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  • 1.
    Ahad, Abdul
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Nick, Peter
    Actin is bundled in activation-tagged tobacco mutants that tolerate aluminum2007In: Planta, ISSN 0032-0935, E-ISSN 1432-2048, Vol. 225, no 2, p. 451-468Article in journal (Refereed)
    Abstract [en]

    A panel of aluminum-tolerant (AlRes) mutants was isolated by protoplast-based T-DNA activation tagging in the tobacco cultivar SR1. The mutants fell into two phenotypic classes: a minority of the mutants were fertile and developed similarly to the wild type (type I), the majority was male-sterile and grew as semi-dwarfs (type II). These traits, along with the aluminum tolerance, were inherited in a monogenic dominant manner. Both types of mutants were characterized by excessive bundling of actin microfilaments and by a strongly increased abundance of actin, a phenotype that could be partially phenocopied in the wild type by treatment with aluminum chloride. The actin bundles could be dissociated into finer strands by addition of exogenous auxin in both types of mutants. However, actin microfilaments and leaf expansion were sensitive to blockers of actin assembly in the wild type and in the mutants of type I, whereas they were more tolerant in the mutants of type II. The mutants of type II displayed a hypertrophic development of vasculature, manifest in form of supernumerary leaf veins and extended xylem layers in stems and petioles. Whereas mutants of type I were characterized by a normal, but aluminum-tolerant polar auxin-transport, auxin-transport was strongly promoted in the mutants of type II. The phenotype of these mutants is discussed in terms of reduced endocytosis leading, concomitantly with aluminum tolerance, to changes in polar auxin transport.

  • 2.
    Akhter, Shirin
    et al.
    Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentre, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Westrin, Karl Johan
    Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden.
    Zivi, Nathan
    Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentre, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden; Skogforsk, Uppsala Science Park, Uppsala, Sweden.
    Nordal, Veronika
    Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentre, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Kretzschmar, Warren W.
    Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden.
    Delhomme, Nicolas
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Street, Nathaniel R.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Nilsson, Ove
    Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences (SLU), Umeå, Sweden.
    Emanuelsson, Olof
    Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Solna, Sweden.
    Sundström, Jens F.
    Department of Plant Biology, Linnean Center for Plant Biology, Uppsala BioCentre, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway2022In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 236, no 5, p. 1951-1963Article in journal (Refereed)
    Abstract [en]

    Reproductive phase change is well characterized in angiosperm model species, but less studied in gymnosperms. We utilize the early cone-setting acrocona mutant to study reproductive phase change in the conifer Picea abies (Norway spruce), a gymnosperm. The acrocona mutant frequently initiates cone-like structures, called transition shoots, in positions where wild-type P. abies always produces vegetative shoots.

    We collect acrocona and wild-type samples, and RNA-sequence their messenger RNA (mRNA) and microRNA (miRNA) fractions. We establish gene expression patterns and then use allele-specific transcript assembly to identify mutations in acrocona. We genotype a segregating population of inbred acrocona trees.

    A member of the SQUAMOSA BINDING PROTEIN-LIKE (SPL) gene family, PaSPL1, is active in reproductive meristems, whereas two putative negative regulators of PaSPL1, miRNA156 and the conifer specific miRNA529, are upregulated in vegetative and transition shoot meristems. We identify a mutation in a putative miRNA156/529 binding site of the acrocona PaSPL1 allele and show that the mutation renders the acrocona allele tolerant to these miRNAs. We show co-segregation between the early cone-setting phenotype and trees homozygous for the acrocona mutation.

    In conclusion, we demonstrate evolutionary conservation of the age-dependent flowering pathway and involvement of this pathway in regulating reproductive phase change in the conifer P. abies.

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  • 3. Ali, Muhammad Amjad
    et al.
    Azeem, Farrukh
    Nawaz, Muhammad Amjad
    Acet, Tuba
    Abbas, Amjad
    Imran, Qari Muhammad
    Laboratory of Plant Functional Genomics, College of Agriculture & Life Sciences, Kyngpook National University, Buk-gu Daegu, South Korea.
    Shah, Kausar Hussain
    Rehman, Hafiz Mamoon
    Chung, Gyuhwa
    Yang, Seung Hwan
    Transcription factors WRKY11 and WRKY17 are involved in abiotic stress responses in Arabidopsis2018In: Journal of plant physiology (Print), ISSN 0176-1617, E-ISSN 1618-1328, Vol. 226, p. 12-21Article in journal (Refereed)
    Abstract [en]

    Plant WRKY transcription factors play a vital role in abiotic stress tolerance and regulation of plant defense responses. This study examined AtWRKY11 and AtWRKY17 expression under ABA, salt, and osmotic stress at different developmental stages in Arabidopsis. We used reverse transcriptase PCR, quantitative real-time PCR, and promoter:GUS lines to analyze expression. Both genes were upregulated in response to abiotic stress. Next, we applied the same stressors to seedlings of T-DNA insertion wrky11 and 17 knock-out mutants (single and double). Under stress, the mutants exhibited slower germination and compromised root growth compared with the wild type. In most cases, double-mutant seedlings were more affected than single mutants. These results suggest that wrky11 and wrky17 are not strictly limited to plant defense responses but are also involved in conferring stress tolerance.

  • 4.
    Amith, Abraham
    et al.
    Rubber Research Institute of India, Kottayam, Kerala, India.
    Philip, Shaji
    Rubber Research Institute of India, Kottayam, Kerala, India.
    Joby, Joseph
    Rubber Research Institute of India, Kottayam, Kerala, India.
    Sivan, Pramod
    Rubber Research Institute of India, Kottayam, Kerala, India.
    Kuruvila, Jacob
    Rubber Research Institute of India, Kottayam, Kerala, India.
    Raveendran, Sindhu
    Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (NIIST), Thiruvananthapuram-695 019, Kerala, India.
    Pandey, Ashok
    Centre for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research (IITR), Lucknow-226 001, Uttar Pradesh, India.
    Byoung, Sang
    Kochupurackal, Jayachandran
    School of Biosciences, Mahatma Gandhi University, Kottayam, Kerala, India.
    Growth promoting activities of antagonistic bacterial endophytes from Hevea brasiliensis (Willd. ex A.Juss.) Müll.Arg.2021In: Indian Journal of Experimental Biology, ISSN 0019-5189, Vol. 59, no 12, p. 827-833Article in journal (Refereed)
    Abstract [en]

    Rubber plantations are known to udergo various biotic and abiotic stresses. However, the symbiotic bacterial endophytes that inhabit them provide protection. Here, we isolated bacterial endophytes from the rubber tree, Hevea brasiliensis (Willd. ex A.Juss.) Müll.Arg. and studied their antagonistic activity against major pathogens such as Phytophthora meadii, Corynespora cassiicola and Corticium salmonicolar. The antifungal metabolites such as HCN, siderophores and salicylic acid were produced by the antagonistic endophytes under in vitro conditions. Bioassay showed the growth promotion by a consortium of selected antagonistic endophytes in H. brasiliensis seedlings. The photosynthetic efficiency of seedlings increased after endophyte inoculation. Endophyte-treated plants showed accumulation of starch granules in root tissues. The selected antagonistic isolates belong to Bacillus sp. and Pseudomonas sp. The study revealed the biocontrol and growth promoting potential of bacterial endophytes from H. brasiliensis.

  • 5.
    Andersson, Jessica
    et al.
    Halmstad University, School of Business, Innovation and Sustainability.
    Magnusson, Carl
    Halmstad University, School of Business, Innovation and Sustainability.
    Alternativa urbana odlingsmetodernas potential för självförsörjning i Sverige2024Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    During the COVID pandemic of 2019, Sweden saw a huge increase in food prices, as many of the country's grocery chains import a large amount of all foods. This research is motivated by the Swedish Parliament's motion "Self-Sufficiency of Food in Sweden" and the need for innovative solutions to enhance Sweden's food supply. This study focuses on alternative urban agriculture methods, with a focus on aeroponics, aquaponics, hydroponics, and vertical farming, and their potential for self-sufficiency in Sweden. This study aims to fill the gap in Swedish research on soilless urban farming methods and contribute to the understanding and acceptance of the alternative methods above. The study seeks to determine whether the yield of alternative cultivation methods is comparable to traditional methods, soil-based and greenhouse-based farming, in terms of resources invested and to identify the alternative method with the highest yield. Resources in this thesis will be defined as the amount of water that is used. Our thesis aims to support businesses and local governance in decision-making regarding implementation of alternative urban farming in Sweden. A literature search was conducted using keywords such as hydroponic, vertical farming and sustainability. Statistical analysis of collected data indicates significant differences in yield and water usage among the collected examples which resulted in vertical hydroponic farming offering the highest yield in terms of space utilization, with significant statistical significance (p < 0.05). Additionally, hydroponic farming requires the least amount of water compared to other methods although this is not a certainty as there was no significant statistical difference between the different methods. The study demonstrates that hydroponic farming can achieve higher yields compared to traditional soil-based farming and other alternative farming methods. The study emphasizes organizational and governmental solutions to improve self-sufficiency at the local and national levels. Alternative urban farming methods offer a sustainable contribution to increasing self-sufficiency while minimizing resource usage.

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  • 6. Andersson-Gunnerås, Sara
    et al.
    Mellerowicz, Ewa J
    Love, Jonathan
    Segerman, Bo
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ohmiya, Yasunori
    Coutinho, Pedro M
    Nilsson, Peter
    Henrissat, Bernard
    Moritz, Thomas
    Sundberg, Björn
    Biosynthesis of cellulose-enriched tension wood in Populus: global analysis of transcripts and metabolites identifies biochemical and developmental regulators in secondary wall biosynthesis2006In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 45, no 2, p. 144-165Article in journal (Refereed)
    Abstract [en]

    Stems and branches of angiosperm trees form tension wood (TW) when exposed to a gravitational stimulus. One of the main characteristics of TW, which distinguishes it from normal wood, is the formation of fibers with a thick inner gelatinous cell wall layer mainly composed of crystalline cellulose. Hence TW is enriched in cellulose, and deficient in lignin and hemicelluloses. An expressed sequence tag library made from TW-forming tissues in Populus tremula (L.) x tremuloides (Michx.) and data from transcript profiling using microarray and metabolite analysis were obtained during TW formation in Populus tremula (L.) in two growing seasons. The data were examined with the aim of identifying the genes responsible for the change in carbon (C) flow into various cell wall components, and the mechanisms important for the formation of the gelatinous cell wall layer (G-layer). A specific effort was made to identify carbohydrate-active enzymes with a putative function in cell wall biosynthesis. An increased C flux to cellulose was suggested by a higher abundance of sucrose synthase transcripts. However, genes related to the cellulose biosynthetic machinery were not generally affected, although the expression of secondary wall-specific CesA genes was modified in both directions. Other pathways for which the data suggested increased activity included lipid and glucosamine biosynthesis and the pectin degradation machinery. In addition, transcripts encoding fasciclin-like arabinogalactan proteins were particularly increased and found to lack true Arabidopsis orthologs. Major pathways for which the transcriptome and metabolome analysis suggested decreased activity were the pathway for C flux through guanosine 5'-diphosphate (GDP) sugars to mannans, the pentose phosphate pathway, lignin biosynthesis, and biosynthesis of cell wall matrix carbohydrates. Several differentially expressed auxin- and ethylene-related genes and transcription factors were also identified.

  • 7.
    Armada Moreira, Adam
    et al.
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Diacci, Chiara
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Manan Dar, Abdul Manan
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Berggren, Magnus
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Simon, Daniel
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Stavrinidou, Eleni
    Linköping University, Department of Science and Technology, Laboratory of Organic Electronics. Linköping University, Faculty of Science & Engineering. Swedish Univ Agr Sci, Sweden.
    Benchmarking organic electrochemical transistors for plant electrophysiology2022In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 13, article id 916120Article in journal (Refereed)
    Abstract [en]

    Plants are able to sense and respond to a myriad of external stimuli, using different signal transduction pathways, including electrical signaling. The ability to monitor plant responses is essential not only for fundamental plant science, but also to gain knowledge on how to interface plants with technology. Still, the field of plant electrophysiology remains rather unexplored when compared to its animal counterpart. Indeed, most studies continue to rely on invasive techniques or on bulky inorganic electrodes that oftentimes are not ideal for stable integration with plant tissues. On the other hand, few studies have proposed novel approaches to monitor plant signals, based on non-invasive conformable electrodes or even organic transistors. Organic electrochemical transistors (OECTs) are particularly promising for electrophysiology as they are inherently amplification devices, they operate at low voltages, can be miniaturized, and be fabricated in flexible and conformable substrates. Thus, in this study, we characterize OECTs as viable tools to measure plant electrical signals, comparing them to the performance of the current standard, Ag/AgCl electrodes. For that, we focused on two widely studied plant signals: the Venus flytrap (VFT) action potentials elicited by mechanical stimulation of its sensitive trigger hairs, and the wound response of Arabidopsis thaliana. We found that OECTs are able to record these signals without distortion and with the same resolution as Ag/AgCl electrodes and that they offer a major advantage in terms of signal noise, which allow them to be used in field conditions. This work establishes these organic bioelectronic devices as non-invasive tools to monitor plant signaling that can provide insight into plant processes in their natural environment.

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  • 8. Asaf, Sajjad
    et al.
    Khan, Abdul Latif
    Aaqil Khan, Muhammad
    Imran, Qari Muhammad
    School of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea.
    Kang, Sang-Mo
    Al-Hosni, Khdija
    Jeong, Eun Ju
    Lee, Ko Eun
    Lee, In-Jung
    Comparative analysis of complete plastid genomes from wild soybean (Glycine soja) and nine other Glycine species2017In: PLOS ONE, E-ISSN 1932-6203, Vol. 12, no 8Article in journal (Refereed)
    Abstract [en]

    The plastid genomes of different plant species exhibit significant variation, thereby providing valuable markers for exploring evolutionary relationships and population genetics. Glycine soja (wild soybean) is recognized as the wild ancestor of cultivated soybean (G. max), representing a valuable genetic resource for soybean breeding programmes. In the present study, the complete plastid genome of Gsoja was sequenced using Illumina paired-end sequencing and then compared it for the first time with previously reported plastid genome sequences from nine other Glycine species. The Gsoja plastid genome was 152,224 bp in length and possessed a typical quadripartite structure, consisting of a pair of inverted repeats (IRa/IRb; 25,574 bp) separated by small (178,963 bp) and large (83,181 bp) single-copy regions, with a 51-kb inversion in the large single-copy region. The genome encoded 134 genes, including 87 protein-coding genes, eight ribosomal RNA genes, and 39 transfer RNA genes, and possessed 204 randomly distributed microsatellites, including 15 forward, 25 tandem, and 34 palindromic repeats. Whole-plastid genome comparisons revealed an overall high degree of sequence similarity between Gmax and Ggracilis and some divergence in the intergenic spacers of other species. Greater numbers of indels and SNP substitutions were observed compared with Gcyrtoloba. The sequence of the accD gene from Gsoja was highly divergent from those of the other species except for Gmax and Ggracilis. Phylogenomic analyses of the complete plastid genomes and 76 shared genes yielded an identical topology and indicated that Gsoja is closely related to Gmax and Ggracilis. The complete Gsoja genome sequenced in the present study is a valuable resource for investigating the population and evolutionary genetics of Glycine species and can be used to identify related species.

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  • 9. Asaf, Sajjad
    et al.
    Khan, Abdul Latif
    Khan, Muhammad Aaqil
    Imran, Qari Muhammad
    School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea.
    Yun, Byung-Wook
    Lee, In-Jung
    Osmoprotective functions conferred to soybean plants via inoculation with Sphingomonas sp. LK11 and exogenous trehalose2017In: Microbiology Research, ISSN 0944-5013, E-ISSN 1618-0623, Vol. 205, p. 135-145Article in journal (Refereed)
    Abstract [en]

    Osmotic stress induced by drought can hinder the growth and yield of crop plants. To understand the eco-physiological role of osmoprotectants, the combined utilization of endophytes and osmolytes (trehalose) can be an ideal strategy used to overcome the adverse effects of drought. Hence, in the present study, we aimed to investigate the role of Sphingomonas sp. LK11, which produces phytohormones and synthesizes trehalose, in improving soybean plant growth under drought-induced osmotic stress (−0.4, −0.9, and −1.2 MPa). The results showed that the inoculation of soybean plants with Sphingomonas sp. LK11 significantly increased plant length, dry biomass, photosynthetic pigments, glutathione, amino acids (proline, glycine, and glutamate), and primary sugars as compared to control plants under varying drought stresses. Trehalose applied to the plant with or without endophyte-inoculation also showed similar plant growth-promoting attributes under stress. Stress exposure significantly enhanced endogenous jasmonic (JA) and abscisic (ABA) acid contents in control plants. In contrast, Sphingomonas sp. LK11-inoculation significantly lowered ABA and JA levels in soybean plants, but these phytohormones increased in response to combined treatments during stress. The drought-induced osmotic stress resistance associated with Sphingomonas sp. LK11 and trehalose was also evidenced by increased mRNA gene expression of soybean dehydration responsive element binding protein (DREB)-type transcription factors (GmDREBa and GmDREB2) and the MYB (myeloblastosis) transcription factor (GmMYBJ1) as compared to the control. In conclusion, our findings demonstrated that inoculation with this endophyte and trehalose improved the negative effects of drought-induced osmotic stress, and it enhanced soybean plant growth and tolerance.

  • 10. Asaf, Sajjad
    et al.
    Waqas, Muhammad
    Khan, Abdul L.
    Khan, Muhammad A.
    Kang, Sang-Mo
    Imran, Qari Muhammad
    School of Applied Biosciences, Kyungpook National University, Daegu, South Korea.
    Shahzad, Raheem
    Bilal, Saqib
    Yun, Byung-Wook
    Lee, In-Jung
    The complete chloroplast genome of wild rice (Oryza minuta) and its comparison to related species2017In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 8, article id 304Article in journal (Refereed)
    Abstract [en]

    Oryza minuta, a tetraploid wild relative of cultivated rice (family Poaceae), possesses a BBCC genome and contains genes that confer resistance to bacterial blight (BB) and white-backed (WBPH) and brown (BPH) plant hoppers. Based on the importance of this wild species, this study aimed to understand the phylogenetic relationships of O. minuta with other Oryza species through an in-depth analysis of the composition and diversity of the chloroplast (cp) genome. The analysis revealed a cp genome size of 135,094 bp with a typical quadripartite structure and consisting of a pair of inverted repeats separated by small and large single copies, 139 representative genes, and 419 randomly distributed microsatellites. The genomic organization, gene order, GC content and codon usage are similar to those of typical angiosperm cp genomes. Approximately 30 forward, 28 tandem and 20 palindromic repeats were detected in the Ominuta cp genome. Comparison of the complete O. minuta cp genome with another eleven Oryza species showed a high degree of sequence similarity and relatively high divergence of intergenic spacers. Phylogenetic analyses were conducted based on the complete genome sequence, 65 shared genes and matK gene showed same topologies and O. minuta forms a single clade with parental O. punctata. Thus, the complete Ominuta cp genome provides interesting insights and valuable information that can be used to identify related species and reconstruct its phylogeny.

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  • 11.
    Aspeborg, Henrik
    et al.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Bhalerao, Rishikeshi
    Hertzberg, Magnus
    Johansson, Karin
    Johnsson, P.
    Karlsson, Ann
    Sandberg, Göran
    Schrader, Jarmo
    Sundberg, Björn
    Teeri, Tuula
    Trygg, Johan
    Wallbäcks, Lars
    Vegetabile material, plants and a method of producing a plant having altered lignin properties2008Patent (Other (popular science, discussion, etc.))
    Abstract [en]

    The present invention is related to a set of genes, which when modified in plants gives altered lignin properties. The invention provides DNA construct such as a vector useful in the method of the invention. Further, the invention relates to a plant cell or plant progeny of the plants and wood produced by the plants according to the invention Lower lignin levels will result in improved saccharification for bio-refining and ethanol production and improved pulp and paper. Increased lignin levels will utilise lignin properties for energy production. The genes and DNA constructs may be used for the identification of plants having altered lignin characteristics as compared to the wild-type. According to the invention genes and DNA constructs may also be used as candidate genes in marker assisted breeding.

  • 12.
    Aspeborg, Henrik
    et al.
    KTH, School of Biotechnology (BIO).
    Schrader, J.
    Coutinho, P. M.
    Stam, M.
    Kallas, A.
    Djerbi, S.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics.
    Denman, S.
    Amini, B.
    Sterky, Fredrik
    KTH, School of Biotechnology (BIO), Proteomics.
    Master, E.
    Sandberg, G.
    Mellerowicz, E.
    Sundberg, B.
    Henrissat, B.
    Teeri, Tuula T.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Carbohydrate-active enzymes involved in the secondary cell wall biogenesis in hybrid aspen2005In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 137, no 3, p. 983-997Article in journal (Refereed)
    Abstract [en]

    Wood formation is a fundamental biological process with significant economic interest. While lignin biosynthesis is currently relatively well understood, the pathways leading to the synthesis of the key structural carbohydrates in wood fibers remain obscure. We have used a functional genomics approach to identify enzymes involved in carbohydrate biosynthesis and remodeling during xylem development in the hybrid aspen Populus tremula x tremuloides. Microarrays containing cDNA clones from different tissue-specific libraries were hybridized with probes obtained from narrow tissue sections prepared by cryosectioning of the developing xylem. Bioinformatic analyses using the sensitive tools developed for carbohydrate-active enzymes allowed the identification of 25 xylem-specific glycosyltransferases belonging to the Carbohydrate-Active EnZYme families GT2, GT8, GT14, GT31, GT43, GT47, and GT61 and nine glycosidases (or transglycosidases) belonging to the Carbohydrate-Active EnZYme families GH9, GH10, GH16, GH17, GH19, GH28, GH35, and GH51. While no genes encoding either polysaccharide lyases or carbohydrate esterases were found among the secondary wall-specific genes, one putative O-acetyltransferase was identified. These wood-specific enzyme genes constitute a valuable resource for future development of engineered fibers with improved performance in different applications.

  • 13.
    Auffret, Alistair G
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Meineri, Eric
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Bruun, Hans Henrik
    Ejrnaes, Rasmus
    Graae, Bente J
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Ontogenetic niche shifts in three Vaccinium species on a sub-alpine mountain side2010In: Plant Ecology & Diversity, ISSN 1755-0874, E-ISSN 1755-1668, Vol. 3, no 2, p. 131-139Article in journal (Refereed)
    Abstract [en]

    Background: Climate warming in arctic and alpine regions is expected to result in the altitudinal migration of plant species, but current predictions neglect differences between species' regeneration niche and established niche.

    Aims: To examine potential recruitment of Vaccinium myrtillus, V. uliginosum and V. vitis-idaea on a mountain slope in northern Sweden in relation to current adult occurrence.

    Methods: We combined a seed-sowing experiment in seven community types with adult occurrence observations and species distribution mapping. Results: Emergence of V. myrtillus and V. vitis-idaea seedlings was significantly related to community type, while V. uliginosum was indifferent, but exhibited the highest average emergence. Adult occurrence was related to community, and ontogenetic niche shifts were observed for all three study species. V. myrtillus was shown to have the highest potential recruitment in habitats at altitudes above its current populations.

    Conclusions: The potential for migration exists, but incongruence between regenerative and established niches presents a challenge for colonisers, as well as for plant migration modelling.

  • 14.
    Azeem, Muhammad
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
    Iqbal, Z.
    Emami, S. N.
    Nordlander, G.
    Nordenhem, H.
    Mozūratis, R.
    El-Seedi, Hesham
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
    Borg-Karlson, Anna-Karin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Organic chemistry.
    Chemical composition and antifeedant activity of some aromatic plants against pine weevil (Hylobius abietis)2020In: Annals of Applied Biology, ISSN 0003-4746, E-ISSN 1744-7348Article in journal (Refereed)
    Abstract [en]

    The pine weevil Hylobius abietis is an important pest causing severe damage to conifer seedlings in reforestation areas in Europe and Asia. Plants that have no evolutionary history with the pine weevil are of special interest in the search for compounds with a strong antifeedant activity. Thus, the essential oils of nine aromatic plants, viz Amomum subulatum, Cinnamomum tamala, Curcuma longa, Laurus nobilis, Ocimum basilicum, Origanum majorana, Origanum vulgare, Syzygium aromaticum and Trachyspermum ammi were extracted by hydrodistillation. The essential oil constituents were identified by gas chromatography–mass spectrometry, and antifeedant properties towards the pine weevil were assessed using choice feeding bioassay. The essential oils of C. longa, O. majorana, S. aromaticum and T. ammi showed an excellent antifeedant activity towards the pine weevil for 24 hr, whereas the essential oil of other plants showed the activity for 6 hr. There was a positive correlation between the amount of benzenoid compounds and the antifeedant activity of the essential oils. This study suggests that pine weevil non-host plant compounds have potential to be used for the protection of seedlings against pine weevil feeding. However, further study will be needed to explore the antifeedant activity of individual components and oils in the laboratory as well as in the field. 

  • 15.
    Bacete, Laura
    et al.
    Univ Politecn Madrid UPM, Ctr Biotecnol & Genom Plantas, Inst Nacl Invest & Tecnol Agr & Alimentaria INIA, Campus Montegancedo UPM, Pozuelo De Alarcon 28223, Madrid, Spain.;Univ Politecn Madrid, Dept Biotecnol Biol Vegetal, Escuela Tecn Super Ingn Agron Alimentaria & Biosi, Madrid 28040, Spain..
    Melida, Hugo
    Univ Politecn Madrid UPM, Ctr Biotecnol & Genom Plantas, Inst Nacl Invest & Tecnol Agr & Alimentaria INIA, Campus Montegancedo UPM, Pozuelo De Alarcon 28223, Madrid, Spain..
    Lopez, Gemma
    Univ Politecn Madrid UPM, Ctr Biotecnol & Genom Plantas, Inst Nacl Invest & Tecnol Agr & Alimentaria INIA, Campus Montegancedo UPM, Pozuelo De Alarcon 28223, Madrid, Spain..
    Dabos, Patrick
    Univ Toulouse, INRA, UPS, CNRS,LIPM, Castanet Tolosan, France..
    Tremousaygue, Dominique
    Univ Toulouse, INRA, UPS, CNRS,LIPM, Castanet Tolosan, France..
    Denance, Nicolas
    Univ Toulouse, INRA, UPS, CNRS,LIPM, Castanet Tolosan, France.;Univ Paul Sabatier, Lab Rech Sci Vegetales, CNRS, UMR 5546, Chemin Borde Rouge, F-31326 Castanet Tolosan, France..
    Miedes, Eva
    Univ Politecn Madrid UPM, Ctr Biotecnol & Genom Plantas, Inst Nacl Invest & Tecnol Agr & Alimentaria INIA, Campus Montegancedo UPM, Pozuelo De Alarcon 28223, Madrid, Spain.;Univ Politecn Madrid, Dept Biotecnol Biol Vegetal, Escuela Tecn Super Ingn Agron Alimentaria & Biosi, Madrid 28040, Spain..
    Bulone, Vincent
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. AlbaNova Univ Ctr, Sch Engn Sci Chem Biotechnol & Hlth, Royal IUniv Adelaide, RC Ctr Excellence Plant Cell Walls, Waite Campus, Urrbrae, SA 5064, Australia.;Univ Adelaide, Sch Agr Food & Wine, Waite Campus, Urrbrae, SA 5064, Australia..
    Goffner, Deborah
    Univ Paul Sabatier, Lab Rech Sci Vegetales, CNRS, UMR 5546, Chemin Borde Rouge, F-31326 Castanet Tolosan, France..
    Molina, Antonio
    Univ Politecn Madrid UPM, Ctr Biotecnol & Genom Plantas, Inst Nacl Invest & Tecnol Agr & Alimentaria INIA, Campus Montegancedo UPM, Pozuelo De Alarcon 28223, Madrid, Spain.;Univ Politecn Madrid, Dept Biotecnol Biol Vegetal, Escuela Tecn Super Ingn Agron Alimentaria & Biosi, Madrid 28040, Spain..
    Arabidopsis Response Regulator 6 (ARR6) Modulates Plant Cell-Wall Composition and Disease Resistance2020In: Molecular Plant-Microbe Interactions, ISSN 0894-0282, E-ISSN 1943-7706, Vol. 33, no 5, p. 767-780Article in journal (Refereed)
    Abstract [en]

    The cytokinin signaling pathway, which is mediated by Arabidopsis response regulator (ARR) proteins, has been involved in the modulation of some disease-resistance responses. Here, we describe novel functions of ARR6 in the control of plant disease-resistance and cell-wall composition. Plants impaired in ARR6 function (arr6) were more resistant and susceptible, respectively, to the necrotrophic fungus Plectosphaerella cucumerina and to the vascular bacterium Ralstonia solanacearum, whereas Arabidopsis plants that overexpress ARR6 showed the opposite phenotypes, which further support a role of ARR6 in the modulation of disease-resistance responses against these pathogens. Transcriptomics and metabolomics analyses revealed that, in arr6 plants, canonical disease-resistance pathways, like those activated by defensive phytohormones, were not altered, whereas immune responses triggered by microbe-associated molecular patterns were slightly enhanced. Cell-wall composition of arr6 plants was found to be severely altered compared with that of wild-type plants. Remarkably, pectin-enriched cell-wall fractions extracted from arr6 walls triggered more intense immune responses than those activated by similar wall fractions from wild-type plants, suggesting that an-6 pectin fraction is enriched in wall-related damage-associated molecular patterns, which trigger immune responses. This work supports a novel function of ARR6 in the control of cell-wall composition and disease resistance and reinforces the role of the plant cell wall in the modulation of specific immune responses.

  • 16.
    Barajas-Lopez, Juan de Dios
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Kremnev, Dmitry
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Shaikhali, Jehad
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Pinas-Fernandez, Aurora
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Strand, Åsa
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    PAPP5 is involved in the tetrapyrrole mediated plastid signalling during chloroplast development2013In: PLOS ONE, E-ISSN 1932-6203, Vol. 8, no 3, article id e60305Article in journal (Refereed)
    Abstract [en]

    The initiation of chloroplast development in the light is dependent on nuclear encoded components. The nuclear genes encoding key components in the photosynthetic machinery are regulated by signals originating in the plastids. These plastid signals play an essential role in the regulation of photosynthesis associated nuclear genes (PhANGs) when proplastids develop into chloroplasts. One of the plastid signals is linked to the tetrapyrrole biosynthesis and accumulation of the intermediates the Mg-ProtoIX and its methyl ester Mg-ProtoIX-ME. Phytochrome-Associated Protein Phosphatase 5 (PAPP5) was isolated in a previous study as a putative Mg-ProtoIX interacting protein. In order to elucidate if there is a biological link between PAPP5 and the tetrapyrrole mediated signal we generated double mutants between the Arabidopsis papp5 and the crd mutants. The crd mutant over-accumulates Mg-ProtoIX and Mg-ProtoIX-ME and the tetrapyrrole accumulation triggers retrograde signalling. The crd mutant exhibits repression of PhANG expression, altered chloroplast morphology and a pale phenotype. However, in the papp5crd double mutant, the crd phenotype is restored and papp5crd accumulated wild type levels of chlorophyll, developed proper chloroplasts and showed normal induction of PhANG expression in response to light. Tetrapyrrole feeding experiments showed that PAPP5 is required to respond correctly to accumulation of tetrapyrroles in the cell and that PAPP5 is most likely a component in the plastid signalling pathway down stream of the tetrapyrrole Mg-ProtoIX/Mg-ProtoIX-ME. Inhibition of phosphatase activity phenocopied the papp5crd phenotype in the crd single mutant demonstrating that PAPP5 phosphatase activity is essential to mediate the retrograde signal and to suppress PhANG expression in the crd mutant. Thus, our results suggest that PAPP5 receives an inbalance in the tetrapyrrole biosynthesis through the accumulation of Mg-ProtoIX and acts as a negative regulator of PhANG expression during chloroplast biogenesis and development.

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  • 17.
    Basso, Marcos Fernando
    et al.
    W5 Norte, Brazil; Natl Inst Sci & Technol, Brazil.
    Lourenco-Tessutti, Isabela Tristan
    W5 Norte, Brazil; Natl Inst Sci & Technol, Brazil.
    Moreira-Pinto, Clidia Eduarda
    W5 Norte, Brazil; Natl Inst Sci & Technol, Brazil; Fed Univ Brasilia, Brazil.
    Mendes, Reneida Aparecida Godinho
    W5 Norte, Brazil; Fed Univ Brasilia, Brazil.
    Paes-de-Melo, Bruno
    W5 Norte, Brazil; Natl Inst Sci & Technol, Brazil.
    das Neves, Maysa Rosa
    W5 Norte, Brazil.
    Macedo, Amanda Ferreira
    Univ Sao Paulo, Brazil.
    Figueiredo, Viviane
    Fed Univ Rio Janeiro, Brazil.
    Grandis, Adriana
    Univ Sao Paulo, Brazil.
    Macedo, Leonardo Lima Pepino
    W5 Norte, Brazil; Natl Inst Sci & Technol, Brazil.
    Arraes, Fabricio Barbosa Monteiro
    W5 Norte, Brazil; Natl Inst Sci & Technol, Brazil.
    Costa, Marcos Mota do Carmo
    W5 Norte, Brazil.
    Togawa, Roberto Coiti
    W5 Norte, Brazil; Natl Inst Sci & Technol, Brazil.
    Enrich Prast, Alex
    Linköping University, Department of Thematic Studies, Tema Environmental Change. Linköping University, Faculty of Arts and Sciences. Linköping University, Biogas Research Center. Fed Univ Rio Janeiro, Brazil.
    Marcelino-Guimaraes, Francismar Correa
    Natl Inst Sci & Technol, Brazil; Embrapa Soybean, Brazil.
    Gomes, Ana Cristina Meneses Mendes
    W5 Norte, Brazil.
    Silva, Maria Cristina Mattar
    W5 Norte, Brazil; Natl Inst Sci & Technol, Brazil.
    Floh, Eny Iochevet Segal
    Univ Sao Paulo, Brazil.
    Buckeridge, Marcos Silveira
    Univ Sao Paulo, Brazil.
    Engler, Janice de Almeida
    Natl Inst Sci & Technol, Brazil; Univ Cote dAzur, France.
    Grossi-de-Sa, Maria Fatima
    W5 Norte, Brazil; Natl Inst Sci & Technol, Brazil; Univ Catolica Brasilia, Brazil.
    Overexpression of a soybean Globin (GmGlb1-1) gene reduces plant susceptibility to Meloidogyne incognita2022In: Planta, ISSN 0032-0935, E-ISSN 1432-2048, Vol. 256, no 4, article id 83Article in journal (Refereed)
    Abstract [en]

    Non-symbiotic globin class #1 (Glb1) genes are expressed in different plant organs, have a high affinity for oxygen, and are related to nitric oxide (NO) turnover. Previous studies showed that soybean Glb1 genes are upregulated in soybean plants under flooding conditions. Herein, the GmGlb1-1 gene was identified in soybean as being upregulated in the nematode-resistant genotype PI595099 compared to the nematode-susceptible cultivar BRS133 during plant parasitism by Meloidogyne incognita. The Arabidopsis thaliana and Nicotiana tabacum transgenic lines overexpressing the GmGlb1-1 gene showed reduced susceptibility to M. incognita. Consistently, gall morphology data indicated that pJ2 nematodes that infected the transgenic lines showed developmental alterations and delayed parasitism progress. Although no significant changes in biomass and seed yield were detected, the transgenic lines showed an elongated, etiolation-like growth under well-irrigation, and also developed more axillary roots under flooding conditions. In addition, transgenic lines showed upregulation of some important genes involved in plant defense response to oxidative stress. In agreement, higher hydrogen peroxide accumulation and reduced activity of reactive oxygen species (ROS) detoxification enzymes were also observed in these transgenic lines. Thus, based on our data and previous studies, it was hypothesized that constitutive overexpression of the GmGlb1-1 gene can interfere in the dynamics of ROS production and NO scavenging, enhancing the acquired systemic acclimation to biotic and abiotic stresses, and improving the cellular homeostasis. Therefore, these collective data suggest that ectopic or nematode-induced overexpression, or enhanced expression of the GmGlb1-1 gene using CRISPR/dCas9 offers great potential for application in commercial soybean cultivars aiming to reduce plant susceptibility to M. incognita.

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  • 18.
    Bautista, Rocí­o
    et al.
    University of Malaga.
    Villalobos, David, P.
    University of Malaga.
    Diaz-Moreno, Sara M
    University of Malaga.
    Cantón, Francisco, R.
    University of Malaga.
    Cánovas, Francisco, M.
    University of Malaga.
    Gonzalo Claros, M.
    University of Malaga.
    Toward a Pinus pinaster bacterial artificial chromosome library2007In: Annals of Forest Science, ISSN 1286-4560, E-ISSN 1297-966X, Vol. 64, no 8, p. 855-864Article in journal (Refereed)
    Abstract [en]

    Conifers are of great economic and ecological importance, but little is known concerning their genomic organization. This study is an attempt to obtain high-quality high-molecular-weight DNA from Pinus pinaster cotyledons and the construction of a pine BAC library. The preparation incorporates modifications like low centrifugation speeds, increase of EDTA concentration for plug maintenance, use of DNase inhibitors to reduce DNA degradation, use of polyvinylpyrrolidone and ascorbate to avoid secondary metabolites, and a brief electrophoresis of the plugs prior to their use. A total of 72 192 clones with an average insert size of 107 kb, which represents an equivalent of 11X pine haploid genomes, were obtained. The proportions of clones lacking inserts or containing chloroplast DNA are both approximately 1.6%. The library was screened with cDNA probes for seven genes, and two clones containing Fd-GOGAT sequences were found, one of them seemingly functional. Ongoing projects aimed at constructing a pinebacterial artificial chromosome library may benefit from the methods described here.

  • 19.
    Bellini, Catherine
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, France.
    A synthetic auxin for cloning mature trees2024In: Nature Biotechnology, ISSN 1087-0156, E-ISSN 1546-1696Article in journal (Other academic)
  • 20. Benson, Samuel L
    et al.
    Maheswaran, Pratheesh
    Ware, Maxwell A
    Hunter, C Neil
    Horton, Peter
    Jansson, Stefan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ruban, Alexander V
    Johnson, Matthew P
    An intact light harvesting complex I antenna system is required for complete state transitions in Arabidopsis2015In: Nature plants, ISSN 2055-026X, Vol. 1, no 12, article id 15176Article in journal (Refereed)
    Abstract [en]

    Efficient photosynthesis depends on maintaining balance between the rate of light-driven electron transport occurring in photosystem I (PSI) and photosystem II (PSII), located in the chloroplast thylakoid membranes. Balance is achieved through a process of 'state transitions' that increases energy transfer towards PSI when PSII is overexcited (state II), and towards PSII when PSI is overexcited (state I). This is achieved through redox control of the phosphorylation state of light-harvesting antenna complex II (LHCII). PSI is served by both LHCII and four light-harvesting antenna complex I (LHCI) subunits, Lhca1, 2, 3 and 4. Here we demonstrate that despite unchanged levels of LHCII phosphorylation, absence of specific Lhca subunits reduces state transitions in Arabidopsis. The severest phenotype-observed in a mutant lacking Lhca4 (Delta Lhca4)-displayed a 69% reduction compared with the wild type. Yet, surprisingly, the amounts of the PSI-LHCI-LHCII supercomplex isolated by blue native polyacrylamide gel electrophoresis (BN-PAGE) from digitonin-solubilized thylakoids were similar in the wild type and Delta Lhca mutants. Fluorescence excitation spectroscopy revealed that in the wild type this PSI-LHCI-LHCII supercomplex is supplemented by energy transfer from additional LHCII trimers in state II, whose binding is sensitive to digitonin, and which are absent in Delta Lhca4. The grana margins of the thylakoid membrane were found to be the primary site of interaction between this 'extra' LHCII and the PSI-LHCI-LHCII supercomplex in state II. The results suggest that the LHCI complexes mediate energetic interactions between LHCII and PSI in the intact membrane.

  • 21.
    Berglund, Jennie
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Fibre- and Polymer Technology, Wood Chemistry and Pulp Technology. Wallenberg Wood Science Center.
    Wood Hemicelluloses - Fundamental Insights on Biological and Technical Properties2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Hemicelluloses are a group of heterogeneous polysaccharides representing around 30 % of wood where the dominating types are xylans, glucomannans and xyloglucans. Hemicelluloses complex molecular structure makes it difficult to understand the relationship between structure and properties entirely, and their biological role is not yet fully verified. Additionally, hemicelluloses are sensitive to chemical processing and are not utilized to their full potentials for production of value-added products such as materials, additives to food and pharmaceutical products, etc. Increased knowledge regarding their functions is important for the development of both processes and products. The aim with this work has therefore been to increase the fundamental understanding about how the structure and properties of wood hemicelluloses are correlated, and properties such as flexibility, interaction with cellulose, solubility, resistance to chemical-, thermal-, and enzymatic degradation have been explored.

    Molecular dynamics (MD) simulations were used to, in detail, study the structures found in wood hemicelluloses. The flexibility was evaluated by comparing the impact of backbone sugars on the conformational space and also the impact of side groups was considered. Based on the conformational space of backbone glycosidic linkages the flexibility order of hemicelluloses in an aqueous environment was determined to be: xylan > glucomannan > xyloglucan. Additionally, the impact of xylan structure on cellulose interaction was evaluated by MD methods.

    Hemicelluloses were extracted from birch and spruce, and were used to fabricate different composite hydrogels with bacterial cellulose. These materials were studied with regards to mechanical properties, and it was shown that galactoglucomannans mainly contributed to an increased modulus in compression, whereas the most significant effect from xylan was increased strain under uniaxial tensile testing. Besides, other polysaccharides of similar structure as galactoglucomannans were modified and used as pure, well defined, models. Acetyl groups are naturally occurring decorations of wood hemicelluloses and can also be chemically introduced. Here, mannans with different degrees of acetylation were prepared and the influence of structure on solubility in water and the organic solvent DMSO were evaluated. Furthermore, the structure and water solubility influenced the interaction with cellulose. Acetylation also showed to increase the thermal and biological stability of mannans.

    With chemical pulping processes in mind, the degradability of spruce galactoglucomannans in alkaline solution were studied with regards to the structure, and the content of more or less stable structural regions were proposed.

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  • 22. Bitocchi, Elena
    et al.
    Rau, Domenico
    Benazzo, Andrea
    Bellucci, Elisa
    Goretti, Daniela
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Biagetti, Eleonora
    Panziera, Alex
    Laido, Giovanni
    Rodriguez, Monica
    Gioia, Tania
    Attene, Giovanna
    McClean, Phillip
    Lee, Rian K.
    Jackson, Scott A.
    Bertorelle, Giorgio
    Papa, Roberto
    High Level of Nonsynonymous Changes in Common Bean Suggests That Selection under Domestication Increased Functional Diversity at Target Traits2017In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 7, article id 2005Article in journal (Refereed)
    Abstract [en]

    Crop species have been deeply affected by the domestication process, and there have been many efforts to identify selection signatures at the genome level. This knowledge will help geneticists to better understand the evolution of organisms, and at the same time, help breeders to implement successful breeding strategies. Here, we focused on domestication in the Mesoamerican gene pool of Phaseolus vulgaris by sequencing 49 gene fragments from a sample of 45 P. vulgaris wild and domesticated accessions, and as controls, two accessions each of the closely related species Phaseolus coccineus and Phaseolus dumosus. An excess of nonsynonymous mutations within the domesticated germplasm was found. Our data suggest that the cost of domestication alone cannot explain fully this finding. Indeed, the significantly higher frequency of polymorphisms in the coding regions observed only in the domesticated plants (compared to noncoding regions), the fact that these mutations were mostly nonsynonymous and appear to be recently derived mutations, and the investigations into the functions of their relative genes (responses to biotic and abiotic stresses), support a scenario that involves new functional mutations selected for adaptation during domestication. Moreover, consistent with this hypothesis, selection analysis and the possibility to compare data obtained for the same genes in different studies of varying sizes, data types, and methodologies allowed us to identify four genes that were strongly selected during domestication. Each selection candidate is involved in plant resistance/tolerance to abiotic stresses, such as heat, drought, and salinity. Overall, our study suggests that domestication acted to increase functional diversity at target loci, which probably controlled traits related to expansion and adaptation to new agro-ecological growing conditions.

  • 23. Bollhoner, Benjamin
    et al.
    Jokipii-Lukkari, Soile
    Bygdell, Joakim
    Stael, Simon
    Adriasola, Mathilda
    KTH, School of Biotechnology (BIO).
    Muniz, Luis
    Van Breusegem, Frank
    Ezcurra, Ines
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Wingsle, Gunnar
    Tuominen, Hannele
    The function of two type II metacaspases in woody tissues of Populus trees2018In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 217, no 4, p. 1551-1565Article in journal (Refereed)
    Abstract [en]

    Metacaspases (MCs) are cysteine proteases that are implicated in programmed cell death of plants. AtMC9 (Arabidopsis thaliana Metacaspase9) is a member of the Arabidopsis MC family that controls the rapid autolysis of the xylem vessel elements, but its downstream targets in xylem remain uncharacterized. PttMC13 and PttMC14 were identified as AtMC9 homologs in hybrid aspen (Populustremulaxtremuloides). A proteomic analysis was conducted in xylem tissues of transgenic hybrid aspen trees which carried either an overexpression or an RNA interference construct for PttMC13 and PttMC14. The proteomic analysis revealed modulation of levels of both previously known targets of metacaspases, such as Tudor staphylococcal nuclease, heat shock proteins and 14-3-3 proteins, as well as novel proteins, such as homologs of the PUTATIVE ASPARTIC PROTEASE3 (PASPA3) and the cysteine protease RD21 by PttMC13 and PttMC14. We identified here the pathways and processes that are modulated by PttMC13 and PttMC14 in xylem tissues. In particular, the results indicate involvement of PttMC13 and/or PttMC14 in downstream proteolytic processes and cell death of xylem elements. This work provides a valuable reference dataset on xylem-specific metacaspase functions for future functional and biochemical analyses.

  • 24.
    Bollhöner, Benjamin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Jokipii-Lukkari, Soile
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Bygdell, Joakim
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Stael, Simon
    Adriasola, Mathilda
    Muñiz, Luis
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Van Breusegem, Frank
    Ezcurra, Inés
    Wingsle, Gunnar
    Tuominen, Hannele
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The function of two type II metacaspases in woody tissues of Populus trees2018In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 217, no 4, p. 1551-1565Article in journal (Refereed)
    Abstract [en]

    Metacaspases (MCs) are cysteine proteases that are implicated in programmed cell death of plants. AtMC9 (Arabidopsis thaliana Metacaspase9) is a member of the Arabidopsis MC family that controls the rapid autolysis of the xylem vessel elements, but its downstream targets in xylem remain uncharacterized. PttMC13 and PttMC14 were identified as AtMC9 homologs in hybrid aspen (Populustremulaxtremuloides). A proteomic analysis was conducted in xylem tissues of transgenic hybrid aspen trees which carried either an overexpression or an RNA interference construct for PttMC13 and PttMC14. The proteomic analysis revealed modulation of levels of both previously known targets of metacaspases, such as Tudor staphylococcal nuclease, heat shock proteins and 14-3-3 proteins, as well as novel proteins, such as homologs of the PUTATIVE ASPARTIC PROTEASE3 (PASPA3) and the cysteine protease RD21 by PttMC13 and PttMC14. We identified here the pathways and processes that are modulated by PttMC13 and PttMC14 in xylem tissues. In particular, the results indicate involvement of PttMC13 and/or PttMC14 in downstream proteolytic processes and cell death of xylem elements. This work provides a valuable reference dataset on xylem-specific metacaspase functions for future functional and biochemical analyses.

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  • 25. Bot, Phearom
    et al.
    Mun, Bong-Gyu
    Imran, Qari Muhammad
    Hussain, Adil
    Lee, Sang-Uk
    Loake, Gary
    Yun, Byung-Wook
    Differential expression of AtWAKL10 in response to nitric oxide suggests a putative role in biotic and abiotic stress responses2019In: PeerJ, Vol. 7Article in journal (Refereed)
  • 26. Botterweg-Paredes, Esther
    et al.
    Blaakmeer, Anko
    Hong, Shin-Young
    Sun, Bin
    Mineri, Lorenzo
    Kruusvee, Valdeko
    Xie, Yakun
    Straub, Daniel
    Ménard, Delphine
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Pesquet, Edouard
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Wenkel, Stephan
    Light affects tissue patterning of the hypocotyl in the shade-avoidance response2020In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 16, no 3, article id e1008678Article in journal (Refereed)
    Abstract [en]

    Plants have evolved strategies to avoid shade and optimize the capture of sunlight. While some species are tolerant to shade, plants such as Arabidopsis thaliana are shade-intolerant and induce elongation of their hypocotyl to outcompete neighboring plants. We report the identification of a developmental module acting downstream of shade perception controlling vascular patterning. We show that Arabidopsis plants react to shade by increasing the number and types of water-conducting tracheary elements in the vascular cylinder to maintain vascular density constant. Mutations in genes affecting vascular patterning impair the production of additional xylem and also show defects in the shade-induced hypocotyl elongation response. Comparative analysis of the shade-induced transcriptomes revealed differences between wild type and vascular patterning mutants and it appears that the latter mutants fail to induce sets of genes encoding biosynthetic and cell wall modifying enzymes. Our results thus set the stage for a deeper understanding of how growth and patterning are coordinated in a dynamic environment.

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  • 27.
    Bourdon, Matthieu
    et al.
    The Sainsbury Laboratory, University of Cambridge, Cambridge, UK; Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland.
    Vilaplana, Francisco
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center.
    Bulone, Vincent
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Glycoscience. College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia.
    Helariutta, Ykä
    The Sainsbury Laboratory, University of Cambridge, Cambridge, UK; Wood Development Group, University of Helsinki, Helsinki, Finland; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
    et al.,
    Ectopic callose deposition into woody biomass modulates the nano-architecture of macrofibrils2023In: Nature Plants, E-ISSN 2055-0278, Vol. 9, no 9, p. 1530-1546Article in journal (Refereed)
    Abstract [en]

    Plant biomass plays an increasingly important role in the circular bioeconomy, replacing non-renewable fossil resources. Genetic engineering of this lignocellulosic biomass could benefit biorefinery transformation chains by lowering economic and technological barriers to industrial processing. However, previous efforts have mostly targeted the major constituents of woody biomass: cellulose, hemicellulose and lignin. Here we report the engineering of wood structure through the introduction of callose, a polysaccharide novel to most secondary cell walls. Our multiscale analysis of genetically engineered poplar trees shows that callose deposition modulates cell wall porosity, water and lignin contents and increases the lignin–cellulose distance, ultimately resulting in substantially decreased biomass recalcitrance. We provide a model of the wood cell wall nano-architecture engineered to accommodate the hydrated callose inclusions. Ectopic polymer introduction into biomass manifests in new physico-chemical properties and offers new avenues when considering lignocellulose engineering.

  • 28.
    Boutté, Yohann
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Frescatada-Rosa, Márcia
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Men, Shuzhen
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Chow, Cheung-Ming
    Ebine, Kazuo
    Gustavsson, Anna
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Johansson, Lenore
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Ueda, Takashi
    Moore, Ian
    Jürgens, Gerd
    Grebe, Markus
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Endocytosis restricts Arabidopsis KNOLLE syntaxin to the cell division plane during late cytokinesis2010In: EMBO Journal, ISSN 0261-4189, E-ISSN 1460-2075, Vol. 29, no 3, p. 546-58Article in journal (Refereed)
    Abstract [en]

    Cytokinesis represents the final stage of eukaryotic cell division during which the cytoplasm becomes partitioned between daughter cells. The process differs to some extent between animal and plant cells, but proteins of the syntaxin family mediate membrane fusion in the plane of cell division in diverse organisms. How syntaxin localization is kept in check remains elusive. Here, we report that localization of the Arabidopsis KNOLLE syntaxin in the plane of cell division is maintained by sterol-dependent endocytosis involving a clathrin- and DYNAMIN-RELATED PROTEIN1A-dependent mechanism. On genetic or pharmacological interference with endocytosis, KNOLLE mis-localizes to lateral plasma membranes after cell-plate fusion. Fluorescence-loss-in-photo-bleaching and fluorescence-recovery-after-photo-bleaching experiments reveal lateral diffusion of GFP-KNOLLE from the plane of division to lateral membranes. In an endocytosis-defective sterol biosynthesis mutant displaying lateral KNOLLE diffusion, KNOLLE secretory trafficking remains unaffected. Thus, restriction of lateral diffusion by endocytosis may serve to maintain specificity of syntaxin localization during late cytokinesis.

  • 29. Bygdell, Joakim
    et al.
    Srivastava, Vaibhav
    KTH, School of Biotechnology (BIO), Glycoscience.
    Obudulu, Ogonna
    Srivastava, Manoj K.
    Nilsson, Robert
    Sundberg, Bjorn
    Trygg, Johan
    Mellerowicz, Ewa J.
    Wingsle, Gunnar
    Protein expression in tension wood formation monitored at high tissue resolution in Populus2017In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 68, no 13, p. 3405-3417Article in journal (Refereed)
    Abstract [en]

    Tension wood (TW) is a specialized tissue with contractile properties that is formed by the vascular cambium in response to gravitational stimuli. We quantitatively analysed the proteomes of Populus tremula cambium and its xylem cell derivatives in stems forming normal wood (NW) and TW to reveal the mechanisms underlying TW formation. Phloem-, cambium-, and wood-forming tissues were sampled by tangential cryosectioning and pooled into nine independent samples. The proteomes of TW and NW samples were similar in the phloem and cambium samples, but diverged early during xylogenesis, demonstrating that reprogramming is an integral part of TW formation. For example, 14-3-3, reactive oxygen species, ribosomal and ATPase complex proteins were found to be up-regulated at early stages of xylem differentiation during TW formation. At later stages of xylem differentiation, proteins involved in the biosynthesis of cellulose and enzymes involved in the biosynthesis of rhamnogalacturonan-I, rhamnogalacturonan-II, arabinogalactan-II and fasciclin-like arabinogalactan proteins were up-regulated in TW. Surprisingly, two isoforms of exostosin family proteins with putative xylan xylosyl transferase function and several lignin biosynthesis proteins were also up-regulated, even though xylan and lignin are known to be less abundant in TW than in NW. These data provided new insight into the processes behind TW formation.

  • 30.
    Bygdell, Joakim
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Srivastava, Vaibhav
    Obudulu, Ogonna
    Srivastava, Manoj K.
    Nilsson, Robert
    Sundberg, Björn
    Trygg, Johan
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mellerowicz, Ewa J.
    Wingsle, Gunnar
    Protein expression in tension wood formation monitored at high tissue resolution in Populus2017In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 68, no 13, p. 3405-3417Article in journal (Refereed)
    Abstract [en]

    Tension wood (TW) is a specialized tissue with contractile properties that is formed by the vascular cambium in response to gravitational stimuli. We quantitatively analysed the proteomes of Populus tremula cambium and its xylem cell derivatives in stems forming normal wood (NW) and TW to reveal the mechanisms underlying TW formation. Phloem-, cambium-, and wood-forming tissues were sampled by tangential cryosectioning and pooled into nine independent samples. The proteomes of TW and NW samples were similar in the phloem and cambium samples, but diverged early during xylogenesis, demonstrating that reprogramming is an integral part of TW formation. For example, 14-3-3, reactive oxygen species, ribosomal and ATPase complex proteins were found to be up-regulated at early stages of xylem differentiation during TW formation. At later stages of xylem differentiation, proteins involved in the biosynthesis of cellulose and enzymes involved in the biosynthesis of rhamnogalacturonan-I, rhamnogalacturonan-II, arabinogalactan-II and fasciclin-like arabinogalactan proteins were up-regulated in TW. Surprisingly, two isoforms of exostosin family proteins with putative xylan xylosyl transferase function and several lignin biosynthesis proteins were also up-regulated, even though xylan and lignin are known to be less abundant in TW than in NW. These data provided new insight into the processes behind TW formation.

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  • 31. Bünder, Anne
    et al.
    Sundman, Ola
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Mahboubi, Amir
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Persson, Staffan
    Mansfield, Shawn D.
    Rüggeberg, Markus
    Niittylä, Totte
    CELLULOSE SYNTHASE INTERACTING 1 is required for wood mechanics and leaf morphology in aspen2020In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 103, no 5, p. 1858-1868Article in journal (Refereed)
    Abstract [en]

    Cellulose microfibrils synthesized by CELLULOSE SYNTHASE COMPLEXES (CSCs) are the main load‐bearing polymers in wood. CELLULOSE SYNTHASE INTERACTING1 (CSI1) connects CSCs with cortical microtubules, which align with cellulose microfibrils. Mechanical properties of wood are dependent on cellulose microfibril alignment and structure in the cell walls, but the molecular mechanism(s) defining these features is unknown. Herein, we investigated the role of CSI1 in hybrid aspen (Populus tremula  × Populus tremuloides ) by characterizing transgenic lines with significantly reduced CSI1 transcript abundance. Reduction in leaves (50–80%) caused leaf twisting and misshaped pavement cells, while reduction (70–90%) in developing xylem led to impaired mechanical wood properties evident as a decrease in the elastic modulus and rupture. X‐ray diffraction measurements indicate that microfibril angle was not impacted by the altered CSI1 abundance in developing wood fibres. Instead, the augmented wood phenotype of the transgenic trees was associated with a reduced cellulose degree of polymerization. These findings establish a function for CSI1 in wood mechanics and in defining leaf cell shape. Furthermore, the results imply that the microfibril angle in wood is defined by CSI1 independent mechanism(s).

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  • 32.
    Canales, Javier
    et al.
    University of Malaga.
    Ávila, Concepción
    University of Malaga.
    Cantón, Francisco
    University of Malaga.
    Pacheco-Villalobos, David
    University of Malaga.
    Díaz-Moreno, Sara
    University of Malaga.
    Ariza, David
    University of Cordoba.
    Molina-Rueda, Juan
    University of Malaga.
    Navarro-Cerrillo, Rafael
    University of Cordoba.
    Claros, M.
    University of Malaga.
    Cánovas, Francisco
    University of Malaga.
    Gene expression profiling in the stem of young maritime pine trees: detection of ammonium stress-responsive genes in the apex2011In: Trees, ISSN 0931-1890, E-ISSN 1432-2285, Vol. 26, no 2, p. 609-619Article in journal (Refereed)
    Abstract [en]

    The shoots of young conifer trees represent an interesting model to study the development and growth of conifers from meristematic cells in the shoot apex to differentiated tissues at the shoot base. In this work, microarray analysis was used to monitor contrasting patterns of gene expression between the apex and the base ofmaritime pine shoots. A group of differentially expressed genes were selected and validated by examining their relative expression levels in different sections along thestem, from the top to the bottom. After validation of the microarray data, additional geneexpression analyses were also performed in the shoots of young maritime pine treesexposed to different levels of ammonium nutrition. Our results show that the apex ofmaritime pine trees is extremely sensitive to conditions of ammonium excess or deficiency, as revealed by the observed changes in the expression of stress-responsivegenes. This new knowledge may be used to precocious detection of early symptoms of nitrogen nutritional stresses, thereby increasing survival and growth rates of young treesin managed forests. 

  • 33.
    Carlsbecker, Annelie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Physiological Botany.
    Augstein, Frauke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Physiological Botany.
    Xylem versus phloem in secondary growth: a balancing act mediated by gibberellins2021In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 72, no 10, p. 3489-3492Article in journal (Other academic)
    Abstract [en]

    Secondary growth generates wood, which constitutes most of the plant biomass. Despite considerable efforts over the last decade to uncover the genetic and molecular regulation of the vascular cambium, there is still much to learn about how it produces wood (xylem) inward and bast (phloem) outward. Ben-Targem et al. (2021) now provide novel insight into how the hormones auxin and gibberellic acid (GA) govern the activity of the cambium, promoting a transition from formation of equal amounts of xylem and phloem to a stage where xylem formation dominates phloem in Arabidopsis hypocotyls, resembling wood formation in trees.

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  • 34.
    Castro Alves, Victor
    et al.
    Örebro University, School of Science and Technology.
    Kalbina, Irina
    Örebro University, School of Science and Technology.
    Nilsen, Asgeir
    Örebro University, School of Hospitality, Culinary Arts & Meal Science.
    Mats, Aronsson
    Svegro AB, Svartsjö, Sweden.
    Rosenqvist, Eva
    Section of Crop Sciences, Institute of Plant and Environmental Sciences, University of Copenhagen, Tåstrup, Denmark.
    Jansen, Marcel A K
    School of Biological, Earth and Environmental Sciences, Environmental Research Institute, University College Cork, North Mall, Cork, Ireland.
    Qian, Minjie
    School of Science and Technology, Örebro University, Örebro, Sweden.
    Öström, Åsa
    Örebro University, School of Hospitality, Culinary Arts & Meal Science.
    Hyötyläinen, Tuulia
    Örebro University, School of Science and Technology.
    Strid, Åke
    Örebro University, School of Science and Technology.
    Integration of non-target metabolomics and sensory analysis unravels vegetable plant metabolite signatures associated with sensory quality: A case study using dill (Anethum graveolens)2021In: Food Chemistry, ISSN 0308-8146, E-ISSN 1873-7072, Vol. 344, article id 128714Article in journal (Refereed)
    Abstract [en]

    Using dill (Anethum graveolens L.) as a model herb, we revealnovel associations between metabolite profile and sensory quality, by integrating non-target metabolomics with sensory data. Low night temperatures and exposure to UV-enriched light was used to modulate plant metabolism, thereby improving sensory quality. Plant age is a crucial factor associated with accumulation of dill ether and α-phellandrene, volatile compounds associated with dill flavour. However, sensory analysis showed that neither of these compounds has any strong association with dill taste. Rather, amino acids alanine, phenylalanine, glutamic acid, valine, and leucine increased in samples exposed to eustress and were positively associated with dill and sour taste. Increases in amino acids and organic acids changed the taste from lemon/grass to a more bitter/pungent dill-related taste. Our approach reveals a novel approach to establish links between effects of eustressors on sensory quality, and may be applicable to a broad range of crops.

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    Integration of non-target metabolomics and sensory analysis unravels vegetable plant metabolite signatures associated with sensory quality: A case study using dill (Anethum graveolens)
  • 35.
    Cañas, Rafael A
    et al.
    University of Malaga.
    Villalobos, David P
    University of Malaga.
    Díaz-Moreno, Sara
    University of Malaga.
    Cánovas, Francisco M
    University of Malaga.
    Cantón, Francisco R
    University of Malaga.
    Molecular and functional analyses support a role of Ornithine-{delta}-aminotransferase in the provision of glutamate for glutamine biosynthesis during pine germination2008In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 148, no 1, p. 77-88Article in journal (Refereed)
    Abstract [en]

    We report the molecular characterization and functional analysis of a gene (PsdeltaOAT) from Scots pine (Pinus sylvestris) encoding Orn-delta-aminotransferase (delta-OAT; EC 2.6.1.13), an enzyme of arginine metabolism. The deduced amino acid sequence contains a putative N-terminal signal peptide for mitochondrial targeting. The polypeptide is similar to other delta-OATs from plants, yeast, and mammals and encoded by a single-copy gene in pine. PsdeltaOAT encodes a functional delta-OAT as determined by expression of the recombinant protein in Escherichia coli and analysis of the active enzyme. The expression of PsdeltaOAT was undetectable in the embryo, but highly induced at early stages of germination and seedling development in all different organs. Transcript levels decreased in later developmental stages, although an increase was observed in lignified stems of 90-d-old plants. An increase of delta-OAT activity was observed in germinating embryos and seedlings and appears to mirror the observed alterations in PsdeltaOAT transcript levels. Similar expression patterns were also observed for genes encoding arginase and isocitrate dehydrogenase. Transcripts of PsdeltaOAT and the arginase gene were found widely distributed in different cell types of pine organs. Consistent with these results a metabolic pathway is proposed for the nitrogen flow from the megagametophyte to the developing seedling, which is also supported by the relative abundance of free amino acids in embryos and seedlings. Taken together, our data support that delta-OAT plays an important role in this process providing glutamate for glutamine biosynthesis during early pine growth.

  • 36.
    Chawade, Aakash
    et al.
    CropTailor AB, Lund, Sweden.
    Lindlöf, Angelica
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre. CropTailor AB, Lund, Sweden.
    Olsson, Björn
    University of Skövde, School of Life Sciences. University of Skövde, The Systems Biology Research Centre.
    Olsson, Olof
    CropTailor AB, Lund, Sweden ; Department of Pure and Applied Biochemistry, Lund University, Sweden.
    Global expression profiling of low temperature induced genes in the chilling tolerant japonica rice jumli marshi2013In: PLOS ONE, E-ISSN 1932-6203, Vol. 8, no 12, p. e81729-, article id e81729Article in journal (Refereed)
    Abstract [en]

    Low temperature is a key factor that limits growth and productivity of many important agronomical crops worldwide. Rice (Oryza sativa L.) is negatively affected already at temperatures below +10°C and is therefore denoted as chilling sensitive. However, chilling tolerant rice cultivars exist and can be commercially cultivated at altitudes up to 3,050 meters with temperatures reaching as low as +4°C. In this work, the global transcriptional response to cold stress (+4°C) was studied in the Nepalese highland variety Jumli Marshi (spp. japonica) and 4,636 genes were identified as significantly differentially expressed within 24 hours of cold stress. Comparison with previously published microarray data from one chilling tolerant and two sensitive rice cultivars identified 182 genes differentially expressed (DE) upon cold stress in all four rice cultivars and 511 genes DE only in the chilling tolerant rice. Promoter analysis of the 182 genes suggests a complex cross-talk between ABRE and CBF regulons. Promoter analysis of the 511 genes identified over-represented ABRE motifs but not DRE motifs, suggesting a role for ABA signaling in cold tolerance. Moreover, 2,101 genes were DE in Jumli Marshi alone. By chromosomal localization analysis, 473 of these cold responsive genes were located within 13 different QTLs previously identified as cold associated.

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  • 37.
    Chen, Yang-Er
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry. College of Life Sciences, Sichuan Agricultural University, Ya'an, China.
    Yuan, Shu
    Schröder, Wolfgang P.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Comparison of methods for extracting thylakoid membranes of Arabidopsis plants2016In: Physiologia Plantarum, ISSN 0031-9317, E-ISSN 1399-3054, Vol. 156, no 1, p. 3-12Article in journal (Refereed)
    Abstract [en]

    Robust and reproducible methods for extracting thylakoid membranes are required for the analysis of photosynthetic processes in higher plants such as Arabidopsis. Here, we compare three methods for thylakoid extraction using two different buffers. Method I involves homogenizing the plant material witha metal/glass blender; method II involves manually grinding the plant materialin ice-cold grinding buffer with a mortar and method III entails snap-freezing followed by manual grinding with a mortar, after which the frozen powder is thawed in isolation buffer. Thylakoid membrane samples extracted using each method were analyzed with respect to protein and chlorophyll content, yields relative to starting material, oxygen-evolving activity, protein complex content and phosphorylation. We also examined how the use of fresh and frozen thylakoid material affected the extracts’ contents of protein complexes. The use of different extraction buffers did not significantly alter the protein contentof the extracts in any case. Method I yielded thylakoid membranes with the highest purity and oxygen-evolving activity. Method III used low amounts of starting material and was capable of capturing rapid phosphorylation changes in the sample at the cost of higher levels of contamination. Method II yielded thylakoid membrane extracts with properties intermediate between those obtained with the other two methods. Finally, frozen and freshly isolated thylakoid membranes performed identically in blue native-polyacrylamide gel electrophoresis experiments conducted in order to separate multimeric protein supracomplexes.

  • 38. Cho, Sung Hyun
    et al.
    Purushotham, Pallinti
    Fang, Chao
    Maranas, Cassandra
    Diaz-Moreno, Sara M
    KTH, School of Biotechnology (BIO), Glycoscience.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Zimmer, Jochen
    Kumar, Manish
    Nixon, B. Tracy
    Synthesis and Self-Assembly of Cellulose Microfibrils from Reconstituted Cellulose Synthase2017In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 175, no 1, p. 146-156Article in journal (Refereed)
    Abstract [en]

    Cellulose, the major component of plant cell walls, can be converted to bioethanol and is thus highly studied. In plants, cellulose is produced by cellulose synthase, a processive family-2 glycosyltransferase. In plant cell walls, individual beta-1,4-glucan chains polymerized by CesA are assembled into microfibrils that are frequently bundled into macrofibrils. An in vitro system in which cellulose is synthesized and assembled into fibrils would facilitate detailed study of this process. Here, we report the heterologous expression and partial purification of His-tagged CesA5 from Physcomitrella patens. Immunoblot analysis and mass spectrometry confirmed enrichment of PpCesA5. The recombinant protein was functional when reconstituted into liposomes made from yeast total lipid extract. The functional studies included incorporation of radiolabeled Glc, linkage analysis, and imaging of cellulose microfibril formation using transmission electron microscopy. Several microfibrils were observed either inside or on the outer surface of proteoliposomes, and strikingly, several thinner fibrils formed ordered bundles that either covered the surfaces of proteoliposomes or were spawned from liposome surfaces. We also report this arrangement of fibrils made by proteoliposomes bearing CesA8 from hybrid aspen. These observations describe minimal systems of membrane-reconstituted CesAs that polymerize beta-1,4-glucan chains that coalesce to form microfibrils and higher-ordered macrofibrils. How these micro-and macrofibrils relate to those found in primary and secondary plant cell walls is uncertain, but their presence enables further study of the mechanisms that govern the formation and assembly of fibrillar cellulosic structures and cell wall composites during or after the polymerization process controlled by CesA proteins.

  • 39.
    Choong, Ferdinand X.
    et al.
    Karolinska Inst, Dept Neurosci, Swedish Med Nanosci Ctr, SE-17177 Stockholm, Sweden..
    Back, Marcus
    Linkoping Univ, IFM, Dept Chem, SE-58183 Linkoping, Sweden..
    Schulz, Anette
    Karolinska Inst, Dept Neurosci, Swedish Med Nanosci Ctr, SE-17177 Stockholm, Sweden..
    Nilsson, K. Peter. R.
    Linkoping Univ, IFM, Dept Chem, SE-58183 Linkoping, Sweden..
    Edlund, Ulrica
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Richter-Dahlfors, Agneta
    Karolinska Inst, Dept Neurosci, Swedish Med Nanosci Ctr, SE-17177 Stockholm, Sweden..
    Stereochemical identification of glucans by oligothiophenes enables cellulose anatomical mapping in plant tissues2018In: Scientific Reports, E-ISSN 2045-2322, Vol. 8, article id 3108Article in journal (Refereed)
    Abstract [en]

    Efficient use of plant-derived materials requires enabling technologies for non-disruptive composition analysis. The ability to identify and spatially locate polysaccharides in native plant tissues is difficult but essential. Here, we develop an optical method for cellulose identification using the structure-responsive, heptameric oligothiophene h-FTAA as molecular fluorophore. Spectrophotometric analysis of h-FTAA interacting with closely related glucans revealed an exceptional specificity for beta-linked glucans. This optical, non-disruptive method for stereochemical differentiation of glycosidic linkages was next used for in situ composition analysis in plants. Multi-laser/multi-detector analysis developed herein revealed spatial localization of cellulose and structural cell wall features such as plasmodesmata and perforated sieve plates of the phloem. Simultaneous imaging of intrinsically fluorescent components revealed the spatial relationship between cell walls and other organelles, such as chloroplasts and lignified annular thickenings of the trachea, with precision at the sub-cellular scale. Our non-destructive method for cellulose identification lays the foundation for the emergence of anatomical maps of the chemical constituents in plant tissues. This rapid and versatile method will likely benefit the plant science research fields and may serve the biorefinery industry as reporter for feedstock optimization as well as in-line monitoring of cellulose reactions during standard operations.

  • 40. Chow, Wah Soon
    et al.
    Lee, Hae-Youn
    He, Jie
    Hendrickson, Luke
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Research School of Biological Sciences, Australian National University, GPO Box 475, Canberra, ACT 2601, Australia.
    Hong, Young-Nam
    Matsubara, Shizue
    Photoinactivation of photosystem II in leaves2005In: Photosynthesis Research, ISSN 0166-8595, E-ISSN 1573-5079, Vol. 84, no 1-3, p. 35-41Article in journal (Refereed)
    Abstract [en]

    Photoinactivation of Photosystem II (PS II), the light-induced loss of ability to evolve oxygen, inevitably occurs under any light environment in nature, counteracted by repair. Under certain conditions, the extent of photoinactivation of PS II depends on the photon exposure (light dosage, x), rather than the irradiance or duration of illumination per se, thus obeying the law of reciprocity of irradiance and duration of illumination, namely, that equal photon exposure produces an equal effect. If the probability of photoinactivation (p) of PS II is directly proportional to an increment in photon exposure (p = kDeltax, where k is the probability per unit photon exposure), it can be deduced that the number of active PS II complexes decreases exponentially as a function of photon exposure: N = Noexp(-kx). Further, since a photon exposure is usually achieved by varying the illumination time (t) at constant irradiance (I), N = Noexp(-kI t), i.e., N decreases exponentially with time, with a rate coefficient of photoinactivation kI, where the product kI is obviously directly proportional to I. Given that N = Noexp(-kx), the quantum yield of photoinactivation of PS II can be defined as -dN/dx = kN, which varies with the number of active PS II complexes remaining. Typically, the quantum yield of photoinactivation of PS II is ca. 0.1micromol PS II per mol photons at low photon exposure when repair is inhibited. That is, when about 10(7) photons have been received by leaf tissue, one PS II complex is inactivated. Some species such as grapevine have a much lower quantum yield of photoinactivation of PS II, even at a chilling temperature. Examination of the longer-term time course of photoinactivation of PS II in capsicum leaves reveals that the decrease in N deviates from a single-exponential decay when the majority of the PS II complexes are inactivated in the absence of repair. This can be attributed to the formation of strong quenchers in severely-photoinactivated PS II complexes, able to dissipate excitation energy efficiently and to protect the remaining active neighbours against damage by light.

  • 41. Cifuentes, Carolina
    et al.
    Bulone, Vincent
    KTH, School of Biotechnology (BIO), Glycoscience.
    Emons, Anne Mie C.
    Biosynthesis of Callose and Cellulose by Detergent Extracts of Tobacco Cell Membranes and Quantification of the Polymers Synthesized in vitro2010In: J INTEGR PLANT BIOL, ISSN 1672-9072, Vol. 52, no 2, p. 221-233Article in journal (Refereed)
    Abstract [en]

    The conditions that favor the in vitro synthesis of cellulose from tobacco BY-2 cell extracts were determined. The procedure leading to the highest yield of cellulose consisted of incubating digitonin extracts of membranes from 11-day-old tobacco BY-2 cells in the presence of 1 mM UDP-glucose, 8 mM Ca2+ and 8 mM Mg2+. Under these conditions, up to nearly 40% of the polysaccharides synthesized in vitro corresponded to cellulose, the other polymer synthesized being callose. Transmission electron microscopy analysis revealed the occurrence of two types of structures in the synthetic reactions. The first type consisted of small aggregates with a diameter between 3 and 5 nm that associated to form fibrillar strings of a maximum length of 400 nm. These structures were sensitive to the acetic/nitric acid treatment of Updegraff and corresponded to callose. The second type of structures was resistant to the Updegraff reagent and corresponded to straight cellulose microfibrils of 2-3 nm in diameter and 200 nm to up to 5 mu m in length. In vitro reactions performed on electron microscopy grids indicated that the minimal rate of microfibril elongation in vitro is 120 nm/min. Measurements of retardance by liquid crystal polarization microscopy as a function of time showed that small groups of microfibrils increased in retardance by up to 0.047 nm/min per pixel, confirming the formation of organized structures.

  • 42.
    Clergeot, Pierre-Henri
    et al.
    Stockholm University.
    Rivetti, Claudia
    Stockholm University.
    Hamiduzzaman, M. Md.
    Stockholm University.
    Ekengren, Sophia
    Stockholm University.
    The corky root rot pathogen, Pyrenochaeta lycopersici manipulates tomato roots with molecules secreted early during their interaction2012In: Acta Agriculturae Scandinavica - Section B, ISSN 0906-4710, E-ISSN 1651-1913, Vol. 62, no 4, p. 300-310Article in journal (Refereed)
    Abstract [en]

    Corky root rot is a ubiquitous soil-borne disease of tomato caused by the pathogen Pyrenochaeta lycopersici. This filamentous fungus is found on the roots of many crops and can persist in the soil up to 15 years as microsclerotia. High prevalence of corky root rot can be partly explained by the endurance and the broad host range of P. lycopersici, but how this fungus can gain access to host roots is still poorly understood, as its competitive saprophytic ability is very low. We have combined microscopy and reporter gene techniques to investigate the tomato-P. lycopersici interaction in vitro, and discovered the pathogen secretes molecules that change the direction of root growth and induce cell necrosis specifically in the apical part of the root of tomato ( apex, elongation zone and beginning of the root hair zone). Moreover, we found that the fungus preferentially infects immature root cells that are sensitive to these secreted fungal molecules, whereas infection is blocked in mature and insensitive parts of the root. Our study sheds light on novel and important features of the biology of this pathogen, which could contribute to its fitness in the rhizosphere.

  • 43.
    Cocco, Emma
    et al.
    Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, Università degli Studi di Cagliari, Cagliari, Italy; Laboratory of Economic and Pharmaceutical Botany, Department of Life and Environmental Sciences, Università degli Studi di Cagliari, Cagliari, Italy.
    Farci, Domenica
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Haniewicz, Patrycja
    Department of Plant Physiology, Warsaw University of Life Sciences—SGGW, Warsaw, Poland.
    Schröder, Wolfgang P.
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Maxia, Andrea
    Laboratory of Economic and Pharmaceutical Botany, Department of Life and Environmental Sciences, Università degli Studi di Cagliari, Cagliari, Italy.
    Piano, Dario
    Laboratory of Plant Physiology and Photobiology, Department of Life and Environmental Sciences, Università degli Studi di Cagliari, Cagliari, Italy.
    The Influence of Blue and Red Light on Seed Development and Dormancy in Nicotiana tabacum L.2022In: Seeds, ISSN 2674-1024, Vol. 1, no 3, p. 152-163Article in journal (Refereed)
    Abstract [en]

    The correct development of seeds is a pivotal requirement for species preservation. This process depends on the balance between sensing the environmental stimuli/stressors and hormone-mediated transduction, which results in physiological responses. The red and blue regions of the electromagnetic spectrum are known to influence seed dormancy and germination. Here, we report on the effects induced by the blue (peak at 430 nm) and red (peak at 650 nm) regions of the electromagnetic spectrum on seeds from photo- and skotomorphogenetic capsules developed under white, blue, or red light. Regardless of exposure, seeds from skotomorphogenetic capsules showed an almost absent dormancy in association with altered germination kinetics. Conversely, in seeds from photomorphogenetic capsules, the exposure to the blue region induced skotomorphogenetic-like effects, while the exposure to the whole visible range (350–750 nm), as well as to only the red region, showed a dose-related trend. The observed differences appeared to be dependent on the wavelengths in the red and to be based on transduction mechanisms taking place in fruits. While the molecular bases of this differential effect need to be clarified, the results hint at the role played by different light wavelengths and intensities in seed development and germination. These findings may be relevant for applications in crop production and species safeguarding.

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  • 44.
    Collazos Matute, Álvaro
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science.
    Use of Feruloyl Esterases and Xylanases for the valorization of Feruloylated-Arabinoxylans from Wheat bran2021Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    This research work studied the use of CAZymes for the sustainable valorization of wheat bran as a potential source for bioactive carbohydrates, in the form feruloylated-arabinoxylans (F-AXs) present in this cereal by-product. In order to extract the recalcitrant fraction of F-AXs, specific CAZymes have been tested. Feruloyl esterases (FAEs) have been characterized in model and commercial substrates, showing that the FAE with highest activity and substrate specificity is the enzyme 29492, the one that, together with the FAE U2BHX, also has an unexpected activity rapidly creating other compounds, like a dimer 5,5-diFA’ from free FA. Also, Xylanases and FAEs have been analyzed in insoluble real substrate (wheat bran), demonstrating that the best enzymes to extract this antioxidant biopolymers are FAE 22198 and xylanase AcXyn10A CBM1C, due to the presence of CBM in both structures. Then, the use of CAZymes, combined with destaching pre-treatments and SWE extractions would allow a better use of residual matter, thus promoting a more eco-friendly circular economy.

  • 45.
    Curci, Pasquale Luca
    et al.
    Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, Belgium; Institute of Biosciences and Bioresources, National Research Council (CNR), Via Amendola 165/A, Bari, Italy.
    Zhang, Jie
    Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, Belgium.
    Mähler, Niklas
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Seyfferth, Carolin
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, Belgium.
    Mannapperuma, Chanaka
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Diels, Tim
    Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, Belgium.
    Van Hautegem, Tom
    Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, Belgium.
    Jonsen, David
    SweTree Technologies AB, Skogsmarksgränd 7, Umeå, Sweden.
    Street, Nathaniel
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Hvidsten, Torgeir R.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.
    Hertzberg, Magnus
    SweTree Technologies AB, Umeå, Sweden.
    Nilsson, Ove
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre (UPSC), Swedish University of Agricultural Sciences, Umeå, Sweden.
    Inzé, Dirk
    Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, Belgium.
    Nelissen, Hilde
    Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, Belgium.
    Vandepoele, Klaas
    Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Technologiepark 71, Ghent, Belgium.
    Identification of growth regulators using cross-species network analysis in plants2022In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 190, no 4, p. 2350-2365Article in journal (Refereed)
    Abstract [en]

    With the need to increase plant productivity, one of the challenges plant scientists are facing is to identify genes that play a role in beneficial plant traits. Moreover, even when such genes are found, it is generally not trivial to transfer this knowledge about gene function across species to identify functional orthologs. Here, we focused on the leaf to study plant growth. First, we built leaf growth transcriptional networks in Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and aspen (Populus tremula). Next, known growth regulators, here defined as genes that when mutated or ectopically expressed alter plant growth, together with cross-species conserved networks, were used as guides to predict novel Arabidopsis growth regulators. Using an in-depth literature screening, 34 out of 100 top predicted growth regulators were confirmed to affect leaf phenotype when mutated or overexpressed and thus represent novel potential growth regulators. Globally, these growth regulators were involved in cell cycle, plant defense responses, gibberellin, auxin, and brassinosteroid signaling. Phenotypic characterization of loss-of-function lines confirmed two predicted growth regulators to be involved in leaf growth (NPF6.4 and LATE MERISTEM IDENTITY2). In conclusion, the presented network approach offers an integrative cross-species strategy to identify genes involved in plant growth and development.

  • 46.
    Danielsson, Marie
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry.
    Zhao, Tao
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Organic chemistry. Department of Science and Technology, Örebro University, Örebro, Sweden.
    Borg-Karlson, Anna-Karin
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Chemistry, Organic chemistry.
    Arthropod infestation sites and induced defence can be traced by emission from single spruce needles2019In: Arthropod-Plant Interactions, ISSN 1872-8855, E-ISSN 1872-8847, Vol. 13, no 2, p. 253-259Article in journal (Refereed)
    Abstract [en]

    Emissions of defence chemicals from Norway spruce seedlings can be induced by feeding arthropods or by exogenous hormonal application. Some defence chemicals may attract or repel associated arthropods. The aim of this study was to show that it is possible to detect and collect stress-induced volatiles from micro sites, such as at the scale of a single needle, in vivo by using SPME. Methyl jasmonate application on the stem of Norway spruce seedlings induced emission of (E)-beta-farnesene only from the needles closest to the application site. Emissions of (E)-beta-farnesene, (E,E)-alpha-farnesene and (E)-alpha-bisabolene were only detected from needles infested by the spider mite Oligonychus ununguis. The total volatile amount detected by SPME-GC-MS reached a considerable mass of 14 ng/needle/24 h, suggesting that emission from damaged and stressed conifers might have a larger impact on the macro climate than previously estimated.

  • 47. Dauphinee, Adrian N.
    et al.
    Cardoso, Catarina
    Dalman, Kerstin
    Ohlsson, Jonas A.
    Berglund Fick, Stina
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Robert, Stephanie
    Hicks, Glenn R.
    Bozhkov, Peter V
    Minina, Elena A.
    Chemical Screening Pipeline for Identification of Specific Plant Autophagy Modulators2019In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 181, no 3, p. 855-866Article in journal (Refereed)
    Abstract [en]

    Autophagy is a major catabolic process in eukaryotes with a key role in homeostasis, programmed cell death, and aging. In plants, autophagy is also known to regulate agronomically important traits such as stress resistance, longevity, vegetative biomass, and seed yield. Despite its significance, there is still a shortage of reliable tools modulating plant autophagy. Here, we describe the first robust pipeline for identification of specific plant autophagy-modulating compounds. Our screening protocol comprises four phases: (1) high-throughput screening of chemical compounds in cell cultures of tobacco (Nicotiana tabacum); (2) confirmation of the identified hits in planta using Arabidopsis (Arabidopsis thaliana); (3) further characterization of the effect using conventional molecular biology methods; and (4) verification of chemical specificity on autophagy in planta. The methods detailed here streamline the identification of specific plant autophagy modulators and aid in unraveling the molecular mechanisms of plant autophagy.

  • 48.
    Decker, Daniel
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    UDP-sugar metabolizing pyrophosphorylases in plants: formation of precursors for essential glycosylation-reactions2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    UDP-sugar metabolizing pyrophosphorylases provide the primary mechanism for de novo synthesis of UDP-sugars, which can then be used for myriads of glycosyltranferase reactions, producing cell wall carbohydrates, sucrose, glycoproteins and glycolipids, as well as many other glycosylated compounds. The pyrophosphorylases can be divided into three families: UDP-Glc pyrophosphorylase (UGPase), UDP-sugar pyrophosphorylase (USPase) and UDP-N-acety lglucosamine pyrophosphorylase (UAGPase), which can be discriminated both by differences in accepted substrate range and amino acid sequences.

    This thesis focuses both on experimental examination (and re-examination) of some enzymatic/ biochemical properties of selected members of the UGPases and USPases and UAGPase families and on the design and implementation of a strategy to study in vivo roles of these pyrophosphorylases using specific inhibitors. In the first part, substrate specificities of members of the Arabidopsis UGPase, USPase and UAGPase families were comprehensively surveyed and kinetically analyzed, with barley UGPase also further studied with regard to itspH dependency, regulation by oligomerization, etc. Whereas all the enzymes preferentially used UTP as nucleotide donor, they differed in their specificity for sugar-1-P. UGPases had high activity with D-Glc-1-P, but could also react with Frc-1-P, whereas USPase reacted with arange of sugar-1-phosphates, including D-Glc-1-P, D-Gal-1-P, D-GalA-1-P, β-L-Ara-1-P and α-D-Fuc-1-P. In contrast, UAGPase2 reacted only with D-GlcNAc-1-P, D-GalNAc-1-P and, to some extent, with D-Glc-1-P. A structure activity relationship was established to connect enzyme activity, the examined sugar-1-phosphates and the three pyrophosphorylases. The UGPase/USPase/UAGPase active sites were subsequently compared in an attempt to identify amino acids which may contribute to the experimentally determined differences in substrate specificities.

    The second part of the thesis deals with identification and characterization of inhibitors of the pyrophosphorylases and with studies on in vivo effects of those inhibitors in Arabidopsis-based systems. A novel luminescence-based high-throughput assay system was designed, which allowed for quantitative measurement of UGPase and USPase activities, down to a pmol per min level. The assay was then used to screen a chemical library (which contained 17,500 potential inhibitors) to identify several compounds affecting UGPase and USPase. Hit-optimization on one of the compounds revealed even stronger inhibitors of UGPase and USPase which also strongly inhibited Arabidopsis pollen germination, by disturbing UDP-sugar metabolism. The inhibitors may represent useful tools to study in vivo roles of the pyrophosphorylases, as a complement to previous genetics-based studies.

    The thesis also includes two review papers on mechanisms of synthesis of NDP-sugars. The first review covered the characterization of USPase from both prokaryotic and eukaryotic organisms, whereas the second review was a comprehensive survey of NDP-sugar producing enzymes (not only UDP-sugar producing and not only pyrophosphorylases). All these enzymes were discussed with respect to their substrate specificities and structural features (if known) and their proposed in vivo functions.

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  • 49.
    Decker, Daniel
    et al.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Öberg, Christopher
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Kleczkowski, Leszek A.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Identification and characterization of inhibitors of UDP-glucose and UDP-sugar pyrophosphorylases for in vivo studies2017In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 90, no 6, p. 1093-1107Article in journal (Other academic)
    Abstract [en]

    UDP-sugars serve as ultimate precursors in hundreds of glycosylation reactions (e.g. for protein and lipid glycosylation, synthesis of sucrose, cell wall polysaccharides, etc.), underlying an important role of UDP-sugar-producing enzymes in cellular metabolism. However, genetic studies on mechanisms of UDP-sugar formation were frequently hampered by reproductive impairment of the resulting mutants, making it difficult to assess an in vivo role of a given enzyme. Here, a chemical library containing 17 500 compounds was separately screened against purified UDP-glucose pyrophosphorylase (UGPase) and UDP-sugar pyrophosphorylase (USPase), both enzymes representing the primary mechanisms of UDP-sugar formation. Several compounds have been identified which, at 50 μm, exerted at least 50% inhibition of the pyrophosphorylase activity. In all cases, both UGPase and USPase activities were inhibited, probably reflecting common structural features of active sites of these enzymes. One of these compounds (cmp #6), a salicylamide derivative, was found as effective inhibitor of Arabidopsis pollen germination and Arabidopsis cell culture growth. Hit optimization on cmp #6 yielded two analogs (cmp #6D and cmp #6D2), which acted as uncompetitive inhibitors against both UGPase and USPase, and were strong inhibitors in the pollen test, with apparent inhibition constants of less than 1 μm. Their effects on pollen germination were relieved by addition of UDP-glucose and UDP-galactose, suggesting that the inhibitors targeted UDP-sugar formation. The results suggest that cmp #6 and its analogs may represent useful tools to study in vivo roles of the pyrophosphorylases, helping to overcome the limitations of genetic approaches.

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  • 50. Derba-Maceluch, Marta
    et al.
    Amini, Fariba
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Biology Department, Faculty of Science, Arak University, Arak, Iran.
    Donev, Evgeniy N.
    Pawar, Prashant Mohan-Anupama
    Michaud, Lisa
    Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Johansson, Ulf
    Albrectsen, Benedicte Riber
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Mellerowicz, Ewa J.
    Cell Wall Acetylation in Hybrid Aspen Affects Field Performance, Foliar Phenolic Composition and Resistance to Biological Stress Factors in a Construct-Dependent Fashion2020In: Frontiers in Plant Science, E-ISSN 1664-462X, Vol. 11, article id 651Article in journal (Refereed)
    Abstract [en]

    The production of biofuels and "green" chemicals from the lignocellulose of fast-growing hardwood species is hampered by extensive acetylation of xylan. Different strategies have been implemented to reduce xylan acetylation, resulting in transgenic plants that show good growth in the greenhouse, improved saccharification and fermentation, but the field performance of such plants has not yet been reported. The aim of this study was to evaluate the impact of reduced acetylation on field productivity and identify the best strategies for decreasing acetylation. Growth and biological stress data were evaluated for 18 hybrid aspen lines with 10-20% reductions in the cell wall acetyl content from a five year field experiment in Southern Sweden. The reduction in acetyl content was achieved either by suppressing the process of acetylation in the Golgi by reducing expression of REDUCED WALL ACETYLATION (RWA) genes, or by post-synthetic acetyl removal by fungal acetyl xylan esterases (AXEs) from two different families, CE1 and CE5, targeting them to cell walls. Transgene expression was regulated by either a constitutive promoter (35S) or a wood-specific promoter (WP). For the majority of transgenic lines, growth was either similar to that in WT and transgenic control (WP:GUS) plants, or slightly reduced. The slight reduction was observed in the AXE-expressing lines regulated by the 35S promoter, not those with the WP promoter which limits expression to cells developing secondary walls. Expressing AXEs regulated by the 35S promoter resulted in increased foliar arthropod chewing, and altered condensed tannins and salicinoid phenolic glucosides (SPGs) profiles. Greater growth inhibition was observed in the case of CE5 than with CE1 AXE, and it was associated with increased foliar necrosis and distinct SPG profiles, suggesting that CE5 AXE could be recognized by the pathogen-associated molecular pattern system. For each of three different constructs, there was a line with dwarfism and growth abnormalities, suggesting random genetic/epigenetic changes. This high frequency of dwarfism (17%) is suggestive of a link between acetyl metabolism and chromatin function. These data represent the first evaluation of acetyl-reduced plants from the field, indicating some possible pitfalls, and identifying the best strategies, when developing highly productive acetyl-reduced feedstocks.

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