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Lu K, Wang F, Chen L, Zhang W. Overexpression of S-R enhances the accumulation of biomass, fatty acids, and β-carotene in Schizochytrium. BIORESOURCE TECHNOLOGY 2023; 385:129452. [PMID: 37406830 DOI: 10.1016/j.biortech.2023.129452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 07/07/2023]
Abstract
Strategies for enhancing biomass accumulation and increasing the production of fatty acids and β-carotene in Schizochytrium are hindered by the lack of suitable targets. In this study, S-R, a RING (really interesting new gene) finger domain-containing protein, was identified in Schizochytrium, with homologs found in the family Thraustochytriaceae. Transgenic strains overexpressing S-R showed a minor improvement in cell growth but a significant increase in total fatty acids content by 1.29- to 1.36-fold. Almost all individual saturated fatty acids exhibited significant increases, with the greatest increase observed in the C14:0 content, by 1.52- to 1.78-fold. Additionally, the β-carotene content of S-R strains was significantly upregulated. Overexpression of s-r conferred hypersaline tolerance in Schizochytrium, with a significant increase in dry cell weight, total fatty acids and β-carotene, likely due to the upregulation of glycerol and proline. This study provides a feasible strategy to engineer Thraustochytriaceae for efficient biomass and biochemical production.
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Affiliation(s)
- Kongyong Lu
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China; Frontier Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, PR China
| | - Fangzhong Wang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China; Frontier Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, PR China; Center for Biosafety Research and Strategy, Tianjin University, Tianjin, PR China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China; Frontier Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, PR China.
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, PR China; Frontier Science Center of Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, PR China; Center for Biosafety Research and Strategy, Tianjin University, Tianjin, PR China
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2
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Li Y, Qin P, Sun A, Xiao W, Chen F, He Y, Yu K, Li Y, Zhang M, Guo X. Genome-wide identification, new classification, expression analysis and screening of drought & heat resistance related candidates in the RING zinc finger gene family of bread wheat (Triticum aestivum L.). BMC Genomics 2022; 23:696. [PMID: 36207690 PMCID: PMC9547421 DOI: 10.1186/s12864-022-08905-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 09/23/2022] [Indexed: 11/12/2022] Open
Abstract
Background RING (Really Interesting New Gene) zinc finger (RING-zf) proteins belong to an important subclass of zinc fingers superfamily, which play versatile roles during various developmental stages and in abiotic stress responses. Based on the conserved cysteine and histidine residues, the RING-zf domains are classified into RING-HC (C3HC4), RING-H2 (C3H2C3), RING-v, RING-D, RING-S/T, RING-G, and RING-C2. However, little is known about the function of the RING-zfs of wheat. Results In this study, 129 (93.5%) of 138 members were found in nucleus, indicating TaRING-zf were primarily engaged in the degradation of transcription factors and other nuclear-localized proteins. 138 TaRING-zf domains can be divided into four canonical or modified types (RING-H2, RING-HC, RING-D, and RING-M). The RING-M was newly identified in T. aestivum, and might represent the intermediate other states between RING-zf domain and other modified domains. The consensus sequence of the RING-M domain can be described as M-X2-R-X14-Cys-X1-H-X2-Cys-X2-Cys-X10-Cys-X2-Cys. Further interspecies collinearity analyses showed that TaRING-zfs were more closely related to the genes in Poaceae. According to the public transcriptome data, most of the TaRING-zfs were expressed at different 15 stages of plant growth, development, and some of them exhibited specific responses to drought/heat stress. Moreover, 4 RING-HC (TraesCS2A02G526800.1, TraesCS4A02G290600.1, TraesCS4B02G023600.1 and TraesCS4D02G021200.1) and 2 RING-H2 (TraesCS3A02G288900.1 and TraesCS4A02G174600.1) were significantly expressed at different development stages and under drought stress. These findings provide valuable reference data for further study of their physiological functions in wheat varieties. Conclusions Taken together, the characterization and classifications of the TaRING-zf family were extensively studied and some new features about it were revealed. This study could provide some valuable targets for further studies on their functions in growth and development, and abiotic stress responses in wheat. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08905-x.
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Affiliation(s)
- Yongliang Li
- College of Biology, Hunan University, Changsha, 410082, China
| | - Pai Qin
- College of Biology, Hunan University, Changsha, 410082, China
| | - Aolong Sun
- College of Biology, Hunan University, Changsha, 410082, China
| | - Wenjun Xiao
- College of Biology, Hunan University, Changsha, 410082, China.
| | - Fenglin Chen
- College of Biology, Hunan University, Changsha, 410082, China
| | - Yang He
- College of Biology, Hunan University, Changsha, 410082, China
| | - Keyao Yu
- College of Biology, Hunan University, Changsha, 410082, China
| | - You Li
- College of Biology, Hunan University, Changsha, 410082, China
| | - Meng Zhang
- College of Biology, Hunan University, Changsha, 410082, China
| | - Xinhong Guo
- College of Biology, Hunan University, Changsha, 410082, China.
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Han G, Qiao Z, Li Y, Yang Z, Wang C, Zhang Y, Liu L, Wang B. RING Zinc Finger Proteins in Plant Abiotic Stress Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:877011. [PMID: 35498666 PMCID: PMC9047180 DOI: 10.3389/fpls.2022.877011] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/22/2022] [Indexed: 05/03/2023]
Abstract
RING zinc finger proteins have a conserved RING domain, mainly function as E3 ubiquitin ligases, and play important roles in plant growth, development, and the responses to abiotic stresses such as drought, salt, temperature, reactive oxygen species, and harmful metals. RING zinc finger proteins act in abiotic stress responses mainly by modifying and degrading stress-related proteins. Here, we review the latest progress in research on RING zinc finger proteins, including their structural characteristics, classification, subcellular localization, and physiological functions, with an emphasis on abiotic stress tolerance. Under abiotic stress, RING zinc finger proteins on the plasma membrane may function as sensors or abscisic acid (ABA) receptors in abiotic stress signaling. Some RING zinc finger proteins accumulate in the nucleus may act like transcription factors to regulate the expression of downstream abiotic stress marker genes through direct or indirect ways. Most RING zinc finger proteins usually accumulate in the cytoplasm or nucleus and act as E3 ubiquitin ligases in the abiotic stress response through ABA, mitogen-activated protein kinase (MAPK), and ethylene signaling pathways. We also highlight areas where further research on RING zinc finger proteins in plants is needed.
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Affiliation(s)
- Guoliang Han
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
- Dongying Institute, Shandong Normal University, Dongying, China
| | - Ziqi Qiao
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Yuxia Li
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Zongran Yang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Chengfeng Wang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Yuanyuan Zhang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Lili Liu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Baoshan Wang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
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Meng X, Liu J, Zhao M. Genome-wide identification of RING finger genes in flax ( Linum usitatissimum) and analyses of their evolution. PeerJ 2021; 9:e12491. [PMID: 34820204 PMCID: PMC8601054 DOI: 10.7717/peerj.12491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 10/25/2021] [Indexed: 01/05/2023] Open
Abstract
Background Flax (Linum usitatissimum) is an important crop for its seed oil and stem fiber. Really Interesting New Gene (RING) finger genes play essential roles in growth, development, and biotic and abiotic stress responses in plants. However, little is known about these genes in flax. Methods Here, we performed a systematic genome-wide analysis to identify RING finger genes in flax. Results We identified 587 RING domains in 574 proteins and classified them into RING-H2 (292), RING-HCa (181), RING-HCb (23), RING-v (53), RING-C2 (31), RING-D (2), RING-S/T (3), and RING-G (2). These proteins were further divided into 45 groups according to domain organization. These genes were located in 15 chromosomes and clustered into three clades according to their phylogenetic relationships. A total of 312 segmental duplicated gene pairs were inferred from 411 RING finger genes, indicating a major contribution of segmental duplications to the RING finger gene family expansion. The non-synonymous/synonymous substitution ratio of the segmentally duplicated gene pairs was less than 1, suggesting that the gene family was under negative selection since duplication. Further, most RING genes in flax were differentially expressed during seed development or in the shoot apex. This study provides useful information for further functional analysis of RING finger genes in flax and to develop gene-derived molecular markers in flax breeding.
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Affiliation(s)
- Xianwen Meng
- The College of Ecological Environmental and Resources, Qinghai Provincial Key Laboratory of High Value Utilization of Characteristic Economic Plants, Qinghai Tibet Alpine Wetland Restoration Engineering Technology Research Center, Qinghai Minzu University, Xining, China
| | - Jing Liu
- The College of Ecological Environmental and Resources, Qinghai Provincial Key Laboratory of High Value Utilization of Characteristic Economic Plants, Qinghai Tibet Alpine Wetland Restoration Engineering Technology Research Center, Qinghai Minzu University, Xining, China
| | - Mingde Zhao
- The College of Ecological Environmental and Resources, Qinghai Provincial Key Laboratory of High Value Utilization of Characteristic Economic Plants, Qinghai Tibet Alpine Wetland Restoration Engineering Technology Research Center, Qinghai Minzu University, Xining, China
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Evolutionary and Characteristic Analysis of RING-DUF1117 E3 Ubiquitin Ligase Genes in Gossypium Discerning the Role of GhRDUF4D in Verticillium dahliae Resistance. Biomolecules 2021; 11:biom11081145. [PMID: 34439811 PMCID: PMC8392396 DOI: 10.3390/biom11081145] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/30/2021] [Accepted: 07/31/2021] [Indexed: 11/16/2022] Open
Abstract
Verticillium wilt, primarily induced by the soil-borne fungus Verticillium dahliae, is a serious threat to cotton fiber production. There are a large number of really interesting new gene (RING) domain-containing E3 ubiquitin ligases in Arabidopsis, of which three (At2g39720 (AtRHC2A), At3g46620 (AtRDUF1), and At5g59550 (AtRDUF2)) have a domain of unknown function (DUF) 1117 domain in their C-terminal regions. This study aimed to detect and characterize the RDUF members in cotton, to gain an insight into their roles in cotton’s adaptation to environmental stressors. In this study, a total of 6, 7, 14, and 14 RDUF (RING-DUF1117) genes were detected in Gossypium arboretum, G. raimondii, G. hirsutum, and G. barbadense, respectively. These RDUF genes were classified into three groups. The genes in each group were highly conserved based on gene structure and domain analysis. Gene duplication analysis revealed that segmental duplication occurred during cotton evolution. Expression analysis revealed that the GhRDUF genes were widely expressed during cotton growth and under abiotic stresses. Many cis-elements related to hormone response and environment stressors were identified in GhRDUF promoters. The predicted target miRNAs and transcription factors implied that GhRDUFs might be regulated by gra-miR482c, as well as by transcription factors, including MYB, C2H2, and Dof. The GhRDUF genes responded to cold, drought, and salt stress and were sensitive to jasmonic acid, salicylic acid, and ethylene signals. Meanwhile, GhRDUF4D expression levels were enhanced after V. dahliae infection. Subsequently, GhRDUF4D was verified by overexpression in Arabidopsis and virus-induced gene silencing treatment in upland cotton. We observed that V. dahliae resistance was significantly enhanced in transgenic Arabidopsis, and weakened in GhRDUF4D silenced plants. This study conducted a comprehensive analysis of the RDUF genes in Gossypium, hereby providing basic information for further functional studies.
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Research Progress on Plant RING-Finger Proteins. Genes (Basel) 2019; 10:genes10120973. [PMID: 31779262 PMCID: PMC6969932 DOI: 10.3390/genes10120973] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 11/21/2019] [Accepted: 11/21/2019] [Indexed: 12/17/2022] Open
Abstract
E3 ubiquitin ligases are the most expanded components of the ubiquitin proteasome system (UPS). They mediate the recognition of substrates and later transfer the ubiquitin (Ub) of the system. Really Interesting New Gene (RING) finger proteins characterized by the RING domain, which contains 40–60 residues, are thought to be E3 ubiquitin ligase. RING-finger proteins play significant roles in plant growth, stress resistance, and signal transduction. In this study, we mainly describe the structural characteristics, classifications, and subcellular localizations of RING-finger proteins, as well the physiological processes of RING-finger proteins in plant growth and development. We also summarize the functions of plant RING-finger proteins in plant stress resistance. Finally, further research on plant RING-finger proteins is suggested, thereby establishing a strong foundation for the future study of plant RING-finger proteins.
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Yang L, Miao M, Lyu H, Cao X, Li J, Li Y, Li Z, Chang W. Genome-Wide Identification, Evolution, and Expression Analysis of RING Finger Gene Family in Solanum lycopersicum. Int J Mol Sci 2019; 20:ijms20194864. [PMID: 31574992 PMCID: PMC6801689 DOI: 10.3390/ijms20194864] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/27/2019] [Accepted: 09/29/2019] [Indexed: 01/11/2023] Open
Abstract
RING domain proteins generally have E3 ubiquitin ligase activity and are involved in degrading their substrate proteins. The roles of these proteins in growth, development, and responses to different abiotic stresses have been described well in various plant species, but little is available on tomatoes. Here, we identified 474 RING domains in 469 potential proteins encoded in the tomato genome. These RING genes were found to be located in 12 chromosomes and could be divided into 51 and 11 groups according to the conserved motifs outside the RING domain and phylogenetic analysis, respectively. Segmental duplication could be the major driver in the expansion of the tomato RING gene family. Further comparative syntenic analysis suggested that there have been functional divergences of RING genes during plant evolution and most of the RING genes in various species are under negative selection. Expression profiles derived from a transcriptomic analysis showed that most tomato RING genes exhibited tissue-specific expression patterning. Further RT-qPCR validation showed that almost all genes were upregulated by salt treatment, which was consistent with the microarray results. This study provides the first comprehensive understanding of the RING gene family in the tomato genome. Our results pave the way for further investigation of the classification, evolution, and potential functions of the RING domain genes in tomato.
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Affiliation(s)
- Liang Yang
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.
- Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement in Southwest Regions, Ministry of Agriculture, Chengdu 610066, China.
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
| | - Mingjun Miao
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.
- Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement in Southwest Regions, Ministry of Agriculture, Chengdu 610066, China.
| | - Hongjun Lyu
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China.
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Shandong Province Key Laboratory for Biology of Greenhouse Vegetables, Shandong Branch of National Improvement Center for Vegetables, Jinan 250100, China.
| | - Xue Cao
- College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Ju Li
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.
- Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement in Southwest Regions, Ministry of Agriculture, Chengdu 610066, China.
| | - Yuejian Li
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.
| | - Zhi Li
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.
- Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement in Southwest Regions, Ministry of Agriculture, Chengdu 610066, China.
| | - Wei Chang
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan Province, Horticulture Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.
- Key Laboratory of Horticultural Crops Biology and Germplasm Enhancement in Southwest Regions, Ministry of Agriculture, Chengdu 610066, China.
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Jiménez-López D, Muñóz-Belman F, González-Prieto JM, Aguilar-Hernández V, Guzmán P. Repertoire of plant RING E3 ubiquitin ligases revisited: New groups counting gene families and single genes. PLoS One 2018; 13:e0203442. [PMID: 30169501 PMCID: PMC6118397 DOI: 10.1371/journal.pone.0203442] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/21/2018] [Indexed: 01/12/2023] Open
Abstract
E3 ubiquitin ligases of the ubiquitin proteasome system (UPS) mediate recognition of substrates and later transfer the ubiquitin (Ub). They are the most expanded components of the system. The Really Interesting New Gene (RING) domain contains 40-60 residues that are highly represented among E3 ubiquitin ligases. The Arabidopsis thaliana E3 ubiquitin ligases with a RING finger primarily contain RING-HC or RING-H2 type domains or less frequently RING-v, RING-C2, RING-D, RING-S/T and RING-G type domains. Our previous work on three E3 ubiquitin ligase families with a RING-H2 type domain, ATL, BTL, and CTL, suggested that a phylogenetic distribution based on the RING domain allowed for the creation a catalog of known domains or unknown conserved motifs. This work provided a useful and comprehensive view of particular families of RING E3 ubiquitin ligases. We updated the annotation of A. thaliana RING proteins and surveyed RING proteins from 30 species across eukaryotes. Based on domain architecture profile of the A. thaliana proteins, we catalogued 4711 RING finger proteins into 107 groups, including 66 previously described gene families or single genes and 36 novel families or undescribed genes. Forty-four groups were specific to a plant lineage while 41 groups consisted of proteins found in all eukaryotic species. Our present study updates the current classification of plant RING finger proteins and reiterates the importance of these proteins in plant growth and adaptation.
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Affiliation(s)
- Domingo Jiménez-López
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, Gto., México
- Biotecnología Vegetal, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Tamaulipas, México
| | - Francisco Muñóz-Belman
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, Gto., México
| | - Juan Manuel González-Prieto
- Biotecnología Vegetal, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Tamaulipas, México
| | - Victor Aguilar-Hernández
- CONACYT, Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Col. Chuburná de Hidalgo, Mérida, Yucatán, México
| | - Plinio Guzmán
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, Gto., México
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Jiménez-López D, Aguilar-Henonin L, González-Prieto JM, Aguilar-Hernández V, Guzmán P. CTLs, a new class of RING-H2 ubiquitin ligases uncovered by YEELL, a motif close to the RING domain that is present across eukaryotes. PLoS One 2018; 13:e0190969. [PMID: 29324855 PMCID: PMC5764321 DOI: 10.1371/journal.pone.0190969] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 12/22/2017] [Indexed: 12/12/2022] Open
Abstract
RING ubiquitin E3 ligases enclose a RING domain for ubiquitin ligase activity and associated domains and/or conserved motifs outside the RING domain that collectively facilitate their classification and usually reveal some of key information related to mechanism of action. Here we describe a new family of E3 ligases that encodes a RING-H2 domain related in sequence to the ATL and BTL RING-H2 domains. This family, named CTL, encodes a motif designed as YEELL that expands 21 amino acids next to the RING-H2 domain that is present across most eukaryotic lineages. E3 ubiquitin ligase BIG BROTHER is a plant CTL that regulates organ size, and SUMO-targeted ubiquitin E3 ligase RNF111/ARKADIA is a vertebrate CTL. Basal animal and vertebrate, as well as fungi species, encode a single CTL gene that constraints the number of paralogs observed in vertebrates. Conversely, as previously described in ATL and BTL families in plants, CTL genes range from a single copy in green algae and 3 to 5 copies in basal species to 9 to 35 copies in angiosperms. Our analysis describes key structural features of a novel family of E3 ubiquitin ligases as an integral component of the set of core eukaryotic genes.
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Affiliation(s)
- Domingo Jiménez-López
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, Guanajuato, México
- Biotecnología Vegetal, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Tamaulipas, México
| | - Laura Aguilar-Henonin
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, Guanajuato, México
| | - Juan Manuel González-Prieto
- Biotecnología Vegetal, Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Tamaulipas, México
| | - Victor Aguilar-Hernández
- CONACYT, Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, México
| | - Plinio Guzmán
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, Guanajuato, México
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Genome-wide identification, evolution and expression analysis of RING finger protein genes in Brassica rapa. Sci Rep 2017; 7:40690. [PMID: 28094809 PMCID: PMC5240574 DOI: 10.1038/srep40690] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 12/08/2016] [Indexed: 12/31/2022] Open
Abstract
More and more RING finger genes were found to be implicated in various important biological processes. In the present study, a total of 731 RING domains in 715 predicted proteins were identified in Brassica rapa genome (AA, 2n = 20), which were further divided into eight types: RING-H2 (371), RING-HCa (215), RING-HCb (47), RING-v (44), RING-C2 (38), RING-D (10), RING-S/T (5) and RING-G (1). The 715 RING finger proteins were further classified into 51 groups according to the presence of additional domains. 700 RING finger protein genes were mapped to the 10 chromosomes of B. rapa with a range of 47 to 111 genes for each chromosome. 667 RING finger protein genes were expressed in at least one of the six tissues examined, indicating their involvement in various physiological and developmental processes in B. rapa. Hierarchical clustering analysis of RNA-seq data divided them into seven major groups, one of which includes 231 members preferentially expressed in leaf, and constitutes then a panel of gene candidates for studying the genetic and molecular mechanisms of leafy head traits in Brassica crops. Our results lay the foundation for further studies on the classification, evolution and putative functions of RING finger protein genes in Brassica species.
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