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Liu M, Wang L, Yu Q, Song J, Zhu L, Jia KH, Qin X. The response of LncRNAs associated with photosynthesis-and pigment synthesis-related genes to green light in Chlamydomonas reinhardtii. PHOTOSYNTHESIS RESEARCH 2024; 161:65-78. [PMID: 38108929 DOI: 10.1007/s11120-023-01062-6] [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: 07/18/2023] [Accepted: 11/11/2023] [Indexed: 12/19/2023]
Abstract
The quality of light is an important abiotic factor that affects the growth and development of green plants. Ultraviolet, red, blue, and far-red light all have demonstrated roles in regulating green plant growth and development, as well as light morphogenesis. However, the mechanism underlying photosynthetic organism responses to green light throughout the life of them are not clear. In this study, we exposed the unicellular green alga Chlamydomonas reinhardtii to green light and analyzed the dynamics of transcriptome changes. Based on the whole transcriptome data from C. reinhardtii, a total of 9974 differentially expressed genes (DEGs) were identified under green light. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that these DEGs were mainly related to "carboxylic acid metabolic process," "enzyme activity," "carbon metabolism," and "photosynthesis and other processes." At the same time, 253 differentially expressed long non-coding RNAs (DELs) were characterized as green light responsive. We also made a detailed analysis of the responses of photosynthesis- and pigment synthesis-related genes in C. reinhardtii to green light and found that these genes exhibited obvious dynamic expression. Lastly, we constructed a co-expression regulatory network, comprising 49 long non-coding RNAs (lncRNAs) and 20 photosynthesis and pigment related genes, of which 9 mRNAs were also the predicted trans/cis-targets of 8 lncRNAs, these results suggested that lncRNAs may affect the expression of mRNAs related to photosynthesis and pigment synthesis. Our findings give a preliminary explanation of the response mechanism of C. reinhardtii to green light at the transcriptional level.
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Affiliation(s)
- Menghua Liu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Longxin Wang
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Qianqian Yu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Jialin Song
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
- Shandong University of Arts, Jinan, China
| | - Lixia Zhu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Kai-Hua Jia
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Xiaochun Qin
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China.
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2
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Huang L, Ökmen B, Stolze SC, Kastl M, Khan M, Hilbig D, Nakagami H, Djamei A, Doehlemann G. The fungal pathogen Ustilago maydis targets the maize corepressor RELK2 to modulate host transcription for tumorigenesis. THE NEW PHYTOLOGIST 2024; 241:1747-1762. [PMID: 38037456 DOI: 10.1111/nph.19448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/08/2023] [Indexed: 12/02/2023]
Abstract
Ustilago maydis is a biotrophic fungus that causes tumor formation on all aerial parts of maize. U. maydis secretes effector proteins during penetration and colonization to successfully overcome the plant immune response and reprogram host physiology to promote infection. In this study, we functionally characterized the U. maydis effector protein Topless (TPL) interacting protein 6 (Tip6). We found that Tip6 interacts with the N-terminus of RELK2 through its two Ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motifs. We show that the EAR motifs are essential for the virulence function of Tip6 and critical for altering the nuclear distribution pattern of RELK2. We propose that Tip6 mimics the recruitment of RELK2 by plant repressor proteins, thus disrupting host transcriptional regulation. We show that a large group of AP2/ERF B1 subfamily transcription factors are misregulated in the presence of Tip6. Our study suggests a regulatory mechanism where the U. maydis effector Tip6 utilizes repressive domains to recruit the corepressor RELK2 to disrupt the transcriptional networks of the host plant.
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Affiliation(s)
- Luyao Huang
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, 50674, Germany
| | - Bilal Ökmen
- Department of Microbial Interactions, IMIT/ZMBP, University of Tübingen, Tübingen, 72076, Germany
| | - Sara Christina Stolze
- Protein Mass Spectrometry, Max-Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Melanie Kastl
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, 50674, Germany
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, 53127, Germany
| | - Mamoona Khan
- Department of Plant Pathology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53115, Germany
| | - Daniel Hilbig
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, 50674, Germany
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, 53127, Germany
| | - Hirofumi Nakagami
- Protein Mass Spectrometry, Max-Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
- Basic Immune System of Plants, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Armin Djamei
- Department of Plant Pathology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, 53115, Germany
| | - Gunther Doehlemann
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, 50674, Germany
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3
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Hu M, Xie M, Cui X, Huang J, Cheng X, Liu L, Yan S, Liu S, Tong C. Characterization and Potential Function Analysis of the SRS Gene Family in Brassica napus. Genes (Basel) 2023; 14:1421. [PMID: 37510325 PMCID: PMC10379590 DOI: 10.3390/genes14071421] [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: 06/15/2023] [Revised: 07/07/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
SRS (SHI-related sequence) transcription factors play a crucial role in plant growth, development, and abiotic stress response. Although Brassica napus (B. napus) is one of the most important oil crops in the world, the role of SRS genes in B. napus (BnSRS) has not been well investigated. Therefore, we employed a bioinformatics approach to identify BnSRS genes from genomic data and investigated their characteristics, functions, and expression patterns, to gain a better understanding of how this gene family is involved in plant development and growth. The results revealed that there were 34 BnSRS gene family members in the genomic sequence of B. napus, unevenly distributed throughout the sequence. Based on the phylogenetic analysis, these BnSRS genes could be divided into four subgroups, with each group sharing comparable conserved motifs and gene structure. Analysis of the upstream promoter region showed that BnSRS genes may regulate hormone responses, biotic and abiotic stress response, growth, and development in B. napus. The protein-protein interaction analysis revealed the involvement of BnSRS genes in various biological processes and metabolic pathways. Our analysis of BnSRS gene expression showed that 23 BnSRS genes in the callus tissue exhibited a dominant expression pattern, suggesting their critical involvement in cell dedifferentiation, cell division, and tissue development. In addition, association analysis between genotype and agronomic traits revealed that BnSRS genes may be linked to some important agronomic traits in B. napus, suggesting that BnSRS genes were widely involved in the regulation of important agronomic traits (including C16.0, C18.0, C18.1, C18.2 C18.3, C20.1, C22.1, GLU, protein, TSW, and FFT). In this study, we predicted the evolutionary relationships and potential functions of BnSRS gene family members, providing a basis for the development of BnSRS gene functions which could facilitate targeted functional studies and genetic improvement for elite breeding in B. napus.
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Affiliation(s)
- Ming Hu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Meili Xie
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Xiaobo Cui
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Junyan Huang
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Xiaohui Cheng
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Lijiang Liu
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Shunping Yan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Chaobo Tong
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
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4
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Huang H, Song J, Feng Y, Zheng L, Chen Y, Luo K. Genome-Wide Identification and Expression Analysis of the SHI-Related Sequence Family in Cassava. Genes (Basel) 2023; 14:genes14040870. [PMID: 37107628 PMCID: PMC10138042 DOI: 10.3390/genes14040870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
The SHORT INTERNODES (SHI)-related sequences (SRS) are plant-specific transcription factors that have been quantitatively characterized during plant growth, regeneration, and stress responses. However, the genome-wide discovery of SRS family genes and their involvement in abiotic stress-related activities in cassava have not been documented. A genome-wide search strategy was used to identify eight family members of the SRS gene family in cassava (Manihot esculenta Crantz). Based on their evolutionary linkages, all MeSRS genes featured homologous RING-like zinc finger and IXGH domains. Genetic architecture and conserved motif analysis validated the categorization of MeSRS genes into four groups. Eight pairs of segmental duplications were detected, resulting in an increase in the number of MeSRS genes. Orthologous studies of SRS genes among cassava and three different plant species (Arabidopsis thaliana, Oryza sativa, and Populus trichocarpa) provided important insights into the probable history of the MeSRS gene family. The functionality of MeSRS genes was elucidated through the prediction of protein–protein interaction networks and cis-acting domains. RNA-seq data demonstrated tissue/organ expression selectivity and preference of the MeSRS genes. Furthermore, qRT-PCR investigation of MeSRS gene expression after exposure to salicylic acid (SA) and methyl jasmonate (MeJA) hormone treatments, as well as salt (NaCl) and osmotic (polyethylene glycol, PEG) stresses, showed their stress-responsive patterns. This genome-wide characterization and identification of the evolutionary relationships and expression profiles of the cassava MeSRS family genes will be helpful for further research into this gene family and its function in stress response. It may also assist future agricultural efforts to increase the stress tolerance of cassava.
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Affiliation(s)
- Huling Huang
- Sanya Nanfan Research Institute, School of Tropical Crops, Hainan University, Haikou 572025, China
| | - Jiming Song
- Institute of Tropical and subtropical Economic Crops, Yunnan Provincial Academy of Agricultural Sciences, Baoshan 678000, China
| | - Yating Feng
- Sanya Nanfan Research Institute, School of Tropical Crops, Hainan University, Haikou 572025, China
| | - Linling Zheng
- Sanya Nanfan Research Institute, School of Tropical Crops, Hainan University, Haikou 572025, China
| | - Yinhua Chen
- Sanya Nanfan Research Institute, School of Tropical Crops, Hainan University, Haikou 572025, China
| | - Kai Luo
- Sanya Nanfan Research Institute, School of Tropical Crops, Hainan University, Haikou 572025, China
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5
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Sun C, Yu L, Zhang S, Gu Q, Wang M. Genome-wide characterization of the SHORT INTER-NODES/STYLISH and Shi-Related Sequence family in Gossypium hirsutum and functional identification of GhSRS21 under salt stress. FRONTIERS IN PLANT SCIENCE 2023; 13:1078083. [PMID: 36684735 PMCID: PMC9846857 DOI: 10.3389/fpls.2022.1078083] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Saline stress is a significant factor that caused crop growth inhibition and yield decline. SHORT INTERNODES/STYLISH (SHI/STY) and SHI-RELATED SEQUENCE (SRS) transcription factors are specific to plants and share a conserved RING-like zinc-finger domain (CX2CX7CX4CX2C2X6C). However, the functions of SHI/STY and SRS genes in cotton responses to salt stress remain unclear. In this study, 26 GhSRSs were identified in Gossypium hirsutum, which further divided into three subgroups. Phylogenetic analysis of 88 SRSs from8 plant species revealed independent evolutionary pattern in some of SRSs derived from monocots. Conserved domain and subcellular location predication of GhSRSs suggested all of them only contained the conserved RING-like zinc-finger domain (DUF702) domain and belonged to nucleus-localized transcription factors except for the GhSRS22. Furthermore, synteny analysis showed structural variation on chromosomes during the process of cotton polyploidization. Subsequently, expression patterns of GhSRS family members in response to salt and drought stress were analyzed in G. hirsutum and identified a salt stress-inducible gene GhSRS21. The GhSRS21 was proved to localize in the nuclear and silencing it in G. hirsutum increased the cotton resistance to salt using the virus-induced gene silencing (VIGS) system. Finally, our transcriptomic data revealed that GhSRS21 negatively controlled cotton salt tolerance by regulating the balance between ROS production and scavenging. These results will increase our understanding of the SRS gene family in cotton and provide the candidate resistant gene for cotton breeding.
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Affiliation(s)
- Chendong Sun
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Li Yu
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shuojun Zhang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Qijuan Gu
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, China
| | - Mei Wang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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6
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Fang D, Zhang W, Ye Z, Hu F, Cheng X, Cao J. The plant specific SHORT INTERNODES/STYLISH (SHI/STY) proteins: Structure and functions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:685-695. [PMID: 36565613 DOI: 10.1016/j.plaphy.2022.12.018] [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: 05/24/2022] [Revised: 12/02/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
Plant specific SHORT INTERNODES/STYLISH (SHI/STY) protein is a transcription factor involved in the formation and development of early lateral organs in plants. However, research on the SHI/STY protein family is not focused enough. In this article, we review recent studies on SHI/STY genes and explore the evolution and structure of SHI/STY. The biological functions of SHI/STYs are discussed in detail in this review, and the application of each biological function to modern agriculture is discussed. All SHI/STY proteins contain typical conserved RING-like zinc finger domain and IGGH domain. SHI/STYs are involved in the formation and development of lateral root, stem extension, leaf morphogenesis, and root nodule development. They are also involved in the regulation of pistil and stamen development and flowering time. At the same time, the regulation of some GA, JA, and auxin signals also involves these family proteins. For each aspect, unanswered or poorly understood questions were identified to help define future research areas. This review will provide a basis for further functional study of this gene family.
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Affiliation(s)
- Da Fang
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Weimeng Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Ziyi Ye
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Fei Hu
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xiuzhu Cheng
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jun Cao
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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7
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Morais ERDC, de Medeiros NMC, da Silva FL, de Sousa IAL, de Oliveira IGB, Meneses CHSG, Scortecci KC. Redox homeostasis at SAM: a new role of HINT protein. PLANTA 2022; 257:12. [PMID: 36520227 DOI: 10.1007/s00425-022-04044-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
ScHINT1 was identified at sugarcane SAM using subtractive libraries. Here, by bioinformatic tools, two-hybrid approach, and biochemical assays, we proposed that its role might be associated to control redox homeostasis. Such control is important for plant development and flowering transition, and this is ensured with some protein partners such as PAL and SBT that interact with ScHINT1. The shoot apical meristem transition from vegetative to reproductive is a crucial step for plants. In sugarcane (Saccharum spp.), this process is not well known, and it has an important impact on production due to field reduction. In view of this, ScHINT1 (Sugarcane HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN) was identified previously by subtractive cDNA libraries using Shoot Apical Meristem (SAM) by our group. This protein is a member of the HIT superfamily that was composed of hydrolase with an AMP site ligation. To better understand the role of ScHINT1 in sugarcane flowering, here its function in SAM was characterized using different approaches such as bioinformatics, two-hybrid assays, transgenic plants, and biochemical assays. ScHINT1 was conserved in plants, and it was grouped into four clades (HINT1, HINT2, HINT3, and HINT4). The 3D model proposed that ScHINT1 might be active as it was able to ligate to AMP subtract. Moreover, the two-hybrid approach identified two protein interactions: subtilase and phenylalanine ammonia-lyase. The evolutionary tree highlighted the relationships that each sequence has with specific subfamilies and different proteins. The 3D models constructed reveal structure conservation when compared with other PDB-related crystals, which indicates probable functional activity for the sugarcane models assessed. The interactome analysis showed a connection to different proteins that have antioxidative functions in apical meristems. Lastly, the transgenic plants with 35S::ScHINT1_AS (anti-sense orientation) produced more flowers than wild-type or 35S::ScHINT1_S (sense). Alpha-tocopherol and antioxidant enzymes measurement showed that their levels were higher in 35S::ScHINT_S plants than in 35S::ScHINT1_AS or wild-type plants. These results proposed that ScHINT1 might have an important role with other proteins in orchestrating this complex network for plant development and flowering.
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Affiliation(s)
- Emanoelly Roberta de Carvalho Morais
- Departamento de Biologia Celular e Genética - Centro de Biociências, Universidade Federal do Rio Grande do Norte, Campus Universitário UFRN, Bairro Lagoa Nova, Natal, RN, 59072-970, Brazil
- Programa de Pós-Graduação em Bioquímica e Biologia Molecular, Universidade Federal do Rio Grande do Norte, Campus Universitário UFRN, Bairro Lagoa Nova, Natal, RN, 59072-970, Brazil
| | - Nathalia Maira Cabral de Medeiros
- Departamento de Biologia Celular e Genética - Centro de Biociências, Universidade Federal do Rio Grande do Norte, Campus Universitário UFRN, Bairro Lagoa Nova, Natal, RN, 59072-970, Brazil
- Programa de Pós-Graduação em Bioquímica e Biologia Molecular, Universidade Federal do Rio Grande do Norte, Campus Universitário UFRN, Bairro Lagoa Nova, Natal, RN, 59072-970, Brazil
| | - Francinaldo Leite da Silva
- Departamento de Biologia Celular e Genética - Centro de Biociências, Universidade Federal do Rio Grande do Norte, Campus Universitário UFRN, Bairro Lagoa Nova, Natal, RN, 59072-970, Brazil
| | - Isabel Andrade Lopes de Sousa
- Departamento de Biologia Celular e Genética - Centro de Biociências, Universidade Federal do Rio Grande do Norte, Campus Universitário UFRN, Bairro Lagoa Nova, Natal, RN, 59072-970, Brazil
- Programa de Pós-Graduação em Bioquímica e Biologia Molecular, Universidade Federal do Rio Grande do Norte, Campus Universitário UFRN, Bairro Lagoa Nova, Natal, RN, 59072-970, Brazil
| | - Izamara Gesiele Bezerra de Oliveira
- Departamento de Biologia - Centro de Ciências Biológicas e da Saúde/Programa de Pós-Graduação em Ciências Agrárias, Universidade Estadual da Paraíba, Rua Baraúnas, 351, Bairro Universitário, Campina Grande, PB, 58429-500, Brazil
| | - Carlos Henrique Salvino Gadelha Meneses
- Departamento de Biologia - Centro de Ciências Biológicas e da Saúde/Programa de Pós-Graduação em Ciências Agrárias, Universidade Estadual da Paraíba, Rua Baraúnas, 351, Bairro Universitário, Campina Grande, PB, 58429-500, Brazil
| | - Katia Castanho Scortecci
- Departamento de Biologia Celular e Genética - Centro de Biociências, Universidade Federal do Rio Grande do Norte, Campus Universitário UFRN, Bairro Lagoa Nova, Natal, RN, 59072-970, Brazil.
- Programa de Pós-Graduação em Bioquímica e Biologia Molecular, Universidade Federal do Rio Grande do Norte, Campus Universitário UFRN, Bairro Lagoa Nova, Natal, RN, 59072-970, Brazil.
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8
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Ma B, Nian L, Ain NU, Liu X, Yang Y, Zhu X, Haider FU, Lv Y, Bai P, Zhang X, Li Q, Mao Z, Xue Z. Genome-Wide Identification and Expression Profiling of the SRS Gene Family in Melilotus albus Reveals Functions in Various Stress Conditions. PLANTS (BASEL, SWITZERLAND) 2022; 11:3101. [PMID: 36432830 PMCID: PMC9693462 DOI: 10.3390/plants11223101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/06/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
The plant-specific SHI-related sequence (SRS) family of transcription factors plays a vital role in growth regulation, plant development, phytohormone biosynthesis, and stress response. However, the genome-wide identification and role in the abiotic stress-related functions of the SRS gene family were not reported in white sweet clover (Melilotus albus). In this study, nine M. albus SRS genes (named MaSRS01-MaSRS09) were identified via a genome-wide search method. All nine genes were located on six out of eight chromosomes in the genome of M. albus and duplication analysis indicated eight segmentally duplicated genes in the MaSRS family. These MaSRS genes were classified into six groups based on their phylogenetic relationships. The gene structure and motif composition results indicated that MaSRS members in the same group contained analogous intron/exon and motif organizations. Further, promoter region analysis of MaSRS genes uncovered various growth, development, and stress-responsive cis-acting elements. Protein interaction networks showed that each gene has both functions of interacting with other genes and members within the family. Moreover, real-time quantitative PCR was also performed to verify the expression patterns of nine MaSRS genes in the leaves of M. albus. The results showed that nine MaSRSs were up- and down-regulated at different time points after various stress treatments, such as salinity, low-temperature, salicylic acid (SA), and methyl jasmonate (MeJA). This is the first systematic study of the M. albus SRS gene family, and it can serve as a strong foundation for further elucidation of the stress response and physiological improvement of the growth functions in M. albus.
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Affiliation(s)
- Biao Ma
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
| | - Lili Nian
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China
| | - Noor ul Ain
- Centre of Genomics and Biotechnology, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China
| | - Xuelu Liu
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China
| | - Yingbo Yang
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaolin Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Fasih Ullah Haider
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Ying Lv
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
| | - Pengpeng Bai
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaoning Zhang
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China
| | - Quanxi Li
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
| | - Zixuan Mao
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
| | - Zongyang Xue
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
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9
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Zhu X, Wang B, Wang X, Wei X. Genome-wide identification, structural analysis and expression profiles of short internodes related sequence gene family in quinoa. Front Genet 2022; 13:961925. [PMID: 36072673 PMCID: PMC9443693 DOI: 10.3389/fgene.2022.961925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 07/01/2022] [Indexed: 11/27/2022] Open
Abstract
Based on the whole genome data information of Chenopodium quinoa Willd, the CqSRS gene family members were systematically identified and analyzed by bioinformatics methods, and the responses of CqSRS genes to NaCl (100 mmol/L), salicylic acid (200 umol/L) and low temperature (4°C) were detected by qRT-PCR. The results showed that a total of 10 SHI related sequence genes were identified in quinoa, and they were distributed on 9 chromosomes, and there were four pairs of duplicated genes. The number of amino acids encoded ranged from 143 aa to 370 aa, and the isoelectric point ranged from 4.81 to 8.90. The secondary structure was mainly composed of random coil (Cc). Most of the SRS gene encoding proteins were located in the cytoplasm (5 CqSRS). Phylogenetic analysis showed that the CqSRS genes were divided into three groups, and the gene structure showed that the number of exons of CqSRS was between two-five. Promoter analysis revealed that there are a total of 44 elements related to plant hormone response elements, light response elements, stress response elements and tissue-specific expression in the upstream regin of the gene. Protein interaction showed that all 10 CqSRS proteins appeared in the known protein interaction network diagram in Arabidopsis. Expression profile analysis showed that CqSRS genes had different expression patterns, and some genes had tissue-specific expression. qRT-PCR showed that all SRS family genes responded to ABA、NaCl、drought and low-temperature treatments, but the expression levels of different CqSRS genes were significantly different under various stresses. This study lays a foundation for further analyzed the function of CqSRS genes.
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Affiliation(s)
- Xiaolin Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Baoqiang Wang
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xian Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaohong Wei
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Xiaohong Wei,
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10
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Lim PK, Zheng X, Goh JC, Mutwil M. Exploiting plant transcriptomic databases: Resources, tools, and approaches. PLANT COMMUNICATIONS 2022; 3:100323. [PMID: 35605200 PMCID: PMC9284291 DOI: 10.1016/j.xplc.2022.100323] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/03/2022] [Accepted: 04/06/2022] [Indexed: 05/11/2023]
Abstract
There are now more than 300 000 RNA sequencing samples available, stemming from thousands of experiments capturing gene expression in organs, tissues, developmental stages, and experimental treatments for hundreds of plant species. The expression data have great value, as they can be re-analyzed by others to ask and answer questions that go beyond the aims of the study that generated the data. Because gene expression provides essential clues to where and when a gene is active, the data provide powerful tools for predicting gene function, and comparative analyses allow us to study plant evolution from a new perspective. This review describes how we can gain new knowledge from gene expression profiles, expression specificities, co-expression networks, differential gene expression, and experiment correlation. We also introduce and demonstrate databases that provide user-friendly access to these tools.
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Affiliation(s)
- Peng Ken Lim
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Xinghai Zheng
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Jong Ching Goh
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Marek Mutwil
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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11
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Genome-Wide Profiling of Alternative Splicing and Gene Fusion during Rice Black-Streaked Dwarf Virus Stress in Maize (Zea mays L.). Genes (Basel) 2022; 13:genes13030456. [PMID: 35328010 PMCID: PMC8955601 DOI: 10.3390/genes13030456] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/28/2022] [Accepted: 02/28/2022] [Indexed: 12/26/2022] Open
Abstract
Rice black-streaked dwarf virus (RBSDV) causes maize rough dwarf disease (MRDD), which is a viral disease that significantly affects maize yields worldwide. Plants tolerate stress through transcriptional reprogramming at the alternative splicing (AS), transcriptional, and fusion gene (FG) levels. However, it is unclear whether and how AS and FG interfere with transcriptional reprogramming in MRDD. In this study, we performed global profiling of AS and FG on maize response to RBSDV and compared it with transcriptional changes. There are approximately 1.43 to 2.25 AS events per gene in maize infected with RBSDV. GRMZM2G438622 was only detected in four AS modes (A3SS, A5SS, RI, and SE), whereas GRMZM2G059392 showed downregulated expression and four AS events. A total of 106 and 176 FGs were detected at two time points, respectively, including six differentially expressed genes and five differentially spliced genes. The gene GRMZM2G076798 was the only FG that occurred at two time points and was involved in two FG events. Among these, 104 GOs were enriched, indicating that nodulin-, disease resistance-, and chloroplastic-related genes respond to RBSDV stress in maize. These results provide new insights into the mechanisms underlying post-transcriptional and transcriptional regulation of maize response to RBSDV stress.
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Xanthopoulou A, Moysiadis T, Bazakos C, Karagiannis E, Karamichali I, Stamatakis G, Samiotaki M, Manioudaki M, Michailidis M, Madesis P, Ganopoulos I, Molassiotis A, Tanou G. The perennial fruit tree proteogenomics atlas: a spatial map of the sweet cherry proteome and transcriptome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1319-1336. [PMID: 34842310 DOI: 10.1111/tpj.15612] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
Genome-wide transcriptome analysis provides systems-level insights into plant biology. Due to the limited depth of quantitative proteomics our understanding of gene-protein-complex stoichiometry is largely unknown in plants. Recently, the complexity of the proteome and its cell-/tissue-specific distribution have boosted the research community to the integration of transcriptomics and proteomics landscapes in a proteogenomic approach. Herein, we generated a quantitative proteome and transcriptome abundance atlas of 15 major sweet cherry (Prunus avium L., cv 'Tragana Edessis') tissues represented by 29 247 genes and 7584 proteins. Additionally, 199 984 alternative splicing events, particularly exon skipping and alternative 3' splicing, were identified in 23 383 transcribed regions of the analyzed tissues. Common signatures as well as differences between mRNA and protein quantities, including genes encoding transcription factors and allergens, within and across the different tissues are reported. Using our integrated dataset, we identified key putative regulators of fruit development, notably genes involved in the biosynthesis of anthocyanins and flavonoids. We also provide proteogenomic-based evidence for the involvement of ethylene signaling and pectin degradation in cherry fruit ripening. Moreover, clusters of genes and proteins with similar and different expression and suppression trends across diverse tissues and developmental stages revealed a relatively low RNA abundance-to-protein correlation. The present proteogenomic analysis allows us to identify 17 novel sweet cherry proteins without prior protein-level annotation evidenced in the currently available databases. To facilitate use by the community, we also developed the Sweet Cherry Atlas Database (https://grcherrydb.com/) for viewing and data mining these resources. This work provides new insights into the proteogenomics workflow in plants and a rich knowledge resource for future investigation of gene and protein functions in Prunus species.
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Affiliation(s)
- Aliki Xanthopoulou
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki-Thermi, 57001, Greece
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thessaloniki-Thermi, 57001, Greece
| | - Theodoros Moysiadis
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki-Thermi, 57001, Greece
- Department of Computer Science, School of Sciences and Engineering, University of Nicosia, Nicosia, 2417, Cyprus
| | - Christos Bazakos
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thessaloniki-Thermi, 57001, Greece
- Joint Laboratory of Horticulture, ELGO-DIMITRA, Thessaloniki-Thermi, 57001, Greece
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne, 50829, Germany
| | - Evangelos Karagiannis
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki-Thermi, 57001, Greece
| | - Ioanna Karamichali
- Institute of Applied Biosciences, CERTH, Thessaloniki-Thermi, 57001, Greece
| | - George Stamatakis
- Institute of Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Vari, 16672, Greece
| | - Martina Samiotaki
- Institute of Bioinnovation, Biomedical Sciences Research Center "Alexander Fleming", Vari, 16672, Greece
| | - Maria Manioudaki
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki-Thermi, 57001, Greece
| | - Michail Michailidis
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki-Thermi, 57001, Greece
| | - Panagiotis Madesis
- Institute of Applied Biosciences, CERTH, Thessaloniki-Thermi, 57001, Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thessaloniki-Thermi, 57001, Greece
- Joint Laboratory of Horticulture, ELGO-DIMITRA, Thessaloniki-Thermi, 57001, Greece
| | - Athanassios Molassiotis
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki-Thermi, 57001, Greece
| | - Georgia Tanou
- Joint Laboratory of Horticulture, ELGO-DIMITRA, Thessaloniki-Thermi, 57001, Greece
- Institute of Soil and Water Resources, ELGO-DIMITRA, Thessaloniki-Thermi, 57001, Greece
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