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Controlled processivity in glycosyltransferases: A way to expand the enzymatic toolbox. Biotechnol Adv 2023; 63:108081. [PMID: 36529206 DOI: 10.1016/j.biotechadv.2022.108081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/20/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022]
Abstract
Glycosyltransferases (GT) catalyse the biosynthesis of complex carbohydrates which are the most abundant group of molecules in nature. They are involved in several key mechanisms such as cell signalling, biofilm formation, host immune system invasion or cell structure and this in both prokaryotic and eukaryotic cells. As a result, research towards complete enzyme mechanisms is valuable to understand and elucidate specific structure-function relationships in this group of molecules. In a next step this knowledge could be used in GT protein engineering, not only for rational drug design but also for multiple biotechnological production processes, such as the biosynthesis of hyaluronan, cellooligosaccharides or chitooligosaccharides. Generation of these poly- and/or oligosaccharides is possible due to a common feature of several of these GTs: processivity. Enzymatic processivity has the ability to hold on to the growing polymer chain and some of these GTs can even control the number of glycosyl transfers. In a first part, recent advances in understanding the mechanism of various processive enzymes are discussed. To this end, an overview is given of possible engineering strategies for the purpose of new industrial and fundamental applications. In the second part of this review, we focused on specific chain length-controlling mechanisms, i.e., key residues or conserved regions, and this for both eukaryotic and prokaryotic enzymes.
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Maceda-López LF, Góngora-Castillo EB, Ibarra-Laclette E, Morán-Velázquez DC, Girón Ramírez A, Bourdon M, Villalpando-Aguilar JL, Toomer G, Tang JZ, Azadi P, Santamaría JM, López-Rosas I, López MG, Simpson J, Alatorre-Cobos F. Transcriptome Mining Provides Insights into Cell Wall Metabolism and Fiber Lignification in Agave tequilana Weber. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11111496. [PMID: 35684270 PMCID: PMC9182668 DOI: 10.3390/plants11111496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 05/08/2023]
Abstract
Resilience of growing in arid and semiarid regions and a high capacity of accumulating sugar-rich biomass with low lignin percentages have placed Agave species as an emerging bioenergy crop. Although transcriptome sequencing of fiber-producing agave species has been explored, molecular bases that control wall cell biogenesis and metabolism in agave species are still poorly understood. Here, through RNAseq data mining, we reconstructed the cellulose biosynthesis pathway and the phenylpropanoid route producing lignin monomers in A. tequilana, and evaluated their expression patterns in silico and experimentally. Most of the orthologs retrieved showed differential expression levels when they were analyzed in different tissues with contrasting cellulose and lignin accumulation. Phylogenetic and structural motif analyses of putative CESA and CAD proteins allowed to identify those potentially involved with secondary cell wall formation. RT-qPCR assays revealed enhanced expression levels of AtqCAD5 and AtqCESA7 in parenchyma cells associated with extraxylary fibers, suggesting a mechanism of formation of sclerenchyma fibers in Agave similar to that reported for xylem cells in model eudicots. Overall, our results provide a framework for understanding molecular bases underlying cell wall biogenesis in Agave species studying mechanisms involving in leaf fiber development in monocots.
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Affiliation(s)
- Luis F. Maceda-López
- Colegio de Postgraduados, Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico; (L.F.M.-L.); (D.C.M.-V.); (J.L.V.-A.)
| | - Elsa B. Góngora-Castillo
- CONACYT-Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 × 32 y 34, Chuburná de Hidalgo, Mérida 97205, Mexico;
| | - Enrique Ibarra-Laclette
- Red de Estudios Moleculares Avanzados, Instituto de Ecología A. C. Carretera Antigua a Coatepec 351, El Haya, Xalapa 91070, Mexico;
| | - Dalia C. Morán-Velázquez
- Colegio de Postgraduados, Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico; (L.F.M.-L.); (D.C.M.-V.); (J.L.V.-A.)
| | - Amaranta Girón Ramírez
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 × 32 y 34, Chuburná de Hidalgo, Mérida 97205, Mexico; (A.G.R.); (J.M.S.)
| | - Matthieu Bourdon
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK;
| | - José L. Villalpando-Aguilar
- Colegio de Postgraduados, Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico; (L.F.M.-L.); (D.C.M.-V.); (J.L.V.-A.)
| | - Gabriela Toomer
- Division of Microbiology and Molecular Biology, IIT Research Institute, Chicago, IL 60616, USA;
| | - John Z. Tang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (J.Z.T.); (P.A.)
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (J.Z.T.); (P.A.)
| | - Jorge M. Santamaría
- Centro de Investigación Científica de Yucatán, Unidad de Biotecnología, Calle 43 No. 130 × 32 y 34, Chuburná de Hidalgo, Mérida 97205, Mexico; (A.G.R.); (J.M.S.)
| | - Itzel López-Rosas
- CONACYT-Colegio de Postgraduados Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico;
| | - Mercedes G. López
- Departmento de Biotecnología y Bioquímica, Centro de Investigación y Estudios Avanzados del IPN, Irapuato 36824, Mexico;
| | - June Simpson
- Departmento de Ingeniería Genetica, Centro de Investigación y Estudios Avanzados del IPN, Irapuato 36824, Mexico;
| | - Fulgencio Alatorre-Cobos
- CONACYT-Colegio de Postgraduados Campus Campeche, Carretera Haltunchén-Edzná km 17.5, Sihochac, Campeche 24450, Mexico;
- Correspondence:
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Pancaldi F, van Loo EN, Schranz ME, Trindade LM. Genomic Architecture and Evolution of the Cellulose synthase Gene Superfamily as Revealed by Phylogenomic Analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:870818. [PMID: 35519813 PMCID: PMC9062648 DOI: 10.3389/fpls.2022.870818] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
The Cellulose synthase superfamily synthesizes cellulose and different hemicellulosic polysaccharides in plant cell walls. While much has been discovered about the evolution and function of these genes, their genomic architecture and relationship with gene (sub-)functionalization and evolution remains unclear. By using 242 genomes covering plant evolution from green algae to eudicots, we performed a large-scale analysis of synteny, phylogenetic, and functional data of the CesA superfamily. Results revealed considerable gene copy number variation across species and gene families, and also two patterns - singletons vs. tandem arrays - in chromosomic gene arrangement. Synteny analysis revealed exceptional conservation of gene architecture across species, but also lineage-specific patterns across gene (sub-)families. Synteny patterns correlated with gene sub-functionalization into primary and secondary CesAs and distinct CslD functional isoforms. Furthermore, a genomic context shift of a group of cotton secondary CesAs was associated with peculiar properties of cotton fiber synthesis. Finally, phylogenetics suggested that primary CesA sequences appeared before the secondary CesAs, while phylogenomic analyses unveiled the genomic trace of the CslD duplication that initiated the CslF family. Our results describe in detail the genomic architecture of the CesA superfamily in plants, highlighting its crucial relevance for gene diversification and sub-functionalization, and for understanding their evolution.
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Affiliation(s)
- Francesco Pancaldi
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | | | - M. Eric Schranz
- Biosystematics group, Wageningen University & Research, Wageningen, Netherlands
| | - Luisa M. Trindade
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
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Liu X, Zhang H, Zhang W, Xu W, Li S, Chen X, Chen H. Genome-wide bioinformatics analysis of Cellulose Synthase gene family in common bean (Phaseolus vulgaris L.) and the expression in the pod development. BMC Genom Data 2022; 23:9. [PMID: 35093018 PMCID: PMC8801070 DOI: 10.1186/s12863-022-01026-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 01/10/2022] [Indexed: 11/18/2022] Open
Abstract
Background CesA and Csl gene families, which belong to the cellulose synthase gene superfamily, plays an important role in the biosynthesis of the plant cell wall. Although researchers have investigated this gene superfamily in several model plants, to date, no comprehensive analysis has been conducted in the common bean. Results In this study, we identified 39 putative cellulose synthase genes from the common bean genome sequence. Then, we performed a bioinformatics analysis of this gene family involving sequence alignment, phylogenetic analysis, gene structure, collinearity analysis and chromosome location. We found all members possess a cellulose_synt domain. Phylogenetic analysis revealed that these cellulose synthase genes may be classified into five subfamilies, and that members in the same subfamily share conserved exon-intron distribution and motif compositions. Abundant and distinct cis-acting elements in the 2 k basepairs upstream regulatory regions indicate that the cellulose synthase gene family may plays a vital role in the growth and development of common bean. Moreover, the 39 cellulose synthase genes are distributed on 10 of the 11 chromosomes. Additionally expression analysis shows that all CesA/Csl genes selected are constitutively expressed in the pod development. Conclusions This research reveals both the putative biochemical and physiological functions of cellulose synthase genes in common bean and implies the importance of studying non-model plants to understand the breadth and diversity of cellulose synthase genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01026-0.
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Affiliation(s)
- Xiaoqing Liu
- Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Nanjing, 210014, China
| | - Hongmei Zhang
- Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Nanjing, 210014, China
| | - Wei Zhang
- Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Nanjing, 210014, China
| | - Wenjing Xu
- Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Nanjing, 210014, China
| | - Songsong Li
- Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Nanjing, 210014, China
| | - Xin Chen
- Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Nanjing, 210014, China.
| | - Huatao Chen
- Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Industrial Crops, Nanjing, 210014, China.
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Malik P, Kumar J, Sharma S, Sharma R, Sharma S. Multi-locus genome-wide association mapping for spike-related traits in bread wheat (Triticum aestivum L.). BMC Genomics 2021; 22:597. [PMID: 34353288 PMCID: PMC8340506 DOI: 10.1186/s12864-021-07834-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 06/23/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Bread wheat (Triticum aestivum L.) is one of the most important cereal food crops for the global population. Spike-layer uniformity (the consistency of the spike distribution in the vertical space)-related traits (SLURTs) are quantitative and have been shown to directly affect yield potential by modifying the plant architecture. Therefore, these parameters are important breeding targets for wheat improvement. The present study is the first genome-wide association study (GWAS) targeting SLURTs in wheat. In this study, a set of 225 diverse spring wheat accessions were used for multi-locus GWAS to evaluate SLURTs, including the number of spikes per plant (NSPP), spike length (SL), number of spikelets per spike (NSPS), grain weight per spike (GWPS), lowest tiller height (LTH), spike-layer thickness (SLT), spike-layer number (SLN) and spike-layer uniformity (SLU). RESULTS In total, 136 significant marker trait associations (MTAs) were identified when the analysis was both performed individually and combined for two environments. Twenty-nine MTAs were detected in environment one, 48 MTAs were discovered in environment two and 59 MTAs were detected using combined data from the two environments. Altogether, 15 significant MTAs were found for five traits in one of the two environments, and four significant MTAs were detected for the two traits, LTH and SLU, in both environments i.e. E1, E2 and also in combined data from the two environments. In total, 279 candidate genes (CGs) were identified, including Chaperone DnaJ, ABC transporter-like, AP2/ERF, SWEET sugar transporter, as well as genes that have previously been associated with wheat spike development, seed development and grain yield. CONCLUSIONS The MTAs detected through multi-locus GWAS will be useful for improving SLURTs and thus yield in wheat production through marker-assisted and genomic selection.
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Affiliation(s)
- Parveen Malik
- Department of Genetics and Plant Breeding, ChaudharyCharan Singh University (CCSU), Meerut, 250 004, India
| | - Jitendra Kumar
- Department of Genetics and Plant Breeding, ChaudharyCharan Singh University (CCSU), Meerut, 250 004, India.,National Agri-Food Biotechnology Institute (NABI), Sector 81(Knowledge City), SahibzadaAjit Singh Nagar, Punjab, 140306, India
| | - Shiveta Sharma
- Department of Genetics and Plant Breeding, ChaudharyCharan Singh University (CCSU), Meerut, 250 004, India
| | - Rajiv Sharma
- Scotland's Rural College (SRUC), Peter Wilson Building, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, ChaudharyCharan Singh University (CCSU), Meerut, 250 004, India.
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Zhang W, Zhang S, Lu X, Li C, Liu X, Dong G, Xia T. Tissue-specific Transcriptome analysis reveals lignocellulose synthesis regulation in elephant grass (Pennisetum purpureum Schum). BMC PLANT BIOLOGY 2020; 20:528. [PMID: 33213376 PMCID: PMC7678330 DOI: 10.1186/s12870-020-02735-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 11/10/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND The characteristics of elephant grass, especially its stem lignocellulose, are of great significance for its quality as feed or other industrial raw materials. However, the research on lignocellulose biosynthesis pathway and key genes is limited because the genome of elephant grass has not been deciphered. RESULTS In this study, RNA sequencing (RNA-seq) combined with lignocellulose content analysis and cell wall morphology observation using elephant grass stems from different development stages as materials were applied to reveal the genes that regulate the synthesis of cellulose and lignin. A total of 3852 differentially expressed genes (DEGs) were identified in three periods of T1, T2, and T3 through RNA-seq analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of all DEGs showed that the two most abundant metabolic pathways were phenylpropane metabolism, starch and sucrose metabolism, which were closely related to cell wall development, hemicellulose, lignin and cellulose synthesis. Through weighted gene co-expression network analysis (WGCNA) of DEGs, a 'blue' module highly associated with cellulose synthesis and a 'turquoise' module highly correlated with lignin synthesis were exhibited. A total of 43 candidate genes were screened, of which 17 had function annotations in other species. Besides, by analyzing the content of lignocellulose in the stem tissues of elephant grass at different developmental stages and the expression levels of genes such as CesA, PAL, CAD, C4H, COMT, CCoAMT, F5H and CCR, it was found that the content of lignocellulose was related to the expression level of these structural genes. CONCLUSIONS This study provides a basis for further understanding the molecular mechanisms of cellulose and lignin synthesis pathways of elephant grass, and offers a unique and extensive list of candidate genes for future specialized functional studies which may promote the development of high-quality elephant grass varieties with high cellulose and low lignin content.
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Affiliation(s)
- Wenqing Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, Jinan, China
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Shengkui Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, Jinan, China
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Xianqin Lu
- State Key Laboratory of Biobased Material and Green Papermaking, Jinan, China
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Can Li
- State Key Laboratory of Biobased Material and Green Papermaking, Jinan, China
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Xingwang Liu
- State Key Laboratory of Biobased Material and Green Papermaking, Jinan, China
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Geyu Dong
- State Key Laboratory of Biobased Material and Green Papermaking, Jinan, China
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China
| | - Tao Xia
- State Key Laboratory of Biobased Material and Green Papermaking, Jinan, China.
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, Shandong, People's Republic of China.
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Iqbal I, Tripathi RK, Wilkins O, Singh J. Thaumatin-Like Protein ( TLP) Gene Family in Barley: Genome-Wide Exploration and Expression Analysis during Germination. Genes (Basel) 2020; 11:E1080. [PMID: 32947963 PMCID: PMC7564728 DOI: 10.3390/genes11091080] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/17/2020] [Accepted: 09/09/2020] [Indexed: 12/21/2022] Open
Abstract
Thaumatin-like Proteins (TLPs) are known to play a vital role in plant defense, developmental processes and seed germination. We identified 19 TLP genes from the reference genome of barley and 37, 28 and 35 TLP genes from rice, Brachypodium and sorghum genomes, respectively. Comparative phylogenetic analysis classified the TLP family into nine groups. Localized gene duplications with diverse exon/intron structures contributed to the expansion of the TLP gene family in cereals. Most of the barley TLPs were localized on chromosome 5H. The spatiotemporal expression pattern of HvTLP genes indicated their predominant expression in the embryo, developing grains, root and shoot tissues. Differential expression of HvTLP14, HvTLP17 and HvTLP18 in the malting variety (Morex) over 16-96 h of grain germination revealed their possible role in malting. This study provides a description of the TLP gene family in barley and their possible involvement in seed germination and the malting process.
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Affiliation(s)
| | | | | | - Jaswinder Singh
- Plant Science Department, McGill University, 21111 Lakeshore Rd., Quebec, QC H9X3V9, Canada; (I.I.); (R.K.T.); (O.W.)
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Gigli-Bisceglia N, Engelsdorf T, Hamann T. Plant cell wall integrity maintenance in model plants and crop species-relevant cell wall components and underlying guiding principles. Cell Mol Life Sci 2020; 77:2049-2077. [PMID: 31781810 PMCID: PMC7256069 DOI: 10.1007/s00018-019-03388-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 10/28/2019] [Accepted: 11/19/2019] [Indexed: 02/06/2023]
Abstract
The walls surrounding the cells of all land-based plants provide mechanical support essential for growth and development as well as protection from adverse environmental conditions like biotic and abiotic stress. Composition and structure of plant cell walls can differ markedly between cell types, developmental stages and species. This implies that wall composition and structure are actively modified during biological processes and in response to specific functional requirements. Despite extensive research in the area, our understanding of the regulatory processes controlling active and adaptive modifications of cell wall composition and structure is still limited. One of these regulatory processes is the cell wall integrity maintenance mechanism, which monitors and maintains the functional integrity of the plant cell wall during development and interaction with environment. It is an important element in plant pathogen interaction and cell wall plasticity, which seems at least partially responsible for the limited success that targeted manipulation of cell wall metabolism has achieved so far. Here, we provide an overview of the cell wall polysaccharides forming the bulk of plant cell walls in both monocotyledonous and dicotyledonous plants and the effects their impairment can have. We summarize our current knowledge regarding the cell wall integrity maintenance mechanism and discuss that it could be responsible for several of the mutant phenotypes observed.
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Affiliation(s)
- Nora Gigli-Bisceglia
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, 6708 PB, The Netherlands
| | - Timo Engelsdorf
- Division of Plant Physiology, Department of Biology, Philipps University of Marburg, 35043, Marburg, Germany
| | - Thorsten Hamann
- Institute for Biology, Faculty of Natural Sciences, Norwegian University of Science and Technology, 5 Høgskoleringen, 7491, Trondheim, Norway.
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Zhao Y, Xie P, Guan P, Wang Y, Li Y, Yu K, Xin M, Hu Z, Yao Y, Ni Z, Sun Q, Xie C, Peng H. Btr1-A Induces Grain Shattering and Affects Spike Morphology and Yield-Related Traits in Wheat. PLANT & CELL PHYSIOLOGY 2019; 60:1342-1353. [PMID: 30994893 DOI: 10.1093/pcp/pcz050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/21/2019] [Indexed: 06/09/2023]
Abstract
Spike brittleness represents an important domestication trait in crops. Although the brittle rachis of wild wheat was cloned, however, the molecular mechanism underlying spike brittleness is yet to be elucidated. Here, we identified a single dominant brittle rachis gene Br-Ab on chromosome arm 3AbS using an F2 population of diploid wheat and designated Btr1-Ab. Sequence analysis of the Btr1-A gene in 40 diploid wheat accessions, 80 tetraploid wheat accessions and 38 hexaploid wheat accessions showed that two independent mutations (Ala119Thr for diploid and Gly97* for polyploids) in the Btr1-A coding region resulting in the nonbrittle rachis allele. Overexpression of Btr1-Ab in nonbrittle hexaploid wheat led to brittle rachis in transgenic plants. RNA-Seq analysis revealed that Btr1-A represses the expression of cell wall biosynthesis genes during wheat rachis development. In addition, we found that Btr1-A can modify spike morphology and reduce threshability, grain size and thousand grain weight in transgenic wheat. These results demonstrated that Btr1-A reduces cell wall synthesis in rachis nodes, resulting in natural spikelet shattering, and that the transition from Btr1-A to btr1-A during wheat domestication had profound effects on evolution of spike morphology and yield-related traits.
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Affiliation(s)
- Yue Zhao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
- These authors contributed equally to this work
| | - Peng Xie
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
- These authors contributed equally to this work
| | - Panfeng Guan
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
- These authors contributed equally to this work
| | - Yongfa Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Yinghui Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Kuohai Yu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Chaojie Xie
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
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10
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Nawaz MA, Lin X, Chan TF, Imtiaz M, Rehman HM, Ali MA, Baloch FS, Atif RM, Yang SH, Chung G. Characterization of Cellulose Synthase A (CESA) Gene Family in Eudicots. Biochem Genet 2018; 57:248-272. [PMID: 30267258 DOI: 10.1007/s10528-018-9888-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 09/20/2018] [Indexed: 12/30/2022]
Abstract
Cellulose synthase A (CESA) is a key enzyme involved in the complex process of plant cell wall biosynthesis, and it remains a productive subject for research. We employed systems biology approaches to explore structural diversity of eudicot CESAs by exon-intron organization, mode of duplication, synteny, and splice site analyses. Using a combined phylogenetics and comparative genomics approach coupled with co-expression networks we reconciled the evolution of cellulose synthase gene family in eudicots and found that the basic forms of CESA proteins are retained in angiosperms. Duplications have played an important role in expansion of CESA gene family members in eudicots. Co-expression networks showed that primary and secondary cell wall modules are duplicated in eudicots. We also identified 230 simple sequence repeat markers in 103 eudicot CESAs. The 13 identified conserved motifs in eudicots will provide a basis for gene identification and functional characterization in other plants. Furthermore, we characterized (in silico) eudicot CESAs against senescence and found that expression levels of CESAs decreased during leaf senescence.
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Affiliation(s)
- Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Xiao Lin
- Center for Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Ting-Fung Chan
- Center for Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Muhammad Imtiaz
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510275, China
| | - Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea
| | - Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, 14280, Bolu, Turkey
| | - Rana Muhammad Atif
- US-Pakistan Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam, 59626, Republic of Korea.
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11
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Scavuzzo-Duggan TR, Chaves AM, Singh A, Sethaphong L, Slabaugh E, Yingling YG, Haigler CH, Roberts AW. Cellulose synthase 'class specific regions' are intrinsically disordered and functionally undifferentiated. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:481-497. [PMID: 29380536 DOI: 10.1111/jipb.12637] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 01/27/2018] [Indexed: 05/16/2023]
Abstract
Cellulose synthases (CESAs) are glycosyltransferases that catalyze formation of cellulose microfibrils in plant cell walls. Seed plant CESA isoforms cluster in six phylogenetic clades, whose non-interchangeable members play distinct roles within cellulose synthesis complexes (CSCs). A 'class specific region' (CSR), with higher sequence similarity within versus between functional CESA classes, has been suggested to contribute to specific activities or interactions of different isoforms. We investigated CESA isoform specificity in the moss, Physcomitrella patens (Hedw.) B. S. G. to gain evolutionary insights into CESA structure/function relationships. Like seed plants, P. patens has oligomeric rosette-type CSCs, but the PpCESAs diverged independently and form a separate CESA clade. We showed that P. patens has two functionally distinct CESAs classes, based on the ability to complement the gametophore-negative phenotype of a ppcesa5 knockout line. Thus, non-interchangeable CESA classes evolved separately in mosses and seed plants. However, testing of chimeric moss CESA genes for complementation demonstrated that functional class-specificity is not determined by the CSR. Sequence analysis and computational modeling showed that the CSR is intrinsically disordered and contains predicted molecular recognition features, consistent with a possible role in CESA oligomerization and explaining the evolution of class-specific sequences without selection for class-specific function.
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Affiliation(s)
- Tess R Scavuzzo-Duggan
- Department of Biological Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI, 02881, USA
| | - Arielle M Chaves
- Department of Biological Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI, 02881, USA
| | - Abhishek Singh
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Latsavongsakda Sethaphong
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Erin Slabaugh
- Department of Crop and Soil Sciences and Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Yaroslava G Yingling
- Department of Materials Science and Engineering, North Carolina State University, Raleigh, NC, 27695, USA
| | - Candace H Haigler
- Department of Crop and Soil Sciences and Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Alison W Roberts
- Department of Biological Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI, 02881, USA
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12
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Hernández-Altamirano JM, Largo-Gosens A, Martínez-Rubio R, Pereda D, Álvarez JM, Acebes JL, Encina A, García-Angulo P. Effect of ancymidol on cell wall metabolism in growing maize cells. PLANTA 2018; 247:987-999. [PMID: 29330614 DOI: 10.1007/s00425-018-2840-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/02/2018] [Indexed: 06/07/2023]
Abstract
Ancymidol inhibits the incorporation of cellulose into cell walls of maize cell cultures in a gibberellin-independent manner, impairing cell growth; the reduction in the cellulose content is compensated with xylans. Ancymidol is a plant growth retardant which impairs gibberellin biosynthesis. It has been reported to inhibit cellulose synthesis by tobacco cells, based on its cell-malforming effects. To ascertain the putative role of ancymidol as a cellulose biosynthesis inhibitor, we conducted a biochemical study of its effect on cell growth and cell wall metabolism in maize cultured cells. Ancymidol concentrations ≤ 500 µM progressively reduced cell growth and induced globular cell shape without affecting cell viability. However, cell growth and viability were strongly reduced by ancymidol concentrations ≥ 1.5 mM. The I50 value for the effect of ancymidol on FW gain was 658 µM. A reversal of the inhibitory effects on cell growth was observed when 500 µM ancymidol-treated cultures were supplemented with 100 µM GA3. Ancymidol impaired the accumulation of cellulose in cell walls, as monitored by FTIR spectroscopy. Cells treated with 500 µM ancymidol showed a ~ 60% reduction in cellulose content, with no further change as the ancymidol concentration increased. Cellulose content was partially restored by 100 µM GA3. Radiolabeling experiments confirmed that ancymidol reduced the incorporation of [14C]glucose into α-cellulose and this reduction was not reverted by the simultaneous application of GA3. RT-PCR analysis indicated that the cellulose biosynthesis inhibition caused by ancymidol is not related to a downregulation of ZmCesA gene expression. Additionally, ancymidol treatment increased the incorporation of [3H]arabinose into a hemicellulose-enriched fraction, and up-regulated ZmIRX9 and ZmIRX10L gene expression, indicating an enhancement in the biosynthesis of arabinoxylans as a compensatory response to cellulose reduction.
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Affiliation(s)
- J Mabel Hernández-Altamirano
- Departamento de Ingeniería y Ciencias Agrarias, Área de Fisiología Vegetal, Universidad de León, 24071, León, Spain
| | - Asier Largo-Gosens
- Departamento de Ingeniería y Ciencias Agrarias, Área de Fisiología Vegetal, Universidad de León, 24071, León, Spain
- Centro de Biotecnología Vegetal, Facultad de Ciencias Biológicas, Universidad Nacional Andrés Bello, 8370146, Santiago, Chile
| | - Romina Martínez-Rubio
- Departamento de Ingeniería y Ciencias Agrarias, Área de Fisiología Vegetal, Universidad de León, 24071, León, Spain
| | - Diego Pereda
- Departamento de Ingeniería y Ciencias Agrarias, Área de Fisiología Vegetal, Universidad de León, 24071, León, Spain
| | - Jesús M Álvarez
- Departamento de Ingeniería y Ciencias Agrarias, Área de Fisiología Vegetal, Universidad de León, 24071, León, Spain
| | - José L Acebes
- Departamento de Ingeniería y Ciencias Agrarias, Área de Fisiología Vegetal, Universidad de León, 24071, León, Spain.
| | - Antonio Encina
- Departamento de Ingeniería y Ciencias Agrarias, Área de Fisiología Vegetal, Universidad de León, 24071, León, Spain
| | - Penélope García-Angulo
- Departamento de Ingeniería y Ciencias Agrarias, Área de Fisiología Vegetal, Universidad de León, 24071, León, Spain
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13
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Zou X, Zhen Z, Ge Q, Fan S, Liu A, Gong W, Li J, Gong J, Shi Y, Wang Y, Liu R, Duan L, Lei K, Zhang Q, Jiang X, Zhang S, Jia T, Zhang L, Shang H, Yuan Y. Genome-wide identification and analysis of the evolution and expression patterns of the cellulose synthase gene superfamily in Gossypium species. Gene 2017; 646:28-38. [PMID: 29278771 DOI: 10.1016/j.gene.2017.12.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 12/03/2017] [Accepted: 12/20/2017] [Indexed: 12/30/2022]
Abstract
The cellulose synthase gene superfamily, which includes the cellulose synthase (Ces) and cellulose synthase-like (Csl) families, is involved in the synthesis of cellulose and hemicellulose. This superfamily is critical for cotton fiber development in Gossypium species. Applying a series of bioinformatic methods, we identified 228 Ces/Csl genes from four Gossypium species (G. hirsutum, G. barbadense, G. arboreum, and G. raimondii). These genes were then grouped into 11 subfamilies based on phylogenetic relationships. A subsequent analysis of gene evolution revealed sites in CSLG and CSLJ genes that were under long-term positive selection pressure, with a posterior probability >0.95. Moreover, the dN:dS value for the CSLJ clade was 1.305, suggesting this subfamily was under positive selection pressure. Our data indicated that the dN:dS value ranged from 0.0084 to 0.9693 among the homologous Ces/Csl genes, implying they were under purifying selection pressure. Our transcriptome and qRT-PCR analyses revealed that CesA genes were more highly expressed in tetraploids than in diploids. However, the Csl expression levels exhibited the opposite trend. Furthermore, changes to promoter sequences may have influenced the expression of homologous Ces/Csl genes. Our findings may provide novel insights into the evolutionary relationships and expression patterns of the Ces/Csl genes in Gossypium species.
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Affiliation(s)
- Xianyan Zou
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Zhang Zhen
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Senmiao Fan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Aiying Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Junwen Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Juwu Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Yanling Wang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Ruixian Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Li Duan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Kang Lei
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Qi Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Xiao Jiang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Shuya Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Tingting Jia
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Lipeng Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan, China.
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14
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Kaur S, Zhang X, Mohan A, Dong H, Vikram P, Singh S, Zhang Z, Gill KS, Dhugga KS, Singh J. Genome-Wide Association Study Reveals Novel Genes Associated with Culm Cellulose Content in Bread Wheat ( Triticum aestivum, L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1913. [PMID: 29163625 PMCID: PMC5681534 DOI: 10.3389/fpls.2017.01913] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 10/23/2017] [Indexed: 05/30/2023]
Abstract
Plant cell wall formation is a complex, coordinated and developmentally regulated process. Cellulose is the most dominant constituent of plant cell walls. Because of its paracrystalline structure, cellulose is the main determinant of mechanical strength of plant tissues. As the most abundant polysaccharide on earth, it is also the focus of cellulosic biofuel industry. To reduce culm lodging in wheat and for improved ethanol production, delineation of the variation for stem cellulose content could prove useful. We present results on the analysis of the stem cellulose content of 288 diverse wheat accessions and its genome-wide association study (GWAS). Cellulose concentration ranged from 35 to 52% (w/w). Cellulose content was normally distributed in the accessions around a mean and median of 45% (w/w). Genome-wide marker-trait association study using 21,073 SNPs helped identify nine SNPs that were associated (p < 1E-05) with cellulose content. Four strongly associated (p < 8.17E-05) SNP markers were linked to wheat unigenes, which included β-tubulin, Auxin-induced protein 5NG4, and a putative transmembrane protein of unknown function. These genes may be directly or indirectly involved in the formation of cellulose in wheat culms. GWAS results from this study have the potential for genetic manipulation of cellulose content in bread wheat and other small grain cereals to enhance culm strength and improve biofuel production.
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Affiliation(s)
- Simerjeet Kaur
- Department of Plant Science, McGill University, Sainte Anne de Bellevue, QC, Canada
| | - Xu Zhang
- Department of Crop and Soil Science, Washington State University, Pullman, WA, United States
| | - Amita Mohan
- Department of Crop and Soil Science, Washington State University, Pullman, WA, United States
| | - Haixiao Dong
- Department of Crop and Soil Science, Washington State University, Pullman, WA, United States
| | - Prashant Vikram
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco, Mexico
| | - Sukhwinder Singh
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco, Mexico
| | - Zhiwu Zhang
- Department of Crop and Soil Science, Washington State University, Pullman, WA, United States
| | - Kulvinder S. Gill
- Department of Crop and Soil Science, Washington State University, Pullman, WA, United States
| | - Kanwarpal S. Dhugga
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco, Mexico
| | - Jaswinder Singh
- Department of Plant Science, McGill University, Sainte Anne de Bellevue, QC, Canada
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15
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Kaur S, Dhugga KS, Beech R, Singh J. Genome-wide analysis of the cellulose synthase-like (Csl) gene family in bread wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2017; 17:193. [PMID: 29100539 PMCID: PMC5670714 DOI: 10.1186/s12870-017-1142-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 10/26/2017] [Indexed: 05/24/2023]
Abstract
BACKGROUND Hemicelluloses are a diverse group of complex, non-cellulosic polysaccharides, which constitute approximately one-third of the plant cell wall and find use as dietary fibres, food additives and raw materials for biofuels. Genes involved in hemicellulose synthesis have not been extensively studied in small grain cereals. RESULTS In efforts to isolate the sequences for the cellulose synthase-like (Csl) gene family from wheat, we identified 108 genes (hereafter referred to as TaCsl). Each gene was represented by two to three homeoalleles, which are named as TaCslXY_ZA, TaCslXY_ZB, or TaCslXY_ZD, where X denotes the Csl subfamily, Y the gene number and Z the wheat chromosome where it is located. A quarter of these genes were predicted to have 2 to 3 splice variants, resulting in a total of 137 putative translated products. Approximately 45% of TaCsl genes were located on chromosomes 2 and 3. Sequences from the subfamilies C and D were interspersed between the dicots and grasses but those from subfamily A clustered within each group of plants. Proximity of the dicot-specific subfamilies B and G, to the grass-specific subfamilies H and J, respectively, points to their common origin. In silico expression analysis in different tissues revealed that most of the genes were expressed ubiquitously and some were tissue-specific. More than half of the genes had introns in phase 0, one-third in phase 2, and a few in phase 1. CONCLUSION Detailed characterization of the wheat Csl genes has enhanced the understanding of their structural, functional, and evolutionary features. This information will be helpful in designing experiments for genetic manipulation of hemicellulose synthesis with the goal of developing improved cultivars for biofuel production and increased tolerance against various stresses.
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Affiliation(s)
- Simerjeet Kaur
- Department of Plant Science, McGill University, Sainte Anne de Bellevue, QC, Canada
| | - Kanwarpal S. Dhugga
- International Maize and Wheat Improvement Center (CIMMYT), El Batán, Texcoco, Estado de México Mexico
| | - Robin Beech
- Institute of Parasitology, McGill University, Sainte Anne de Bellevue, Montreal, QC Canada
| | - Jaswinder Singh
- Department of Plant Science, McGill University, Sainte Anne de Bellevue, QC, Canada
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16
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Yurkevich OY, Kirov IV, Bolsheva NL, Rachinskaya OA, Grushetskaya ZE, Zoschuk SA, Samatadze TE, Bogdanova MV, Lemesh VA, Amosova AV, Muravenko OV. Integration of Physical, Genetic, and Cytogenetic Mapping Data for Cellulose Synthase ( CesA) Genes in Flax ( Linum usitatissimum L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1467. [PMID: 28878799 PMCID: PMC5572355 DOI: 10.3389/fpls.2017.01467] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 08/07/2017] [Indexed: 05/07/2023]
Abstract
Flax, Linum usitatissimum L., is a valuable multi-purpose plant, and currently, its genome is being extensively investigated. Nevertheless, mapping of genes in flax genome is still remaining a challenging task. The cellulose synthase (CesA) multigene family involving in the process of cellulose synthesis is especially important for metabolism of this fiber crop. For the first time, fluorescent in situ hybridization (FISH)-based chromosomal localization of the CesA conserved fragment (KF011584.1), 5S, and 26S rRNA genes was performed in landrace, oilseed, and fiber varieties of L. usitatissimum. Intraspecific polymorphism in chromosomal distribution of KF011584.1 and 5S DNA loci was revealed, and the generalized chromosome ideogram was constructed. Using BLAST analysis, available data on physical/genetic mapping and also whole-genome sequencing of flax, localization of KF011584.1, 45S, and 5S rRNA sequences on genomic scaffolds, and their anchoring to the genetic map were conducted. The alignment of the results of FISH and BLAST analyses indicated that KF011584.1 fragment revealed on chromosome 3 could be anchored to linkage group (LG) 11. The common LG for 45S and 5S rDNA was not found probably due to the polymorphic localization of 5S rDNA on chromosome 1. Our findings indicate the complexity of integration of physical, genetic, and cytogenetic mapping data for multicopy gene families in plants. Nevertheless, the obtained results can be useful for future progress in constructing of integrated physical/genetic/cytological maps in L. usitatissimum which are essential for flax breeding.
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Affiliation(s)
- Olga Y. Yurkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Ilya V. Kirov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of SciencesMoscow, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Olga A. Rachinskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Zoya E. Grushetskaya
- Institute of Genetics and Cytology, National Academy of Sciences of BelarusMinsk, Belarus
| | - Svyatoslav A. Zoschuk
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Tatiana E. Samatadze
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Marina V. Bogdanova
- Institute of Genetics and Cytology, National Academy of Sciences of BelarusMinsk, Belarus
| | - Valentina A. Lemesh
- Institute of Genetics and Cytology, National Academy of Sciences of BelarusMinsk, Belarus
| | - Alexandra V. Amosova
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
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17
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Nawaz MA, Rehman HM, Baloch FS, Ijaz B, Ali MA, Khan IA, Lee JD, Chung G, Yang SH. Genome and transcriptome-wide analyses of cellulose synthase gene superfamily in soybean. JOURNAL OF PLANT PHYSIOLOGY 2017; 215:163-175. [PMID: 28704793 DOI: 10.1016/j.jplph.2017.04.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 04/12/2017] [Accepted: 04/14/2017] [Indexed: 05/28/2023]
Abstract
The plant cellulose synthase gene superfamily belongs to the category of type-2 glycosyltransferases, and is involved in cellulose and hemicellulose biosynthesis. These enzymes are vital for maintaining cell-wall structural integrity throughout plant life. Here, we identified 78 putative cellulose synthases (CS) in the soybean genome. Phylogenetic analysis against 40 reference Arabidopsis CS genes clustered soybean CSs into seven major groups (CESA, CSL A, B, C, D, E and G), located on 19 chromosomes (except chromosome 18). Soybean CS expansion occurred in 66 duplication events. Additionally, we identified 95 simple sequence repeat makers related to 44 CSs. We next performed digital expression analysis using publically available datasets to understand potential CS functions in soybean. We found that CSs were highly expressed during soybean seed development, a pattern confirmed with an Affymatrix soybean IVT array and validated with RNA-seq profiles. Within CS groups, CESAs had higher relative expression than CSLs. Soybean CS models were designed based on maximum average RPKM values. Gene co-expression networks were developed to explore which CSs could work together in soybean. Finally, RT-PCR analysis confirmed the expression of 15 selected CSs during all four seed developmental stages.
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Affiliation(s)
- Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Republic of Korea
| | - Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Republic of Korea
| | | | - Babar Ijaz
- Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, Faisalabad 38040, Pakistan
| | - Iqrar Ahmad Khan
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad 38040, Pakistan
| | - Jeong Dong Lee
- Division of Plant Biosciences, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Republic of Korea.
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, 59626, Republic of Korea.
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18
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Redox-dependent interaction between thaumatin-like protein and β-glucan influences malting quality of barley. Proc Natl Acad Sci U S A 2017. [PMID: 28634304 DOI: 10.1073/pnas.1701824114] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Barley is the cornerstone of the malting and brewing industry. It is known that 250 quantitative trait loci (QTLs) of the grain are associated with 19 malting-quality phenotypes. However, only a few of the contributing genetic components have been identified. One of these, on chromosome 4H, contains a major malting QTL, QTL2, located near the telomeric region that accounts, respectively, for 28.9% and 37.6% of the variation in the β-glucan and extract fractions of malt. In the current study, we dissected the QTL2 region using an expression- and microsynteny-based approach. From a set of 22 expressed sequence tags expressed in seeds at the malting stage, we identified a candidate gene, TLP8 (thaumatin-like protein 8), which was differentially expressed and influenced malting quality. Transcript abundance and protein profiles of TLP8 were studied in different malt and feed varieties using quantitative PCR, immunoblotting, and enzyme-linked immunosorbent assay (ELISA). The experiments demonstrated that TLP8 binds to insoluble (1, 3, 1, 4)-β-D glucan in grain extracts, thereby facilitating the removal of this undesirable polysaccharide during malting. Further, the binding of TLP8 to β-glucan was dependent on redox. These findings represent a stride forward in our understanding of the malting process and provide a foundation for future improvements in the final beer-making process.
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19
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Wang Y, Xu L, Thilmony R, You FM, Gu YQ, Coleman-Derr D. PIECE 2.0: an update for the plant gene structure comparison and evolution database. Nucleic Acids Res 2016; 45:1015-1020. [PMID: 27742820 PMCID: PMC5210635 DOI: 10.1093/nar/gkw935] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/04/2016] [Accepted: 10/12/2016] [Indexed: 11/30/2022] Open
Abstract
PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron–exon organization and provides valuable insights into the evolution of gene structure in plant genomes. Recently, we updated PIECE to a new version, PIECE 2.0 (http://probes.pw.usda.gov/piece or http://aegilops.wheat.ucdavis.edu/piece). PIECE 2.0 contains annotated genes from 49 sequenced plant species as compared to 25 species in the previous version. In the current version, we also added several new features: (i) a new viewer was developed to show phylogenetic trees displayed along with the structure of individual genes; (ii) genes in the phylogenetic tree can now be also grouped according to KOG (The annotation of Eukaryotic Orthologous Groups) and KO (KEGG Orthology) in addition to Pfam domains; (iii) information on intronless genes are now included in the database; (iv) a statistical summary of global gene structure information for each species and its comparison with other species was added; and (v) an improved GSDraw tool was implemented in the web server to enhance the analysis and display of gene structure. The updated PIECE 2.0 database will be a valuable resource for the plant research community for the study of gene structure and evolution.
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Affiliation(s)
- Yi Wang
- USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.,USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA
| | - Ling Xu
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA.,USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA
| | - Roger Thilmony
- USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA
| | - Frank M You
- Cereal Research Centre, Agriculture and Agri-Food Canada, Morden R6M 1Y5 MB, Canada
| | - Yong Q Gu
- USDA-ARS, Western Regional Research Center, Crop Improvement and Genetics Research Unit, Albany, CA 94710, USA
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA .,USDA-ARS, Plant Gene Expression Center, Albany, CA 94710, USA
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Sethi S, Saini JS, Mohan A, Brar NK, Verma S, Sarao NK, Gill KS. Comparative and evolutionary analysis of α-amylase gene across monocots and dicots. Funct Integr Genomics 2016; 16:545-55. [PMID: 27481351 DOI: 10.1007/s10142-016-0505-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 06/30/2016] [Accepted: 07/05/2016] [Indexed: 10/21/2022]
Abstract
α-amylase is an important enzyme involved in starch degradation to provide energy to the germinating seedling. The present study was conducted to reveal structural and functional evolution of this gene among higher plants. Discounting polyploidy, most plant species showed only a single copy of the gene making multiple isoforms in different tissues and developmental stages. Genomic length of the gene ranged from 1472 bp in wheat to 2369 bp in soybean, and the size variation was mainly due to differences in the number and size of introns. In spite of this variation, the intron phase distribution and insertion sites were mostly conserved. The predicted protein size ranged from 414 amino acid (aa) in soybean to 449aa in Brachypodium. Overall, the protein sequence similarity among orthologs ranged from 56.4 to 97.4 %. Key motifs and domains along with their relative distances were conserved among plants although several species, genera, and class specific motifs were identified. The glycosyl hydrolase superfamily domain length varied from 342aa in soybean to 384aa in maize and sorghum while length of the C-terminal β-sheet domain was highly conserved with 61aa in all monocots and Arabidopsis but was 59aa in soybean and Medicago. Compared to rice, 3D structure of the proteins showed 89.8 to 91.3 % similarity among the monocots and 72.7 to 75.8 % among the dicots. Sequence and relative location of the five key aa required for the ligand binding were highly conserved in all species except rice.
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Affiliation(s)
- Sorabh Sethi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Johar S Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India.
| | - Amita Mohan
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Navreet K Brar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Shabda Verma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Navraj K Sarao
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Kulvinder S Gill
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
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