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Yang R, Wu Z, Sun Y, Liu Y, Hang Y, Liu M, Liu Y, Wang X, Liu W, Fu C. miR156-PvSPL2 controls culm development by transcriptional repression of switchgrass CYTOKININ OXIDASE/DEHYDROGENASE4. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2055-2067. [PMID: 38507513 DOI: 10.1111/tpj.16728] [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: 10/07/2023] [Revised: 02/07/2024] [Accepted: 03/09/2024] [Indexed: 03/22/2024]
Abstract
Culm development in grasses can be controlled by both miR156 and cytokinin. However, the crosstalk between the miR156-SPL module and the cytokinin metabolic pathway remains largely unknown. Here, we found CYTOKININ OXIDASE/DEHYDROGENASE4 (PvCKX4) plays a negative regulatory role in culm development of the bioenergy grass Panicum virgatum (switchgrass). Overexpression of PvCKX4 in switchgrass reduced the internode diameter and length without affecting tiller number. Interestingly, we also found that PvCKX4 was always upregulated in miR156 overexpressing (miR156OE) transgenic switchgrass lines. Additionally, upregulation of either miR156 or PvCKX4 in switchgrass reduced the content of isopentenyl adenine (iP) without affecting trans-zeatin (tZ) accumulation. It is consistent with the evidence that the recombinant PvCKX4 protein exhibited much higher catalytic activity against iP than tZ in vitro. Furthermore, our results showed that miR156-targeted SPL2 bound directly to the promoter of PvCKX4 to repress its expression. Thus, alleviating the SPL2-mediated transcriptional repression of PvCKX4 through miR156 overexpression resulted in a significant increase in cytokinin degradation and impaired culm development in switchgrass. On the contrary, suppressing PvCKX4 in miR156OE transgenic plants restored iP content, internode diameter, and length to wild-type levels. Most strikingly, the double transgenic lines retained the same increased tiller numbers as the miR156OE transgenic line, which yielded more biomass than the wild type. These findings indicate that the miR156-SPL module can control culm development through transcriptional repression of PvCKX4 in switchgrass, which provides a promising target for precise design of shoot architecture to yield more biomass from grasses.
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Affiliation(s)
- Ruijuan Yang
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Zhenying Wu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Sun
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Yangzhou University, Yangzhou, 225009, China
| | - Yuchen Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Yuqing Hang
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Min Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Yajun Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Wenwen Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
| | - Chunxiang Fu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
- Shandong Energy Institute, Qingdao, 266101, China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
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Machado KLDG, Faria DV, Duarte MBS, Silva LAS, de Oliveira TDR, Falcão TCA, Batista DS, Costa MGC, Santa-Catarina C, Silveira V, Romanel E, Otoni WC, Nogueira FTS. Plant age-dependent dynamics of annatto pigment (bixin) biosynthesis in Bixa orellana. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1390-1406. [PMID: 37975812 DOI: 10.1093/jxb/erad458] [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: 06/08/2023] [Accepted: 11/15/2023] [Indexed: 11/19/2023]
Abstract
Age affects the production of secondary metabolites, but how developmental cues regulate secondary metabolism remains poorly understood. The achiote tree (Bixa orellana L.) is a source of bixin, an apocarotenoid used in diverse industries worldwide. Understanding how age-dependent mechanisms control bixin biosynthesis is of great interest for plant biology and for economic reasons. Here we overexpressed miRNA156 (miR156) in B. orellana to comprehensively study the effects of the miR156-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) module on age-dependent bixin biosynthesis in leaves. Overexpression of miR156 in annatto plants (miR156ox) reduced BoSPL transcript levels, impacted leaf ontogeny, lessened bixin production, and increased abscisic acid levels. Modulation of expression of BoCCD4-4 and BoCCD1, key genes in carotenoid biosynthesis, was associated with diverting the carbon flux from bixin to abscisic acid in miR156ox leaves. Proteomic analyses revealed an overall low accumulation of most secondary metabolite-related enzymes in miR156ox leaves, suggesting that miR156-targeted BoSPLs may be required to activate several secondary metabolic pathways. Our findings suggest that the conserved BomiR156-BoSPL module is deployed to regulate leaf dynamics of bixin biosynthesis, and may create novel opportunities to fine-tune bixin output in B. orellana breeding programs.
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Affiliation(s)
- Kleiton Lima de Godoy Machado
- Departamento de Biologia Vegetal/Laboratório de Cultura de Tecidos Vegetais/BIOAGRO, Campus Universitário, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Daniele Vidal Faria
- Departamento de Biologia Vegetal/Laboratório de Cultura de Tecidos Vegetais/BIOAGRO, Campus Universitário, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Marcos Bruno Silva Duarte
- Departamento de Biologia Vegetal/Laboratório de Cultura de Tecidos Vegetais/BIOAGRO, Campus Universitário, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Lázara Aline Simões Silva
- Departamento de Biologia Vegetal/Laboratório de Cultura de Tecidos Vegetais/BIOAGRO, Campus Universitário, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Tadeu Dos Reis de Oliveira
- Laboratório de Biologia Celular e Tecidual (LBCT), Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), 28013-602, Campos dos Goytacazes, RJ, Brazil
| | - Thais Castilho Arruda Falcão
- Laboratório de Genômica de Plantas e Bioenergia (PGEMBL), Departamento de Biotecnologia, Escola de Engenharia de Lorena (EEL), Universidade de São Paulo (USP), 12602-810, Lorena, SP, Brazil
| | - Diego Silva Batista
- Departamento de Agricultura, Universidade Federal da Paraíba, Campus III, 58220-000, Bananeiras, PB, Brazil
| | | | - Claudete Santa-Catarina
- Laboratório de Biologia Celular e Tecidual (LBCT), Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), 28013-602, Campos dos Goytacazes, RJ, Brazil
| | - Vanildo Silveira
- Laboratório de Biotecnologia (LBT), CBB-UENF, Campos dos Goytacazes, RJ, Brazil
| | - Elisson Romanel
- Laboratório de Genômica de Plantas e Bioenergia (PGEMBL), Departamento de Biotecnologia, Escola de Engenharia de Lorena (EEL), Universidade de São Paulo (USP), 12602-810, Lorena, SP, Brazil
| | - Wagner Campos Otoni
- Departamento de Biologia Vegetal/Laboratório de Cultura de Tecidos Vegetais/BIOAGRO, Campus Universitário, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
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Xue G, Wu W, Fan Y, Ma C, Xiong R, Bai Q, Yao X, Weng W, Cheng J, Ruan J. Genome-wide identification, evolution, and role of SPL gene family in beet (Beta vulgaris L.) under cold stress. BMC Genomics 2024; 25:101. [PMID: 38262939 PMCID: PMC10804631 DOI: 10.1186/s12864-024-09995-5] [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: 11/14/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND SPL transcription factors play vital roles in regulating plant growth, development, and abiotic stress responses. Sugar beet (Beta vulgaris L.), one of the world's main sugar-producing crops, is a major source of edible and industrial sugars for humans. Although the SPL gene family has been extensively identified in other species, no reports on the SPL gene family in sugar beet are available. RESULTS Eight BvSPL genes were identified at the whole-genome level and were renamed based on their positions on the chromosome. The gene structure, SBP domain sequences, and phylogenetic relationship with Arabidopsis were analyzed for the sugar beet SPL gene family. The eight BvSPL genes were divided into six groups (II, IV, V, VI, VII, and VIII). Of the BvSPL genes, no tandem duplication events were found, but one pair of segmental duplications was present. Multiple cis-regulatory elements related to growth and development were identified in the 2000-bp region upstream of the BvSPL gene start codon (ATG). Using quantitative real-time polymerase chain reaction (qRT-PCR), the expression profiles of the eight BvSPL genes were examined under eight types of abiotic stress and during the maturation stage. BvSPL transcription factors played a vital role in abiotic stress, with BvSPL3 and BvSPL6 being particularly noteworthy. CONCLUSION Eight sugar beet SPL genes were identified at the whole-genome level. Phylogenetic trees, gene structures, gene duplication events, and expression profiles were investigated. The qRT-PCR analysis indicated that BvSPLs play a substantial role in the growth and development of sugar beet, potentially participating in the regulation of root expansion and sugar accumulation.
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Affiliation(s)
- Guoxing Xue
- College of Agriculture, Guizhou University, 550025, Guiyang, People's Republic of China
| | - Weijiao Wu
- College of Agriculture, Guizhou University, 550025, Guiyang, People's Republic of China
| | - Yue Fan
- College of Food Science and Engineering, Xinjiang Institute of Technology, 843199, Aksu, People's Republic of China
| | - Chao Ma
- College of Agriculture, Guizhou University, 550025, Guiyang, People's Republic of China
| | - Ruiqi Xiong
- College of Agriculture, Guizhou University, 550025, Guiyang, People's Republic of China
| | - Qing Bai
- College of Agriculture, Guizhou University, 550025, Guiyang, People's Republic of China
| | - Xin Yao
- College of Agriculture, Guizhou University, 550025, Guiyang, People's Republic of China
| | - Wenfeng Weng
- College of Agriculture, Guizhou University, 550025, Guiyang, People's Republic of China
| | - Jianping Cheng
- College of Agriculture, Guizhou University, 550025, Guiyang, People's Republic of China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, 550025, Guiyang, People's Republic of China.
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Yang L, Ping T, Lu W, Song S, Wang J, Wang Q, Chai G, Bai Y, Chen Y. Genome-wide identification of auxin-responsive microRNAs in the poplar stem. Genes Genomics 2023:10.1007/s13258-023-01385-7. [PMID: 37336805 DOI: 10.1007/s13258-023-01385-7] [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: 09/27/2022] [Accepted: 04/01/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND Wood (secondary xylem) of forests is a material of great economic importance. Wood development is strictly controlled by both the phytohormone auxin and microRNAs (miRNAs). Currently, the regulatory mechanisms underlying wood formation by auxin-associated miRNAs remain unclear. OBJECTIVE This report was designed to identify auxin-responsive miRNAs during wood formation. METHODS Morphological observation of wood development in the poplar stems was performed under the treatment of different concentrations (0 mg/L, CK; 5 mg/L, Low; 10 mg/L, High) of indol-3-butyric acid (IBA). Using a small RNA sequencing strategy, the effect of IBA treatment on miRNAs expression was genome-widely analyzed. RESULTS In this study, we found that wood development of poplar was promoted by low concentration of IBA treatment but inhibited by high concentration of IBA treatment. Stringent bioinformatic analysis led to identification of 118 known and 134 novel miRNAs candidates. Sixty-nine unique developmental-related miRNAs, corresponding to 269 target genes, exhibited specific expression patterns in response to auxin, as was consistent with the influence of auxin application on wood formation. Three novel miRNAs had the most number (≥ 9) of target genes, belonging to SPL, GRF and ARF gene families. The evolutionary relationships and tissue expression patterns of 41 SPL, GRF and ARF genes in poplar were thus analyzed. Of them, four representative members and corresponding miRNAs were confirmed using RT-qPCR. CONCLUSIONS Our results may be helpful for a better understanding of auxin-induced regulation of wood formation in tree species.
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Affiliation(s)
- Lihua Yang
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Tao Ping
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Wenjin Lu
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Sangfa Song
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jianli Wang
- Grass and Science Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Qiao Wang
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Guohua Chai
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying, 257000, China
| | - Yue Bai
- Forestry College, Inner Mongolia Agricultural University, Huhhot, 010018, China.
| | - Yan Chen
- Forestry College, Inner Mongolia Agricultural University, Huhhot, 010018, China.
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266109, China.
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Yang R, Liu W, Sun Y, Sun Z, Wu Z, Wang Y, Wang M, Wang H, Bai S, Fu C. LATERAL BRANCHING OXIDOREDUCTASE, one novel target gene of Squamosa Promoter Binding Protein-like 2, regulates tillering in switchgrass. THE NEW PHYTOLOGIST 2022; 235:563-575. [PMID: 35383390 PMCID: PMC9321131 DOI: 10.1111/nph.18140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Strigolactones (SLs) play a critical role in regulating plant tiller number. LATERAL BRANCHING OXIDOREDUCTASE (LBO) encodes an important late-acting enzyme for SL biosynthesis and regulates shoot branching in Arabidopsis. However, little is known about the function of LBO in monocots including switchgrass (Panicum virgatum L.), a dual-purpose fodder and biofuel crop. We studied the function of PvLBO via the genetic manipulation of its expression levels in both the wild-type and miR156 overexpressing (miR156OE ) switchgrass. Co-expression analysis, quantitative real-time polymerase chain reaction (qRT-PCR), transient dual luciferase assay, and chromatin immunoprecipitation-qPCR were all used to determine the activation of PvLBO by miR156-targeted Squamosa Promoter Binding Protein-like 2 (PvSPL2) in regulating tillering of switchgrass. PvLBOtranscripts dramatically declined in miR156OE transgenic switchgrass, and the overexpression of PvLBO in the miR156OE transgenic line produce fewer tillers than the control. Furthermore, we found that PvSPL2 can directly bind to the promoter of PvLBO and activate its transcription, suggesting that PvLBO is a novel downstream gene of PvSPL2. We propose that PvLBO functions as an SL biosynthetic gene to mediate tillering and acts as an important downstream factor in the crosstalk between the SL biosynthetic pathway and the miR156-SPL module in switchgrass.
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Affiliation(s)
- Ruijuan Yang
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao266101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Wenwen Liu
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao266101China
| | - Ying Sun
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao266101China
| | - Zhichao Sun
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao266101China
| | - Zhenying Wu
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao266101China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yamei Wang
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao266101China
| | - Mengqi Wang
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao266101China
| | - Honglun Wang
- CAS Key Laboratory of Tibetan Medicine ResearchNorthwest Institute of Plateau BiologyChinese Academy of SciencesXining810008China
| | - Shiqie Bai
- Sichuan Academy of Grassland ScienceChengdu611731China
| | - Chunxiang Fu
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdao266101China
- University of Chinese Academy of SciencesBeijing100049China
- CAS Key Laboratory of Tibetan Medicine ResearchNorthwest Institute of Plateau BiologyChinese Academy of SciencesXining810008China
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He F, Long R, Wei C, Zhang Y, Li M, Kang J, Yang Q, Wang Z, Chen L. Genome-wide identification, phylogeny and expression analysis of the SPL gene family and its important role in salt stress in Medicago sativa L. BMC PLANT BIOLOGY 2022; 22:295. [PMID: 35705909 PMCID: PMC9199161 DOI: 10.1186/s12870-022-03678-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 06/03/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND SQUAMOSA promoter-binding protein-like (SPL) transcription factors are widely present in plants and are involved in signal transduction, the stress response and development. The SPL gene family has been characterized in several model species, such as A. thaliana and G. max. However, there is no in-depth analysis of the SPL gene family in forage, especially alfalfa (Medicago sativa L.), one of the most important forage crops worldwide. RESULT In total, 76 putative MsSPL genes were identified in the alfalfa genome with an uneven distribution. Based on their identity and gene structure, these MsSPLs were divided into eight phylogenetic groups. Seventy-three MsSPL gene pairs arose from segmental duplication events, and the MsSPLs on the four subgenomes of individual chromosomes displayed high collinearity with the corresponding M. truncatula genome. The prediction of the cis-elements in the promoter regions of the MsSPLs detected two copies of ABA (abscisic acid)-responsive elements (ABREs) on average, implying their potential involvement in alfalfa adaptation to adverse environments. The transcriptome sequencing of MsSPLs in roots and leaves revealed that 54 MsSPLs were expressed in both tissues. Upon salt treatment, three MsSPLs (MsSPL17, MsSPL23 and MsSPL36) were significantly regulated, and the transcription level of MsSPL36 in leaves was repressed to 46.6% of the control level. CONCLUSION In this study, based on sequence homology, we identified 76 SPL genes in the alfalfa. The SPLs with high identity shared similar gene structures and motifs. In total, 71.1% (54 of 76) of the MsSPLs were expressed in both roots and leaves, and the majority (74.1%) preferred underground tissues to aerial tissues. MsSPL36 in leaves was significantly repressed under salt stress. These findings provide comprehensive information regarding the SPB-box gene family for improve alfalfa tolerance to high salinity.
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Affiliation(s)
- Fei He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ruicai Long
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Chunxue Wei
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yunxiu Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Mingna Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Junmei Kang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qingchuan Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zhen Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Lin Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Cai J, Liu W, Li W, Zhao L, Chen G, Bai Y, Ma D, Fu C, Wang Y, Zhang X. Downregulation of miR156-Targeted PvSPL6 in Switchgrass Delays Flowering and Increases Biomass Yield. FRONTIERS IN PLANT SCIENCE 2022; 13:834431. [PMID: 35251105 PMCID: PMC8894730 DOI: 10.3389/fpls.2022.834431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
MiR156/SQUAMOSA PROMOTER BINDING-LIKEs (SPLs) module is the key regulatory hub of juvenile-to-adult phase transition as a critical flowering regulator. In this study, a miR156-targeted PvSPL6 was identified and characterized in switchgrass (Panicum virgatum L.), a dual-purpose fodder and biofuel crop. Overexpression of PvSPL6 in switchgrass promoted flowering and reduced internode length, internode number, and plant height, whereas downregulation of PvSPL6 delayed flowering and increased internode length, internode number, and plant height. Protein subcellular localization analysis revealed that PvSPL6 localizes to both the plasma membrane and nucleus. We produced transgenic switchgrass plants that overexpressed a PvSPL6-GFP fusion gene, and callus were induced from inflorescences of selected PvSPL6-GFPOE transgenic lines. We found that the PvSPL6-GFP fusion protein accumulated mainly in the nucleus in callus and was present in both the plasma membrane and nucleus in regenerating callus. However, during subsequent development, the signal of the PvSPL6-GFP fusion protein was detected only in the nucleus in the roots and leaves of plantlets. In addition, PvSPL6 protein was rapidly transported from the nucleus to the plasma membrane after exogenous GA3 application, and returned from the plasma membrane to nucleus after treated with the GA3 inhibitor (paclobutrazol). Taken together, our results demonstrate that PvSPL6 is not only an important target that can be used to develop improved cultivars of forage and biofuel crops that show delayed flowering and high biomass yields, but also has the potential to regulate plant regeneration in response to GA3.
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Affiliation(s)
- Jinjun Cai
- College of Natural Resources and Environment, Northwest Agriculture and Forestry University, Yangling, China
- Institute of Agricultural Resources and Environment, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Wenwen Liu
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Weiqian Li
- Institute of Agricultural Resources and Environment, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Lijuan Zhao
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan, China
| | - Gang Chen
- Institute of Agricultural Resources and Environment, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Yangyang Bai
- Institute of Agricultural Resources and Environment, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Dongmei Ma
- Breeding Base for State Key Laboratory of Land Degradation and Ecological Restoration in Northwest China, Ningxia University, Yinchuan, China
| | - Chunxiang Fu
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- CAS Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Xining, China
| | - Yamei Wang
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Xinchang Zhang
- College of Natural Resources and Environment, Northwest Agriculture and Forestry University, Yangling, China
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Su K, Wu Z, Liu Y, Jiang S, Ma D, Wang Y, Fu C. Highly efficient detoxification of dinitrotoluene by transgenic switchgrass overexpressing bacterial nitroreductase. PLANT, CELL & ENVIRONMENT 2021; 44:3173-3183. [PMID: 34008171 DOI: 10.1111/pce.14099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/12/2021] [Indexed: 06/12/2023]
Abstract
Dinitrotoluene (DNT) has been extensively used in manufacturing munitions, polyurethane foams and other important chemical products. However, it is highly toxic and mutagenic to most organisms. Here, we synthesized a codon-optimized bacterial nitroreductase gene, NfsI, for plant expression. The kinetic analysis indicates that the recombinant NfsI can detoxify both 2,4-DNT and its sulfonate (DNTS), while it has a 97.6-fold higher catalytic efficiency for 2,4-DNT than DNTS. Furthermore, we overexpressed NfsI in switchgrass (Panicum virgatum L.), which is a multiple-purpose crop used for fodder and biofuel production as well as phytoremediation. The 2,4-DNT treatment inhibited root elongation of wild-type switchgrass plants and promoted reactive oxygen species (ROS) accumulation in roots. In contrast, overexpression of NfsI in switchgrass significantly alleviated 2,4-DNT-induced root growth inhibition and ROS overproduction. Thus, the NfsI overexpressing transgenic switchgrass plant removed 94.1% 2,4-DNT after 6 days, whose efficiency was 1.7-fold higher than control plants. Moreover, the comparative transcriptome analysis suggests that 22.9% of differentially expressed genes induced by 2,4-DNT may participate in NfsI-mediated 2,4-DNT detoxification in switchgrass. Our work sheds light on the function of NfsI during DNT phytoremediation for the first time, revealing the application potential of switchgrass plants engineered with NfsI.
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Affiliation(s)
- Kunlong Su
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhenying Wu
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Yuchen Liu
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Shanshan Jiang
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Dongmei Ma
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- School of ecology environment, Ningxia University, Yinchuan, China
| | - Yan Wang
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chunxiang Fu
- Shandong Provincial Key Laboratory of Energy Genetics and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
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Liu Y, Yan J, Wang K, Li D, Yang R, Luo H, Zhang W. MiR396-GRF module associates with switchgrass biomass yield and feedstock quality. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1523-1536. [PMID: 33567151 PMCID: PMC8384596 DOI: 10.1111/pbi.13567] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 05/10/2023]
Abstract
Improving plant biomass yield and/or feedstock quality for highly efficient lignocellulose conversion has been the main research focus in genetic modification of switchgrass (Panicum virgatum L.), a dedicated model plant for biofuel production. Here, we proved that overexpression of miR396 (OE-miR396) leads to reduced plant height and lignin content mainly by reducing G-lignin monomer content. We identified nineteen PvGRFs in switchgrass and proved thirteen of them were cleaved by miR396. MiR396-targeted PvGRF1, PvGRF9 and PvGRF3 showed significantly higher expression in stem. By separately overexpressing rPvGRF1, 3 and 9, in which synonymous mutations abolished the miR396 target sites, and suppression of PvGRF1/3/9 activity via PvGRF1/3/9-SRDX overexpression in switchgrass, we confirmed PvGRF1 and PvGRF9 played positive roles in improving plant height and G-lignin content. Overexpression of PvGRF9 was sufficient to complement the defective phenotype of OE-miR396 plants. MiR396-PvGRF9 modulates these traits partly by interfering GA and auxin biosynthesis and signalling transduction and cell wall lignin, glucose and xylan biosynthesis pathways. Moreover, by enzymatic hydrolysis analyses, we found that overexpression of rPvGRF9 significantly enhanced per plant sugar yield. Our results suggest that PvGRF9 can be utilized as a candidate molecular tool in modifying plant biomass yield and feedstock quality.
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Affiliation(s)
- Yanrong Liu
- College of Grassland Science and technologyChina Agricultural UniversityBeijingChina
| | - Jianping Yan
- College of Grassland Science and technologyChina Agricultural UniversityBeijingChina
| | - Kexin Wang
- College of Grassland Science and technologyChina Agricultural UniversityBeijingChina
| | - Dayong Li
- College of Life SciencesShandong Normal UniversityJinanShandongChina
| | - Rui Yang
- Beijing Key Laboratory of New Technology in Agricultural ApplicationCollege of Plant Science and TechnologyBeijing University of AgricultureBeijingChina
| | - Hong Luo
- Department of Genetics and BiochemistryClemson UniversityClemsonSCUSA
| | - Wanjun Zhang
- College of Grassland Science and technologyChina Agricultural UniversityBeijingChina
- Key Lab of Grassland Science in BeijingChina Agricultural UniversityBeijingChina
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Lin CY, Donohoe BS, Bomble YJ, Yang H, Yunes M, Sarai NS, Shollenberger T, Decker SR, Chen X, McCann MC, Tucker MP, Wei H, Himmel ME. Iron incorporation both intra- and extra-cellularly improves the yield and saccharification of switchgrass (Panicum virgatum L.) biomass. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:55. [PMID: 33663584 PMCID: PMC7931346 DOI: 10.1186/s13068-021-01891-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 01/27/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Pretreatments are commonly used to facilitate the deconstruction of lignocellulosic biomass to its component sugars and aromatics. Previously, we showed that iron ions can be used as co-catalysts to reduce the severity of dilute acid pretreatment of biomass. Transgenic iron-accumulating Arabidopsis and rice plants exhibited higher iron content in grains, increased biomass yield, and importantly, enhanced sugar release from the biomass. RESULTS In this study, we used intracellular ferritin (FerIN) alone and in combination with an improved version of cell wall-bound carbohydrate-binding module fused iron-binding peptide (IBPex) specifically targeting switchgrass, a bioenergy crop species. The FerIN switchgrass improved by 15% in height and 65% in yield, whereas the FerIN/IBPex transgenics showed enhancement up to 30% in height and 115% in yield. The FerIN and FerIN/IBPex switchgrass had 27% and 51% higher in planta iron accumulation than the empty vector (EV) control, respectively, under normal growth conditions. Improved pretreatability was observed in FerIN switchgrass (~ 14% more glucose release than the EV), and the FerIN/IBPex plants showed further enhancement in glucose release up to 24%. CONCLUSIONS We conclude that this iron-accumulating strategy can be transferred from model plants and applied to bioenergy crops, such as switchgrass. The intra- and extra-cellular iron incorporation approach improves biomass pretreatability and digestibility, providing upgraded feedstocks for the production of biofuels and bioproducts.
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Affiliation(s)
- Chien-Yuan Lin
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
- Present Address: Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608 USA
- Present Address: Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Bryon S. Donohoe
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Yannick J. Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Haibing Yang
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 USA
- Present Address: South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 China
| | - Manal Yunes
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
- Present Address: Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO 80309 USA
| | - Nicholas S. Sarai
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
- Present Address: Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 USA
| | - Todd Shollenberger
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Stephen R. Decker
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Xiaowen Chen
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Maureen C. McCann
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 USA
| | - Melvin P. Tucker
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Hui Wei
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Michael E. Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
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Zhang HX, Feng XH, Jin JH, Khan A, Guo WL, Du XH, Gong ZH. CaSBP11 Participates in the Defense Response of Pepper to Phytophthora capsici through Regulating the Expression of Defense-Related Genes. Int J Mol Sci 2020; 21:E9065. [PMID: 33260627 PMCID: PMC7729508 DOI: 10.3390/ijms21239065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/21/2022] Open
Abstract
Squamosa promoter binding protein (SBP)-box genes are plant-specific transcription factors involved in plant growth and development, morphogenesis and biotic and abiotic stress responses. However, these genes have been understudied in pepper, especially with respect to defense responses to Phytophthora capsici infection. CaSBP11 is a SBP-box family gene in pepper that was identified in our previous research. Silencing CaSBP11 enhanced the defense response of pepper plants to Phytophthora capsici. Without treatment, the expression of defense-related genes (CaBPR1, CaPO1, CaSAR8.2 and CaDEF1) increased in CaSBP11-silenced plants. However, the expression levels of these genes were inhibited under transient CaSBP11 expression. CaSBP11 overexpression in transgenic Nicotiana benthamiana decreased defense responses, while in Arabidopsis, it induced or inhibited the expression of genes in the salicylic acid and jasmonic acid signaling pathways. CaSBP11 overexpression in sid2-2 mutants induced AtNPR1, AtNPR3, AtNPR4, AtPAD4, AtEDS1, AtEDS5, AtMPK4 and AtNDR1 expression, while AtSARD1 and AtTGA6 expression was inhibited. CaSBP11 overexpression in coi1-21 and coi1-22 mutants, respectively, inhibited AtPDF1.2 expression and induced AtPR1 expression. These results indicate CaSBP11 has a negative regulatory effect on defense responses to Phytophthora capsici. Moreover, it may participate in the defense response of pepper to Phytophthora capsici by regulating defense-related genes and the salicylic and jasmonic acid-mediated disease resistance signaling pathways.
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Affiliation(s)
- Huai-Xia Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; (H.-X.Z.); (X.-H.F.); (J.-H.J.)
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China; (W.-L.G.); (X.-H.D.)
| | - Xiao-Hui Feng
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; (H.-X.Z.); (X.-H.F.); (J.-H.J.)
| | - Jing-Hao Jin
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; (H.-X.Z.); (X.-H.F.); (J.-H.J.)
| | - Abid Khan
- Department of Horticulture, The University of Haripur, Haripur 22620, Pakistan;
| | - Wei-Li Guo
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China; (W.-L.G.); (X.-H.D.)
| | - Xiao-Hua Du
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xinxiang 453003, China; (W.-L.G.); (X.-H.D.)
| | - Zhen-Hui Gong
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; (H.-X.Z.); (X.-H.F.); (J.-H.J.)
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Wang Y, Liu W, Wang X, Yang R, Wu Z, Wang H, Wang L, Hu Z, Guo S, Zhang H, Lin J, Fu C. MiR156 regulates anthocyanin biosynthesis through SPL targets and other microRNAs in poplar. HORTICULTURE RESEARCH 2020; 7:118. [PMID: 32821401 PMCID: PMC7395715 DOI: 10.1038/s41438-020-00341-w] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/23/2020] [Accepted: 05/12/2020] [Indexed: 05/20/2023]
Abstract
Anthocyanins biosynthesized from the flavonoid pathway are types of pigments that are involved in the protection of poplar from biotic and abiotic stresses. Previous researchers studying anthocyanin-related transcription factors and structural genes in poplar have made significant discoveries. However, little is known about the regulatory role of microRNAs in anthocyanin biosynthesis in poplar. Here, we overexpressed miR156 in poplar to study the comprehensive effects of the miR156-SPL module on the biosynthesis of anthocyanins. Small RNA sequencing analysis revealed 228 microRNAs differentially expressed in transgenic poplar plants with dramatically increased miR156 levels. Furthermore, integrated microRNAomic and transcriptomic analysis suggested that two microRNAs, miR160h, and miR858, have the potential to affect anthocyanin accumulation in poplar by regulating auxin response factors and MYB transcription factors, respectively. Additionally, the accumulation of miR160h and miR858 displayed a positive correlation with miR156 levels, suggesting a possible interaction between the miR156-SPL module and these microRNAs in poplar. Last, metabolomics analysis revealed that the levels of anthocyanins, flavones, and flavonols were substantially elevated in transgenic poplar plants overexpressing miR156 compared with the wild type, whereas the total lignin content was reduced in the transgenic plants. Taken together, our results indicate that miR156 can fine tune the anthocyanin biosynthetic pathway via multiple factors, including microRNAs, transcription factors, and the levels of structural genes, in poplar. This provides additional clues for understanding the complex regulatory network of anthocyanin biosynthesis in woody plants.
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Affiliation(s)
- Yamei Wang
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Wenwen Liu
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Xinwei Wang
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, 10083 China
| | - Ruijuan Yang
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhenying Wu
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Han Wang
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Lei Wang
- Collaborative Innovation Center of Crop Stress Biology, Henan Province and Institute of Plant Stress Biology, Henan University, Kaifeng, 475001 China
| | - Zhubing Hu
- Collaborative Innovation Center of Crop Stress Biology, Henan Province and Institute of Plant Stress Biology, Henan University, Kaifeng, 475001 China
| | - Siyi Guo
- Collaborative Innovation Center of Crop Stress Biology, Henan Province and Institute of Plant Stress Biology, Henan University, Kaifeng, 475001 China
| | - Hailing Zhang
- Grass and Science Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang China
| | - Jinxing Lin
- College of Biological Sciences & Biotechnology, Beijing Forestry University, Beijing, 10083 China
| | - Chunxiang Fu
- Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
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13
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Lai T, Wang X, Ye B, Jin M, Chen W, Wang Y, Zhou Y, Blanks AM, Gu M, Zhang P, Zhang X, Li C, Wang H, Liu Y, Gallusci P, Tör M, Hong Y. Molecular and functional characterization of the SBP-box transcription factor SPL-CNR in tomato fruit ripening and cell death. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2995-3011. [PMID: 32016417 PMCID: PMC7260717 DOI: 10.1093/jxb/eraa067] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/01/2020] [Indexed: 05/19/2023]
Abstract
SlSPL-CNR, an SBP-box transcription factor (TF) gene residing at the epimutant Colourless non-ripening (Cnr) locus, is involved in tomato ripening. This epimutant provides a unique model to investigate the (epi)genetic basis of fruit ripening. Here we report that SlSPL-CNR is a nucleus-localized protein with a distinct monopartite nuclear localization signal (NLS). It consists of four consecutive residues ' 30KRKR33' at the N-terminus of the protein. Mutation of the NLS abolishes SlSPL-CNR's ability to localize in the nucleus. SlSPL-CNR comprises two zinc-finger motifs (ZFMs) within the C-terminal SBP-box domain. Both ZFMs contribute to zinc-binding activity. SlSPL-CNR can induce cell death in tomato and tobacco, dependent on its nuclear localization. However, the two ZFMs have differential impacts on SlSPL-CNR's induction of severe necrosis or mild necrotic ringspot. NLS and ZFM mutants cannot complement Cnr fruits to ripen. SlSPL-CNR interacts with SlSnRK1. Virus-induced SlSnRK1 silencing leads to reduction in expression of ripening-related genes and inhibits ripening in tomato. We conclude that SlSPL-CNR is a multifunctional protein that consists of a distinct monopartite NLS, binds to zinc, and interacts with SlSnRK1 to affect cell death and tomato fruit ripening.
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Affiliation(s)
- Tongfei Lai
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xiaohong Wang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Bishun Ye
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Mingfei Jin
- School of Life Sciences, East China Normal University, Shanghai, China
- Warwick-Hangzhou Joint RNA Signaling Laboratory, School of Life Sciences, University of Warwick, Coventry, UK
| | - Weiwei Chen
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Ying Wang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yingying Zhou
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Andrew M Blanks
- Cell and Developmental Biology, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Mei Gu
- The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xinlian Zhang
- Department of Family Medicine and Public Health, Division of Biostatistics & Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Chunyang Li
- Warwick-Hangzhou Joint RNA Signaling Laboratory, School of Life Sciences, University of Warwick, Coventry, UK
| | - Huizhong Wang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Philippe Gallusci
- Laboratory of Grape Ecophysiology and Functional Biology, Bordeaux University, INRA, Bordeaux Science Agro, Villenave d’Ornon, France
| | - Mahmut Tör
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, School of Science and the Environment, University of Worcester, Worcester, UK
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Warwick-Hangzhou Joint RNA Signaling Laboratory, School of Life Sciences, University of Warwick, Coventry, UK
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, School of Science and the Environment, University of Worcester, Worcester, UK
- Correspondence: , or
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14
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Yu N, Yang JC, Yin GT, Li RS, Zou WT. Genome-wide characterization of the SPL gene family involved in the age development of Jatropha curcas. BMC Genomics 2020; 21:368. [PMID: 32434522 PMCID: PMC7238634 DOI: 10.1186/s12864-020-06776-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/10/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND SPL (SQUAMOSA-promoter binding protein-like) proteins form a large family of plant-specific transcription factors that play essential roles in various aspects of plant growth and development. They are potentially important candidates for genetic improvement of agronomic traits. However, there were limited information about the SPL genes in Jatropha curcas, an important biofuel plant. RESULTS In Jatropha, 15 JcSPL genes were identified. Phylogenetic analysis revealed that most of the JcSPLs were closely related to SPLs from woody plant rather than herbaceous plant and distantly related to monocotyledon SPLs. Gene structure, conserved motif and repetitive sequence analysis indicated diverse and specific functions of some JcSPL genes. By combination of target prediction and degradome sequencing analysis, 10 of the 15 JcSPLs were shown to be targets of JcmiR156. Quantitative PCR analysis showed diversified spatial-temporal expression patterns of JcSPLs. It is interesting that the expression levels of JcSPL3 were the highest in all tissues examined in 7- or 10-year-old plants and exhibited increasing trend with plant age, suggesting its important role in the regulation of age development in Jatropha. Overexpression of JcSPL3 in Arabidopsis resulted in earlier flowering time, shorter silique length and reduced biomass of roots. CONCLUSIONS Through comprehensive and systematic analysis of phylogenetic relationships, conserved motifs, gene structures, chromosomal locations, repetitive sequence and expression patterns, 15 JcSPL genes were identified in Jatropha and characterized in great detail. These results provide deep insight into the evolutionary origin and biological significance of plant SPLs and lay the foundation for further functional characterization of JcSPLs with the purpose of genetic improvement in Jatropha.
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Affiliation(s)
- Niu Yu
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Number 682, Guang Shan Yi Road, Longdong District, Guangzhou, 510520, China.
| | - Jin-Chang Yang
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Number 682, Guang Shan Yi Road, Longdong District, Guangzhou, 510520, China
| | - Guang-Tian Yin
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Number 682, Guang Shan Yi Road, Longdong District, Guangzhou, 510520, China
| | - Rong-Sheng Li
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Number 682, Guang Shan Yi Road, Longdong District, Guangzhou, 510520, China
| | - Wen-Tao Zou
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Number 682, Guang Shan Yi Road, Longdong District, Guangzhou, 510520, China
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15
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Ma J, Zhao P, Liu S, Yang Q, Guo H. The Control of Developmental Phase Transitions by microRNAs and Their Targets in Seed Plants. Int J Mol Sci 2020; 21:E1971. [PMID: 32183075 PMCID: PMC7139601 DOI: 10.3390/ijms21061971] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 02/29/2020] [Accepted: 03/12/2020] [Indexed: 12/18/2022] Open
Abstract
Seed plants usually undergo various developmental phase transitions throughout their lifespan, mainly including juvenile-to-adult and vegetative-to-reproductive transitions, as well as developmental transitions within organ/tissue formation. MicroRNAs (miRNAs), as a class of small endogenous non-coding RNAs, are involved in the developmental phase transitions in plants by negatively regulating the expression of their target genes at the post-transcriptional level. In recent years, cumulative evidence has revealed that five miRNAs, miR156, miR159, miR166, miR172, and miR396, are key regulators of developmental phase transitions in plants. In this review, the advanced progress of the five miRNAs and their targets in regulating plant developmental transitions, especially in storage organ formation, are summarized and discussed, combining our own findings with the literature. In general, the functions of the five miRNAs and their targets are relatively conserved, but their functional divergences also emerge to some extent. In addition, potential research directions of miRNAs in regulating plant developmental phase transitions are prospected.
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Affiliation(s)
- Jingyi Ma
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, China; (J.M.); (P.Z.); (Q.Y.)
| | - Pan Zhao
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, China; (J.M.); (P.Z.); (Q.Y.)
| | - Shibiao Liu
- College of Biology and Environmental Sciences, Jishou University, Jishou 416000, China;
| | - Qi Yang
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, China; (J.M.); (P.Z.); (Q.Y.)
| | - Huihong Guo
- College of Biological Sciences and Biotechnology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, No. 35, Tsing Hua East Road, Haidian District, Beijing 100083, China; (J.M.); (P.Z.); (Q.Y.)
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Liu Y, Yan J, Wang K, Li D, Han Y, Zhang W. Heteroexpression of Osa- miR319b improved switchgrass biomass yield and feedstock quality by repression of PvPCF5. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:56. [PMID: 32206089 PMCID: PMC7081615 DOI: 10.1186/s13068-020-01693-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/02/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Switchgrass (Panicum virgatum L.), a C4 perennial grass, has been recognized as one of the most potentially important lignocellulose biofuel crops. MicroRNA319 (miR319) plays a key role in plant development, abiotic resistance, and cell wall biosynthesis by repressing expression of its target TCP genes. We hypothesized miR319-TCP pathway could play important roles in switchgrass feedstock characteristics for biofuel production, and produced switchgrass transgenic plants overexpressing miR319 (by ectopic expressing Osa-MIR319b gene), blocking miR319 (by overexpressing a target mimicry of miR319/MIM319) and repression of miR319 target gene PvPCF5. Plant phenotype, biomass yield, and feedstock quality of transgenic plants were analyzed. RESULTS Overexpression of miR319 in switchgrass promoted leaf elongation and expansion of transgenic plants, increased plant height, stem diameter, and resulted in a significant increase in plant biomass yield. Transgenic plants overexpressing of miR319 reduced lignin content, showed significantly higher enzymatic hydrolysis efficiency compared to the wild type plant. However, opposite results were observed in the MIM319 plants. Furthermore, suppression of miR319 target gene PvPCF5 activity also reduced lignin content, increased lignin monomer S/G ratio and the proportion of β-O-4 linkages, while significantly improving the sugar production per plant. Quantitative real-time (qRT-PCR) analysis indicated that expression of PvMYB58/63B and PvHCT with predicted TCP binding sites in their promoter regions was negatively regulated by miR319-PvPCF5 module. CONCLUSIONS MiR319-PvPCF5 module plays positive roles in regulating biomass yield and quality of switchgrass. It can be utilized as a candidate molecular tool in regulating biomass yield and feedstock quality. The finding could also be transferred to other grasses for forage quality improvement through genetic manipulation.
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Affiliation(s)
- Yanrong Liu
- College of Biological Science, China Agricultural University, Beijing, 100193 People’s Republic of China
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Jianping Yan
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Kexin Wang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Dayong Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097 People’s Republic of China
| | - Yejun Han
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190 China
| | - Wanjun Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193 People’s Republic of China
- National Energy R &D Center for Biomass (NECB), China Agricultural University, Beijing, 100193 People’s Republic of China
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17
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Zhang X, Xie S, Han J, Zhou Y, Liu C, Zhou Z, Wang F, Cheng Z, Zhang J, Hu Y, Hao Z, Li M, Zhang D, Yong H, Huang Y, Weng J, Li X. Integrated transcriptome, small RNA, and degradome analysis reveals the complex network regulating starch biosynthesis in maize. BMC Genomics 2019; 20:574. [PMID: 31296166 PMCID: PMC6625009 DOI: 10.1186/s12864-019-5945-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 06/30/2019] [Indexed: 12/18/2022] Open
Abstract
Background Starch biosynthesis in endosperm is a key process influencing grain yield and quality in maize. Although a number of starch biosynthetic genes have been well characterized, the mechanisms by which the expression of these genes is regulated, especially in regard to microRNAs (miRNAs), remain largely unclear. Results Sequence data for small RNAs, degradome, and transcriptome of maize endosperm at 15 and 25 d after pollination (DAP) from inbred lines Mo17 and Ji419, which exhibit distinct starch content and starch granule structure, revealed the mediation of starch biosynthetic pathways by miRNAs. Transcriptome analysis of these two lines indicated that 33 of 40 starch biosynthetic genes were differentially expressed, of which 12 were up-regulated in Ji419 at 15 DAP, one was up-regulated in Ji419 at 25 DAP, 14 were up-regulated in Ji419 at both 15 and 25 DAP, one was down-regulated in Ji419 at 15 DAP, two were down-regulated in Ji419 at 25 DAP, and three were up-regulated in Ji419 at 15 DAP and down-regulated in Ji419 at 25 DAP, compared with Mo17. Through combined analyses of small RNA and degradome sequences, 22 differentially expressed miRNAs were identified, including 14 known and eight previously unknown miRNAs that could target 35 genes. Furthermore, a complex co-expression regulatory network was constructed, in which 19 miRNAs could modulate starch biosynthesis in endosperm by tuning the expression of 19 target genes. Moreover, the potential operation of four miRNA-mediated pathways involving transcription factors, miR169a-NF-YA1-GBSSI/SSIIIa and miR169o-GATA9-SSIIIa/SBEIIb, was validated via analyses of expression pattern, transient transformation assays, and transactivation assays. Conclusion Our results suggest that miRNAs play a critical role in starch biosynthesis in endosperm, and that miRNA-mediated networks could modulate starch biosynthesis in this tissue. These results have provided important insights into the molecular mechanism of starch biosynthesis in developing maize endosperm. Electronic supplementary material The online version of this article (10.1186/s12864-019-5945-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaocong Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sidi Xie
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jienan Han
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Chang Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Zhiqiang Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Feifei Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zixiang Cheng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junjie Zhang
- College of Life Science, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Yufeng Hu
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhuanfang Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingshun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Degui Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongjun Yong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yubi Huang
- College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
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18
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Genome-Wide Analysis of the TCP Gene Family in Switchgrass ( Panicum virgatum L.). Int J Genomics 2019; 2019:8514928. [PMID: 31093492 PMCID: PMC6481156 DOI: 10.1155/2019/8514928] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/09/2019] [Accepted: 02/20/2019] [Indexed: 01/07/2023] Open
Abstract
The plant-specific transcription factor TCPs play multiple roles in plant growth, development, and stress responses. However, a genome-wide analysis of TCP proteins and their roles in salt stress has not been declared in switchgrass (Panicum virgatum L.). In this study, 42 PvTCP genes (PvTCPs) were identified from the switchgrass genome and 38 members can be anchored to its chromosomes unevenly. Nine PvTCPs were predicted to be microRNA319 (miR319) targets. Furthermore, PvTCPs can be divided into three clades according to the phylogeny and conserved domains. Members in the same clade have the similar gene structure and motif localization. Although all PvTCPs were expressed in tested tissues, their expression profiles were different under normal condition. The specific expression may indicate their different roles in plant growth and development. In addition, approximately 20 cis-acting elements were detected in the promoters of PvTCPs, and 40% were related to stress response. Moreover, the expression profiles of PvTCPs under salt stress were also analyzed and 29 PvTCPs were regulated after NaCl treatment. Taken together, the PvTCP gene family was analyzed at a genome-wide level and their possible functions in salt stress, which lay the basis for further functional analysis of PvTCPs in switchgrass.
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19
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Wu Z, Wang N, Hisano H, Cao Y, Wu F, Liu W, Bao Y, Wang Z, Fu C. Simultaneous regulation of F5H in COMT-RNAi transgenic switchgrass alters effects of COMT suppression on syringyl lignin biosynthesis. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:836-845. [PMID: 30267599 PMCID: PMC6419721 DOI: 10.1111/pbi.13019] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/12/2018] [Accepted: 09/24/2018] [Indexed: 05/06/2023]
Abstract
Ferulate 5-hydroxylase (F5H) catalyses the hydroxylation of coniferyl alcohol and coniferaldehyde for the biosynthesis of syringyl (S) lignin in angiosperms. However, the coordinated effects of F5H with caffeic acid O-methyltransferase (COMT) on the metabolic flux towards S units are largely unknown. We concomitantly regulated F5H expression in COMT-down-regulated transgenic switchgrass (Panicum virgatum L.) lines and studied the coordination of F5H and COMT in lignin biosynthesis. Down-regulation of F5H in COMT-RNAi transgenic switchgrass plants further impeded S lignin biosynthesis and, consequently, increased guaiacyl (G) units and reduced 5-OH G units. Conversely, overexpression of F5H in COMT-RNAi transgenic plants reduced G units and increased 5-OH units, whereas the deficiency of S lignin biosynthesis was partially compensated or fully restored, depending on the extent of COMT down-regulation in switchgrass. Moreover, simultaneous regulation of F5H and COMT expression had different effects on cell wall digestibility of switchgrass without biomass loss. Our results indicate that up-regulation and down-regulation of F5H expression, respectively, have antagonistic and synergistic effects on the reduction in S lignin resulting from COMT suppression. The coordinated effects between lignin genes should be taken into account in future studies aimed at cell wall bioengineering.
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Affiliation(s)
- Zhenying Wu
- Shandong Provincial Key Laboratory of Energy GeneticsKey Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoShandongChina
| | - Nengfei Wang
- Key Lab of Marine Bioactive SubstancesThe First Institute of OceanographyState Oceanic AdministrationQingdaoShandongChina
| | - Hiroshi Hisano
- Noble Research Institute, LLCArdmoreOKUSA
- Institute of Plant Science and ResourcesOkayama UniversityKurashikiOkayamaJapan
| | - Yingping Cao
- Shandong Provincial Key Laboratory of Energy GeneticsKey Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoShandongChina
| | - Fengyan Wu
- Noble Research Institute, LLCArdmoreOKUSA
| | - Wenwen Liu
- Shandong Provincial Key Laboratory of Energy GeneticsKey Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoShandongChina
| | - Yan Bao
- Shandong Provincial Key Laboratory of Energy GeneticsKey Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoShandongChina
| | | | - Chunxiang Fu
- Shandong Provincial Key Laboratory of Energy GeneticsKey Laboratory of BiofuelsQingdao Institute of Bioenergy and Bioprocess TechnologyChinese Academy of SciencesQingdaoShandongChina
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20
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Zhang HX, Ali M, Feng XH, Jin JH, Huang LJ, Khan A, Lv JG, Gao SY, Luo DX, Gong ZH. A Novel Transcription Factor CaSBP12 Gene Negatively Regulates the Defense Response against Phytophthora capsici in Pepper ( Capsicum annuum L.). Int J Mol Sci 2018; 20:E48. [PMID: 30583543 PMCID: PMC6337521 DOI: 10.3390/ijms20010048] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 12/16/2018] [Accepted: 12/20/2018] [Indexed: 01/24/2023] Open
Abstract
SBP-box (Squamosa-promoter binding protein) genes are a type of plant-specific transcription factor and play important roles in plant growth, signal transduction and stress response. However, little is known about the SBP-box genes in pepper (CaSBP), especially in the process of Phytophthora capsici infection. In this study, a novel gene (CaSBP12) was selected from the CaSBP gene family, which was isolated from the pepper genome database in our previous study. The CaSBP12 gene was located in the nucleus of the cell and its silencing in the pepper plant enhanced the defense response against Phytophthora capsici infection. After inoculation with Phytophthora capsici, the root activity of the CaSBP12-silenced plants is compared to control plants, while malondialdehyde (MDA) content is compared viceversa. Additionally, the expression of defense related genes (CaPO1, CaSAR8.2, CaBPR1, and CaDEF1) in the silenced plants were induced to different degrees and the peak of CaSAR8.2 and CaBPR1 were higher than that of CaDEF1. The CaSBP12 over-expressed Nicotiana benthamiana plants were more susceptible to Phytophthora capsici infection with higher EC (electrical conductivity) and MDA contents as compared to the wild-type. The relative expression of defense related genes (NbDEF, NbNPR1, NbPR1a, and NbPR1b) in transgenic and wild-type Nicotiana benthamiana plants were induced, especially the NbPR1a and NbPR1b. In conclusion, these results indicate that CaSBP12 gene negative regulates the defense response against Phytophthora capsici infection which suggests their potentially significant role in plant defense. To our knowledge, this is the first report on CaSBP gene which negative regulate defense response.
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Affiliation(s)
- Huai-Xia Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Muhammad Ali
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Xiao-Hui Feng
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Jing-Hao Jin
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Liu-Jun Huang
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Abid Khan
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
| | - Jing-Gang Lv
- Tianjin Vegetable Research Center, Tianjin 300192, China.
| | - Su-Yan Gao
- Tianjin Vegetable Research Center, Tianjin 300192, China.
| | - De-Xu Luo
- Xuhuai Region Huaiyin Institute of Agricultural Sciences, Jiangsu 223001, China.
| | - Zhen-Hui Gong
- College of Horticulture, Northwest A&F University, Yangling 712100, China.
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21
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Chen K, Luan M, Xiong H, Chen P, Chen J, Gao G, Huang K, Zhu A, Yu C. Genome-wide association study discovered favorable single nucleotide polymorphisms and candidate genes associated with ramet number in ramie (Boehmeria nivea L.). BMC PLANT BIOLOGY 2018; 18:345. [PMID: 30541445 PMCID: PMC6292125 DOI: 10.1186/s12870-018-1573-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 11/26/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Ramie (Boehmeria nivea L.) is one of the most important natural fiber crops and an important forage grass in south China. Ramet number, which is a quantitative trait controlled by multigenes, is one of the most important agronomic traits in plants because the ramet number per plant is a key component of grain yield and biomass. However, the genetic variation and genetic architecture of ramie ramet number are rarely known. RESULTS A genome-wide association study was performed using a panel of 112 core germplasms and 108,888 single nucleotide polymorphisms (SNPs) detected using specific-locus amplified fragment sequencing technology. Trait-SNP association analysis detected 44 significant SNPs that were associated with ramet number at P < 0.01. The favorable SNP Marker20170-64 emerged at least twice in the three detected stages and was validated to be associated with the ramie ramet number using genomic DNA polymerase chain reaction with an F1 hybrid progeny population. Comparative genome analysis predicted nine candidate genes for ramet number based on Marker20170-64. Real-time quantitative polymerase chain reaction analysis indicated that six of the genes were specific to upregulation in the ramie variety with high ramet number. These results suggest that these genes could be considered as ramet number-associated candidates in ramie. CONCLUSIONS The identified loci or genes may be promising targets for genetic engineering and selection for modulating the ramet number in ramie. Our work improves understanding of the genetics of ramet number in ramie core germplasms and provides tools for marker-assisted selection for improvement of agricultural traits.
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Affiliation(s)
- Kunmei Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, West Xianjiahu Road, Changsha, 410205 Hunan Province China
| | - Mingbao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, West Xianjiahu Road, Changsha, 410205 Hunan Province China
| | - Heping Xiong
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, West Xianjiahu Road, Changsha, 410205 Hunan Province China
| | - Ping Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, West Xianjiahu Road, Changsha, 410205 Hunan Province China
| | - Jikang Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, West Xianjiahu Road, Changsha, 410205 Hunan Province China
| | - Gang Gao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, West Xianjiahu Road, Changsha, 410205 Hunan Province China
| | - Kunyong Huang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, West Xianjiahu Road, Changsha, 410205 Hunan Province China
| | - Aiguo Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, West Xianjiahu Road, Changsha, 410205 Hunan Province China
| | - Chunming Yu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348, West Xianjiahu Road, Changsha, 410205 Hunan Province China
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22
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Yan J, Liu Y, Wang K, Li D, Hu Q, Zhang W. Overexpression of OsPIL1 enhanced biomass yield and saccharification efficiency in switchgrass. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 276:143-151. [PMID: 30348312 DOI: 10.1016/j.plantsci.2018.08.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/14/2018] [Accepted: 08/23/2018] [Indexed: 05/20/2023]
Abstract
Switchgrass (Panicum virgatum L.) is a herbaceous cellulosic biofuel plant with broad adaptability. However, the intrinsic recalcitrance of biomass and limited land for switchgrass planting hinder its utilization as feedstock for biofuel ethanol production. The OsPIL1 (PHYTOCHROME INTERACTING FACTOR 3-LIKE 1) gene encodes a basic helix-loop-helix transcription factor. Its expression is induced by light, which facilitated the expression of cell wall-related genes, promoted cell elongation and resulted in longer internode in rice. Here, we introduced the OsPIL1 gene into switchgrass by Agrobacterium-mediated transformation with the aim of improving biomass yield of transgenic switchgrass plants. The transgenic plants were verified by PCR, Southern-blotting, RT-PCR and qRT-PCR tests, respectively. The transgenic plants overexpression of OsPIL1 showed increased plant height and biomass yield. Microscopy analysis showed that the length of epidermal cells of transgenic plants was longer than that of wild type. OsPIL1 overexpressed transgenic switchgrass plants also released more soluble sugar after enzymatic hydrolysis, indicating improved saccharification efficiency. The results suggest OsPIL1 can be used as a useful molecular tool in improving plant biomass and saccharification efficiency with the purpose of plant fiber biofuel ethanol production.
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Affiliation(s)
- Jianping Yan
- Department of Grassland Science, China Agricultural University, Beijing, 100193, PR China.
| | - Yanrong Liu
- Department of Grassland Science, China Agricultural University, Beijing, 100193, PR China.
| | - Kexin Wang
- Department of Grassland Science, China Agricultural University, Beijing, 100193, PR China.
| | - Dayong Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, PR China.
| | - Qingquan Hu
- Yunnan Animal Science and Veterinary Institute, Kunming, 650224, PR China.
| | - Wanjun Zhang
- Department of Grassland Science, China Agricultural University, Beijing, 100193, PR China; National Energy R&D Center for Biomass (NECB), China Agricultural University, Beijing, 100193, PR China.
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23
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Susila H, Nasim Z, Ahn JH. Ambient Temperature-Responsive Mechanisms Coordinate Regulation of Flowering Time. Int J Mol Sci 2018; 19:ijms19103196. [PMID: 30332820 PMCID: PMC6214042 DOI: 10.3390/ijms19103196] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/09/2018] [Accepted: 10/13/2018] [Indexed: 12/23/2022] Open
Abstract
In plants, environmental conditions such as temperature affect survival, growth, and fitness, particularly during key stages such as seedling growth and reproduction. To survive and thrive in changing conditions, plants have evolved adaptive responses that tightly regulate developmental processes such as hypocotyl elongation and flowering time in response to environmental temperature changes. Increases in temperature, coupled with increasing fluctuations in local climate and weather, severely affect our agricultural systems; therefore, understanding the mechanisms by which plants perceive and respond to temperature is critical for agricultural sustainability. In this review, we summarize recent findings on the molecular mechanisms of ambient temperature perception as well as possible temperature sensing components in plants. Based on recent publications, we highlight several temperature response mechanisms, including the deposition and eviction of histone variants, DNA methylation, alternative splicing, protein degradation, and protein localization. We discuss roles of each proposed temperature-sensing mechanism that affects plant development, with an emphasis on flowering time. Studies of plant ambient temperature responses are advancing rapidly, and this review provides insights for future research aimed at understanding the mechanisms of temperature perception and responses in plants.
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Affiliation(s)
- Hendry Susila
- Department of Life Sciences, Korea University, Seoul 02841, Korea.
| | - Zeeshan Nasim
- Department of Life Sciences, Korea University, Seoul 02841, Korea.
| | - Ji Hoon Ahn
- Department of Life Sciences, Korea University, Seoul 02841, Korea.
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24
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Li G, Jones KC, Eudes A, Pidatala VR, Sun J, Xu F, Zhang C, Wei T, Jain R, Birdseye D, Canlas PE, Baidoo EEK, Duong PQ, Sharma MK, Singh S, Ruan D, Keasling JD, Mortimer JC, Loqué D, Bartley LE, Scheller HV, Ronald PC. Overexpression of a rice BAHD acyltransferase gene in switchgrass (Panicum virgatum L.) enhances saccharification. BMC Biotechnol 2018; 18:54. [PMID: 30180895 PMCID: PMC6123914 DOI: 10.1186/s12896-018-0464-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 08/27/2018] [Indexed: 11/10/2022] Open
Abstract
Background Switchgrass (Panicum virgatum L.) is a promising bioenergy feedstock because it can be grown on marginal land and produces abundant biomass. Recalcitrance of the lignocellulosic components of the switchgrass cell wall to enzymatic degradation into simple sugars impedes efficient biofuel production. We previously demonstrated that overexpression of OsAT10, a BAHD acyltransferase gene, enhances saccharification efficiency in rice. Results Here we show that overexpression of the rice OsAT10 gene in switchgrass decreased the levels of cell wall-bound ferulic acid (FA) in green leaf tissues and to a lesser extent in senesced tissues, and significantly increased levels of cell wall-bound p-coumaric acid (p-CA) in green leaves but decreased its level in senesced tissues of the T0 plants under greenhouse conditions. The engineered switchgrass lines exhibit an approximate 40% increase in saccharification efficiency in green tissues and a 30% increase in senesced tissues. Conclusion Our study demonstrates that overexpression of OsAT10, a rice BAHD acyltransferase gene, enhances saccharification of lignocellulosic biomass in switchgrass. Electronic supplementary material The online version of this article (10.1186/s12896-018-0464-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guotian Li
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant Pathology and the Genome Center, University of California, Davis, CA, 95616, USA
| | - Kyle C Jones
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant Pathology and the Genome Center, University of California, Davis, CA, 95616, USA
| | - Aymerick Eudes
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | | | - Jian Sun
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Biomass Science and Conversion Technology Department, Sandia National Laboratories, CA94551, Livermore, USA
| | - Feng Xu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chengcheng Zhang
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Tong Wei
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant Pathology and the Genome Center, University of California, Davis, CA, 95616, USA
| | - Rashmi Jain
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant Pathology and the Genome Center, University of California, Davis, CA, 95616, USA
| | - Devon Birdseye
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Patrick E Canlas
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, 95616, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Phat Q Duong
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA, 95616, USA
| | - Manoj K Sharma
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant Pathology and the Genome Center, University of California, Davis, CA, 95616, USA.,School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Seema Singh
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Biomass Science and Conversion Technology Department, Sandia National Laboratories, CA94551, Livermore, USA
| | - Deling Ruan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant Pathology and the Genome Center, University of California, Davis, CA, 95616, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Bioengineering and Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
| | - Jenny C Mortimer
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Dominique Loqué
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Laura E Bartley
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Henrik V Scheller
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Pamela C Ronald
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Plant Pathology and the Genome Center, University of California, Davis, CA, 95616, USA.
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Ambavaram MMR, Ali A, Ryan KP, Peoples O, Snell KD, Somleva MN. Novel transcription factors PvBMY1 and PvBMY3 increase biomass yield in greenhouse-grown switchgrass (Panicum virgatum L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:100-109. [PMID: 29907302 DOI: 10.1016/j.plantsci.2018.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 06/08/2023]
Abstract
Increasing crop yield requires the coordination of multiple metabolic pathways spanning photosynthetic carbon fixation, central carbon metabolism, and finally targeted carbon deposition to end product. In this study, we used a transcriptome-based gene regulatory association network to search for transcription factor genes that could play a role in increasing carbon flow through pathways associated with these processes to increase biomass yield in switchgrass. Two novel switchgrass transcription factors, PvBMY1 (BioMass Yield 1, belonging to the APETALA2/Ethylene Response Factor family of transcription factors) and PvBMY3 (BioMass Yield 3, a member of the Nuclear-Factor Y family of transcription factors), with predicted roles in the regulation of photosynthesis and related metabolism were identified. These genes were overexpressed in switchgrass to determine their impact on biomass yield. A significant increase in both aboveground and root biomass was observed in transgenic greenhouse grown plants compared to wild-type control plants with the best line producing 160% more aboveground biomass than controls. Transgenic lines with elevated electron transport rate of photosystems I and II as well as increased levels of starch and soluble sugars were identified.
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Affiliation(s)
| | - Aminat Ali
- Yield10 Bioscience, Inc., 19 Presidential Way, Woburn, MA 01801, United States
| | - Kieran P Ryan
- Yield10 Bioscience, Inc., 19 Presidential Way, Woburn, MA 01801, United States
| | - Oliver Peoples
- Yield10 Bioscience, Inc., 19 Presidential Way, Woburn, MA 01801, United States
| | - Kristi D Snell
- Yield10 Bioscience, Inc., 19 Presidential Way, Woburn, MA 01801, United States.
| | - Maria N Somleva
- Yield10 Bioscience, Inc., 19 Presidential Way, Woburn, MA 01801, United States
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26
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Zuo C, Blow M, Sreedasyam A, Kuo RC, Ramamoorthy GK, Torres-Jerez I, Li G, Wang M, Dilworth D, Barry K, Udvardi M, Schmutz J, Tang Y, Xu Y. Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:170. [PMID: 29951114 PMCID: PMC6009963 DOI: 10.1186/s13068-018-1167-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/08/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Switchgrass (Panicum virgatum L.) is an important bioenergy crop widely used for lignocellulosic research. While extensive transcriptomic analyses have been conducted on this species using short read-based sequencing techniques, very little has been reliably derived regarding alternatively spliced (AS) transcripts. RESULTS We present an analysis of transcriptomes of six switchgrass tissue types pooled together, sequenced using Pacific Biosciences (PacBio) single-molecular long-read technology. Our analysis identified 105,419 unique transcripts covering 43,570 known genes and 8795 previously unknown genes. 45,168 are novel transcripts of known genes. A total of 60,096 AS transcripts are identified, 45,628 being novel. We have also predicted 1549 transcripts of genes involved in cell wall construction and remodeling, 639 being novel transcripts of known cell wall genes. Most of the predicted transcripts are validated against Illumina-based short reads. Specifically, 96% of the splice junction sites in all the unique transcripts are validated by at least five Illumina reads. Comparisons between genes derived from our identified transcripts and the current genome annotation revealed that among the gene set predicted by both analyses, 16,640 have different exon-intron structures. CONCLUSIONS Overall, substantial amount of new information is derived from the PacBio RNA data regarding both the transcriptome and the genome of switchgrass.
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Affiliation(s)
- Chunman Zuo
- College of Computer Science and Technology, Jilin University, Changchun, China
- Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA USA
- BESC BioEnergy Research Center, Oak Ridge National Lab, Oak Ridge, TN USA
| | - Matthew Blow
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | | | - Rita C. Kuo
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | | | | | - Guifen Li
- Noble Research Institute, LLC, Ardmore, OK USA
| | - Mei Wang
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - David Dilworth
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | | | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, CA USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Yuhong Tang
- BESC BioEnergy Research Center, Oak Ridge National Lab, Oak Ridge, TN USA
- Noble Research Institute, LLC, Ardmore, OK USA
| | - Ying Xu
- College of Computer Science and Technology, Jilin University, Changchun, China
- Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA USA
- BESC BioEnergy Research Center, Oak Ridge National Lab, Oak Ridge, TN USA
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27
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Genome-Wide Identification, Phylogeny, and Expression Analysis of ARF Genes Involved in Vegetative Organs Development in Switchgrass. Int J Genomics 2018; 2018:7658910. [PMID: 29854720 PMCID: PMC5949158 DOI: 10.1155/2018/7658910] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 04/11/2018] [Indexed: 11/18/2022] Open
Abstract
Auxin response factors (ARFs) have been reported to play vital roles during plant growth and development. In order to reveal specific functions related to vegetative organs in grasses, an in-depth study of the ARF gene family was carried out in switchgrass (Panicum virgatum L.), a warm-season C4 perennial grass that is mostly used as bioenergy and animal feedstock. A total of 47 putative ARF genes (PvARFs) were identified in the switchgrass genome (2n = 4x = 36), 42 of which were anchored to the seven pairs of chromosomes and found to be unevenly distributed. Sixteen PvARFs were predicted to be potential targets of small RNAs (microRNA160 and 167). Phylogenetically speaking, PvARFs were divided into seven distinct subgroups based on the phylogeny, exon/intron arrangement, and conserved motif distribution. Moreover, 15 pairs of PvARFs have different temporal-spatial expression profiles in vegetative organs (2nd, 3rd, and 4th internode and leaves), which implies that different PvARFs have specific functions in switchgrass growth and development. In addition, at least 14 pairs of PvARFs respond to naphthylacetic acid (NAA) treatment, which might be helpful for us to study on auxin response in switchgrass. The comprehensive analysis, described here, will facilitate the future functional analysis of ARF genes in grasses.
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Zhang C, Tang G, Peng X, Sun F, Liu S, Xi Y. Long non-coding RNAs of switchgrass (Panicum virgatum L.) in multiple dehydration stresses. BMC PLANT BIOLOGY 2018; 18:79. [PMID: 29728055 PMCID: PMC5936019 DOI: 10.1186/s12870-018-1288-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 04/22/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) play important roles in plant growth and stress responses. Studies of lncRNAs in non-model plants are quite limited, especially those investigating multiple dehydration stresses. In this study, we identified novel lncRNAs and analyzed their functions in dehydration stress memory in switchgrass, an excellent biofuel feedstock and soil-conserving plant in the Gramineae family. RESULTS We analyzed genome-wide transcriptional profiles of leaves of 5-week-old switchgrass plantlets grown via tissue culture after primary and secondary dehydration stresses (D1 and D2) and identified 16,551 novel lncRNAs, including 4554 annotated lncRNAs (targeting 3574 genes), and 11,997 unknown lncRNAs. Gene ontology and pathway enrichment analysis of annotated genes showed that the differentially expressed lncRNAs were related to abscisic acid (ABA) and ethylene (ETH) biosynthesis and signal transduction, and to starch and sucrose metabolism. The upregulated lncRNAs and genes were related to ABA synthesis and its signal transduction, and to trehalose synthesis. Meanwhile, lncRNAs and genes related to ETH biosynthesis and signal transduction were suppressed. LncRNAs and genes involved in ABA metabolism were verified using quantitative real-time PCR, and the endogenous ABA content was determined via high performance liquid chromatography mass spectrometry (HPLC-MS). These results showed that ABA accumulated significantly during dehydration stress, especially in D2. Furthermore, we identified 307 dehydration stress memory lncRNAs, and the ratios of different memory types in switchgrass were similar to those in Arabidopsis and maize. CONCLUSIONS The molecular responses of switchgrass lncRNAs to multiple dehydration stresses were researched systematically, revealing novel information about their transcriptional regulatory behavior. This study provides new insights into the response mechanism to dehydration stress in plants. The lncRNAs and pathways identified in this study provide valuable information for genetic modification of switchgrass and other crops.
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Affiliation(s)
- Chao Zhang
- College of Agronomy, Northwest A & F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Wheat Biology and Genetic Breeding, Ministry of Agriculture, Yangling, 712100 Shaanxi China
| | - Gaijuan Tang
- College of Plant Protection, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Xi Peng
- College of Agronomy, Northwest A & F University, Yangling, 712100 Shaanxi China
| | - Fengli Sun
- College of Agronomy, Northwest A & F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Wheat Biology and Genetic Breeding, Ministry of Agriculture, Yangling, 712100 Shaanxi China
| | - Shudong Liu
- College of Agronomy, Northwest A & F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Wheat Biology and Genetic Breeding, Ministry of Agriculture, Yangling, 712100 Shaanxi China
| | - Yajun Xi
- College of Agronomy, Northwest A & F University, Yangling, 712100 Shaanxi China
- Key Laboratory of Wheat Biology and Genetic Breeding, Ministry of Agriculture, Yangling, 712100 Shaanxi China
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29
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Liu H, Yu H, Tang G, Huang T. Small but powerful: function of microRNAs in plant development. PLANT CELL REPORTS 2018; 37:515-528. [PMID: 29318384 DOI: 10.1007/s00299-017-2246-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/15/2017] [Indexed: 05/02/2023]
Abstract
MicroRNAs (miRNAs) are a group of endogenous noncoding small RNAs frequently 21 nucleotides long. miRNAs act as negative regulators of their target genes through sequence-specific mRNA cleavage, translational repression, or chromatin modifications. Alterations of the expression of a miRNA or its targets often result in a variety of morphological and physiological abnormalities, suggesting the strong impact of miRNAs on plant development. Here, we review the recent advances on the functional studies of plant miRNAs. We will summarize the regulatory networks of miRNAs in a series of developmental processes, including meristem development, establishment of lateral organ polarity and boundaries, vegetative and reproductive organ growth, etc. We will also conclude the conserved and species-specific roles of plant miRNAs in evolution and discuss the strategies for further elucidating the functional mechanisms of miRNAs during plant development.
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Affiliation(s)
- Haiping Liu
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA
| | - Hongyang Yu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Guiliang Tang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, 49931, USA
| | - Tengbo Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, People's Republic of China.
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30
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Genome-wide identification and characterization of SPL transcription factor family and their evolution and expression profiling analysis in cotton. Sci Rep 2018; 8:762. [PMID: 29335584 PMCID: PMC5768680 DOI: 10.1038/s41598-017-18673-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 12/04/2017] [Indexed: 12/01/2022] Open
Abstract
Plant specific transcription factors, SQUAMOSA promoter-binding protein-like (SPL), are involved in many biological processes. However, no systematical study has been reported in cotton. In this study, a total of 177 SPL genes were identified, including 29, 30, 59 and 59 SPLs in Gossypium arboreum, G. raimondii, G. barbadense, and G. hirsutum, respectively. These SPL genes were classified into eight phylogenetical groups. The gene structure, conserved motif, and clustering were highly conserved within each orthologs. Two zinc finger-like structures (Cys3His and Cys2HisCys) and NLS segments were existed in all GrSPLs. Segmental duplications play important roles in SPL family expansion, with 20 genes involved in segmental duplications and 2 in tandem duplications, and ten ortholog pairs in syntenic regions between G. raimondii and A. thaliana. Several putative cis-elements, involved in light, stresses and phytohormones response, were found in the promoter regions of GhSPLs, suggesting that plant responses to those environmental changes may be induced through targeting SPL transcription factors. RNA-seq analysis shows that SPL genes were differentially expressed in cotton; some were highly expressed during fiber initiation and early development. Comparing with other plants, SPL genes show subfunctionalization, lost and/or gain functions in cotton during long-term domestication and evolution.
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31
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Zhang C, Peng X, Guo X, Tang G, Sun F, Liu S, Xi Y. Transcriptional and physiological data reveal the dehydration memory behavior in switchgrass ( Panicum virgatum L.). BIOTECHNOLOGY FOR BIOFUELS 2018; 11:91. [PMID: 29619087 PMCID: PMC5879616 DOI: 10.1186/s13068-018-1088-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 03/21/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Switchgrass (Panicum virgatum L.) is a model biofuel plant because of its high biomass, cellulose-richness, easy degradation to ethanol, and the availability of extensive genomic information. However, a little is currently known about the molecular responses of switchgrass plants to dehydration stress, especially multiple dehydration stresses. RESULTS Studies on the transcriptional profiles of 35-day-old tissue culture plants revealed 741 dehydration memory genes. Gene Ontology and pathway analysis showed that these genes were enriched in phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant hormone signal transduction. Further analysis of specific pathways combined with physiological data suggested that switchgrass improved its dehydration resistance by changing various aspects of its responses to secondary dehydration stress (D2), including the regulation of abscisic acid (ABA) and jasmonic acid (JA) biosynthesis and signal transduction, the biosynthesis of osmolytes (l-proline, stachyose and trehalose), energy metabolism (i.e., metabolic process relating to photosynthetic systems, glycolysis, and the TCA cycle), and lignin biosynthesis. The transcriptional data and chemical substance assays showed that ABA was significantly accumulated during both primary (D1) and secondary (D2) dehydration stresses, whereas JA accumulated during D1 but became significantly less abundant during D2. This suggests the existence of a complicated signaling network of plant hormones in response to repeated dehydration stresses. A homology analysis focusing on switchgrass, maize, and Arabidopsis revealed the conservation and species-specific distribution of dehydration memory genes. CONCLUSIONS The molecular responses of switchgrass plants to successive dehydration stresses have been systematically characterized, revealing a previously unknown transcriptional memory behavior. These results provide new insights into the mechanisms of dehydration stress responses in plants. The genes and pathways identified in this study will be useful for the genetic improvement of switchgrass and other crops.
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Affiliation(s)
- Chao Zhang
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Xi Peng
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Xiaofeng Guo
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Gaijuan Tang
- College of Plant Protection, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Fengli Sun
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Shudong Liu
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Yajun Xi
- College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100 Shaanxi China
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Baxter HL, Mazarei M, Dumitrache A, Natzke JM, Rodriguez M, Gou J, Fu C, Sykes RW, Turner GB, Davis MF, Brown SD, Davison BH, Wang Z, Stewart CN. Transgenic miR156 switchgrass in the field: growth, recalcitrance and rust susceptibility. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:39-49. [PMID: 28436149 PMCID: PMC5785337 DOI: 10.1111/pbi.12747] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 03/16/2017] [Accepted: 04/10/2017] [Indexed: 05/02/2023]
Abstract
Sustainable utilization of lignocellulosic perennial grass feedstocks will be enabled by high biomass production and optimized cell wall chemistry for efficient conversion into biofuels. MicroRNAs are regulatory elements that modulate the expression of genes involved in various biological functions in plants, including growth and development. In greenhouse studies, overexpressing a microRNA (miR156) gene in switchgrass had dramatic effects on plant architecture and flowering, which appeared to be driven by transgene expression levels. High expressing lines were extremely dwarfed, whereas low and moderate-expressing lines had higher biomass yields, improved sugar release and delayed flowering. Four lines with moderate or low miR156 overexpression from the prior greenhouse study were selected for a field experiment to assess the relationship between miR156 expression and biomass production over three years. We also analysed important bioenergy feedstock traits such as flowering, disease resistance, cell wall chemistry and biofuel production. Phenotypes of the transgenic lines were inconsistent between the greenhouse and the field as well as among different field growing seasons. One low expressing transgenic line consistently produced more biomass (25%-56%) than the control across all three seasons, which translated to the production of 30% more biofuel per plant during the final season. The other three transgenic lines produced less biomass than the control by the final season, and the two lines with moderate expression levels also exhibited altered disease susceptibilities. Results of this study emphasize the importance of performing multiyear field studies for plants with altered regulatory transgenes that target plant growth and development.
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Affiliation(s)
- Holly L. Baxter
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
| | - Mitra Mazarei
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
| | - Alexandru Dumitrache
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Jace M. Natzke
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Miguel Rodriguez
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Jiqing Gou
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
- Samuel Roberts Noble FoundationArdmoreOKUSA
| | - Chunxiang Fu
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
- Samuel Roberts Noble FoundationArdmoreOKUSA
| | - Robert W. Sykes
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
- National Renewable Energy LaboratoryGoldenCOUSA
| | - Geoffrey B. Turner
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
- National Renewable Energy LaboratoryGoldenCOUSA
| | - Mark F. Davis
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
- National Renewable Energy LaboratoryGoldenCOUSA
| | - Steven D. Brown
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Brian H. Davison
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Zeng‐Yu Wang
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
- Samuel Roberts Noble FoundationArdmoreOKUSA
| | - C. Neal Stewart
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
- BioEnergy Science Center (BESC)Oak Ridge National LaboratoryOak RidgeTNUSA
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Liu Y, Wang K, Li D, Yan J, Zhang W. Enhanced Cold Tolerance and Tillering in Switchgrass (Panicum virgatum L.) by Heterologous Expression of Osa-miR393a. PLANT & CELL PHYSIOLOGY 2017; 58:2226-2240. [PMID: 29069481 DOI: 10.1093/pcp/pcx157] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 10/13/2017] [Indexed: 05/16/2023]
Abstract
The microRNA393 (miR393) family is one of the conserved miRNA families in the plant kingdom. MiR393 was reported to regulate rice tillering and abiotic stress resistance positively through an auxin signaling pathway. However, little is known about the function of miR393 in switchgrass (Panicum virgatum L.), an important bioenergy C4 grass plant. We tested the expression level of miR393 and its four putative target genes (PvAFB1, PvAFB2, PvAFB3 and PvTIR1) in switchgrass, and found that these genes all responded to cold stress and exogenous 1-naphthaleneacetic acid (NAA) treatment. To investigate the function of miR393 in switchgrass, we enhanced miR393 expression by introducing an Osa-miR393a gene into switchgrass. The results showed that cold tolerance of the transgenic T0 and T1 generation plants was highly improved. Cold tolerance-related genes PvCOR47, PvICE1 and PvRAV1 were negatively regulated by exogenous NAA, and the expression of these genes was significantly higher in transgenic plants than in wild-type plants. The transgenic T1 seedlings were more tolerant to exogenous NAA treatment, accumulating less H2O2 after cold treatments. It was also observed that the miR393/target module regulates cold tolerance responses in Arabidopsis. In addition, transgenic plants overexpressing miR393 had significantly more tillers and higher biomass yield per plant in greenhouse and field tests. Forage quality analyses revealed that the soluble sugar contents of transgenic plants were increased markedly. Overall, the results suggested that overexpression of miR393 improved cold tolerance and tillering of switchgrass through regulation of auxin signaling transduction.
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Affiliation(s)
- Yanrong Liu
- Department of Grassland Science, China Agricultural University, Beijing, 100193, PR China
| | - Kexin Wang
- Department of Grassland Science, China Agricultural University, Beijing, 100193, PR China
| | - Dayong Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Jianping Yan
- Department of Grassland Science, China Agricultural University, Beijing, 100193, PR China
| | - Wanjun Zhang
- Department of Grassland Science, China Agricultural University, Beijing, 100193, PR China
- National Energy R&D Center for Biomass (NECB), China Agricultural University, Beijing, 100193, PR China
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D'Ario M, Griffiths-Jones S, Kim M. Small RNAs: Big Impact on Plant Development. TRENDS IN PLANT SCIENCE 2017; 22:1056-1068. [PMID: 29032035 DOI: 10.1016/j.tplants.2017.09.009] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/13/2017] [Accepted: 09/18/2017] [Indexed: 05/19/2023]
Abstract
While the role of proteins in determining cell identity has been extensively studied, the contribution of small noncoding RNA molecules such as miRNAs and siRNAs has been also recognised. miRNAs bind to complementary sites in target mRNA molecules to trigger the degradation or translational inhibition of those targets. Recent studies have revealed that miRNAs play pivotal roles in key developmental processes such as patterning of the embryo, meristem, leaf, and flower. Furthermore, these miRNAs have been recruited throughout plant evolution into pathways that create diverse plant organ forms and shapes. This review focuses on the roles of miRNAs in establishing plant cell identity during key plant development processes and creating morphological diversity during plant evolution.
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Affiliation(s)
- Marco D'Ario
- Faculty of Biology, Medicine, and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Sam Griffiths-Jones
- Faculty of Biology, Medicine, and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK.
| | - Minsung Kim
- Faculty of Biology, Medicine, and Health, University of Manchester, Oxford Road, Manchester M13 9PT, UK.
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35
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Wang J, Ma L, Shen Z, Sun D, Zhong P, Bai Z, Zhang H, Cao Y, Bao Y, Fu C. Lignification of Sheepgrass Internodes at Different Developmental Stages and Associated Alteration of Cell Wall Saccharification Efficiency. FRONTIERS IN PLANT SCIENCE 2017; 8:414. [PMID: 28396679 PMCID: PMC5366342 DOI: 10.3389/fpls.2017.00414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/10/2017] [Indexed: 05/30/2023]
Abstract
Sheepgrass (Leymus chinensis) is a high-quality cool-season forage crop used as pasture and hay for livestock feeds. The presence of lignin in cell walls, however, impairs forage digestibility of such lignocellulosic feedstock. Here, the structural characterization and cell wall composition of sheepgrass internodes were studied, and a progressive increase in cell wall lignification was observed with internode maturation. Lignin composition analysis further revealed a gradual accumulation of guaiacyl and syringyl lignin units during internode development. Consistently, the transcript abundance of lignin-related genes was upregulated in mature internodes, suggesting their potential roles in lignin biosynthesis. Furthermore, the effects of cell wall composition and lignification extent on biomass saccharification efficiency were examined in sheepgrass. The results showed that lignin content, guaiacyl and syringyl lignin unit levels inversely correlated with cell wall digestibility, indicating that lignin is a crucial obstacle for utilizing sheepgrass feedstock. The baseline information obtained in this work will facilitate establishment, grazing management, harvesting and feedstock utilization of sheepgrass in future.
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Affiliation(s)
- Jianli Wang
- Grass and Science Institute of Heilongjiang Academy of Agricultural SciencesHarbin, China
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
| | - Lichao Ma
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
| | - Zhongbao Shen
- Grass and Science Institute of Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Dequan Sun
- Grass and Science Institute of Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Peng Zhong
- Rural Energy Research Institute of Heilongjiang Academy of Agricultural SciencesHarbin, China
| | - Zetao Bai
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
| | - Hailing Zhang
- Grass and Science Institute of Heilongjiang Academy of Agricultural SciencesHarbin, China
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
| | - Yingping Cao
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
| | - Yan Bao
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
| | - Chunxiang Fu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
- Qingdao Engineering Research Center of Biomass Resources and Environment, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdao, China
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Johnson CR, Millwood RJ, Tang Y, Gou J, Sykes RW, Turner GB, Davis MF, Sang Y, Wang ZY, Stewart CN. Field-grown miR156 transgenic switchgrass reproduction, yield, global gene expression analysis, and bioconfinement. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:255. [PMID: 29213314 PMCID: PMC5707911 DOI: 10.1186/s13068-017-0939-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/19/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND Genetic engineering has been effective in altering cell walls for biofuel production in the bioenergy crop, switchgrass (Panicum virgatum). However, regulatory issues arising from gene flow may prevent commercialization of engineered switchgrass in the eastern United States where the species is native. Depending on its expression level, microRNA156 (miR156) can reduce, delay, or eliminate flowering, which may serve to decrease transgene flow. In this unique field study of transgenic switchgrass that was permitted to flower, two low (T14 and T35) and two medium (T27 and T37) miR156-overexpressing 'Alamo' lines with the transgene under the control of the constitutive maize (Zea mays) ubiquitin 1 promoter, along with nontransgenic control plants, were grown in eastern Tennessee over two seasons. RESULTS miR156 expression was positively associated with decreased and delayed flowering in switchgrass. Line T27 did not flower during the 2-year study. Line T37 did flower, but not all plants produced panicles. Flowering was delayed in T37, resulting in 70.6% fewer flowers than controls during the second field year with commensurate decreased seed yield: 1205 seeds per plant vs. 18,539 produced by each control. These results are notable given that line T37 produced equivalent vegetative aboveground biomass to the controls. miR156 transcript abundance of field-grown plants was congruent with greenhouse results. The five miR156 SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) target genes had suppressed expression in one or more of the transgenic lines. Line T27, which had the highest miR156 overexpression, showed significant downregulation for all five SPL genes. On the contrary, line T35 had the lowest miR156 overexpression and had no significant change in any of the five SPL genes. CONCLUSIONS Because of the research field's geographical features, this study was the first instance of any genetically engineered trait in switchgrass, in which experimental plants were allowed to flower in the field in the eastern U.S.; USDA-APHIS-BRS regulators allowed open flowering. We found that medium overexpression of miR156, e.g., line T37, resulted in delayed and reduced flowering accompanied by high biomass production. We propose that induced miR156 expression could be further developed as a transgenic switchgrass bioconfinement tool to enable eventual commercialization.
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Affiliation(s)
- Chelsea R. Johnson
- Department of Plant Sciences, University of Tennessee, Knoxville, TN USA
| | - Reginald J. Millwood
- Department of Plant Sciences, University of Tennessee, Knoxville, TN USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
| | - Yuhong Tang
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Noble Research Institute, Ardmore, OK USA
| | - Jiqing Gou
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Noble Research Institute, Ardmore, OK USA
| | - Robert W. Sykes
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- National Renewable Energy Laboratory, Golden, CO USA
| | - Geoffrey B. Turner
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- National Renewable Energy Laboratory, Golden, CO USA
| | - Mark F. Davis
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- National Renewable Energy Laboratory, Golden, CO USA
| | - Yi Sang
- Department of Plant Sciences, University of Tennessee, Knoxville, TN USA
| | - Zeng-Yu Wang
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
- Noble Research Institute, Ardmore, OK USA
| | - C. Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN USA
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Park JJ, Yoo CG, Flanagan A, Pu Y, Debnath S, Ge Y, Ragauskas AJ, Wang ZY. Defined tetra-allelic gene disruption of the 4-coumarate:coenzyme A ligase 1 (Pv4CL1) gene by CRISPR/Cas9 in switchgrass results in lignin reduction and improved sugar release. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:284. [PMID: 29213323 PMCID: PMC5708096 DOI: 10.1186/s13068-017-0972-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 11/18/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND The development of genome editing technologies offers new prospects in improving bioenergy crops like switchgrass (Panicum virgatum). Switchgrass is an outcrossing species with an allotetraploid genome (2n = 4x = 36), a complexity which forms an impediment to generating homozygous knock-out plants. Lignin, a major component of the plant cell wall and a contributor to cellulosic feedstock's recalcitrance to decomposition, stands as a barrier to efficient biofuel production by limiting enzyme access to cell wall polymers during the fermentation process. RESULTS We developed a CRISPR/Cas9 genome editing system in switchgrass to target a key enzyme involved in the early steps of monolignol biosynthesis, 4-Coumarate:coenzyme A ligase (4CL). Three 4CL genes, Pv4CL1, Pv4CL2, and Pv4CL3, were identified in switchgrass. Expression analysis revealed that Pv4CL1 transcripts were more abundant in the stem than in the leaf, while Pv4CL2 transcripts were barely detectable and Pv4CL3 was mainly expressed in the leaf. Pv4CL1 was selected as the target for CRISPR/Cas9 editing because of its preferential expression in highly lignified stem tissues. Specific guide RNA was constructed to target Pv4CL1. After introducing the construct into switchgrass calli, 39 transgenic plants were regenerated. Using two rounds of PCR screening and sequencing, four plants were confirmed to have tetra-allelic mutations simultaneously. The Pv4CL1 knock-out plants had reduced cell wall thickness, an 8-30% reduction in total lignin content, a 7-11% increase in glucose release, and a 23-32% increase in xylose release. CONCLUSION This study established a successful CRISPR/Cas9 system in switchgrass with mutation efficiency reaching 10%. The system allows the precise targeting of the selected Pv4CL1 gene to create switchgrass knock-out mutant plants with decreased lignin content and reduced recalcitrance.
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Affiliation(s)
- Jong-Jin Park
- Noble Research Institute, Ardmore, OK 73401 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Chang Geun Yoo
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | - Amy Flanagan
- Noble Research Institute, Ardmore, OK 73401 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Yunqiao Pu
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
| | | | - Yaxin Ge
- Noble Research Institute, Ardmore, OK 73401 USA
| | - Arthur J. Ragauskas
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996 USA
- Center for Renewable Carbon, Department of Forestry, Wildlife, and Fisheries, University of Tennessee Institute of Agriculture, Knoxville, TN 37996 USA
| | - Zeng-Yu Wang
- Noble Research Institute, Ardmore, OK 73401 USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
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