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Shu M, Yates TB, John C, Harman-Ware AE, Happs RM, Bryant N, Jawdy SS, Ragauskas AJ, Tuskan GA, Muchero W, Chen JG. Providing biological context for GWAS results using eQTL regulatory and co-expression networks in Populus. THE NEW PHYTOLOGIST 2024; 244:603-617. [PMID: 39169686 DOI: 10.1111/nph.20026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 07/16/2024] [Indexed: 08/23/2024]
Abstract
Our study utilized genome-wide association studies (GWAS) to link nucleotide variants to traits in Populus trichocarpa, a species with rapid linkage disequilibrium decay. The aim was to overcome the challenge of interpreting statistical associations at individual loci without sufficient biological context, which often leads to reliance solely on gene annotations from unrelated model organisms. We employed an integrative approach that included GWAS targeting multiple traits using three individual techniques for lignocellulose phenotyping, expression quantitative trait loci (eQTL) analysis to construct transcriptional regulatory networks around each candidate locus and co-expression analysis to provide biological context for these networks, using lignocellulose biosynthesis in Populus trichocarpa as a case study. The research identified three candidate genes potentially involved in lignocellulose formation, including one previously recognized gene (Potri.005G116800/VND1, a critical regulator of secondary cell wall formation) and two genes (Potri.012G130000/AtSAP9 and Potri.004G202900/BIC1) with newly identified putative roles in lignocellulose biosynthesis. Our integrative approach offers a framework for providing biological context to loci associated with trait variation, facilitating the discovery of new genes and regulatory networks.
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Affiliation(s)
- Mengjun Shu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831, TN, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, 37831, TN, USA
| | - Timothy B Yates
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831, TN, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, 37831, TN, USA
| | - Cai John
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831, TN, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, 37831, TN, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, 37996, TN, USA
| | - Anne E Harman-Ware
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, 80401, CO, USA
| | - Renee M Happs
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, 80401, CO, USA
| | - Nathan Bryant
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, 37996, TN, USA
| | - Sara S Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831, TN, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, 37831, TN, USA
| | - Arthur J Ragauskas
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831, TN, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, 37831, TN, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, 37996, TN, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831, TN, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, 37831, TN, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831, TN, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, 37831, TN, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831, TN, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, 37831, TN, USA
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2
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Gushino S, Tsai AYL, Otani M, Demura T, Sawa S. VND Genes Redundantly Regulate Cell Wall Thickening during Parasitic Nematode Infection. PLANT & CELL PHYSIOLOGY 2024; 65:1224-1230. [PMID: 38662403 DOI: 10.1093/pcp/pcae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/22/2024] [Accepted: 04/25/2024] [Indexed: 04/26/2024]
Abstract
Plant parasitic root-knot nematodes are major agricultural pests worldwide, as they infect plant roots and cause substantial damages to crop plants. Root-knot nematodes induce specialized feeding cells known as giant cells (GCs) in the root vasculature, which serve as nutrient reservoirs for the infecting nematodes. Here, we show that the cell walls of GCs thicken to form pitted patterns that superficially resemble metaxylem cells. Interestingly, VASCULAR-RELATED NAC-DOMAIN1 (VND1) was found to be upregulated, while the xylem-type programmed cell death marker XYLEM CYSTEINE PEPTIDASE 1 was downregulated upon nematode infection. The vnd2 and vnd3 mutants showed reduced secondary cell wall pore size, while the vnd1 vnd2 vnd3 triple mutant produced significantly fewer nematode egg masses when compared with the wild type. These results suggest that the GC development pathway likely shares common signaling modules with the metaxylem differentiation pathway and VND1, VND2, and VND3 redundantly regulate plant-nematode interaction through secondary cell wall formation.
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Affiliation(s)
- Saki Gushino
- Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto, 860-8555 Japan
| | - Allen Yi-Lun Tsai
- Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto, 860-8555 Japan
- International Research Center for Agricultural and Environmental Biology (IRCAEB), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555 Japan
| | - Misato Otani
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha, 5-1-5, Kashiwa, 277-8562 Japan
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0192 Japan
| | - Taku Demura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara, 630-0192 Japan
| | - Shinichiro Sawa
- Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto, 860-8555 Japan
- International Research Center for Agricultural and Environmental Biology (IRCAEB), Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555 Japan
- International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, 2-39-1 Kurokami, Chuo-ku,Kumamoto, 860-8555 Japan
- Institute of Industrial Nanomaterials, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555 Japan
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3
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Li Q, Zhang H, Yang Y, Tang K, Yang Y, Ouyang W, Du G. Genome-Wide Identification of NAC Family Genes and Their Expression Analyses in Response to Osmotic Stress in Cannabis sativa L. Int J Mol Sci 2024; 25:9466. [PMID: 39273412 PMCID: PMC11394811 DOI: 10.3390/ijms25179466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 08/25/2024] [Accepted: 08/28/2024] [Indexed: 09/15/2024] Open
Abstract
NAC (NAM, ATAF1/2, and CUC2) transcription factors are unique and essential for plant growth and development. Although the NAC gene family has been identified in a wide variety of plants, its chromosomal location and function in Cannabis sativa are still unknown. In this study, a total of 69 putative CsNACs were obtained, and chromosomal location analysis indicated that the CsNAC genes mapped unevenly to 10 chromosomes. Phylogenetic analyses showed that the 69 CsNACs could be divided into six subfamilies. Additionally, the CsNAC genes in group IV-a are specific to Cannabis sativa and contain a relatively large number of exons. Promoter analysis revealed that most CsNAC promoters contained cis-elements related to plant hormones, the light response, and abiotic stress. Furthermore, transcriptome expression profiling revealed that 24 CsNAC genes in two Cannabis sativa cultivars (YM1 and YM7) were significantly differentially expressed under osmotic stress, and these 12 genes presented differential expression patterns across different cultivars according to quantitative real-time PCR (RT-qPCR) analysis. Among these, the genes homologous to the CsNAC18, CsNAC24, and CsNAC61 genes have been proven to be involved in the response to abiotic stress and might be candidate genes for further exploration to determine their functions. The present study provides a comprehensive insight into the sequence characteristics, structural properties, evolutionary relationships, and expression patterns of NAC family genes under osmotic stress in Cannabis sativa and provides a basis for further functional characterization of CsNAC genes under osmotic stress to improve agricultural traits in Cannabis sativa.
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Affiliation(s)
- Qi Li
- School of Agriculture, Yunnan University, Kunming 650500, China
| | - Hanxue Zhang
- School of Agriculture, Yunnan University, Kunming 650500, China
| | - Yulei Yang
- School of Agriculture, Yunnan University, Kunming 650500, China
| | - Kailei Tang
- School of Agriculture, Yunnan University, Kunming 650500, China
| | - Yang Yang
- School of Agriculture, Yunnan University, Kunming 650500, China
| | - Wenjing Ouyang
- School of Agriculture, Yunnan University, Kunming 650500, China
| | - Guanghui Du
- School of Agriculture, Yunnan University, Kunming 650500, China
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4
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Xue JS, Feng YF, Zhang MQ, Xu QL, Xu YM, Shi JQ, Liu LF, Wu XF, Wang S, Yang ZN. The regulatory mechanism of rapid lignification for timely anther dehiscence. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1788-1800. [PMID: 38888227 DOI: 10.1111/jipb.13715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 05/16/2024] [Indexed: 06/20/2024]
Abstract
Anther dehiscence is a crucial event in plant reproduction, tightly regulated and dependent on the lignification of the anther endothecium. In this study, we investigated the rapid lignification process that ensures timely anther dehiscence in Arabidopsis. Our findings reveal that endothecium lignification can be divided into two distinct phases. During Phase I, lignin precursors are synthesized without polymerization, while Phase II involves simultaneous synthesis of lignin precursors and polymerization. The transcription factors MYB26, NST1/2, and ARF17 specifically regulate the pathway responsible for the synthesis and polymerization of lignin monomers in Phase II. MYB26-NST1/2 is the key regulatory pathway responsible for endothecium lignification, while ARF17 facilitates this process by interacting with MYB26. Interestingly, our results demonstrate that the lignification of the endothecium, which occurs within approximately 26 h, is much faster than that of the vascular tissue. These findings provide valuable insights into the regulation mechanism of rapid lignification in the endothecium, which enables timely anther dehiscence and successful pollen release during plant reproduction.
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Affiliation(s)
- Jing-Shi Xue
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yi-Feng Feng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Ming-Qi Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Qin-Lin Xu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Ya-Min Xu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jun-Qin Shi
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Li-Fang Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xiao-Feng Wu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Shui Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zhong-Nan Yang
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
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5
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Ohashi-Ito K, Iwamoto K, Fukuda H. LONESOME HIGHWAY-TARGET OF MONOPTEROS5 transcription factor complex promotes a predifferentiation state for xylem vessel differentiation in the root apical meristem by inducing the expression of VASCULAR-RELATED NAC-DOMAIN genes. THE NEW PHYTOLOGIST 2024; 242:1146-1155. [PMID: 38462819 DOI: 10.1111/nph.19670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/24/2024] [Indexed: 03/12/2024]
Abstract
In Arabidopsis thaliana, heterodimers comprising two bHLH family proteins, LONESOME HIGHWAY (LHW) and TARGET OF MONOPTEROS5 (TMO5) or its homolog TMO5-LIKE 1 (T5L1) control vascular development in the root apical meristem (RAM). The LHW-TMO5/T5L1 complex regulates vascular cell proliferation, vascular pattern organization, and xylem vessel differentiation; however, the mechanism of preparation for xylem vessel differentiation in the RAM remains elusive. We examined the relationship between LHW-T5L1 and VASCULAR-RELATED NAC-DOMAIN (VND) genes, which are key regulators of vessel differentiation, using reverse genetics approaches. LHW-T5L1 upregulated the expression of VND1, VND2, VND3, VND6, and VND7 but not that of other VNDs. The expression of VND1-VND3 in the RAM was decreased in lhw. In vnd1 vnd2 vnd3 triple loss-of-function mutant roots, metaxylem differentiation was delayed, and VND6 and VND7 expression was reduced. Furthermore, transcriptome analysis of VND1-overexpressing cells revealed that VND1 upregulates genes involved in the synthesis of secondary cell wall components. These results suggest that LHW-T5L1 upregulates VND1-VND3 at the early stages of vascular development in the RAM, and VNDs promote a predifferentiation state for xylem vessels by triggering low levels of VND6 and VND7 as well as genes for the synthesis of secondary cell wall materials.
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Affiliation(s)
- Kyoko Ohashi-Ito
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Kuninori Iwamoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiroo Fukuda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
- Akita Prefectural University, Akita, 010-0195, Japan
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6
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Li J, Ren J, Lei X, Fan W, Tang L, Zhang Q, Bao Z, Zhou W, Bai J, Zhang Y, Gong C. CsREV-CsTCP4-CsVND7 module shapes xylem patterns differentially between stem and leaf to enhance tea plant tolerance to drought. Cell Rep 2024; 43:113987. [PMID: 38517888 DOI: 10.1016/j.celrep.2024.113987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/22/2024] [Accepted: 03/07/2024] [Indexed: 03/24/2024] Open
Abstract
Cultivating drought-tolerant tea varieties enhances both yield and quality of tea plants in northern China. However, the mechanisms underlying their drought tolerance remain largely unknown. Here we identified a key regulator called CsREV, which differentially regulates xylem patterns between leaves and stems, thereby conferring drought tolerance in tea plants. When drought occurs, upregulation of CsREV activates the CsVND7a-dependent xylem vessel differentiation. However, when drought persists, the vessel differentiation is hindered as CsVND7a is downregulated by CsTCP4a. This, combined with the CsREV-promoted secondary-cell-wall thickness of xylem vessel, leads to the enhanced curling of leaves, a characteristic closely associated with plant drought tolerance. Notably, this inhibitory effect of CsTCP4a on CsVND7a expression is absent in stems, allowing stem xylem vessels to continuously differentiate. Overall, the CsREV-CsTCP4-CsVND7 module is differentially utilized to shape the xylem patterns in leaves and stems, potentially balancing water transportation and utilization to improve tea plant drought tolerance.
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Affiliation(s)
- Jiayang Li
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiejie Ren
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xingyu Lei
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wenmin Fan
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lei Tang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qiqi Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhulatai Bao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wenfei Zhou
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Juan Bai
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuzhou Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chunmei Gong
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China.
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7
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Zhu Y, Guo J, Wu F, Yu H, Min J, Zhao Y, Tan C, Liu Y, Xu C. Exogenous Melatonin Application Accelerated the Healing Process of Oriental Melon Grafted onto Squash by Promoting Lignin Accumulation. Int J Mol Sci 2024; 25:3690. [PMID: 38612499 PMCID: PMC11011509 DOI: 10.3390/ijms25073690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/24/2024] [Accepted: 03/24/2024] [Indexed: 04/14/2024] Open
Abstract
Melatonin (MT) is a vital hormone factor in plant growth and development, yet its potential to influence the graft union healing process has not been reported. In this study, we examined the effects of MT on the healing of oriental melon scion grafted onto squash rootstock. The studies indicate that the exogenous MT treatment promotes the lignin content of oriental melon and squash stems by increasing the enzyme activities of hydroxycinnamoyl CoA ligase (HCT), hydroxy cinnamaldehyde dehydrogenase (HCALDH), caffeic acid/5-hydroxy-conifer aldehyde O-methyltransferase (COMT), caffeoyl-CoA O-methyltransferase (CCoAOMT), phenylalanine ammonia-lyase (PAL), 4-hydroxycinnamate CoA ligase (4CL), and cinnamyl alcohol dehydrogenase (CAD). Using the oriental melon and squash treated with the exogenous MT to graft, the connection of oriental melon scion and squash rootstock was more efficient and faster due to higher expression of wound-induced dedifferentiation 1 (WIND1), cyclin-dependent kinase (CDKB1;2), target of monopteros 6 (TMO6), and vascular-related NAC-domain 7 (VND7). Further research found that the exogenous MT increased the lignin content of the oriental melon scion stem by regulating CmCAD1 expression, and then accelerated the graft healing process. In addition, the root growth of grafted seedlings treated with the exogenous MT was more vigorous.
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Affiliation(s)
- Yulei Zhu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (J.G.); (F.W.); (H.Y.); (J.M.); (Y.Z.); (C.T.)
- Key Laboratory of Protected Horticulture (Ministry of Education), Shenyang Agricultural University, Shenyang 110866, China
- Modern Protected Horticultural Engineering & Technology Center, Shenyang Agricultural University, Shenyang 110866, China
| | - Jieying Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (J.G.); (F.W.); (H.Y.); (J.M.); (Y.Z.); (C.T.)
- Key Laboratory of Protected Horticulture (Ministry of Education), Shenyang Agricultural University, Shenyang 110866, China
- Modern Protected Horticultural Engineering & Technology Center, Shenyang Agricultural University, Shenyang 110866, China
| | - Fang Wu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (J.G.); (F.W.); (H.Y.); (J.M.); (Y.Z.); (C.T.)
- Key Laboratory of Protected Horticulture (Ministry of Education), Shenyang Agricultural University, Shenyang 110866, China
- Modern Protected Horticultural Engineering & Technology Center, Shenyang Agricultural University, Shenyang 110866, China
| | - Hanqi Yu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (J.G.); (F.W.); (H.Y.); (J.M.); (Y.Z.); (C.T.)
- Key Laboratory of Protected Horticulture (Ministry of Education), Shenyang Agricultural University, Shenyang 110866, China
- Modern Protected Horticultural Engineering & Technology Center, Shenyang Agricultural University, Shenyang 110866, China
| | - Jiahuan Min
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (J.G.); (F.W.); (H.Y.); (J.M.); (Y.Z.); (C.T.)
- Key Laboratory of Protected Horticulture (Ministry of Education), Shenyang Agricultural University, Shenyang 110866, China
- Modern Protected Horticultural Engineering & Technology Center, Shenyang Agricultural University, Shenyang 110866, China
| | - Yingtong Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (J.G.); (F.W.); (H.Y.); (J.M.); (Y.Z.); (C.T.)
- Key Laboratory of Protected Horticulture (Ministry of Education), Shenyang Agricultural University, Shenyang 110866, China
- Modern Protected Horticultural Engineering & Technology Center, Shenyang Agricultural University, Shenyang 110866, China
| | - Changhua Tan
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (J.G.); (F.W.); (H.Y.); (J.M.); (Y.Z.); (C.T.)
- Key Laboratory of Protected Horticulture (Ministry of Education), Shenyang Agricultural University, Shenyang 110866, China
- Modern Protected Horticultural Engineering & Technology Center, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Horticultural Equipment (Ministry of Agriculture and Rural Affairs), Shenyang Agricultural University, Shenyang 110866, China
| | - Yuanwei Liu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China;
| | - Chuanqiang Xu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (J.G.); (F.W.); (H.Y.); (J.M.); (Y.Z.); (C.T.)
- Key Laboratory of Protected Horticulture (Ministry of Education), Shenyang Agricultural University, Shenyang 110866, China
- Modern Protected Horticultural Engineering & Technology Center, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Horticultural Equipment (Ministry of Agriculture and Rural Affairs), Shenyang Agricultural University, Shenyang 110866, China
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8
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Han K, Zhao Y, Sun Y, Li Y. NACs, generalist in plant life. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2433-2457. [PMID: 37623750 PMCID: PMC10651149 DOI: 10.1111/pbi.14161] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023]
Abstract
Plant-specific NAC proteins constitute a major transcription factor family that is well-known for its roles in plant growth, development, and responses to abiotic and biotic stresses. In recent years, there has been significant progress in understanding the functions of NAC proteins. NAC proteins have a highly conserved DNA-binding domain; however, their functions are diverse. Previous understanding of the structure of NAC transcription factors can be used as the basis for their functional diversity. NAC transcription factors consist of a target-binding domain at the N-terminus and a highly versatile C-terminal domain that interacts with other proteins. A growing body of research on NAC transcription factors helps us comprehend the intricate signalling network and transcriptional reprogramming facilitated by NAC-mediated complexes. However, most studies of NAC proteins have been limited to a single function. Here, we discuss the upstream regulators, regulatory components and targets of NAC in the context of their prospective roles in plant improvement strategies via biotechnology intervention, highlighting the importance of the NAC transcription factor family in plants and the need for further research.
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Affiliation(s)
- Kunjin Han
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Ye Zhao
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yuhan Sun
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yun Li
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
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9
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Sun Y, Yang B, De Rybel B. Hormonal control of the molecular networks guiding vascular tissue development in the primary root meristem of Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6964-6974. [PMID: 37343122 PMCID: PMC7615341 DOI: 10.1093/jxb/erad232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]
Abstract
Vascular tissues serve a dual function in plants, both providing physical support and controlling the transport of nutrients, water, hormones, and other small signaling molecules. Xylem tissues transport water from root to shoot; phloem tissues transfer photosynthates from shoot to root; while divisions of the (pro)cambium increase the number of xylem and phloem cells. Although vascular development constitutes a continuous process from primary growth in the early embryo and meristem regions to secondary growth in the mature plant organs, it can be artificially separated into distinct processes including cell type specification, proliferation, patterning, and differentiation. In this review, we focus on how hormonal signals orchestrate the molecular regulation of vascular development in the Arabidopsis primary root meristem. Although auxin and cytokinin have taken center stage in this aspect since their discovery, other hormones including brassinosteroids, abscisic acid, and jasmonic acid also take leading roles during vascular development. All these hormonal cues synergistically or antagonistically participate in the development of vascular tissues, forming a complex hormonal control network.
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Affiliation(s)
- Yanbiao Sun
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Centre for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Baojun Yang
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Centre for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Bert De Rybel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Centre for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
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10
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Zhang Y, Qu X, Li X, Ren M, Tong Y, Wu X, Sun Y, Wu F, Yang A, Chen S. Comprehensive transcriptome and WGCNA analysis reveals the potential function of anthocyanins in low-temperature resistance of a red flower mutant tobacco. Genomics 2023; 115:110728. [PMID: 37858843 DOI: 10.1016/j.ygeno.2023.110728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/21/2023]
Abstract
The anthocyanin is a protective substance in various plants, and plays important roles in resisting to low-temperature. Here, we explored transcriptome analysis of pink flower (as CK) and the natural mutant red flower (as research objects) under low-temperature conditions, and aimed to reveal the potential functions of anthocyanins and anthocyanin-related regulatory factors in resistance to low-temperature. Our results showed that most of the differentially expressed genes (DEGs) encoding key enzymes in the late stage of anthocyanin metabolism in the mutant were significantly up-regulated. Meanwhile, several genes significantly differentially expressed in CK or mutant were obtained by classification and analysis of transcription factors (TFs), phytohormones and osmoregulators. Additionally, WGCNA was carried out to mine hub genes resistanted to low-temperature stress in flavonoid pathway. Finally, one UFGT family gene, three MYB and one bHLH were obtained as the future hub genes of this study. Combined with the above information, we concluded that the ability of the red flower mutant to grow and develop normally at low-temperatures was the result of a combination of flavonoids and cold resistance genes.
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Affiliation(s)
- Yinchao Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Xiaoling Qu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Xiuchun Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Min Ren
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Ying Tong
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Xiuming Wu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Yangyang Sun
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Fengyan Wu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Aiguo Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
| | - Shuai Chen
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China.
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11
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Yu A, Zou H, Li P, Yao X, Zhou Z, Gu X, Sun R, Liu A. Genomic characterization of the NAC transcription factors, directed at understanding their functions involved in endocarp lignification of iron walnut ( Juglans sigillata Dode). Front Genet 2023; 14:1168142. [PMID: 37229193 PMCID: PMC10203416 DOI: 10.3389/fgene.2023.1168142] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/17/2023] [Indexed: 05/27/2023] Open
Abstract
The NAC (NAM, ATAF1/2, and CUC2) transcription factors (TF), one of the largest plant-specific gene families, play important roles in the regulation of plant growth and development, stress response and disease resistance. In particular, several NAC TFs have been identified as master regulators of secondary cell wall (SCW) biosynthesis. Iron walnut (Juglans sigillata Dode), an economically important nut and oilseed tree, has been widely planted in the southwest China. The thick and high lignified shell derived endocarp tissues, however, brings troubles in processing processes of products in industry. It is indispensable to dissect the molecular mechanism of thick endocarp formation for further genetic improvement of iron walnut. In the present study, based on genome reference of iron walnut, 117 NAC genes, in total, were identified and characterized in silico, which involves only computational analysis to provide insight into gene function and regulation. We found that the amino acids encoded by these NAC genes varied from 103 to 1,264 in length, and conserved motif numbers ranged from 2 to 10. The JsiNAC genes were unevenly distributed across the genome of 16 chromosomes, and 96 of these genes were identified as segmental duplication genes. Furthermore, 117 JsiNAC genes were divided into 14 subfamilies (A-N) according to the phylogenetic tree based on NAC family members of Arabidopsis thaliana and common walnut (Juglans regia). Furthermore, tissue-specific expression pattern analysis demonstrated that a majority of NAC genes were constitutively expressed in five different tissues (bud, root, fruit, endocarp, and stem xylem), while a total of 19 genes were specifically expressed in endocarp, and most of them also showed high and specific expression levels in the middle and late stages during iron walnut endocarp development. Our result provided a new insight into the gene structure and function of JsiNACs in iron walnut, and identified key candidate JsiNAC genes involved in endocarp development, probably providing mechanistic insight into shell thickness formation across nut species.
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12
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Zhang B, Dang X, Chen H, Li T, Zhu F, Nagawa S. Ectopic Expression of FvVND4c Promotes Secondary Cell Wall Thickening and Flavonoid Accumulation in Fragaria vesca. Int J Mol Sci 2023; 24:ijms24098110. [PMID: 37175817 PMCID: PMC10179399 DOI: 10.3390/ijms24098110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 04/23/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Secondary cell wall (SCW) thickening has a significant effect on the growth and development of plants, as well as in the resistance to various biotic and abiotic stresses. Lignin accounts for the strength of SCW. It is synthesized through the phenylpropanoid pathway that also leads to flavonoid synthesis. The coupling strategies for lignin and flavonoid syntheses are diverse in plants. How their syntheses are balanced by transcriptional regulation in fleshy fruits is still unclear. The diploid strawberry (Fragaria vesca) is a model for fleshy fruits research due to its small genome and wide scope of genetic transformation. SCW thickening is regulated by a multilevel transcriptional regulatory network wherein vascular-related NAC domains (VNDs) act as key regulators. In this study, we systematically characterized VNDs in Fragaria vesca and explored their functions. The overexpression of FvVND4c in diploid strawberry fruits resulted in SCW thickening and fruit color changes accompanied with the accumulation of lignin and flavonoids. Genes related to these phenotypes were also induced upon FvVND4c overexpression. Among the induced genes, we found FvMYB46 to be a direct downstream regulator of FvVND4c. The overexpression of FvMYB46 resulted in similar phenotypes as FvVND4c, except for the color change. Transcriptomic analyses suggest that both FvVND4c and FvMYB46 act on phenylpropanoid and flavonoid biosynthesis pathways, and induce lignin synthesis for SCW. These results suggest that FvVND4c and FvMYB46 cooperatively regulate SCW thickening and flavonoid accumulation in Fragaria vesca.
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Affiliation(s)
- Bei Zhang
- College of Horticulture, Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China
| | - Xiaofei Dang
- College of Horticulture, Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China
| | - Hao Chen
- College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China
| | - Tian Li
- College of Future Technology, Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China
| | - Fangjie Zhu
- College of Life Science, Fujian Agriculture and Forestry University (FAFU), Fuzhou 350002, China
- Fujian Agriculture and Forestry University-University of California, Riverside, Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shingo Nagawa
- Fujian Agriculture and Forestry University-University of California, Riverside, Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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13
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Blanco-Touriñán N, Torres-Martínez HH, Augstein F, Champeyroux C, von der Mark C, Carlsbecker A, Dubrovsky JG, Rodriguez-Villalón A. The primary root procambium contributes to lateral root formation through its impact on xylem connection. Curr Biol 2023; 33:1716-1727.e3. [PMID: 37071995 DOI: 10.1016/j.cub.2023.03.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/21/2023] [Accepted: 03/21/2023] [Indexed: 04/20/2023]
Abstract
The postembryonic formation of lateral roots (LRs) starts in internal root tissue, the pericycle. An important question of LR development is how the connection of the primary root vasculature with that of the emerging LR is established and whether the pericycle and/or other cell types direct this process. Here, using clonal analysis and time-lapse experiments, we show that both the procambium and pericycle of the primary root (PR) affect the LR vascular connectivity in a coordinated manner. We show that during LR formation, procambial derivates switch their identity and become precursors of xylem cells. These cells, together with the pericycle-origin xylem, participate in the formation of what we call a "xylem bridge" (XB), which establishes the xylem connection between the PR and the nascent LR. If the parental protoxylem cell fails to differentiate, XB is still sometimes formed but via a connection with metaxylem cells, highlighting that this process has some plasticity. Using mutant analyses, we show that the early specification of XB cells is determined by CLASS III HOMEODOMAIN-LEUCINE ZIPPER (HD-ZIP III) transcription factors (TFs). Subsequent XB cell differentiation is marked by the deposition of secondary cell walls (SCWs) in spiral and reticulate/scalariform patterns, which is dependent on the VASCULAR-RELATED NAC-DOMAIN (VND) TFs. XB elements were also observed in Solanum lycopersicum, suggesting that this mechanism may be more widely conserved in plants. Together, our results suggest that plants maintain vascular procambium activity, which safeguards the functionality of newly established lateral organs by assuring the continuity of the xylem strands throughout the root system.
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Affiliation(s)
- Noel Blanco-Touriñán
- Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, 8092 Zurich, Switzerland.
| | - Héctor H Torres-Martínez
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad, 2001, Cuernavaca 62250, Mexico
| | - Frauke Augstein
- Department of Organismal Biology, Physiological Botany, Linnean Centre for Plant Biology, Uppsala University, Ullsv. 24E, 756 51 Uppsala, Sweden
| | - Chloé Champeyroux
- Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, 8092 Zurich, Switzerland
| | - Claudia von der Mark
- Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, 8092 Zurich, Switzerland
| | - Annelie Carlsbecker
- Department of Organismal Biology, Physiological Botany, Linnean Centre for Plant Biology, Uppsala University, Ullsv. 24E, 756 51 Uppsala, Sweden
| | - Joseph G Dubrovsky
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad, 2001, Cuernavaca 62250, Mexico.
| | - Antia Rodriguez-Villalón
- Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, 8092 Zurich, Switzerland.
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14
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Zhang L, He C, Lai Y, Wang Y, Kang L, Liu A, Lan C, Su H, Gao Y, Li Z, Yang F, Li Q, Mao H, Chen D, Chen W, Kaufmann K, Yan W. Asymmetric gene expression and cell-type-specific regulatory networks in the root of bread wheat revealed by single-cell multiomics analysis. Genome Biol 2023; 24:65. [PMID: 37016448 PMCID: PMC10074895 DOI: 10.1186/s13059-023-02908-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/23/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Homoeologs are defined as homologous genes resulting from allopolyploidy. Bread wheat, Triticum aestivum, is an allohexaploid species with many homoeologs. Homoeolog expression bias, referring to the relative contribution of homoeologs to the transcriptome, is critical for determining the traits that influence wheat growth and development. Asymmetric transcription of homoeologs has been so far investigated in a tissue or organ-specific manner, which could be misleading due to a mixture of cell types. RESULTS Here, we perform single nuclei RNA sequencing and ATAC sequencing of wheat root to study the asymmetric gene transcription, reconstruct cell differentiation trajectories and cell-type-specific gene regulatory networks. We identify 22 cell types. We then reconstruct cell differentiation trajectories that suggest different origins between epidermis/cortex and endodermis, distinguishing bread wheat from Arabidopsis. We show that the ratio of asymmetrically transcribed triads varies greatly when analyzing at the single-cell level. Hub transcription factors determining cell type identity are also identified. In particular, we demonstrate that TaSPL14 participates in vasculature development by regulating the expression of BAM1. Combining single-cell transcription and chromatin accessibility data, we construct the pseudo-time regulatory network driving root hair differentiation. We find MYB3R4, REF6, HDG1, and GATAs as key regulators in this process. CONCLUSIONS Our findings reveal the transcriptional landscape of root organization and asymmetric gene transcription at single-cell resolution in polyploid wheat.
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Affiliation(s)
- Lihua Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yuting Lai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yating Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Lu Kang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Ankui Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Handong Su
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yuwen Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Zeqing Li
- Wuhan Igenebook Biotechnology Co., Ltd, Wuhan, 430014 China
| | - Fang Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023 China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität Zu Berlin, 10115 Berlin, Germany
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070 China
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15
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Pedersen GB, Blaschek L, Frandsen KEH, Noack LC, Persson S. Cellulose synthesis in land plants. MOLECULAR PLANT 2023; 16:206-231. [PMID: 36564945 DOI: 10.1016/j.molp.2022.12.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
All plant cells are surrounded by a cell wall that provides cohesion, protection, and a means of directional growth to plants. Cellulose microfibrils contribute the main biomechanical scaffold for most of these walls. The biosynthesis of cellulose, which typically is the most prominent constituent of the cell wall and therefore Earth's most abundant biopolymer, is finely attuned to developmental and environmental cues. Our understanding of the machinery that catalyzes and regulates cellulose biosynthesis has substantially improved due to recent technological advances in, for example, structural biology and microscopy. Here, we provide a comprehensive overview of the structure, function, and regulation of the cellulose synthesis machinery and its regulatory interactors. We aim to highlight important knowledge gaps in the field, and outline emerging approaches that promise a means to close those gaps.
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Affiliation(s)
- Gustav B Pedersen
- Copenhagen Plant Science Center (CPSC), Department of Plant & Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Leonard Blaschek
- Copenhagen Plant Science Center (CPSC), Department of Plant & Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Kristian E H Frandsen
- Copenhagen Plant Science Center (CPSC), Department of Plant & Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Lise C Noack
- Copenhagen Plant Science Center (CPSC), Department of Plant & Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Staffan Persson
- Copenhagen Plant Science Center (CPSC), Department of Plant & Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark; Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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16
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Ge Y, Gao Y, Jiao Y, Wang Y. A conserved module in the formation of moss midribs and seed plant axillary meristems. SCIENCE ADVANCES 2022; 8:eadd7275. [PMID: 36399581 PMCID: PMC9674282 DOI: 10.1126/sciadv.add7275] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Different evolutionary lineages have evolved distinct characteristic body plans and anatomical structures, but their origins are largely elusive. For example, seed plants evolve axillary meristems to enable lateral branching. In moss, the phyllid (leaf) midrib containing specialized cells is responsible for water conduction and support. Midribs function like vascular tissues in flowering plants but may have risen from a different evolutionary path. Here, we demonstrate that midrib formation in the model moss Physcomitrium patens is regulated by orthologs of Arabidopsis LATERAL SUPPRESSOR (LAS), a key regulator of axillary meristem initiation. Midribs are missing in loss-of-function mutants, and ectopic formation of midrib-like structures is induced in overexpression lines. Furthermore, the PpLAS/AtLAS genes have conserved functions in the promotion of cell division in both lineages, which alleviates phenotypes in both Physcomitrium and Arabidopsis las mutants. Our results show that a conserved regulatory module is reused in divergent developmental programs, water-conducting and supporting tissues in moss, and axillary meristem initiation in seed plants.
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Affiliation(s)
- Yanhua Ge
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Gao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ying Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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17
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Augstein F, Carlsbecker A. Salinity induces discontinuous protoxylem via a DELLA-dependent mechanism promoting salt tolerance in Arabidopsis seedlings. THE NEW PHYTOLOGIST 2022; 236:195-209. [PMID: 35746821 PMCID: PMC9545557 DOI: 10.1111/nph.18339] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 06/11/2022] [Indexed: 06/15/2023]
Abstract
Salinity is detrimental to plants and developmental adjustments limiting salt uptake and transport is therefore important for acclimation to high salt. These parameters may be influenced by xylem morphology, however how plant root xylem development is affected by salt stress remains unclear. Using molecular and genetic techniques and detailed phenotypic analyses, we demonstrate that salt causes distinct effects on Arabidopsis seedling root xylem and reveal underlying molecular mechanisms. Salinity causes intermittent inhibition of protoxylem cell differentiation, generating protoxylem gaps, in Arabidopsis and several other eudicot seedlings. The extent of protoxylem gaps in seedlings positively correlates with salt tolerance. Reduced gibberellin signalling is required for protoxylem gap formation. Mutant analyses reveal that the xylem differentiation regulator VASCULAR RELATED NAC DOMAIN 6 (VND6), along with secondary cell wall producing and cell wall modifying enzymes, including EXPANSIN A1 (EXP1), are involved in protoxylem gap formation, in a DELLA-dependent manner. Salt stress is likely to reduce levels of bioactive gibberellins, stabilising DELLAs, which in turn activates multiple factors modifying protoxylem differentiation. Salt stress impacts seedling survival and formation of protoxylem gaps may be a measure to enhance salt tolerance.
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Affiliation(s)
- Frauke Augstein
- Department of Organismal Biology, Physiological Botany, and Linnean Centre for Plant BiologyUppsala UniversityUllsv. 24ESE‐756 51UppsalaSweden
| | - Annelie Carlsbecker
- Department of Organismal Biology, Physiological Botany, and Linnean Centre for Plant BiologyUppsala UniversityUllsv. 24ESE‐756 51UppsalaSweden
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18
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Sakamoto S, Nomura T, Kato Y, Ogita S, Mitsuda N. High-transcriptional activation ability of bamboo SECONDARY WALL NAC transcription factors is derived from C-terminal domain. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2022; 39:229-240. [PMID: 36349231 PMCID: PMC9592943 DOI: 10.5511/plantbiotechnology.22.0501a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/01/2022] [Indexed: 06/16/2023]
Abstract
The secondary cell wall, which is mainly composed of cellulose, hemicellulose, and lignin, constitutes woody tissues and gives physical strength and hydrophobic properties for resistance against environmental stresses. We cloned and functionally analyzed the homologous transcription factor (TF) genes of SECONDARY WALL NAC (SWN) proteins from Hachiku bamboo (Phyllostachys nigra; PnSWNs). An RT-PCR analysis showed that PnSWNs are expressed in young tissues in bamboo. Their transcriptional activation activities were higher than that of the Arabidopsis NAC SECONDARY WALL THICKENING PROMOTING FACTOR 3 (NST3) TF, which was equivalent to SWN TFs in monocot. PnSWNs preferred to activate the genes related to secondary cell wall formation but not the genes related to programmed cell death. When PnSWNs were expressed in Arabidopsis, they highly induced secondary cell wall formation, like previously-shown rice SWN1. Dissection analysis revealed that this high activity largely depends on C-terminal domain. These results demonstrate that the cloned bamboo SWNs function as regulators of secondary cell wall formation with strong activation ability derived from C-terminal domain, and could be served as new genetic tools for secondary cell wall manipulation.
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Affiliation(s)
- Shingo Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1 Tsukuba, Ibaraki 305-8566, Japan
- Global Zero Emission Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1 Tsukuba, Ibaraki 305-8566, Japan
| | - Taiji Nomura
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yasuo Kato
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Shinjiro Ogita
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
- Faculty of Bioresource Sciences, Prefectural University of Hiroshima, 5562 Nanatsukacho, Shobara, Hiroshima 727-0023, Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1 Tsukuba, Ibaraki 305-8566, Japan
- Global Zero Emission Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1 Tsukuba, Ibaraki 305-8566, Japan
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19
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The Regulation of Xylem Development by Transcription Factors and Their Upstream MicroRNAs. Int J Mol Sci 2022; 23:ijms231710134. [PMID: 36077531 PMCID: PMC9456210 DOI: 10.3390/ijms231710134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/27/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
Xylem, as a unique organizational structure of vascular plants, bears water transport and supports functions necessary for plant survival. Notably, secondary xylem in the stem (i.e., wood) also has important economic and ecological value. In view of this, the regulation of xylem development has been widely concerned. In recent years, studies on model plants Arabidopsis and poplar have shown that transcription factors play important regulatory roles in various processes of xylem development, including the directional differentiation of procambium and cambium into xylem, xylem arrangement patterns, secondary cell wall formation and programmed cell death. This review focuses on the regulatory roles of widely and thoroughly studied HD-ZIP, MYB and NAC transcription factor gene families in xylem development, and it also pays attention to the regulation of their upstream microRNAs. In addition, the existing questions in the research and future research directions are prospected.
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20
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Current Understanding of the Genetics and Molecular Mechanisms Regulating Wood Formation in Plants. Genes (Basel) 2022; 13:genes13071181. [PMID: 35885964 PMCID: PMC9319765 DOI: 10.3390/genes13071181] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/24/2022] [Accepted: 06/29/2022] [Indexed: 11/17/2022] Open
Abstract
Unlike herbaceous plants, woody plants undergo volumetric growth (a.k.a. secondary growth) through wood formation, during which the secondary xylem (i.e., wood) differentiates from the vascular cambium. Wood is the most abundant biomass on Earth and, by absorbing atmospheric carbon dioxide, functions as one of the largest carbon sinks. As a sustainable and eco-friendly energy source, lignocellulosic biomass can help address environmental pollution and the global climate crisis. Studies of Arabidopsis and poplar as model plants using various emerging research tools show that the formation and proliferation of the vascular cambium and the differentiation of xylem cells require the modulation of multiple signals, including plant hormones, transcription factors, and signaling peptides. In this review, we summarize the latest knowledge on the molecular mechanism of wood formation, one of the most important biological processes on Earth.
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21
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Xu H, Giannetti A, Sugiyama Y, Zheng W, Schneider R, Watanabe Y, Oda Y, Persson S. Secondary cell wall patterning-connecting the dots, pits and helices. Open Biol 2022; 12:210208. [PMID: 35506204 PMCID: PMC9065968 DOI: 10.1098/rsob.210208] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 04/07/2022] [Indexed: 01/04/2023] Open
Abstract
All plant cells are encased in primary cell walls that determine plant morphology, but also protect the cells against the environment. Certain cells also produce a secondary wall that supports mechanically demanding processes, such as maintaining plant body stature and water transport inside plants. Both these walls are primarily composed of polysaccharides that are arranged in certain patterns to support cell functions. A key requisite for patterned cell walls is the arrangement of cortical microtubules that may direct the delivery of wall polymers and/or cell wall producing enzymes to certain plasma membrane locations. Microtubules also steer the synthesis of cellulose-the load-bearing structure in cell walls-at the plasma membrane. The organization and behaviour of the microtubule array are thus of fundamental importance to cell wall patterns. These aspects are controlled by the coordinated effort of small GTPases that probably coordinate a Turing's reaction-diffusion mechanism to drive microtubule patterns. Here, we give an overview on how wall patterns form in the water-transporting xylem vessels of plants. We discuss systems that have been used to dissect mechanisms that underpin the xylem wall patterns, emphasizing the VND6 and VND7 inducible systems, and outline challenges that lay ahead in this field.
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Affiliation(s)
- Huizhen Xu
- School of Biosciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Alessandro Giannetti
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Yuki Sugiyama
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - Wenna Zheng
- School of Biosciences, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - René Schneider
- Institute of Biochemistry and Biology, Plant Physiology Department, University of Potsdam, 14476 Potsdam, Germany
| | - Yoichiro Watanabe
- Institute for Research Initiatives, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Yoshihisa Oda
- Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Staffan Persson
- School of Biosciences, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Center, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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22
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Huang X, Wang W, Gong T, Wickell D, Kuo LY, Zhang X, Wen J, Kim H, Lu F, Zhao H, Chen S, Li H, Wu W, Yu C, Chen S, Fan W, Chen S, Bao X, Li L, Zhang D, Jiang L, Khadka D, Yan X, Liao Z, Zhou G, Guo Y, Ralph J, Sederoff RR, Wei H, Zhu P, Li FW, Ming R, Li Q. The flying spider-monkey tree fern genome provides insights into fern evolution and arborescence. NATURE PLANTS 2022; 8:500-512. [PMID: 35534720 PMCID: PMC9122828 DOI: 10.1038/s41477-022-01146-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 03/30/2022] [Indexed: 05/03/2023]
Abstract
To date, little is known about the evolution of fern genomes, with only two small genomes published from the heterosporous Salviniales. Here we assembled the genome of Alsophila spinulosa, known as the flying spider-monkey tree fern, onto 69 pseudochromosomes. The remarkable preservation of synteny, despite resulting from an ancient whole-genome duplication over 100 million years ago, is unprecedented in plants and probably speaks to the uniqueness of tree ferns. Our detailed investigations into stem anatomy and lignin biosynthesis shed new light on the evolution of stem formation in tree ferns. We identified a phenolic compound, alsophilin, that is abundant in xylem, and we provided the molecular basis for its biosynthesis. Finally, analysis of demographic history revealed two genetic bottlenecks, resulting in rapid demographic declines of A. spinulosa. The A. spinulosa genome fills a crucial gap in the plant genomic landscape and helps elucidate many unique aspects of tree fern biology.
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Affiliation(s)
- Xiong Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Wenling Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Ting Gong
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - David Wickell
- Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
| | - Li-Yaung Kuo
- Institute of Molecular & Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jialong Wen
- Beijing Key Laboratory of Lignocellulosic Chemistry, Beijing Forestry University, Beijing, China
| | - Hoon Kim
- Department of Biochemistry and DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, USA
| | - Fachuang Lu
- Department of Biochemistry and DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, USA
| | - Hansheng Zhao
- State Forestry Administration Key Open Laboratory on the Science and Technology of Bamboo and Rattan, Institute of Gene for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing, China
| | - Song Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Hui Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Wenqi Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Changjiang Yu
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Wei Fan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Shuai Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiuqi Bao
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Li Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Dan Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Longyu Jiang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Dipak Khadka
- GoldenGate International College, Tribhuvan University, Battisputali, Kathmandu, Nepal
| | - Xiaojing Yan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Zhenyang Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Gongke Zhou
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, China
| | - Yalong Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, China
| | - John Ralph
- Department of Biochemistry and DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, USA
| | - Ronald R Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, USA
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, USA.
| | - Ping Zhu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; NHC Key Laboratory of Biosynthesis of Natural Products; CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Fay-Wei Li
- Thompson Institute, Ithaca, NY, USA.
- Plant Biology Section, Cornell University, Ithaca, NY, USA.
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.
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23
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Hirai R, Wang S, Demura T, Ohtani M. Histone Deacetylation Controls Xylem Vessel Cell Differentiation via Transcriptional Regulation of a Transcription Repressor Complex OFP1/4-MYB75-KNAT7-BLH6. FRONTIERS IN PLANT SCIENCE 2022; 12:825810. [PMID: 35154217 PMCID: PMC8829346 DOI: 10.3389/fpls.2021.825810] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Xylem vessels are indispensable tissues in vascular plants that transport water and minerals. The differentiation of xylem vessel cells is characterized by secondary cell wall deposition and programmed cell death. These processes are initiated by a specific set of transcription factors, called VASCULAR-RELATED NAC-DOMAIN (VND) family proteins, through the direct and/or indirectly induction of genes required for secondary cell wall deposition and programmed cell death. In this study, we explored novel regulatory factors for xylem vessel cell differentiation in Arabidopsis thaliana. We tested the effects of cellular stress inducers on VND7-induced differentiation of xylem vessel cells with the VND7-VP16-GR system, in which VND7 activity is post-translationally induced by dexamethasone application. We established that the histone deacetylase (HDAC) inhibitors trichostatin A (TSA) and sirtinol inhibited VND7-induced xylem vessel cell differentiation. The inhibitory effects of TSA and sirtinol treatment were detected only when they were added at the same time as the dexamethasone application, suggesting that TSA and sirtinol mainly influence the early stages of xylem vessel cell differentiation. Expression analysis revealed that these HDAC inhibitors downregulated VND7-downstream genes, including both direct and indirect targets of transcriptional activation. Notably, the HDAC inhibitors upregulated the transcript levels of negative regulators of xylem vessel cells, OVATE FAMILY PROTEIN1 (OFP1), OFP4, and MYB75, which are known to form a protein complex with BEL1-LIKE HOMEODOMAIN6 (BLH6) to repress gene transcription. The KDB system, another in vitro induction system of ectopic xylem vessel cells, demonstrated that TSA and sirtinol also inhibited ectopic formation of xylem vessel cells, and this inhibition was partially suppressed in knat7-1, bhl6-1, knat7-1 bhl6-1, and quintuple ofp1 ofp2 ofp3 ofp4 ofp5 mutants. Thus, the negative effects of HDAC inhibitors on xylem vessel cell differentiation are mediated, at least partly, by the abnormal upregulation of the transcriptional repressor complex OFP1/4-MYB75-KNAT7-BLH6. Collectively, our findings suggest that active regulation of histone deacetylation by HDACs is involved in xylem vessel cell differentiation via the OFP1/4-MYB75-KNAT7-BLH6 complex.
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Affiliation(s)
- Risaku Hirai
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Shumin Wang
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Taku Demura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Center for Digital Green-Innovation, Nara Institute of Science and Technology, Ikoma, Japan
| | - Misato Ohtani
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
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24
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Chen Y, Tong S, Jiang Y, Ai F, Feng Y, Zhang J, Gong J, Qin J, Zhang Y, Zhu Y, Liu J, Ma T. Transcriptional landscape of highly lignified poplar stems at single-cell resolution. Genome Biol 2021; 22:319. [PMID: 34809675 PMCID: PMC8607660 DOI: 10.1186/s13059-021-02537-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/10/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Plant secondary growth depends on the activity of the vascular cambium, which produces xylem and phloem. Wood derived from xylem is the most abundant form of biomass globally and has played key socio-economic and subsistence roles throughout human history. However, despite intensive study of vascular development, the full diversity of cell types and the gene networks engaged are still poorly understood. RESULTS Here, we have applied an optimized protoplast isolation protocol and RNA sequencing to characterize the high-resolution single-cell transcriptional landscape of highly lignified poplar stems. We identify 20 putative cell clusters with a series of novel cluster-specific marker genes and find that these cells are highly heterogeneous based on the transcriptome. Analysis of these marker genes' expression dynamics enables reconstruction of the cell differentiation trajectories involved in phloem and xylem development. We find that different cell clusters exhibit distinct patterns of phytohormone responses and emphasize the use of our data to predict potential gene redundancy and identify candidate genes related to vascular development in trees. CONCLUSIONS These findings establish the transcriptional landscape of major cell types of poplar stems at single-cell resolution and provide a valuable resource for investigating basic principles of vascular cell specification and differentiation in trees.
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Affiliation(s)
- Yang Chen
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Shaofei Tong
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yuanzhong Jiang
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Fandi Ai
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yanlin Feng
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Junlin Zhang
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jue Gong
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jiajia Qin
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yuanyuan Zhang
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yingying Zhu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Tao Ma
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
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25
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Liu Y, Cao S, Liu X, Li Y, Wang B, Sun Y, Zhang C, Guo X, Li H, Lu H. PtrLAC16 plays a key role in catalyzing lignin polymerization in the xylem cell wall of Populus. Int J Biol Macromol 2021; 188:983-992. [PMID: 34403677 DOI: 10.1016/j.ijbiomac.2021.08.077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/06/2021] [Accepted: 08/10/2021] [Indexed: 10/20/2022]
Abstract
Plant laccases have been proposed to participate in lignin biosynthesis. However, there is no direct evidence that individual laccases in Populus can polymerize lignin monomers and alter cell wall structure. Here, a Populus laccase, PtrLAC16, was expressed and purified in a eukaryotic system. Enzymatic analysis of PtrLAC16 showed that it could polymerize lignin monomers in vitro. PtrLAC16 preferred sinapyl alcohol, and this preference is associated with an altered S/G ratio in transgenic Populus lines. PtrLAC16 was localized exclusively in the cell walls of stem vascular tissue, and a reduction in PtrLAC16 expression led to a significant decrease in lignin content and altered cell wall structure. There was a direct correlation between the inhibition of PtrLAC16 expression and structural changes in the stem cell wall of Populus. This study provides direct evidence that PtrLAC16 plays a key role in the polymerization of lignin monomers, especially for sinapyl lignin, and affects the formation of xylem cell walls in Populus.
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Affiliation(s)
- Yadi Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Shan Cao
- School of Management, Qingdao Agricultural University, Shandong 266109, China
| | - Xiatong Liu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Ying Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Bing Wang
- Guizhou Academy of Tobacco Science, Molecular Genetics Key Laboratory of China Tobacco, Guiyang 550081, China
| | - Yu Sun
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Chong Zhang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Xiaorui Guo
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Hui Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Hai Lu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
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26
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Dvořák Tomaštíková E, Hafrén A, Trejo-Arellano MS, Rasmussen SR, Sato H, Santos-González J, Köhler C, Hennig L, Hofius D. Polycomb Repressive Complex 2 and KRYPTONITE regulate pathogen-induced programmed cell death in Arabidopsis. PLANT PHYSIOLOGY 2021; 185:2003-2021. [PMID: 33566101 PMCID: PMC8133635 DOI: 10.1093/plphys/kiab035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/08/2021] [Indexed: 05/10/2023]
Abstract
The Polycomb Repressive Complex 2 (PRC2) is well-known for its role in controlling developmental transitions by suppressing the premature expression of key developmental regulators. Previous work revealed that PRC2 also controls the onset of senescence, a form of developmental programmed cell death (PCD) in plants. Whether the induction of PCD in response to stress is similarly suppressed by the PRC2 remained largely unknown. In this study, we explored whether PCD triggered in response to immunity- and disease-promoting pathogen effectors is associated with changes in the distribution of the PRC2-mediated histone H3 lysine 27 trimethylation (H3K27me3) modification in Arabidopsis thaliana. We furthermore tested the distribution of the heterochromatic histone mark H3K9me2, which is established, to a large extent, by the H3K9 methyltransferase KRYPTONITE, and occupies chromatin regions generally not targeted by PRC2. We report that effector-induced PCD caused major changes in the distribution of both repressive epigenetic modifications and that both modifications have a regulatory role and impact on the onset of PCD during pathogen infection. Our work highlights that the transition to pathogen-induced PCD is epigenetically controlled, revealing striking similarities to developmental PCD.
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Affiliation(s)
- Eva Dvořák Tomaštíková
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
- Present address: Institute of Experimental Botany, Czech Academy of Sciences; Centre of the Region Haná for Biotechnological and Agricultural Research, Šlechtitelů 31, 779 00 Olomouc, Czech Republic
| | - Anders Hafrén
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Minerva S Trejo-Arellano
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
- Present address: Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Sheena Ricafranca Rasmussen
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Hikaru Sato
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Juan Santos-González
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Lars Hennig
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Daniel Hofius
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
- Author for communication:
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27
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Li M, Yang Y, Xu R, Mu W, Li Y, Mao X, Zheng Z, Bi H, Hao G, Li X, Xu X, Xi Z, Shrestha N, Liu J. A chromosome-level genome assembly for the tertiary relict plant Tetracentron sinense oliv. (trochodendraceae). Mol Ecol Resour 2021; 21:1186-1199. [PMID: 33486895 DOI: 10.1111/1755-0998.13334] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 12/01/2020] [Accepted: 01/18/2021] [Indexed: 12/13/2022]
Abstract
Tetracentron sinense and Trochodendron aralioides are two Tertiary relict species of large trees in the family Trochodendraceae with narrow distributions on the mainland and islands of eastern Asia. They belong to the order Trochodendrales, which is one of the four early-diverged eudicot lineages. These two relict species provide a good system in which to examine genomic changes that occurred as they survived during repeated climatic oscillations in the Quaternary. We sequenced the genome of Te. sinense and compared it with that of Tr. aralioides. We found that Te. sinense has a smaller genome size (986.3 Mb) than that of Tr. aralioides (1610 Mb). Repetitive elements made the major contribution to the contrasting genome sizes in the two species, with most bursts of repeats occurring within the past four million years when the climate oscillated greatly. These species share two rounds of whole-genome duplications. The mainland species Te. sinense had a larger effective population size than the island species Tr. aralioides after the largest glaciation during the Quaternary climatic oscillation. However, soon after this recovery stage, the effective population sizes of both species continued to decrease, although the current effective population size of Te. sinense is still larger than that of Tr. aralioides. We recovered three distinctly diverged clades through resequencing the genomes of 50 individuals across the distributional range of Te. sinense in China. Our results provide an important genomic resource with which to examine early trait evolution in the core eudicots and assist efforts to conserve this relict tree species.
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Affiliation(s)
- Minjie Li
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Renping Xu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Wenjie Mu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ying Li
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xingxing Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zeyu Zheng
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Hao Bi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Guoqian Hao
- Biodiversity Institute of Mount Emei, Mount Emei Scenic Area Management Committee, Leshan, China
| | - Xiaojie Li
- Emeishan Biological Resources Experimental Station, Emei, China
| | - Xiaoting Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhenxiang Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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28
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Zheng L, Yang J, Chen Y, Ding L, Wei J, Wang H. An improved and efficient method of Agrobacterium syringe infiltration for transient transformation and its application in the elucidation of gene function in poplar. BMC PLANT BIOLOGY 2021; 21:54. [PMID: 33478390 PMCID: PMC7818742 DOI: 10.1186/s12870-021-02833-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 01/11/2021] [Indexed: 05/23/2023]
Abstract
BACKGROUND Forest trees have important economic and ecological value. As a model tree, poplar has played a significant role in elucidating the molecular mechanisms underlying tree biology. However, a lack of mutant libraries and time-consuming stable genetic transformation processes severely limit progress into the functional characterization of poplar genes. A convenient and fast transient transformation method is therefore needed to enhance progress on functional genomics in poplar. METHODS A total of 11 poplar clones were screened for amenability to syringe infiltration. Syringe infiltration was performed on the lower side of the leaves of young soil-grown plants. Transient expression was evaluated by visualizing the reporters β-glucuronidase (GUS) and green fluorescent protein (GFP). The experimental parameters of the syringe agroinfiltration were optimized based on the expression levels of the reporter luciferase (LUC). Stably transformed plants were regenerated from transiently transformed leaf explants through callus-induced organogenesis. The functions of Populus genes in secondary cell wall-thickening were characterized by visualizing lignin deposition therein after staining with basic fuchsin. RESULTS We greatly improved the transient transformation efficiency of syringe Agrobacterium infiltration in poplar through screening for a suitable poplar clone from a variety of clones and optimizing the syringe infiltration procedure. The selected poplar clone, Populus davidiana × P. bolleana, is amenable to Agrobacterium syringe infiltration, as indicated by the easy diffusion of the bacterial suspension inside the leaf tissues. Using this technique, we localized a variety of poplar proteins in specific intracellular organelles and illustrated the protein-protein and protein-DNA interactions. The transiently transformed leaves could be used to generate stably transformed plants with high efficiency through callus induction and differentiation processes. Furthermore, transdifferentiation of the protoxylem-like vessel element and ectopic secondary wall thickening were induced in the agroinfiltrated leaves via the transient overexpression of genes associated with secondary wall formation. CONCLUSIONS The application of P. davidiana × P. bolleana in Agrobacterium syringe infiltration provides a foundation for the rapid and high-throughput functional characterization of Populus genes in intact poplar plants, including those involved in wood formation, and provides an effective alternative to Populus stable genetic transformation.
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Affiliation(s)
- Lin Zheng
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097, People's Republic of China
| | - Jixiu Yang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097, People's Republic of China
- College of Bioscience and Resources Environment, Beijing University of Agriculture, No. 7, Beinong Road, Huilongguan, Changping District, Beijing, 102206, People's Republic of China
| | - Yajuan Chen
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097, People's Republic of China
| | - Liping Ding
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097, People's Republic of China
| | - Jianhua Wei
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097, People's Republic of China.
| | - Hongzhi Wang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, No. 9, Shuguang Huayuan Middle Road, Haidian District, Beijing, 100097, People's Republic of China.
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Zhang B, Gao Y, Zhang L, Zhou Y. The plant cell wall: Biosynthesis, construction, and functions. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:251-272. [PMID: 33325153 DOI: 10.1111/jipb.13055] [Citation(s) in RCA: 185] [Impact Index Per Article: 61.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 12/15/2020] [Indexed: 05/19/2023]
Abstract
The plant cell wall is composed of multiple biopolymers, representing one of the most complex structural networks in nature. Hundreds of genes are involved in building such a natural masterpiece. However, the plant cell wall is the least understood cellular structure in plants. Due to great progress in plant functional genomics, many achievements have been made in uncovering cell wall biosynthesis, assembly, and architecture, as well as cell wall regulation and signaling. Such information has significantly advanced our understanding of the roles of the cell wall in many biological and physiological processes and has enhanced our utilization of cell wall materials. The use of cutting-edge technologies such as single-molecule imaging, nuclear magnetic resonance spectroscopy, and atomic force microscopy has provided much insight into the plant cell wall as an intricate nanoscale network, opening up unprecedented possibilities for cell wall research. In this review, we summarize the major advances made in understanding the cell wall in this era of functional genomics, including the latest findings on the biosynthesis, construction, and functions of the cell wall.
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Affiliation(s)
- Baocai Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yihong Gao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lanjun Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yihua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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Ramachandran V, Tobimatsu Y, Masaomi Y, Sano R, Umezawa T, Demura T, Ohtani M. Plant-specific Dof transcription factors VASCULAR-RELATED DOF1 and VASCULAR-RELATED DOF2 regulate vascular cell differentiation and lignin biosynthesis in Arabidopsis. PLANT MOLECULAR BIOLOGY 2020; 104:263-281. [PMID: 32740898 DOI: 10.1007/s11103-020-01040-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 07/23/2020] [Indexed: 05/28/2023]
Abstract
Plant-specific Dof transcription factors VDOF1 and VDOF2 are novel regulators of vascular cell differentiation through the course of a lifetime in Arabidopsis, with shifting their transcriptional target genes. Vascular system is one of critical tissues for vascular plants to transport low-molecular compounds, such as water, minerals, and the photosynthetic product, sucrose. Here, we report the involvement of two Dof transcription factors, named VASCULAR-RELATED DOF1 (VDOF1)/VDOF4.6 and VDOF2/VDOF1.8, in vascular cell differentiation and lignin biosynthesis in Arabidopsis. VDOF genes were expressed in vascular tissues, but the detailed expression sites were partly different between VDOF1 and VDOF2. Vein patterning and lignin analysis of VDOF overexpressors and double mutant vdof1 vdof2 suggested that VDOF1 and VDOF2 would function as negative regulators of vein formation in seedlings, and lignin deposition in inflorescence stems. Interestingly, effects of VDOF overexpression in lignin deposition were different by developmental stages of inflorescence stems, and total lignin contents were increased and decreased in VDOF1 and VDOF2 overexpressors, respectively. RNA-seq analysis of inducible VDOF overexpressors demonstrated that the genes for cell wall biosynthesis, including lignin biosynthetic genes, and the transcription factor genes related to stress response and brassinosteroid signaling were commonly affected by VDOF1 and VDOF2 overexpression. Taken together, we concluded that VDOF1 and VDOF2 are novel regulators of vascular cell differentiation through the course of a lifetime, with shifting their transcriptional target genes: in seedlings, the VDOF genes negatively regulate vein formation, while at reproductive stages, the VDOF proteins target lignin biosynthesis.
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Affiliation(s)
- Vasagi Ramachandran
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Yuki Tobimatsu
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Yamamura Masaomi
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Ryosuke Sano
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, 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, Gokasho, Kyoto, 611-0011, Japan
| | - Taku Demura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan.
| | - Misato Ohtani
- Graduate School of Science and Technology, 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.
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Guo Z, Xu H, Lei Q, Du J, Li C, Wang C, Yang Y, Yang Y, Sun X. The Arabidopsis transcription factor LBD15 mediates ABA signaling and tolerance of water-deficit stress by regulating ABI4 expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:510-521. [PMID: 32744432 DOI: 10.1111/tpj.14942] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 06/23/2020] [Accepted: 07/07/2020] [Indexed: 06/11/2023]
Abstract
To survive, sessile plants must adapt to grow and develop when facing water-deficit stress. However, the molecular mechanisms underlying fine-tuning of the antagonistic action between stress response and growth remain to be determined. Here, plants overexpressing Lateral Organ Boundaries Domain 15 (LBD15) showed abscisic acid (ABA) hypersensitivity and tolerance of water-deficit stress, whereas the loss-of-function mutant lbd15 presented decreased sensitivity to ABA and increased sensitivity to water-deficit stress. Further analysis revealed that LBD15 directly binds to the promoter of the ABA signaling pathway gene ABSCISIC ACID INSENSITIVE4 (ABI4) to activate its expression, thereby forming an LBD15-ABI4 cascade to optimally regulate ABA signaling-mediated plant growth and tolerance of water-deficit stress. In addition, drought stress-induced ABA signaling promoted LBD15 expression, which directly activates expression of ABI4 to close stomata. As a result, water loss is reduced, and then water-deficit stress tolerance is increased. The results of this study reveal a molecular mechanism by which LBD15 coordinates and balances plant growth and resistance to water-deficit stress.
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Affiliation(s)
- Zhaolai Guo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650224, China
| | - Huini Xu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650224, China
| | - Qidong Lei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650224, China
| | - Jiancan Du
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Cheng Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chongde Wang
- College of Plant Protection, Yunnan Agricultural University, Kunming, 650201, China
| | - Yunqiang Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yongping Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xudong Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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Hernandez Y, Goswami K, Sanan‐Mishra N. Stress induced dynamic adjustment of conserved miR164:NAC module. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2020; 1:134-151. [PMID: 37283725 PMCID: PMC10168063 DOI: 10.1002/pei3.10027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 07/02/2020] [Accepted: 07/14/2020] [Indexed: 06/08/2023]
Abstract
Aims including the rationale Salinity and drought are the two major stresses limiting the productivity of economically important crops such as Glycine max (soybean). The incidence of these stresses during the pod development stages affects the quality and quantity of seeds, which compromise the yield of soybean. The miR164:NAC module has been shown to play a critical role in regulating the response to salt and drought stress in several plant species. However, biological role of miR164:NAC module in salt stress in soybean is not fully understood. Methods In this study, we identified 215 salt responsive miRNAs, using miScript miRNA array with a sensitive and a tolerant soybean genotype, William82 and INCASoy36, respectively. The targets of these salt regulated miRNAs were searched in the degradome datasets. Key results It was found that four salt stress deregulated miRNAs targeted the NAC transcription factor and among these miR164k and miR408d showed antagonistic expression in the two soybean genotypes. The expression of miR164k was higher in salt tolerant INCASoy36 as compared to salt sensitive William82, under unstressed conditions. However under salt stress, miR164k was downregulated in INCASoy36 (-2.65 fold), whereas it was upregulated in William82 (4.68 fold). A transient co-expression assay validated that gma-miR164k directs the cleavage of GmNAC1 transcript. Bioinformatics analysis revealed that the regulation of NAC transcription factor family by members of miR164 family is conserved across many species. The dynamic expression profiles of miR164 and NAC-TFs were captured in different tissues of rice, tobacco, and two soybean genotypes under drought and salt stress conditions. Main conclusion Collectively, our results suggest that genetically determined dynamic modulation of the conserved miR164:NAC-TF module may play an important role in determining the adaptive response of plants to stress.
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Affiliation(s)
- Yuniet Hernandez
- Plant RNAi Biology GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
| | - Kavita Goswami
- Plant RNAi Biology GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
| | - Neeti Sanan‐Mishra
- Plant RNAi Biology GroupInternational Centre for Genetic Engineering and BiotechnologyNew DelhiIndia
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Yao W, Li C, Lin S, Wang J, Zhou B, Jiang T. Transcriptome analysis of salt-responsive and wood-associated NACs in Populus simonii × Populus nigra. BMC PLANT BIOLOGY 2020; 20:317. [PMID: 32631231 PMCID: PMC7336439 DOI: 10.1186/s12870-020-02507-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 06/19/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND NAC (NAM, ATAF1-2, and CUC2) family is one of the largest plant-specific transcription factor families known to play significant roles in plant development processes and stress responses. RESULTS In the study, a total of 112 NACs were identified to be differentially expressed in the comparisons of leaves and stems, leaves and roots, roots and stems of Populus simonii×P. nigra among 289 members by RNA-Seq. And 148, 144 and 134 NACs were detected to be salt-responsive in the roots, stems and leaves under 150 mM NaCl stress, respectively. Among them, a total of 53 salt-responsive NACs were shared across the three tissues. Under salt stress, 41/37 NACs were identified to be up/down-regulated in the leaves of Populus simonii × P.nigra among 170 non-redundant NACs by RT-qPCR, which was similar with RNA-Seq results. The expression pattern analysis of 6 NACs including four randomly up-regulated genes (NAC86, NAC105, NAC139 and NAC163) and two down-regulated genes (NAC15 and NAC149) indicated a few NACs showed specific temporal and spatial expression patterns in the three tissues of Populus simonii×P.nigra. Based on transcriptome screening and phylogenic analysis of differentially expressed NACs in different tissues under salt stress, 18 potential NACs associated with wood formation and 20 involved in stress responses were identified in Populus simonii×P.nigra. CONCLUSIONS The study further gains an understanding of the connection of tissue specificity and gene function in poplar, and lays the foundation of functional analysis of poplar NACs in stress responses.
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Affiliation(s)
- Wenjing Yao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China
- Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Chuanzhe Li
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Shuyan Lin
- Co-Innovation Center for Sustainable Forestry in Southern China/Bamboo Research Institute, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Jianping Wang
- Department of Agronomy, University of Florida, 2033 Mowry Road, Gainesville, FL32610, USA
| | - Boru Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China.
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 51 Hexing Road, Harbin, 150040, China.
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Lin W, Sun L, Huang RZ, Liang W, Liu X, He H, Fukuda H, He XQ, Qian W. Active DNA demethylation regulates tracheary element differentiation in Arabidopsis. SCIENCE ADVANCES 2020; 6:eaaz2963. [PMID: 32637594 PMCID: PMC7319731 DOI: 10.1126/sciadv.aaz2963] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 05/13/2020] [Indexed: 05/16/2023]
Abstract
DNA demethylation is important for the erasure of DNA methylation. The role of DNA demethylation in plant development remains poorly understood. Here, we found extensive DNA demethylation in the CHH context around pericentromeric regions and DNA demethylation in the CG, CHG, and CHH contexts at discrete genomic regions during ectopic xylem tracheary element (TE) differentiation. While loss of pericentromeric methylation occurs passively, DNA demethylation at a subset of regions relies on active DNA demethylation initiated by DNA glycosylases ROS1, DML2, and DML3. The ros1 and rdd mutations impair ectopic TE differentiation and xylem development in the young roots of Arabidopsis seedlings. Active DNA demethylation targets and regulates many genes for TE differentiation. The defect of xylem development in rdd is proposed to be caused by dysregulation of multiple genes. Our study identifies a role of active DNA demethylation in vascular development and reveals an epigenetic mechanism for TE differentiation.
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Affiliation(s)
- Wei Lin
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Linhua Sun
- Academy for Advanced Interdisciplinary Studies, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Run-Zhou Huang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wenjie Liang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xinyu Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hiroo Fukuda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Xin-Qiang He
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Corresponding author. (X.-Q.H.); (W.Q.)
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Corresponding author. (X.-Q.H.); (W.Q.)
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Zhang L, Liu B, Zhang J, Hu J. Insights of Molecular Mechanism of Xylem Development in Five Black Poplar Cultivars. FRONTIERS IN PLANT SCIENCE 2020; 11:620. [PMID: 32547574 PMCID: PMC7271880 DOI: 10.3389/fpls.2020.00620] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 04/22/2020] [Indexed: 06/11/2023]
Abstract
Black poplar (Populus deltoides, P. nigra, and their hybrids) is the main poplar cultivars in China. It offers interesting options of large-scale biomass production for bioenergy due to its rapid growth and high yield. Poplar wood properties were associated with chemical components and physical structures during wood formation. In this study, five poplar cultivars, P. euramericana 'Zhonglin46' (Pe1), P. euramericana 'Guariento' (Pe2), P. nigra 'N179' (Pn1), P. deltoides 'Danhong' (Pd1), and P. deltoides 'Nanyang' (Pd2), were used to explore the molecular mechanism of xylem development. We analyzed the structural differences of developing xylem in the five cultivars and profiled the transcriptome-wide gene expression patterns through RNA sequencing. The cross sections of the developing xylem showed that the cell wall thickness of developed fiber in Pd1 was thickest and the number of xylem vessels of Pn1 was the least. A total of 10,331 differentially expressed genes were identified among 10 pairwise comparisons of the five cultivars, most of them were related to programmed cell death and secondary cell wall thickening. K-means cluster analysis and Gene Ontology enrichment analysis showed that the genes highly expressed in Pd1 were related to nucleotide decomposition, metabolic process, transferase, and microtubule cytoskeleton; whereas the genes highly expressed in Pn1 were involved in cell wall macromolecule decomposition and polysaccharide binding processes. Based on a weighted gene co-expression network analysis, a large number of candidate regulators for xylem development were identified. And their potential regulatory roles to cell wall biosynthesis genes were validated by a transient overexpression system. This study provides a set of promising candidate regulators for genetic engineering to improve feedstock and enhance biofuel conversion in the bioenergy crop Populus.
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Affiliation(s)
- Lei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Bobin Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Ramachandran P, Augstein F, Nguyen V, Carlsbecker A. Coping With Water Limitation: Hormones That Modify Plant Root Xylem Development. FRONTIERS IN PLANT SCIENCE 2020; 11:570. [PMID: 32499804 PMCID: PMC7243681 DOI: 10.3389/fpls.2020.00570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/17/2020] [Indexed: 05/23/2023]
Abstract
Periods of drought, that threaten crop production, are expected to become more prominent in large parts of the world, making it necessary to explore all aspects of plant growth and development, to breed, modify and select crops adapted to such conditions. One such aspect is the xylem, where influencing the size and number of the water-transporting xylem vessels, may impact on hydraulic conductance and drought tolerance. Here, we focus on how plants adjust their root xylem as a response to reduced water availability. While xylem response has been observed in a wide array of species, most of our knowledge on the molecular mechanisms underlying xylem plasticity comes from studies on the model plant Arabidopsis thaliana. When grown under water limiting conditions, Arabidopsis rapidly adjusts its development to produce more xylem strands with altered identity in an abscisic acid (ABA) dependent manner. Other hormones such as auxin and cytokinin are essential for vascular patterning and differentiation. Their balance can be perturbed by stress, as evidenced by the effects of enhanced jasmonic acid signaling, which results in similar xylem developmental alterations as enhanced ABA signaling. Furthermore, brassinosteroids and other signaling molecules involved in drought tolerance can also impact xylem development. Hence, a multitude of signals affect root xylem properties and, potentially, influence survival under water limiting conditions. Here, we review the likely entangled signals that govern root vascular development, and discuss the importance of taking root anatomical traits into account when breeding crops for enhanced resilience toward changes in water availability.
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Hennet L, Berger A, Trabanco N, Ricciuti E, Dufayard JF, Bocs S, Bastianelli D, Bonnal L, Roques S, Rossini L, Luquet D, Terrier N, Pot D. Transcriptional Regulation of Sorghum Stem Composition: Key Players Identified Through Co-expression Gene Network and Comparative Genomics Analyses. FRONTIERS IN PLANT SCIENCE 2020; 11:224. [PMID: 32194601 PMCID: PMC7064007 DOI: 10.3389/fpls.2020.00224] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 02/12/2020] [Indexed: 06/10/2023]
Abstract
Most sorghum biomass accumulates in stem secondary cell walls (SCW). As sorghum stems are used as raw materials for various purposes such as feed, energy and fiber reinforced polymers, identifying the genes responsible for SCW establishment is highly important. Taking advantage of studies performed in model species, most of the structural genes contributing at the molecular level to the SCW biosynthesis in sorghum have been proposed while their regulatory factors have mostly not been determined. Validation of the role of several MYB and NAC transcription factors in SCW regulation in Arabidopsis and a few other species has been provided. In this study, we contributed to the recent efforts made in grasses to uncover the mechanisms underlying SCW establishment. We reported updated phylogenies of NAC and MYB in 9 different species and exploited findings from other species to highlight candidate regulators of SCW in sorghum. We acquired expression data during sorghum internode development and used co-expression analyses to determine groups of co-expressed genes that are likely to be involved in SCW establishment. We were able to identify two groups of co-expressed genes presenting multiple evidences of involvement in SCW building. Gene enrichment analysis of MYB and NAC genes provided evidence that while NAC SECONDARY WALL THICKENING PROMOTING FACTOR NST genes and SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN gene functions appear to be conserved in sorghum, NAC master regulators of SCW in sorghum may not be as tissue compartmentalized as in Arabidopsis. We showed that for every homolog of the key SCW MYB in Arabidopsis, a similar role is expected for sorghum. In addition, we unveiled sorghum MYB and NAC that have not been identified to date as being involved in cell wall regulation. Although specific validation of the MYB and NAC genes uncovered in this study is needed, we provide a network of sorghum genes involved in SCW both at the structural and regulatory levels.
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Affiliation(s)
- Lauriane Hennet
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Angélique Berger
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Noemi Trabanco
- Parco Tecnologico Padano, Lodi, Italy
- Centro de Biotecnología y Genómica de Plantas, UPM-INIA, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Emeline Ricciuti
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Jean-François Dufayard
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Stéphanie Bocs
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Denis Bastianelli
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
- CIRAD, UMR SELMET, Montpellier, France
| | - Laurent Bonnal
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
- CIRAD, UMR SELMET, Montpellier, France
| | - Sandrine Roques
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Laura Rossini
- Parco Tecnologico Padano, Lodi, Italy
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Delphine Luquet
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Nancy Terrier
- AGAP, CIRAD, INRAE, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - David Pot
- CIRAD, UMR AGAP, Montpellier, France
- CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
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De La Torre AR, Piot A, Liu B, Wilhite B, Weiss M, Porth I. Functional and morphological evolution in gymnosperms: A portrait of implicated gene families. Evol Appl 2020; 13:210-227. [PMID: 31892953 PMCID: PMC6935586 DOI: 10.1111/eva.12839] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/25/2019] [Accepted: 07/02/2019] [Indexed: 12/12/2022] Open
Abstract
Gymnosperms diverged from their sister plant clade of flowering plants 300 Mya. Morphological and functional divergence between the two major seed plant clades involved significant changes in their reproductive biology, water-conducting systems, secondary metabolism, stress defense mechanisms, and small RNA-mediated epigenetic silencing. The relatively recent sequencing of several gymnosperm genomes and the development of new genomic resources have enabled whole-genome comparisons within gymnosperms, and between angiosperms and gymnosperms. In this paper, we aim to understand how genes and gene families have contributed to the major functional and morphological differences in gymnosperms, and how this information can be used for applied breeding and biotechnology. In addition, we have analyzed the angiosperm versus gymnosperm evolution of the pleiotropic drug resistance (PDR) gene family with a wide range of functionalities in plants' interaction with their environment including defense mechanisms. Some of the genes reviewed here are newly studied members of gene families that hold potential for biotechnological applications related to commercial and pharmacological value. Some members of conifer gene families can also be exploited for their potential in phytoremediation applications.
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Affiliation(s)
| | - Anthony Piot
- Department of Wood and Forest SciencesLaval UniversityQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Laval UniversityQuebec CityQuebecCanada
- Centre for Forest Research (CEF)Laval UniversityQuebec CityQuebecCanada
| | - Bobin Liu
- School of ForestryNorthern Arizona UniversityFlagstaffAZUSA
- College of ForestryFujian Agricultural and Forestry UniversityFuzhouFujianChina
| | | | - Matthew Weiss
- School of ForestryNorthern Arizona UniversityFlagstaffAZUSA
| | - Ilga Porth
- Department of Wood and Forest SciencesLaval UniversityQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Laval UniversityQuebec CityQuebecCanada
- Centre for Forest Research (CEF)Laval UniversityQuebec CityQuebecCanada
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Kaga Y, Yokoyama R, Sano R, Ohtani M, Demura T, Kuroha T, Shinohara N, Nishitani K. Interspecific Signaling Between the Parasitic Plant and the Host Plants Regulate Xylem Vessel Cell Differentiation in Haustoria of Cuscuta campestris. FRONTIERS IN PLANT SCIENCE 2020; 11:193. [PMID: 32231674 PMCID: PMC7082356 DOI: 10.3389/fpls.2020.00193] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/10/2020] [Indexed: 05/13/2023]
Abstract
The genus Cuscuta is stem parasitic angiosperms that parasitize a wide range of vascular plants via de novo formation of a distinctive parasitic organ called a haustorium. In the developing haustorium, meristematic cells, which are initiated from the stem cortical tissue, differentiate into haustorial parenchyma cells, which elongate, penetrate into the host tissues, and finally connect with the host vasculature. This interspecific vasculature connection allows the parasite to uptake water and nutrients from the host plant. Although histological aspects of haustorium development have been studied extensively, the molecular mechanisms underlying vasculature development and the interspecific connection with the host vasculature remain largely unknown. To gain insights into the interspecific cell-to-cell interactions involved in haustorium development, we established an in vitro haustorium induction system for Cuscuta campestris using Arabidopsis thaliana rosette leaves as the host plant tissue. The in vitro induction system was used to show that interaction with host tissue was required for the differentiation of parasite haustorial cells into xylem vessel cells. To further characterize the molecular events occurring during host-dependent xylem vessel cell differentiation in C. campestris, we performed a transcriptome analysis using samples from the in vitro induction system. The results showed that orthologs of genes involved in development and proliferation of vascular stem cells were up-regulated even in the absence of host tissue, whereas orthologs of genes required for xylem vessel cell differentiation were up-regulated only after some haustorial cells had elongated and contacted the host xylem. Consistent results were obtained by another transcriptome analysis of the haustorium development in C. campestris undergoing parasitization of an intact host plant. These findings suggest the involvement of host-derived signals in the regulation of non-autonomous xylem vessel differentiation and suggest that its connection to the host xylem during the haustorium development activates a set of key genes for differentiation into xylem vessel cells.
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Affiliation(s)
- Yuki Kaga
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Ryusuke Yokoyama
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Ryosuke Sano
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Misato Ohtani
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Taku Demura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Takeshi Kuroha
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Naoki Shinohara
- Faculty of Science, Kanagawa University, Hiratsuka, Kanagawa, Japan
| | - Kazuhiko Nishitani
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
- Faculty of Science, Kanagawa University, Hiratsuka, Kanagawa, Japan
- *Correspondence: Kazuhiko Nishitani,
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40
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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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41
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Lieberman-Lazarovich M, Yahav C, Israeli A, Efroni I. Deep Conservation of cis-Element Variants Regulating Plant Hormonal Responses. THE PLANT CELL 2019; 31:2559-2572. [PMID: 31467248 PMCID: PMC6881130 DOI: 10.1105/tpc.19.00129] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 08/27/2019] [Indexed: 05/14/2023]
Abstract
Phytohormones regulate many aspects of plant life by activating transcription factors (TFs) that bind sequence-specific response elements (REs) in regulatory regions of target genes. Despite their short length, REs are degenerate, with a core of just 3 to 4 bp. This degeneracy is paradoxical, as it reduces specificity and REs are extremely common in the genome. To study whether RE degeneracy might serve a biological function, we developed an algorithm for the detection of regulatory sequence conservation and applied it to phytohormone REs in 45 angiosperms. Surprisingly, we found that specific RE variants are highly conserved in core hormone response genes. Experimental evidence showed that specific variants act to regulate the magnitude and spatial profile of hormonal response in Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum). Our results suggest that hormone-regulated TFs bind a spectrum of REs, each coding for a distinct transcriptional response profile. Our approach has implications for precise genome editing and for rational promoter design.
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Affiliation(s)
- Michal Lieberman-Lazarovich
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, The Hebrew University, Rehovot 7610001, Israel
| | - Chen Yahav
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, The Hebrew University, Rehovot 7610001, Israel
| | - Alon Israeli
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, The Hebrew University, Rehovot 7610001, Israel
| | - Idan Efroni
- Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, The Hebrew University, Rehovot 7610001, Israel
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42
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Tamura T, Endo H, Suzuki A, Sato Y, Kato K, Ohtani M, Yamaguchi M, Demura T. Affinity-based high-resolution analysis of DNA binding by VASCULAR-RELATED NAC-DOMAIN7 via fluorescence correlation spectroscopy. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:298-313. [PMID: 31313414 DOI: 10.1111/tpj.14443] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/30/2019] [Accepted: 06/11/2019] [Indexed: 06/10/2023]
Abstract
VASCULAR-RELATED NAC-DOMAIN7 (VND7) is the master transcription factor for vessel element differentiation in Arabidopsis thaliana. To identify the cis-acting sequence(s) bound by VND7, we employed fluorescence correlation spectroscopy (FCS) to find VND7-DNA interactions quantitatively. This identified an 18-bp sequence from the promoter of XYLEM CYSTEINE PEPTIDASE1 (XCP1), a direct target of VND7. A quantitative assay for binding affinity between VND7 and the 18-bp sequence revealed the core nucleotides contributing to specific binding between VND7 and the 18-bp sequence. Moreover, by combining the systematic evolution of ligands by exponential enrichment (SELEX) technique with known consensus sequences, we defined a motif termed the Ideal Core Structure for binding by VND7 (ICSV). We also used FCS to search for VND7 binding sequences in the promoter regions of other direct targets. Taking these data together, we proposed that VND7 preferentially binds to the ICSV sequence. Additionally, we found that substitutions among the core nucleotides affected transcriptional regulation by VND7 in vivo, indicating that the core nucleotides contribute to vessel-element-specific gene expression. Furthermore, our results demonstrate that FCS is a powerful tool for unveiling the DNA-binding properties of transcription factors.
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Affiliation(s)
- Taizo Tamura
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Hitoshi Endo
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Aichi, 464-8602, Japan
| | - Atsunobu Suzuki
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Yutaka Sato
- Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Ko Kato
- 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
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Masatoshi Yamaguchi
- Graduate School of Science and Engineering, Saitama University, Saitama, Saitama, 338-8570, Japan
| | - Taku Demura
- 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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43
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Wang C, Chen L, Yang H, Yang S, Wang J. Genome-wide identification, expression and functional analysis of Populus xylogen-like genes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 287:110191. [PMID: 31481222 DOI: 10.1016/j.plantsci.2019.110191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 05/26/2023]
Abstract
As an extracellular arabinogalactan protein (AGP) containing a non-specific lipid transfer protein (nsLTP) domain, xylogen mediates the local intercellular communication required for tracheary element (TE) differentiation in Zinnia cell culture. Although XYLP (xylogen-like protein) gene families have been reported in Arabidopsis and rice, no comprehensive analysis has been performed in woody plants. In this work, 31 XYLP genes in five phylogenetic groups were identified from Populus trichocarpa genome and a comprehensive bioinformatic analysis including gene and protein structures, chromosomal locations and duplication events were conducted. In-silico data and qRT-PCR results indicated that PtXYLP1 is predominantly expressed in poplar apex, young leaves and roots, while PtXYLP2 is uniformly expressed across a variety of tissues with a low abundance. Analysis on PtXYLP1pro:GUS and PtXYLP2pro:GUS in Arabidopsis revealed their differential expression patterns during seed germination and specific inductions by exogenously applied phytohormones including auxin, cytokinin and GA. When overexpressed in Arabidopsis, PtXYLP1 but not PtXYLP2 resulted in cotyledons with defective venation patterns and interrupted secondary (2°) vein loops, which phenotype was underpinned by the down-regulation of genes indispensably required by embryonic venation development at procambium and/or vessel level.
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Affiliation(s)
- Caili Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Lincai Chen
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Heyu Yang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Shaohui Yang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Jiehua Wang
- School of Environmental Science and Engineering, Tianjin University, Tianjin, 300072, China.
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44
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Jean-Baptiste K, McFaline-Figueroa JL, Alexandre CM, Dorrity MW, Saunders L, Bubb KL, Trapnell C, Fields S, Queitsch C, Cuperus JT. Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana. THE PLANT CELL 2019; 31:993-1011. [PMID: 30923229 PMCID: PMC8516002 DOI: 10.1105/tpc.18.00785] [Citation(s) in RCA: 225] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/12/2019] [Accepted: 03/26/2019] [Indexed: 05/20/2023]
Abstract
Single cell RNA sequencing can yield high-resolution cell-type-specific expression signatures that reveal new cell types and the developmental trajectories of cell lineages. Here, we apply this approach to Arabidopsis (Arabidopsis thaliana) root cells to capture gene expression in 3,121 root cells. We analyze these data with Monocle 3, which orders single cell transcriptomes in an unsupervised manner and uses machine learning to reconstruct single cell developmental trajectories along pseudotime. We identify hundreds of genes with cell-type-specific expression, with pseudotime analysis of several cell lineages revealing both known and novel genes that are expressed along a developmental trajectory. We identify transcription factor motifs that are enriched in early and late cells, together with the corresponding candidate transcription factors that likely drive the observed expression patterns. We assess and interpret changes in total RNA expression along developmental trajectories and show that trajectory branch points mark developmental decisions. Finally, by applying heat stress to whole seedlings, we address the longstanding question of possible heterogeneity among cell types in the response to an abiotic stress. Although the response of canonical heat-shock genes dominates expression across cell types, subtle but significant differences in other genes can be detected among cell types. Taken together, our results demonstrate that single cell transcriptomics holds promise for studying plant development and plant physiology with unprecedented resolution.
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Affiliation(s)
- Ken Jean-Baptiste
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | | | - Cristina M Alexandre
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Michael W Dorrity
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Lauren Saunders
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Kerry L Bubb
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
- Department of Medicine, University of Washington, Seattle, Washington 98195
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
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45
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Jean-Baptiste K, McFaline-Figueroa JL, Alexandre CM, Dorrity MW, Saunders L, Bubb KL, Trapnell C, Fields S, Queitsch C, Cuperus JT. Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana. THE PLANT CELL 2019. [PMID: 30923229 DOI: 10.1101/448514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Single cell RNA sequencing can yield high-resolution cell-type-specific expression signatures that reveal new cell types and the developmental trajectories of cell lineages. Here, we apply this approach to Arabidopsis (Arabidopsis thaliana) root cells to capture gene expression in 3,121 root cells. We analyze these data with Monocle 3, which orders single cell transcriptomes in an unsupervised manner and uses machine learning to reconstruct single cell developmental trajectories along pseudotime. We identify hundreds of genes with cell-type-specific expression, with pseudotime analysis of several cell lineages revealing both known and novel genes that are expressed along a developmental trajectory. We identify transcription factor motifs that are enriched in early and late cells, together with the corresponding candidate transcription factors that likely drive the observed expression patterns. We assess and interpret changes in total RNA expression along developmental trajectories and show that trajectory branch points mark developmental decisions. Finally, by applying heat stress to whole seedlings, we address the longstanding question of possible heterogeneity among cell types in the response to an abiotic stress. Although the response of canonical heat-shock genes dominates expression across cell types, subtle but significant differences in other genes can be detected among cell types. Taken together, our results demonstrate that single cell transcriptomics holds promise for studying plant development and plant physiology with unprecedented resolution.
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Affiliation(s)
- Ken Jean-Baptiste
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | | | - Cristina M Alexandre
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Michael W Dorrity
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Lauren Saunders
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Kerry L Bubb
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
- Department of Medicine, University of Washington, Seattle, Washington 98195
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
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46
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Tan TT, Demura T, Ohtani M. Creating vessel elements in vitro: Towards a comprehensive understanding of the molecular basis of xylem vessel element differentiation. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2019; 36:1-6. [PMID: 31275042 PMCID: PMC6566013 DOI: 10.5511/plantbiotechnology.18.1119b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 11/19/2018] [Indexed: 05/30/2023]
Abstract
Xylem is an essential conductive tissue in vascular plants, and secondary cell wall polymers found in xylem vessel elements, such as cellulose, hemicellulose, and lignin, are promising sustainable bioresources. Thus, understanding the molecular mechanisms underlying xylem vessel element differentiation is an important step towards increasing woody biomass and crop yields. Establishing in vitro induction systems, in which vessel element differentiation is induced by phytohormonal stimuli or by overexpression of specific transcription factors, has been vital to this research. In this review, we present an overview of these in vitro induction systems, and describe two recently developed in vitro induction systems, VISUAL (Vascular cell Induction culture System Using Arabidopsis Leaves) and the KDB system. Furthermore, we discuss the potentials and limitations of each of these new in vitro induction systems for advancing our understanding of the molecular mechanisms driving xylem vessel element differentiation.
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Affiliation(s)
- Tian Tian Tan
- Graduate School of Science and Technology, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia
| | - Taku Demura
- 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
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47
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48
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Cubría-Radío M, Nowack MK. Transcriptional networks orchestrating programmed cell death during plant development. Curr Top Dev Biol 2018; 131:161-184. [PMID: 30612616 PMCID: PMC7116394 DOI: 10.1016/bs.ctdb.2018.10.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Transcriptional gene regulation is a fundamental biological principle in the development of eukaryotes. It does control not only cell proliferation, specification, and differentiation, but also cell death processes as an integral feature of an organism's developmental program. As in animals, developmentally regulated cell death in plants occurs in numerous contexts and is of vital importance for plant vegetative and reproductive development. In comparison with the information available on the molecular regulation of programmed cell death (PCD) in animals, however, our knowledge on plant PCD still remains scarce. Here, we discuss the functions of different classes of transcription factors that have been implicated in the control of developmentally regulated cell death. Though doubtlessly representing but a first layer of PCD regulation, information on PCD-regulating transcription factors and their targets represents a promising strategy to understand the complex machinery that ensures the precise and failsafe execution of PCD processes in plant development.
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Affiliation(s)
- Marta Cubría-Radío
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Moritz K Nowack
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium.
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