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Xu W, Wu D, Yang T, Sun C, Wang Z, Han B, Wu S, Yu A, Chapman MA, Muraguri S, Tan Q, Wang W, Bao Z, Liu A, Li DZ. Genomic insights into the origin, domestication and genetic basis of agronomic traits of castor bean. Genome Biol 2021; 22:113. [PMID: 33874982 PMCID: PMC8056531 DOI: 10.1186/s13059-021-02333-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/29/2021] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Castor bean (Ricinus communis L.) is an important oil crop, which belongs to the Euphorbiaceae family. The seed oil of castor bean is currently the only commercial source of ricinoleic acid that can be used for producing about 2000 industrial products. However, it remains largely unknown regarding the origin, domestication, and the genetic basis of key traits of castor bean. RESULTS Here we perform a de novo chromosome-level genome assembly of the wild progenitor of castor bean. By resequencing and analyzing 505 worldwide accessions, we reveal that the accessions from East Africa are the extant wild progenitors of castor bean, and the domestication occurs ~ 3200 years ago. We demonstrate that significant genetic differentiation between wild populations in Kenya and Ethiopia is associated with past climate fluctuation in the Turkana depression ~ 7000 years ago. This dramatic change in climate may have caused the genetic bottleneck in wild castor bean populations. By a genome-wide association study, combined with quantitative trait locus analysis, we identify important candidate genes associated with plant architecture and seed size. CONCLUSIONS This study provides novel insights of domestication and genome evolution of castor bean, which facilitates genomics-based breeding of this important oilseed crop and potentially other tree-like crops in future.
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Affiliation(s)
- Wei Xu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Di Wu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Tianquan Yang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Chao Sun
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zaiqing Wang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Bing Han
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Shibo Wu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Anmin Yu
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China
| | - Mark A Chapman
- Biological Sciences and Centre for Underutilised Crops, University of Southampton, Southampton, SO17 1BJ, UK
| | - Sammy Muraguri
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Qing Tan
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Wenbo Wang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhigui Bao
- Shanghai OE Biotech Co., Ltd, Shanghai, 201114, China
| | - Aizhong Liu
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
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Xiao R, Zhang C, Guo X, Li H, Lu H. MYB Transcription Factors and Its Regulation in Secondary Cell Wall Formation and Lignin Biosynthesis during Xylem Development. Int J Mol Sci 2021; 22:3560. [PMID: 33808132 PMCID: PMC8037110 DOI: 10.3390/ijms22073560] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 01/12/2023] Open
Abstract
The secondary wall is the main part of wood and is composed of cellulose, xylan, lignin, and small amounts of structural proteins and enzymes. Lignin molecules can interact directly or indirectly with cellulose, xylan and other polysaccharide molecules in the cell wall, increasing the mechanical strength and hydrophobicity of plant cells and tissues and facilitating the long-distance transportation of water in plants. MYBs (v-myb avian myeloblastosis viral oncogene homolog) belong to one of the largest superfamilies of transcription factors, the members of which regulate secondary cell-wall formation by promoting/inhibiting the biosynthesis of lignin, cellulose, and xylan. Among them, MYB46 and MYB83, which comprise the second layer of the main switch of secondary cell-wall biosynthesis, coordinate upstream and downstream secondary wall synthesis-related transcription factors. In addition, MYB transcription factors other than MYB46/83, as well as noncoding RNAs, hormones, and other factors, interact with one another to regulate the biosynthesis of the secondary wall. Here, we discuss the biosynthesis of secondary wall, classification and functions of MYB transcription factors and their regulation of lignin polymerization and secondary cell-wall formation during wood formation.
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Affiliation(s)
- Ruixue Xiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (R.X.); (H.L.)
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (X.G.)
| | - Chong Zhang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (X.G.)
| | - Xiaorui Guo
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (X.G.)
| | - Hui Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (R.X.); (H.L.)
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (X.G.)
| | - Hai Lu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (R.X.); (H.L.)
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (C.Z.); (X.G.)
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Chen L, Wu F, Zhang J. NAC and MYB Families and Lignin Biosynthesis-Related Members Identification and Expression Analysis in Melilotus albus. PLANTS 2021; 10:plants10020303. [PMID: 33562564 PMCID: PMC7914948 DOI: 10.3390/plants10020303] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/28/2020] [Accepted: 12/11/2020] [Indexed: 11/26/2022]
Abstract
Melilotus albus is an annual or biennial legume species that adapts to extreme environments via its high stress tolerance. NAC and MYB transcription factors (TFs) are involved in the regulation of lignin biosynthesis, which has not been studied in M. albus. A total of 101 MaNAC and 299 MaMYB members were identified based on M. albus genome. Chromosome distribution and synteny analysis indicated that some genes underwent tandem duplication. Ka/Ks analysis suggested that MaNACs and MaMYBs underwent strong purifying selection. Stress-, hormone- and development-related cis-elements and MYB-binding sites were identified in the promoter regions of MaNACs and MaMYBs. Five MaNACs, two MaMYBs and ten lignin biosynthesis genes were identified as presenting coexpression relationships according to weighted gene coexpression network analysis (WGCNA). Eleven and thirteen candidate MaNAC and MaMYB genes related to lignin biosynthesis were identified, respectively, and a network comprising these genes was constructed which further confirmed the MaNAC and MaMYB relationship. These candidate genes had conserved gene structures and motifs and were highly expressed in the stems and roots, and qRT-PCR further verified the expression patterns. Overall, our results provide a reference for determining the precise role of NAC and MYB genes in M. albus and may facilitate efforts to breed low-lignin-content forage cultivars in the future.
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Li L, Zhang Y, Zheng T, Zhuo X, Li P, Qiu L, Liu W, Wang J, Cheng T, Zhang Q. Comparative gene expression analysis reveals that multiple mechanisms regulate the weeping trait in Prunus mume. Sci Rep 2021; 11:2675. [PMID: 33514804 PMCID: PMC7846751 DOI: 10.1038/s41598-021-81892-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 01/13/2021] [Indexed: 11/23/2022] Open
Abstract
Prunus mume (also known as Mei) is an important ornamental plant that is popular with Asians. The weeping trait in P. mume has attracted the attention of researchers for its high ornamental value. However, the formation of the weeping trait of woody plants is a complex process and the molecular basis of weeping stem development is unclear. Here, the morphological and histochemical characteristics and transcriptome profiles of upright and weeping stems from P. mume were studied. Significant alterations in the histochemical characteristics of upright and weeping stems were observed, and the absence of phloem fibres and less xylem in weeping stems might be responsible for their inability to resist gravity and to grow downward. Transcriptome analysis showed that differentially expressed genes (DEGs) were enriched in phenylpropanoid biosynthesis and phytohormone signal transduction pathways. To investigate the differential responses to hormones, upright and weeping stems were treated with IAA (auxin) and GA3 (gibberellin A3), respectively, and the results revealed that weeping stems had a weaker IAA response ability and reduced upward bending angles than upright stems. On the contrary, weeping stems had increased upward bending angles than upright stems with GA3 treatment. Compared to upright stems, interestingly, DEGs associated with diterpenoid biosynthesis and phenylpropanoid biosynthesis were significantly enriched after being treated with IAA, and expression levels of genes associated with phenylpropanoid biosynthesis, ABC transporters, glycosylphosphatidylinositol (GPI)—anchor biosynthesis were altered after being treated with GA3 in weeping stems. Those results reveal that multiple molecular mechanisms regulate the formation of weeping trait in P. mume, which lays a theoretical foundation for the cultivation of new varieties.
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Affiliation(s)
- Lulu Li
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Yichi Zhang
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Tangchun Zheng
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
| | - Xiaokang Zhuo
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Ping Li
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Like Qiu
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Weichao Liu
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Jia Wang
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Tangren Cheng
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Qixiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
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Rajavel A, Klees S, Schlüter JS, Bertram H, Lu K, Schmitt AO, Gültas M. Unravelling the Complex Interplay of Transcription Factors Orchestrating Seed Oil Content in Brassica napus L. Int J Mol Sci 2021; 22:1033. [PMID: 33494188 PMCID: PMC7864344 DOI: 10.3390/ijms22031033] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/13/2021] [Accepted: 01/17/2021] [Indexed: 11/16/2022] Open
Abstract
Transcription factors (TFs) and their complex interplay are essential for directing specific genetic programs, such as responses to environmental stresses, tissue development, or cell differentiation by regulating gene expression. Knowledge regarding TF-TF cooperations could be promising in gaining insight into the developmental switches between the cultivars of Brassica napus L., namely Zhongshuang11 (ZS11), a double-low accession with high-oil- content, and Zhongyou821 (ZY821), a double-high accession with low-oil-content. In this regard, we analysed a time series RNA-seq data set of seed tissue from both of the cultivars by mainly focusing on the monotonically expressed genes (MEGs). The consideration of the MEGs enables the capturing of multi-stage progression processes that are orchestrated by the cooperative TFs and, thus, facilitates the understanding of the molecular mechanisms determining seed oil content. Our findings show that TF families, such as NAC, MYB, DOF, GATA, and HD-ZIP are highly involved in the seed developmental process. Particularly, their preferential partner choices as well as changes in their gene expression profiles seem to be strongly associated with the differentiation of the oil content between the two cultivars. These findings are essential in enhancing our understanding of the genetic programs in both cultivars and developing novel hypotheses for further experimental studies.
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Affiliation(s)
- Abirami Rajavel
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (A.R.); (S.K.); (J.-S.S.); (H.B.); (A.O.S.)
| | - Selina Klees
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (A.R.); (S.K.); (J.-S.S.); (H.B.); (A.O.S.)
| | - Johanna-Sophie Schlüter
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (A.R.); (S.K.); (J.-S.S.); (H.B.); (A.O.S.)
| | - Hendrik Bertram
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (A.R.); (S.K.); (J.-S.S.); (H.B.); (A.O.S.)
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China;
- Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology, Southern Mountainous Land of Southwest University, Beibei, Chongqing 400715, China
| | - Armin Otto Schmitt
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (A.R.); (S.K.); (J.-S.S.); (H.B.); (A.O.S.)
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
| | - Mehmet Gültas
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (A.R.); (S.K.); (J.-S.S.); (H.B.); (A.O.S.)
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
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Holmquist L, Dölfors F, Fogelqvist J, Cohn J, Kraft T, Dixelius C. Major latex protein-like encoding genes contribute to Rhizoctonia solani defense responses in sugar beet. Mol Genet Genomics 2020; 296:155-164. [PMID: 33118051 PMCID: PMC7840631 DOI: 10.1007/s00438-020-01735-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/09/2020] [Indexed: 12/15/2022]
Abstract
Sugar beets are attacked by several pathogens that cause root damages. Rhizoctonia (Greek for “root killer”) is one of them. Rhizoctonia root rot has become an increasing problem for sugar beet production and to decrease yield losses agronomical measures are adopted. Here, two partially resistant and two susceptible sugar beet genotypes were used for transcriptome analysis to discover new defense genes to this fungal disease, information to be implemented in molecular resistance breeding. Among 217 transcripts with increased expression at 2 days post-infection (dpi), three resistance-like genes were found. These genes were not significantly elevated at 5 dpi, a time point when increased expression of three Bet v I/Major latex protein (MLP) homologous genes BvMLP1, BvMLP2 and BvML3 was observed in the partially resistant genotypes. Quantitative RT-PCR analysis on diseased sugar beet seedlings validated the activity of BvMLP1 and BvMLP3 observed in the transcriptome during challenge by R. solani. The three BvMLP genes were cloned and overexpressed in Arabidopsis thaliana to further dissect their individual contribution. Transgenic plants were also compared to T-DNA mutants of orthologous MLP genes. Plants overexpressing BvMLP1 and BvMLP3 showed significantly less infection whereas additive effects were seen on Atmlp1/Atmlp3 double mutants. The data suggest that BvMLP1 and BvMLP3 may contribute to the reduction of the Rhizoctonia root rot disease in sugar beet. Impact on the defense reaction from other differential expressed genes observed in the study is discussed.
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Affiliation(s)
- Louise Holmquist
- MariboHilleshög Research AB, Säbyholmsvägen 24, 26191, Landskrona, Sweden.,Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, 75007, Uppsala, Sweden
| | - Fredrik Dölfors
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, 75007, Uppsala, Sweden
| | - Johan Fogelqvist
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, 75007, Uppsala, Sweden
| | - Jonathan Cohn
- Syngenta, Crop Protection, 9 Davis Drive, Research Triangle Park, NC, 27709, USA
| | - Thomas Kraft
- MariboHilleshög Research AB, Säbyholmsvägen 24, 26191, Landskrona, Sweden
| | - Christina Dixelius
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, P.O. Box 7080, 75007, Uppsala, Sweden.
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Seo M, Kim H, Lee JY. Information on the move: vascular tissue development in space and time during postembryonic root growth. CURRENT OPINION IN PLANT BIOLOGY 2020; 57:110-117. [PMID: 32905917 DOI: 10.1016/j.pbi.2020.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/08/2020] [Accepted: 08/04/2020] [Indexed: 05/27/2023]
Abstract
Cascades of temporal and spatial regulation of gene expression play crucial roles in the vascular development in plant roots. Once vascular cell fates are determined, the timing of their differentiation is tightly controlled in a cell-autonomous manner. In contrast, extensive cell-to-cell communication contributes to the positioning and specifying of vascular cell types in the root meristem. Diverse factors moving short distances in a radial direction were found to be key contributors to these processes. Furthermore, signals from differentiated phloem were found to influence the phloem precursor and determine how the corresponding asymmetric cell division proceeded. These findings highlight the potential importance of underexplored types of intercellular communication in relation to vascular tissue development during postembryonic root growth.
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Affiliation(s)
- Minji Seo
- School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyoujin Kim
- School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji-Young Lee
- School of Biological Sciences, College of Natural Science, Seoul National University, Seoul 08826, Republic of Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea.
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58
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Qin W, Yin Q, Chen J, Zhao X, Yue F, He J, Yang L, Liu L, Zeng Q, Lu F, Mitsuda N, Ohme-Takagi M, Wu AM. The class II KNOX transcription factors KNAT3 and KNAT7 synergistically regulate monolignol biosynthesis in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5469-5483. [PMID: 32474603 DOI: 10.1093/jxb/eraa266] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/22/2020] [Indexed: 05/21/2023]
Abstract
The function of the transcription factor KNOTTED ARABIDOPSIS THALIANA7 (KNAT7) is still unclear since it appears to be either a negative or a positive regulator for secondary cell wall deposition with its loss-of-function mutant displaying thicker interfascicular and xylary fiber cell walls but thinner vessel cell walls in inflorescence stems. To explore the exact function of KNAT7, class II KNOTTED1-LIKE HOMEOBOX (KNOX II) genes in Arabidopsis including KNAT3, KNAT4, and KNAT5 were studied together. By chimeric repressor technology, we found that both KNAT3 and KNAT7 repressors exhibited a similar dwarf phenotype. Both KNAT3 and KNAT7 genes were expressed in the inflorescence stems and the knat3 knat7 double mutant exhibited a dwarf phenotype similar to the repressor lines. A stem cross-section of knat3 knat7 displayed an enhanced irregular xylem phenotype as compared with the single mutants, and its cell wall thickness in xylem vessels and interfascicular fibers was significantly reduced. Analysis of cell wall chemical composition revealed that syringyl lignin was significantly decreased while guaiacyl lignin was increased in the knat3 knat7 double mutant. Coincidently, the knat3 knat7 transcriptome showed that most lignin pathway genes were activated, whereas the syringyl lignin-related gene Ferulate 5-Hydroxylase (F5H) was down-regulated. Protein interaction analysis revealed that KNAT3 and KNAT7 can form a heterodimer, and KNAT3, but not KNAT7, can interact with the key secondary cell wall formation transcription factors NST1/2, which suggests that the KNAT3-NST1/2 heterodimer complex regulates F5H to promote syringyl lignin synthesis. These results indicate that KNAT3 and KNAT7 synergistically work together to promote secondary cell wall biosynthesis.
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Affiliation(s)
- Wenqi Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Qi Yin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Jiajun Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xianhai Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Fengxia Yue
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, China
| | - Junbo He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Linjie Yang
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, China
| | - Lijun Liu
- State Forestry and Grassland Administration Key Laboratory of Silviculture in downstream areas of the Yellow River, College of Forestry, Shandong Agriculture University, Taian, Shandong, China
| | - Qingyin Zeng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Fachuang Lu
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, China
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | | | - Ai-Min Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
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Tu M, Wang X, Yin W, Wang Y, Li Y, Zhang G, Li Z, Song J, Wang X. Grapevine VlbZIP30 improves drought resistance by directly activating VvNAC17 and promoting lignin biosynthesis through the regulation of three peroxidase genes. HORTICULTURE RESEARCH 2020; 7:150. [PMID: 32922822 PMCID: PMC7458916 DOI: 10.1038/s41438-020-00372-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/19/2020] [Accepted: 06/23/2020] [Indexed: 05/20/2023]
Abstract
Drought stress severely affects grapevine quality and yield, and recent reports have revealed that lignin plays an important role in protection from drought stress. Since little is known about lignin-mediated drought resistance in grapevine, we investigated its significance. Herein, we show that VlbZIP30 mediates drought resistance by activating the expression of lignin biosynthetic genes and increasing lignin deposition. Transgenic grapevine plants overexpressing VlbZIP30 exhibited lignin deposition (mainly G and S monomers) in the stem secondary xylem under control conditions, which resulted from the upregulated expression of VvPRX4 and VvPRX72. Overexpression of VlbZIP30 improves drought tolerance, characterized by a reduction in the water loss rate, maintenance of an effective photosynthesis rate, and increased lignin content (mainly G monomer) in leaves under drought conditions. Electrophoretic mobility shift assay, luciferase reporter assays, and chromatin immunoprecipitation-qPCR assays indicated that VlbZIP30 directly binds to the G-box cis-element in the promoters of lignin biosynthetic (VvPRX N1) and drought-responsive (VvNAC17) genes to regulate their expression. In summary, we report a novel VlbZIP30-mediated mechanism linking lignification and drought tolerance in grapevine. The results of this study may be of value for the development of molecular breeding strategies to produce drought-resistant fruit crops.
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Affiliation(s)
- Mingxing Tu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Xianhang Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- College of Enology, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Wuchen Yin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Ya Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Yajuan Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Guofeng Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Zhi Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Junyang Song
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Xiping Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
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Characterization of the UDP-glycosyltransferase UGT72 Family in Poplar and Identification of Genes Involved in the Glycosylation of Monolignols. Int J Mol Sci 2020; 21:ijms21145018. [PMID: 32708651 PMCID: PMC7404001 DOI: 10.3390/ijms21145018] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/11/2020] [Accepted: 07/13/2020] [Indexed: 12/28/2022] Open
Abstract
Monolignols are the building blocks for lignin polymerization in the apoplastic domain. Monolignol biosynthesis, transport, storage, glycosylation, and deglycosylation are the main biological processes partaking in their homeostasis. In Arabidopsis thaliana, members of the uridine diphosphate-dependent glucosyltransferases UGT72E and UGT72B subfamilies have been demonstrated to glycosylate monolignols. Here, the poplar UGT72 family, which is clustered into four groups, was characterized: Group 1 UGT72AZ1 and UGT72AZ2, homologs of Arabidopsis UGT72E1-3, as well as group 4 UGT72B37 and UGT72B39, homologs of Arabidopsis UGT72B1-3, glycosylate monolignols. In addition, promoter-GUS analyses indicated that poplar UGT72 members are expressed within vascular tissues. At the subcellular level, poplar UGT72s belonging to group 1 and group 4 were found to be associated with the nucleus and the endoplasmic reticulum. However, UGT72A2, belonging to group 2, was localized in bodies associated with chloroplasts, as well as possibly in chloroplasts. These results show a partial conservation of substrate recognition between Arabidopsis and poplar homologs, as well as divergent functions between different groups of the UGT72 family, for which the substrates remain unknown.
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61
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Sun Y, Ren S, Ye S, Tian Q, Luo K. Identification and Functional Characterization of PtoMYB055 Involved in the Regulation of the Lignin Biosynthesis Pathway in Populus tomentosa. Int J Mol Sci 2020; 21:ijms21144857. [PMID: 32659969 PMCID: PMC7402297 DOI: 10.3390/ijms21144857] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/04/2020] [Accepted: 07/06/2020] [Indexed: 01/23/2023] Open
Abstract
Wood, which is mainly composed of lignified secondary cell wall, is the most abundant biomass in woody plants. Previous studies have revealed that R2R3-type MYB transcription factors are important regulators of the formation of the secondary cell wall in vascular plants. In this study, we isolated the R2R3-type MYB transcription factor gene PtoMYB055, which is mainly expressed in xylem and phloem tissue, from Populus tomentosa and demonstrate that PtoMYB055 is a key regulator of lignin biosynthesis. PtoMYB055 as a transcriptional activator is localized to the nucleus. Overexpression of PtoMYB055 upregulates expression of lignin biosynthetic genes in transgenic poplar plants, resulting in ectopic deposition of lignin in phloem tissue and an increase in thickness of the secondary cell wall. In sum, PtoMYB055 is a transcriptional activator that is involved in regulating lignin biosynthesis during the formation of the secondary cell wall in poplar.
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Miyamoto T, Takada R, Tobimatsu Y, Suzuki S, Yamamura M, Osakabe K, Osakabe Y, Sakamoto M, Umezawa T. Double knockout of OsWRKY36 and OsWRKY102 boosts lignification with altering culm morphology of rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 296:110466. [PMID: 32539998 DOI: 10.1016/j.plantsci.2020.110466] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/18/2020] [Accepted: 03/08/2020] [Indexed: 06/11/2023]
Abstract
Breeding to enrich lignin, a major component of lignocelluloses, in plants contributes to enhanced applications of lignocellulosic biomass into solid biofuels and valuable aromatic chemicals. To collect information on enhancing lignin deposition in grass species, important lignocellulose feedstocks, we generated rice (Oryza sativa) transgenic lines deficient in OsWRKY36 and OsWRKY102, which encode putative transcriptional repressors for secondary cell wall formation. We used CRISPR/Cas9-mediated targeted mutagenesis and closely characterized their altered cell walls using chemical and nuclear magnetic resonance (NMR) methods. Both OsWRKY36 and OsWRKY102 mutations significantly increased lignin content by up to 28 % and 32 %, respectively. Additionally, OsWRKY36/OsWRKY102-double-mutant lines displayed lignin enrichment of cell walls (by up to 41 %) with substantially altered culm morphology over the single-mutant lines as well as the wild-type controls. Our chemical and NMR analyses showed that relative abundances of guaiacyl and p-coumarate units were slightly higher and lower, respectively, in the WRKY mutant lignins compared with those in the wild-type lignins. Our results provide evidence that both OsWRKY36 and OsWRKY102 are associated with repression of rice lignification.
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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
| | - 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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63
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Akiyoshi N, Nakano Y, Sano R, Kunigita Y, Ohtani M, Demura T. Involvement of VNS NAC-domain transcription factors in tracheid formation in Pinus taeda. TREE PHYSIOLOGY 2020; 40:704-716. [PMID: 31821470 DOI: 10.1093/treephys/tpz106] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 08/22/2019] [Accepted: 09/24/2019] [Indexed: 05/19/2023]
Abstract
Vascular plants have two types of water-conducting cells, xylem vessel cells (in angiosperms) and tracheid cells (in ferns and gymnosperms). These cells are commonly characterized by secondary cell wall (SCW) formation and programmed cell death (PCD), which increase the efficiency of water conduction. The differentiation of xylem vessel cells is regulated by a set of NAC (NAM, ATAF1/2 and CUC2) transcription factors, called the VASCULAR-RELATED NAC-DOMAIN (VND) family, in Arabidopsis thaliana Linne. The VNDs regulate the transcriptional induction of genes required for SCW formation and PCD. However, information on the transcriptional regulation of tracheid cell differentiation is still limited. Here, we performed functional analysis of loblolly pine (Pinus taeda Linne) VND homologs (PtaVNS, for VND, NST/SND, SMB-related protein). We identified five PtaVNS genes in the loblolly pine genome, and four of these PtaVNS genes were highly expressed in tissues with tracheid cells, such as shoot apices and developing xylem. Transient overexpression of PtaVNS genes induced xylem vessel cell-like patterning of SCW deposition in tobacco (Nicotiana benthamiana Domin) leaves, and up-regulated the promoter activities of loblolly pine genes homologous to SCW-related MYB transcription factor genes and cellulose synthase genes, as well as to cysteine protease genes for PCD. Collectively, our data indicated that PtaVNS proteins possess transcriptional activity to induce the molecular programs required for tracheid formation, i.e., SCW formation and PCD. Moreover, these findings suggest that the VNS-MYB-based transcriptional network regulating water-conducting cell differentiation in angiosperm and moss plants is conserved in gymnosperms.
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Affiliation(s)
- Nobuhiro Akiyoshi
- Graduate School of Science and Technology, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Yoshimi Nakano
- Graduate School of Science and Technology, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Ryosuke Sano
- Graduate School of Science and Technology, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Yusuke Kunigita
- Graduate School of Science and Technology, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Misato Ohtani
- Graduate School of Science and Technology, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8562, Japan
| | - Taku Demura
- Graduate School of Science and Technology, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
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64
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Wei H. Construction of a hierarchical gene regulatory network centered around a transcription factor. Brief Bioinform 2020; 20:1021-1031. [PMID: 29186304 DOI: 10.1093/bib/bbx152] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 10/11/2017] [Indexed: 12/24/2022] Open
Abstract
We have modified a multitude of transcription factors (TFs) in numerous plant species and some animal species, and obtained transgenic lines that exhibit phenotypic alterations. Whenever we observe phenotypic changes in a TF's transgenic lines, we are always eager to identify its target genes, collaborative regulators and even upstream high hierarchical regulators. This issue can be addressed by establishing a multilayered hierarchical gene regulatory network (ML-hGRN) centered around a given TF. In this article, a practical approach for constructing an ML-hGRN centered on a TF using a combined approach of top-down and bottom-up network construction methods is described. Strategies for constructing ML-hGRNs are vitally important, as these networks provide key information to advance our understanding of how biological processes are regulated.
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Affiliation(s)
- Hairong Wei
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.,School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA
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65
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Geng P, Zhang S, Liu J, Zhao C, Wu J, Cao Y, Fu C, Han X, He H, Zhao Q. MYB20, MYB42, MYB43, and MYB85 Regulate Phenylalanine and Lignin Biosynthesis during Secondary Cell Wall Formation. PLANT PHYSIOLOGY 2020; 182:1272-1283. [PMID: 31871072 PMCID: PMC7054866 DOI: 10.1104/pp.19.01070] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/09/2019] [Indexed: 05/18/2023]
Abstract
Lignin is a phenylpropanoid-derived polymer that functions as a major component of cell walls in plant vascular tissues. Biosynthesis of the aromatic amino acid Phe provides precursors for many secondary metabolites, including lignins and flavonoids. Here, we discovered that MYB transcription factors MYB20, MYB42, MYB43, and MYB85 are transcriptional regulators that directly activate lignin biosynthesis genes and Phe biosynthesis genes during secondary wall formation in Arabidopsis (Arabidopsis thaliana). Disruption of MYB20, MYB42, MYB43, and MYB85 resulted in growth development defects and substantial reductions in lignin biosynthesis. In addition, our data showed that these MYB proteins directly activated transcriptional repressors that specifically inhibit flavonoid biosynthesis, which competes with lignin biosynthesis for Phe precursors. Together, our results provide important insights into the molecular framework for the lignin biosynthesis pathway.
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Affiliation(s)
- Pan Geng
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Su Zhang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua University-Peking University, Joint Center for Life Sciences, Beijing 100084, China
| | - Jinyue Liu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Cuihuan Zhao
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jie Wu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua University-Peking University, Joint Center for Life Sciences, Beijing 100084, China
| | - Yingping Cao
- Shandong Technology Innovation Center of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Chunxiang Fu
- Shandong Technology Innovation Center of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Xue Han
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, 100871 Beijing, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, 100871 Beijing, China
| | - Qiao Zhao
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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Xu W, Tang W, Wang C, Ge L, Sun J, Qi X, He Z, Zhou Y, Chen J, Xu Z, Ma YZ, Chen M. SiMYB56 Confers Drought Stress Tolerance in Transgenic Rice by Regulating Lignin Biosynthesis and ABA Signaling Pathway. FRONTIERS IN PLANT SCIENCE 2020; 11:785. [PMID: 32625221 PMCID: PMC7314972 DOI: 10.3389/fpls.2020.00785] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/18/2020] [Indexed: 05/19/2023]
Abstract
Foxtail millet (Setaria italica) originated in China and is generally cultivated in arid and barren soil. Through long-term harsh environmental selection, foxtail millet has acquired significant drought resistance. However, the molecular mechanism of foxtail millet drought resistance is still unknown. Here, we identified a drought-induced R2R3-MYB transcription factor SiMYB56 in foxtail millet. Overexpression of SiMYB56 significantly enhances tolerance to drought stress in transgenic rice plants at both the vegetative and the reproductive stage and has no adverse effect on its normal growth. Compared with wild-type controls, SiMYB56-overexpressing rice plants had lower MDA content and higher lignin content under drought conditions. Quantitative real-time PCR and Transcriptional activity assays demonstrated that SiMYB56 could activate expression of lignin biosynthesis genes under drought conditions. Also, we found that overexpression of SiMYB56 can led to ABA accumulation in the seeds transgenic rice plants. Further experiments showed that Overexpression of SiMYB56 can upregulate the expression of ABA synthesis and response related genes under drought conditions. In conclusion, SiMYB56 may enhance the drought resistance of transgenic rice plants by regulating lignin biosynthesis and ABA signaling pathway, making SiMYB56 a candidate gene for drought resistance improvement in gramineous crops.
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Affiliation(s)
- Weiya Xu
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wensi Tang
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunxiao Wang
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Linhao Ge
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianchang Sun
- Institute of Crop Sciences, Ningxia Academy of Agriculture and Forestry Sciences, Yongning, China
| | - Xin Qi
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhang He
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongbin Zhou
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun Chen
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhaoshi Xu
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - You-Zhi Ma
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: You-Zhi Ma,
| | - Ming Chen
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Ming Chen,
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Zhang Z, Zhang X, Lin Z, Wang J, Liu H, Zhou L, Zhong S, Li Y, Zhu C, Lai J, Li X, Yu J, Lin Z. A Large Transposon Insertion in the stiff1 Promoter Increases Stalk Strength in Maize. THE PLANT CELL 2020; 32:152-165. [PMID: 31690654 PMCID: PMC6961635 DOI: 10.1105/tpc.19.00486] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/08/2019] [Accepted: 11/01/2019] [Indexed: 05/11/2023]
Abstract
Stalk lodging, which is generally determined by stalk strength, results in considerable yield loss and has become a primary threat to maize (Zea mays) yield under high-density planting. However, the molecular genetic basis of maize stalk strength remains unclear, and improvement methods remain inefficient. Here, we combined map-based cloning and association mapping and identified the gene stiff1 underlying a major quantitative trait locus for stalk strength in maize. A 27.2-kb transposable element insertion was present in the promoter of the stiff1 gene, which encodes an F-box domain protein. This transposable element insertion repressed the transcription of stiff1, leading to the increased cellulose and lignin contents in the cell wall and consequently greater stalk strength. Furthermore, a precisely edited allele of stiff1 generated through the CRISPR/Cas9 system resulted in plants with a stronger stalk than the unedited control. Nucleotide diversity analysis revealed that the promoter of stiff1 was under strong selection in the maize stiff-stalk group. Our cloning of stiff1 reveals a case in which a transposable element played an important role in maize improvement. The identification of stiff1 and our edited stiff1 allele pave the way for efficient improvement of maize stalk strength.
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Affiliation(s)
- Zhihai Zhang
- National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Xuan Zhang
- National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Zhelong Lin
- National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Jian Wang
- National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Hangqin Liu
- National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Leina Zhou
- National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Shuyang Zhong
- National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Yan Li
- National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Can Zhu
- National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Jinsheng Lai
- National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Xianran Li
- Department of Agronomy, Iowa State University, Ames, Iowa 50011
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, Iowa 50011
| | - Zhongwei Lin
- National Maize Improvement Center; Center for Crop Functional Genomics and Molecular Breeding; Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education; Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
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Zhang J, Tuskan GA, Tschaplinski TJ, Muchero W, Chen JG. Transcriptional and Post-transcriptional Regulation of Lignin Biosynthesis Pathway Genes in Populus. FRONTIERS IN PLANT SCIENCE 2020; 11:652. [PMID: 32528504 PMCID: PMC7262965 DOI: 10.3389/fpls.2020.00652] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/28/2020] [Indexed: 05/04/2023]
Abstract
Lignin is a heterogeneous polymer of aromatic subunits derived from phenylalanine. It is polymerized in intimate proximity to the polysaccharide components in plant cell walls and provides additional rigidity and compressive strength for plants. Understanding the regulatory mechanisms of lignin biosynthesis is important for genetic modification of the plant cell wall for agricultural and industrial applications. Over the past 10 years the transcriptional regulatory model of lignin biosynthesis has been established in plants. However, the role of post-transcriptional regulation is still largely unknown. Increasing evidence suggests that lignin biosynthesis pathway genes are also regulated by alternative splicing, microRNA, and long non-coding RNA. In this review, we briefly summarize recent progress on the transcriptional regulation, then we focus on reviewing progress on the post-transcriptional regulation of lignin biosynthesis pathway genes in the woody model plant Populus.
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Affiliation(s)
- Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- *Correspondence: Jin Zhang,
| | - 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
| | - 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
| | - 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
- Jin-Gui Chen,
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Hirai R, Higaki T, Takenaka Y, Sakamoto Y, Hasegawa J, Matsunaga S, Demura T, Ohtani M. The Progression of Xylem Vessel Cell Differentiation is Dependent on the Activity Level of VND7 in Arabidopsis thaliana. PLANTS 2019; 9:plants9010039. [PMID: 31881731 PMCID: PMC7020236 DOI: 10.3390/plants9010039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 12/17/2022]
Abstract
Xylem vessels are important for water conduction in vascular plants. The VASCULAR-RELATED NAC-DOMAIN (VND) family proteins, master regulators of xylem vessel cell differentiation in Arabidopsis thaliana, can upregulate a set of genes required for xylem vessel cell differentiation, including those involved in secondary cell wall (SCW) formation and programmed cell death (PCD); however, it is not fully understood how VND activity levels influence these processes. Here, we examined the Arabidopsis VND7-VP16-GR line, in which VND7 activity is post-translationally activated by treatments with different concentrations of dexamethasone (DEX), a synthetic glucocorticoid. Our observations showed that 1 nM DEX induced weak SCW deposition, but not PCD, whereas 10 or 100 nM DEX induced both SCW deposition and PCD. The decreased chlorophyll contents and SCW deposition were apparent after 24 h of 100 nM DEX treatment, but became evident only after 48 h of 10 nM DEX treatment. Moreover, the lower DEX concentrations delayed the upregulation of VND7 downstream genes, and decreased their induction levels. They collectively suggest that the regulation of VND activity is important not only to initiate xylem vessel cell differentiation, but also regulate the quality of the xylem vessels through VND-activity-dependent upregulation of the PCD- and SCW-related genes.
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Affiliation(s)
- Risaku Hirai
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan; (R.H.); (Y.T.)
| | - Takumi Higaki
- International Research Organization for Advanced Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan;
| | - Yuto Takenaka
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan; (R.H.); (Y.T.)
| | - Yuki Sakamoto
- Faculty of Science and Technology, Department of Applied Biological Science, Tokyo University of Science, Noda 278-8510, Japan; (Y.S.); (J.H.); (S.M.)
| | - Junko Hasegawa
- Faculty of Science and Technology, Department of Applied Biological Science, Tokyo University of Science, Noda 278-8510, Japan; (Y.S.); (J.H.); (S.M.)
| | - Sachihiro Matsunaga
- Faculty of Science and Technology, Department of Applied Biological Science, Tokyo University of Science, Noda 278-8510, Japan; (Y.S.); (J.H.); (S.M.)
| | - Taku Demura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan; (R.H.); (Y.T.)
- Correspondence: (T.D.); (M.O.); Tel.: +81-743-72-5460 (T.D.); +81-4-7136-3673 (M.O.)
| | - Misato Ohtani
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan; (R.H.); (Y.T.)
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
- Correspondence: (T.D.); (M.O.); Tel.: +81-743-72-5460 (T.D.); +81-4-7136-3673 (M.O.)
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Matias Hurtado FM, Pinto MDS, de Oliveira PN, Riaño-Pachón DM, Inocente LB, Carrer H. Analysis of NAC Domain Transcription Factor Genes of Tectona grandis L.f. Involved in Secondary Cell Wall Deposition. Genes (Basel) 2019; 11:E20. [PMID: 31878092 PMCID: PMC7016782 DOI: 10.3390/genes11010020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 11/16/2022] Open
Abstract
NAC proteins are one of the largest families of plant-specific transcription factors (TFs). They regulate diverse complex biological processes, including secondary xylem differentiation and wood formation. Recent genomic and transcriptomic studies of Tectona grandis L.f. (teak), one of the most valuable hardwood trees in the world, have allowed identification and analysis of developmental genes. In the present work, T. grandis NAC genes were identified and analyzed regarding to their evolution and expression profile during wood formation. We analyzed the recently published T. grandis genome, and identified 130 NAC proteins that are coded by 107 gene loci. These proteins were classified into 23 clades of the NAC family, together with Populus, Eucalyptus, and Arabidopsis. Data on transcript expression revealed specific temporal and spatial expression patterns for the majority of teak NAC genes. RT-PCR indicated expression of VND genes (Tg11g04450-VND2 and Tg15g08390-VND4) related to secondary cell wall formation in xylem vessels of 16-year-old juvenile trees. Our findings open a way to further understanding of NAC transcription factor genes in T. grandis wood biosynthesis, while they are potentially useful for future studies aiming to improve biomass and wood quality using biotechnological approaches.
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Affiliation(s)
- Fernando Manuel Matias Hurtado
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Av. Pádua Dias, 11, CP 9, Piracicaba, SP 13418-900, Brazil; (F.M.M.H.); (M.d.S.P.); (P.N.d.O.)
| | - Maísa de Siqueira Pinto
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Av. Pádua Dias, 11, CP 9, Piracicaba, SP 13418-900, Brazil; (F.M.M.H.); (M.d.S.P.); (P.N.d.O.)
| | - Perla Novais de Oliveira
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Av. Pádua Dias, 11, CP 9, Piracicaba, SP 13418-900, Brazil; (F.M.M.H.); (M.d.S.P.); (P.N.d.O.)
| | - Diego Mauricio Riaño-Pachón
- Computational, Evolutionary and Systems Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of São Paulo. Av. Centenário 303, Piracicaba, SP 13416-000, Brazil;
| | - Laura Beatriz Inocente
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Av. Pádua Dias, 11, CP 9, Piracicaba, SP 13418-900, Brazil; (F.M.M.H.); (M.d.S.P.); (P.N.d.O.)
| | - Helaine Carrer
- Department of Biological Sciences, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Av. Pádua Dias, 11, CP 9, Piracicaba, SP 13418-900, Brazil; (F.M.M.H.); (M.d.S.P.); (P.N.d.O.)
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Li Q, Wu Z, Wu H, Fang W, Chen F, Teng N. Transcriptome Profiling Unravels a Vital Role of Pectin and Pectinase in Anther Dehiscence in Chrysanthemum. Int J Mol Sci 2019; 20:E5865. [PMID: 31766739 PMCID: PMC6928809 DOI: 10.3390/ijms20235865] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/15/2019] [Accepted: 11/21/2019] [Indexed: 01/08/2023] Open
Abstract
Chrysanthemum (Chrysanthemum morifolium (Ramat.) Kitamura) plants have great ornamental value, but their flowers can also be a source of pollen contamination. Previously, morphological and cytological studies have shown that anthers of some chrysanthemum cultivars such as 'Qx-115' fail to dehisce, although the underlying mechanism is largely unknown. In this study, we investigated the molecular basis of anther indehiscence in chrysanthemum via transcriptome analysis of a dehiscent cultivar ('Qx-097') and an indehiscent cultivar ('Qx-115'). We also measured related physiological indicators during and preceding the period of anther dehiscence. Our results showed a difference in pectinase accumulation and activity between the two cultivars during dehiscence. Detection of de-esterified pectin and highly esterified pectin in anthers during the period preceding anther dehiscence using LM19 and LM20 monoclonal antibodies showed that both forms of pectin were absent in the stomium region of 'Qx-097' anthers but were abundant in that of 'Qx-115' anthers. Analysis of transcriptome data revealed a significant difference in the expression levels of two transcription factor-encoding genes, CmLOB27 and CmERF72, between 'Qx-097' and 'Qx-115' during anther development. Transient overexpression of CmLOB27 and CmERF72 separately in tobacco leaves promoted pectinase biosynthesis. We conclude that CmLOB27 and CmERF72 are involved in the synthesis of pectinase, which promotes the degradation of pectin. Our results lay a foundation for further investigation of the role of CmLOB27 and CmERF72 transcription factors in the process of anther dehiscence in chrysanthemum.
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Affiliation(s)
- Qian Li
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
- Baguazhou Science and Technology Innovation Center of Modern Horticulture Industry, Nanjing 210095, China
| | - Ze Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
- Baguazhou Science and Technology Innovation Center of Modern Horticulture Industry, Nanjing 210095, China
| | - Huijun Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
- Baguazhou Science and Technology Innovation Center of Modern Horticulture Industry, Nanjing 210095, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
| | - Nianjun Teng
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, Nanjing 210095, China
- Baguazhou Science and Technology Innovation Center of Modern Horticulture Industry, Nanjing 210095, China
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72
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Su X, Zhao Y, Wang H, Li G, Cheng X, Jin Q, Cai Y. Transcriptomic analysis of early fruit development in Chinese white pear (Pyrus bretschneideri Rehd.) and functional identification of PbCCR1 in lignin biosynthesis. BMC PLANT BIOLOGY 2019; 19:417. [PMID: 31604417 PMCID: PMC6788021 DOI: 10.1186/s12870-019-2046-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/20/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND The content of stone cells and lignin is one of the key factors affecting the quality of pear fruit. In a previous study, we determined the developmental regularity of stone cells and lignin in 'Dangshan Su' pear fruit 15-145 days after pollination (DAP). However, the development of fruit stone cells and lignin before 15 DAP has not been heavily researched. RESULTS In this study, we found that primordial stone cells began to appear at 7 DAP and that the fruit had formed a large number of stone cells at 15 DAP. Subsequently, transcriptome sequencing was performed on fruits at 0, 7, and 15 DAP and identified 3834 (0 vs. 7 DAP), 4049 (7 vs. 15 DAP) and 5763 (0 vs. 15 DAP) DEGs. During the 7-15 DAP period, a large number of key enzyme genes essential for lignin biosynthesis are gradually up-regulated, and their expression pattern is consistent with the accumulation of lignin in this period. Further analysis found that the biosynthesis of S-type lignin in 'Dangshan Su' pear does not depend on the catalytic activity of PbSAD but is primarily generated by the catalytic activity of caffeoyl-CoA through CCoAOMT, CCR, F5H, and CAD. We cloned PbCCR1, 2 and analysed their functions in Chinese white pear lignin biosynthesis. PbCCR1 and 2 have a degree of functional redundancy; both demonstrate the ability to participate in lignin biosynthesis. However, PbCCR1 may be the major gene for lignin biosynthesis, while PbCCR2 has little effect on lignin biosynthesis. CONCLUSIONS Our results revealed that 'Dangshan Su' pear began to form a large number of stone cells and produce lignin after 7 DAP and mainly accumulated materials from 0 to 7 DAP. PbCCR1 is mainly involved in the biosynthesis of lignin in 'Dangshan Su' pear and plays a positive role in lignin biosynthesis.
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Affiliation(s)
- Xueqiang Su
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Yu Zhao
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Han Wang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Guohui Li
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Xi Cheng
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Qing Jin
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
| | - Yongping Cai
- School of Life Science, Anhui Agricultural University, Hefei, Anhui China
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73
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Mining MYB transcription factors from the genomes of orchids (Phalaenopsis and Dendrobium) and characterization of an orchid R2R3-MYB gene involved in water-soluble polysaccharide biosynthesis. Sci Rep 2019; 9:13818. [PMID: 31554868 PMCID: PMC6761160 DOI: 10.1038/s41598-019-49812-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 08/20/2019] [Indexed: 12/20/2022] Open
Abstract
Members of the MYB superfamily act as regulators in a wide range of biological processes in plants. Despite this, the MYB superfamily from the Orchidaceae has not been identified, and MYB genes related to bioactive water-soluble polysaccharide (WSP) biosynthesis are relatively unknown. In this study, we identified 159 and 165 MYB genes from two orchids, Phalaenopsis equestris and Dendrobium officinale, respectively. The MYB proteins were classified into four MYB classes in both orchids: MYB-related (MYBR), R2R3-MYB, 3R-MYB and atypical MYB proteins. The MYBR proteins in both orchids were classified into five subfamilies and 12 genes were strongly up-regulated in response to cold stress in D. officinale. The R2R3-MYB proteins were both divided into 31 clades in P. equestris and D. officinale. Among these clades, nine contained MYB TFs related to secondary cell wall biosynthesis or testa mucilage biosynthesis in Arabidopsis thaliana. In D. officinale, 10 candidate genes showed an expression pattern corresponding to changes in the WSP content. Overexpression of one of these candidate genes (DoMYB75) in A. thaliana increased seed WSP content by about 14%. This study provides information about MYB genes in two orchids that will further help to understand the transcriptional regulation of WSP biosynthesis in these orchids as well as other plant species.
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74
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He C, Teixeira da Silva JA, Wang H, Si C, Zhang M, Zhang X, Li M, Tan J, Duan J. Mining MYB transcription factors from the genomes of orchids (Phalaenopsis and Dendrobium) and characterization of an orchid R2R3-MYB gene involved in water-soluble polysaccharide biosynthesis. Sci Rep 2019. [PMID: 31554868 DOI: 10.1038/s41598-019-49812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Members of the MYB superfamily act as regulators in a wide range of biological processes in plants. Despite this, the MYB superfamily from the Orchidaceae has not been identified, and MYB genes related to bioactive water-soluble polysaccharide (WSP) biosynthesis are relatively unknown. In this study, we identified 159 and 165 MYB genes from two orchids, Phalaenopsis equestris and Dendrobium officinale, respectively. The MYB proteins were classified into four MYB classes in both orchids: MYB-related (MYBR), R2R3-MYB, 3R-MYB and atypical MYB proteins. The MYBR proteins in both orchids were classified into five subfamilies and 12 genes were strongly up-regulated in response to cold stress in D. officinale. The R2R3-MYB proteins were both divided into 31 clades in P. equestris and D. officinale. Among these clades, nine contained MYB TFs related to secondary cell wall biosynthesis or testa mucilage biosynthesis in Arabidopsis thaliana. In D. officinale, 10 candidate genes showed an expression pattern corresponding to changes in the WSP content. Overexpression of one of these candidate genes (DoMYB75) in A. thaliana increased seed WSP content by about 14%. This study provides information about MYB genes in two orchids that will further help to understand the transcriptional regulation of WSP biosynthesis in these orchids as well as other plant species.
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Affiliation(s)
- Chunmei He
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | | | - Haobin Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Can Si
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingze Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoming Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Mingzhi Li
- Biodata Biotechnology Co. Ltd, Heifei, 230031, China
| | - Jianwen Tan
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Jun Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Gene Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
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75
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Brown K, Takawira LT, O'Neill MM, Mizrachi E, Myburg AA, Hussey SG. Identification and functional evaluation of accessible chromatin associated with wood formation in Eucalyptus grandis. THE NEW PHYTOLOGIST 2019; 223:1937-1951. [PMID: 31063599 DOI: 10.1111/nph.15897] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/29/2019] [Indexed: 05/03/2023]
Abstract
Accessible chromatin changes dynamically during development and harbours functional regulatory regions which are poorly understood in the context of wood development. We explored the importance of accessible chromatin in Eucalyptus grandis in immature xylem generally, and MYB transcription factor-mediated transcriptional programmes specifically. We identified biologically reproducible DNase I Hypersensitive Sites (DHSs) and assessed their functional significance in immature xylem through their associations with gene expression, epigenomic data and DNA sequence conservation. We identified in vitro DNA binding sites for six secondary cell wall-associated Eucalyptus MYB (EgrMYB) transcription factors using DAP-seq, reconstructed protein-DNA networks of predicted targets based on binding sites within or outside DHSs and assessed biological enrichment of these networks with published datasets. 25 319 identified immature xylem DHSs were associated with increased transcription and significantly enriched for various epigenetic signatures (H3K4me3, H3K27me3, RNA pol II), conserved noncoding sequences and depleted single nucleotide variants. Predicted networks built from EgrMYB binding sites located in accessible chromatin were significantly enriched for systems biology datasets relevant to wood formation, whereas those occurring in inaccessible chromatin were not. Our study demonstrates that DHSs in E. grandis immature xylem, most of which are intergenic, are of functional significance to gene regulation in this tissue.
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Affiliation(s)
- Katrien Brown
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa
| | - Lazarus T Takawira
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa
| | - Marja M O'Neill
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa
| | - Alexander A Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa
| | - Steven G Hussey
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa
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76
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Defoort J, Van de Peer Y, Vermeirssen V. Function, dynamics and evolution of network motif modules in integrated gene regulatory networks of worm and plant. Nucleic Acids Res 2019; 46:6480-6503. [PMID: 29873777 PMCID: PMC6061849 DOI: 10.1093/nar/gky468] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/14/2018] [Indexed: 12/29/2022] Open
Abstract
Gene regulatory networks (GRNs) consist of different molecular interactions that closely work together to establish proper gene expression in time and space. Especially in higher eukaryotes, many questions remain on how these interactions collectively coordinate gene regulation. We study high quality GRNs consisting of undirected protein–protein, genetic and homologous interactions, and directed protein–DNA, regulatory and miRNA–mRNA interactions in the worm Caenorhabditis elegans and the plant Arabidopsis thaliana. Our data-integration framework integrates interactions in composite network motifs, clusters these in biologically relevant, higher-order topological network motif modules, overlays these with gene expression profiles and discovers novel connections between modules and regulators. Similar modules exist in the integrated GRNs of worm and plant. We show how experimental or computational methodologies underlying a certain data type impact network topology. Through phylogenetic decomposition, we found that proteins of worm and plant tend to functionally interact with proteins of a similar age, while at the regulatory level TFs favor same age, but also older target genes. Despite some influence of the duplication mode difference, we also observe at the motif and module level for both species a preference for age homogeneity for undirected and age heterogeneity for directed interactions. This leads to a model where novel genes are added together to the GRNs in a specific biological functional context, regulated by one or more TFs that also target older genes in the GRNs. Overall, we detected topological, functional and evolutionary properties of GRNs that are potentially universal in all species.
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Affiliation(s)
- Jonas Defoort
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium.,Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Vanessa Vermeirssen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
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77
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Cho J, Jeon H, Kim M, Vo TK, Kim J, Park E, Choi Y, Lee H, Han K, Ko J. Wood forming tissue-specific bicistronic expression of PdGA20ox1 and PtrMYB221 improves both the quality and quantity of woody biomass production in a hybrid poplar. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1048-1057. [PMID: 30515982 PMCID: PMC6523601 DOI: 10.1111/pbi.13036] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/27/2018] [Accepted: 10/28/2018] [Indexed: 05/22/2023]
Abstract
With the exponential growth of the human population and industrial developments, research on renewable energy resources is required to alleviate environmental and economic impacts caused by the consumption of fossil fuels. In this study, we present a synthetic biological application of a wood forming tissue-specific bicistronic gene expression system to improve both the quantity and quality of woody biomass to minimize undesirable growth penalties. Our transgenic poplars, designed to express both PdGA20ox1 (a GA20-oxidase from Pinus densiflora producing bioactive gibberellin, GA) and PtrMYB221 (a MYB transcription factor negatively regulating lignin biosynthesis) under the developing xylem (DX) tissue-specific promoter (i.e., DX15::PdGA20ox1-2A-PtrMYB221 poplar), resulted in a 2-fold increase in biomass quantity compared to wild-type (WT), without undesirable growth defects. A similar phenotype was observed in transgenic Arabidopsis plants harboring the same gene constructs. These phenotypic consequences were further verified in the field experiments. Importantly, our transgenic poplars exhibited an improved quality of biomass with reduced lignin content (~16.0 wt%) but increased holocellulose content (~6.6 wt%). Furthermore, the saccharification efficiency of our transgenic poplar increased significantly by up to 8%. Our results demonstrate that the controlled production of both GA and a secondary wall modifying regulator in the same spatio-temporal manner can be utilized as an efficient biotechnological tool for producing the desired multi-purpose woody biomass.
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Affiliation(s)
- Jin‐Seong Cho
- Department of Plant & Environmental New ResourcesKyung Hee UniversityYonginKorea
| | - Hyung‐Woo Jeon
- Department of Plant & Environmental New ResourcesKyung Hee UniversityYonginKorea
| | - Min‐Ha Kim
- Department of Plant & Environmental New ResourcesKyung Hee UniversityYonginKorea
| | - The K. Vo
- Department of Chemical EngineeringKyung Hee UniversityYonginKorea
| | - Jinsoo Kim
- Department of Chemical EngineeringKyung Hee UniversityYonginKorea
| | - Eung‐Jun Park
- Division of Forest BiotechnologyKorea Forest Research InstituteSuwonKorea
| | - Young‐Im Choi
- Division of Forest BiotechnologyKorea Forest Research InstituteSuwonKorea
| | - Hyoshin Lee
- Division of Forest BiotechnologyKorea Forest Research InstituteSuwonKorea
| | - Kyung‐Hwan Han
- Department of Horticulture and Department of ForestryMichigan State UniversityEast LansingMIUSA
| | - Jae‐Heung Ko
- Department of Plant & Environmental New ResourcesKyung Hee UniversityYonginKorea
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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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79
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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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80
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Kalemba EM, Stolarska E. Regulation of Gene Expression of Methionine Sulfoxide Reductases and Their New Putative Roles in Plants. Int J Mol Sci 2019; 20:ijms20061309. [PMID: 30875880 PMCID: PMC6471524 DOI: 10.3390/ijms20061309] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 02/07/2023] Open
Abstract
Oxidation of methionine to methionine sulfoxide is a type of posttranslational modification reversed by methionine sulfoxide reductases (Msrs), which present an exceptionally high number of gene copies in plants. The side-form general antioxidant function-specific role of each Msr isoform has not been fully studied. Thirty homologous genes of Msr type A (MsrA) and type B (MsrB) that originate from the genomes of Arabidopsis thaliana, Populus trichocarpa, and Oryza sativa were analyzed in silico. From 109 to 201 transcription factors and responsive elements were predicted for each gene. Among the species, 220 and 190 common transcription factors and responsive elements were detected for the MsrA and MsrB isoforms, respectively. In a comparison of 14 MsrA and 16 MsrB genes, 424 transcription factors and responsive elements were reported in both types of genes, with almost ten times fewer unique elements. The transcription factors mainly comprised plant growth and development regulators, transcription factors important in stress responses with significant overrepresentation of the myeloblastosis viral oncogene homolog (MYB) and no apical meristem, Arabidopsis transcription activation factor and cup-shaped cotyledon (NAC) families and responsive elements sensitive to ethylene, jasmonate, sugar, and prolamine. Gene Ontology term-based functional classification revealed that cellular, metabolic, and developmental process terms and the response to stimulus term dominated in the biological process category. Available experimental transcriptomic and proteomic data, in combination with a set of predictions, gave coherent results validating this research. Thus, new manners Msr gene expression regulation, as well as new putative roles of Msrs, are proposed.
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Affiliation(s)
- Ewa M Kalemba
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland.
| | - Ewelina Stolarska
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland.
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81
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Chen H, Wang JP, Liu H, Li H, Lin YCJ, Shi R, Yang C, Gao J, Zhou C, Li Q, Sederoff RR, Li W, Chiang VL. Hierarchical Transcription Factor and Chromatin Binding Network for Wood Formation in Black Cottonwood ( Populus trichocarpa). THE PLANT CELL 2019; 31:602-626. [PMID: 30755461 PMCID: PMC6482634 DOI: 10.1105/tpc.18.00620] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 01/15/2019] [Accepted: 02/07/2019] [Indexed: 05/18/2023]
Abstract
Wood remains the world's most abundant and renewable resource for timber and pulp and is an alternative to fossil fuels. Understanding the molecular regulation of wood formation can advance the engineering of wood for more efficient material and energy productions. We integrated a black cottonwood (Populus trichocarpa) wood-forming cell system with quantitative transcriptomics and chromatin binding assays to construct a transcriptional regulatory network (TRN) directed by a key transcription factor (TF), PtrSND1-B1 (secondary wall-associated NAC-domain protein). The network consists of four layers of TF-target gene interactions with quantitative regulatory effects, describing the specificity of how the regulation is transduced through these interactions to activate cell wall genes (effector genes) for wood formation. PtrSND1-B1 directs 57 TF-DNA interactions through 17 TFs transregulating 27 effector genes. Of the 57 interactions, 55 are novel. We tested 42 of these 57 interactions in 30 genotypes of transgenic P. trichocarpa and verified that ∼90% of the tested interactions function in vivo. The TRN reveals common transregulatory targets for distinct TFs, leading to the discovery of nine TF protein complexes (dimers and trimers) implicated in regulating the biosynthesis of specific types of lignin. Our work suggests that wood formation may involve regulatory homeostasis determined by combinations of TF-DNA and TF-TF (protein-protein) regulations.
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Affiliation(s)
- Hao Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
- Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695
| | - Jack P. Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Huizi Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Huiyu Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Ying-Chung Jimmy Lin
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Department of Life Sciences, College of Life Science, National Taiwan University, Taipei, 10617, Taiwan
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Rui Shi
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Chenmin Yang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Jinghui Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
| | - Ronald R. Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina 27695
- Department of Forest Biomaterials, North Carolina State University, Raleigh, North Carolina 27695
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82
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Furches A, Kainer D, Weighill D, Large A, Jones P, Walker AM, Romero J, Gazolla JGFM, Joubert W, Shah M, Streich J, Ranjan P, Schmutz J, Sreedasyam A, Macaya-Sanz D, Zhao N, Martin MZ, Rao X, Dixon RA, DiFazio S, Tschaplinski TJ, Chen JG, Tuskan GA, Jacobson D. Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence. FRONTIERS IN PLANT SCIENCE 2019; 10:1249. [PMID: 31649710 PMCID: PMC6791931 DOI: 10.3389/fpls.2019.01249] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 09/09/2019] [Indexed: 05/05/2023]
Abstract
Understanding the regulatory network controlling cell wall biosynthesis is of great interest in Populus trichocarpa, both because of its status as a model woody perennial and its importance for lignocellulosic products. We searched for genes with putatively unknown roles in regulating cell wall biosynthesis using an extended network-based Lines of Evidence (LOE) pipeline to combine multiple omics data sets in P. trichocarpa, including gene coexpression, gene comethylation, population level pairwise SNP correlations, and two distinct SNP-metabolite Genome Wide Association Study (GWAS) layers. By incorporating validation, ranking, and filtering approaches we produced a list of nine high priority gene candidates for involvement in the regulation of cell wall biosynthesis. We subsequently performed a detailed investigation of candidate gene GROWTH-REGULATING FACTOR 9 (PtGRF9). To investigate the role of PtGRF9 in regulating cell wall biosynthesis, we assessed the genome-wide connections of PtGRF9 and a paralog across data layers with functional enrichment analyses, predictive transcription factor binding site analysis, and an independent comparison to eQTN data. Our findings indicate that PtGRF9 likely affects the cell wall by directly repressing genes involved in cell wall biosynthesis, such as PtCCoAOMT and PtMYB.41, and indirectly by regulating homeobox genes. Furthermore, evidence suggests that PtGRF9 paralogs may act as transcriptional co-regulators that direct the global energy usage of the plant. Using our extended pipeline, we show multiple lines of evidence implicating the involvement of these genes in cell wall regulatory functions and demonstrate the value of this method for prioritizing candidate genes for experimental validation.
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Affiliation(s)
- Anna Furches
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States
| | - David Kainer
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Deborah Weighill
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States
| | - Annabel Large
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Oak Ridge Associated Universities (ORAU), Oak Ridge, TN, United States
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, United States
| | - Piet Jones
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States
| | - Angelica M. Walker
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Oak Ridge Associated Universities (ORAU), Oak Ridge, TN, United States
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, United States
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
| | - Jonathon Romero
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States
| | | | - Wayne Joubert
- Oak Ridge Leadership Computing Facility, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Manesh Shah
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jared Streich
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Priya Ranjan
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Plant Sciences, The University of Tennessee Institute of Agriculture, University of Tennessee, Knoxville, TN, United States
| | - Jeremy Schmutz
- Joint Genome Institute, Walnut Creek, CA, United States
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | | | - David Macaya-Sanz
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Nan Zhao
- Department of Plant Sciences, The University of Tennessee Institute of Agriculture, University of Tennessee, Knoxville, TN, United States
| | - Madhavi Z. Martin
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Xiaolan Rao
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
| | - Richard A. Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
| | - Stephen DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Timothy J. Tschaplinski
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jin-Gui Chen
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Gerald A. Tuskan
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Daniel Jacobson
- Biosciences Division, and The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States
- *Correspondence: Daniel Jacobson,
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83
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Saelim L, Akiyoshi N, Tan TT, Ihara A, Yamaguchi M, Hirano K, Matsuoka M, Demura T, Ohtani M. Arabidopsis Group IIId ERF proteins positively regulate primary cell wall-type CESA genes. JOURNAL OF PLANT RESEARCH 2019; 132:117-129. [PMID: 30478480 DOI: 10.1007/s10265-018-1074-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 10/21/2018] [Indexed: 05/22/2023]
Abstract
The cell wall determines morphology and the environmental responses of plant cells. The primary cell wall (PCW) is produced during cell division and expansion, determining the cell shape and volume. After cell expansion, specific types of plant cells produce a lignified wall, known as a secondary cell wall (SCW). We functionally analyzed Group IIId Arabidopsis AP2/EREBP genes, namely ERF34, ERF35, ERF38, and ERF39, which are homologs of a rice ERF gene previously proposed to be related to SCW biosynthesis. Expression analysis revealed that these four genes are expressed in regions related to cell division and/or cell differentiation in seedlings (i.e., shoot apical meristems, the primordia of leaves and lateral roots, trichomes, and central cylinder of primary roots) and flowers (i.e., vascular tissues of floral organs and replums and/or valve margins of pistils). Overexpression of ERF genes significantly upregulated PCW-type, but not SCW-type, CESA genes encoding cellulose synthase catalytic subunits in Arabidopsis seedlings. Transient co-expression reporter analysis indicated that ERF35, ERF38, and ERF39 possess transcriptional activator activity, and that ERF34, ERF35, ERF38, and ERF39 upregulated the promoter activity of CESA1, a PCW-type CESA gene, through the DRECRTCOREAT elements, the core cis-acting elements known to be recognized by AP2/ERF proteins. Together, our findings show that Group IIId ERF genes are positive transcriptional regulators of PCW-type CESA genes in Arabidopsis and are possibly involved in modulating cellulose biosynthesis in response to developmental requirements and environmental stimuli.
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Affiliation(s)
- Laddawan Saelim
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Nobuhiro Akiyoshi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Tian Tian Tan
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
- Centre for Research in Biotechnology for Agriculture, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Ayumi Ihara
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Masatoshi Yamaguchi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
- Graduate School of Science and Engineering, Saitama University, Saitama, Saitama, 338-8570, Japan
| | - Ko Hirano
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Makoto Matsuoka
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Taku Demura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan.
| | - Misato Ohtani
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan.
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84
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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: 10] [Impact Index Per Article: 1.7] [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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85
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Geng D, Chen P, Shen X, Zhang Y, Li X, Jiang L, Xie Y, Niu C, Zhang J, Huang X, Ma F, Guan Q. MdMYB88 and MdMYB124 Enhance Drought Tolerance by Modulating Root Vessels and Cell Walls in Apple. PLANT PHYSIOLOGY 2018; 178:1296-1309. [PMID: 30190418 PMCID: PMC6236628 DOI: 10.1104/pp.18.00502] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/26/2018] [Indexed: 05/18/2023]
Abstract
Water deficit is one of the main limiting factors in apple (Malus × domestica Borkh.) cultivation. Root architecture plays an important role in the drought tolerance of plants; however, research efforts to improve drought tolerance of apple trees have focused on aboveground targets. Due to the difficulties associated with visualization and data analysis, there is currently a poor understanding of the genetic players and molecular mechanisms involved in the root architecture of apple trees under drought conditions. We previously observed that MdMYB88 and its paralog MdMYB124 regulate apple tree root morphology. In this study, we found that MdMYB88 and MdMYB124 play important roles in maintaining root hydraulic conductivity under long-term drought conditions and therefore contribute toward adaptive drought tolerance. Further investigation revealed that MdMYB88 and MdMYB124 regulate root xylem development by directly binding MdVND6 and MdMYB46 promoters and thus influence expression of their target genes under drought conditions. In addition, MdMYB88 and MdMYB124 were shown to regulate the deposition of cellulose and lignin root cell walls in response to drought. Taken together, our results provide novel insights into the importance of MdMYB88 and MdMYB124 in root architecture, root xylem development, and secondary cell wall deposition in response to drought in apple trees.
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Affiliation(s)
- Dali Geng
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Pengxiang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaoxia Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yi Zhang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lijuan Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yinpeng Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chundong Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jing Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaohua Huang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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Ohtani M, Demura T. The quest for transcriptional hubs of lignin biosynthesis: beyond the NAC-MYB-gene regulatory network model. Curr Opin Biotechnol 2018; 56:82-87. [PMID: 30390602 DOI: 10.1016/j.copbio.2018.10.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/05/2018] [Accepted: 10/05/2018] [Indexed: 01/15/2023]
Abstract
Lignin is an important secondary metabolite in plants. The biosynthesis of lignin is initiated by the transcriptional upregulation of genes encoding enzymes involved in monolignol biosynthesis and lignin polymerization. Based on studies of xylem differentiation over the last two decades, the NAC-MYB-based gene regulatory network (NAC-MYB-GRN) model is widely considered to underpin developmental lignin biosynthesis. We are now standing on the threshold of a new direction in transcriptional regulation research; the search for novel molecular hubs connecting developmental/environmental signals in lignin biosynthesis. Emerging genome-wide 'omics' technologies are a promising approach for understanding such hubs. Elucidating these molecular hubs may enable us to control lignification in harmony with plant development and environmental adaptation.
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Affiliation(s)
- Misato Ohtani
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Taku Demura
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.
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87
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Li C, Ma X, Yu H, Fu Y, Luo K. Ectopic Expression of PtoMYB74 in Poplar and Arabidopsis Promotes Secondary Cell Wall Formation. FRONTIERS IN PLANT SCIENCE 2018; 9:1262. [PMID: 30364214 PMCID: PMC6191708 DOI: 10.3389/fpls.2018.01262] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 08/10/2018] [Indexed: 05/21/2023]
Abstract
In vascular plants, R2R3-MYB transcription factors are important regulators of secondary cell wall formation. Although 192 annotated R2R3 MYB genes were identified in the poplar genome, only a few members were characterized to participate in the regulation of the secondary cell wall biosynthesis. In this paper, we identify an R2R3-MYB transcription factor, PtoMYB74, which is predicted to be an ortholog of Arabidopsis AtMYB61, a transcription activator that regulates the secondary cell wall formation, lignin biosynthesis, stomatal aperture, and the mucilage of seed coat. PtoMYB74 is mainly expressed in the stems, especially in the xylem tissues and organs. PtoMYB74 as a transcriptional activator is localized to the nucleus. The overexpression of PtoMYB74 increased the secondary cell wall thickness of vessels in transgenic poplar and changed the secondary cell wall compositions. The expression levels of lignin and cellulose biosynthetic genes were elevated in the transgenic poplar overexpressing PtoMYB74 compared to the wild type, while there was no change in the xylan biosynthetic genes. Transcriptional activation assays demonstrated that PtoMYB74 could activate the promoters of structural genes in the lignin and cellulose biosynthetic pathways. Taken together, our data show that PtoMYB74 positively regulates the secondary cell wall biosynthesis in poplar.
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Affiliation(s)
- Chaofeng Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaodong Ma
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Ecology and Environmental Resources, Qinghai University for Nationalities, Xining, China
| | - Hong Yu
- School of Life Sciences, Southwest University, Chongqing, China
| | - Yongyao Fu
- School of Life Sciences, Southwest University, Chongqing, China
| | - Keming Luo
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
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88
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Zhang LM, Leng CY, Luo H, Wu XY, Liu ZQ, Zhang YM, Zhang H, Xia Y, Shang L, Liu CM, Hao DY, Zhou YH, Chu CC, Cai HW, Jing HC. Sweet Sorghum Originated through Selection of Dry, a Plant-Specific NAC Transcription Factor Gene. THE PLANT CELL 2018; 30:2286-2307. [PMID: 30309900 PMCID: PMC6241255 DOI: 10.1105/tpc.18.00313] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 09/04/2018] [Accepted: 10/02/2018] [Indexed: 05/20/2023]
Abstract
Sorghum (Sorghum bicolor) is the fifth most popular crop worldwide and a C4 model plant. Domesticated sorghum comes in many forms, including sweet cultivars with juicy stems and grain sorghum with dry, pithy stems at maturity. The Dry locus, which controls the pithy/juicy stem trait, was discovered over a century ago. Here, we found that Dry gene encodes a plant-specific NAC transcription factor. Dry was either deleted or acquired loss-of-function mutations in sweet sorghum, resulting in cell collapse and altered secondary cell wall composition in the stem. Twenty-three Dry ancestral haplotypes, all with dry, pithy stems, were found among wild sorghum and wild sorghum relatives. Two of the haplotypes were detected in domesticated landraces, with four additional dry haplotypes with juicy stems detected in improved lines. These results imply that selection for Dry gene mutations was a major step leading to the origin of sweet sorghum. The Dry gene is conserved in major cereals; fine-tuning its regulatory network could provide a molecular tool to control crop stem texture.
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Affiliation(s)
- Li-Min Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Chuan-Yuan Leng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Luo
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiao-Yuan Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhi-Quan Liu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Inner Mongolia Research Centre for Prataculture, Chinese Academy of Sciences, Beijing 100093, China
| | - Yu-Miao Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Zhang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Xia
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Li Shang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Chun-Ming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Dong-Yun Hao
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, Jilin 130124, China
| | - Yi-Hua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Cheng-Cai Chu
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hong-Wei Cai
- Department of Plant Genetics and Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Forage Crop Research Institute, Japan Grassland Agricultural and Forage Seed Association, Nasushiobara, Tochigi 329-2742, Japan
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Inner Mongolia Research Centre for Prataculture, Chinese Academy of Sciences, Beijing 100093, China
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89
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Van de Wouwer D, Boerjan W, Vanholme B. Plant cell wall sugars: sweeteners for a bio-based economy. PHYSIOLOGIA PLANTARUM 2018; 164:27-44. [PMID: 29430656 DOI: 10.1111/ppl.12705] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 02/07/2018] [Accepted: 02/07/2018] [Indexed: 05/23/2023]
Abstract
Global warming and the consequent climate change is one of the major environmental challenges we are facing today. The driving force behind the rise in temperature is our fossil-based economy, which releases massive amounts of the greenhouse gas carbon dioxide into the atmosphere. In order to reduce greenhouse gas emission, we need to scale down our dependency on fossil resources, implying that we need other sources for energy and chemicals to feed our economy. Here, plants have an important role to play; by means of photosynthesis, plants capture solar energy to split water and fix carbon derived from atmospheric carbon dioxide. A significant fraction of the fixed carbon ends up as polysaccharides in the plant cell wall. Fermentable sugars derived from cell wall polysaccharides form an ideal carbon source for the production of bio-platform molecules. However, a major limiting factor in the use of plant biomass as feedstock for the bio-based economy is the complexity of the plant cell wall and its recalcitrance towards deconstruction. To facilitate the release of fermentable sugars during downstream biomass processing, the composition and structure of the cell wall can be engineered. Different strategies to reduce cell wall recalcitrance will be described in this review. The ultimate goal is to obtain a tailor-made biomass, derived from plants with a cell wall optimized for particular industrial or agricultural applications, without affecting plant growth and development.
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Affiliation(s)
- Dorien Van de Wouwer
- Ghent University, Department of Plant Biotechnology and Bioinformatics, (Technologiepark 927), 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, (Technologiepark 927), 9052, Ghent, Belgium
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, (Technologiepark 927), 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, (Technologiepark 927), 9052, Ghent, Belgium
| | - Bartel Vanholme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, (Technologiepark 927), 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, (Technologiepark 927), 9052, Ghent, Belgium
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90
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Laubscher M, Brown K, Tonfack LB, Myburg AA, Mizrachi E, Hussey SG. Temporal analysis of Arabidopsis genes activated by Eucalyptus grandis NAC transcription factors associated with xylem fibre and vessel development. Sci Rep 2018; 8:10983. [PMID: 30030488 PMCID: PMC6054625 DOI: 10.1038/s41598-018-29278-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 07/09/2018] [Indexed: 11/12/2022] Open
Abstract
Secondary cell wall (SCW) deposition in Arabidopsis is regulated among others by NAC transcription factors, where SND1 chiefly initiates xylem fibre differentiation while VND6 controls metaxylem vessel SCW development, especially programmed cell death and wall patterning. The translational relevance of Arabidopsis SCW regulation theory and the utility of characterized transcription factors as modular synthetic biology tools for improving commercial fibre crops is unclear. We investigated inter-lineage gene activation dynamics for potential fibre and vessel differentiation regulators from the widely grown hardwood Eucalyptus grandis (Myrtales). EgrNAC26, a VND6 homolog, and EgrNAC61, an SND1 homolog, were transiently expressed in Arabidopsis mesophyll protoplasts in parallel to determine early and late (i.e. 7 and 14 hours post-transfection) gene targets. Surprisingly, across the time series EgrNAC26 activated only a subset of SCW-related transcription factors and biosynthetic genes activated by EgrNAC61, specializing instead in targeting vessel-specific wall pit and programmed cell death markers. Promoters of EgrNAC26 and EgrNAC61 both induced reporter gene expression in vessels of young Arabidopsis plants, with EgrNAC61 also conferring xylem- and cork cambium-preferential expression in Populus. Our results demonstrate partial conservation, with notable exceptions, of SND1 and VND6 homologs in Eucalyptus and a first report of cork cambium expression for EgrNAC61.
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Affiliation(s)
- M Laubscher
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa
| | - K Brown
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa
| | - L B Tonfack
- Plant Physiology and Improvement Unit, Laboratory of Biotechnology and Environment, Department of Plant Biology, University of Yaoundé I, P.O. Box 812, Yaoundé, Cameroon
| | - A A Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa
| | - E Mizrachi
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa
| | - S G Hussey
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X28, Pretoria, 0002, South Africa.
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91
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Xia J, Zhao Y, Burks P, Pauly M, Brown PJ. A sorghum NAC gene is associated with variation in biomass properties and yield potential. PLANT DIRECT 2018; 2:e00070. [PMID: 31245734 PMCID: PMC6508854 DOI: 10.1002/pld3.70] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/12/2018] [Accepted: 06/19/2018] [Indexed: 05/13/2023]
Abstract
Sorghum bicolor is a C4 grass widely cultivated for grain, forage, sugar, and biomass. The sorghum Dry Stalk (D) locus controls a qualitative difference between juicy green (dd) and dry white (D-) stalks and midribs, and co-localizes with a quantitative trait locus for sugar yield. Here, we apply fine-mapping and genome-wide association study (GWAS) to identify a candidate gene underlying D, and use nearly isogenic lines (NILs) to characterize the transcriptional, compositional, and agronomic effects of variation at the D locus. The D locus was fine-mapped to a 36 kb interval containing four genes. One of these genes is a NAC transcription factor that contains a stop codon in the NAC domain in the recessive (dd) parent. Allelic variation at D affects grain yield, sugar yield, and biomass composition in NILs. Green midrib (dd) NILs show reductions in lignin in stalk tissue and produce higher sugar and grain yields under well-watered field conditions. Increased yield potential in dd NILs is associated with increased stalk mass and moisture, higher biomass digestibility, and an extended period of grain filling. Transcriptome profiling of midrib tissue at the 4-6 leaf stages, when NILs first become phenotypically distinct, reveals that dd NILs have increased expression of a miniature zinc finger (MIF) gene. MIF genes dimerize with and suppress zinc finger homeodomain (ZF-HD) transcription factors, and a ZF-HD gene is associated with midrib color variation in a GWAS analysis across 1,694 diverse sorghum inbreds. A premature stop codon in a NAC gene is the most likely candidate polymorphism underlying the sorghum D locus. More detailed understanding of the sorghum D locus could help improve agronomic potential in cereals.
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Affiliation(s)
- Jingnu Xia
- Department of Crop SciencesUniversity of Illinois at Urbana ChampaignUrbanaIllinois
- Present address:
Department of BiochemistryUniversity of OxfordOxfordUK
| | - Yunjun Zhao
- Department of Plant and Microbial BiologyUniversity of California, BerkeleyBerkeleyCalifornia
- Present address:
Brookhaven National LabUptonNew York
| | - Payne Burks
- Department of Crop SciencesUniversity of Illinois at Urbana ChampaignUrbanaIllinois
- Present address:
Chromatin Inc.LubbockTexas
| | - Markus Pauly
- Department of Plant and Microbial BiologyUniversity of California, BerkeleyBerkeleyCalifornia
- Present address:
Heinrich‐Heine UniversityDuesseldorfGermany
| | - Patrick J. Brown
- Department of Crop SciencesUniversity of Illinois at Urbana ChampaignUrbanaIllinois
- Present address:
University of California, DavisDavisCalifornia
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92
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Tyagi A, Nigam D, S. V. AM, Solanke AU, Singh NK, Sharma TR, Gaikwad K. Genome-wide discovery of tissue-specific miRNAs in clusterbean (Cyamopsis tetragonoloba) indicates their association with galactomannan biosynthesis. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1241-1257. [PMID: 29193664 PMCID: PMC5978871 DOI: 10.1111/pbi.12866] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 11/15/2017] [Accepted: 11/22/2017] [Indexed: 05/13/2023]
Abstract
Owing to the presence of 80% soluble dietary fibre, high protein content and high value gum, clusterbean (Cyamopsis tetragonoloba) has recently emerged as an economically important legume. The developing clusterbean seeds accumulate 90% galactomannans in the endosperm and, therefore, can be used as a model crop to understand galactomannan biosynthesis and its regulation. miRNAs are tiny master regulators of their corresponding target genes, resulting in variations in the amounts of their metabolic end products. To understand the role of these regulators in galactomannan biosynthesis regulation, small RNA libraries were prepared and sequenced from five tissues of clusterbean genotype RGC-936, and miRanalyzer and DSAP programs were used to identify conserved miRNAs and novel small RNAs. A total of 187 known and 171 novel miRNAs were found to be differentially expressed, of which 10 miRNAs were validated. A complicated network topology and 35% sharing of the target mRNAs between known and novel miRNAs suggest random evolution of novel miRNAs. The gene ontology (GO) annotation of potential target genes revealed the genes coding for signalling and carbohydrate metabolism (50.10%), kinases and other enzymes (20.75%), transcription factors (10.20%), transporters (8.35%) and other targets (10.6%). Two novel unigenes were annotated as ManS (mannosyltransferase/mannan synthase) and UGE (UDP- D-glucose 4-epimerase) and validated as targets for three novel miRNAs, that is Ct-miR3130, Ct-miR3135 and Ct-miR3157. Our findings reveal that these novel miRNAs could play an important role in the regulation of the galactomannan pathway in C. tetragonoloba and possibly other galactomannan-producing species.
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Affiliation(s)
- Anshika Tyagi
- ICAR‐National Research Centre on Plant BiotechnologyNew DelhiIndia
| | - Deepti Nigam
- ICAR‐National Research Centre on Plant BiotechnologyNew DelhiIndia
| | | | | | | | - Tilak R. Sharma
- ICAR‐National Research Centre on Plant BiotechnologyNew DelhiIndia
- Present address:
National Agri‐Food Biotechnology InstituteMohaliIndia
| | - Kishor Gaikwad
- ICAR‐National Research Centre on Plant BiotechnologyNew DelhiIndia
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93
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Seyfferth C, Wessels B, Jokipii-Lukkari S, Sundberg B, Delhomme N, Felten J, Tuominen H. Ethylene-Related Gene Expression Networks in Wood Formation. FRONTIERS IN PLANT SCIENCE 2018; 9:272. [PMID: 29593753 PMCID: PMC5861219 DOI: 10.3389/fpls.2018.00272] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/16/2018] [Indexed: 05/27/2023]
Abstract
Thickening of tree stems is the result of secondary growth, accomplished by the meristematic activity of the vascular cambium. Secondary growth of the stem entails developmental cascades resulting in the formation of secondary phloem outwards and secondary xylem (i.e., wood) inwards of the stem. Signaling and transcriptional reprogramming by the phytohormone ethylene modifies cambial growth and cell differentiation, but the molecular link between ethylene and secondary growth remains unknown. We addressed this shortcoming by analyzing expression profiles and co-expression networks of ethylene pathway genes using the AspWood transcriptome database which covers all stages of secondary growth in aspen (Populus tremula) stems. ACC synthase expression suggests that the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) is synthesized during xylem expansion and xylem cell maturation. Ethylene-mediated transcriptional reprogramming occurs during all stages of secondary growth, as deduced from AspWood expression profiles of ethylene-responsive genes. A network centrality analysis of the AspWood dataset identified EIN3D and 11 ERFs as hubs. No overlap was found between the co-expressed genes of the EIN3 and ERF hubs, suggesting target diversification and hence independent roles for these transcription factor families during normal wood formation. The EIN3D hub was part of a large co-expression gene module, which contained 16 transcription factors, among them several new candidates that have not been earlier connected to wood formation and a VND-INTERACTING 2 (VNI2) homolog. We experimentally demonstrated Populus EIN3D function in ethylene signaling in Arabidopsis thaliana. The ERF hubs ERF118 and ERF119 were connected on the basis of their expression pattern and gene co-expression module composition to xylem cell expansion and secondary cell wall formation, respectively. We hereby establish data resources for ethylene-responsive genes and potential targets for EIN3D and ERF transcription factors in Populus stem tissues, which can help to understand the range of ethylene targeted biological processes during secondary growth.
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Affiliation(s)
- Carolin Seyfferth
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Bernard Wessels
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Soile Jokipii-Lukkari
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Björn Sundberg
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Nicolas Delhomme
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Judith Felten
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Hannele Tuominen
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
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94
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QTL delineation for five fiber quality traits based on an intra-specific Gossypium hirsutum L. recombinant inbred line population. Mol Genet Genomics 2018; 293:831-843. [PMID: 29423657 DOI: 10.1007/s00438-018-1424-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 02/03/2018] [Indexed: 12/20/2022]
Abstract
Gossypium hirsutum L. is the most important fiber crop worldwide and contributes to more than 95% of global cotton production. Marker-assisted selection (MAS) is an effective approach for improving fiber quality, and quantitative trait loci (QTL) mapping of fiber quality traits is important for cotton breeding. In this study, a permanent intra-specific recombinant inbred line (RIL) population containing 137 families was used for fiber quality testing. Based on a previously reported high-density genetic map with an average marker distance of 0.63 cM, 186 additive QTLs were obtained for five fiber quality traits over five consecutive years, including 39 for fiber length (FL), 36 for fiber strength (FS), 50 for fiber uniformity (FU), 33 for micronaire (MC) and 28 for fiber elongation (FE). Three stable QTLs, qMC-A4-1, qMC-D2-3 and qFS-D9-1, were detected in four datasets, and another eight stable QTLs, qMC-A4-2, qMC-D11-2, qFU-A9-1, qFU-A10-4, qFS-D11-1, qFL-D9-2, qFL-D11-1 and qFE-A3-2, were detected in three datasets. The annotated genes in these 11 stable QTLs were collected, and these genes included many transcription factors with functions during fiber development. 33 QTL coincidence regions were found, and these involved nearly half of the total QTLs. Four chromosome regions containing at least 6 QTLs were promising for fine mapping. In addition, 41 pairs of epistatic QTLs (e-QTLs) were screened, including 6 for FL, 30 for FS, 2 for FU and 3 for MC. The identification of stable QTLs adds valuable information for further QTL fine mapping and gene positional cloning for fiber quality genetic detection and provides useful markers for further molecular breeding in enhancing fiber quality.
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95
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Liu C, Ha CM, Dixon RA. Functional Genomics in the Study of Metabolic Pathways in Medicago truncatula: An Overview. Methods Mol Biol 2018; 1822:315-337. [PMID: 30043312 DOI: 10.1007/978-1-4939-8633-0_20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In addition to its value as a model system for studies on symbiotic nitrogen fixation, Medicago truncatula has recently become an organism of choice for dissection of complex pathways of secondary metabolism. This work has been driven by two main reasons, both with practical implications. First Medicago species possess a wide range of flavonoid and terpenoid natural products, many of which, for example, the isoflavonoids and triterpene saponins, have important biological activities impacting both plant and animal (including human) health. Second, M. truncatula serves as an excellent model for alfalfa, the world's major forage legume, and forage quality is determined in large part by the concentrations of products of secondary metabolism, particularly lignin and condensed tannins. We here review recent progress in understanding the pathways leading to flavonoids, lignin, and triterpene saponins through utilization of genetic resources in M. truncatula.
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Affiliation(s)
- Chenggang Liu
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, USA
| | - Chan Man Ha
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, USA
| | - Richard A Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, USA.
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96
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Zhang J, Xie M, Tuskan GA, Muchero W, Chen JG. Recent Advances in the Transcriptional Regulation of Secondary Cell Wall Biosynthesis in the Woody Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:1535. [PMID: 30405670 PMCID: PMC6206300 DOI: 10.3389/fpls.2018.01535] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/28/2018] [Indexed: 05/19/2023]
Abstract
Plant cell walls provide structural support for growth and serve as a barrier for pathogen attack. Plant cell walls are also a source of renewable biomass for conversion to biofuels and bioproducts. Understanding plant cell wall biosynthesis and its regulation is of critical importance for the genetic modification of plant feedstocks for cost-effective biofuels and bioproducts conversion and production. Great progress has been made in identifying enzymes involved in plant cell wall biosynthesis, and in Arabidopsis it is generally recognized that the regulation of genes encoding these enzymes is under a transcriptional regulatory network with coherent feedforward and feedback loops. However, less is known about the transcriptional regulation of plant secondary cell wall (SCW) biosynthesis in woody species despite of its high relevance to biofuels and bioproducts conversion and production. In this article, we synthesize recent progress on the transcriptional regulation of SCW biosynthesis in Arabidopsis and contrast to what is known in woody species. Furthermore, we evaluate progress in related emerging regulatory machineries targeting transcription factors in this complex regulatory network of SCW biosynthesis.
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Affiliation(s)
- Jin Zhang
- 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
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Plant Sciences, University of Tennessee, Knoxville, 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
- *Correspondence: Wellington Muchero, Jin-Gui Chen,
| | - 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
- *Correspondence: Wellington Muchero, Jin-Gui Chen,
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Camel Paucar V, Galeano E, Carrer H. Análisis in silico y expresión génica del factor de transcripción TgNAC01 implicado en xilogénesis y estrés abiótico en Tectona grandis. ACTA BIOLÓGICA COLOMBIANA 2017. [DOI: 10.15446/abc.v22n3.62164] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
El xilema secundario es el componente más abundante de la biomasa vegetal. Por tanto, conocer los genes que regulan su formación ayudaría a diseñar estrategias para el mejoramiento genético de la madera. Así, el objetivo de este trabajo fue realizar el análisis computacional de la estructura primaria y secundaria del factor de transcripción (FT) TgNAC01 de Tectona grandis, además de evaluar su historia evolutiva, dominios conservados y expresión génica en tejidos lignificados de árboles de 12 y 60 años. Para ello, se realizó una evaluación del potencial de interacción ion-electrón (PIIE), mediante el método del espectro de la información (MEI) utilizando la librería SFAPS de R-Project, seguido del modelamiento estructural utilizando el software MODELLER y visualizado mediante PyMol. Además, el análisis de alineamiento de secuencia múltiple y filogenia fue mediante el software Bioedit y MrBayes respectivamente. También se evaluó los niveles de síntesis del FT TgNAC01 mediante qRT-PCR. Como resultados, se evidencio que el FT mantiene una estructura β-hoja antiparalela retorcida, que se compacta contra una α-hélice en la región N-terminal, teniendo así tres dominios α hélice y siete dominios β plegada. Asimismo, mediante el MEI se demostró que tiene alrededor de cinco funciones biológicas y mutaciones sobre los aminoácidos con mayor PIIE, lo que conlleva a evoluciones sobre las redes de regulación genética. Finalmente, el FT TgNAC01 juega un papel fundamental en la organización y desarrollo de las partes que componen la albura, como las células radiales de la zona cambial, los vasos, fibras y los anillos de crecimiento.
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MacMillan CP, Birke H, Chuah A, Brill E, Tsuji Y, Ralph J, Dennis ES, Llewellyn D, Pettolino FA. Tissue and cell-specific transcriptomes in cotton reveal the subtleties of gene regulation underlying the diversity of plant secondary cell walls. BMC Genomics 2017; 18:539. [PMID: 28720072 PMCID: PMC5516393 DOI: 10.1186/s12864-017-3902-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 06/22/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Knowledge of plant secondary cell wall (SCW) regulation and deposition is mainly based on the Arabidopsis model of a 'typical' lignocellulosic SCW. However, SCWs in other plants can vary from this. The SCW of mature cotton seed fibres is highly cellulosic and lacks lignification whereas xylem SCWs are lignocellulosic. We used cotton as a model to study different SCWs and the expression of the genes involved in their formation via RNA deep sequencing and chemical analysis of stem and seed fibre. RESULTS Transcriptome comparisons from cotton xylem and pith as well as from a developmental series of seed fibres revealed tissue-specific and developmentally regulated expression of several NAC transcription factors some of which are likely to be important as top tier regulators of SCW formation in xylem and/or seed fibre. A so far undescribed hierarchy was identified between the top tier NAC transcription factors SND1-like and NST1/2 in cotton. Key SCW MYB transcription factors, homologs of Arabidopsis MYB46/83, were practically absent in cotton stem xylem. Lack of expression of other lignin-specific MYBs in seed fibre relative to xylem could account for the lack of lignin deposition in seed fibre. Expression of a MYB103 homolog correlated with temporal expression of SCW CesAs and cellulose synthesis in seed fibres. FLAs were highly expressed and may be important structural components of seed fibre SCWs. Finally, we made the unexpected observation that cell walls in the pith of cotton stems contained lignin and had a higher S:G ratio than in xylem, despite that tissue's lacking many of the gene transcripts normally associated with lignin biosynthesis. CONCLUSIONS Our study in cotton confirmed some features of the currently accepted gene regulatory cascade for 'typical' plant SCWs, but also revealed substantial differences, especially with key downstream NACs and MYBs. The lignocellulosic SCW of cotton xylem appears to be achieved differently from that in Arabidopsis. Pith cell walls in cotton stems are compositionally very different from that reported for other plant species, including Arabidopsis. The current definition of a 'typical' primary or secondary cell wall might not be applicable to all cell types in all plant species.
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Affiliation(s)
| | - Hannah Birke
- CSIRO Agriculture and Food, PO Box 1700, Canberra, ACT, 2601, Australia.,Present address: Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Aaron Chuah
- John Curtin School of Medical Research, The Australian National University, ACT, Canberra, 2601, Australia
| | - Elizabeth Brill
- CSIRO Agriculture and Food, PO Box 1700, Canberra, ACT, 2601, Australia
| | - Yukiko Tsuji
- Department of Biochemistry and the Department of Energy's Great Lakes BioEnergy Research Center, The Wisconsin Energy Institute, 1552 University Avenue, Madison, WI, 53726-4084, USA
| | - John Ralph
- Department of Biochemistry and the Department of Energy's Great Lakes BioEnergy Research Center, The Wisconsin Energy Institute, 1552 University Avenue, Madison, WI, 53726-4084, USA
| | | | - Danny Llewellyn
- CSIRO Agriculture and Food, PO Box 1700, Canberra, ACT, 2601, Australia
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de Luis Balaguer MA, Sozzani R. Inferring Gene Regulatory Networks in the Arabidopsis Root Using a Dynamic Bayesian Network Approach. Methods Mol Biol 2017. [PMID: 28623595 DOI: 10.1007/978-1-4939-7125-1_21] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Gene regulatory network (GRN) models have been shown to predict and represent interactions among sets of genes. Here, we first show the basic steps to implement a simple but computationally efficient algorithm to infer GRNs based on dynamic Bayesian networks (DBNs), and we then explain how to approximate DBN-based GRN models with continuous models. In addition, we show a MATLAB implementation of the key steps of this method, which we use to infer an Arabidopsis root GRN.
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Affiliation(s)
- Maria Angels de Luis Balaguer
- Department of Plant and Microbial Biology, North Carolina State University, 2552A Thomas Hall, Raleigh, NC, 27695, USA
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, 2552A Thomas Hall, Raleigh, NC, 27695, USA.
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Kwenda S, Motlolometsi TV, Birch PRJ, Moleleki LN. RNA-seq Profiling Reveals Defense Responses in a Tolerant Potato Cultivar to Stem Infection by Pectobacterium carotovorum ssp. brasiliense. FRONTIERS IN PLANT SCIENCE 2016; 7:1905. [PMID: 28066465 PMCID: PMC5167753 DOI: 10.3389/fpls.2016.01905] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 12/01/2016] [Indexed: 05/28/2023]
Abstract
Pectobacterium carotovorum subsp. brasiliense is a member of the soft rot Enterobacteriaceae (SRE) family that causes tuber soft rot and blackleg diseases of stems in potato plants. Currently, there are no effective chemical strategies for the control of members of the SRE. Thus, an understanding of the inducible defense responses in stems of potato plants is important, particularly during colonization of the vascular system. Here, time-course RNA-sequencing analysis was used to compare expressed genes between a susceptible potato cultivar (Solanum tuberosum cv Valor) and a tolerant cultivar (S. tuberosum cv BP1) at 0, 6, 12, 24, and 72 h post-inoculation with P. c. brasiliense. In total, we identified 6139 and 8214 differentially expressed genes (DEGs) in the tolerant and susceptible cultivars, compared to mock-inoculated controls, respectively. Key DEGs distinguishing between tolerance and susceptibility were associated with negative regulation of cell death and plant-type cell wall organization/biogenesis biological processes in the tolerant and susceptible cultivars, respectively. Among these were DEGs involved in signaling (mainly MAPK cascade and ethylene pathway), defense-related transcription regulation including WRKY transcription factors, and downstream secondary cell biosynthesis. Together, our results suggest that S. tuberosum cv BP1 likely employs quantitative defense response against P. c. brasiliense. Overall, our study provides the first transcriptome-wide insight into the molecular basis of tolerance and/or resistance of potato stems to SRE infection.
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Affiliation(s)
- Stanford Kwenda
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Tshepiso V. Motlolometsi
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Paul R. J. Birch
- Division of Plant Sciences, James Hutton Institute, College of Life Sciences, University of DundeeDundee, UK
| | - Lucy N. Moleleki
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
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