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Zhou Y, Gao YH, Zhang BC, Yang HL, Tian YB, Huang YH, Yin CC, Tao JJ, Wei W, Zhang WK, Chen SY, Zhou YH, Zhang JS. CELLULOSE SYNTHASE-LIKE C proteins modulate cell wall establishment during ethylene-mediated root growth inhibition in rice. THE PLANT CELL 2024; 36:3751-3769. [PMID: 38943676 PMCID: PMC11371184 DOI: 10.1093/plcell/koae195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 05/29/2024] [Accepted: 06/07/2024] [Indexed: 07/01/2024]
Abstract
The cell wall shapes plant cell morphogenesis and affects the plasticity of organ growth. However, the way in which cell wall establishment is regulated by ethylene remains largely elusive. Here, by analyzing cell wall patterns, cell wall composition and gene expression in rice (Oryza sativa, L.) roots, we found that ethylene induces cell wall thickening and the expression of cell wall synthesis-related genes, including CELLULOSE SYNTHASE-LIKE C1, 2, 7, 9, 10 (OsCSLC1, 2, 7, 9, 10) and CELLULOSE SYNTHASE A3, 4, 7, 9 (OsCESA3, 4, 7, 9). Overexpression and mutant analyses revealed that OsCSLC2 and its homologs function in ethylene-mediated induction of xyloglucan biosynthesis mainly in the cell wall of root epidermal cells. Moreover, OsCESA-catalyzed cellulose deposition in the cell wall was enhanced by ethylene. OsCSLC-mediated xyloglucan biosynthesis likely plays an important role in restricting cell wall extension and cell elongation during the ethylene response in rice roots. Genetically, OsCSLC2 acts downstream of ETHYLENE-INSENSITIVE3-LIKE1 (OsEIL1)-mediated ethylene signaling, and OsCSLC1, 2, 7, 9 are directly activated by OsEIL1. Furthermore, the auxin signaling pathway is synergistically involved in these regulatory processes. These findings link plant hormone signaling with cell wall establishment, broadening our understanding of root growth plasticity in rice and other crops.
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Affiliation(s)
- Yang Zhou
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi-Hong Gao
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bao-Cai Zhang
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Han-Lei Yang
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan-Bao Tian
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi-Hua Huang
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Cui-Cui Yin
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian-Jun Tao
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Wei
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wan-Ke Zhang
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shou-Yi Chen
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi-Hua Zhou
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin-Song Zhang
- Key Lab of Seed Innovation, State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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Shabab Z, Sarada DL. 24-Epibrassinolide mitigates arsenate stress in seedlings of Oryza sativa (IR-20) via the induction of phenylpropanoid pathway. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:109023. [PMID: 39146914 DOI: 10.1016/j.plaphy.2024.109023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 07/29/2024] [Accepted: 08/06/2024] [Indexed: 08/17/2024]
Abstract
The introduction of arsenic, a hazardous metalloid, into the soil system due to heavy industrialization has negatively affected agricultural productivity, resulting in limited crop yields. A recent breakthrough in stress-responsive hormones, specifically brassinosteroids, has extensively covered the role of antioxidant enzyme defense systems in heavy metal stress mitigation. Considering the antioxidant properties and metal complex formation abilities of polyphenols, our study focuses on examining their role in arsenate toxicity amelioration by 24-epibrassinolide. We demonstrate enhanced growth parameters of sodium arsenate-stressed seedlings upon application of 24-epibrassinolide, with increased root and shoot polyphenol levels analyzed by high-performance liquid chromatography. Specifically, the concentration of catechin, sinapic acid, 4-hydroxy benzoic acid, protocatechuic acid, 4-coumaric acid, and myricetin were elevated, indicating induction of phenylpropanoid signaling pathway. Further, we also report a decrease in the generation of superoxide anions and hydrogen peroxide validated the antioxidant effects of these metabolites through the nitrobluetetrazolium and diaminobenzidine staining method. In addition, evaluation of transcript level of genes encoding for specific enzymes of the phenylpropanoid pathway in shoot and root showed a significant upregulation in mRNA expression of phenylalanine ammonia-lyase-1, cinnamate-4-hydroxylase, and caffeic acid o-methyltransferase-1 upon exogenous application of 24-epibrassinolide in arsenate stressed Oryza sativa.
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Affiliation(s)
- Ziya Shabab
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603 203, Tamil Nadu, India
| | - DronamrajuV L Sarada
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603 203, Tamil Nadu, India.
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3
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Lee EB, Lee K. Coptis rhizome extract influence on Streptococcus pneumoniae through autolysin activation. AMB Express 2024; 14:79. [PMID: 38965154 PMCID: PMC11224187 DOI: 10.1186/s13568-024-01736-x] [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: 01/05/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
This study investigated the antibacterial properties of Coptis rhizome, a plant traditionally used for respiratory infections, against Streptoccus pneumonia (S. pneumoniae), for which there has been minimal empirical evidence of effectiveness. The study particularly examined autolysis, indirectly associated with antibacterial resistance, when using Coptis rhizome for bacterial infections. In our methodology, Coptis rhizome was processed with ethanol and distilled water to produce four different extracts: CRET30, CRET50, CRET70, and CRDW. The antibacterial activity of these extracts were tested through Minimum Inhibitory Concentration (MIC) assays, disk diffusion tests, and time-kill assays, targeting both standard (ATCC 49619) and resistant (ATCC 70067) strains. The study also evaluated the extracts' biofilm inhibition properties and monitored the expression of the lyt gene, integral to autolysis. The results prominently showed that the CRET70 extract demonstrated remarkable antibacterial strength. It achieved an MIC of 0.125 µg/mL against both tested S. pneumoniae strains. The disk diffusion assay recorded inhibition zones of 22.17 mm for ATCC 49619 and 17.20 mm for ATCC 70067. Impressively, CRET70 resulted in a 2-log decrease in bacterial numbers for both strains, showcasing its potent bactericidal capacity. The extract was also effective in inhibiting 77.40% of biofilm formation. Additionally, the significant overexpression of the lytA gene in the presence of CRET70 pointed to a potential mechanism of action for its antibacterial effects. The outcomes provided new perspectives on the use of Coptis rhizome in combating S. pneumoniae, especially significant in an era of escalating antibiotic resistance.
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Affiliation(s)
- Eon-Bee Lee
- Laboratory of Veterinary Pharmacokinetics and Pharmacodynamics, College of Veterinary Medicine, Kyungpook National University, Daegu, 41566, Republic of Korea
- Veterinary Drugs and Biologics Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Republic of Korea
| | - Kyubae Lee
- Department of Biomedical Materials, Konyang University, Daejeon, 35365, Republic of Korea.
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Wang R, Cheng Y, Jiang N, Jiang T, Wei Z. Overexpression of the PtrNF-YA6 gene inhibits secondary cell wall thickening in poplar. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 343:112058. [PMID: 38447913 DOI: 10.1016/j.plantsci.2024.112058] [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: 12/18/2023] [Revised: 02/20/2024] [Accepted: 03/03/2024] [Indexed: 03/08/2024]
Abstract
The NF-Y gene family in plants plays a crucial role in numerous biological processes, encompassing hormone response, stress response, as well as growth and development. In this study, we first used bioinformatics techniques to identify members of the NF-YA family that may function in wood formation. We then used molecular biology techniques to investigate the role and molecular mechanism of PtrNF-YA6 in secondary cell wall (SCW) formation in Populus trichocarpa. We found that PtrNF-YA6 protein was localized in the nucleus and had no transcriptional activating activity. Overexpression of PtrNF-YA6 had an inhibitory effect on plant growth and development and significantly suppressed hemicellulose synthesis and SCW thickening in transgenic plants. Yeast one-hybrid and ChIP-PCR assays revealed that PtrNF-YA6 directly regulated the expression of hemicellulose synthesis genes (PtrGT47A-1, PtrGT8C, PtrGT8F, PtrGT43B, PtrGT47C, PtrGT8A and PtrGT8B). In conclusion, PtrNF-YA6 can inhibit plant hemicellulose synthesis and SCW thickening by regulating the expression of downstream SCW formation-related target genes.
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Affiliation(s)
- Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Yujia Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Nan Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China.
| | - Zhigang Wei
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang 150040, China; Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China.
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Wei S, Yu Z, Du F, Cao F, Yang M, Liu C, Qi Z, Chen Q, Zou J, Wang J. Integrated Transcriptomic and Proteomic Characterization of a Chromosome Segment Substitution Line Reveals the Regulatory Mechanism Controlling the Seed Weight in Soybean. PLANTS (BASEL, SWITZERLAND) 2024; 13:908. [PMID: 38592937 PMCID: PMC10975824 DOI: 10.3390/plants13060908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
Soybean is the major global source of edible oils and vegetable proteins. Seed size and weight are crucial traits determining the soybean yield. Understanding the molecular regulatory mechanism underlying the seed weight and size is helpful for improving soybean genetic breeding. The molecular regulatory pathways controlling the seed weight and size were investigated in this study. The 100-seed weight, seed length, seed width, and seed weight per plant of a chromosome segment substitution line (CSSL) R217 increased compared with those of its recurrent parent 'Suinong14' (SN14). Transcriptomic and proteomic analyses of R217 and SN14 were performed at the seed developmental stages S15 and S20. In total, 2643 differentially expressed genes (DEGs) and 208 differentially accumulated proteins (DAPs) were detected at S15, and 1943 DEGs and 1248 DAPs were detected at S20. Furthermore, integrated transcriptomic and proteomic analyses revealed that mitogen-activated protein kinase signaling and cell wall biosynthesis and modification were potential pathways associated with seed weight and size control. Finally, 59 candidate genes that might control seed weight and size were identified. Among them, 25 genes were located on the substituted segments of R217. Two critical pathways controlling seed weight were uncovered in our work. These findings provided new insights into the seed weight-related regulatory network in soybean.
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Affiliation(s)
- Siming Wei
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Zhenhai Yu
- Heilongjiang Province Green Food Science Institute, Harbin 150028, China;
| | - Fangfang Du
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Fubin Cao
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Mingliang Yang
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Chunyan Liu
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Zhaoming Qi
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Qingshan Chen
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Jianan Zou
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
| | - Jinhui Wang
- National Key Laboratory of Smart Farm Technology and System, Key Laboratory of Soybean Biology in Chinese Ministry of Education, College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.W.); (F.D.); (F.C.); (M.Y.); (C.L.); (Z.Q.)
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Lv S, Lin Z, Shen J, Luo L, Xu Q, Li L, Gui J. OsTCP19 coordinates inhibition of lignin biosynthesis and promotion of cellulose biosynthesis to modify lodging resistance in rice. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:123-136. [PMID: 37724960 DOI: 10.1093/jxb/erad367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/18/2023] [Indexed: 09/21/2023]
Abstract
Lignin and cellulose are two essential elements of plant secondary cell walls that shape the mechanical characteristics of the culm to prevent lodging. However, how the regulation of the lignin and cellulose composition is combined to achieve optimal mechanical characteristics is unclear. Here, we show that increasing OsTCP19 expression in rice coordinately repressed lignin biosynthesis and promoted cellulose biosynthesis, resulting in enhanced lodging resistance. In contrast, repression of OsTCP19 coordinately promoted lignin biosynthesis and inhibited cellulose biosynthesis, leading to greater susceptibility to lodging. We found that OsTCP19 binds to the promoters of both MYB108 and MYB103L to increase their expression, with the former being responsible for repressing lignin biosynthesis and the latter for promoting cellulose biosynthesis. Moreover, up-regulation of OsTCP19 in fibers improved grain yield and lodging resistance. Thus, our results identify the OsTCP19-OsMYB108/OsMYB103L module as a key regulator of lignin and cellulose production in rice, and open up the possibility for precisely manipulating lignin-cellulose composition to improve culm mechanical properties for lodging resistance.
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Affiliation(s)
- Siwei Lv
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Zengshun Lin
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Junhui Shen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Laifu Luo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qingguo Xu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Laigeng Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jinshan Gui
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
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Li G, Song C, Manzoor MA, Li D, Cao Y, Cai Y. Functional and kinetics of two efficient phenylalanine ammonia lyase from Pyrus bretschneideri. BMC PLANT BIOLOGY 2023; 23:612. [PMID: 38041062 PMCID: PMC10693048 DOI: 10.1186/s12870-023-04586-0] [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: 06/21/2023] [Accepted: 11/06/2023] [Indexed: 12/03/2023]
Abstract
BACKGROUND The enzyme phenylalanine ammonia lyase (PAL) controls the transition from primary to secondary metabolism by converting L-phenylalanine (L-Phe) to cinnamic acid. However, the function of PAL in pear plants (Pyrus bretschneideri) has not yet been fully elucidated. RESULTS We identified three PAL genes (PbPAL1, PbPAL2 and PbPAL3) from the pear genome by exploring pear genome databases. The evolutionary tree revealed that three PbPALs were classified into one group. We expressed PbPAL1 and PbPAL2 recombinant proteins, and the purified PbPAL1 and PbPAL2 proteins showed strict substrate specificity for L-Phe, no activity toward L-Tyr in vitro, and modest changes in kinetics and enzyme characteristics. Furthermore, overexpression of PbAL1 and PbPAL1-RNAi, respectively, and resulted in significant changes in stone cell and lignin contents in pear fruits. The results of yeast one-hybrid (Y1H) assays that PbWLIM1 could bind to the conserved PAL box in the PbPAL promoter and regulate the transcription level of PbPAL2. CONCLUSIONS Our findings not only showed PbPAL's potential role in lignin biosynthesis but also laid the foundation for future studies on the regulation of lignin synthesis and stone cell development in pear fruit utilizing molecular biology approaches.
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Affiliation(s)
- Guohui Li
- Anhui Engineering Research Center for Eco-Agriculture of Traditional Chinese Medicine, Anhui Provincial Key Laboratory for Quality Evaluation and Improvement of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
| | - Cheng Song
- Anhui Engineering Research Center for Eco-Agriculture of Traditional Chinese Medicine, Anhui Provincial Key Laboratory for Quality Evaluation and Improvement of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
| | - Muhammad Aamir Manzoor
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Daoyuan Li
- Anhui Engineering Research Center for Eco-Agriculture of Traditional Chinese Medicine, Anhui Provincial Key Laboratory for Quality Evaluation and Improvement of Traditional Chinese Medicine, College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
| | - Yunpeng Cao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Yongping Cai
- Anhui Agricultural University, Hefei, 230036, China.
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8
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Takawira LT, Hadj Bachir I, Ployet R, Tulloch J, San Clemente H, Christie N, Ladouce N, Dupas A, Rai A, Grima-Pettenati J, Myburg AA, Mizrachi E, Mounet F, Hussey SG. Functional investigation of five R2R3-MYB transcription factors associated with wood development in Eucalyptus using DAP-seq-ML. PLANT MOLECULAR BIOLOGY 2023; 113:33-57. [PMID: 37661236 DOI: 10.1007/s11103-023-01376-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 07/31/2023] [Indexed: 09/05/2023]
Abstract
A multi-tiered transcriptional network regulates xylem differentiation and secondary cell wall (SCW) formation in plants, with evidence of both conserved and lineage-specific SCW network architecture. We aimed to elucidate the roles of selected R2R3-MYB transcription factors (TFs) linked to Eucalyptus wood formation by identifying genome-wide TF binding sites and direct target genes through an improved DAP-seq protocol combined with machine learning for target gene assignment (DAP-seq-ML). We applied this to five TFs including a well-studied SCW master regulator (EgrMYB2; homolog of AtMYB83), a repressor of lignification (EgrMYB1; homolog of AtMYB4), a TF affecting SCW thickness and vessel density (EgrMYB137; homolog of PtrMYB074) and two TFs with unclear roles in SCW regulation (EgrMYB135 and EgrMYB122). Each DAP-seq TF peak set (average 12,613 peaks) was enriched for canonical R2R3-MYB binding motifs. To improve the reliability of target gene assignment to peaks, a random forest classifier was developed from Arabidopsis DAP-seq, RNA-seq, chromatin, and conserved noncoding sequence data which demonstrated significantly higher precision and recall to the baseline method of assigning genes to proximal peaks. EgrMYB1, EgrMYB2 and EgrMYB137 predicted targets showed clear enrichment for SCW-related biological processes. As validation, EgrMYB137 overexpression in transgenic Eucalyptus hairy roots increased xylem lignification, while its dominant repression in transgenic Arabidopsis and Populus reduced xylem lignification, stunted growth, and caused downregulation of SCW genes. EgrMYB137 targets overlapped significantly with those of EgrMYB2, suggesting partial functional redundancy. Our results show that DAP-seq-ML identified biologically relevant R2R3-MYB targets supported by the finding that EgrMYB137 promotes SCW lignification in planta.
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Affiliation(s)
- Lazarus T Takawira
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Ines Hadj Bachir
- Laboratoire de Recherche en Sciences Végétales, Université Toulouse, CNRS, INP, Castanet-Tolosan, France
| | - Raphael Ployet
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Jade Tulloch
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Helene San Clemente
- Laboratoire de Recherche en Sciences Végétales, Université Toulouse, CNRS, INP, Castanet-Tolosan, France
| | - Nanette Christie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Nathalie Ladouce
- Laboratoire de Recherche en Sciences Végétales, Université Toulouse, CNRS, INP, Castanet-Tolosan, France
| | - Annabelle Dupas
- Laboratoire de Recherche en Sciences Végétales, Université Toulouse, CNRS, INP, Castanet-Tolosan, France
| | - Avanish Rai
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Jacqueline Grima-Pettenati
- Laboratoire de Recherche en Sciences Végétales, Université Toulouse, CNRS, INP, Castanet-Tolosan, France
| | - Alexander A Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Eshchar Mizrachi
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Fabien Mounet
- Laboratoire de Recherche en Sciences Végétales, Université Toulouse, CNRS, INP, Castanet-Tolosan, France.
| | - Steven G Hussey
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa.
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Yang J, Xu J, Zhang Y, Cui J, Hu H, Xue J, Zhu L. Two R2R3-MYB transcription factors from Chinese cedar (Cryptomeria fortunei Hooibrenk) are involved in the regulation of secondary cell wall formation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107879. [PMID: 37422947 DOI: 10.1016/j.plaphy.2023.107879] [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: 03/02/2022] [Revised: 06/06/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023]
Abstract
As the most abundant renewable energy source, wood comprises the secondary cell wall (SCW). SCW biosynthesis involves lignin and cellulose deposition. Increasing studies have illustrated that R2R3-MYB transcription factors (TFs) play pivotal roles in affecting lignin accumulation and SCW formation. Nevertheless, the regulatory roles of R2R3-MYBs are still unresolved in Cryptomeria fortunei Hooibrenk cambium and wood formation. To dissect the potentials of CfMYBs, we successfully cloned and intensively studied the functions of CfMYB4 and CfMYB5 in SCW formation and abiotic stress response. They both contained the conserved MYB domain capable of forming a special structure that could bind to the core motifs of downstream genes. The phylogenetic tree implied that two CfMYBs clustered into different evolutionary branches. They were predominantly expressed in the stem and were localized to the nucleus. Furthermore, CfMYB4 functioned as an activator to enhance lignin and cellulose accumulation, and increase the SCW thickness by elevating the expression levels of SCW-related genes. By contrast, CfMYB5 negatively regulated lignin and cellulose biosynthesis, and decreased SCW formation by reducing the expression of SCW biosynthetic genes. Our data not only highlight the regulatory functions of CfMYBs in lignin deposition but also provide critical insights into the development of strategies for the genetic improvement of Cryptomeria fortunei wood biomass.
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Affiliation(s)
- Junjie Yang
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China; College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Jin Xu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China; College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.
| | - Yingting Zhang
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China; College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Jiebing Cui
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China; College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Hailiang Hu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China; College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Jinyu Xue
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China; College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Lijuan Zhu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, 210037, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China; College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
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10
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Cao S, Wang Y, Gao Y, Xu R, Ma J, Xu Z, Shang-Guan K, Zhang B, Zhou Y. The RLCK-VND6 module coordinates secondary cell wall formation and adaptive growth in rice. MOLECULAR PLANT 2023:S1674-2052(23)00104-1. [PMID: 37050877 DOI: 10.1016/j.molp.2023.04.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 03/05/2023] [Accepted: 04/08/2023] [Indexed: 05/27/2023]
Abstract
The orderly deposition of secondary cell wall (SCW) in plants is implicated in various biological programs and is precisely controlled. Although many positive and negative regulators of SCW have been documented, the molecular mechanisms underlying SCW formation coordinated with distinct cellular physiological processes during plant adaptive growth remain largely unclear. Here, we report the identification of Cellulose Synthase co-expressed Kinase1 (CSK1), which encodes a receptor-like cytoplasmic kinase, as a negative regulator of SCW formation and its signaling cascade in rice. Transcriptome deep sequencing of developing internodes and genome-wide co-expression assays revealed that CSK1 is co-expressed with cellulose synthase genes and is responsive to various stress stimuli. The increased SCW thickness and vigorous vessel transport in csk1 indicate that CSK1 functions as a negative regulator of SCW biosynthesis. Through observation of green fluorescent protein-tagged CSK1 in rice protoplasts and stable transgenic plants, we found that CSK1 is localized in the nucleus and cytoplasm adjacent to the plasma membrane. Biochemical and molecular assays demonstrated that CSK1 phosphorylates VASCULAR-RELATED NAC-DOMAIN 6 (VND6), a master SCW-associated transcription factor, in the nucleus, which reduces the transcription of a suite of SCW-related genes, thereby attenuating SCW accumulation. Consistently, genetic analyses show that CSK1 functions upstream of VND6 in regulating SCW formation. Interestingly, our physiological analyses revealed that CSK1 and VND6 are involved in abscisic acid-mediated regulation of cell growth and SCW deposition. Taken together, these results indicate that the CSK1-VND6 module is an important component of the SCW biosynthesis machinery, which coordinates SCW accumulation and adaptive growth in rice. Our study not only identifies a new regulator of SCW biosynthesis but also reveals a fine-tuned mechanism for precise control of SCW deposition, offering tools for rationally tailoring agronomic traits.
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Affiliation(s)
- Shaoxue Cao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yihong Gao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Xu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianing Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zuopeng Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, College of Agriculture, Yangzhou University, Yangzhou, 225009, China
| | - Keke Shang-Guan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Baocai Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yihua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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11
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Tung CC, Kuo SC, Yang CL, Yu JH, Huang CE, Liou PC, Sun YH, Shuai P, Su JC, Ku C, Lin YCJ. Single-cell transcriptomics unveils xylem cell development and evolution. Genome Biol 2023; 24:3. [PMID: 36624504 PMCID: PMC9830878 DOI: 10.1186/s13059-022-02845-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/31/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Xylem, the most abundant tissue on Earth, is responsible for lateral growth in plants. Typical xylem has a radial system composed of ray parenchyma cells and an axial system of fusiform cells. In most angiosperms, fusiform cells comprise vessel elements for water transportation and libriform fibers for mechanical support, while both functions are performed by tracheids in other vascular plants such as gymnosperms. Little is known about the developmental programs and evolutionary relationships of these xylem cell types. RESULTS Through both single-cell and laser capture microdissection transcriptomic profiling, we determine the developmental lineages of ray and fusiform cells in stem-differentiating xylem across four divergent woody angiosperms. Based on cross-species analyses of single-cell clusters and overlapping trajectories, we reveal highly conserved ray, yet variable fusiform, lineages across angiosperms. Core eudicots Populus trichocarpa and Eucalyptus grandis share nearly identical fusiform lineages, whereas the more basal angiosperm Liriodendron chinense has a fusiform lineage distinct from that in core eudicots. The tracheids in the basal eudicot Trochodendron aralioides, an evolutionarily reversed trait, exhibit strong transcriptomic similarity to vessel elements rather than libriform fibers. CONCLUSIONS This evo-devo framework provides a comprehensive understanding of the formation of xylem cell lineages across multiple plant species spanning over a hundred million years of evolutionary history.
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Affiliation(s)
- Chia-Chun Tung
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Shang-Che Kuo
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan
| | - Chia-Ling Yang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Jhong-He Yu
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Chia-En Huang
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Pin-Chien Liou
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Ying-Hsuan Sun
- Department of Forestry, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Peng Shuai
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jung-Chen Su
- Department of Pharmacy, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Chuan Ku
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan.
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan.
| | - Ying-Chung Jimmy Lin
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan.
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, 10617, Taiwan.
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan.
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12
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Zhang Q, Qin B, Wang GD, Zhang WJ, Li M, Yin ZG, Yuan X, Sun HY, Du JD, Du YL, Jia P. Exogenous melatonin enhances cell wall response to salt stress in common bean ( Phaseolus vulgaris) and the development of the associated predictive molecular markers. FRONTIERS IN PLANT SCIENCE 2022; 13:1012186. [PMID: 36325547 PMCID: PMC9619082 DOI: 10.3389/fpls.2022.1012186] [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: 08/05/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Common bean (Phaseolus vulgaris) is an important food crop; however, its production is affected by salt stress. Salt stress can inhibit seed germination, promote senescence, and modify cell wall biosynthesis, assembly, and architecture. Melatonin, an indole heterocycle, has been demonstrated to greatly impact cell wall structure, composition, and regulation in plants under stress. However, the molecular basis for such assumptions is still unclear. In this study, a common bean variety, "Naihua" was treated with water (W), 70 mmol/L NaCl solution (S), and 100 μmol/L melatonin supplemented with salt solution (M+S) to determine the response of common bean to exogenous melatonin and explore regulatory mechanism of melatonin against salt stress. The results showed that exogenous melatonin treatment alleviated salt stress-induced growth inhibition of the common bean by increasing the length, surface area, volume, and diameter of common bean sprouts. Moreover, RNA sequencing (RNA-seq) and real-time quantitative PCR (qRT-PCR) indicated that the cell wall regulation pathway was involved in the salt stress tolerance of the common bean enhanced by melatonin. Screening of 120 germplasm resources revealed that melatonin treatment improved the salt tolerance of more than 65% of the common bean germplasm materials. Melatonin also up-regulated cell wall pathway genes by at least 46%. Furthermore, we analyzed the response of the common bean germplasm materials to melatonin treatment under salt stress using the key genes associated with the synthesis of the common bean cell wall as the molecular markers. The results showed that two pairs of markers were significantly associated with melatonin, and these could be used as candidate markers to predict whether common bean respond to exogenous melatonin and then enhance salt tolerance at the sprouting stage. This study shows that cell wall can respond to exogenous melatonin and enhance the salt tolerance of common bean. The makers identified in this study can be used to select common bean varieties that can respond to melatonin under stress. Overall, the study found that cell wall could response melatonin and enhance the salt tolerance and developed the makers for predicting varieties fit for melatonin under stress in common bean, which may be applied in the selection or development of common bean varieties with abiotic stress tolerance.
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Affiliation(s)
- Qi Zhang
- College of Agriculture, Herlongjiang Bayi Agricultural University, Daqing, China
| | - Bin Qin
- College of Agriculture, Herlongjiang Bayi Agricultural University, Daqing, China
| | - Guang-da Wang
- College of Agriculture, Herlongjiang Bayi Agricultural University, Daqing, China
| | - Wen-jing Zhang
- College of Agriculture, Herlongjiang Bayi Agricultural University, Daqing, China
| | - Ming Li
- College of Agriculture, Herlongjiang Bayi Agricultural University, Daqing, China
| | - Zhen-gong Yin
- Crop Resources Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xiankai Yuan
- College of Agriculture, Herlongjiang Bayi Agricultural University, Daqing, China
| | - Hao-yue Sun
- Qiqihar Branch, Heilongjiang Academy of Agricultural Sciences, Qiqihaer, China
| | - Ji-dao Du
- College of Agriculture, Herlongjiang Bayi Agricultural University, Daqing, China
- National Coarse Cereals Engineering Research Center, Herlongjiang Bayi Agricultural University, Daqing, China
| | - Yan-li Du
- College of Agriculture, Herlongjiang Bayi Agricultural University, Daqing, China
- National Coarse Cereals Engineering Research Center, Herlongjiang Bayi Agricultural University, Daqing, China
| | - Pengyu Jia
- College of Agriculture, Herlongjiang Bayi Agricultural University, Daqing, China
- National Coarse Cereals Engineering Research Center, Herlongjiang Bayi Agricultural University, Daqing, China
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13
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Zhang Y, Shan X, Zhao Q, Shi F. The MicroRNA397a-LACCASE17 module regulates lignin biosynthesis in Medicago ruthenica (L.). FRONTIERS IN PLANT SCIENCE 2022; 13:978515. [PMID: 36061772 PMCID: PMC9434696 DOI: 10.3389/fpls.2022.978515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Mechanical strength is essential for the upright growth habit, which is one of the most important characteristics of terrestrial plants. Lignin, a phenylpropanoid-derived polymer mainly present in secondary cell walls plays critical role in providing mechanical support. Here, we report that the prostrate-stem cultivar of the legume forage Medicago ruthenica cultivar 'Mengnong No. 1' shows compromised mechanical strength compared with the erect-stem cultivar 'Zhilixing'. The erect-stem cultivar, 'Zhilixing' has significantly higher lignin content, leading to higher mechanical strength than the prostrate-stem cultivar. The low abundance of miRNA397a in the Zhiixing cultivar causes reduced cleavage of MrLAC17 transcript, which results in enhanced expression level of MrLAC17 compared to that in the prostrate-stem cultivar Mengnong No. 1. Complementation of the Arabidopsis lac4 lac17 double mutants with MrLAC17 restored the lignin content to wild-type levels, confirming that MrLAC17 perform an exchangeable role with Arabidopsis laccases. LAC17-mediated lignin polymerization is therefore increased in the 'Zhilixing', causing the erect stem phenotype. Our data reveal the importance of the miR397a in the lignin biosynthesis and suggest a strategy for molecular breeding targeting plant architecture in legume forage.
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Affiliation(s)
- Yutong Zhang
- Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, College of Grassland Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaotong Shan
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Qiao Zhao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Fengling Shi
- Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, College of Grassland Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
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14
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Wang X, Yao S, Htet WPPM, Yue Y, Zhang Z, Sun K, Chen S, Luo K, Fan D. MicroRNA828 negatively regulates lignin biosynthesis in stem of Populus tomentosa through MYB targets. TREE PHYSIOLOGY 2022; 42:1646-1661. [PMID: 35220431 DOI: 10.1093/treephys/tpac023] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Lignin biosynthesis in the sclerenchyma cells is strictly controlled by a complex network of genetic and environmental signals. In the last decades, the transcriptional regulation of lignin synthesis in woody species has been established. However, the role of microRNA-mediated post-transcriptional modulation in secondary cell wall biosynthesis remains poorly understood. Here, we identified a microRNA, miR828, involved in the regulation specific to lignin biosynthesis during stem development in Populus tomentosa Carr. miR828 is preferentially expressed in the secondary vascular tissues during stem development. Two MYB genes (MYB171 and MYB011) were validated as direct targets of miR828 by degradome analysis and green fluorescent protein signal detection. Overexpression of miR828 in poplar downregulated genes for lignin biosynthesis, resulting in reduced lignin content in cell walls. Conversely, suppression of miR828 in plants by the short tandem target mimics elevated the expression of lignin biosynthetic genes and increased lignin deposition. We further revealed that poplar MYB171, as the most abundant miR828 target in the stem, is a positive regulator for lignin biosynthesis. Transient expression assays showed that both MYB171 and MYB011 activated PAL1 and CCR2 transcription, whereas the introduction of miR828 significantly suppressed their expression that was induced by MYB171 or MYB011. Collectively, our results demonstrate that the miR828-MYBs module precisely regulates lignin biosynthesis during the stem development in P. tomentosa through transcriptional and post-transcriptional manners.
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Affiliation(s)
- Xianqiang Wang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Shu Yao
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Win Pa Pa Myo Htet
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Yuchen Yue
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Zhuanzhuan Zhang
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Kuan Sun
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Sijie Chen
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
| | - Di Fan
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China
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15
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Li G, Zeng X, Li Y, Li J, Huang X, Zhao D. BRITTLE CULM17, a Novel Allele of TAC4, Affects the Mechanical Properties of Rice Plants. Int J Mol Sci 2022; 23:ijms23105305. [PMID: 35628116 PMCID: PMC9140386 DOI: 10.3390/ijms23105305] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 01/27/2023] Open
Abstract
Lodging resistance of rice (Oryza sativa L.) has always been a hot issue in agricultural production. A brittle stem mutant, osbc17, was identified by screening an EMS (Ethylmethane sulfonate) mutant library established in our laboratory. The stem segments and leaves of the mutant were obviously brittle and fragile, with low mechanical strength. Examination of paraffin sections of flag leaf and internode samples indicated that the number of cell layers in mechanical tissue of the mutant was decreased compared with the wild type, Pingtangheinuo, and scanning electron microscopy revealed that the mechanical tissue cell walls of the mutant were thinner. Lignin contents of the internodes of mature-stage rice were significantly lower in the mutant than in the wild type. By the MutMap method, we found candidate gene OsBC17, which was located on rice chromosome 2 and had a 2433 bp long coding sequence encoding a protein sequence of 810 amino acid residues with unknown function. According to LC-MS/MS analysis of intermediate products of the lignin synthesis pathway, the accumulation of caffeyl alcohol in the osbc17 mutant was significantly higher than in Pingtangheinuo. Caffeyl alcohol can be polymerized to the catechyl lignin monomer by laccase ChLAC8; however, ChLAC8 and OsBC17 are not homologous proteins, which suggests that the osbc17 gene is involved in this process by regulating laccase expression.
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Affiliation(s)
- Guangzheng Li
- The State Key Laboratory of Green Pesticide and Agricultural Biological Engineering, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China;
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, Guiyang 550025, China; (X.Z.); (Y.L.); (J.L.); (X.H.)
| | - Xiaofang Zeng
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, Guiyang 550025, China; (X.Z.); (Y.L.); (J.L.); (X.H.)
| | - Yan Li
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, Guiyang 550025, China; (X.Z.); (Y.L.); (J.L.); (X.H.)
| | - Jianrong Li
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, Guiyang 550025, China; (X.Z.); (Y.L.); (J.L.); (X.H.)
| | - Xiaozhen Huang
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, Guiyang 550025, China; (X.Z.); (Y.L.); (J.L.); (X.H.)
| | - Degang Zhao
- The State Key Laboratory of Green Pesticide and Agricultural Biological Engineering, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China;
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Institute of Agro-Bioengineering, College of Life Sciences, Guizhou University, Guiyang 550025, China; (X.Z.); (Y.L.); (J.L.); (X.H.)
- Guizhou Plant Conservation Center, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
- Correspondence:
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16
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Li X, Huang H, Rizwan HM, Wang N, Jiang J, She W, Zheng G, Pan H, Guo Z, Pan D, Pan T. Transcriptome Analysis Reveals Candidate Lignin-Related Genes and Transcription Factors during Fruit Development in Pomelo ( Citrus maxima). Genes (Basel) 2022; 13:845. [PMID: 35627230 PMCID: PMC9140673 DOI: 10.3390/genes13050845] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/27/2022] [Accepted: 05/03/2022] [Indexed: 02/01/2023] Open
Abstract
Juice sac granulation (a physiological disorder) leads to large postharvest losses of pomelo (Citrus maxima). Previous studies have shown that juice sac granulation is closely related to lignin accumulation, while the molecular mechanisms underlying this disorder remain elusive in pomelo. Our results showed that the lignin content in NC (near the core) and FC (far away from the core) juice sacs overall increased from 157 DPA (days post anthesis) to 212 DPA and reached a maximum at 212 DPA. Additionally, the lignin content of NC juice sacs was higher than that of FC juice sacs. In this study, we used transcriptome-based weighted gene co-expression network analysis (WGCNA) to address how lignin formation in NC and FC juice sacs is generated during the development of pomelo. After data assembly and bioinformatic analysis, we found a most correlated module (black module) to the lignin content, then we used the 11 DEGs in this module as hub genes for lignin biosynthesis. Among these DEGs, PAL (phenylalanine ammonia lyase), HCT (hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase), 4CL2 (4-coumarate: CoA ligase), C4H (cinnamate 4-hydroxylase), C3'H (p-coumarate 3-hydroxylase), and CCoAOMT1 (caffeoyl CoA 3-Omethyltransferase) were the most distinct DEGs in granulated juice sacs. Co-expression analysis revealed that the expression patterns of several transcription factors such as MYB, NAC, OFP6, and bHLH130 are highly correlated with lignin formation. In addition, the expression patterns of the DEGs related to lignin biosynthesis and transcription factors were validated by qRT-PCR, and the results were highly concordant with the RNA-seq results. These results would be beneficial for further studies on the molecular mechanism of lignin accumulation in pomelo juice sacs and would help with citrus breeding.
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Affiliation(s)
- Xiaoting Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (H.M.R.); (N.W.); (J.J.); (W.S.); (G.Z.); (H.P.); (Z.G.); (T.P.)
| | - Hantang Huang
- College of Horticulture, China Agricultural University, Beijing 100083, China;
| | - Hafiz Muhammad Rizwan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (H.M.R.); (N.W.); (J.J.); (W.S.); (G.Z.); (H.P.); (Z.G.); (T.P.)
| | - Naiyu Wang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (H.M.R.); (N.W.); (J.J.); (W.S.); (G.Z.); (H.P.); (Z.G.); (T.P.)
| | - Jingyi Jiang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (H.M.R.); (N.W.); (J.J.); (W.S.); (G.Z.); (H.P.); (Z.G.); (T.P.)
| | - Wenqin She
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (H.M.R.); (N.W.); (J.J.); (W.S.); (G.Z.); (H.P.); (Z.G.); (T.P.)
| | - Guohua Zheng
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (H.M.R.); (N.W.); (J.J.); (W.S.); (G.Z.); (H.P.); (Z.G.); (T.P.)
| | - Heli Pan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (H.M.R.); (N.W.); (J.J.); (W.S.); (G.Z.); (H.P.); (Z.G.); (T.P.)
| | - Zhixiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (H.M.R.); (N.W.); (J.J.); (W.S.); (G.Z.); (H.P.); (Z.G.); (T.P.)
| | - Dongming Pan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (H.M.R.); (N.W.); (J.J.); (W.S.); (G.Z.); (H.P.); (Z.G.); (T.P.)
| | - Tengfei Pan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (H.M.R.); (N.W.); (J.J.); (W.S.); (G.Z.); (H.P.); (Z.G.); (T.P.)
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17
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Li H, Dai X, Huang X, Xu M, Wang Q, Yan X, Sederoff RR, Li Q. Single-cell RNA sequencing reveals a high-resolution cell atlas of xylem in Populus. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1906-1921. [PMID: 34347368 DOI: 10.1111/jipb.13159] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/02/2021] [Indexed: 05/24/2023]
Abstract
High-throughput single-cell RNA sequencing (scRNA-seq) has advantages over traditional RNA-seq to explore spatiotemporal information on gene dynamic expressions in heterogenous tissues. We performed Drop-seq, a method for the dropwise sequestration of single cells for sequencing, on protoplasts from the differentiating xylem of Populus alba × Populus glandulosa. The scRNA-seq profiled 9,798 cells, which were grouped into 12 clusters. Through characterization of differentially expressed genes in each cluster and RNA in situ hybridizations, we identified vessel cells, fiber cells, ray parenchyma cells and xylem precursor cells. Diffusion pseudotime analyses revealed the differentiating trajectory of vessels, fiber cells and ray parenchyma cells and indicated a different differentiation process between vessels and fiber cells, and a similar differentiation process between fiber cells and ray parenchyma cells. We identified marker genes for each cell type (cluster) and key candidate regulators during developmental stages of xylem cell differentiation. Our study generates a high-resolution expression atlas of wood formation at the single cell level and provides valuable information on wood formation.
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Affiliation(s)
- Hui Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xinren Dai
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiong Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Mengxuan Xu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Qiao Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiaojing Yan
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Ronald R Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
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18
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Gao J, Chen T, Jiang C, Wang T, Huang O, Zhang X, Liu J. Comparative anatomical and transcriptomic analyses of the color variation of leaves in Aquilaria sinensis. PeerJ 2021; 9:e11586. [PMID: 34221719 PMCID: PMC8231315 DOI: 10.7717/peerj.11586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 05/20/2021] [Indexed: 11/20/2022] Open
Abstract
Color variation in plant tissues is a common phenomenon accompanied with a series of biological changes. In this study, a special-phenotype Aquilaria sinensis (GS) with color variation of leaf was firstly reported, and DNA barcode sequences showed GS samples could not be discriminated clearly with the normal A. sinensis sample (NS), which suggested that the variety was not the cause of the GS formation. To reveal the characteristics of GS compared to NS, the anatomical and transcriptome sequencing studies were carried out. In microscopic observation, the leaves of golden-vein-leaf sample (LGS) and normal-vein-leaf sample (LNS) showed significant differences including the area of the included phloem in midrib and the thickness parameters of palisade and spongy tissues; the stems of golden-vein-leaf sample (SGS) and normal-vein-leaf sample (SNS) were also different in many aspects such as the area of vessels and included phloem. In addition, the structure of chloroplast was more complete in the midrib of LNS than that of LGS, and some particles suspected as virus were found through transmission electron microscope as well. Genes upregulated in LGS in contrast with LNS were mainly enriched in photosynthesis. As for stems, most of the genes upregulated in SGS compared to SNS were involved in translation and metabolism processes. The pathways about photosynthesis and chlorophyll metabolism as well as some important transcription factors may explain the molecular mechanism of the unique phenotypes of leaves and the genes related to suberin biosynthesis may result in the difference of stems. In addition, the genes about defense response especially biotic stress associated with numerous pathogenesis-related (PR) genes upregulated in LGS compared to LNS indicated that the pathogen may be the internal factor. Taken together, our results reveal the macro- and micro-phenotype variations as well as gene expression profiles between GS and NS, which could provide valuable clues for elucidating the mechanism of the color variation of Aquilaria.
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Affiliation(s)
- Jiaqi Gao
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- School of Pharmacy, Jiangsu University, Zhenjiang, China
| | - Tong Chen
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chao Jiang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Tielin Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ou Huang
- Guangdong Shangzhengtang Group Co., Ltd, Dongguan, China
| | - Xiang Zhang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Juan Liu
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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19
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Yuan H, Guo W, Zhao L, Yu Y, Chen S, Tao L, Cheng L, Kang Q, Song X, Wu J, Yao Y, Huang W, Wu Y, Liu Y, Yang X, Wu G. Genome-wide identification and expression analysis of the WRKY transcription factor family in flax (Linum usitatissimum L.). BMC Genomics 2021; 22:375. [PMID: 34022792 PMCID: PMC8141250 DOI: 10.1186/s12864-021-07697-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 05/10/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Members of the WRKY protein family, one of the largest transcription factor families in plants, are involved in plant growth and development, signal transduction, senescence, and stress resistance. However, little information is available about WRKY transcription factors in flax (Linum usitatissimum L.). RESULTS In this study, comprehensive genome-wide characterization of the flax WRKY gene family was conducted that led to prediction of 102 LuWRKY genes. Based on bioinformatics-based predictions of structural and phylogenetic features of encoded LuWRKY proteins, 95 LuWRKYs were classified into three main groups (Group I, II, and III); Group II LuWRKYs were further assigned to five subgroups (IIa-e), while seven unique LuWRKYs (LuWRKYs 96-102) could not be assigned to any group. Most LuWRKY proteins within a given subgroup shared similar motif compositions, while a high degree of motif composition variability was apparent between subgroups. Using RNA-seq data, expression patterns of the 102 predicted LuWRKY genes were also investigated. Expression profiling data demonstrated that most genes associated with cellulose, hemicellulose, or lignin content were predominantly expressed in stems, roots, and less in leaves. However, most genes associated with stress responses were predominantly expressed in leaves and exhibited distinctly higher expression levels in developmental stages 1 and 8 than during other stages. CONCLUSIONS Ultimately, the present study provides a comprehensive analysis of predicted flax WRKY family genes to guide future investigations to reveal functions of LuWRKY proteins during plant growth, development, and stress responses.
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Affiliation(s)
- Hongmei Yuan
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China.
| | - Wendong Guo
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Sciences, Harbin, 150040, China
| | - Lijuan Zhao
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Ying Yu
- School of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Si Chen
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Lei Tao
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Lili Cheng
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Qinghua Kang
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Xixia Song
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Jianzhong Wu
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Yubo Yao
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Wengong Huang
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Ying Wu
- College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Yan Liu
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Xue Yang
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Guangwen Wu
- Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
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20
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Lee DY, Jeon J, Kim KT, Cheong K, Song H, Choi G, Ko J, Opiyo SO, Correll JC, Zuo S, Madhav S, Wang GL, Lee YH. Comparative genome analyses of four rice-infecting Rhizoctonia solani isolates reveal extensive enrichment of homogalacturonan modification genes. BMC Genomics 2021; 22:242. [PMID: 33827423 PMCID: PMC8028249 DOI: 10.1186/s12864-021-07549-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/23/2021] [Indexed: 11/24/2022] Open
Abstract
Background Plant pathogenic isolates of Rhizoctonia solani anastomosis group 1-intraspecific group IA (AG1-IA) infect a wide range of crops causing diseases such as rice sheath blight (ShB). ShB has become a serious disease in rice production worldwide. Additional genome sequences of the rice-infecting R. solani isolates from different geographical regions will facilitate the identification of important pathogenicity-related genes in the fungus. Results Rice-infecting R. solani isolates B2 (USA), ADB (India), WGL (India), and YN-7 (China) were selected for whole-genome sequencing. Single-Molecule Real-Time (SMRT) and Illumina sequencing were used for de novo sequencing of the B2 genome. The genomes of the other three isolates were then sequenced with Illumina technology and assembled using the B2 genome as a reference. The four genomes ranged from 38.9 to 45.0 Mbp in size, contained 9715 to 11,505 protein-coding genes, and shared 5812 conserved orthogroups. The proportion of transposable elements (TEs) and average length of TE sequences in the B2 genome was nearly 3 times and 2 times greater, respectively, than those of ADB, WGL and YN-7. Although 818 to 888 putative secreted proteins were identified in the four isolates, only 30% of them were predicted to be small secreted proteins, which is a smaller proportion than what is usually found in the genomes of cereal necrotrophic fungi. Despite a lack of putative secondary metabolite biosynthesis gene clusters, the rice-infecting R. solani genomes were predicted to contain the most carbohydrate-active enzyme (CAZyme) genes among all 27 fungal genomes used in the comparative analysis. Specifically, extensive enrichment of pectin/homogalacturonan modification genes were found in all four rice-infecting R. solani genomes. Conclusion Four R. solani genomes were sequenced, annotated, and compared to other fungal genomes to identify distinctive genomic features that may contribute to the pathogenicity of rice-infecting R. solani. Our analyses provided evidence that genomic conservation of R. solani genomes among neighboring AGs was more diversified than among AG1-IA isolates and the presence of numerous predicted pectin modification genes in the rice-infecting R. solani genomes that may contribute to the wide host range and virulence of this necrotrophic fungal pathogen. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07549-7.
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Affiliation(s)
- Da-Young Lee
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA
| | - Jongbum Jeon
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Ki-Tae Kim
- Department of Agricultural Life Science, Sunchon National University, Suncheon, 57922, South Korea
| | - Kyeongchae Cheong
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Hyeunjeong Song
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Gobong Choi
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Jaeho Ko
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | - Stephen O Opiyo
- Ohio Agricultural Research and Development Center (OARDC) Molecular & Cellular Imaging Center (MCIC)-Columbus, The Ohio State University, Columbus, OH, 43210, USA
| | - James C Correll
- Department of Entomology & Plant Pathology, University of Arkansas, Fayetteville, AK, 72701, USA
| | - Shimin Zuo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Sheshu Madhav
- Indian Council of Agricultural Research-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, 500030, Telangana, India
| | - Guo-Liang Wang
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA.
| | - Yong-Hwan Lee
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea. .,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea. .,Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea. .,Center for Fungal Genetic Resources, Plant Immunity Research Center, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, 08826, Seoul, South Korea.
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21
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Zhang B, Gao Y, Zhang L, Zhou Y. The plant cell wall: Biosynthesis, construction, and functions. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:251-272. [PMID: 33325153 DOI: 10.1111/jipb.13055] [Citation(s) in RCA: 172] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 12/15/2020] [Indexed: 05/19/2023]
Abstract
The plant cell wall is composed of multiple biopolymers, representing one of the most complex structural networks in nature. Hundreds of genes are involved in building such a natural masterpiece. However, the plant cell wall is the least understood cellular structure in plants. Due to great progress in plant functional genomics, many achievements have been made in uncovering cell wall biosynthesis, assembly, and architecture, as well as cell wall regulation and signaling. Such information has significantly advanced our understanding of the roles of the cell wall in many biological and physiological processes and has enhanced our utilization of cell wall materials. The use of cutting-edge technologies such as single-molecule imaging, nuclear magnetic resonance spectroscopy, and atomic force microscopy has provided much insight into the plant cell wall as an intricate nanoscale network, opening up unprecedented possibilities for cell wall research. In this review, we summarize the major advances made in understanding the cell wall in this era of functional genomics, including the latest findings on the biosynthesis, construction, and functions of the cell wall.
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Affiliation(s)
- Baocai Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yihong Gao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lanjun Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yihua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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22
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Overexpression of PtrMYB121 Positively Regulates the Formation of Secondary Cell Wall in Arabidopsis thaliana. Int J Mol Sci 2020; 21:ijms21207734. [PMID: 33086706 PMCID: PMC7589094 DOI: 10.3390/ijms21207734] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/15/2020] [Accepted: 10/17/2020] [Indexed: 12/30/2022] Open
Abstract
MYB transcription factors have a wide range of functions in plant growth, hormone signaling, salt, and drought tolerances. In this study, two homologous transcription factors, PtrMYB55 and PtrMYB121, were isolated and their functions were elucidated. Tissue expression analysis revealed that PtrMYB55 and PtrMYB121 had a similar expression pattern, which had the highest expression in stems. Their expression continuously increased with the growth of poplar, and the expression of PtrMYB121 was significantly upregulated in the process. The full length of PtrMYB121 was 1395 bp, and encoded protein contained 464 amino acids including conserved R2 and R3 MYB domains. We overexpressed PtrMYB121 in Arabidopsis thaliana, and the transgenic lines had the wider xylem as compared with wild-type Arabidopsis. The contents of cellulose and lignin were obviously higher than those in wild-type materials, but there was no significant change in hemicellulose. Quantitative real-time PCR demonstrated that the key enzyme genes regulating the synthesis of lignin and cellulose were significantly upregulated in the transgenic lines. Furthermore, the effector-reporter experiment confirmed that PtrMYB121 bound directly to the promoters of genes relating to the synthesis of lignin and cellulose. These results suggest that PtrMYB121 may positively regulate the formation of secondary cell wall by promoting the synthesis of lignin and cellulose.
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23
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Suetsugu K. A novel seed dispersal mode of Apostasia nipponica could provide some clues to the early evolution of the seed dispersal system in Orchidaceae. Evol Lett 2020; 4:457-464. [PMID: 33014421 PMCID: PMC7523560 DOI: 10.1002/evl3.188] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/08/2020] [Accepted: 07/08/2020] [Indexed: 11/11/2022] Open
Abstract
Despite being one of the most diverse families, scant attention has been paid to the seed dispersal system in Orchidaceae, owing to the widely accepted notion that wind dispersal is the dominant strategy. However, the indehiscent fruits, with seeds immersed in fleshy tissue, evoke the possibility of endozoochory in Apostasioideae, the earliest diverging lineage of orchids. In the present study, I investigated the seed dispersal system of Apostasia nipponica by direct observation, time-lapse photography, and investigation of the viability of seeds passing through the digestive tract of orthopterans. This study revealed a previously undocumented seed dispersal system in A. nipponica, in which the cricket, Eulandrevus ivani, and the camel cricket, Diestrammena yakumontana, consume the fruit and defecate viable seeds. Orthopterans are rarely considered seed dispersers, but the gross fruit morphology and pigmentation patterns of some Apostasia species parallel those seen in A. nipponica, suggesting that similar seed dispersal systems could be widespread among Apostasia species. Whether seed dispersal by orthopteran frugivores is common in Apostasioideae warrants further investigation.
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Affiliation(s)
- Kenji Suetsugu
- Department of BiologyGraduate School of ScienceKobe UniversityKobeHyogo657–8501Japan
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24
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Petit J, Salentijn EMJ, Paulo MJ, Denneboom C, van Loo EN, Trindade LM. Elucidating the Genetic Architecture of Fiber Quality in Hemp ( Cannabis sativa L.) Using a Genome-Wide Association Study. Front Genet 2020; 11:566314. [PMID: 33093845 PMCID: PMC7527631 DOI: 10.3389/fgene.2020.566314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/25/2020] [Indexed: 01/12/2023] Open
Abstract
Hemp (Cannabis sativa L.) is a bast-fiber crop with a great potential in the emerging bio-based economy. Yet, hemp breeding for fiber quality is restricted and that is mainly due to the limited knowledge of the genetic architecture of its fiber quality. A panel of 123 hemp accessions, with large phenotypic variability, was used to study the genetic basis of seven cell wall and bast fiber traits relevant to fiber quality. These traits showed large genetic variance components and high values of broad sense heritability in this hemp panel, as concluded from the phenotypic evaluation across three test locations with contrasting environments. The hemp panel was genotyped using restriction site associated DNA sequencing (RAD-seq). Subsequently, a large set (> 600,000) of selected genome-wide single nucleotide polymorphism (SNP) markers was used for a genome-wide association study (GWAS) approach to get insights into quantitative trait loci (QTLs) controlling fiber quality traits. In absence of a complete hemp genome sequence, identification of QTLs was based on the following characteristics: (i) association level to traits, (ii) fraction of explained trait variance, (iii) collinearity between QTLs, and (iv) detection across different environments. Using this approach, 16 QTLs were identified across locations for different fiber quality traits, including contents of glucose, glucuronic acid, mannose, xylose, lignin, and bast fiber content. Among them, six were found across the three environments. The genetic markers composing the QTLs that are common across locations are valuable tools to develop novel genotypes of hemp with improved fiber quality. Underneath the QTLs, 12 candidate genes were identified which are likely to be involved in the biosynthesis and modification of monosaccharides, polysaccharides, and lignin. These candidate genes were suggested to play an important role in determining fiber quality in hemp. This study provides new insights into the genetic architecture of fiber traits, identifies QTLs and candidate genes that form the basis for molecular breeding for high fiber quality hemp cultivars.
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Affiliation(s)
- Jordi Petit
- Wageningen UR Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Elma M J Salentijn
- Wageningen UR Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Maria-João Paulo
- Biometris, Wageningen University & Research, Wageningen, Netherlands
| | - Christel Denneboom
- Wageningen UR Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Eibertus N van Loo
- Wageningen UR Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Luisa M Trindade
- Wageningen UR Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
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25
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Coomey JH, Sibout R, Hazen SP. Grass secondary cell walls, Brachypodium distachyon as a model for discovery. THE NEW PHYTOLOGIST 2020; 227:1649-1667. [PMID: 32285456 DOI: 10.1111/nph.16603] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/05/2020] [Indexed: 05/20/2023]
Abstract
A key aspect of plant growth is the synthesis and deposition of cell walls. In specific tissues and cell types including xylem and fibre, a thick secondary wall comprised of cellulose, hemicellulose and lignin is deposited. Secondary cell walls provide a physical barrier that protects plants from pathogens, promotes tolerance to abiotic stresses and fortifies cells to withstand the forces associated with water transport and the physical weight of plant structures. Grasses have numerous cell wall features that are distinct from eudicots and other plants. Study of the model species Brachypodium distachyon as well as other grasses has revealed numerous features of the grass cell wall. These include the characterisation of xylosyl and arabinosyltransferases, a mixed-linkage glucan synthase and hydroxycinnamate acyltransferases. Perhaps the most fertile area for discovery has been the formation of lignins, including the identification of novel substrates and enzyme activities towards the synthesis of monolignols. Other enzymes function as polymerising agents or transferases that modify lignins and facilitate interactions with polysaccharides. The regulatory aspects of cell wall biosynthesis are largely overlapping with those of eudicots, but salient differences among species have been resolved that begin to identify the determinants that define grass cell walls.
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Affiliation(s)
- Joshua H Coomey
- Biology Department, University of Massachusetts, Amherst, MA, 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, 01003, USA
| | - Richard Sibout
- Biopolymères Interactions Assemblages, INRAE, UR BIA, F-44316, Nantes, France
| | - Samuel P Hazen
- Biology Department, University of Massachusetts, Amherst, MA, 01003, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, 01003, USA
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26
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El-Azaz J, de la Torre F, Pascual MB, Debille S, Canlet F, Harvengt L, Trontin JF, Ávila C, Cánovas FM. Transcriptional analysis of arogenate dehydratase genes identifies a link between phenylalanine biosynthesis and lignin biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3080-3093. [PMID: 32090267 PMCID: PMC7260716 DOI: 10.1093/jxb/eraa099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/17/2020] [Indexed: 05/29/2023]
Abstract
Biogenesis of the secondary cell wall in trees involves the massive biosynthesis of the phenylalanine-derived polymer lignin. Arogenate dehydratase (ADT) catalyzes the last, and rate-limiting, step of the main pathway for phenylalanine biosynthesis. In this study, we found that transcript levels for several members of the large ADT gene family, including ADT-A and ADT-D, were enhanced in compression wood of maritime pine, a xylem tissue enriched in lignin. Transcriptomic analysis of maritime pine silenced for PpMYB8 revealed that this gene plays a critical role in coordinating the deposition of lignin with the biosynthesis of phenylalanine. Specifically, it was found that ADT-A and ADT-D were strongly down-regulated in PpMYB8-silenced plants and that they were transcriptionally regulated through direct interaction of this transcription factor with regulatory elements present in their promoters. Another transcription factor, PpHY5, exhibited an expression profile opposite to that of PpMYB8 and also interacted with specific regulatory elements of ADT-A and ADT-D genes, suggesting that it is involved in transcriptional regulation of phenylalanine biosynthesis. Taken together, our results reveal that PpMYB8 and PpHY5 are involved in the control of phenylalanine formation and its metabolic channeling for lignin biosynthesis and deposition during wood formation in maritime pine.
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Affiliation(s)
- Jorge El-Azaz
- Grupo de Biología Molecular y Biotecnología de Plantas (BIO-114), Universidad de Málaga, Málaga, Spain
| | - Fernando de la Torre
- Grupo de Biología Molecular y Biotecnología de Plantas (BIO-114), Universidad de Málaga, Málaga, Spain
| | - María Belén Pascual
- Grupo de Biología Molecular y Biotecnología de Plantas (BIO-114), Universidad de Málaga, Málaga, Spain
| | - Sandrine Debille
- Institut Technologique FCBA, Pôle Biotechnologies et Sylviculture Avancée (BSA), Pierroton, Cestas, France
| | - Francis Canlet
- Institut Technologique FCBA, Pôle Biotechnologies et Sylviculture Avancée (BSA), Pierroton, Cestas, France
| | - Luc Harvengt
- Institut Technologique FCBA, Pôle Biotechnologies et Sylviculture Avancée (BSA), Pierroton, Cestas, France
| | - Jean-François Trontin
- Institut Technologique FCBA, Pôle Biotechnologies et Sylviculture Avancée (BSA), Pierroton, Cestas, France
| | - Concepción Ávila
- Grupo de Biología Molecular y Biotecnología de Plantas (BIO-114), Universidad de Málaga, Málaga, Spain
| | - Francisco M Cánovas
- Grupo de Biología Molecular y Biotecnología de Plantas (BIO-114), Universidad de Málaga, Málaga, Spain
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Zhang SW, Yuan C, An LY, Niu Y, Song M, Tang QL, Wei DY, Tian SB, Wang YQ, Yang Y, Wang ZM. SmCOI1 affects anther dehiscence in a male-sterile Solanum melongena line. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2020; 37:1-8. [PMID: 32362742 PMCID: PMC7193836 DOI: 10.5511/plantbiotechnology.19.1107a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Anther indehiscence is an important form of functional male sterility that can facilitate the production of hybrid seed; however, the molecular mechanisms of anther indehiscence-based male sterility have not been thoroughly explored in eggplant (Solanum melongena L.). Here, we used two-dimensional gel electrophoresis to compare the protein profiles in the anthers of normally developing (F142) and anther indehiscent (S16) S. melongena plants. Four differentially expressed proteins were identified using matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry. Of these proteins, the transcript accumulation of the eggplant CORONATINE INSENSITIVE1 (SmCOI1) was significantly downregulated in S16 relative to F142. Phylogenetic analysis showed that SmCOI1 has high amino acid sequence similarity and clustered into the same subgroup as its homologs in other members of the Solanaceae. Subcellular localization analysis showed that SmCOI1 localized to the nucleus. Moreover, reverse-transcription quantitative PCR revealed that the jasmonic acid pathway genes SmJAZ1 and SmOPR3 are upregulated in F142 relative to S16. Protein-protein interaction studies identified a direct interaction between SmCOI1 and SmOPR3, but SmCOI1 failed to interact with SmJAZ1. These findings shed light on the regulatory mechanisms of anther dehiscence in eggplant.
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Affiliation(s)
- Shao-Wei Zhang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing 400715, China
| | - Chao Yuan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing 400715, China
| | - Li-Yu An
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing 400715, China
| | - Yi Niu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing 400715, China
| | - Ming Song
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing 400715, China
| | - Qing-Lin Tang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing 400715, China
| | - Da-Yong Wei
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing 400715, China
| | - Shi-Bing Tian
- The Institute of Vegetables and Flowers, Chongqing Academy of Agricultural Sciences, Chongqing 400055, China
| | - Yong-Qing Wang
- The Institute of Vegetables and Flowers, Chongqing Academy of Agricultural Sciences, Chongqing 400055, China
| | - Yang Yang
- The Institute of Vegetables and Flowers, Chongqing Academy of Agricultural Sciences, Chongqing 400055, China
- E-mail: Tel: +86-23-6825-0974 Fax: +86-6825-1274
| | - Zhi-Ming Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions, Ministry of Education, Chongqing 400715, China
- E-mail: Tel: +86-23-6825-0974 Fax: +86-6825-1274
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Cao S, Huang C, Luo L, Zheng S, Zhong Y, Sun J, Gui J, Li L. Cell-Specific Suppression of 4-Coumarate-CoA Ligase Gene Reveals Differential Effect of Lignin on Cell Physiological Function in Populus. FRONTIERS IN PLANT SCIENCE 2020; 11:589729. [PMID: 33281849 PMCID: PMC7705072 DOI: 10.3389/fpls.2020.589729] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/19/2020] [Indexed: 05/20/2023]
Abstract
Lignin is a main component of the secondary cell wall in vessels and fibers of xylem tissue. However, the significance of lignin in cell physiology during plant growth is unclear. In this study, we generated lignin-modified Populus via cell-specific downregulation of the 4-coumarate-CoA ligase gene (4CL). The transgenic plants with selective lignin modification in vessel elements or fiber cells allowed us to investigate how lignin affects the physiology of vessel or fiber cells in relation to plant growth. Results showed that vessel-specific suppression of lignin biosynthesis resulted in deformed vessels and normal fibers, while fiber-specific suppression of lignin biosynthesis led to less-lignified fibers and normal vessels. Further analyses revealed that the efficiency of long distance water transport was severely affected in transgenics with vessel-specific lignin modification, while minimal effect was detected in transgenics with fiber-specific lignin modification. Vessel-specific lignin reduction led to high susceptibility to drought stress and poor growth in field, likely due to vessel defects in long distance transport of water. The distinct physiological significance of lignin in different cell types provides insights into the selective modification of lignin for improvement of lignocellulosic biomass utilization.
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Affiliation(s)
- Shumin Cao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Cheng Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Laifu Luo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Shuai Zheng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Yu Zhong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Jiayan Sun
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Jinshan Gui
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Jinshan Gui,
| | - Laigeng Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Laigeng Li,
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Köbölkuti ZA, Cseke K, Benke A, Báder M, Borovics A, Németh R. Allelic variation in candidate genes associated with wood properties of cultivated poplars (Populus). Biol Futur 2019; 70:286-294. [PMID: 34554544 DOI: 10.1556/019.70.2019.32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 10/26/2019] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Since Populus has veritable value as timber, plywood, pulp, and paper, genomic research should create the sound basis for further breeding toward desirable wood quality attributes. MATERIALS AND METHODS In this study, we addressed the need for a research methodology that initially identifies and then characterize candidate genes encoding enzymes with wood property phenotypic traits, toward the aim of developing a genomics-based breeding technology. RESULTS On 23 different poplar species/hybrid samples, we successfully amplified 55 primers designed on Populus trichocarpa L. Considering the number of polymorphic sites, out of 73,206 bp, 51 SNPs and 31 indel events were found. Non-synonymous single base mutations could be detected in number of 30, 21 out of 164 sequences were the number of minimum recombination events and 41 significant pairwise comparisons between loci could be detected. DISCUSSION AND CONCLUSION Our results provide a roadmap for a future association genetic study between nucleotide diversity and precise evaluation of phenotype.
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Affiliation(s)
- Zoltán Attila Köbölkuti
- Department of Tree Breeding, National Agricultural Research and Innovation Centre, Forest Research Institute, Várkerulet 30/A, Sárvár, 9600, Hungary.
| | - Klára Cseke
- Department of Tree Breeding, National Agricultural Research and Innovation Centre, Forest Research Institute, Várkerulet 30/A, Sárvár, 9600, Hungary
| | - Attila Benke
- Department of Tree Breeding, National Agricultural Research and Innovation Centre, Forest Research Institute, Várkerulet 30/A, Sárvár, 9600, Hungary
| | - Mátyás Báder
- Simonyi Karoly Faculty of Engineering, Wood Sciences and Applied Arts, University of Sopron, Bajcsy Zs. u. 4, 9400, Sopron, Hungary
| | - Attila Borovics
- Department of Tree Breeding, National Agricultural Research and Innovation Centre, Forest Research Institute, Várkerulet 30/A, Sárvár, 9600, Hungary
| | - Róbert Németh
- Simonyi Karoly Faculty of Engineering, Wood Sciences and Applied Arts, University of Sopron, Bajcsy Zs. u. 4, 9400, Sopron, Hungary
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Li M, Cheng C, Zhang X, Zhou S, Wang C, Ma C, Yang S. PpNAC187 Enhances Lignin Synthesis in 'Whangkeumbae' Pear ( Pyrus pyrifolia) 'Hard-End' Fruit. Molecules 2019; 24:E4338. [PMID: 31783586 PMCID: PMC6930614 DOI: 10.3390/molecules24234338] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/23/2019] [Accepted: 11/25/2019] [Indexed: 11/16/2022] Open
Abstract
A disorder in pears that is known as 'hard-end' fruit affects the appearance, edible quality, and market value of pear fruit. RNA-Seq was carried out on the calyx end of 'Whangkeumbae' pear fruit with and without the hard-end symptom to explore the mechanism underlying the formation of hard-end. The results indicated that the genes in the phenylpropanoid pathway affecting lignification were up-regulated in hard-end fruit. An analysis of differentially expressed genes (DEGs) identified three NAC transcription factors, and RT-qPCR analysis of PpNAC138, PpNAC186, and PpNAC187 confirmed that PpNAC187 gene expression was correlated with the hard-end disorder in pear fruit. A transient increase in PpNAC187 was observed in the calyx end of 'Whangkeumbae' fruit when they began to exhibit hard-end symptom. Concomitantly, the higher level of PpCCR and PpCOMT transcripts was observed, which are the key genes in lignin biosynthesis. Notably, lignin content in the stem and leaf tissues of transgenic tobacco overexpressing PpNAC187 was significantly higher than in the control plants that were transformed with an empty vector. Furthermore, transgenic tobacco overexpressing PpNAC187 had a larger number of xylem vessel elements. The results of this study confirmed that PpNAC187 functions in inducing lignification in pear fruit during the development of the hard-end disorder.
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Affiliation(s)
- Mingtong Li
- College of Horticulture, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang, Qingdao 266109, China; (M.L.); (C.C.); (X.Z.); (C.W.); (C.M.)
| | - Chenxia Cheng
- College of Horticulture, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang, Qingdao 266109, China; (M.L.); (C.C.); (X.Z.); (C.W.); (C.M.)
| | - Xinfu Zhang
- College of Horticulture, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang, Qingdao 266109, China; (M.L.); (C.C.); (X.Z.); (C.W.); (C.M.)
| | - Suping Zhou
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John Merritt Blvd, Nashville, TN 37209, USA;
| | - Caihong Wang
- College of Horticulture, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang, Qingdao 266109, China; (M.L.); (C.C.); (X.Z.); (C.W.); (C.M.)
| | - Chunhui Ma
- College of Horticulture, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang, Qingdao 266109, China; (M.L.); (C.C.); (X.Z.); (C.W.); (C.M.)
| | - Shaolan Yang
- College of Horticulture, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang, Qingdao 266109, China; (M.L.); (C.C.); (X.Z.); (C.W.); (C.M.)
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Mao X, Weake VM, Chapple C. Mediator function in plant metabolism revealed by large-scale biology. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5995-6003. [PMID: 31504746 DOI: 10.1093/jxb/erz372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/07/2019] [Indexed: 05/16/2023]
Abstract
Mediator is a multisubunit transcriptional co-regulator that is involved in the regulation of an array of processes including plant metabolism. The pathways regulated by Mediator-dependent processes include those for the synthesis of phenylpropanoids (MED5), cellulose (MED16), lipids (MED15 and CDK8), and the regulation of iron homeostasis (MED16 and MED25). Traditional genetic and biochemical approaches laid the foundation for our understanding of Mediator function, but recent transcriptomic and metabolomic studies have provided deeper insights into how specific subunits cooperate in the regulation of plant metabolism. In this review, we highlight recent developments in the investigation of Mediator and plant metabolism, with particular emphasis on the large-scale biology studies of med mutants.
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Affiliation(s)
- Xiangying Mao
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Vikki M Weake
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, USA
| | - Clint Chapple
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA
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Gui J, Luo L, Zhong Y, Sun J, Umezawa T, Li L. Phosphorylation of LTF1, an MYB Transcription Factor in Populus, Acts as a Sensory Switch Regulating Lignin Biosynthesis in Wood Cells. MOLECULAR PLANT 2019; 12:1325-1337. [PMID: 31145998 DOI: 10.1016/j.molp.2019.05.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/01/2019] [Accepted: 05/20/2019] [Indexed: 05/03/2023]
Abstract
Lignin is specifically deposited in plant secondary cell walls, and initiation of lignin biosynthesis is regulated by a variety of developmental and environmental signals. However, the mechanisms governing the regulation of lignin biosynthesis remain to be elucidated. In this study, we identified a lignin biosynthesis-associated transcription factor (LTF) from Populus, LTF1, which binds the promoter of a key lignin biosynthetic gene encoding 4-coumarate-CoA ligase (4CL). We showed that LTF1 in its unphosphorylated state functions as a regulator restraining lignin biosynthesis. When LTF1 becomes phosphorylated by PdMPK6 in response to external stimuli such as wounding, it undergoes degradation through a proteasome pathway, resulting in activation of lignification. Expression of a phosphorylation-null mutant version of LTF1 led to stable protein accumulation and persistent attenuation of lignification in wood cells. Taken together, our study reveals a mechanism whereby LTF1 phosphorylation acts as a sensory switch to regulate lignin biosynthesis in response to environmental stimuli. The discovery of novel modulators and mechanisms modifying lignin biosynthesis has important implications for improving the utilization of cell-wall biomass.
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Affiliation(s)
- Jinshan Gui
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Laifu Luo
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science, Lanzhou University, Lanzhou 730000, China
| | - Yu Zhong
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jiayan Sun
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Toshiaki Umezawa
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Laigeng Li
- National Key Laboratory of Plant Molecular Genetics and CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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Aleamotu'a M, McCurdy DW, Collings DA. Phi thickenings in roots: novel secondary wall structures responsive to biotic and abiotic stresses. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4631-4642. [PMID: 31106830 DOI: 10.1093/jxb/erz240] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 05/14/2019] [Indexed: 06/09/2023]
Abstract
Phi thickenings are specialized secondary walls found in root cortical cells. Despite their widespread occurrence throughout the plant kingdom, these specialized thickenings remain poorly understood. First identified by Van Tieghem in 1871, phi thickenings are a lignified and thickened cell wall band that is deposited inside the primary wall, as a ring around the cells' radial walls. Phi thickenings can, however, display structural variations including a fine, reticulate network of wall thickenings extending laterally from the central lignified band. While phi thickenings have been proposed to mechanically strengthen roots, act as a permeability barrier to modulate solute movement, and regulate fungal interactions, these possibilities remain to be experimentally confirmed. Furthermore, since temporal and spatial development of phi thickenings varies widely between species, thickenings may perform diverse roles in different species. Phi thickenings can be induced by abiotic stresses in different species; they can, for example, be induced by heavy metals in the Zn/Cd hyperaccumulator Thlaspi caerulescens, and in a cultivar-specific manner by water stress in Brassica. This latter observation provides an experimental platform to probe phi thickening function, and to identify genetic pathways responsible for their formation. These pathways might be expected to differ from those involved in secondary wall formation in xylem, since phi thickening deposition in not linked to programmed cell death.
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Affiliation(s)
- Maketalena Aleamotu'a
- Centre for Plant Science, School of Environmental and Life Sciences, The University of Newcastle, Callaghan NSW, Australia
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Li Y, Yang Y, Liu Y, Li D, Zhao Y, Li Z, Liu Y, Jiang D, Li J, Zhou H, Chen J, Zhuang C, Liu Z. Overexpression of OsAGO1b Induces Adaxially Rolled Leaves by Affecting Leaf Abaxial Sclerenchymatous Cell Development in Rice. RICE (NEW YORK, N.Y.) 2019; 12:60. [PMID: 31396773 PMCID: PMC6687834 DOI: 10.1186/s12284-019-0323-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 08/02/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND ARGONAUTE 1 (AGO1) proteins can recruit small RNAs to regulate gene expression, involving several growth and development processes in Arabidopsis. Rice genome contains four AGO1 genes, OsAGO1a to OsAGO1d. However, the regulatory functions to rice growth and development of each AGO1 gene are still unknown. RESULTS We obtained overexpression and RNAi transgenic lines of each OsAGO1 gene. However, only up- and down-regulation of OsAGO1b caused multiple abnormal phenotypic changes in rice, indicating that OsAGO1b is the key player in rice growth and organ development compared with other three OsAGO1s. qRT-PCR assays showed that OsAGO1b was almost unanimously expressed in leaves at different developmental stages, and strongly expressed in spikelets at S1 to S3 stages. OsAGO1b is a typical AGO protein, and co-localized in both the nucleus and cytoplasm simultaneously. Overexpression of OsAGO1b caused adaxially rolled leaves and a series of abnormal phenotypes, such as the reduced tiller number and plant height. Knockdown lines of OsAGO1b showed almost normal leaves, but the seed setting percentage was significantly reduced accompanied by the disturbed anther patterning and reduced pollen fertility. Further anatomical observation revealed that OsAGO1b overexpression plants showed the partially defective development of sclerenchymatous cells on the abaxial side of leaves. In situ hybridization showed OsAGO1b mRNA was uniformly accumulated in P1 to P3 primordia without polarity property, suggesting OsAGO1b did not regulate the adaxial-abaxial polarity development directly. The expression levels of several genes related to leaf polarity development and vascular bundle differentiation were observably changed. Notably, the accumulation of miR166 and TAS3-siRNA was decreased, and their targeted OSHBs and OsARFs were significantly up-regulated. The mRNA distribution patterns of OSHB3 and OsARF4 in leaves remained almost unchanged between ZH11 and OsAGO1b overexpression lines, but their expression levels were enhanced at the regions of vascular bundles and sclerenchymatous cell differentiation. CONCLUSIONS In summary, we demonstrated OsAGO1b is the leading player among four OsAGO1s in rice growth and development. We propose that OsAGO1b may regulate the abaxial sclerenchymatous cell differentiation by affecting the expression of OSHBs in rice.
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Affiliation(s)
- Youhan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223 China
| | - Yiqi Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
| | - Ye Liu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223 China
- School of Life Sciences, University of Science and Technology of China, Hefei, 230026 China
| | - Dexia Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
| | - Yahuan Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
| | - Zhijie Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
| | - Ying Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
| | - Dagang Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
| | - Jing Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
| | - Hai Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
| | - Jianghua Chen
- Key Laboratory of Tropical Plant Resources and Sustainable Use, CAS Center for Excellence in Molecular Plant Sciences, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223 China
| | - Chuxiong Zhuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
| | - Zhenlan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, 510642 China
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Deng Q, Kong Z, Wu X, Ma S, Yuan Y, Jia H, Ma Z. Cloning of a COBL gene determining brittleness in diploid wheat using a MapRseq approach. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 285:141-150. [PMID: 31203879 DOI: 10.1016/j.plantsci.2019.05.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 05/06/2019] [Accepted: 05/12/2019] [Indexed: 05/24/2023]
Abstract
Plant tissue brittleness is related to cellular structure and lodging. MED0031 is a mutant identified previously from ethyl methane sulfonate treatment of diploid wheat accession TA2726, showing brittleness in both stem and leaf. In microscopic and histological observations, the mutant was found to have less large vascular bundles per unit area, a thinner sclerenchyma cell wall, and a broader parenchyma, compared with the wild type. The mutated gene, TmBr1, was mapped to a 0.056 cM interval on chromosome 5Am. This gene was cloned using a MapRseq approach that searched the candidate gene through combination of the prior target gene mapping information with SNP calling and discovery of differentially expressed genes from RNA_seq data of the wild type and a BC3F2 bulk showing the mutant phenotype. TmBr1 encodes a COBL protein and a nonsense mutation within the region coding for the conserved COBRA domain caused premature translation termination. Introduction of TmBr1 to Arabidopsis AtCOBL4 mutant rescued the phenotype, demonstrating their functional conservation. Apart from the effect on cellulose content, the TmBr1 mutation might modulate synthesis of noncellulosic polysaccharide pectin as well. Application of the MapRseq approach to isolation of genes present in recombination cold spots and complicated genomes was discussed.
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Affiliation(s)
- Qingyan Deng
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Jiangsu, China
| | - Zhongxin Kong
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Jiangsu, China
| | - Xiaoxia Wu
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Jiangsu, China
| | - Shengwei Ma
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Jiangsu, China
| | - Yang Yuan
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Jiangsu, China
| | - Haiyan Jia
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Jiangsu, China
| | - Zhengqiang Ma
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Jiangsu, China.
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Xia X, Li H, Cao D, Luo X, Yang X, Chen L, Liu B, Wang Q, Jing D, Cao S. Characterization of a NAC transcription factor involved in the regulation of pomegranate seed hardness (Punica granatum L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 139:379-388. [PMID: 30954020 DOI: 10.1016/j.plaphy.2019.01.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 06/09/2023]
Abstract
The pomegranate, Punica granatum L., which has been cultivated since antiquity, is known to be a superfruit, possessing an array of functional anti-oxidants and various other health benefits. The hardness of pomegranate seeds is an important indicator of fruit quality, which in turn affects economic value and market demand. However, the molecular mechanism underlying pomegranate seed hardness remains to be fully understood. In this study, we found a positive correlation between seed hardness and lignin content in two pomegranate varieties: "Tunisia" and "Sanbai". Specifically, genes associated with lignin biosynthesis were differentially expressed in soft-seed and hard-seed pomegranate varieties. Among these differential genes, we cloned and characterized the NAC transcription factor PgSND1-like. Sequence alignment found a single base replacement at the 166-bp position of CDS in the PgSND1-like gene from "Tunisia" and "Sanbai". Both PgSND1-like (Sanbai) and PgSND1-like (Tunisia) proteins are localized in the cell nucleus and have a transcription activation domain in the C-terminus. Yeast two-hybrid analysis indicated that PgSND1-like protein interacts with itself to form a homodimer. Overexpression of PgSND1-like (Sanbai) in Arabidopsis showed a higher lignin content in inflorescence stem and mature seed compared with wild-type Arabidopsis. Accordingly, the expression levels of several lignin biosynthesis-associated genes were upregulated in stem cells and mature seeds of transgenic plants. However, PgSND1-like (Tunisia) transgenic Arabidopsis showed no phenotypic differences with wild-type Arabidopsis. Taken together, we suggest that PgSND1-like may regulate at least two different functions in two pomegranate varieties, promoting lignin biosynthesis and seed hardness of pomegranate.
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Affiliation(s)
- Xiaocong Xia
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Zhengzhou, 450009, China
| | - Haoxian Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Zhengzhou, 450009, China
| | - Da Cao
- The University of Queensland , St Lucia, QLD 4072, Australia
| | - Xiang Luo
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Zhengzhou, 450009, China
| | - Xuanwen Yang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Zhengzhou, 450009, China
| | - Lina Chen
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Zhengzhou, 450009, China
| | - Beibei Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Zhengzhou, 450009, China
| | - Qi Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Zhengzhou, 450009, China
| | - Dan Jing
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Zhengzhou, 450009, China
| | - Shangyin Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Zhengzhou, 450009, China.
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Ke S, Luan X, Liang J, Hung YH, Hsieh TF, Zhang XQ. Rice OsPEX1, an extensin-like protein, affects lignin biosynthesis and plant growth. PLANT MOLECULAR BIOLOGY 2019; 100:151-161. [PMID: 30840202 DOI: 10.1007/s11103-019-00849-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 02/23/2019] [Indexed: 05/06/2023]
Abstract
Rice leucine-rich repeat extensin-like protein OsPEX1 mediates the intersection of lignin deposition and plant growth. Lignin, a major structural component of secondary cell wall, is essential for normal plant growth and development. However, the molecular and genetic regulation of lignin biosynthesis is not fully understood in rice. Here we report the identification and characterization of a rice semi-dominant dwarf mutant (pex1) with stiff culm. Molecular and genetic analyses revealed that the pex1 phenotype was caused by ectopic expression of a leucine-rich repeat extension-like gene, OsPEX1. Interestingly, the pex1 mutant showed significantly higher lignin content and increased expression levels of lignin-related genes compared with wild type plants. Conversely, OsPEX1-suppresssed transgenics displayed low lignin content and reduced transcriptional abundance of genes associated with lignin biosynthesis, indicating that the OsPEX1 mediates lignin biosynthesis and/or deposition in rice. When OsPEX1 was ectopically expressed in rice cultivars with tall stature that lacks the allele of semi-dwarf 1, well-known green revolution gene, the resulting transgenic plants displayed reduced height and enhanced lodging resistance. Our study uncovers a causative effect between the expression of OsPEX1 and lignin deposition. Lastly, we demonstrated that modulating OsPEX1 expression could provide a tool for improving rice lodging resistance.
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Affiliation(s)
- Shanwen Ke
- Guangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Xin Luan
- Guangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Jiayan Liang
- Guangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Yu-Hung Hung
- Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC, 28081, USA
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Tzung-Fu Hsieh
- Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC, 28081, USA.
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Xiang-Qian Zhang
- Guangdong Engineering Research Center of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China.
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Ectopic expression of SOD and APX genes in Arabidopsis alters metabolic pools and genes related to secondary cell wall cellulose biosynthesis and improve salt tolerance. Mol Biol Rep 2019; 46:1985-2002. [PMID: 30706357 DOI: 10.1007/s11033-019-04648-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/24/2019] [Indexed: 10/27/2022]
Abstract
Hydrogen peroxide (H2O2) is known to accumulate in plants during abiotic stress conditions and also acts as a signalling molecule. In this study, Arabidopsis thaliana transgenics overexpressing cytosolic CuZn-superoxide dismutase (PaSOD) from poly-extremophile high-altitude Himalayan plant Potentilla atrosanguinea, cytosolic ascorbate peroxidase (RaAPX) from Rheum australe and dual transgenics overexpressing both the genes were developed and analyzed under salt stress. In comparison to wild-type (WT) or single transgenics, the performance of dual transgenics under salt stress was better with higher biomass accumulation and cellulose content. We identified genes involved in cell wall biosynthesis, including nine cellulose synthases (CesA), seven cellulose synthase-like proteins together with other wall-related genes. RNA-seq analysis and qPCR revealed differential regulation of genes (CesA 4, 7 and 8) and transcription factors (MYB46 and 83) involved in secondary cell wall cellulose biosynthesis, amongst which most of the cellulose biosynthesis gene showed upregulation in single (PaSOD line) and dual transgenics at 100 mM salt stress. A positive correlation between cellulose content and H2O2 accumulation was observed in these transgenic lines. Further, cellulose content was 1.6-2 folds significantly higher in PaSOD and dual transgenic lines, 1.4 fold higher in RaAPX lines as compared to WT plants under stress conditions. Additionally, transgenics overexpressing PaSOD and RaAPX also displayed higher amounts of phenolics as compared to WT. The novelty of present study is that H2O2 apart from its role in signalling, it also provides mechanical strength to plants and aid in plant biomass production during salt stress by transcriptional activation of cellulose biosynthesis pathway. This modulation of the cellulose biosynthetic machinery in plants has the potential to provide insight into plant growth, morphogenesis and to create plants with enhanced cellulose content for biofuel use.
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Jia N, Liu J, Sun Y, Tan P, Cao H, Xie Y, Wen B, Gu T, Liu J, Li M, Huang Y, Lu J, Jin N, Sun L, Xin F, Fan B. Citrus sinensis MYB transcription factors CsMYB330 and CsMYB308 regulate fruit juice sac lignification through fine-tuning expression of the Cs4CL1 gene. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:334-343. [PMID: 30466599 DOI: 10.1016/j.plantsci.2018.10.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/05/2018] [Accepted: 10/06/2018] [Indexed: 05/06/2023]
Abstract
Lignin is one of the most important components of the plant cell wall, and the expression and transcriptional regulation of lignin biosynthesis-related genes have been studied widely in Arabidopsis and other plants. Citrus fruit juice sacs often undergo lignification, particularly during fruit ripening and storage periods; however, the underlying genetic mechanisms have been little investigated. In this study, we isolated and identified CsMYB330 and CsMYB308 transcription factors, and found that their expression levels are significantly altered during the lignification of citrus fruit juice sacs. We found that CsMYB330 and CsMYB308 can recognize and bind AC elements in the Cs4CL1 promoter and finely regulate expression of the Cs4CL1 gene. In this regulatory process, CsMYB330 was identified as a transcriptional activator, whereas CsMYB308 appears to be a transcriptional repressor. In addition, using a transient assay, we demonstrated that expression of the Cs4CL1 gene is significantly altered in fruit juice sacs overexpressing these two transcription factors. These results indicate that the transcription factors CsMYB330 and CsMYB308 play important roles in the lignification of citrus fruit juice sacs and provide novel insights into the transcriptional regulation associated with fruit juice sac lignification.
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Affiliation(s)
- Ning Jia
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Science, Beijing 100193, China; Laboratory of Quality & Safety Risk Assessment on Agro-products Processing, Ministry of Agriculture and Rural Affairs, Beijing 100193, China; Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiqin Liu
- Qinhuangdao Customs, Hebei, Qinhuangdao 066004, China
| | - Yufeng Sun
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Science, Beijing 100193, China; Laboratory of Quality & Safety Risk Assessment on Agro-products Processing, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Penghui Tan
- Turfgrass Research Institute, Beijing Forestry University, Beijing, 100083, China
| | - Hao Cao
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yingying Xie
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Boting Wen
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tianyi Gu
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiameng Liu
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Science, Beijing 100193, China; Laboratory of Quality & Safety Risk Assessment on Agro-products Processing, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Minmin Li
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Science, Beijing 100193, China; Laboratory of Quality & Safety Risk Assessment on Agro-products Processing, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Yatao Huang
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Science, Beijing 100193, China; Laboratory of Quality & Safety Risk Assessment on Agro-products Processing, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Jia Lu
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Science, Beijing 100193, China; Laboratory of Quality & Safety Risk Assessment on Agro-products Processing, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Nuo Jin
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Science, Beijing 100193, China; Laboratory of Quality & Safety Risk Assessment on Agro-products Processing, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Lichao Sun
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fengjiao Xin
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Bei Fan
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Science, Beijing 100193, China; Laboratory of Quality & Safety Risk Assessment on Agro-products Processing, Ministry of Agriculture and Rural Affairs, Beijing 100193, China.
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Suetsugu K. Seed dispersal in the mycoheterotrophic orchid Yoania japonica: Further evidence for endozoochory by camel crickets. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:707-712. [PMID: 29656468 DOI: 10.1111/plb.12731] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/04/2018] [Indexed: 05/26/2023]
Abstract
Although orthopterans are rarely considered to be effective seed dispersal agents, the large flightless crickets known as 'weta' have been suggested to function as ecological replacements for small mammals in New Zealand, where such mammals are absent. In addition, a recent study reported that camel crickets mediate seed dispersal of several heterotrophic plants, including Yoania amagiensis in Japan. I investigated the seed dispersal mechanism of Yoania japonica because the fruit morphology is similar to Y. amagiensis. Specifically, I aimed to determine whether Y. japonica fruits are consumed by camel crickets and, if so, whether the seeds defecated by camel crickets remains intact, by checking seed viability with TTC staining, and whether germination rate is different between seeds collected directly from fruits and defecated seeds by comparing in situ seed germinability. The present study provides evidence that camel crickets function as seed dispersal agents of Y. japonica. Camel crickets were important consumers of Y. japonica fruits, and a substantial portion of the consumed seeds remained viable after passing through the digestive tract. In situ seed germination experiments revealed that the seeds defecated by camel crickets actually germinated in the field. In addition, the germination rate of defecated seeds was even higher than that of intact seeds, although the difference was not significant. Taken together with recent reports of insect-mediated endozoochory, such a seed dispersal system may be common in plants with fleshy indehiscent fruits and small seeds, even in locations where other seed dispersal agents are present.
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Affiliation(s)
- K Suetsugu
- Department of Biology, Graduate School of Science, Kobe University, Kobe, Japan
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An YH, Zhou H, Yuan YH, Li L, Sun J, Shu S, Guo SR. 24-Epibrassinolide-induced alterations in the root cell walls of Cucumis sativus L. under Ca(NO 3) 2 stress. PROTOPLASMA 2018; 255:841-850. [PMID: 29243177 DOI: 10.1007/s00709-017-1187-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 11/19/2017] [Indexed: 06/07/2023]
Abstract
Brassinosteroids (BRs) can effectively alleviate the oxidative stress caused by Ca(NO3)2 in cucumber seedlings. The root system is an essential organ in plants due to its roles in physical anchorage, water and nutrient uptake, and metabolite synthesis and storage. In this study, 24-epibrassinolide (EBL) was applied to the cucumber seedling roots under Ca(NO3)2 stress, and the resulting chemical and anatomical changes were characterized to investigate the roles of BRs in alleviating salinity stress. Ca(NO3)2 alone significantly induced changes in the components of cell wall, anatomical structure, and expression profiles of several lignin biosynthetic genes. Salt stress damaged several metabolic pathways, leading to cell wall reassemble. However, EBL promoted cell expansion and maintained optimum length of root system, alleviating the oxidative stress caused by Ca(NO3)2. The continuous transduction of EBL signal thickened the secondary cell wall of casparian band cells, thus resisting against ion toxicity and maintaining water transport.
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Affiliation(s)
- Ya-Hong An
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- Jiangsu Province Engineering Laboratory for Modern Facility Agriculture Technology and Equipment, Nanjing, 210095, People's Republic of China
| | - Heng Zhou
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- Jiangsu Province Engineering Laboratory for Modern Facility Agriculture Technology and Equipment, Nanjing, 210095, People's Republic of China
| | - Ying-Hui Yuan
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- Jiangsu Province Engineering Laboratory for Modern Facility Agriculture Technology and Equipment, Nanjing, 210095, People's Republic of China
| | - Lin Li
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- Jiangsu Province Engineering Laboratory for Modern Facility Agriculture Technology and Equipment, Nanjing, 210095, People's Republic of China
| | - Jin Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- Jiangsu Province Engineering Laboratory for Modern Facility Agriculture Technology and Equipment, Nanjing, 210095, People's Republic of China
- Nanjing Agricultural University (Suqian) Academy of Protected Horticulture, Suqian, 223800, People's Republic of China
| | - Sheng Shu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- Jiangsu Province Engineering Laboratory for Modern Facility Agriculture Technology and Equipment, Nanjing, 210095, People's Republic of China
- Nanjing Agricultural University (Suqian) Academy of Protected Horticulture, Suqian, 223800, People's Republic of China
| | - Shi-Rong Guo
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
- Jiangsu Province Engineering Laboratory for Modern Facility Agriculture Technology and Equipment, Nanjing, 210095, People's Republic of China.
- Nanjing Agricultural University (Suqian) Academy of Protected Horticulture, Suqian, 223800, People's Republic of China.
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Hossain Z, Pillai BVS, Gruber MY, Yu M, Amyot L, Hannoufa A. Transcriptome profiling of Brassica napus stem sections in relation to differences in lignin content. BMC Genomics 2018; 19:255. [PMID: 29661131 PMCID: PMC5903004 DOI: 10.1186/s12864-018-4645-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 04/03/2018] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Brassica crops are cultivated widely for human consumption and animal feed purposes, and oilseed rape/canola (Brassica napus and rapa) is the second most important oilseed worldwide. Because of its natural diversity and genetic complexity, genomics studies on oilseed rape will be a useful resource base to modify the quantity and quality of biomass in various crops, and therefore, should have a positive impact on lignocellulosic biofuel production. The objective of this study was to perform microarray analysis on two variable lignin containing oilseed rape cultivars to target novel genes and transcription factors of importance in Brassica lignin regulation for applied research. RESULTS To gain insight into the molecular networks controlling cell wall biosynthetic and regulatory events, we conducted lignin and microarray analysis of top and basal stem sections of brown seeded Brassica napus DH12075 and yellow seeded YN01-429 cultivars. A total of 9500 genes were differentially expressed 2-fold or higher in the stem between the cultivars, with a higher number of expressed genes in the basal section. Of the upregulated genes, many were transcription factors and a considerable number of these were associated with secondary wall synthesis and lignification in B. napus and other plant species. The three largest groups of transcription factors with differential expression were C2H2 and C3HC4 zinc fingers and bHLH. A significant number of genes related to lignin and carbohydrate metabolism also showed differential expression patterns between the stem sections of the two cultivars. Within the same cultivar, the number of upregulated genes was higher in the top section relative to the basal one. CONCLUSION In this study, we identified and established expression patterns of many new genes likely involved in cell wall biosynthesis and regulation. Some genes with known roles in other biochemical pathways were also identified to have a potential role in cell wall biosynthesis. This stem transcriptome profiling will allow for selecting novel regulatory and structural genes for functional characterization, a strategy which may provide tools for modifying cell wall composition to facilitate fermentation for biofuel production.
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Affiliation(s)
- Zakir Hossain
- Agriculture and Agri-Food Canada, London Research and Development Centre, 1391 Sandford Street, London, ON N5V 4T3 Canada
- Agriculture and Agri-Food Canada, Swift Current Research and Development Centre, 1 Airport Road, Swift Current, SK S9H 3X2 Canada
| | - Bhinu V.-S. Pillai
- Agriculture and Agri-Food Canada, London Research and Development Centre, 1391 Sandford Street, London, ON N5V 4T3 Canada
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, 6947 Highway 7, Post Office Box 1000, Agassiz, BC V0M 1A0 Canada
| | - Margaret Y. Gruber
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | - Min Yu
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | - Lisa Amyot
- Agriculture and Agri-Food Canada, London Research and Development Centre, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, London Research and Development Centre, 1391 Sandford Street, London, ON N5V 4T3 Canada
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Transcriptome analysis provides insights into xylogenesis formation in Moso bamboo (Phyllostachys edulis) shoot. Sci Rep 2018; 8:3951. [PMID: 29500441 PMCID: PMC5834459 DOI: 10.1038/s41598-018-21766-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 02/07/2018] [Indexed: 01/21/2023] Open
Abstract
Maturation-related changes in cell wall composition and the molecular mechanisms underlying cell wall changes were investigated from the apical, middle and basal segments in moso bamboo shoot (MBS). With maturation extent from apical to basal regions in MBS, lignin and cellulose content increased, whereas heteroxylan exhibited a decreasing trend. Activities of phenylalanine amonnialyase (PAL), cinnamyl alcohol dehydrogenase (CAD) and cinnamate-4-hydroxylase (C4H), which are involved in lignin biosynthesis, increased rapidly from the apex to the base sections. The comparative transcriptomic analysis was carried out to identify some key genes involved in secondary cell walls (SCW) formation underlying the cell wall compositions changes including 63, 8, 18, and 31 functional unigenes encoding biosynthesis of lignin, cellulose, xylan and NAC-MYB-based transcription factors, respectively. Genes related to secondary cell wall formation and lignin biosynthesis had higher expression levels in the middle and basal segments compared to those in the apical segments. Furthermore, the expression profile of PePAL gene showed positive relationships with cellulose-related gene PeCESA4, xylan-related genes PeIRX9 and PeIRX10. Our results indicated that lignification occurred in the more mature middle and basal segments in MBS at harvest while lignification of MBS were correlated with higher expression levels of PeCESA4, PeIRX9 and PeIRX10 genes.
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Prajapati AS, Pawar VA, Panchal KJ, Sudhir AP, Dave BR, Patel DH, Subramanian RB. Effects of substrate binding site residue substitutions of xynA from Bacillus amyloliquefaciens on substrate specificity. BMC Biotechnol 2018; 18:9. [PMID: 29439688 PMCID: PMC5812043 DOI: 10.1186/s12896-018-0420-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/30/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The aromatic residues of xylanase enzyme, W187, Y124, W144, Y128 and W63 of substrate binding pocket from Bacillus amyloliquefaciens were investigated for their role in substrate binding by homology modelling and sequence analysis. These residues are highly conserved and play an important role in substrate binding through steric hindrance. The substitution of these residues with alanine allows the enzyme to accommodate nonspecific substrates. RESULTS Wild type and mutated genes were cloned and overexpressed in BL21. Optimum pH and temperature of rBAxn exhibited pH 9.0 and 50 °C respectively and it was stable up to 215 h. Along with the physical properties of rBAxn, kinetic parameters (Km 19.34 ± 0.72 mg/ml; kcat 6449.12 ± 155.37 min- 1 and kcat/Km 333.83 ± 6.78 ml min- 1 mg- 1) were also compared with engineered enzymes. Out of five mutations, W63A, Y128A and W144A lost almost 90% activity and Y124A and W187A retained almost 40-45% xylanase activity. CONCLUSIONS The site-specific single mutation, led to alteration in substrate specificity from xylan to CMC while in case of double mutant the substrate specificity was altered from xylan to CMC, FP and avicel, indicating the role of aromatic residues on substrate binding, catalytic process and overall catalytic efficiency.
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Affiliation(s)
- Anil S. Prajapati
- P. G. Department of Biosciences, UGC-Centre of advanced studies, Satellite campus, Sardar Patel University, Sardar Patel Maidan, Bakrol-Vadtal Road, PO Box 39, Vallabh Vidyanagar, Gujarat 388 120 India
| | - Vishakha A. Pawar
- P. G. Department of Biosciences, UGC-Centre of advanced studies, Satellite campus, Sardar Patel University, Sardar Patel Maidan, Bakrol-Vadtal Road, PO Box 39, Vallabh Vidyanagar, Gujarat 388 120 India
| | - Ketankumar J. Panchal
- P. G. Department of Biosciences, UGC-Centre of advanced studies, Satellite campus, Sardar Patel University, Sardar Patel Maidan, Bakrol-Vadtal Road, PO Box 39, Vallabh Vidyanagar, Gujarat 388 120 India
| | - Ankit P. Sudhir
- P. G. Department of Biosciences, UGC-Centre of advanced studies, Satellite campus, Sardar Patel University, Sardar Patel Maidan, Bakrol-Vadtal Road, PO Box 39, Vallabh Vidyanagar, Gujarat 388 120 India
| | - Bhaumik R. Dave
- P. G. Department of Biosciences, UGC-Centre of advanced studies, Satellite campus, Sardar Patel University, Sardar Patel Maidan, Bakrol-Vadtal Road, PO Box 39, Vallabh Vidyanagar, Gujarat 388 120 India
| | - Darshan H. Patel
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology (CHARUSAT), Changa, Anand, Gujarat India
| | - R. B. Subramanian
- P. G. Department of Biosciences, UGC-Centre of advanced studies, Satellite campus, Sardar Patel University, Sardar Patel Maidan, Bakrol-Vadtal Road, PO Box 39, Vallabh Vidyanagar, Gujarat 388 120 India
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Negi S, Tak H, Ganapathi TR. Xylem specific activation of 5' upstream regulatory region of two NAC transcription factors (MusaVND6 and MusaVND7) in banana is regulated by SNBE-like sites. PLoS One 2018; 13:e0192852. [PMID: 29438404 PMCID: PMC5811034 DOI: 10.1371/journal.pone.0192852] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/31/2018] [Indexed: 11/18/2022] Open
Abstract
Deposition of secondary cell wall in the xylem elements is controlled by a subgroup of NAC (NAM, ATAF, CUC) family, known as vascular-related NAC transcription factors (VNDs). In the present study, we analyzed the 5' upstream regulatory region of two banana NAC transcription factors (MusaVND6 and MusaVND7) for tissue specific expression and presence of 19-bp secondary-wall NAC binding element (SNBE)-like motifs. Transgenic banana plants of Musa cultivar Rasthali harboring either PMusaVND7::GUS or PMusaVND6::GUS showed specific GUS (β-D-Glucuronidase) activity in cells of the xylem tissue. Approximately 1.2kb promoter region of either MusaVND6 or MusaVND7 showed presence of at least two SNBE-like motifs. This 1.2kb promoter region was retarded in a gel shift assay by three banana VND protein (VND1,VND2 and VND3). The banana VND1-VND3 could also retard the mobility of isolated SNBE-like motifs of MusaVND6 or MusaVND7 in a gel shift assay. Transcript levels of MusaVND6 and MusaVND7 were elevated in transgenic banana overexpressing either banana VND1, VND2 or VND3. Present study suggested a probable regulation of banana VND6 and VND7 expression through direct interaction of banana VND1- VND3 with SNBE-like motifs. Our study also indicated two promoter elements for possible utilization in cell wall modifications in plants especially banana, which is being recently considered as a potential biofuel crop.
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Affiliation(s)
- Sanjana Negi
- Plant Cell Culture Technology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
- Homi Bhabha National Institute, AnushaktiNagar, Mumbai, India
| | - Himanshu Tak
- Plant Cell Culture Technology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
- Homi Bhabha National Institute, AnushaktiNagar, Mumbai, India
| | - T. R. Ganapathi
- Plant Cell Culture Technology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, India
- Homi Bhabha National Institute, AnushaktiNagar, Mumbai, India
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46
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Prajapati AS, Panchal KJ, Pawar VA, Noronha MJ, Patel DH, Subramanian RB. Review on Cellulase and Xylanase Engineering for Biofuel Production. Ind Biotechnol (New Rochelle N Y) 2018. [DOI: 10.1089/ind.2017.0027] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Anil S. Prajapati
- P.G. Department of Biosciences, UGC-Centre of Advanced Studies, Satellite campus, Sardar Patel Maidan, Sardar Patel University, Gujarat, India
| | - Ketankumar J. Panchal
- P.G. Department of Biosciences, UGC-Centre of Advanced Studies, Satellite campus, Sardar Patel Maidan, Sardar Patel University, Gujarat, India
| | - Vishakha A. Pawar
- P.G. Department of Biosciences, UGC-Centre of Advanced Studies, Satellite campus, Sardar Patel Maidan, Sardar Patel University, Gujarat, India
| | - Monica J. Noronha
- P.G. Department of Biosciences, UGC-Centre of Advanced Studies, Satellite campus, Sardar Patel Maidan, Sardar Patel University, Gujarat, India
| | - Darshan H. Patel
- P. D. Patel Institute of Applied Sciences, Charotar University of Science and Technology Gujarat, India
| | - R. B. Subramanian
- P.G. Department of Biosciences, UGC-Centre of Advanced Studies, Satellite campus, Sardar Patel Maidan, Sardar Patel University, Gujarat, India
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47
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Joshi R, Singla-Pareek SL, Pareek A. Engineering abiotic stress response in plants for biomass production. J Biol Chem 2018; 293:5035-5043. [PMID: 29339553 DOI: 10.1074/jbc.tm117.000232] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
One of the major challenges in today's agriculture is to achieve enhanced plant growth and biomass even under adverse environmental conditions. Recent advancements in genetics and molecular biology have enabled the identification of a complex signaling network contributing toward plant growth and development on the one hand and abiotic stress response on the other hand. As an outcome of these studies, three major approaches have been identified as having the potential to improve biomass production in plants under abiotic stress conditions. These approaches deal with having changes in the following: (i) plant-microbe interactions; (ii) cell wall biosynthesis; and (iii) phytohormone levels. At the same time, employing functional genomics and genetics-based approaches, a very large number of genes have been identified that play a key role in abiotic stress tolerance. Our Minireview is an attempt to unveil the cross-talk that has just started to emerge between the transcriptional circuitries for biomass production and abiotic stress response. This knowledge may serve as a valuable resource to eventually custom design the crop plants for higher biomass production, in a more sustainable manner, in marginal lands under variable climatic conditions.
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Affiliation(s)
- Rohit Joshi
- From the Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sneh L Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India, and
| | - Ashwani Pareek
- From the Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India, .,the UWA Institute of Agriculture, School of Agriculture and Environment, University of Western Australia, Perth, Western Australia 6009, Australia
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48
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Zhang D, Xu Z, Cao S, Chen K, Li S, Liu X, Gao C, Zhang B, Zhou Y. An Uncanonical CCCH-Tandem Zinc-Finger Protein Represses Secondary Wall Synthesis and Controls Mechanical Strength in Rice. MOLECULAR PLANT 2018; 11:163-174. [PMID: 29175437 DOI: 10.1016/j.molp.2017.11.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 11/09/2017] [Accepted: 11/13/2017] [Indexed: 05/26/2023]
Abstract
Secondary walls, which represent the bulk of biomass, have a large impact on plant growth and adaptation to environments. Secondary wall synthesis is switched and regulated by a sophisticated signaling transduction network. However, there is limited understanding of these regulatory pathways. Here, we report that ILA1-interacting protein 4 (IIP4) can repress secondary wall synthesis. IIP4 is a phosphorylation substrate of an Raf-like MAPKKK, but its function is unknown. By generating iip4 mutants and relevant transgenic plants, we found that lesions in IIP4 enhance secondary wall formation. Gene expression and transactivation activity assays revealed that IIP4 negatively regulates the expression of MYB61 and CESAs but does not bind their promoters. IIP4 interacts with NAC29/NAC31, the upstream regulators of secondary wall synthesis, and suppresses the downstream regulatory pathways in plants. Mutagenesis analyses showed that phosphomimic IIP4 proteins translocate from the nucleus to the cytoplasm, which releases interacting NACs and attenuates its repression function. Moreover, we revealed that IIPs are evolutionarily conserved and share unreported CCCH motifs, referred to as uncanonical CCCH-tandem zinc-finger proteins. Collectively, our study provides mechanistic insights into the control of secondary wall synthesis and presents an opportunity for improving relevant agronomic traits in crops.
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Affiliation(s)
- Dongmei Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zuopeng Xu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shaoxue Cao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kunling Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Shance Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangling Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Baocai Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yihua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Suetsugu K. Independent recruitment of a novel seed dispersal system by camel crickets in achlorophyllous plants. THE NEW PHYTOLOGIST 2018; 217:828-835. [PMID: 29120037 DOI: 10.1111/nph.14859] [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: 09/14/2017] [Accepted: 09/23/2017] [Indexed: 05/26/2023]
Abstract
The seeds of most heterotrophic plants, commonly referred to as dust seeds, are typically dispersed in the air like dust particles. Therefore, little attention has been paid to how seeds of heterotrophic plants are dispersed, owing to the notion that wind dispersal is the dominant strategy. However, inconspicuous but fleshy, indehiscent fruit can be observed in distantly related plants that have independently evolved full heterotrophy. Here I investigated the seed dispersal system in three unrelated fully heterotrophic plants with fleshy, indehiscent fruits (Yoania amagiensis, Monotropastrum humile and Phacellanthus tubiflorus) by direct observation, a differential exclusion experiment of fruit feeders and investigation on seed viability through the digestive tract. The present study revealed that camel crickets are the major seed disperser in three achlorophyllous plants in the study population. This represents the first evidence of seed dispersal by camel crickets in any angiosperm species. These heterotrophic plants grow in the understorey of densely vegetated forests where wind is probably an ineffective seed dispersal agent. Life-history traits of the achlorophyllous plants associated with heterotrophic lifestyles, such as colonization of dark understorey habitats and dust seeds, could facilitate independent recruitment of the novel endozoochorous seed dispersal system by camel crickets.
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Affiliation(s)
- Kenji Suetsugu
- Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, 657-8501, Japan
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50
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Li WQ, Zhang MJ, Gan PF, Qiao L, Yang SQ, Miao H, Wang GF, Zhang MM, Liu WT, Li HF, Shi CH, Chen KM. CLD1/SRL1 modulates leaf rolling by affecting cell wall formation, epidermis integrity and water homeostasis in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:904-923. [PMID: 28960566 DOI: 10.1111/tpj.13728] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 08/29/2017] [Accepted: 09/22/2017] [Indexed: 05/20/2023]
Abstract
Leaf rolling is considered as one of the most important agronomic traits in rice breeding. It has been previously reported that SEMI-ROLLED LEAF 1 (SRL1) modulates leaf rolling by regulating the formation of bulliform cells in rice (Oryza sativa); however, the regulatory mechanism underlying SRL1 has yet to be further elucidated. Here, we report the functional characterization of a novel leaf-rolling mutant, curled leaf and dwarf 1 (cld1), with multiple morphological defects. Map-based cloning revealed that CLD1 is allelic with SRL1, and loses function in cld1 through DNA methylation. CLD1/SRL1 encodes a glycophosphatidylinositol (GPI)-anchored membrane protein that modulates leaf rolling and other aspects of rice growth and development. The cld1 mutant exhibits significant decreases in cellulose and lignin contents in secondary cell walls of leaves, indicating that the loss of function of CLD1/SRL1 affects cell wall formation. Furthermore, the loss of CLD1/SRL1 function leads to defective leaf epidermis such as bulliform-like epidermal cells. The defects in leaf epidermis decrease the water-retaining capacity and lead to water deficits in cld1 leaves, which contribute to the main cause of leaf rolling. As a result of the more rapid water loss and lower water content in leaves, cld1 exhibits reduced drought tolerance. Accordingly, the loss of CLD1/SRL1 function causes abnormal expression of genes and proteins associated with cell wall formation, cuticle development and water stress. Taken together, these findings suggest that the functional roles of CLD1/SRL1 in leaf-rolling regulation are closely related to the maintenance of cell wall formation, epidermal integrity and water homeostasis.
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Affiliation(s)
- Wen-Qiang Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Min-Juan Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Peng-Fei Gan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Lei Qiao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shuai-Qi Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hai Miao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Gang-Feng Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Mao-Mao Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Wen-Ting Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hai-Feng Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Chun-Hai Shi
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
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