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Zhao Y, Wang T, Wan S, Tong Y, Wei Y, Li P, Hu N, Liu Y, Chen H, Pan X, Zhang B, Peng R, Hu S. Genome-wide identification and functional analysis of the SiCIN gene family in foxtail millet (Setaria italica L.). Gene 2024; 921:148499. [PMID: 38718970 DOI: 10.1016/j.gene.2024.148499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024]
Abstract
Cell wall invertase (CIN) is a vital member of plant invertase (INV) and plays a key role in the breakdown of sucrose. This enzyme facilitates the hydrolysis of sucrose into glucose and fructose, which is crucial for various aspects of plant growth and development. However, the function of CIN genes in foxtail millet (Setaria italica) is less studied. In this research, we used the blast-p of NCBI and TBtools for bidirectional comparison, and a total of 13 CIN genes (named SiCINs) were identified from foxtail millet by using Arabidopsis and rice CIN sequences as reference sequences. The phylogenetic tree analysis revealed that the CIN genes can be categorized into three subfamilies: group 1, group 2, and group 3. Furthermore, upon conducting chromosomal localization analysis, it was observed that the 13 SiCINs were distributed unevenly across five chromosomes. Cis-acting elements of SiCIN genes can be classified into three categories: plant growth and development, stress response, and hormone response. The largest number of cis-acting elements were those related to light response (G-box) and the cis-acting elements related to seed-specific regulation (RY-element). qRT-PCR analysis further confirmed that the expression of SiCIN7 and SiCIN8 in the grain was higher than that in any other tissues. The overexpression of SiCIN7 in Arabidopsis improved the grain size and thousand-grain weight, suggesting that SiCIN7 could positively regulate grain development. Our findings will help to further understand the grain-filling mechanism of SiCIN and elucidate the biological mechanism underlying the grain development of SiCIN.
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Affiliation(s)
- Yongqing Zhao
- College of Agricultural, Tarim University, Alar 843300, Xinjiang, China; College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China; Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corp, China
| | - Tao Wang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
| | - Sumei Wan
- College of Agricultural, Tarim University, Alar 843300, Xinjiang, China; Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corp, China
| | - Yan Tong
- Anyang Academy of Agriculture Sciences, Anyang 455000, Henan, China
| | - Yangyang Wei
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
| | - Pengtao Li
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
| | - Nan Hu
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
| | - Yuling Liu
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China
| | - Hongqi Chen
- Anyang Academy of Agriculture Sciences, Anyang 455000, Henan, China
| | - Xiaoping Pan
- Department of Biology, East Carolina University, Greenville, NC 27858, United States
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, United States.
| | - Renhai Peng
- College of Agricultural, Tarim University, Alar 843300, Xinjiang, China; College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, Henan, China; Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corp, China.
| | - Shoulin Hu
- College of Agricultural, Tarim University, Alar 843300, Xinjiang, China; Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corp, China.
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Wang Y, Ruan Q, Zhu X, Wang B, Wei B, Wei X. Identification of Alfalfa SPL gene family and expression analysis under biotic and abiotic stresses. Sci Rep 2023; 13:84. [PMID: 36596810 PMCID: PMC9810616 DOI: 10.1038/s41598-022-26911-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 12/21/2022] [Indexed: 01/04/2023] Open
Abstract
The SQUAMOSA promoter binding-like protein (SPL) is a specific transcription factor that affects plant growth and development. The SPL gene family has been explored in various plants, but information about these genes in alfalfa is limited. This study, based on the whole genome data of alfalfa SPL, the fundamental physicochemical properties, phylogenetic evolution, gene structure, cis-acting elements, and gene expression of members of the MsSPL gene family were analyzed by bioinformatics methods. We identified 82 SPL sequences in the alfalfa, which were annotated into 23 genes, including 7 (30.43%) genes with four alleles, 10 (43.47%) with three, 3 (13.04%) with two, 3 (13.04%) with one allele. These SPL genes were divided into six groups, that are constructed from A. thaliana, M. truncatula and alfalfa. Chromosomal localization of the identified SPL genes showed arbitary distribution. The subcellular localization predictions showed that all MsSPL proteins were located in the nucleus. A total of 71 pairs of duplicated genes were identified, and segmental duplication mainly contributed to the expansion of the MsSPL gene family. Analysis of the Ka/Ks ratios indicated that paralogs of the MsSPL gene family principally underwent purifying selection. Protein-protein interaction analysis of MsSPL proteins were performed to predict their roles in potential regulatory networks. Twelve cis-acting elements including phytohormone and stress elements were detected in the regions of MsSPL genes. We further analyzed that the MsSPLs had apparent responses to abiotic stresses such as drought and salt and the biotic stress of methyl jasmonate. These results provide comprehensive information on the MsSPL gene family in alfalfa and lay a solid foundation for elucidating the biological functions of MsSPLs. This study also provides valuable on the regulation mechanism and function of MsSPLs in response to biotic and abiotic stresses.
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Affiliation(s)
- Yizhen Wang
- grid.411734.40000 0004 1798 5176College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China ,grid.411734.40000 0004 1798 5176Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
| | - Qian Ruan
- grid.411734.40000 0004 1798 5176College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China ,grid.411734.40000 0004 1798 5176Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
| | - Xiaolin Zhu
- grid.411734.40000 0004 1798 5176College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China ,grid.411734.40000 0004 1798 5176Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China ,grid.411734.40000 0004 1798 5176College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 China
| | - Baoqiang Wang
- grid.411734.40000 0004 1798 5176College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China ,grid.411734.40000 0004 1798 5176Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
| | - Bochuang Wei
- grid.411734.40000 0004 1798 5176College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China ,grid.411734.40000 0004 1798 5176Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
| | - Xiaohong Wei
- grid.411734.40000 0004 1798 5176College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China ,grid.411734.40000 0004 1798 5176Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China ,grid.411734.40000 0004 1798 5176College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 China
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3
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Fang Y, Jiang J, Hou X, Guo J, Li X, Zhao D, Xie X. Plant protein-coding gene families: Their origin and evolution. FRONTIERS IN PLANT SCIENCE 2022; 13:995746. [PMID: 36160967 PMCID: PMC9490259 DOI: 10.3389/fpls.2022.995746] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/15/2022] [Indexed: 05/13/2023]
Abstract
Steady advances in genome sequencing methods have provided valuable insights into the evolutionary processes of several gene families in plants. At the core of plant biodiversity is an extensive genetic diversity with functional divergence and expansion of genes across gene families, representing unique phenomena. The evolution of gene families underpins the evolutionary history and development of plants and is the subject of this review. We discuss the implications of the molecular evolution of gene families in plants, as well as the potential contributions, challenges, and strategies associated with investigating phenotypic alterations to explain the origin of plants and their tolerance to environmental stresses.
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Affiliation(s)
- Yuanpeng Fang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Junmei Jiang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Xiaolong Hou
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
| | - Jiyuan Guo
- Department of Resources and Environment, Moutai Institute, Zunyi, China
| | - Xiangyang Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, China
| | - Degang Zhao
- Key Laboratory of Mountain Plant Resources Protection and Germplasm Innovation, Ministry of Education, College of Life Sciences, Institute of Agricultural Bioengineering, Guizhou University, Guiyang, China
- Guizhou Conservation Technology Application Engineering Research Center, Guizhou Institute of Prataculture/Guizhou Institute of Biotechnology/Guizhou Academy of Agricultural Sciences, Guiyang, China
- *Correspondence: Degang Zhao,
| | - Xin Xie
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Conservation Technology Application Engineering Research Center, Guizhou Institute of Prataculture/Guizhou Institute of Biotechnology/Guizhou Academy of Agricultural Sciences, Guiyang, China
- Xin Xie,
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Petersen G, Shyama Prasad Rao R, Anderson B, Zervas A, Seberg O, Rasmusson AG, Max Møller I. Genes from oxidative phosphorylation complexes II-V and two dual-function subunits of complex I are transcribed in Viscum album despite absence of the entire mitochondrial holo-complex I. Mitochondrion 2021; 62:1-12. [PMID: 34740863 DOI: 10.1016/j.mito.2021.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/09/2021] [Accepted: 10/28/2021] [Indexed: 11/30/2022]
Abstract
Mistletoes (Viscum) and close relatives are unique among flowering plants in having a drastically altered electron transport chain. Lack of complex I genes has previously been reported for the mitochondrial genome, and here we report an almost complete absence of nuclear-encoded complex I genes in the transcriptome of Viscum album. Compared to Arabidopsis with approximately 40 nuclear complex I genes, we recover only transcripts of two dual-function genes: gamma carbonic anhydrase and L-galactono-1,4-lactone dehydrogenase. The complement of genes belonging to complexes II-V of the oxidative phosphorylation pathway appears to be in accordance with other vascular plants. Additionally, transcripts encoding alternative NAD(P)H dehydrogenases and alternative oxidase were found. Despite sequence divergence, structural modeling suggests that the encoded proteins are structurally conserved. Complex I loss is a special feature in Viscum species and relatives, as all other parasitic flowering plants investigated to date seem to have a complete OXPHOS system. Hence, Viscum offers a unique system for specifically investigating molecular consequences of complex I absence, such as the role of complex I subunits involved in secondary functions.
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Affiliation(s)
- Gitte Petersen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - R Shyama Prasad Rao
- Biostatistics and Bioinformatics Division, Yenepoya Research Center, Yenepoya University, Mangaluru 575018, Karnataka, India
| | - Benjamin Anderson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Athanasios Zervas
- Department of Environmental Science, Aarhus University, DK-4000 Roskilde, Denmark
| | - Ole Seberg
- Natural History Museum of Denmark, University of Copenhagen, DK-1353 Copenhagen, Denmark
| | | | - Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, DK-4200 Slagelse, Denmark
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Ding CQ, Ng S, Wang L, Wang YC, Li NN, Hao XY, Zeng JM, Wang XC, Yang YJ. Genome-wide identification and characterization of ALTERNATIVE OXIDASE genes and their response under abiotic stresses in Camellia sinensis (L.) O. Kuntze. PLANTA 2018; 248:1231-1247. [PMID: 30097722 DOI: 10.1007/s00425-018-2974-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 08/05/2018] [Indexed: 06/08/2023]
Abstract
Four typical ALTERNATIVE OXIDASE genes have been identified in tea plants, and their sequence features and gene expression profiles have provided useful information for further studies on function and regulation. Alternative oxidase (AOX) is a terminal oxidase located in the respiratory electron transport chain. AOX catalyzes the oxidation of quinol and the reduction of oxygen into water. In this study, a genome-wide search and subsequent DNA cloning were performed to identify and characterize AOX genes in tea plant (Camellia sinensis (L.) O. Kuntze cv. Longjing43). Our results showed that tea plant possesses four AOX genes, i.e., CsAOX1a, CsAOX1d, CsAOX2a and CsAOX2b. Gene structure and protein sequence analyses revealed that all CsAOXs share a four-exon/three-intron structure with highly conserved regions and amino acid residues, which are necessary for AOX secondary structures, catalytic activities and post-translational regulations. All CsAOX were shown to localize in mitochondria using the green fluorescent protein (GFP)-targeting assay. Both CsAOX1a and CsAOX1d were induced by cold, salt and drought stresses, and with different expression patterns in young and mature leaves. Reactive oxygen species (ROS) accumulated strongly after 72 and 96 h cold treatments in both young and mature leaves, while the polyphenol and total catechin decreased significantly only in mature leaves. In comparison to AtAOX1a in Arabidopsis thaliana, CsAOX1a lost almost all of the stress-responsive cis-acting regulatory elements in its promoter region (1500 bp upstream), but possesses a flavonoid biosynthesis-related MBSII cis-acting regulatory element. These results suggest a link between CsAOX1a function and the metabolism of some secondary metabolites in tea plant. Our studies provide a basis for the further elucidation of the biological function and regulation of the AOX pathway in tea plants.
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Affiliation(s)
- Chang-Qing Ding
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, People's Republic of China
| | - Sophia Ng
- ARC Centre of Excellence Plant Energy Biology, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia
- Institut de Biosciences et Biotechnologies, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Cadarache, 13108, St Paul-Lez-Durance, France
| | - Lu Wang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, People's Republic of China
| | - Yu-Chun Wang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, People's Republic of China
| | - Na-Na Li
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, People's Republic of China
| | - Xin-Yuan Hao
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, People's Republic of China
| | - Jian-Ming Zeng
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, People's Republic of China
| | - Xin-Chao Wang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, People's Republic of China.
| | - Ya-Jun Yang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310008, People's Republic of China.
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6
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Selinski J, Scheibe R, Day DA, Whelan J. Alternative Oxidase Is Positive for Plant Performance. TRENDS IN PLANT SCIENCE 2018; 23:588-597. [PMID: 29665989 DOI: 10.1016/j.tplants.2018.03.012] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/15/2018] [Accepted: 03/22/2018] [Indexed: 05/02/2023]
Abstract
The alternative pathway of mitochondrial electron transport, which terminates in the alternative oxidase (AOX), uncouples oxidation of substrate from mitochondrial ATP production, yet plant performance is improved under adverse growth conditions. AOX is regulated at different levels. Identification of regulatory transcription factors shows that Arabidopsis thaliana AOX1a is under strong transcriptional suppression. At the protein level, the primary structure is not optimised for activity. Maximal activity requires the presence of various metabolites, such as tricarboxylic acid-cycle intermediates that act in an isoform-specific manner. In this opinion article we propose that the regulatory mechanisms that keep AOX activity suppressed, at both the gene and protein level, are positive for plant performance due to the flexible short- and long-term fine-tuning.
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Affiliation(s)
- Jennifer Selinski
- Department of Animal, Plant, and Soil Science, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University Bundoora, VIC 3083, Australia.
| | - Renate Scheibe
- Division of Plant Physiology, Department of Biology/Chemistry, University of Osnabrueck, D-49069 Osnabrueck, Germany
| | - David A Day
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - James Whelan
- Department of Animal, Plant, and Soil Science, Australian Research Council Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University Bundoora, VIC 3083, Australia
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