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Singh P, Yadav S, Shah S, Shanker K, Sundaresan V, Shukla AK. Characterization of a CrPME indicates its possible role in determining vindoline accumulation in Catharanthus roseus leaves. PHYSIOLOGIA PLANTARUM 2024; 176:e14276. [PMID: 38566244 DOI: 10.1111/ppl.14276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/10/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024]
Abstract
The leaf-specific Catharanthus roseus alkaloid, vindoline, is the major bottleneck precursor in the production of scarce and costly anticancer bisindoles (vincristine and vinblastine). The final steps of its biosynthesis and storage occur in the laticifers. Earlier, we have shown that vindoline content is directly related to laticifer number. Pectin remodeling enzymes, like pectin methylesterase (PME), are known to be involved in laticifer development. A search in the croFGD yielded a leaf-abundant CrPME isoform that co-expressed with a few vindoline biosynthetic genes. Full-length cloning, tissue-specific expression profiling, and in silico analysis of CrPME were carried out. It was found to possess all the specific characteristics of a typical plant PME. Transient silencing (through VIGS) and overexpression of CrPME in C. roseus indicated a direct relationship between its expression and vindoline content. Comparative analysis of transcript abundance and enzyme activity in three familial C. roseus genotypes differing significantly in their vindoline content and laticifer count (CIM-Sushil > Dhawal > Nirmal) also corroborated the positive relationship of CrPME expression with vindoline content. This study highlights the possible role of CrPME, a cell wall remodeling enzyme, in modulating laticifer-associated secondary metabolism.
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Affiliation(s)
- Pooja Singh
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Seema Yadav
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Saumya Shah
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Karuna Shanker
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
| | - Velusamy Sundaresan
- CSIR-Central Institute of Medicinal and Aromatic Plants, Research Centre, Bengaluru, Karnataka, India
| | - Ashutosh K Shukla
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, Uttar Pradesh, India
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He J, Xu Z, Azhar MT, Zhang Z, Li P, Gong J, Jiang X, Fan S, Ge Q, Yuan Y, Shang H. Comparative transcriptional and co-expression network analysis of two upland cotton accessions with extreme phenotypic differences reveals molecular mechanisms of fiber development. FRONTIERS IN PLANT SCIENCE 2023; 14:1189490. [PMID: 37719229 PMCID: PMC10502173 DOI: 10.3389/fpls.2023.1189490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 07/26/2023] [Indexed: 09/19/2023]
Abstract
Introduction Upland cotton (Gossypium hirsutum) is the main source of natural fiber in the global textile industry, and thus its fiber quality and yield are important parameters. In this study, comparative transcriptomics was used to analyze differentially expressed genes (DEGs) due to its ability to effectively screen candidate genes during the developmental stages of cotton fiber. However, research using this method is limited, particularly on fiber development. The aim of this study was to uncover the molecular mechanisms underlying the whole period of fiber development and the differences in transcriptional levels. Methods Comparative transcriptomes are used to analyze transcriptome data and to screen for differentially expressed genes. STEM and WGCNA were used to screen for key genes involved in fiber development. qRT-PCR was performed to verify gene expression of selected DEGs and hub genes. Results Two accessions of upland cotton with extreme phenotypic differences, namely EZ60 and ZR014121, were used to carry out RNA sequencing (RNA-seq) on fiber samples from different fiber development stages. The results identified 704, 376, 141, 269, 761, and 586 genes that were upregulated, and 1,052, 476, 355, 259, 702, and 847 genes that were downregulated at 0, 5, 10, 15, 20, and 25 days post anthesis, respectively. Similar expression patterns of DEGs were monitored using short time-series expression miner (STEM) analysis, and associated pathways of DEGs within profiles were investigated. In addition, weighted gene co-expression network analysis (WGCNA) identified five key modules in fiber development and screened 20 hub genes involved in the development of fibers. Discussion Through the annotation of the genes, it was found that the excessive expression of resistance-related genes in the early fiber development stages affects the fiber yield, whereas the sustained expression of cell elongation-related genes is critical for long fibers. This study provides new information that can be used to improve fibers in newly developed upland cotton genotypes.
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Affiliation(s)
- Jiasen He
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou Henan, China
| | - Zhongyang Xu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou Henan, China
| | - Muhammad Tehseen Azhar
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou Henan, China
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Zhen Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Pengtao Li
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang Institute of Technology, Anyang, China
| | - Juwu Gong
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiao Jiang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Senmiao Fan
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qun Ge
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Youlu Yuan
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Haihong Shang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou Henan, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
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Jareczek JJ, Grover CE, Hu G, Xiong X, Arick Ii MA, Peterson DG, Wendel JF. Domestication over Speciation in Allopolyploid Cotton Species: A Stronger Transcriptomic Pull. Genes (Basel) 2023; 14:1301. [PMID: 37372480 DOI: 10.3390/genes14061301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/13/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Cotton has been domesticated independently four times for its fiber, but the genomic targets of selection during each domestication event are mostly unknown. Comparative analysis of the transcriptome during cotton fiber development in wild and cultivated materials holds promise for revealing how independent domestications led to the superficially similar modern cotton fiber phenotype in upland (G. hirsutum) and Pima (G. barbadense) cotton cultivars. Here we examined the fiber transcriptomes of both wild and domesticated G. hirsutum and G. barbadense to compare the effects of speciation versus domestication, performing differential gene expression analysis and coexpression network analysis at four developmental timepoints (5, 10, 15, or 20 days after flowering) spanning primary and secondary wall synthesis. These analyses revealed extensive differential expression between species, timepoints, domestication states, and particularly the intersection of domestication and species. Differential expression was higher when comparing domesticated accessions of the two species than between the wild, indicating that domestication had a greater impact on the transcriptome than speciation. Network analysis showed significant interspecific differences in coexpression network topology, module membership, and connectivity. Despite these differences, some modules or module functions were subject to parallel domestication in both species. Taken together, these results indicate that independent domestication led G. hirsutum and G. barbadense down unique pathways but that it also leveraged similar modules of coexpression to arrive at similar domesticated phenotypes.
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Affiliation(s)
- Josef J Jareczek
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50010, USA
- Biology Department, Bellarmine University, Louisville, KY 40205, USA
| | - Corrinne E Grover
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50010, USA
| | - Guanjing Hu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Xianpeng Xiong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Mark A Arick Ii
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Jonathan F Wendel
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50010, USA
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Liu Z, Sun Z, Ke H, Chen B, Gu Q, Zhang M, Wu N, Chen L, Li Y, Meng C, Wang G, Wu L, Zhang G, Ma Z, Zhang Y, Wang X. Transcriptome, Ectopic Expression and Genetic Population Analysis Identify Candidate Genes for Fiber Quality Improvement in Cotton. Int J Mol Sci 2023; 24:ijms24098293. [PMID: 37175999 PMCID: PMC10179096 DOI: 10.3390/ijms24098293] [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: 03/24/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Comparative transcriptome analysis of fiber tissues between Gossypium barbadense and Gossypium hirsutum could reveal the molecular mechanisms underlying high-quality fiber formation and identify candidate genes for fiber quality improvement. In this study, 759 genes were found to be strongly upregulated at the elongation stage in G. barbadense, which showed four distinct expression patterns (I-IV). Among them, the 346 genes of group IV stood out in terms of the potential to promote fiber elongation, in which we finally identified 42 elongation-related candidate genes by comparative transcriptome analysis between G. barbadense and G. hirsutum. Subsequently, we overexpressed GbAAR3 and GbTWS1, two of the 42 candidate genes, in Arabidopsis plants and validated their roles in promoting cell elongation. At the secondary cell wall (SCW) biosynthesis stage, 2275 genes were upregulated and exhibited five different expression profiles (I-V) in G. barbadense. We highlighted the critical roles of the 647 genes of group IV in SCW biosynthesis and further picked out 48 SCW biosynthesis-related candidate genes by comparative transcriptome analysis. SNP molecular markers were then successfully developed to distinguish the SCW biosynthesis-related candidate genes from their G. hirsutum orthologs, and the genotyping and phenotyping of a BC3F5 population proved their potential in improving fiber strength and micronaire. Our results contribute to the better understanding of the fiber quality differences between G. barbadense and G. hirsutum and provide novel alternative genes for fiber quality improvement.
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Affiliation(s)
- Zhengwen Liu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Zhengwen Sun
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Huifeng Ke
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Bin Chen
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Qishen Gu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Man Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Nan Wu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Liting Chen
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Yanbin Li
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Chengsheng Meng
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Guoning Wang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Liqiang Wu
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Guiyin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Zhiying Ma
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Yan Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
| | - Xingfen Wang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Hebei Agricultural University, Baoding 071001, China
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Pieczywek PM, Chibrikov V, Zdunek A. In silico studies of plant primary cell walls - structure and mechanics. Biol Rev Camb Philos Soc 2023; 98:887-899. [PMID: 36692136 DOI: 10.1111/brv.12935] [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: 03/24/2022] [Revised: 12/16/2022] [Accepted: 01/13/2023] [Indexed: 01/25/2023]
Abstract
Primary plant cell wall (PCW) is a highly organized network, its performance is dependent on cellulose, hemicellulose and pectic polysaccharides, their properties, interactions and assemblies. Their mutual relationships and functions in the cell wall can be better understood by means of conceptual models of their higher-order structures. Knowledge unified in the form of a conceptual model allows predictions to be made about the properties and behaviour of the system under study. Ongoing research in this field has resulted in a number of conceptual models of the cell wall. However, due to the currently limited research methods, the community of cell wall researchers have not reached a consensus favouring one model over another. Herein we present yet another research technique - numerical modelling - which is capable of resolving this issue. Even at the current stage of development of numerical techniques, due to their complexity, the in silico reconstruction of PCW remains a challenge for computational simulations. However, some difficulties have been overcome, thereby making it possible to produce advanced approximations of PCW structure and mechanics. This review summarizes the results concerning the simulation of polysaccharide interactions in PCW with regard to network fine structure, supramolecular properties and polysaccharide binding affinity. The in silico mechanical models presented herein incorporate certain physical and biomechanical aspects of cell wall architecture for the purposes of undertaking critical testing to bring about advances in our understanding of the mechanisms controlling cells and limiting cell wall expansion.
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Affiliation(s)
- Piotr Mariusz Pieczywek
- Institute of Agrophysics, Polish Academy of Sciences, ul. Doświadczalna 4, Lublin, 20-290, Poland
| | - Vadym Chibrikov
- Institute of Agrophysics, Polish Academy of Sciences, ul. Doświadczalna 4, Lublin, 20-290, Poland
| | - Artur Zdunek
- Institute of Agrophysics, Polish Academy of Sciences, ul. Doświadczalna 4, Lublin, 20-290, Poland
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Islam MT, Liu J, Das PR, Singh A, Sherif SM. Rootstock effects on bitter pit incidence in 'Honeycrisp' apples are associated with changes in fruit's cell wall chemical properties. FRONTIERS IN PLANT SCIENCE 2022; 13:1034664. [PMID: 36311084 PMCID: PMC9606712 DOI: 10.3389/fpls.2022.1034664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Bitter pit (BP) is a physiological disorder of apples that often appears during or after cold storage. Despite being defined as a calcium deficiency disorder, BP is a complex process that is not only affected by the total Ca2+ content in the fruit but also by the proper cellular Ca2+ homeostasis and partitioning. Early investigations have also suggested that rootstocks could affect BP development and severity. In the present study, rootstock effects on BP development were assessed on 'Honeycrisp' trees that were grafted on 14 different rootstocks (B.10, G.11, G.202, G.214, G.30, G.41, G.935, G.969, M.26 EMLA, M.9, V.1, V.5, V.6, and V.7). We evaluated BP incidence at harvest, and three months after cold storage for four, and three growing seasons, respectively. BP incidence was significantly reduced in 'Honeycrisp' trees on B.10 compared to other rootstocks, whereas trees on V.6 showed the highest percentage of BP at harvest and after cold storage. 'Honeycrisp' apples were collected from three different rootstocks (B.10, G.41, and V.6) two months after cold storage and evaluated for mineral nutrient composition, Ca2+ homeostasis, and cell wall properties, e.g., pectin content, pectin de-esterification rate and pectin methylesterase (PME) activity. Water-soluble and insoluble pectin content was markedly higher in fruits from B.10 than in G.41 and V.6. We also observed increased PME enzyme activity and a greater degree of water-insoluble pectin de-esterification in 'Honeycrisp' apples from V.6 compared to those from B.10. A significantly higher Ca2+ was found in the fruits from B.10 than G.41 and V.6. Higher Ca2+ and lower Mg2+ levels were also observed in the cell wall and water-insoluble pectin fractions of the fruits from B.10 compared to G.41 and V.6. However, the ratio of cell wall-bound Ca2+ to total Ca2+ was lower in B.10 compared to G.41 and V.6. Together, our results indicate that the tolerance of B.10 to BP could be attributed to a reduced PME activity and lower pectin de-esterification level, which in turn reduced the amount of Ca2+ cross-linked with pectin, and probably increased the apoplastic free calcium concentrations that is essential for maintaining cell membrane integrity and reducing BP development.
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Affiliation(s)
- Md Tabibul Islam
- Alson H. Smith Jr. Agricultural Research and Extension Center, School of Plant and Environmental Sciences, Virginia Tech, Winchester, VA, United States
| | - Jianyang Liu
- Alson H. Smith Jr. Agricultural Research and Extension Center, School of Plant and Environmental Sciences, Virginia Tech, Winchester, VA, United States
| | - Protiva Rani Das
- Alson H. Smith Jr. Agricultural Research and Extension Center, School of Plant and Environmental Sciences, Virginia Tech, Winchester, VA, United States
| | - Amritpal Singh
- Summerland Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, Summerland, BC, Canada
| | - Sherif M. Sherif
- Alson H. Smith Jr. Agricultural Research and Extension Center, School of Plant and Environmental Sciences, Virginia Tech, Winchester, VA, United States
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Wu HC, Yu SY, Wang YD, Jinn TL. Guard Cell-Specific Pectin METHYLESTERASE53 Is Required for Abscisic Acid-Mediated Stomatal Function and Heat Response in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:836151. [PMID: 35265095 PMCID: PMC8898962 DOI: 10.3389/fpls.2022.836151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/28/2022] [Indexed: 06/06/2023]
Abstract
Pectin is a major component of the plant cell wall, forming a network that contributes to cell wall integrity and flexibility. Pectin methylesterase (PME) catalyzes the removal of methylester groups from the homogalacturonan backbone, the most abundant pectic polymer, and contributes to intercellular adhesion during plant development and different environmental stimuli stress. In this study, we identified and characterized an Arabidopsis type-II PME, PME53, which encodes a cell wall deposited protein and may be involved in the stomatal lineage pathway and stomatal functions. We demonstrated that PME53 is expressed explicitly in guard cells as an abscisic acid (ABA)-regulated gene required for stomatal movement and thermotolerance. The expression of PME53 is significantly affected by the stomatal differentiation factors SCRM and MUTE. The null mutation in PME53 results in a significant increase in stomatal number and susceptibility to ABA-induced stomatal closure. During heat stress, the pme53 mutant highly altered the activity of PME and significantly lowered the expression level of the calmodulin AtCaM3, indicating that PME53 may be involved in Ca2+-pectate reconstitution to render plant thermotolerance. Here, we present evidence that the PME53-mediated de-methylesterification status of pectin is directed toward stomatal development, movement, and regulation of the flexibility of the guard cell wall required for the heat response.
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Affiliation(s)
- Hui-Chen Wu
- Department of Life Science, Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
- Department of Biological Sciences and Technology, National University of Tainan, Tainan, Taiwan
| | - Shih-Yu Yu
- Department of Life Science, Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - Yin-Da Wang
- Department of Life Science, Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - Tsung-Luo Jinn
- Department of Life Science, Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
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Wang L, Gao Y, Wang S, Zhang Q, Yang S. Genome-wide identification of PME genes, evolution and expression analyses in soybean (Glycine max L.). BMC PLANT BIOLOGY 2021; 21:578. [PMID: 34872520 PMCID: PMC8647493 DOI: 10.1186/s12870-021-03355-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Pectin methylesterase (PME) is one of pectin-modifying enzyme that affects the pectin homeostasis in cell wall and regulates plant growth and diverse biological processes. The PME genes have been well explored and characterized in different plants. Nevertheless, systematic research on the soybean (Glycine max L.) PME genes remain lacking. RESULTS We identified 127 Glycine max PME genes (GmPME) from the soybean Wm82.a2.v1 genome, which unevenly distributed on 20 soybean chromosomes. Phylogenetic analysis classified the GmPME genes into four clades (Group I, Group II, Group III and Group IV). GmPME gene members in the same clades displayed similar gene structures and motif patterns. The gene family expansion analysis demonstrated that segmental duplication was the major driving force to acquire novel GmPME genes compared to the tandem duplication events. Further synteny and evolution analyses showed that the GmPME gene family experienced strong purifying selective pressures during evolution. The cis-element analyses together with the expression patterns of the GmPME genes in various tissues suggested that the GmPME genes broadly participate in distinct biological processes and regulate soybean developments. Importantly, based on the transcriptome data and quantitative RT-PCR validations, we examined the potential roles of the GmPME genes in regulating soybean flower bud development and seed germination. CONCLUSION In conclusion, we provided a comprehensive characterization of the PME genes in soybean, and our work laid a foundation for the functional study of GmPME genes in the future.
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Affiliation(s)
- Liang Wang
- Soybean Research Institute, National Center for Soybean, Key Improvement Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yingqi Gao
- Soybean Research Institute, National Center for Soybean, Key Improvement Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Songming Wang
- Soybean Research Institute, National Center for Soybean, Key Improvement Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qiqi Zhang
- Soybean Research Institute, National Center for Soybean, Key Improvement Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shouping Yang
- Soybean Research Institute, National Center for Soybean, Key Improvement Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 China
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Jiang X, Fan L, Li P, Zou X, Zhang Z, Fan S, Gong J, Yuan Y, Shang H. Co-expression network and comparative transcriptome analysis for fiber initiation and elongation reveal genetic differences in two lines from upland cotton CCRI70 RIL population. PeerJ 2021; 9:e11812. [PMID: 34327061 PMCID: PMC8308610 DOI: 10.7717/peerj.11812] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/28/2021] [Indexed: 01/23/2023] Open
Abstract
Upland cotton is the most widely planted for natural fiber around the world, and either lint percentage (LP) or fiber length (FL) is the crucial component tremendously affecting cotton yield and fiber quality, respectively. In this study, two lines MBZ70-053 and MBZ70-236 derived from G. hirsutum CCRI70 recombinant inbred line (RIL) population presenting different phenotypes in LP and FL traits were chosen to conduct RNA sequencing on ovule and fiber samples, aiming at exploring the differences of molecular and genetic mechanisms during cotton fiber initiation and elongation stages. As a result, 249/128, 369/206, 4296/1198 and 3547/2129 up-/down- regulated differentially expressed genes (DGEs) in L2 were obtained at -3, 0, 5 and 10 days post-anthesis (DPA), respectively. Seven gene expression profiles were discriminated using Short Time-series Expression Miner (STEM) analysis; seven modules and hub genes were identified using weighted gene co-expression network analysis. The DEGs were mainly enriched into energetic metabolism and accumulating as well as auxin signaling pathway in initiation and elongation stages, respectively. Meanwhile, 29 hub genes were identified as 14-3-3ω , TBL35, GhACS, PME3, GAMMA-TIP, PUM-7, etc., where the DEGs and hub genes revealed the genetic and molecular mechanisms and differences during cotton fiber development.
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Affiliation(s)
- Xiao Jiang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Liqiang Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China.,School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Pengtao Li
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, Henan, China
| | - Xianyan Zou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Zhen Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Senmiao Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Juwu Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China.,School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China.,School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
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10
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Graham BP, Haigler CH. Microtubules exert early, partial, and variable control of cotton fiber diameter. PLANTA 2021; 253:47. [PMID: 33484350 DOI: 10.1007/s00425-020-03557-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/30/2020] [Indexed: 05/07/2023]
Abstract
Variable cotton fiber diameter is set early in anisotropic elongation by cell-type-specific processes involving the temporal and spatial regulation of microtubules in the apical region. Cotton fibers are single cells that originate from the seed epidermis of Gossypium species. Then, they undergo extreme anisotropic elongation and limited diametric expansion. The details of cellular morphogenesis determine the quality traits that affect fiber uses and value, such as length, strength, and diameter. Lower and more consistent diameter would increase the competitiveness of cotton fiber with synthetic fiber, but we do not know how this trait is controlled. The complexity of the question is indicated by the existence of fibers in two major width classes in the major commercial species: broad and narrow fibers exist in commonly grown G. hirsutum, whereas G. barbadense produces only narrow fiber. To further understand how fiber diameter is controlled, we used ovule cultures, morphology measurements, and microtubule immunofluorescence to observe the effects of microtubule antagonists on fiber morphology, including shape and diameter within 80 µm of the apex. The treatments were applied at either one or two days post-anthesis during different stages of fiber morphogenesis. The results showed that inhibiting the presence and/or dynamic activity of microtubules caused larger diameter tips to form, with greater effects often observed with earlier treatment. The presence and geometry of a microtubule-depleted-zone below the apex were transiently correlated with the apical diameter of the narrow tip types. Similarly, the microtubule antagonists had somewhat different effects between tip types. Overall, the results demonstrate cell-type-specific mechanisms regulating fiber expansion within 80 µm of the apex, with variation in the impact of microtubules between tip types and over developmental time.
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Affiliation(s)
- Benjamin P Graham
- Department of Crop and Soil Sciences and Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Candace H Haigler
- Department of Crop and Soil Sciences and Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA.
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11
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Genome-Wide Study of the GATL Gene Family in Gossypium hirsutum L. Reveals that GhGATL Genes Act on Pectin Synthesis to Regulate Plant Growth and Fiber Elongation. Genes (Basel) 2020; 11:genes11010064. [PMID: 31935825 PMCID: PMC7016653 DOI: 10.3390/genes11010064] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 01/03/2020] [Indexed: 01/07/2023] Open
Abstract
Pectin is a major polysaccharide component that promotes plant growth and fiber elongation in cotton. In previous studies, the galacturonosyltransferase-like (GATL) gene family has been shown to be involved in pectin synthesis. However, few studies have been performed on cotton GATL genes. Here, a total of 33, 17, and 16 GATL genes were respectively identified in Gossypium hirsutum, Gossypium raimondii, and Gossypium arboreum. In multiple plant species, phylogenetic analysis divided GATL genes into five groups named GATL-a to GATL-e, and the number of groups was found to gradually change over evolution. Whole genome duplication (WGD) and segmental duplication played a significant role in the expansion of the GATL gene family in G. hirsutum. Selection pressure analyses revealed that GATL-a and GATL-b groups underwent a great positive selection pressure during evolution. Moreover, the expression patterns revealed that most of highly expressed GhGATL genes belong to GATL-a and GATL-b groups, which have more segmental duplications and larger positive selection value, suggesting that these genes may play an important role in the evolution of cotton plants. We overexpressed GhGATL2, GhGATL9, GhGATL12, and GhGATL15 in Arabidopsis and silenced the GhGATL15 gene in cotton through a virus induced gene silencing assay (VIGS). The transgenic and VIGS lines showed significant differences in stem diameter, epidermal hair length, stamen length, seed size, and fiber length than the control plant. In addition, the pectin content test proved that the pectin was significantly increased in the transgenic lines and reduced in VIGS plants, demonstrating that GhGATL genes have similar functions and act on the pectin synthesis to regulate plant growth and fiber elongation. In summary, we performed a comprehensive analysis of GhGATL genes in G. hirsutum including evolution, structure and function, in order to better understand GhGATL genes in cotton for further studies.
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12
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Joca TAC, de Oliveira DC, Zotz G, Cardoso JCF, Moreira ASFP. Chemical composition of cell walls in velamentous roots of epiphytic Orchidaceae. PROTOPLASMA 2020; 257:103-118. [PMID: 31402407 DOI: 10.1007/s00709-019-01421-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 07/17/2019] [Indexed: 06/10/2023]
Abstract
The chemical composition of the cell walls strongly affects water permeability and storage in root tissues. Since epiphytic orchids live in a habitat with a highly fluctuating water supply, the root cell walls are functionally important. In the present study, we used histochemistry and immunocytochemistry techniques in order to determine the composition of the cell walls of root tissues of 18 epiphytic species belonging to seven subtribes across the Orchidaceae. The impregnation of lignin in the velamen cells reinforces its function as mechanical support and can facilitate apoplastic flow. Pectins, as well cellulose and lignins, are also essential for the stability and mechanical support of velamen cells. The exodermis and endodermis possess a suberinized lamella and often lignified walls that function as selective barriers to apoplastic flow. Various cortical parenchyma secondary wall thickenings, including phi, reticulated, and uniform, prevent the cortex from collapsing during periods of desiccation. The presence of highly methyl-esterified pectins in the cortical parenchyma facilitates the formation of gels, causing wall loosening and increased porosity, which contributes to water storage and solute transport between cells. Finally, cells with lipid or lignin impregnation in the cortical parenchyma could increase the water flow towards the stele.
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Affiliation(s)
- Thais Arruda Costa Joca
- Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho", Botucatu, São Paulo, Brazil
| | | | - Gerhard Zotz
- Institute of Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
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13
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Zhang Z, Li J, Jamshed M, Shi Y, Liu A, Gong J, Wang S, Zhang J, Sun F, Jia F, Ge Q, Fan L, Zhang Z, Pan J, Fan S, Wang Y, Lu Q, Liu R, Deng X, Zou X, Jiang X, Liu P, Li P, Iqbal MS, Zhang C, Zou J, Chen H, Tian Q, Jia X, Wang B, Ai N, Feng G, Wang Y, Hong M, Li S, Lian W, Wu B, Hua J, Zhang C, Huang J, Xu A, Shang H, Gong W, Yuan Y. Genome-wide quantitative trait loci reveal the genetic basis of cotton fibre quality and yield-related traits in a Gossypium hirsutum recombinant inbred line population. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:239-253. [PMID: 31199554 PMCID: PMC6920336 DOI: 10.1111/pbi.13191] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 05/30/2019] [Accepted: 06/11/2019] [Indexed: 05/02/2023]
Abstract
Cotton is widely cultivated globally because it provides natural fibre for the textile industry and human use. To identify quantitative trait loci (QTLs)/genes associated with fibre quality and yield, a recombinant inbred line (RIL) population was developed in upland cotton. A consensus map covering the whole genome was constructed with three types of markers (8295 markers, 5197.17 centimorgans (cM)). Six fibre yield and quality traits were evaluated in 17 environments, and 983 QTLs were identified, 198 of which were stable and mainly distributed on chromosomes 4, 6, 7, 13, 21 and 25. Thirty-seven QTL clusters were identified, in which 92.8% of paired traits with significant medium or high positive correlations had the same QTL additive effect directions, and all of the paired traits with significant medium or high negative correlations had opposite additive effect directions. In total, 1297 genes were discovered in the QTL clusters, 414 of which were expressed in two RNA-Seq data sets. Many genes were discovered, 23 of which were promising candidates. Six important QTL clusters that included both fibre quality and yield traits were identified with opposite additive effect directions, and those on chromosome 13 (qClu-chr13-2) could increase fibre quality but reduce yield; this result was validated in a natural population using three markers. These data could provide information about the genetic basis of cotton fibre quality and yield and help cotton breeders to improve fibre quality and yield simultaneously.
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14
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Zhang P, Wang H, Qin X, Chen K, Zhao J, Zhao Y, Yue B. Genome-wide identification, phylogeny and expression analysis of the PME and PMEI gene families in maize. Sci Rep 2019; 9:19918. [PMID: 31882640 PMCID: PMC6934449 DOI: 10.1038/s41598-019-56254-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 12/05/2019] [Indexed: 01/09/2023] Open
Abstract
Pectins, the major components of cell walls in plants, are synthesized and secreted to cell walls as highly methyl-esterified polymers and then demethyl-esterified by pectin methylesterases (PMEs). The PMEs are spatially regulated by pectin methylesterase inhibitors (PMEIs). In this study, 43 and 49 putative PME and PMEI genes were identified in maize, respectively. Gene structure and motif analysis revealed that members in the same paralogous pairs or in the same subgroup generally had common motif compositions and gene structure patterns, which indicates functional similarity between the closely related ZmPME/PMEI genes. Gene ontology annotation analysis showed that most of the ZmPME/PMEI genes are involved in cell wall modification and pectin catabolic process with molecular functions of pectinesterase or pectinesterase inhibitor activities. There are 35 ZmPME/PMEI genes expressed higher in anthers than in other tissues from the NimbleGen maize microarray data, and the semiq-RT-PCR assay revealed most of these ZmPME/PMEIs specially expressed in anthers and pollens, indicating they possibly had role in anther and pollen development. In addition, these ZmPME/PMEI genes were highly expressed in the fertile anthers, while lowly or no expressed in sterile anthers. This further indicated these genes might be involved in the development of anther and pollen.
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Affiliation(s)
- Panpan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiner Qin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kuan Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiuran Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yanxin Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Bing Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
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15
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Ruiz‐May E, Segura‐Cabrera A, Elizalde‐Contreras JM, Shannon LM, Loyola‐Vargas VM. A recent advance in the intracellular and extracellular redox post‐translational modification of proteins in plants. J Mol Recognit 2018; 32:e2754. [DOI: 10.1002/jmr.2754] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 06/08/2018] [Accepted: 06/14/2018] [Indexed: 02/01/2023]
Affiliation(s)
- Eliel Ruiz‐May
- Red de Estudios Moleculares AvanzadosInstituto de Ecología A. C., Cluster BioMimic® Xalapa Veracruz Mexico
| | - Aldo Segura‐Cabrera
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute, Wellcome Genome Campus Hinxton Cambridgeshire UK
| | - Jose M. Elizalde‐Contreras
- Red de Estudios Moleculares AvanzadosInstituto de Ecología A. C., Cluster BioMimic® Xalapa Veracruz Mexico
| | - Laura M. Shannon
- Department of Horticultural ScienceUniversity of Minnesota Saint Paul MN USA
| | - Víctor M. Loyola‐Vargas
- Unidad de Bioquímica y Biología Molecular de PlantasCentro de Investigación Científica de Yucatán Mérida Yucatán Mexico
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16
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Bilska-Kos A, Solecka D, Dziewulska A, Ochodzki P, Jończyk M, Bilski H, Sowiński P. Low temperature caused modifications in the arrangement of cell wall pectins due to changes of osmotic potential of cells of maize leaves (Zea mays L.). PROTOPLASMA 2017; 254:713-724. [PMID: 27193139 PMCID: PMC5309300 DOI: 10.1007/s00709-016-0982-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 05/06/2016] [Indexed: 05/17/2023]
Abstract
The cell wall emerged as one of the important structures in plant stress responses. To investigate the effect of cold on the cell wall properties, the content and localization of pectins and pectin methylesterase (PME) activity, were studied in two maize inbred lines characterized by different sensitivity to cold. Low temperature (14/12 °C) caused a reduction of pectin content and PME activity in leaves of chilling-sensitive maize line, especially after prolonged treatment (28 h and 7 days). Furthermore, immunocytohistological studies, using JIM5 and JIM7 antibodies, revealed a decrease of labeling of both low- and high-methylesterified pectins in this maize line. The osmotic potential, quantified by means of incipient plasmolysis was lower in several types of cells of chilling-sensitive maize line which was correlated with the accumulation of sucrose. These studies present new finding on the effect of cold stress on the cell wall properties in conjunction with changes in the osmotic potential of maize leaf cells.
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Affiliation(s)
- Anna Bilska-Kos
- Department of Plant Biochemistry and Physiology, Plant Breeding and Acclimatization Institute - National Research Institute, Radzików, 05-870, Błonie, Poland.
- Department of Plant Physiology, Institute of Applied Biotechnology and Basic Science, University of Rzeszow, Werynia 502, 36-100, Kolbuszowa, Poland.
| | - Danuta Solecka
- Department of Plant Molecular Ecophysiology, Faculty of Biology, Institute of Plant Experimental Biology and Biotechnology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Aleksandra Dziewulska
- Department of Plant Molecular Ecophysiology, Faculty of Biology, Institute of Plant Experimental Biology and Biotechnology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
- Biomedical Sciences Research Complex North Haugh, University of St. Andrews, KY16 9ST, St. Andrews, Fife, Scotland, UK
| | - Piotr Ochodzki
- Department of Plant Pathology, Plant Breeding and Acclimatization Institute - National Research Institute, Radzików, 05-870, Błonie, Poland
| | - Maciej Jończyk
- Department of Plant Molecular Ecophysiology, Faculty of Biology, Institute of Plant Experimental Biology and Biotechnology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Henryk Bilski
- Laboratory of Electron Microscopy, Nencki Institute of Experimental Biology, PAS, Pasteura 3, 02-093, Warsaw, Poland
| | - Paweł Sowiński
- Department of Plant Molecular Ecophysiology, Faculty of Biology, Institute of Plant Experimental Biology and Biotechnology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
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17
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Li W, Shang H, Ge Q, Zou C, Cai J, Wang D, Fan S, Zhang Z, Deng X, Tan Y, Song W, Li P, Koffi PK, Jamshed M, Lu Q, Gong W, Li J, Shi Y, Chen T, Gong J, Liu A, Yuan Y. Genome-wide identification, phylogeny, and expression analysis of pectin methylesterases reveal their major role in cotton fiber development. BMC Genomics 2016; 17:1000. [PMID: 27927181 PMCID: PMC5142323 DOI: 10.1186/s12864-016-3365-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 12/02/2016] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Pectin methylesterase (PME, EC 3.1.1.11) is a hydrolytic enzyme that utilizes pectin as substrates, and plays a significant role in regulating pectin reconstruction thereby regulating plant growth. Pectin is one of the important components of the plant cell wall, which forms the main structural material of cotton fiber. In this research, cotton genome information was used to identify PMEs. RESULTS We identified 80 (GaPME01-GaPME80) PME genes from diploid G. arboreum (A genome), 78 (GrPME01-GrPME78) PME genes from G. raimondii (D genome), and 135 (GhPME001-GhPME135) PME genes from tetraploid cotton G. hirsutum (AD genome). We further analyzed their gene structure, conserved domain, gene expression, and systematic evolution to lay the foundation for deeper research on the function of PMEs. Phylogenetic data indicated that members from the same species demonstrated relatively high sequence identities and genetic similarities. Analysis of gene structures showed that most of the PMEs genes had 2-3 exons, with a few having a variable number of exons from 4 to 6. There are nearly no differences in the gene structure of PMEs among the three (two diploid and one tetraploid) cotton species. Selective pressure analysis showed that the Ka/Ks value for each of the three cotton species PME families was less than one. CONCLUSION Conserved domain analysis showed that PMEs members had a relatively conserved C-terminal pectinesterase domain (PME) while the N-terminus was less conserved. Moreover, some of the family members contained a pectin methylesterase inhibitor (PMEI) domain. The Ka/Ks ratios suggested that the duplicated PMEs underwent purifying selection after the duplication events. This study provided an important basis for further research on the functions of cotton PMEs. Results from qRT-PCR indicated that the expression level of different PMEs at various fiber developmental stages was different. Moreover, some of the PMEs showed fiber predominant expression in secondary wall thickening indicating tissue-specific expression patterns.
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Affiliation(s)
- Weijie Li
- State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.,State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, College of Life Science, Henan University, Kaifeng, 475004, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Changsong Zou
- State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Juan Cai
- State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Daojie Wang
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, College of Life Science, Henan University, Kaifeng, 475004, China
| | - Senmiao Fan
- State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Zhen Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xiaoying Deng
- State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Yunna Tan
- State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Weiwu Song
- State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Pengtao Li
- State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Palanga Kibalou Koffi
- State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Muhammad Jamshed
- State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Quanwei Lu
- State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Junwen Li
- State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Tingting Chen
- State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Juwu Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Aiying Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of biological and genetic breeding of cotton, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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18
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Amsbury S, Hunt L, Elhaddad N, Baillie A, Lundgren M, Verhertbruggen Y, Scheller HV, Knox JP, Fleming AJ, Gray JE. Stomatal Function Requires Pectin De-methyl-esterification of the Guard Cell Wall. Curr Biol 2016; 26:2899-2906. [PMID: 27720618 PMCID: PMC5106435 DOI: 10.1016/j.cub.2016.08.021] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 07/06/2016] [Accepted: 08/05/2016] [Indexed: 12/12/2022]
Abstract
Stomatal opening and closure depends on changes in turgor pressure acting within guard cells to alter cell shape [1]. The extent of these shape changes is limited by the mechanical properties of the cells, which will be largely dependent on the structure of the cell walls. Although it has long been observed that guard cells are anisotropic due to differential thickening and the orientation of cellulose microfibrils [2], our understanding of the composition of the cell wall that allows them to undergo repeated swelling and deflation remains surprisingly poor. Here, we show that the walls of guard cells are rich in un-esterified pectins. We identify a pectin methylesterase gene, PME6, which is highly expressed in guard cells and required for stomatal function. pme6-1 mutant guard cells have walls enriched in methyl-esterified pectin and show a decreased dynamic range in response to triggers of stomatal opening/closure, including elevated osmoticum, suggesting that abrogation of stomatal function reflects a mechanical change in the guard cell wall. Altered stomatal function leads to increased conductance and evaporative cooling, as well as decreased plant growth. The growth defect of the pme6-1 mutant is rescued by maintaining the plants in elevated CO2, substantiating gas exchange analyses, indicating that the mutant stomata can bestow an improved assimilation rate. Restoration of PME6 rescues guard cell wall pectin methyl-esterification status, stomatal function, and plant growth. Our results establish a link between gene expression in guard cells and their cell wall properties, with a corresponding effect on stomatal function and plant physiology. The guard cell wall is distinguished by a relatively low level of methylated pectin Increased methyl pectin leads to stomata with a smaller dynamic range of movement These plants show increased evaporative cooling and decreased growth under drought Elevated CO2 restores mutant plant growth to normal
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Affiliation(s)
- Sam Amsbury
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Lee Hunt
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Nagat Elhaddad
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK; Department of Botany, University of Omar Al-Mukhtar, Al-Baida, Libya
| | - Alice Baillie
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Marjorie Lundgren
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Yves Verhertbruggen
- Biological Systems and Engineering Division and Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Henrik V Scheller
- Biological Systems and Engineering Division and Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - J Paul Knox
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Andrew J Fleming
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
| | - Julie E Gray
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
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19
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Sorieul M, Dickson A, Hill SJ, Pearson H. Plant Fibre: Molecular Structure and Biomechanical Properties, of a Complex Living Material, Influencing Its Deconstruction towards a Biobased Composite. MATERIALS 2016; 9:ma9080618. [PMID: 28773739 PMCID: PMC5509024 DOI: 10.3390/ma9080618] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 07/14/2016] [Accepted: 07/15/2016] [Indexed: 02/07/2023]
Abstract
Plant cell walls form an organic complex composite material that fulfils various functions. The hierarchical structure of this material is generated from the integration of its elementary components. This review provides an overview of wood as a composite material followed by its deconstruction into fibres that can then be incorporated into biobased composites. Firstly, the fibres are defined, and their various origins are discussed. Then, the organisation of cell walls and their components are described. The emphasis is on the molecular interactions of the cellulose microfibrils, lignin and hemicelluloses in planta. Hemicelluloses of diverse species and cell walls are described. Details of their organisation in the primary cell wall are provided, as understanding of the role of hemicellulose has recently evolved and is likely to affect our perception and future study of their secondary cell wall homologs. The importance of the presence of water on wood mechanical properties is also discussed. These sections provide the basis for understanding the molecular arrangements and interactions of the components and how they influence changes in fibre properties once isolated. A range of pulping processes can be used to individualise wood fibres, but these can cause damage to the fibres. Therefore, issues relating to fibre production are discussed along with the dispersion of wood fibres during extrusion. The final section explores various ways to improve fibres obtained from wood.
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Affiliation(s)
| | - Alan Dickson
- Scion, Private Bag 3020, Rotorua 3046, New Zealand.
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20
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Stiff MR, Haigler CH. Cotton fiber tips have diverse morphologies and show evidence of apical cell wall synthesis. Sci Rep 2016; 6:27883. [PMID: 27301434 PMCID: PMC4908599 DOI: 10.1038/srep27883] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/24/2016] [Indexed: 12/31/2022] Open
Abstract
Cotton fibers arise through highly anisotropic expansion of a single seed epidermal cell. We obtained evidence that apical cell wall synthesis occurs through examining the tips of young elongating Gossypium hirsutum (Gh) and G. barbadense (Gb) fibers. We characterized two tip types in Gh fiber (hemisphere and tapered), each with distinct apical diameter, central vacuole location, and distribution of cell wall components. The apex of Gh hemisphere tips was enriched in homogalacturonan epitopes, including a relatively high methyl-esterified form associated with cell wall pliability. Other wall components increased behind the apex including cellulose and the α-Fuc-(1,2)-β-Gal epitope predominantly found in xyloglucan. Gb fibers had only one narrow tip type featuring characters found in each Gh tip type. Pulse-labeling of cell wall glucans indicated wall synthesis at the apex of both Gh tip types and in distal zones. Living Gh hemisphere and Gb tips ruptured preferentially at the apex upon treatment with wall degrading enzymes, consistent with newly synthesized wall at the apex. Gh tapered tips ruptured either at the apex or distantly. Overall, the results reveal diverse cotton fiber tip morphologies and support primary wall synthesis occurring at the apex and discrete distal regions of the tip.
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Affiliation(s)
- Michael R Stiff
- Department of Crop Science, North Carolina State University, Raleigh, North Carolina 27695 USA
| | - Candace H Haigler
- Department of Crop Science, North Carolina State University, Raleigh, North Carolina 27695 USA.,Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695 USA
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Li Y, Tu L, Pettolino FA, Ji S, Hao J, Yuan D, Deng F, Tan J, Hu H, Wang Q, Llewellyn DJ, Zhang X. GbEXPATR, a species-specific expansin, enhances cotton fibre elongation through cell wall restructuring. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:951-63. [PMID: 26269378 DOI: 10.1111/pbi.12450] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 05/08/2015] [Accepted: 05/26/2015] [Indexed: 05/18/2023]
Abstract
Cotton provides us the most important natural fibre. High fibre quality is the major goal of cotton breeding, and introducing genes conferring longer, finer and stronger fibre from Gossypium barbadense to Gossypium hirsutum is an important breeding strategy. We previously analysed the G. barbadense fibre development mechanism by gene expression profiling and found two homoeologous fibre-specific α-expansins from G. barbadense, GbEXPA2 and GbEXPATR. GbEXPA2 (from the DT genome) is a classical α-expansin, while its homoeolog, GbEXPATR (AT genome), encodes a truncated protein lacking the normal C-terminal polysaccharide-binding domain of other α-expansins and is specifically expressed in G. barbadense. Silencing EXPA in G. hirsutum induced shorter fibres with thicker cell walls. GbEXPA2 overexpression in G. hirsutum had no effect on mature fibre length, but produced fibres with a slightly thicker wall and increased crystalline cellulose content. Interestingly, GbEXPATR overexpression resulted in longer, finer and stronger fibres coupled with significantly thinner cell walls. The longer and thinner fibre was associated with lower expression of a number of secondary wall-associated genes, especially chitinase-like genes, and walls with lower cellulose levels but higher noncellulosic polysaccharides which advocated that a delay in the transition to secondary wall synthesis might be responsible for better fibre. In conclusion, we propose that α-expansins play a critical role in fibre development by loosening the cell wall; furthermore, a truncated form, GbEXPATR, has a more dramatic effect through reorganizing secondary wall synthesis and metabolism and should be a candidate gene for developing G. hirsutum cultivars with superior fibre quality.
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Affiliation(s)
- Yang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Filomena A Pettolino
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Plant Industry, Canberra, ACT, Australia
| | - Shengmei Ji
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Juan Hao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Fenglin Deng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jiafu Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Haiyan Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Danny J Llewellyn
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Plant Industry, Canberra, ACT, Australia
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
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22
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Islam MS, Fang DD, Thyssen GN, Delhom CD, Liu Y, Kim HJ. Comparative fiber property and transcriptome analyses reveal key genes potentially related to high fiber strength in cotton (Gossypium hirsutum L.) line MD52ne. BMC PLANT BIOLOGY 2016; 16:36. [PMID: 26833213 PMCID: PMC4736178 DOI: 10.1186/s12870-016-0727-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/28/2016] [Indexed: 05/25/2023]
Abstract
BACKGROUND Individual fiber strength is an important quality attribute that greatly influences the strength of the yarn spun from cotton fibers. Fiber strength is usually measured from bundles of fibers due to the difficulty of reliably measuring strength from individual cotton fibers. However, bundle fiber strength (BFS) is not always correlated with yarn strength since it is affected by multiple fiber properties involved in fiber-to-fiber interactions within a bundle in addition to the individual fiber strength. Molecular mechanisms responsible for regulating individual fiber strength remain unknown. Gossypium hirsutum near isogenic lines (NILs), MD52ne and MD90ne showing variations in BFS provide an opportunity for dissecting the regulatory mechanisms involved in individual fiber strength. RESULTS Comprehensive fiber property analyses of the NILs revealed that the superior bundle strength of MD52ne fibers resulted from high individual fiber strength with minor contributions from greater fiber length. Comparative transcriptome analyses of the NILs showed that the superior bundle strength of MD52ne fibers was potentially related to two signaling pathways: one is ethylene and the interconnected phytohormonal pathways that are involved in cotton fiber elongation, and the other is receptor-like kinases (RLKs) signaling pathways that are involved in maintaining cell wall integrity. Multiple RLKs were differentially expressed in MD52ne fibers and localized in genomic regions encompassing the strength quantitative trait loci (QTLs). Several candidate genes involved in crystalline cellulose assembly were also up-regulated in MD52ne fibers while the secondary cell wall was produced. CONCLUSION Comparative phenotypic and transcriptomic analyses revealed differential expressions of the genes involved in crystalline cellulose assembly, ethylene and RLK signaling pathways between the MD52ne and MD90ne developing fibers. Ethylene and its phytohormonal network might promote the elongation of MD52ne fibers and indirectly contribute to the bundle strength by potentially improving fiber-to-fiber interactions. RLKs that were suggested to mediate a coordination of cell elongation and SCW biosynthesis in other plants might be candidate genes for regulating cotton fiber cell wall assembly and strength.
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Affiliation(s)
- Md S Islam
- USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA, 70124, USA.
| | - David D Fang
- USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA, 70124, USA.
| | - Gregory N Thyssen
- USDA-ARS, Southern Regional Research Center, Cotton Chemistry and Utilization Research Unit, New Orleans, LA, 70124, USA.
| | - Chris D Delhom
- USDA-ARS, Southern Regional Research Center, Cotton Structure and Quality Research Unit, New Orleans, LA, 70124, USA.
| | - Yongliang Liu
- USDA-ARS, Southern Regional Research Center, Cotton Structure and Quality Research Unit, New Orleans, LA, 70124, USA.
| | - Hee Jin Kim
- USDA-ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, LA, 70124, USA.
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23
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Kent LM, Loo TS, Melton LD, Mercadante D, Williams MAK, Jameson GB. Structure and Properties of a Non-processive, Salt-requiring, and Acidophilic Pectin Methylesterase from Aspergillus niger Provide Insights into the Key Determinants of Processivity Control. J Biol Chem 2015; 291:1289-306. [PMID: 26567911 DOI: 10.1074/jbc.m115.673152] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Indexed: 12/17/2022] Open
Abstract
Many pectin methylesterases (PMEs) are expressed in plants to modify plant cell-wall pectins for various physiological roles. These pectins are also attacked by PMEs from phytopathogens and phytophagous insects. The de-methylesterification by PMEs of the O6-methyl ester groups of the homogalacturonan component of pectin, exposing galacturonic acids, can occur processively or non-processively, respectively, describing sequential versus single de-methylesterification events occurring before enzyme-substrate dissociation. The high resolution x-ray structures of a PME from Aspergillus niger in deglycosylated and Asn-linked N-acetylglucosamine-stub forms reveal a 10⅔-turn parallel β-helix (similar to but with less extensive loops than bacterial, plant, and insect PMEs). Capillary electrophoresis shows that this PME is non-processive, halophilic, and acidophilic. Molecular dynamics simulations and electrostatic potential calculations reveal very different behavior and properties compared with processive PMEs. Specifically, uncorrelated rotations are observed about the glycosidic bonds of a partially de-methyl-esterified decasaccharide model substrate, in sharp contrast to the correlated rotations of processive PMEs, and the substrate-binding groove is negatively not positively charged.
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Affiliation(s)
- Lisa M Kent
- From Riddet Institute and Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Trevor S Loo
- From Riddet Institute and Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
| | - Laurence D Melton
- From Riddet Institute and School of Chemical Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Davide Mercadante
- From Riddet Institute and Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg, 69118 Heidelberg, Germany, and
| | - Martin A K Williams
- From Riddet Institute and Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand, MacDiarmid Institute for Advanced Materials and Nanotechnology, Palmerston North 4442, New Zealand
| | - Geoffrey B Jameson
- From Riddet Institute and Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand, MacDiarmid Institute for Advanced Materials and Nanotechnology, Palmerston North 4442, New Zealand
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24
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Tuttle JR, Nah G, Duke MV, Alexander DC, Guan X, Song Q, Chen ZJ, Scheffler BE, Haigler CH. Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall synthesis, represses lignification, and prolongs elongation. BMC Genomics 2015; 16:477. [PMID: 26116072 PMCID: PMC4482290 DOI: 10.1186/s12864-015-1708-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 06/19/2015] [Indexed: 11/20/2022] Open
Abstract
Background The morphogenesis of single-celled cotton fiber includes extreme elongation and staged cell wall differentiation. Designing strategies for improving cotton fiber for textiles and other uses relies on uncovering the related regulatory mechanisms. In this research we compared the transcriptomes and metabolomes of two Gossypium genotypes, Gossypium barbadense cv Phytogen 800 and G. hirsutum cv Deltapine 90. When grown in parallel, the two types of fiber developed similarly except for prolonged fiber elongation in the G. barbadense cultivar. The data were collected from isolated fibers between 10 to 28 days post anthesis (DPA) representing: primary wall synthesis to support elongation; transitional cell wall remodeling; and secondary wall cellulose synthesis, which was accompanied by continuing elongation only in G. barbadense fiber. Results Of 206 identified fiber metabolites, 205 were held in common between the two genotypes. Approximately 38,000 transcripts were expressed in the fiber of each genotype, and these were mapped to the reference set and interpreted by homology to known genes. The developmental changes in the transcriptomes and the metabolomes were compared within and across genotypes with several novel implications. Transitional cell wall remodeling is a distinct stable developmental stage lasting at least four days (18 to 21 DPA). Expression of selected cell wall related transcripts was similar between genotypes, but cellulose synthase gene expression patterns were more complex than expected. Lignification was transcriptionally repressed in both genotypes. Oxidative stress was lower in the fiber of G. barbadense cv Phytogen 800 as compared to G. hirsutum cv Deltapine 90. Correspondingly, the G. barbadense cultivar had enhanced capacity for management of reactive oxygen species during its prolonged elongation period, as indicated by a 138-fold increase in ascorbate concentration at 28 DPA. Conclusions The parallel data on deep-sequencing transcriptomics and non-targeted metabolomics for two genotypes of single-celled cotton fiber showed that a discrete developmental stage of transitional cell wall remodeling occurs before secondary wall cellulose synthesis begins. The data showed how lignification can be transcriptionally repressed during secondary cell wall synthesis, and they implicated enhanced capacity to manage reactive oxygen species through the ascorbate-glutathione cycle as a positive contributor to fiber length. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1708-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John R Tuttle
- Department of Crop Science, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Gyoungju Nah
- Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA.
| | - Mary V Duke
- USDA ARS Genomics and Bioinformatics Research Unit, Stoneville, MS, 38776, USA.
| | | | - Xueying Guan
- Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA.
| | - Qingxin Song
- Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA.
| | - Z Jeffrey Chen
- Institute for Cellular and Molecular Biology and Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, 78712, USA.
| | - Brian E Scheffler
- USDA ARS Genomics and Bioinformatics Research Unit, Stoneville, MS, 38776, USA.
| | - Candace H Haigler
- Department of Crop Science, North Carolina State University, Raleigh, NC, 27695, USA. .,Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA.
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25
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Levesque-Tremblay G, Müller K, Mansfield SD, Haughn GW. HIGHLY METHYL ESTERIFIED SEEDS is a pectin methyl esterase involved in embryo development. PLANT PHYSIOLOGY 2015; 167:725-37. [PMID: 25572606 PMCID: PMC4348785 DOI: 10.1104/pp.114.255604] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 01/06/2015] [Indexed: 05/22/2023]
Abstract
Homogalacturonan pectin domains are synthesized in a highly methyl-esterified form that later can be differentially demethyl esterified by pectin methyl esterase (PME) to strengthen or loosen plant cell walls that contain pectin, including seed coat mucilage, a specialized secondary cell wall of seed coat epidermal cells. As a means to identify the active PMEs in seed coat mucilage, we identified seven PMEs expressed during seed coat development. One of these, HIGHLY METHYL ESTERIFIED SEEDS (HMS), is abundant during mucilage secretion, peaking at 7 d postanthesis in both the seed coat and the embryo. We have determined that this gene is required for normal levels of PME activity and homogalacturonan methyl esterification in the seed. The hms-1 mutant displays altered embryo morphology and mucilage extrusion, both of which are a consequence of defects in embryo development. A significant decrease in the size of cells in the embryo suggests that the changes in embryo morphology are a consequence of lack of cell expansion. Progeny from a cross between hms-1 and the previously characterized PME inhibitor5 overexpression line suggest that HMS acts independently from other cell wall-modifying enzymes in the embryo. We propose that HMS is required for cell wall loosening in the embryo to facilitate cell expansion during the accumulation of storage reserves and that its role in the seed coat is masked by redundancy.
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Affiliation(s)
- Gabriel Levesque-Tremblay
- Departments of Botany (G.L.-T., G.W.H.) andWood Science (S.D.M.), Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andDepartment of Biological Science, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6 (K.M.)
| | - Kerstin Müller
- Departments of Botany (G.L.-T., G.W.H.) andWood Science (S.D.M.), Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andDepartment of Biological Science, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6 (K.M.)
| | - Shawn D Mansfield
- Departments of Botany (G.L.-T., G.W.H.) andWood Science (S.D.M.), Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andDepartment of Biological Science, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6 (K.M.)
| | - George W Haughn
- Departments of Botany (G.L.-T., G.W.H.) andWood Science (S.D.M.), Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4; andDepartment of Biological Science, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6 (K.M.)
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26
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Carneiro RGS, Oliveira DC, Isaias RMS. Developmental anatomy and immunocytochemistry reveal the neo-ontogenesis of the leaf tissues of Psidium myrtoides (Myrtaceae) towards the globoid galls of Nothotrioza myrtoidis (Triozidae). PLANT CELL REPORTS 2014; 33:2093-106. [PMID: 25228569 DOI: 10.1007/s00299-014-1683-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 08/13/2014] [Accepted: 08/31/2014] [Indexed: 05/20/2023]
Abstract
The temporal balance between hyperplasia and hypertrophy, and the new functions of different cell lineages led to cell transformations in a centrifugal gradient that determines the gall globoid shape. Plant galls develop by the redifferentiation of new cell types originated from those of the host plants, with new functional and structural designs related to the composition of cell walls and cell contents. Variations in cell wall composition have just started to be explored with the perspective of gall development, and are herein related to the histochemical gradients previously detected on Psidium myrtoides galls. Young and mature leaves of P. myrtoides and galls of Nothotrioza myrtoidis at different developmental stages were analysed using anatomical, cytometrical and immunocytochemical approaches. The gall parenchyma presents transformations in the size and shape of the cells in distinct tissue layers, and variations of pectin and protein domains in cell walls. The temporal balance between tissue hyperplasia and cell hypertrophy, and the new functions of different cell lineages led to cell transformations in a centrifugal gradient, which determines the globoid shape of the gall. The distribution of cell wall epitopes affected cell wall flexibility and rigidity, towards gall maturation. By senescence, it provided functional stability for the outer cortical parenchyma. The detection of the demethylesterified homogalacturonans (HGAs) denoted the activity of the pectin methylesterases (PMEs) during the senescent phase, and was a novel time-based detection linked to the increased rigidity of the cell walls, and to the gall opening. Current investigation firstly reports the influence of immunocytochemistry of plant cell walls over the development of leaf tissues, determining their neo-ontogenesis towards a new phenotype, i.e., the globoid gall morphotype.
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Affiliation(s)
- Renê G S Carneiro
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos, 6627, Pampulha, Belo Horizonte, Minas Gerais, 31270-901, Brazil
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27
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Domozych DS, Domozych CE. Multicellularity in green algae: upsizing in a walled complex. FRONTIERS IN PLANT SCIENCE 2014; 5:649. [PMID: 25477895 PMCID: PMC4235416 DOI: 10.3389/fpls.2014.00649] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 09/03/2014] [Indexed: 05/09/2023]
Abstract
Modern green algae constitute a large and diverse taxonomic assemblage that encompasses many multicellular phenotypes including colonial, filamentous, and parenchymatous forms. In all multicellular green algae, each cell is surrounded by an extracellular matrix (ECM), most often in the form of a cell wall. Volvocalean taxa like Volvox have an elaborate, gel-like, hydroxyproline rich glycoprotein covering that contains the cells of the colony. In "ulvophytes," uronic acid-rich and sulfated polysaccharides are the likely adhesion agents that maintain the multicellular habit. Charophytes also produce polysaccharide-rich cell walls and in late divergent taxa, pectin plays a critical role in cell adhesion in the multicellular complex. Cell walls are products of coordinated interaction of membrane trafficking, cytoskeletal dynamics and the cell's signal transduction machinery responding both to precise internal clocks and external environmental cues. Most often, these activities must be synchronized with the secretion, deposition and remodeling of the polymers of the ECM. Rapid advances in molecular genetics, cell biology and cell wall biochemistry of green algae will soon provide new insights into the evolution and subcellular processes leading to multicellularity.
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Affiliation(s)
- David S. Domozych
- Skidmore Microscopy Imaging Center, Department of Biology, Skidmore College, Saratoga SpringsNY, USA
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28
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Tang W, He Y, Tu L, Wang M, Li Y, Ruan YL, Zhang X. Down-regulating annexin gene GhAnn2 inhibits cotton fiber elongation and decreases Ca2+ influx at the cell apex. PLANT MOLECULAR BIOLOGY 2014; 85:613-25. [PMID: 24890373 DOI: 10.1007/s11103-014-0208-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 05/26/2014] [Indexed: 05/02/2023]
Abstract
Cotton fiber is a single cell that differentiates from the ovule epidermis and undergoes synchronous elongation with high secretion and growth rate. Apart from economic importance, cotton fiber provides an excellent single-celled model for studying mechanisms of cell-growth. Annexins are Ca(2+)- and phospholipid-binding proteins that have been reported to be localized in multiple cellular compartments and involved in control of vesicle secretions. Although several annexins have been found to be highly expressed in elongating cotton fibers, their functional roles in fiber development remain unknown. Here, 14 annexin family members were identified from the fully sequenced diploid G. raimondii (D5 genome), half of which were expressed in fibers of the cultivated tetraploid species G. hirsutum (cv. YZ1). Among them, GhAnn2 from the D genome of the tetraploid species displayed high expression level in elongating fiber. The expression of GhAnn2 could be induced by some phytohormones that play important roles in fiber elongation, such as IAA and GA3. RNAi-mediated down-regulation of GhAnn2 inhibited fiber elongation and secondary cell wall synthesis, resulting in shorter and thinner mature fibers in the transgenic plants. Measurement with non-invasive scanning ion-selective electrode revealed that the rate of Ca(2+) influx from extracellular to intracellular was decreased at the fiber cell apex of GhAnn2 silencing lines, in comparison to that in the wild type. These results indicate that GhAnn2 may regulate fiber development through modulating Ca(2+) fluxes and signaling.
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Affiliation(s)
- Wenxin Tang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, People's Republic of China,
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29
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Gilbert MK, Kim HJ, Tang Y, Naoumkina M, Fang DD. Comparative transcriptome analysis of short fiber mutants Ligon-lintless 1 and 2 reveals common mechanisms pertinent to fiber elongation in cotton (Gossypium hirsutum L.). PLoS One 2014; 9:e95554. [PMID: 24748059 PMCID: PMC3991655 DOI: 10.1371/journal.pone.0095554] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 03/27/2014] [Indexed: 02/03/2023] Open
Abstract
Understanding the molecular processes affecting cotton (Gossypium hirsutum) fiber development is important for developing tools aimed at improving fiber quality. Short fiber cotton mutants Ligon-lintless 1 (Li1) and Ligon-lintless 2 (Li2) are naturally occurring, monogenic mutations residing on different chromosomes. Both mutations cause early cessation in fiber elongation. These two mutants serve as excellent model systems to elucidate molecular mechanisms relevant to fiber length development. Previous studies of these mutants using transcriptome analysis by our laboratory and others had been limited by the fact that very large numbers of genes showed altered expression patterns in the mutants, making a targeted analysis difficult or impossible. In this research, a comparative microarray analysis was conducted using these two short fiber mutants and their near isogenic wild type (WT) grown under both field and greenhouse environments in order to identify key genes or metabolic pathways common to fiber elongation. Analyses of three transcriptome profiles obtained from different growth conditions and mutant types showed that most differentially expressed genes (DEGs) were affected by growth conditions. Under field conditions, short fiber mutants commanded higher expression of genes related to energy production, manifested by the increasing of mitochondrial electron transport activity or responding to reactive oxygen species when compared to the WT. Eighty-eight DEGs were identified to have altered expression patterns common to both short fiber mutants regardless of growth conditions. Enrichment, pathway and expression analyses suggested that these 88 genes were likely involved in fiber elongation without being affected by growth conditions.
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Affiliation(s)
- Matthew K. Gilbert
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America
| | - Hee Jin Kim
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America
| | - Yuhong Tang
- The Samuel Roberts Noble Foundation, Genomics Core Facility, Ardmore, Oklahoma, United States of America
| | - Marina Naoumkina
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America
| | - David D. Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, Louisiana, United States of America
- * E-mail:
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30
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de Oliveira DC, Magalhães TA, Ferreira BG, Teixeira CT, Formiga AT, Fernandes GW, Isaias RMDS. Variation in the degree of pectin methylesterification during the development of Baccharis dracunculifolia kidney-shaped gall. PLoS One 2014; 9:e94588. [PMID: 24747777 PMCID: PMC3991646 DOI: 10.1371/journal.pone.0094588] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 03/18/2014] [Indexed: 01/12/2023] Open
Abstract
Insect galls may be study models to test the distribution of pectins and arabinogalactan-proteins (AGPs) and their related functions during plant cell cycles. These molecules are herein histochemically and immunocitochemically investigated in the kidney-shaped gall induced by Baccharopelma dracunculifoliae (Psyllidae) on leaves of Baccharis dracunculifolia DC. (Asteraceae) on developmental basis. The homogalacturonans (HGAs) (labeled by JIM5) and the arabinans (labeled by LM6) were detected either in non-galled leaves or in young galls, and indicated stiffening of epidermal cell walls, which is an important step for cell redifferentiation. The labeling of HGAs by JIM7 changed from young to senescent stage, with an increase in the rigidity of cell walls, which is important for the acquaintance of the final gall shape and for the mechanical opening of the gall. The variation on the degree of HGAs during gall development indicated differential PMEs activity during gall development. The epitopes recognized by LM2 (AGP glycan) and LM5 (1–4-β-D-galactans) had poor alterations from non-galled leaves towards gall maturation and senescence. Moreover, the dynamics of pectin and AGPs on two comparable mature kidney-shaped galls on B. dracunculifolia and on B. reticularia revealed specific peculiarities. Our results indicate that similar gall morphotypes in cogeneric host species may present distinct cell responses in the subcelular level, and also corroborate the functions proposed in literature for HGAs.
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Affiliation(s)
- Denis Coelho de Oliveira
- Universidade Federal de Uberlândia (UFU), Instituto de Biologia (INBIO), Campus Umuarama, Uberlândia, Minas Gerais, Brasil
| | - Thiago Alves Magalhães
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Botânica, Belo Horizonte, Minas Gerais, Brasil
| | - Bruno Garcia Ferreira
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Botânica, Belo Horizonte, Minas Gerais, Brasil
| | - Cristiane Trindade Teixeira
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Botânica, Belo Horizonte, Minas Gerais, Brasil
| | - Anete Teixeira Formiga
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Botânica, Belo Horizonte, Minas Gerais, Brasil
| | - Geraldo Wilson Fernandes
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Biologia Geral, Belo Horizonte, Minas Gerais, Brasil
| | - Rosy Mary dos Santos Isaias
- Universidade Federal de Minas Gerais (UFMG), Instituto de Ciências Biológicas, Departamento de Botânica, Belo Horizonte, Minas Gerais, Brasil
- * E-mail:
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