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Peracchi LM, Panahabadi R, Barros-Rios J, Bartley LE, Sanguinet KA. Grass lignin: biosynthesis, biological roles, and industrial applications. FRONTIERS IN PLANT SCIENCE 2024; 15:1343097. [PMID: 38463570 PMCID: PMC10921064 DOI: 10.3389/fpls.2024.1343097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/06/2024] [Indexed: 03/12/2024]
Abstract
Lignin is a phenolic heteropolymer found in most terrestrial plants that contributes an essential role in plant growth, abiotic stress tolerance, and biotic stress resistance. Recent research in grass lignin biosynthesis has found differences compared to dicots such as Arabidopsis thaliana. For example, the prolific incorporation of hydroxycinnamic acids into grass secondary cell walls improve the structural integrity of vascular and structural elements via covalent crosslinking. Conversely, fundamental monolignol chemistry conserves the mechanisms of monolignol translocation and polymerization across the plant phylum. Emerging evidence suggests grass lignin compositions contribute to abiotic stress tolerance, and periods of biotic stress often alter cereal lignin compositions to hinder pathogenesis. This same recalcitrance also inhibits industrial valorization of plant biomass, making lignin alterations and reductions a prolific field of research. This review presents an update of grass lignin biosynthesis, translocation, and polymerization, highlights how lignified grass cell walls contribute to plant development and stress responses, and briefly addresses genetic engineering strategies that may benefit industrial applications.
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Affiliation(s)
- Luigi M. Peracchi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
| | - Rahele Panahabadi
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Jaime Barros-Rios
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Laura E. Bartley
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Karen A. Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, United States
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2
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Zhao K, Rhee SY. Interpreting omics data with pathway enrichment analysis. Trends Genet 2023; 39:308-319. [PMID: 36750393 DOI: 10.1016/j.tig.2023.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/24/2022] [Accepted: 01/13/2023] [Indexed: 02/09/2023]
Abstract
Pathway enrichment analysis is indispensable for interpreting omics datasets and generating hypotheses. However, the foundations of enrichment analysis remain elusive to many biologists. Here, we discuss best practices in interpreting different types of omics data using pathway enrichment analysis and highlight the importance of considering intrinsic features of various types of omics data. We further explain major components that influence the outcomes of a pathway enrichment analysis, including defining background sets and choosing reference annotation databases. To improve reproducibility, we describe how to standardize reporting methodological details in publications. This article aims to serve as a primer for biologists to leverage the wealth of omics resources and motivate bioinformatics tool developers to enhance the power of pathway enrichment analysis.
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Affiliation(s)
- Kangmei Zhao
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94025, USA.
| | - Seung Yon Rhee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94025, USA.
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Genome-Wide Identification Analysis of the R2R3-MYB Transcription Factor Family in Cymbidium sinense for Insights into Drought Stress Responses. Int J Mol Sci 2023; 24:ijms24043235. [PMID: 36834646 PMCID: PMC9959677 DOI: 10.3390/ijms24043235] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Cymbidium sinense represents a distinctive Orchidaceae plant that is more tolerant than other terrestrial orchids. Studies have shown that many members of the MYB transcription factor (TF) family, especially the R2R3-MYB subfamily, are responsive to drought stress. This study identified 103 CsMYBs; phylogenetic analysis classified these genes into 22 subgroups with Arabidopsis thaliana. Structural analysis showed that most CsMYB genes contained the same motifs, three exons and two introns, and showed a helix-turn-helix 3D structure in each R repeat. However, the members of subgroup 22 contained only one exon and no intron. Collinear analysis revealed that C. sinense had more orthologous R2R3-MYB genes with wheat than A. thaliana and rice. Ka/Ks ratios indicated that most CsMYB genes were under purifying negative selection pressure. Cis-acting elements analysis revealed that drought-related elements were mainly focused on subgroups 4, 8, 18, 20, 21, and 22, and Mol015419 (S20) contained the most. The transcriptome analysis results showed that expression patterns of most CsMYB genes were upregulated in leaves in response to slight drought stress and downregulated in roots. Among them, members in S8 and S20 significantly responded to drought stress in C. sinense. In addition, S14 and S17 also participated in these responses, and nine genes were selected for the real-time reverse transcription quantitative PCR (RT-qPCR) experiment. The results were roughly consistent with the transcriptome. Our results, thus, provide an important contribution to understanding the role of CsMYBs in stress-related metabolic processes.
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Lin N, Wang M, Jiang J, Zhou Q, Yin J, Li J, Lian J, Xue Y, Chai Y. Downregulation of Brassica napus MYB69 ( BnMYB69) increases biomass growth and disease susceptibility via remodeling phytohormone, chlorophyll, shikimate and lignin levels. FRONTIERS IN PLANT SCIENCE 2023; 14:1157836. [PMID: 37077631 PMCID: PMC10108680 DOI: 10.3389/fpls.2023.1157836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/07/2023] [Indexed: 05/03/2023]
Abstract
MYB transcription factors are major actors regulating plant development and adaptability. Brassica napus is a staple oil crop and is hampered by lodging and diseases. Here, four B. napus MYB69 (BnMYB69s) genes were cloned and functionally characterized. They were dominantly expressed in stems during lignification. BnMYB69 RNA interference (BnMYB69i) plants showed considerable changes in morphology, anatomy, metabolism and gene expression. Stem diameter, leaves, roots and total biomass were distinctly larger, but plant height was significantly reduced. Contents of lignin, cellulose and protopectin in stems were significantly reduced, accompanied with decrease in bending resistance and Sclerotinia sclerotiorum resistance. Anatomical detection observed perturbation in vascular and fiber differentiation in stems, but promotion in parenchyma growth, accompanied with changes in cell size and cell number. In shoots, contents of IAA, shikimates and proanthocyanidin were reduced, while contents of ABA, BL and leaf chlorophyll were increased. qRT-PCR revealed changes in multiple pathways of primary and secondary metabolisms. IAA treatment could recover many phenotypes and metabolisms of BnMYB69i plants. However, roots showed trends opposite to shoots in most cases, and BnMYB69i phenotypes were light-sensitive. Conclusively, BnMYB69s might be light-regulated positive regulators of shikimates-related metabolisms, and exert profound influences on various internal and external plant traits.
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Affiliation(s)
- Na Lin
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Mu Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Jiayi Jiang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Qinyuan Zhou
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Jiaming Yin
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Jiana Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Academy of Agricultural Science, Southwest University, Chongqing, China
| | - Jianping Lian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yufei Xue
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yourong Chai
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City and Southwest University, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Academy of Agricultural Science, Southwest University, Chongqing, China
- *Correspondence: Yourong Chai,
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Zhang X, Ran D, Wu P, Cao Z, Xu F, Xia N, Gao H, Jiang Y, Yang C, He N, Tang N, Chen Z. Transcriptome and metabolite profiling to identify genes associated with rhizome lignification and the function of ZoCSE in ginger ( Zingiber officinale). FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:689-703. [PMID: 35379382 DOI: 10.1071/fp21267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Ginger (Zingiber officinale Roscoe) is an important spice crop in China, and fresh ginger rhizomes are consumed as vegetable in Sichuan and Chongqing. However, tissue lignification accelerates with rhizome maturation, resulting in the loss of edible quality. To understand the molecular mechanisms of texture modification during rhizome development, we investigated lignin accumulation patterns and identified the key genes associated with lignin biosynthesis using gas chromatography-mass spectrometry (GC-MS), liquid chromatography-tandem mass spectrometry (LC-MS/MS) and RNA-sequencing (RNA-Seq). Results showed that the contents of total lignin and its precursors exhibited notable declines with tissue maturation. However, the lignin composition was remarkably modified and syringyl lignin was deposited in mature rhizomes, leading to ginger lignification. Transcriptome analysis displayed 32 lignin biosynthetic genes were dramatically downregulated with rhizome development, including caffeoylshikimate esterase (CSE ), 4-coumarate-CoA ligase , laccase , cinnamoyl-CoA reductase , cinnamyl-alcohol dehydrogenase , peroxidase and caffeic acid 3-O-methyltransferase , indicating that lignin reduction might be attributed to deficiency in intermediates or the downregulation of key biosynthetic enzymes. Furthermore, overexpressing ZoCSE in Nicotiana benthamiana L. enhanced the total lignin content, suggesting its fundamental role in lignin biosynthesis. RNA-Seq also identified candidate lignin production regulators, including hormone-related genes and NAC/MYB transcription factors (ZoNAC1 , ZoNAC4 , ZoMYB14 and ZoMYB17 ). This result provides a molecular basis for lignin accumulation in ginger.
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Affiliation(s)
- Xian Zhang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; and Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing 400000, China; and College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China
| | - Dongsheng Ran
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China
| | - Peiyin Wu
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; and College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China
| | - Zhengyan Cao
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; and College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China
| | - Ning Xia
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China
| | - Hongmei Gao
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China
| | - Ying Jiang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China
| | - Cheng Yang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China
| | - Na He
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China
| | - Ning Tang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; and Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing 400000, China
| | - Zexiong Chen
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; and Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing 400000, China
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6
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Zhuang Y, Manzitto-Tripp EA. Co-expression network analyses of anthocyanin biosynthesis genes in Ruellia (Wild Petunias; Acanthaceae). BMC Ecol Evol 2022; 22:27. [PMID: 35260074 PMCID: PMC8905905 DOI: 10.1186/s12862-021-01955-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 12/22/2021] [Indexed: 11/26/2022] Open
Abstract
Background Anthocyanins are major pigments contributing to flower coloration and as such knowledge of molecular architecture underlying the anthocyanin biosynthetic pathway (ABP) is key to understanding flower color diversification. To identify ABP structural genes and associated regulatory networks, we sequenced 16 transcriptomes generated from 10 species of Ruellia and then conducted co-expression analyses among resulting data. Results Complete coding sequences for 12 candidate structural loci representing eight genes plus nine candidate regulatory loci were assembled. Analysis of non-synonymous/synonymous (dn/ds) mutation rates indicated all identified loci are under purifying selection, suggesting overall selection to prevent the accumulation of deleterious mutations. Additionally, upstream enzymes have lower rates of molecular evolution compared to downstream enzymes. However, site-specific tests of selection yielded evidence for positive selection at several sites, including four in F3'H2 and five in DFR3, and these sites are located in protein binding regions. A species-level phylogenetic tree constructed using a newly implemented hybrid transcriptome–RADseq approach implicates several flower color transitions among the 10 species. We found evidence of both regulatory and structural mutations to F3′5'H in helping to explain the evolution of red flowers from purple-flowered ancestors. Conclusions Sequence comparisons and co-expression analyses of ABP loci revealed that mutations in regulatory loci are likely to play a greater role in flower color transitions in Ruellia compared to mutations in underlying structural genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01955-x.
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Affiliation(s)
- Yongbin Zhuang
- Department of Ecology and Evolutionary Biology, University of Colorado, UCB 334, Boulder, CO, 80309, USA.,Museum of Natural History, University of Colorado, UCB 350, Boulder, CO, 80309, USA.,College of Agronomy, Shandong Agricultural University, Taian, 271018, Shandong, China
| | - Erin A Manzitto-Tripp
- Department of Ecology and Evolutionary Biology, University of Colorado, UCB 334, Boulder, CO, 80309, USA. .,Museum of Natural History, University of Colorado, UCB 350, Boulder, CO, 80309, USA.
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Wu Y, Wen J, Xia Y, Zhang L, Du H. Evolution and functional diversification of R2R3-MYB transcription factors in plants. HORTICULTURE RESEARCH 2022; 9:uhac058. [PMID: 35591925 PMCID: PMC9113232 DOI: 10.1093/hr/uhac058] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 02/24/2022] [Indexed: 05/31/2023]
Abstract
R2R3-MYB genes (R2R3-MYBs) form one of the largest transcription factor gene families in the plant kingdom, with substantial structural and functional diversity. However, the evolutionary processes leading to this amazing functional diversity have not yet been clearly established. Recently developed genomic and classical molecular technologies have provided detailed insights into the evolutionary relationships and functions of plant R2R3-MYBs. Here, we review recent genome-level and functional analyses of plant R2R3-MYBs, with an emphasis on their evolution and functional diversification. In land plants, this gene family underwent a large expansion by whole genome duplications and small-scale duplications. Along with this population explosion, a series of functionally conserved or lineage-specific subfamilies/groups arose with roles in three major plant-specific biological processes: development and cell differentiation, specialized metabolism, and biotic and abiotic stresses. The rapid expansion and functional diversification of plant R2R3-MYBs are highly consistent with the increasing complexity of angiosperms. In particular, recently derived R2R3-MYBs with three highly homologous intron patterns (a, b, and c) are disproportionately related to specialized metabolism and have become the predominant subfamilies in land plant genomes. The evolution of plant R2R3-MYBs is an active area of research, and further studies are expected to improve our understanding of the evolution and functional diversification of this gene family.
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Affiliation(s)
- Yun Wu
- Department of Landscape Architecture, School of Civil Engineering and Architecture, Zhejiang Sci-Tech University, Hangzhou, 310018, China
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jing Wen
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Yiping Xia
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Liangsheng Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Hai Du
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
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Garcia-Gimenez G, Schreiber M, Dimitroff G, Little A, Singh R, Fincher GB, Burton RA, Waugh R, Tucker MR, Houston K. Identification of candidate MYB transcription factors that influence CslF6 expression in barley grain. FRONTIERS IN PLANT SCIENCE 2022; 13:883139. [PMID: 36160970 PMCID: PMC9493323 DOI: 10.3389/fpls.2022.883139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 08/17/2022] [Indexed: 05/13/2023]
Abstract
(1,3;1,4)-β-Glucan is a non-cellulosic polysaccharide required for correct barley grain fill and plant development, with industrial relevance in the brewing and the functional food sector. Barley grains contain higher levels of (1,3;1,4)-β-glucan compared to other small grain cereals and this influences their end use, having undesirable effects on brewing and distilling and beneficial effects linked to human health. HvCslF6 is the main gene contributing to (1,3;1,4)-β-glucan biosynthesis in the grain. Here, the transcriptional regulation of HvCslF6 was investigated using an in-silico analysis of transcription factor binding sites (TFBS) in its putative promoter, and functional characterization in a barley protoplast transient expression system. Based on TFBS predictions, TF classes AP2/ERF, MYB, and basic helix-loop-helix (bHLH) were over-represented within a 1,000 bp proximal HvCslF6 promoter region. Dual luciferase assays based on multiple HvCslF6 deletion constructs revealed the promoter fragment driving HvCslF6 expression. Highest HvCslF6 promoter activity was narrowed down to a 51 bp region located -331 bp to -382 bp upstream of the start codon. We combined this with TFBS predictions to identify two MYB TFs: HvMYB61 and HvMYB46/83 as putative activators of HvCslF6 expression. Gene network analyses assigned HvMYB61 to the same co-expression module as HvCslF6 and other primary cellulose synthases (HvCesA1, HvCesA2, and HvCesA6), whereas HvMYB46/83 was assigned to a different module. Based on RNA-seq expression during grain development, HvMYB61 was cloned and tested in the protoplast system. The transient over-expression of HvMYB61 in barley protoplasts suggested a positive regulatory effect on HvCslF6 expression.
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Affiliation(s)
| | - Miriam Schreiber
- Plant Sciences Division, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - George Dimitroff
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Alan Little
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Rohan Singh
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Geoffrey B. Fincher
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Rachel A. Burton
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Robbie Waugh
- The James Hutton Institute, Dundee, United Kingdom
- Plant Sciences Division, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Matthew R. Tucker
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Kelly Houston
- The James Hutton Institute, Dundee, United Kingdom
- *Correspondence: Kelly Houston,
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Zhuang H, Chong SL, Priyanka B, Han X, Lin E, Tong Z, Huang H. Full-length transcriptomic identification of R2R3-MYB family genes related to secondary cell wall development in Cunninghamia lanceolata (Chinese fir). BMC PLANT BIOLOGY 2021; 21:581. [PMID: 34879821 PMCID: PMC8653563 DOI: 10.1186/s12870-021-03322-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 11/08/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND R2R3-MYB is a class of transcription factor crucial in regulating secondary cell wall development during wood formation. The regulation of wood formation in gymnosperm has been understudied due to its large genome size. Using Single-Molecule Real-Time sequencing, we obtained full-length transcriptomic libraries from the developmental stem of Cunninghamia lanceolata, a perennial conifer known as Chinese fir. The R2R3-MYB of C. lanceolata (hereafter named as ClMYB) associated with secondary wall development were identified based on phylogenetic analysis, expression studies and functional study on transgenic line. RESULTS The evolutionary relationship of 52 ClMYBs with those from Arabidopsis thaliana, Eucalyptus grandis, Populus trichocarpa, Oryza sativa, two gymnosperm species, Pinus taeda, and Picea glauca were established by neighbour-joining phylogenetic analysis. A large number of ClMYBs resided in the woody-expanded subgroups that predominated with the members from woody dicots. In contrast, the woody-preferential subgroup strictly carrying the members of woody dicots contained only one candidate. The results suggest that the woody-expanded subgroup emerges before the gymnosperm/angiosperm split, while most of the woody-preferential subgroups are likely lineage-specific to woody dicots. Nine candidates shared the same subgroups with the A. thaliana orthologs, with known function in regulating secondary wall development. Gene expression analysis inferred that ClMYB1/2/3/4/5/26/27/49/51 might participate in secondary wall development, among which ClMYB1/2/5/26/27/49 were significantly upregulated in the highly lignified compression wood region, reinforcing their regulatory role associated with secondary wall development. ClMYB1 was experimentally proven a transcriptional activator that localised in the nucleus. The overexpression of ClMYB1 in Nicotiana benthamiana resulted in an increased lignin deposition in the stems. The members of subgroup S4, ClMYB3/4/5 shared the ERF-associated amphiphilic repression motif with AtMYB4, which is known to repress the metabolism of phenylpropanoid derived compounds. They also carried a core motif specific to gymnosperm lineage, suggesting divergence of the regulatory process compared to the angiosperms. CONCLUSIONS This work will enrich the collection of full-length gymnosperm-specific R2R3-MYBs related to stem development and contribute to understanding their evolutionary relationship with angiosperm species.
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Affiliation(s)
- Hebi Zhuang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Sun-Li Chong
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Borah Priyanka
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Xiao Han
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Erpei Lin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Zaikang Tong
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Huahong Huang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China.
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Distinct and Overlapping Functions of Miscanthus sinensis MYB Transcription Factors SCM1 and MYB103 in Lignin Biosynthesis. Int J Mol Sci 2021; 22:ijms222212395. [PMID: 34830276 PMCID: PMC8625797 DOI: 10.3390/ijms222212395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/02/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022] Open
Abstract
Cell wall recalcitrance is a major constraint for the exploitation of lignocellulosic biomass as a renewable resource for energy and bio-based products. Transcriptional regulators of the lignin biosynthetic pathway represent promising targets for tailoring lignin content and composition in plant secondary cell walls. However, knowledge about the transcriptional regulation of lignin biosynthesis in lignocellulosic feedstocks, such as Miscanthus, is limited. In Miscanthus leaves, MsSCM1 and MsMYB103 are expressed at growth stages associated with lignification. The ectopic expression of MsSCM1 and MsMYB103 in N. benthamiana leaves was sufficient to trigger secondary cell wall deposition with distinct sugar and lignin compositions. Moreover, RNA-seq analysis revealed that the transcriptional responses to MsSCM1 and MsMYB103 overexpression showed an extensive overlap with the response to the NAC master transcription factor MsSND1, but were distinct from each other, underscoring the inherent complexity of secondary cell wall formation. Furthermore, conserved and previously described promoter elements as well as novel and specific motifs could be identified from the target genes of the three transcription factors. Together, MsSCM1 and MsMYB103 represent interesting targets for manipulations of lignin content and composition in Miscanthus towards a tailored biomass.
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11
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Yao T, Feng K, Xie M, Barros J, Tschaplinski TJ, Tuskan GA, Muchero W, Chen JG. Phylogenetic Occurrence of the Phenylpropanoid Pathway and Lignin Biosynthesis in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:704697. [PMID: 34484267 PMCID: PMC8416159 DOI: 10.3389/fpls.2021.704697] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/19/2021] [Indexed: 05/19/2023]
Abstract
The phenylpropanoid pathway serves as a rich source of metabolites in plants and provides precursors for lignin biosynthesis. Lignin first appeared in tracheophytes and has been hypothesized to have played pivotal roles in land plant colonization. In this review, we summarize recent progress in defining the lignin biosynthetic pathway in lycophytes, monilophytes, gymnosperms, and angiosperms. In particular, we review the key structural genes involved in p-hydroxyphenyl-, guaiacyl-, and syringyl-lignin biosynthesis across plant taxa and consider and integrate new insights on major transcription factors, such as NACs and MYBs. We also review insight regarding a new transcriptional regulator, 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase, canonically identified as a key enzyme in the shikimate pathway. We use several case studies, including EPSP synthase, to illustrate the evolution processes of gene duplication and neo-functionalization in lignin biosynthesis. This review provides new insights into the genetic engineering of the lignin biosynthetic pathway to overcome biomass recalcitrance in bioenergy crops.
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Affiliation(s)
- Tao Yao
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Kai Feng
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Meng Xie
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Jaime Barros
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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12
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Xing G, Li J, Li W, Lam SM, Yuan H, Shui G, Yang J. AP2/ERF and R2R3-MYB family transcription factors: potential associations between temperature stress and lipid metabolism in Auxenochlorella protothecoides. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:22. [PMID: 33451355 PMCID: PMC7811268 DOI: 10.1186/s13068-021-01881-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/08/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Both APETALA2/Ethylene Responsive Factor (AP2/ERF) superfamily and R2R3-MYB family were from one of the largest diverse families of transcription factors (TFs) in plants, and played important roles in plant development and responses to various stresses. However, no systematic analysis of these TFs had been conducted in the green algae A. protothecoides heretofore. Temperature was a critical factor affecting growth and lipid metabolism of A. protothecoides. It also remained largely unknown whether these TFs would respond to temperature stress and be involved in controlling lipid metabolism process. RESULTS Hereby, a total of six AP2 TFs, six ERF TFs and six R2R3-MYB TFs were identified and their expression profiles were also analyzed under low-temperature (LT) and high-temperature (HT) stresses. Meanwhile, differential adjustments of lipid pathways were triggered, with enhanced triacylglycerol accumulation. A co-expression network was built between these 18 TFs and 32 lipid-metabolism-related genes, suggesting intrinsic associations between TFs and the regulatory mechanism of lipid metabolism. CONCLUSIONS This study represented an important first step towards identifying functions and roles of AP2 superfamily and R2R3-MYB family in lipid adjustments and response to temperature stress. These findings would facilitate the biotechnological development in microalgae-based biofuel production and the better understanding of photosynthetic organisms' adaptive mechanism to temperature stress.
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Affiliation(s)
- Guanlan Xing
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193 China
| | - Jinyu Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193 China
| | - Wenli Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193 China
| | - Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Hongli Yuan
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193 China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jinshui Yang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193 China
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13
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Overexpression of PtrMYB121 Positively Regulates the Formation of Secondary Cell Wall in Arabidopsis thaliana. Int J Mol Sci 2020; 21:ijms21207734. [PMID: 33086706 PMCID: PMC7589094 DOI: 10.3390/ijms21207734] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/15/2020] [Accepted: 10/17/2020] [Indexed: 12/30/2022] Open
Abstract
MYB transcription factors have a wide range of functions in plant growth, hormone signaling, salt, and drought tolerances. In this study, two homologous transcription factors, PtrMYB55 and PtrMYB121, were isolated and their functions were elucidated. Tissue expression analysis revealed that PtrMYB55 and PtrMYB121 had a similar expression pattern, which had the highest expression in stems. Their expression continuously increased with the growth of poplar, and the expression of PtrMYB121 was significantly upregulated in the process. The full length of PtrMYB121 was 1395 bp, and encoded protein contained 464 amino acids including conserved R2 and R3 MYB domains. We overexpressed PtrMYB121 in Arabidopsis thaliana, and the transgenic lines had the wider xylem as compared with wild-type Arabidopsis. The contents of cellulose and lignin were obviously higher than those in wild-type materials, but there was no significant change in hemicellulose. Quantitative real-time PCR demonstrated that the key enzyme genes regulating the synthesis of lignin and cellulose were significantly upregulated in the transgenic lines. Furthermore, the effector-reporter experiment confirmed that PtrMYB121 bound directly to the promoters of genes relating to the synthesis of lignin and cellulose. These results suggest that PtrMYB121 may positively regulate the formation of secondary cell wall by promoting the synthesis of lignin and cellulose.
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Coomey JH, Sibout R, Hazen SP. Grass secondary cell walls, Brachypodium distachyon as a model for discovery. THE NEW PHYTOLOGIST 2020; 227:1649-1667. [PMID: 32285456 DOI: 10.1111/nph.16603] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/05/2020] [Indexed: 05/20/2023]
Abstract
A key aspect of plant growth is the synthesis and deposition of cell walls. In specific tissues and cell types including xylem and fibre, a thick secondary wall comprised of cellulose, hemicellulose and lignin is deposited. Secondary cell walls provide a physical barrier that protects plants from pathogens, promotes tolerance to abiotic stresses and fortifies cells to withstand the forces associated with water transport and the physical weight of plant structures. Grasses have numerous cell wall features that are distinct from eudicots and other plants. Study of the model species Brachypodium distachyon as well as other grasses has revealed numerous features of the grass cell wall. These include the characterisation of xylosyl and arabinosyltransferases, a mixed-linkage glucan synthase and hydroxycinnamate acyltransferases. Perhaps the most fertile area for discovery has been the formation of lignins, including the identification of novel substrates and enzyme activities towards the synthesis of monolignols. Other enzymes function as polymerising agents or transferases that modify lignins and facilitate interactions with polysaccharides. The regulatory aspects of cell wall biosynthesis are largely overlapping with those of eudicots, but salient differences among species have been resolved that begin to identify the determinants that define grass cell walls.
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Affiliation(s)
- Joshua H Coomey
- Biology Department, University of Massachusetts, Amherst, MA, 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, 01003, USA
| | - Richard Sibout
- Biopolymères Interactions Assemblages, INRAE, UR BIA, F-44316, Nantes, France
| | - Samuel P Hazen
- Biology Department, University of Massachusetts, Amherst, MA, 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, 01003, USA
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Singh V, Kumar N, Dwivedi AK, Sharma R, Sharma MK. Phylogenomic Analysis of R2R3 MYB Transcription Factors in Sorghum and their Role in Conditioning Biofuel Syndrome. Curr Genomics 2020; 21:138-154. [PMID: 32655308 PMCID: PMC7324873 DOI: 10.2174/1389202921666200326152119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 11/30/2022] Open
Abstract
Background Large scale cultivation of sorghum for food, feed, and biofuel requires concerted efforts for engineering multipurpose cultivars with optimised agronomic traits. Due to their vital role in regulating the biosynthesis of phenylpropanoid-derived compounds, biomass composition, biotic, and abiotic stress response, R2R3-MYB family transcription factors are ideal targets for improving environmental resilience and economic value of sorghum. Methods We used diverse computational biology tools to survey the sorghum genome to identify R2R3-MYB transcription factors followed by their structural and phylogenomic analysis. We used in-house generated as well as publicly available high throughput expression data to analyse the R2R3 expression patterns in various sorghum tissue types. Results We have identified a total of 134 R2R3-MYB genes from sorghum and developed a framework to predict gene functions. Collating information from the physical location, duplication, structural analysis, orthologous sequences, phylogeny, and expression patterns revealed the role of duplications in clade-wise expansion of the R2R3-MYB family as well as intra-clade functional diversification. Using publicly available and in-house generated RNA sequencing data, we provide MYB candidates for conditioning biofuel syndrome by engineering phenylpropanoid biosynthesis and sugar signalling pathways in sorghum. Conclusion The results presented here are pivotal to prioritize MYB genes for functional validation and optimize agronomic traits in sorghum.
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Affiliation(s)
- Vinay Singh
- 1Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India; 2Crop Genetics & Informatics Group, School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India
| | - Neeraj Kumar
- 1Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India; 2Crop Genetics & Informatics Group, School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India
| | - Anuj K Dwivedi
- 1Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India; 2Crop Genetics & Informatics Group, School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India
| | - Rita Sharma
- 1Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India; 2Crop Genetics & Informatics Group, School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India
| | - Manoj K Sharma
- 1Crop Genetics & Informatics Group, School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India; 2Crop Genetics & Informatics Group, School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Mehrauli Road, New Delhi-110067, India
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16
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Zhang P, Liu X, Yu X, Wang F, Long J, Shen W, Jiang D, Zhao X. The MYB transcription factor CiMYB42 regulates limonoids biosynthesis in citrus. BMC PLANT BIOLOGY 2020; 20:254. [PMID: 32493275 PMCID: PMC7271526 DOI: 10.1186/s12870-020-02475-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/27/2020] [Indexed: 05/21/2023]
Abstract
BACKGROUND Limonoids are major bioactive compounds that are produced by the triterpenoid metabolic pathway. The detailed biochemical process of limonoid biosynthesis and the mechanism of its molecular regulation remain elusive. The identification of transcription factors that regulate limonoid biosynthetic pathways is very important for understanding the underlying regulatory mechanisms. This information could also provide tools for manipulating biosynthesis genes to modulate limonoid production. RESULTS In this study, the CiMYB42 transcription factor was isolated to identify its role in limonoid biosynthesis. Multiple alignment analysis and phylogenetic analysis demonstrated that CiMYB42 is a typical R2R3MYB transcription factor that shares high similarity of its amino acid sequence with AtMYB42. Limonoids contents were higher in Citrus sinensis and Citrus grandis than in other species. Limonoid accumulation during leaf development also showed diverse trends in different genotypes. The expression of CiMYB42 was significantly related to the limonoid content and the expression of CiOSC in some citrus accessions. The overexpression of CiMYB42 in sweet orange resulted in significant accumulation of limonin, whereas the downregulation of CiMYB42 by RNAi resulted in a dwarf phenotype and less nomilin accumulation. Furthermore, the results of a yeast one-hybrid assay and EMSA indicated that CiMYB42 binds exclusively to the TTGTTG sequence (type II MYB core) in the promoter of CiOSC. Together, these results suggest that CiMYB42 positively regulates limonoid biosynthesis by regulating the expression of CiOSC by binding to the TTGTTG sequence (type II MYB core) of its promoter. CONCLUSIONS CiMYB42 is an important transcription activator involved in limonoid biosynthesis that regulates the expression of CiOSC by binding to the TTGTTG sequence (type II MYB core).
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Affiliation(s)
- Pan Zhang
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing, 400712, China
- National Citrus Engineering Research Center, Beibei, Chongqing, 400712, China
| | - Xiaofeng Liu
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing, 400712, China
- National Citrus Engineering Research Center, Beibei, Chongqing, 400712, China
| | - Xin Yu
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing, 400712, China
- National Citrus Engineering Research Center, Beibei, Chongqing, 400712, China
| | - Fusheng Wang
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing, 400712, China
- National Citrus Engineering Research Center, Beibei, Chongqing, 400712, China
| | - Junhong Long
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing, 400712, China
- National Citrus Engineering Research Center, Beibei, Chongqing, 400712, China
| | - Wanxia Shen
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing, 400712, China
- National Citrus Engineering Research Center, Beibei, Chongqing, 400712, China
| | - Dong Jiang
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing, 400712, China
- National Citrus Engineering Research Center, Beibei, Chongqing, 400712, China
| | - Xiaochun Zhao
- Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Beibei, Chongqing, 400712, China.
- National Citrus Engineering Research Center, Beibei, Chongqing, 400712, China.
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17
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Wang D, Xu T, Yin Z, Wu W, Geng H, Li L, Yang M, Cai H, Lian X. Overexpression of OsMYB305 in Rice Enhances the Nitrogen Uptake Under Low-Nitrogen Condition. FRONTIERS IN PLANT SCIENCE 2020; 11:369. [PMID: 32351516 PMCID: PMC7174616 DOI: 10.3389/fpls.2020.00369] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/13/2020] [Indexed: 05/10/2023]
Abstract
Excessive nitrogen fertilizer application causes severe environmental degradation and drives up agricultural production costs. Thus, improving crop nitrogen use efficiency (NUE) is essential for the development of sustainable agriculture. Here, we characterized the roles of the MYB transcription factor OsMYB305 in nitrogen uptake and assimilation in rice. OsMYB305 encoded a transcriptional activator and its expression was induced by N deficiency in rice root. Under low-N condition, OsMYB305 overexpression significantly increased the tiller number, shoot dry weight and total N concentration. In the roots of OsMYB305-OE rice lines, the expression of OsNRT2.1, OsNRT2.2, OsNAR2.1, and OsNiR2 was up-regulated and 15NO3 - influx was significantly increased. In contrast, the expression of lignocellulose biosynthesis-related genes was repressed so that cellulose content decreased, and soluble sugar concentration increased. Certain intermediates in the glycolytic pathway and the tricarboxylic acid cycle were significantly altered and NADH-GOGAT, Pyr-K, and G6PDH were markedly elevated in the roots of OsMYB305-OE rice lines grown under low-N condition. Our results revealed that OsMYB305 overexpression suppressed cellulose biosynthesis under low-nitrogen condition, thereby freeing up carbohydrate for nitrate uptake and assimilation and enhancing rice growth. OsMYB305 is a potential molecular target for increasing NUE in rice.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xingming Lian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
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18
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Hennet L, Berger A, Trabanco N, Ricciuti E, Dufayard JF, Bocs S, Bastianelli D, Bonnal L, Roques S, Rossini L, Luquet D, Terrier N, Pot D. Transcriptional Regulation of Sorghum Stem Composition: Key Players Identified Through Co-expression Gene Network and Comparative Genomics Analyses. FRONTIERS IN PLANT SCIENCE 2020; 11:224. [PMID: 32194601 PMCID: PMC7064007 DOI: 10.3389/fpls.2020.00224] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
Most sorghum biomass accumulates in stem secondary cell walls (SCW). As sorghum stems are used as raw materials for various purposes such as feed, energy and fiber reinforced polymers, identifying the genes responsible for SCW establishment is highly important. Taking advantage of studies performed in model species, most of the structural genes contributing at the molecular level to the SCW biosynthesis in sorghum have been proposed while their regulatory factors have mostly not been determined. Validation of the role of several MYB and NAC transcription factors in SCW regulation in Arabidopsis and a few other species has been provided. In this study, we contributed to the recent efforts made in grasses to uncover the mechanisms underlying SCW establishment. We reported updated phylogenies of NAC and MYB in 9 different species and exploited findings from other species to highlight candidate regulators of SCW in sorghum. We acquired expression data during sorghum internode development and used co-expression analyses to determine groups of co-expressed genes that are likely to be involved in SCW establishment. We were able to identify two groups of co-expressed genes presenting multiple evidences of involvement in SCW building. Gene enrichment analysis of MYB and NAC genes provided evidence that while NAC SECONDARY WALL THICKENING PROMOTING FACTOR NST genes and SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN gene functions appear to be conserved in sorghum, NAC master regulators of SCW in sorghum may not be as tissue compartmentalized as in Arabidopsis. We showed that for every homolog of the key SCW MYB in Arabidopsis, a similar role is expected for sorghum. In addition, we unveiled sorghum MYB and NAC that have not been identified to date as being involved in cell wall regulation. Although specific validation of the MYB and NAC genes uncovered in this study is needed, we provide a network of sorghum genes involved in SCW both at the structural and regulatory levels.
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Affiliation(s)
- Lauriane Hennet
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Angélique Berger
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Noemi Trabanco
- Parco Tecnologico Padano, Lodi, Italy
- Centro de Biotecnología y Genómica de Plantas, UPM-INIA, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Emeline Ricciuti
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Jean-François Dufayard
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Stéphanie Bocs
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Denis Bastianelli
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
- CIRAD, UMR SELMET, Montpellier, France
| | - Laurent Bonnal
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
- CIRAD, UMR SELMET, Montpellier, France
| | - Sandrine Roques
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Laura Rossini
- Parco Tecnologico Padano, Lodi, Italy
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Delphine Luquet
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Nancy Terrier
- AGAP, CIRAD, INRAE, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - David Pot
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
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Zhao Y, Song X, Zhou H, Wei K, Jiang C, Wang J, Cao Y, Tang F, Zhao S, Lu MZ. KNAT2/6b, a class I KNOX gene, impedes xylem differentiation by regulating NAC domain transcription factors in poplar. THE NEW PHYTOLOGIST 2020; 225:1531-1544. [PMID: 31257603 DOI: 10.1111/nph.16036] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 06/22/2019] [Indexed: 05/21/2023]
Abstract
Wood formation is the terminal differentiation of xylem mother cells derived from cambial initials, and negative regulators play important roles in xylem differentiation. The molecular mechanism of the negative regulator of xylem differentiation PagKNAT2/6b was investigated. PagKNAT2/6b is an ortholog of Arabidopsis KNAT2 and KNAT6 that is highly expressed in phloem and xylem. Compared to nontransgenic control plants, transgenic poplar plants overexpressing PagKNAT2/6b present with altered vascular patterns, characterized by decreased secondary xylem with thin cell walls containing less cellulose, xylose and lignin. RNA sequencing analyses revealed that differentially expressed genes are enriched in xylem differentiation and secondary wall synthesis functions. Expression of NAM/ATAF/CUC (NAC) domain genes including PagSND1-A1, PagSND1-A2, PagSND1-B2 and PagVND6-C1 is downregulated by PagKNAT2/6b, while PagXND1a is directly upregulated. Accordingly, the dominant repression form of PagKNAT2/6b leads to increased xylem width per stem diameter through downregulation of PagXND1a. PagKNAT2/6b can inhibit cell differentiation and secondary wall deposition during wood formation in poplar by modulating the expression of NAC domain transcription factors. Direct activation of PagXND1a by PagKNAT2/6b is a key node in the negative regulatory network of xylem differentiation by KNOXs.
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Affiliation(s)
- Yanqiu Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xueqin Song
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, 210037, China
| | - Houjun Zhou
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Kaili Wei
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Cheng Jiang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
| | - Jinnan Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yuan Cao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Fang Tang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, 210037, China
| | - Shutang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, 210037, China
| | - Meng-Zhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Jiangsu, 210037, China
- Zhejiang Agriculture & Forestry University, Hangzhou, 311300, China
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20
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Mazarei M, Baxter HL, Srivastava A, Li G, Xie H, Dumitrache A, Rodriguez M, Natzke JM, Zhang JY, Turner GB, Sykes RW, Davis MF, Udvardi MK, Wang ZY, Davison BH, Blancaflor EB, Tang Y, Stewart CN. Silencing Folylpolyglutamate Synthetase1 ( FPGS1) in Switchgrass ( Panicum virgatum L.) Improves Lignocellulosic Biofuel Production. FRONTIERS IN PLANT SCIENCE 2020; 11:843. [PMID: 32636863 PMCID: PMC7317012 DOI: 10.3389/fpls.2020.00843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/26/2020] [Indexed: 05/12/2023]
Abstract
Switchgrass (Panicum virgatum L.) is a lignocellulosic perennial grass with great potential in bioenergy field. Lignocellulosic bioenergy crops are mostly resistant to cell wall deconstruction, and therefore yield suboptimal levels of biofuel. The one-carbon pathway (also known as C1 metabolism) is critical for polymer methylation, including that of lignin and hemicelluloses in cell walls. Folylpolyglutamate synthetase (FPGS) catalyzes a biochemical reaction that leads to the formation of folylpolyglutamate, an important cofactor for many enzymes in the C1 pathway. In this study, the putatively novel switchgrass PvFPGS1 gene was identified and its functional role in cell wall composition and biofuel production was examined by RNAi knockdown analysis. The PvFPGS1-downregulated plants were analyzed in the field over three growing seasons. Transgenic plants with the highest reduction in PvFPGS1 expression grew slower and produced lower end-of-season biomass. Transgenic plants with low-to-moderate reduction in PvFPGS1 transcript levels produced equivalent biomass as controls. There were no significant differences observed for lignin content and syringyl/guaiacyl lignin monomer ratio in the low-to-moderately reduced PvFPGS1 transgenic lines compared with the controls. Similarly, sugar release efficiency was also not significantly different in these transgenic lines compared with the control lines. However, transgenic plants produced up to 18% more ethanol while maintaining congruent growth and biomass as non-transgenic controls. Severity of rust disease among transgenic and control lines were not different during the time course of the field experiments. Altogether, the unchanged lignin content and composition in the low-to-moderate PvFPGS1-downregulated lines may suggest that partial downregulation of PvFPGS1 expression did not impact lignin biosynthesis in switchgrass. In conclusion, the manipulation of PvFPGS1 expression in bioenergy crops may be useful to increase biofuel potential with no growth penalty or increased susceptibility to rust in feedstock.
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Affiliation(s)
- Mitra Mazarei
- Department of Plant Sciences, The University of Tennessee, Knoxville, TN, United States
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Holly L. Baxter
- Department of Plant Sciences, The University of Tennessee, Knoxville, TN, United States
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Avinash Srivastava
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Noble Research Institute, Ardmore, OK, United States
| | - Guifen Li
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Noble Research Institute, Ardmore, OK, United States
| | - Hongli Xie
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Noble Research Institute, Ardmore, OK, United States
| | - Alexandru Dumitrache
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Miguel Rodriguez
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jace M. Natzke
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Ji-Yi Zhang
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Noble Research Institute, Ardmore, OK, United States
| | - Geoffrey B. Turner
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- National Renewable Energy Laboratory, Golden, CO, United States
| | - Robert W. Sykes
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- National Renewable Energy Laboratory, Golden, CO, United States
| | - Mark F. Davis
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- National Renewable Energy Laboratory, Golden, CO, United States
| | - Michael K. Udvardi
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Noble Research Institute, Ardmore, OK, United States
| | - Zeng-Yu Wang
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Noble Research Institute, Ardmore, OK, United States
| | - Brian H. Davison
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Elison B. Blancaflor
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Noble Research Institute, Ardmore, OK, United States
| | - Yuhong Tang
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Noble Research Institute, Ardmore, OK, United States
- *Correspondence: Yuhong Tang,
| | - Charles Neal Stewart
- Department of Plant Sciences, The University of Tennessee, Knoxville, TN, United States
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Charles Neal Stewart Jr.,
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Induction of PrMADS10 on the lower side of bent pine tree stems: potential role in modifying plant cell wall properties and wood anatomy. Sci Rep 2019; 9:18981. [PMID: 31831838 PMCID: PMC6908731 DOI: 10.1038/s41598-019-55276-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/07/2019] [Indexed: 12/20/2022] Open
Abstract
The molecular mechanisms underlying inclination responses in trees are unclear. In this study, we identified a MADS-box transcription factor differentially expressed early after inclination in the stems of Pinus radiata D. Don. PrMADS10 has a CDS of 582 bp and encodes a group II MADS-box transcription factor. We measured highest accumulation of this transcript on the lower side of inclined pine stems. In an effort to identify putative targets, we stably transformed Arabidopsis thaliana with a 35S::PrMADS10 construct. Transcriptome analysis revealed 1,219 genes differentially-expressed, with 690 and 529 genes up- and down-regulated respectively, when comparing the transgenic and wild-type. Differentially-expressed genes belong to different biological processes, but were enriched in cell wall remodeling and phenylpropanoid metabolic functions. Interestingly, lignin content was 30% higher in transgenic as compared to wild-type plants consistent with observed changes in gene expression. Differentially expressed transcription factors and phenylpropanoid genes were analyzed using STRING. Several MYB and NAC transcription factors showed interactions with genes of the phenylpropanoid pathway. Together, these results implicate PrMADS10 as a regulatory factor, triggering the expression of other transcription factors and genes involved in the synthesis of lignin.
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22
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Miyamoto T, Takada R, Tobimatsu Y, Takeda Y, Suzuki S, Yamamura M, Osakabe K, Osakabe Y, Sakamoto M, Umezawa T. OsMYB108 loss-of-function enriches p-coumaroylated and tricin lignin units in rice cell walls. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:975-987. [PMID: 30773774 DOI: 10.1111/tpj.14290] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/08/2019] [Accepted: 02/14/2019] [Indexed: 05/23/2023]
Abstract
Breeding approaches to enrich lignins in biomass could be beneficial to improving the biorefinery process because lignins increase biomass heating value and represent a potent source of valuable aromatic chemicals. However, despite the fact that grasses are promising lignocellulose feedstocks, limited information is yet available for molecular-breeding approaches to upregulate lignin biosynthesis in grass species. In this study, we generated lignin-enriched transgenic rice (Oryza sativa), a model grass species, via targeted mutagenesis of the transcriptional repressor OsMYB108 using CRISPR/Cas9-mediated genome editing. The OsMYB108-knockout rice mutants displayed increased expressions of lignin biosynthetic genes and enhanced lignin deposition in culm cell walls. Chemical and two-dimensional nuclear magnetic resonance (NMR) analyses revealed that the mutant cell walls were preferentially enriched in γ-p-coumaroylated and tricin lignin units, both of which are typical and unique components in grass lignins. NMR analysis also showed that the relative abundances of major lignin linkage types were altered in the OsMYB108 mutants.
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Affiliation(s)
- Takuji Miyamoto
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Rie Takada
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Yuki Tobimatsu
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Yuri Takeda
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Shiro Suzuki
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Masaomi Yamamura
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Keishi Osakabe
- Faculty of Bioscience and Bioindustry, Tokushima University, Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Yuriko Osakabe
- Faculty of Bioscience and Bioindustry, Tokushima University, Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Masahiro Sakamoto
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Toshiaki Umezawa
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, 611-0011, Japan
- Research Unit for Development of Global Sustainability, Kyoto University, Uji, Kyoto, 611-0011, Japan
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23
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Tombuloglu H. Genome-wide identification and expression analysis of R2R3, 3R- and 4R-MYB transcription factors during lignin biosynthesis in flax (Linum usitatissimum). Genomics 2019; 112:782-795. [PMID: 31128265 DOI: 10.1016/j.ygeno.2019.05.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/06/2019] [Accepted: 05/20/2019] [Indexed: 11/19/2022]
Abstract
MYB transcription factors (TFs) have vital roles in regulating lignin or fiber development. Flax (Linum usitatissimum) is known as one of the plants with high fiber production capacity. However, no studies have been conducted to identify and characterize MYB TFs in the flax genome. Results showed that flax genome harbours 167 R2R3, seven 3R, and one 4R-type MYB TFs. 22 MYB genes (%13) were estimated to be tandem duplicated dated around 13.3-86.98 Mya. 130 flax MYB members have apparent orthologous with Arabidopsis, in which 17 R2R3 MYBs are associated with lignin biosynthesis. MYB062, MYB072, MYB096, MYB141, and MYB146 genes were up-regulated in tissues having higher lignin production capacity. In opposite, MYB012 and MYB113 genes were down-regulated which points out the involvement of those genes in the lignin biosynthesis mechanism. This comprehensive study can provide a basis for understanding the role of MYBs in fiber or lignin production in flax.
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Affiliation(s)
- Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, 31441 Dammam, Saudi Arabia.
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24
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Huang J, Guo Y, Sun Q, Zeng W, Li J, Li X, Xu W. Genome-Wide Identification of R2R3-MYB Transcription Factors Regulating Secondary Cell Wall Thickening in Cotton Fiber Development. PLANT & CELL PHYSIOLOGY 2019; 60:687-701. [PMID: 30576529 DOI: 10.1093/pcp/pcy238] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 12/14/2018] [Indexed: 05/02/2023]
Abstract
MYB proteins represent one of the largest transcription factor (TF) families in plants, some of which act as key transcriptional regulators of secondary cell wall (SCW) biosynthesis. Cotton (Gossypium hirsutum) fiber is thought to be an ideal single-cell model to study cell elongation and SCW biosynthesis. However, little knowledge regarding the TFs controlling fiber SCW biosynthesis, particularly for R2R3-MYBs is known. By far, no comprehensive genome-wide analysis of the secondary wall-associated R2R3-MYBs has been reported in cultivated tetraploid upland cotton. In this study, we identified 419 R2R3-MYB genes by systematically examining the cotton genome. A combination of phylogenetic, RNA-seq and co-expression analyses indicated that 36 R2R3-MYBs were either preferentially or highly expressed in 20 day post anthesis (dpa) fibers and are putative SCW regulators. Among these MYB genes, 22 MYBs are homologs of known SCW MYB proteins and the other 14 MYBs are novel proteins without prior reported SCW biosynthesis-related functions. Finally, we highlighted on the roles of two MYBs named GhMYB46_D13 and GhMYB46_D9, both of which displayed the highest expression in 20 dpa fibers. Expression of GhMYB46_D13 or GhMYB46_D9 individually in Arabidopsis resulted in ectopic SCW deposition in transgenic plants. Furthermore, both GhMYB46_D13 and GhMYB46_D9 were able to activate the cotton fiber SCW cellulose synthase gene promoters. Thus, we have identified 36 R2R3-MYBs as potential SCW regulators in cotton fibers that represent strong candidates for further functional studies during fiber development and SCW thickening.
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Affiliation(s)
- Junfeng Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Yanjun Guo
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Qianwen Sun
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Wei Zeng
- Sino-Australia Plant Cell Wall Research Centre, State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Juan Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Xuebao Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
| | - Wenliang Xu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
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25
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Zhao K, Lin F, Romero-Gamboa SP, Saha P, Goh HJ, An G, Jung KH, Hazen SP, Bartley LE. Rice Genome-Scale Network Integration Reveals Transcriptional Regulators of Grass Cell Wall Synthesis. FRONTIERS IN PLANT SCIENCE 2019; 10:1275. [PMID: 31681374 PMCID: PMC6813959 DOI: 10.3389/fpls.2019.01275] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 09/12/2019] [Indexed: 05/07/2023]
Abstract
Grasses have evolved distinct cell wall composition and patterning relative to dicotyledonous plants. However, despite the importance of this plant family, transcriptional regulation of its cell wall biosynthesis is poorly understood. To identify grass cell wall-associated transcription factors, we constructed the Rice Combined mutual Ranked Network (RCRN). The RCRN covers >90% of annotated rice (Oryza sativa) genes, is high quality, and includes most grass-specific cell wall genes, such as mixed-linkage glucan synthases and hydroxycinnamoyl acyltransferases. Comparing the RCRN and an equivalent Arabidopsis network suggests that grass orthologs of most genetically verified eudicot cell wall regulators also control this process in grasses, but some transcription factors vary significantly in network connectivity between these divergent species. Reverse genetics, yeast-one-hybrid, and protoplast-based assays reveal that OsMYB61a activates a grass-specific acyltransferase promoter, which confirms network predictions and supports grass-specific cell wall synthesis genes being incorporated into conserved regulatory circuits. In addition, 10 of 15 tested transcription factors, including six novel Wall-Associated regulators (WAP1, WACH1, WAHL1, WADH1, OsMYB13a, and OsMYB13b), alter abundance of cell wall-related transcripts when transiently expressed. The results highlight the quality of the RCRN for examining rice biology, provide insight into the evolution of cell wall regulation, and identify network nodes and edges that are possible leads for improving cell wall composition.
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Affiliation(s)
- Kangmei Zhao
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Fan Lin
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | | | - Prasenjit Saha
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Hyung-Jung Goh
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Gynheung An
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
| | - Samuel P. Hazen
- Department of Biology, University of Massachusetts, Amherst, MA, United States
| | - Laura E. Bartley
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
- *Correspondence: Laura E. Bartley,
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26
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Handakumbura PP, Brow K, Whitney IP, Zhao K, Sanguinet KA, Lee SJ, Olins J, Romero-Gamboa SP, Harrington MJ, Bascom CJ, MacKinnon KJM, Veling MT, Liu L, Lee JE, Vogel JP, O'Malley RC, Bezanilla M, Bartley LE, Hazen SP. SECONDARY WALL ASSOCIATED MYB1 is a positive regulator of secondary cell wall thickening in Brachypodium distachyon and is not found in the Brassicaceae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:532-545. [PMID: 30054951 DOI: 10.1111/tpj.14047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/14/2018] [Accepted: 07/18/2018] [Indexed: 05/11/2023]
Abstract
Grass biomass is comprised chiefly of secondary walls that surround fiber and xylem cells. A regulatory network of interacting transcription factors in part regulates cell wall thickening. We identified Brachypodium distachyon SECONDARY WALL ASSOCIATED MYB1 (SWAM1) as a potential regulator of secondary cell wall biosynthesis based on gene expression, phylogeny, and transgenic plant phenotypes. SWAM1 interacts with cellulose and lignin gene promoters with preferential binding to AC-rich sequence motifs commonly found in the promoters of cell wall-related genes. SWAM1 overexpression (SWAM-OE) lines had greater above-ground biomass with only a slight change in flowering time while SWAM1 dominant repressor (SWAM1-DR) plants were severely dwarfed with a striking reduction in lignin of sclerenchyma fibers and stem epidermal cell length. Cellulose, hemicellulose, and lignin genes were significantly down-regulated in SWAM1-DR plants and up-regulated in SWAM1-OE plants. There was no reduction in bioconversion yield in SWAM1-OE lines; however, it was significantly increased for SWAM1-DR samples. Phylogenetic and syntenic analyses strongly suggest that the SWAM1 clade was present in the last common ancestor between eudicots and grasses, but is not in the Brassicaceae. Collectively, these data suggest that SWAM1 is a transcriptional activator of secondary cell wall thickening and biomass accumulation in B. distachyon.
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Affiliation(s)
- Pubudu P Handakumbura
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Kathryn Brow
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
| | - Ian P Whitney
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Kangmei Zhao
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Karen A Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
| | - Scott J Lee
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Jennifer Olins
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
| | - Sandra P Romero-Gamboa
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | | | - Carlisle J Bascom
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Kirk J-M MacKinnon
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Michael T Veling
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
| | - Lifeng Liu
- DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Ji E Lee
- DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - John P Vogel
- DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
| | | | | | - Laura E Bartley
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Samuel P Hazen
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
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27
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Corbin C, Drouet S, Markulin L, Auguin D, Lainé É, Davin LB, Cort JR, Lewis NG, Hano C. A genome-wide analysis of the flax (Linum usitatissimum L.) dirigent protein family: from gene identification and evolution to differential regulation. PLANT MOLECULAR BIOLOGY 2018; 97:73-101. [PMID: 29713868 DOI: 10.1007/s11103-018-0725-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 04/02/2018] [Indexed: 05/21/2023]
Abstract
Identification of DIR encoding genes in flax genome. Analysis of phylogeny, gene/protein structures and evolution. Identification of new conserved motifs linked to biochemical functions. Investigation of spatio-temporal gene expression and response to stress. Dirigent proteins (DIRs) were discovered during 8-8' lignan biosynthesis studies, through identification of stereoselective coupling to afford either (+)- or (-)-pinoresinols from E-coniferyl alcohol. DIRs are also involved or potentially involved in terpenoid, allyl/propenyl phenol lignan, pterocarpan and lignin biosynthesis. DIRs have very large multigene families in different vascular plants including flax, with most still of unknown function. DIR studies typically focus on a small subset of genes and identification of biochemical/physiological functions. Herein, a genome-wide analysis and characterization of the predicted flax DIR 44-membered multigene family was performed, this species being a rich natural grain source of 8-8' linked secoisolariciresinol-derived lignan oligomers. All predicted DIR sequences, including their promoters, were analyzed together with their public gene expression datasets. Expression patterns of selected DIRs were examined using qPCR, as well as through clustering analysis of DIR gene expression. These analyses further implicated roles for specific DIRs in (-)-pinoresinol formation in seed-coats, as well as (+)-pinoresinol in vegetative organs and/or specific responses to stress. Phylogeny and gene expression analysis segregated flax DIRs into six distinct clusters with new cluster-specific motifs identified. We propose that these findings can serve as a foundation to further systematically determine functions of DIRs, i.e. other than those already known in lignan biosynthesis in flax and other species. Given the differential expression profiles and inducibility of the flax DIR family, we provisionally propose that some DIR genes of unknown function could be involved in different aspects of secondary cell wall biosynthesis and plant defense.
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Affiliation(s)
- Cyrielle Corbin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Samantha Drouet
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Lucija Markulin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Daniel Auguin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Éric Lainé
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France
| | - Laurence B Davin
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, USA
| | - John R Cort
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Norman G Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, USA.
| | - Christophe Hano
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRA USC1328, Université d'Orléans, 28000, Chartres, France.
- COSM'ACTIFS, CNRS GDR3711, 28000, Chartres, France.
- Pôle Universitaire d'Eure et Loir, 21 Rue de Loigny la Bataille, 28000, Chartres, France.
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28
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Rao X, Dixon RA. Current Models for Transcriptional Regulation of Secondary Cell Wall Biosynthesis in Grasses. FRONTIERS IN PLANT SCIENCE 2018; 9:399. [PMID: 29670638 PMCID: PMC5893761 DOI: 10.3389/fpls.2018.00399] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 03/13/2018] [Indexed: 05/17/2023]
Abstract
Secondary cell walls mediate many crucial biological processes in plants including mechanical support, water and nutrient transport and stress management. They also provide an abundant resource of renewable feed, fiber, and fuel. The grass family contains the most important food, forage, and biofuel crops. Understanding the regulatory mechanism of secondary wall formation in grasses is necessary for exploiting these plants for agriculture and industry. Previous research has established a detailed model of the secondary wall regulatory network in the dicot model species Arabidopsis thaliana. Grasses, branching off from the dicot ancestor 140-150 million years ago, display distinct cell wall morphology and composition, suggesting potential for a different secondary wall regulation program from that established for dicots. Recently, combined application of molecular, genetic and bioinformatics approaches have revealed more transcription factors involved in secondary cell wall biosynthesis in grasses. Compared with the dicots, grasses exhibit a relatively conserved but nevertheless divergent transcriptional regulatory program to activate their secondary cell wall development and to coordinate secondary wall biosynthesis with other physiological processes.
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Affiliation(s)
- Xiaolan Rao
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN, United States
- *Correspondence: Xiaolan Rao,
| | - Richard A. Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
- BioEnergy Science Center, United States Department of Energy, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, United States Department of Energy, Oak Ridge, TN, United States
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Li W, Ding Z, Ruan M, Yu X, Peng M, Liu Y. Kiwifruit R2R3-MYB transcription factors and contribution of the novel AcMYB75 to red kiwifruit anthocyanin biosynthesis. Sci Rep 2017; 7:16861. [PMID: 29203778 PMCID: PMC5715094 DOI: 10.1038/s41598-017-16905-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 11/20/2017] [Indexed: 12/04/2022] Open
Abstract
Red kiwifruit (Actinidia chinensis) is a popular fresh fruit with a high market value due to its unique color, caused by anthocyanin accumulation. The R2R3-MYB transcription factors (TFs) have important roles in plant development and anthocyanin metabolism. In this first comprehensive study of R2R3-MYBs in kiwifruit, a total of 93 R2R3-MYB genes, including five novel previously unannotated AcMYBs, were identified. Their phylogenic relationship, exon-intron structures, and conserved motifs were analyzed. Based on transcriptome data, 60 AcMYBs were expressed (FPKM > 1) across seven developmental stages of kiwifruit, revealing five expression patterns. One of the 5 newly identified R2R3 TFs, AcMYB75, showed an anthocyanin accumulation-linked expression pattern during fruit development. AcMYB75 localized to the nucleus and has an active transactivation domain, verifying it as a transcription factor. AcMYB75 protein specifically bound the promoter of the anthocyanin biosynthesis gene ANS in yeast one-hybrid system and in vivo. In 35 S:AcMYB75 Arabidopsis plants, anthocyanin significantly accumulated in leaves, and the expression of anthocyanin biosynthetic genes was greatly up-regulated. Together, these results suggest that AcMYB75 is involved in anthocyanin biosynthesis in kiwifruit. These findings will increase our understanding of AcMYBs involved in anthocyanin biosynthesis, and also benefit further functional characterization of R2R3-MYB genes in kiwifruit.
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Affiliation(s)
- Wenbin Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Zehong Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Mengbin Ruan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Xiaoling Yu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Ming Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China.
| | - Yifei Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China.
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Nemesio-Gorriz M, Blair PB, Dalman K, Hammerbacher A, Arnerup J, Stenlid J, Mukhtar SM, Elfstrand M. Identification of Norway Spruce MYB-bHLH-WDR Transcription Factor Complex Members Linked to Regulation of the Flavonoid Pathway. FRONTIERS IN PLANT SCIENCE 2017; 8:305. [PMID: 28337212 PMCID: PMC5343035 DOI: 10.3389/fpls.2017.00305] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/20/2017] [Indexed: 05/16/2023]
Abstract
Transcription factors (TFs) forming MYB-bHLH-WDR complexes are known to regulate the biosynthesis of specialized metabolites in angiosperms through an intricate network. These specialized metabolites participate in a wide range of biological processes including plant growth, development, reproduction as well as in plant immunity. Studying the regulation of their biosynthesis is thus essential. While MYB (TFs) have been previously shown to control specialized metabolism (SM) in gymnosperms, the identity of their partners, in particular bHLH or WDR members, has not yet been revealed. To gain knowledge about MYB-bHLH-WDR transcription factor complexes in gymnosperms and their regulation of SW, we identified two bHLH homologs of AtTT8, six homologs of the MYB transcription factor AtTT2 and one WDR ortholog of AtTTG1 in Norway spruce. We investigated the expression levels of these genes in diverse tissues and upon treatments with various stimuli including methyl-salicylate, methyl-jasmonate, wounding or fungal inoculation. In addition, we also identified protein-protein interactions among different homologs of MYB, bHLH and WDR. Finally, we generated transgenic spruce cell lines overexpressing four of the Norway spruce AtTT2 homologs and observed differential regulation of genes in the flavonoid pathway and flavonoid contents.
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Affiliation(s)
- Miguel Nemesio-Gorriz
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural SciencesUppsala, Sweden
- *Correspondence: Miguel Nemesio-Gorriz
| | - Peter B. Blair
- Department of Biology, University of Alabama at BirminghamBirmingham, AL, USA
| | - Kerstin Dalman
- Department of Chemistry and Biotechnology, Swedish University of Agricultural SciencesUppsala, Sweden
| | - Almuth Hammerbacher
- Department of Microbiology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Jenny Arnerup
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural SciencesUppsala, Sweden
| | - Jan Stenlid
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural SciencesUppsala, Sweden
| | - Shahid M. Mukhtar
- Department of Biology, University of Alabama at BirminghamBirmingham, AL, USA
| | - Malin Elfstrand
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural SciencesUppsala, Sweden
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31
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Koshiba T, Yamamoto N, Tobimatsu Y, Yamamura M, Suzuki S, Hattori T, Mukai M, Noda S, Shibata D, Sakamoto M, Umezawa T. MYB-mediated upregulation of lignin biosynthesis in Oryza sativa towards biomass refinery. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2017; 34:7-15. [PMID: 31275003 PMCID: PMC6543701 DOI: 10.5511/plantbiotechnology.16.1201a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/01/2016] [Indexed: 05/04/2023]
Abstract
Lignin encrusts lignocellulose polysaccharides, and has long been considered an obstacle for the efficient use of polysaccharides during processes such as pulping and bioethanol fermentation. However, lignin is also a potential feedstock for aromatic products and is an important by-product of polysaccharide utilization. Therefore, producing biomass plant species exhibiting enhanced lignin production is an important breeding objective. Herein, we describe the development of transgenic rice plants with increased lignin content. Five Arabidopsis thaliana (Arabidopsis) and one Oryza sativa (rice) MYB transcription factor genes that were implicated to be involved in lignin biosynthesis were transformed into rice (O. sativa L. ssp. japonica cv. Nipponbare). Among them, three Arabidopsis MYBs (AtMYB55, AtMYB61, and AtMYB63) in transgenic rice T1 lines resulted in culms with lignin content about 1.5-fold higher than that of control plants. Furthermore, lignin structures in AtMYB61-overexpressing rice plants were investigated by wet-chemistry and two-dimensional nuclear magnetic resonance spectroscopy approaches. Our data suggested that heterologous expression of AtMYB61 in rice increased lignin content mainly by enriching syringyl units as well as p-coumarate and tricin moieties in the lignin polymers. We contemplate that this strategy is also applicable to lignin upregulation in large-sized grass biomass plants, such as Sorghum, switchgrass, Miscanthus and Erianthus.
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Affiliation(s)
- Taichi Koshiba
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Naoki Yamamoto
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Yuki Tobimatsu
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Masaomi Yamamura
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Shiro Suzuki
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Takefumi Hattori
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Mai Mukai
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Soichiro Noda
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Daisuke Shibata
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Masahiro Sakamoto
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwakecho, Sakyo-ku, Kyoto, Kyoto 606-8502, Japan
- E-mail: Tel: +81-75-753-6464 Fax: +81-75-753-6471
| | - Toshiaki Umezawa
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
- Research Unit for Global Sustainability Studies, Kyoto University, Uji, Kyoto 611-0011, Japan
- E-mail: Tel: +81-774-38-3625 Fax: +81-774-38-3682
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Lei YX, Zhang Y, Li YY, Lai JJ, Gao G, Zhang HQ, Zhou YH, Yang RW. Cloning and molecular characterization of Myb transcription factors from Leymus (Poaceae: Trticeae). Biologia (Bratisl) 2016. [DOI: 10.1515/biolog-2016-0134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Gates DJ, Strickler SR, Mueller LA, Olson BJSC, Smith SD. Diversification of R2R3-MYB Transcription Factors in the Tomato Family Solanaceae. J Mol Evol 2016; 83:26-37. [PMID: 27364496 DOI: 10.1007/s00239-016-9750-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 06/15/2016] [Indexed: 11/26/2022]
Abstract
MYB transcription factors play an important role in regulating key plant developmental processes involving defense, cell shape, pigmentation, and root formation. Within this gene family, sequences containing an R2R3 MYB domain are the most abundant type and exhibit a wide diversity of functions. In this study, we identify 559 R2R3 MYB genes using whole genome data from four species of Solanaceae and reconstruct their evolutionary relationships. We compare the Solanaceae R2R3 MYBs to the well-characterized Arabidopsis thaliana sequences to estimate functional diversity and to identify gains and losses of MYB clades in the Solanaceae. We identify numerous R2R3 MYBs that do not appear closely related to Arabidopsis MYBs, and thus may represent clades of genes that have been lost along the Arabidopsis lineage or gained after the divergence of Rosid and Asterid lineages. Despite differences in the distribution of R2R3 MYBs across functional subgroups and species, the overall size of the R2R3 subfamily has changed relatively little over the roughly 50 million-year history of Solanaceae. We added our information regarding R2R3 MYBs in Solanaceae to other data and performed a meta-analysis to trace the evolution of subfamily size across land plants. The results reveal many shifts in the number of R2R3 genes, including a 54 % increase along the angiosperm stem lineage. The variation in R2R3 subfamily size across land plants is weakly positively correlated with genome size and strongly positively correlated with total number of genes. The retention of such a large number of R2R3 copies over long evolutionary time periods suggests that they have acquired new functions and been maintained by selection. Discovering the nature of this functional diversity will require integrating forward and reverse genetic approaches on an -omics scale.
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Affiliation(s)
- Daniel J Gates
- School of Biological Sciences, University of Nebraska, Lincoln, 68588, USA.
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, 80309, USA.
| | | | - Lukas A Mueller
- Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA
| | - Bradley J S C Olson
- Division of Molecular, Cellular and Developmental Biology, Kansas State University, Manhattan,, KS, 66506, USA
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, 80309, USA
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34
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Ferreira SS, Hotta CT, Poelking VGDC, Leite DCC, Buckeridge MS, Loureiro ME, Barbosa MHP, Carneiro MS, Souza GM. Co-expression network analysis reveals transcription factors associated to cell wall biosynthesis in sugarcane. PLANT MOLECULAR BIOLOGY 2016; 91:15-35. [PMID: 26820137 PMCID: PMC4837222 DOI: 10.1007/s11103-016-0434-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 01/07/2016] [Indexed: 05/18/2023]
Abstract
Sugarcane is a hybrid of Saccharum officinarum and Saccharum spontaneum, with minor contributions from other species in Saccharum and other genera. Understanding the molecular basis of cell wall metabolism in sugarcane may allow for rational changes in fiber quality and content when designing new energy crops. This work describes a comparative expression profiling of sugarcane ancestral genotypes: S. officinarum, S. spontaneum and S. robustum and a commercial hybrid: RB867515, linking gene expression to phenotypes to identify genes for sugarcane improvement. Oligoarray experiments of leaves, immature and intermediate internodes, detected 12,621 sense and 995 antisense transcripts. Amino acid metabolism was particularly evident among pathways showing natural antisense transcripts expression. For all tissues sampled, expression analysis revealed 831, 674 and 648 differentially expressed genes in S. officinarum, S. robustum and S. spontaneum, respectively, using RB867515 as reference. Expression of sugar transporters might explain sucrose differences among genotypes, but an unexpected differential expression of histones were also identified between high and low Brix° genotypes. Lignin biosynthetic genes and bioenergetics-related genes were up-regulated in the high lignin genotype, suggesting that these genes are important for S. spontaneum to allocate carbon to lignin, while S. officinarum allocates it to sucrose storage. Co-expression network analysis identified 18 transcription factors possibly related to cell wall biosynthesis while in silico analysis detected cis-elements involved in cell wall biosynthesis in their promoters. Our results provide information to elucidate regulatory networks underlying traits of interest that will allow the improvement of sugarcane for biofuel and chemicals production.
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Affiliation(s)
| | | | - Viviane Guzzo de Carli Poelking
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
- Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Brazil
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35
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Genome-Wide Identification of R2R3-MYB Genes and Expression Analyses During Abiotic Stress in Gossypium raimondii. Sci Rep 2016; 6:22980. [PMID: 27009386 PMCID: PMC4806351 DOI: 10.1038/srep22980] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 01/29/2016] [Indexed: 11/09/2022] Open
Abstract
The R2R3-MYB is one of the largest families of transcription factors, which have been implicated in multiple biological processes. There is great diversity in the number of R2R3-MYB genes in different plants. However, there is no report on genome-wide characterization of this gene family in cotton. In the present study, a total of 205 putative R2R3-MYB genes were identified in cotton D genome (Gossypium raimondii), that are much larger than that found in other cash crops with fully sequenced genomes. These GrMYBs were classified into 13 groups with the R2R3-MYB genes from Arabidopsis and rice. The amino acid motifs and phylogenetic tree were predicted and analyzed. The sequences of GrMYBs were distributed across 13 chromosomes at various densities. The results showed that the expansion of the G. Raimondii R2R3-MYB family was mainly attributable to whole genome duplication and segmental duplication. Moreover, the expression pattern of 52 selected GrMYBs and 46 GaMYBs were tested in roots and leaves under different abiotic stress conditions. The results revealed that the MYB genes in cotton were differentially expressed under salt and drought stress treatment. Our results will be useful for determining the precise role of the MYB genes during stress responses with crop improvement.
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36
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Zhou C, Li C. A Novel R2R3-MYB Transcription Factor BpMYB106 of Birch (Betula platyphylla) Confers Increased Photosynthesis and Growth Rate through Up-regulating Photosynthetic Gene Expression. FRONTIERS IN PLANT SCIENCE 2016; 7:315. [PMID: 27047502 PMCID: PMC4801893 DOI: 10.3389/fpls.2016.00315] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 02/29/2016] [Indexed: 06/01/2023]
Abstract
We isolated a R2R3-MYB transcription factor BpMYB106, which regulates photosynthesis in birch (Betula platyphylla Suk.). BpMYB106 mainly expresses in the leaf and shoot tip of birch, and its protein is localized in the nucleus. We further fused isolated a 1588 bp promoter of BpMYB106 and analyzed it by PLACE, which showed some cis-acting elements related to photosynthesis. BpMYB106 promoter β-glucuronidase (GUS) reporter fusion studies gene, the result, showed the GUS reporter gene in transgenic birch with BpMYB106 promoter showed strong activities in shoot tip, cotyledon margins, and mature leaf trichomes. The overexpression of BpMYB106 in birch resulted in significantly increased trichome density, net photosynthetic rate, and growth rate as compared with the wild-type birch. RNA-Seq profiling revealed the upregulation of several photosynthesis-related genes in the photosynthesis and oxidative phosphorylation pathways in the leaves of transgenic plants. Yeast one-hybrid analysis, coupled with transient assay in tobacco, revealed that BpMYB106 binds a MYB binding site MYB2 in differentially expressed gene promoters. Thus, BpMYB106 may directly activate the expression of a range of photosynthesis related genes through interacting with the MYB2 element in their promoters. Our study demonstrating the overexpression of BpMYB106-a R2R3-MYB transcription factor-upregulates the genes of the photosynthesis and oxidative phosphorylation pathways to improve photosynthesis.
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37
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Huang J, Chen F, Wu S, Li J, Xu W. Cotton GhMYB7 is predominantly expressed in developing fibers and regulates secondary cell wall biosynthesis in transgenic Arabidopsis. SCIENCE CHINA-LIFE SCIENCES 2016; 59:194-205. [PMID: 26803299 DOI: 10.1007/s11427-015-4991-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 07/20/2015] [Indexed: 12/25/2022]
Abstract
The secondary cell wall in mature cotton fibers contains over 90% cellulose with low quantities of xylan and lignin. However, little is known regarding the regulation of secondary cell wall biosynthesis in cotton fibers. In this study, we characterized an R2R3-MYB transcription factor, GhMYB7, in cotton. GhMYB7 is expressed at a high level in developing fibers and encodes a MYB protein that is targeted to the cell nucleus and has transcriptional activation activity. Ectopic expression of GhMYB7 in Arabidopsis resulted in small, curled, dark green leaves and also led to shorter inflorescence stems. A cross-sectional assay of basal stems revealed that cell wall thickness of vessels and interfascicular fibers was higher in transgenic lines overexpressing GhMYB7 than in the wild type. Constitutive expression of GhMYB7 in Arabidopsis activated the expression of a suite of secondary cell wall biosynthesis-related genes (including some secondary cell wall-associated transcription factors), leading to the ectopic deposition of cellulose and lignin. The ectopic deposition of secondary cell walls may have been initiated before the cessation of cell expansion. Moreover, GhMYB7 was capable of binding to the promoter regions of AtSND1 and AtCesA4, suggesting that GhMYB7 may function upstream of NAC transcription factors. Collectively, these findings suggest that GhMYB7 is a potential transcriptional activator, which may participate in regulating secondary cell wall biosynthesis of cotton fibers.
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Affiliation(s)
- Junfeng Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Feng Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Siyu Wu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Juan Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Wenliang Xu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
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Barrière Y, Courtial A, Chateigner-Boutin AL, Denoue D, Grima-Pettenati J. Breeding maize for silage and biofuel production, an illustration of a step forward with the genome sequence. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:310-329. [PMID: 26566848 DOI: 10.1016/j.plantsci.2015.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 08/04/2015] [Accepted: 08/13/2015] [Indexed: 05/21/2023]
Abstract
The knowledge of the gene families mostly impacting cell wall digestibility variations would significantly increase the efficiency of marker-assisted selection when breeding maize and grass varieties with improved silage feeding value and/or with better straw fermentability into alcohol or methane. The maize genome sequence of the B73 inbred line was released at the end of 2009, opening up new avenues to identify the genetic determinants of quantitative traits. Colocalizations between a large set of candidate genes putatively involved in secondary cell wall assembly and QTLs for cell wall digestibility (IVNDFD) were then investigated, considering physical positions of both genes and QTLs. Based on available data from six RIL progenies, 59 QTLs corresponding to 38 non-overlapping positions were matched up with a list of 442 genes distributed all over the genome. Altogether, 176 genes colocalized with IVNDFD QTLs and most often, several candidate genes colocalized at each QTL position. Frequent QTL colocalizations were found firstly with genes encoding ZmMYB and ZmNAC transcription factors, and secondly with genes encoding zinc finger, bHLH, and xylogen regulation factors. In contrast, close colocalizations were less frequent with genes involved in monolignol biosynthesis, and found only with the C4H2, CCoAOMT5, and CCR1 genes. Close colocalizations were also infrequent with genes involved in cell wall feruloylation and cross-linkages. Altogether, investigated colocalizations between candidate genes and cell wall digestibility QTLs suggested a prevalent role of regulation factors over constitutive cell wall genes on digestibility variations.
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Affiliation(s)
- Yves Barrière
- INRA, UR889, Unité de Génétique et d'Amélioration des Plantes Fourragères, 86600 Lusignan, France.
| | - Audrey Courtial
- LRSV, Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Paul Sabatier Toulouse III / CNRS, Auzeville, BP 42617, 31326 Castanet-Tolosan, France; INRA, US1258, Centre National de Ressources Génomiques Végétales, CS 52627, 31326 Castanet-Tolosan, France
| | | | - Dominique Denoue
- INRA, UR889, Unité de Génétique et d'Amélioration des Plantes Fourragères, 86600 Lusignan, France
| | - Jacqueline Grima-Pettenati
- LRSV, Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Paul Sabatier Toulouse III / CNRS, Auzeville, BP 42617, 31326 Castanet-Tolosan, France
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Exogenous GA₃ Application Enhances Xylem Development and Induces the Expression of Secondary Wall Biosynthesis Related Genes in Betula platyphylla. Int J Mol Sci 2015; 16:22960-75. [PMID: 26404260 PMCID: PMC4613346 DOI: 10.3390/ijms160922960] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 09/09/2015] [Accepted: 09/11/2015] [Indexed: 11/17/2022] Open
Abstract
Gibberellin (GA) is a key signal molecule inducing differentiation of tracheary elements, fibers, and xylogenesis. However the molecular mechanisms underlying the effect of GA on xylem elongation and secondary wall development in tree species remain to be determined. In this study, Betula platyphylla (birch) seeds were treated with 300 ppm GA3 and/or 300 ppm paclobutrazol (PAC), seed germination was recorded, and transverse sections of hypocotyls were stained with toluidine blue; the two-month-old seedlings were treated with 50 μM GA3 and/or 50 μM PAC, transverse sections of seedling stems were stained using phloroglucinol–HCl, and secondary wall biosynthesis related genes expression was analyzed by real-time quantitative PCR. Results indicated that germination percentage, energy and time of seeds, hypocotyl height and seedling fresh weight were enhanced by GA3, and reduced by PAC; the xylem development was wider in GA3-treated plants than in the control; the expression of NAC and MYB transcription factors, CESA, PAL, and GA oxidase was up-regulated during GA3 treatment, suggesting their role in GA3-induced xylem development in the birch. Our results suggest that GA3 induces the expression of secondary wall biosynthesis related genes to trigger xylogenesis in the birch plants.
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40
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Noda S, Koshiba T, Hattori T, Yamaguchi M, Suzuki S, Umezawa T. The expression of a rice secondary wall-specific cellulose synthase gene, OsCesA7, is directly regulated by a rice transcription factor, OsMYB58/63. PLANTA 2015; 242:589-600. [PMID: 26070439 DOI: 10.1007/s00425-015-2343-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 05/21/2015] [Indexed: 05/19/2023]
Abstract
A rice MYB transcription factor, OsMYB58/63, was found to directly upregulate the expression of a rice secondary wall-specific cellulose synthase gene, cellulose synthase A7 ( OsCesA7 ); in contrast, the Arabidopsis putative orthologs AtMYB58 and AtMYB63 have been shown to specifically activate lignin biosynthesis. Although indirect evidence has shown that grass plants are similar to but partially different from dicotyledonous ones in transcriptional regulation of lignocellulose biosynthesis, little is known about the differences. This study showed that a rice MYB transcription factor, OsMYB58/63, directly upregulated the expression of a rice secondary wall-specific cellulose synthase gene, cellulose synthase A7 (OsCesA7). Gene co-expression analysis showed that, in rice, OsMYB58/63 and several rice MYB genes were co-expressed with genes encoding lignocellulose biosynthetic enzymes. The expression levels of OsMYB55/61, OsMYB55/61-L, OsMYB58/63, and OsMYB42/85 were commonly found to be high in culm internodes and nodes. All four MYB transcription factors functioned as transcriptional activators in yeast cells. OsMYB58/63 most strongly transactivated the expression of OsCesA7 in rice protoplasts. Moreover, recombinant OsMYB58/63 protein was bound to two distinct cis-regulatory elements, AC-II and SMRE3, in the OsCesA7 promoter. This is in sharp contrast to the role of Arabidopsis orthologs, AtMYB58 and AtMYB63, which had been reported to specifically activate lignin biosynthesis. The promoter analysis revealed that AC elements, which are the binding sites for MYB58 and MYB63, were lacking in cellulose and xylan biosynthetic genes in Arabidopsis, but present in cellulose, xylan, and lignin biosynthetic genes in rice, implying that the difference of transcriptional regulation between rice and Arabidopsis is due to the distinct composition of promoters. Our results provide a new insight into transcriptional regulation in grass lignocellulose biosynthesis.
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Affiliation(s)
- Soichiro Noda
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, 611-0011, Japan
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41
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Zhong R, Yuan Y, Spiekerman JJ, Guley JT, Egbosiuba JC, Ye ZH. Functional Characterization of NAC and MYB Transcription Factors Involved in Regulation of Biomass Production in Switchgrass (Panicum virgatum). PLoS One 2015; 10:e0134611. [PMID: 26248336 PMCID: PMC4527753 DOI: 10.1371/journal.pone.0134611] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 07/10/2015] [Indexed: 11/18/2022] Open
Abstract
Switchgrass is a promising biofuel feedstock due to its high biomass production and low agronomic input requirements. Because the bulk of switchgrass biomass used for biofuel production is lignocellulosic secondary walls, studies on secondary wall biosynthesis and its transcriptional regulation are imperative for designing strategies for genetic improvement of biomass production in switchgrass. Here, we report the identification and functional characterization of a group of switchgrass transcription factors, including several NACs (PvSWNs) and a MYB (PvMYB46A), for their involvement in regulating secondary wall biosynthesis. PvSWNs and PvMYB46A were found to be highly expressed in stems and their expression was closely associated with sclerenchyma cells. Overexpression of PvSWNs and PvMYB46A in Arabidopsis was shown to result in activation of the biosynthetic genes for cellulose, xylan and lignin and ectopic deposition of secondary walls in normally parenchymatous cells. Transactivation and complementation studies demonstrated that PvSWNs were able to activate the SNBE-driven GUS reporter gene and effectively rescue the secondary wall defects in the Arabidopsis snd1 nst1 double mutant, indicating that they are functional orthologs of Arabidopsis SWNs. Furthermore, we showed that PvMYB46A could activate the SMRE-driven GUS reporter gene and complement the Arabidopsis myb46 myb83 double mutant, suggesting that it is a functional ortholog of Arabidopsis MYB46/MYB83. Together, these results indicate that PvSWNs and PvMYB46A are transcriptional switches involved in regulating secondary wall biosynthesis, which provides molecular tools for genetic manipulation of biomass production in switchgrass.
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Affiliation(s)
- Ruiqin Zhong
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, United States of America
| | - Youxi Yuan
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, United States of America
| | - John J. Spiekerman
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, United States of America
| | - Joshua T. Guley
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, United States of America
| | - Janefrances C. Egbosiuba
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, United States of America
| | - Zheng-Hua Ye
- Department of Plant Biology, University of Georgia, Athens, Georgia, 30602, United States of America
- * E-mail:
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Soler M, Camargo ELO, Carocha V, Cassan-Wang H, San Clemente H, Savelli B, Hefer CA, Paiva JAP, Myburg AA, Grima-Pettenati J. The Eucalyptus grandis R2R3-MYB transcription factor family: evidence for woody growth-related evolution and function. THE NEW PHYTOLOGIST 2015; 206:1364-77. [PMID: 25250741 DOI: 10.1111/nph.13039] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 08/05/2014] [Indexed: 05/19/2023]
Abstract
The R2R3-MYB family, one of the largest transcription factor families in higher plants, controls a wide variety of plant-specific processes including, notably, phenylpropanoid metabolism and secondary cell wall formation. We performed a genome-wide analysis of this superfamily in Eucalyptus, one of the most planted hardwood trees world-wide. A total of 141 predicted R2R3-MYB sequences identified in the Eucalyptus grandis genome sequence were subjected to comparative phylogenetic analyses with Arabidopsis thaliana, Oryza sativa, Populus trichocarpa and Vitis vinifera. We analysed features such as gene structure, conserved motifs and genome location. Transcript abundance patterns were assessed by RNAseq and validated by high-throughput quantitative PCR. We found some R2R3-MYB subgroups with expanded membership in E. grandis, V. vinifera and P. trichocarpa, and others preferentially found in woody species, suggesting diversification of specific functions in woody plants. By contrast, subgroups containing key genes regulating lignin biosynthesis and secondary cell wall formation are more conserved across all of the species analysed. In Eucalyptus, R2R3-MYB tandem gene duplications seem to disproportionately affect woody-preferential and woody-expanded subgroups. Interestingly, some of the genes belonging to woody-preferential subgroups show higher expression in the cambial region, suggesting a putative role in the regulation of secondary growth.
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Affiliation(s)
- Marçal Soler
- LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France
| | - Eduardo Leal Oliveira Camargo
- LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France
| | - Victor Carocha
- LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France
- Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET) Av. da República, Quinta do Marquês, 2781-901, Oeiras, Portugal
| | - Hua Cassan-Wang
- LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France
| | - Hélène San Clemente
- LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France
| | - Bruno Savelli
- LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France
| | - Charles A Hefer
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Jorge A Pinto Paiva
- Instituto de Biologia Experimental e Tecnológica (iBET) Av. da República, Quinta do Marquês, 2781-901, Oeiras, Portugal
- Instituto de Investigaçao Científica e Tropical (IICT/MNE) Palacio Burnay - Rua da Junqueira, 30, 1349-007, Lisboa, Portugal
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
- Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Jacqueline Grima-Pettenati
- LRSV Laboratoire de Recherche en Sciences Végétales, UMR5546, Université Toulouse III/CNRS, BP 42617 Auzeville, 31326, Castanet Tolosan, France
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Nakano Y, Yamaguchi M, Endo H, Rejab NA, Ohtani M. NAC-MYB-based transcriptional regulation of secondary cell wall biosynthesis in land plants. FRONTIERS IN PLANT SCIENCE 2015; 6:288. [PMID: 25999964 PMCID: PMC4419676 DOI: 10.3389/fpls.2015.00288] [Citation(s) in RCA: 274] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 04/09/2015] [Indexed: 05/08/2023]
Abstract
Plant cells biosynthesize primary cell walls (PCW) in all cells and produce secondary cell walls (SCWs) in specific cell types that conduct water and/or provide mechanical support, such as xylem vessels and fibers. The characteristic mechanical stiffness, chemical recalcitrance, and hydrophobic nature of SCWs result from the organization of SCW-specific biopolymers, i.e., highly ordered cellulose, hemicellulose, and lignin. Synthesis of these SCW-specific biopolymers requires SCW-specific enzymes that are regulated by SCW-specific transcription factors. In this review, we summarize our current knowledge of the transcriptional regulation of SCW formation in plant cells. Advances in research on SCW biosynthesis during the past decade have expanded our understanding of the transcriptional regulation of SCW formation, particularly the functions of the NAC and MYB transcription factors. Focusing on the NAC-MYB-based transcriptional network, we discuss the regulatory systems that evolved in land plants to modify the cell wall to serve as a key component of structures that conduct water and provide mechanical support.
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Affiliation(s)
- Yoshimi Nakano
- Graduate School of Biological Sciences, Nara Institute of Science and TechnologyIkoma, Japan
| | - Masatoshi Yamaguchi
- Division of Strategic Research and Development, Graduate School of Science and Engineering, Saitama UniversitySaitama, Japan
- PRESTO (Precursory Research for Embryonic Science and Technology), Japan Science and Technology AgencyKawaguchi, Japan
| | - Hitoshi Endo
- Graduate School of Biological Sciences, Nara Institute of Science and TechnologyIkoma, Japan
| | - Nur Ardiyana Rejab
- Graduate School of Biological Sciences, Nara Institute of Science and TechnologyIkoma, Japan
- Faculty of Science, Institute of Biological Sciences, University of MalayaKuala Lumpur, Malaysia
| | - Misato Ohtani
- Graduate School of Biological Sciences, Nara Institute of Science and TechnologyIkoma, Japan
- Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
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Guerriero G, Hausman JF, Ezcurra I. WD40-Repeat Proteins in Plant Cell Wall Formation: Current Evidence and Research Prospects. FRONTIERS IN PLANT SCIENCE 2015; 6:1112. [PMID: 26734023 PMCID: PMC4686805 DOI: 10.3389/fpls.2015.01112] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 11/24/2015] [Indexed: 05/19/2023]
Abstract
The metabolic complexity of living organisms relies on supramolecular protein structures which ensure vital processes, such as signal transduction, transcription, translation and cell wall synthesis. In eukaryotes WD40-repeat (WDR) proteins often function as molecular "hubs" mediating supramolecular interactions. WDR proteins may display a variety of interacting partners and participate in the assembly of complexes involved in distinct cellular functions. In plants, the formation of lignocellulosic biomass involves extensive synthesis of cell wall polysaccharides, a process that requires the assembly of large transmembrane enzyme complexes, intensive vesicle trafficking, interactions with the cytoskeleton, and coordinated gene expression. Because of their function as supramolecular hubs, WDR proteins could participate in each or any of these steps, although to date only few WDR proteins have been linked to the cell wall by experimental evidence. Nevertheless, several potential cell wall-related WDR proteins were recently identified using in silico approaches, such as analyses of co-expression, interactome and conserved gene neighborhood. Notably, some WDR genes are frequently genomic neighbors of genes coding for GT2-family polysaccharide synthases in eukaryotes, and this WDR-GT2 collinear microsynteny is detected in diverse taxa. In angiosperms, two WDR genes are collinear to cellulose synthase genes, CesAs, whereas in ascomycetous fungi several WDR genes are adjacent to chitin synthase genes, chs. In this Perspective we summarize and discuss experimental and in silico studies on the possible involvement of WDR proteins in plant cell wall formation. The prospects of biotechnological engineering for enhanced biomass production are discussed.
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Affiliation(s)
- Gea Guerriero
- Environmental Research and Innovation, Luxembourg Institute of Science and TechnologyEsch-sur-Alzette, Luxembourg
| | - Jean-Francois Hausman
- Environmental Research and Innovation, Luxembourg Institute of Science and TechnologyEsch-sur-Alzette, Luxembourg
| | - Inés Ezcurra
- School of Biotechnology, Division of Industrial Biotechnology, KTH Royal Institute of Technology, AlbaNova University CenterStockholm, Sweden
- *Correspondence: Inés Ezcurra,
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Amar D, Frades I, Danek A, Goldberg T, Sharma SK, Hedley PE, Proux-Wera E, Andreasson E, Shamir R, Tzfadia O, Alexandersson E. Evaluation and integration of functional annotation pipelines for newly sequenced organisms: the potato genome as a test case. BMC PLANT BIOLOGY 2014; 14:329. [PMID: 25476999 PMCID: PMC4274702 DOI: 10.1186/s12870-014-0329-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 11/10/2014] [Indexed: 05/08/2023]
Abstract
BACKGROUND For most organisms, even if their genome sequence is available, little functional information about individual genes or proteins exists. Several annotation pipelines have been developed for functional analysis based on sequence, 'omics', and literature data. However, researchers encounter little guidance on how well they perform. Here, we used the recently sequenced potato genome as a case study. The potato genome was selected since its genome is newly sequenced and it is a non-model plant even if there is relatively ample information on individual potato genes, and multiple gene expression profiles are available. RESULTS We show that the automatic gene annotations of potato have low accuracy when compared to a "gold standard" based on experimentally validated potato genes. Furthermore, we evaluate six state-of-the-art annotation pipelines and show that their predictions are markedly dissimilar (Jaccard similarity coefficient of 0.27 between pipelines on average). To overcome this discrepancy, we introduce a simple GO structure-based algorithm that reconciles the predictions of the different pipelines. We show that the integrated annotation covers more genes, increases by over 50% the number of highly co-expressed GO processes, and obtains much higher agreement with the gold standard. CONCLUSIONS We find that different annotation pipelines produce different results, and show how to integrate them into a unified annotation that is of higher quality than each single pipeline. We offer an improved functional annotation of both PGSC and ITAG potato gene models, as well as tools that can be applied to additional pipelines and improve annotation in other organisms. This will greatly aid future functional analysis of '-omics' datasets from potato and other organisms with newly sequenced genomes. The new potato annotations are available with this paper.
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Affiliation(s)
- David Amar
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
| | - Itziar Frades
- Deptartment of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
| | - Agnieszka Danek
- Institute of Informatics, Silesian University of Technology, Akademicka 2A, 44-100, Gliwice, Poland.
| | - Tatyana Goldberg
- Department for Bioinformatics and Computational Biology, Technical University of Munich, Arcisstraße 21, 80333, Munich, Germany.
| | - Sanjeev K Sharma
- Cell and Molecular Sciences, The James Hutton Institute, Aberdeen, Scotland, UK.
| | - Pete E Hedley
- Cell and Molecular Sciences, The James Hutton Institute, Aberdeen, Scotland, UK.
| | - Estelle Proux-Wera
- Deptartment of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
- Current affiliation: SciLifeLab, Stockholm University, Universitetsvägen 10, 114 18, Stockholm, Sweden.
| | - Erik Andreasson
- Deptartment of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.
| | - Oren Tzfadia
- Department of Plant Science, The Weizmann Institute of Science, Rehovot, Israel.
| | - Erik Alexandersson
- Deptartment of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
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Contrasting metabolism in perenniating structures of upland and lowland switchgrass plants late in the growing season. PLoS One 2014; 9:e105138. [PMID: 25133804 PMCID: PMC4136849 DOI: 10.1371/journal.pone.0105138] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 07/17/2014] [Indexed: 12/24/2022] Open
Abstract
Background Switchgrass (Panicum virgatum L.) is being developed as a bioenergy crop for many temperate regions of the world. One way to increase biomass yields is to move southern adapted lowland cultivars to more northern latitudes. However, many southerly adapted switchgrass germplasm can suffer significant winter kill in northerly climes. Materials and Methods Here, we have applied next-generation sequencing in combination with biochemical analyses to query the metabolism of crowns and rhizomes obtained from two contrasting switchgrass cultivars. Crowns and rhizomes from field-grown lowland (cv Kanlow) and upland (cv Summer) switchgrass cultivars were collected from three randomly selected post-flowering plants. Summer plants were senescing, whereas Kanlow plants were not at this harvest date. Results Principal component analysis (PCA) differentiated between both the Summer and Kanlow transcriptomes and metabolomes. Significant differences in transcript abundances were detected for 8,050 genes, including transcription factors such as WRKYs and those associated with phenylpropanoid biosynthesis. Gene-set enrichment analyses showed that a number of pathways were differentially up-regulated in the two populations. For both populations, protein levels and enzyme activities agreed well with transcript abundances for genes involved in the phenylpropanoid pathway that were up-regulated in Kanlow crowns and rhizomes. The combination of these datasets suggests that dormancy-related mechanisms had been triggered in the crowns and rhizomes of the Summer plants, whereas the crowns and rhizomes of Kanlow plants had yet to enter dormancy. Conclusions Delayed establishment of dormancy at more northerly latitudes could be one factor that reduces winter-survival in the high-yielding Kanlow plants. Understanding the cellular signatures that accompany the transition to dormancy can be used in the future to select plants with improved winter hardiness.
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