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Nørrevang AF, Shabala S, Palmgren M. A two-sequence motif-based method for the inventory of gene families in fragmented and poorly annotated genome sequences. BMC Genomics 2024; 25:26. [PMID: 38172704 PMCID: PMC10763278 DOI: 10.1186/s12864-023-09859-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024] Open
Abstract
Databases of genome sequences are growing exponentially, but, in some cases, assembly is incomplete and genes are poorly annotated. For evolutionary studies, it is important to identify all members of a given gene family in a genome. We developed a method for identifying most, if not all, members of a gene family from raw genomes in which assembly is of low quality, using the P-type ATPase superfamily as an example. The method is based on the translation of an entire genome in all six reading frames and the co-occurrence of two family-specific sequence motifs that are in close proximity to each other. To test the method's usability, we first used it to identify P-type ATPase members in the high-quality annotated genome of barley (Hordeum vulgare). Subsequently, after successfully identifying plasma membrane H+-ATPase family members (P3A ATPases) in various plant genomes of varying quality, we tested the hypothesis that the number of P3A ATPases correlates with the ability of the plant to tolerate saline conditions. In 19 genomes of glycophytes and halophytes, the total number of P3A ATPase genes was found to vary from 7 to 22, but no significant difference was found between the two groups. The method successfully identified P-type ATPase family members in raw genomes that are poorly assembled.
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Affiliation(s)
- Anton Frisgaard Nørrevang
- NovoCrops Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, DK-1871, Denmark
| | - Sergey Shabala
- School of Biological Sciences, University of Western Australia, Crawley, WA6009, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, 528000, China
| | - Michael Palmgren
- NovoCrops Center, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C, DK-1871, Denmark.
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Zhou Y, Xu K, Gao H, Yao W, Zhang Y, Zhang Y, Azhar Hussain M, Wang F, Yang X, Li H. Comparative Proteomic Analysis of Two Wild Soybean ( Glycine soja) Genotypes Reveals Positive Regulation of Saline-Alkaline Stress Tolerance by Tonoplast Transporters. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:14109-14124. [PMID: 37749803 DOI: 10.1021/acs.jafc.3c02111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Soil saline-alkalization is a significant constraint for soybean production. Owing to higher genetic diversity of wild soybean, we compared the proteomic landscape of saline-alkaline stress-tolerant (SWBY032) and stress-sensitive (SWLJ092) wild soybean (Glycine soja) strains under saline and saline-alkaline stress. Out of 346 differentially expressed proteins (DEPs) specifically involved in saline-alkaline stress, 159 and 133 DEPs were identified in only SWLJ092 and SWBY032, respectively. Functional annotations revealed that more ribosome proteins were downregulated in SWLJ092, whereas more membrane transporters were upregulated in SWBY032. Moreover, protein-protein interaction analysis of 133 DEPs revealed that 14 protein-synthesis- and 2 TCA-cycle-related DEPs might alter saline-alkaline tolerance by affecting protein synthesis and amino acid metabolism. Furthermore, we confirmed G. soja tonoplast intrinsic protein (GsTIP2-1 and GsTIP2-2), inositol transporter (GsINT1), sucrose transport protein (GsSUC4), and autoinhibited Ca2+-ATPase (GsACA11) as tonoplast transporters can synergistically improve saline-alkaline tolerance in soybean, possibly by relieving the inhibition of protein synthesis and amino acid metabolism. Overall, our findings provided a foundation for molecular breeding of a saline-alkaline stress-tolerant soybean.
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Affiliation(s)
- Yonggang Zhou
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 570288, China
| | - Keheng Xu
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
| | - Hongtao Gao
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 570288, China
| | - Wenbo Yao
- College of Tropical Crops, Hainan University, Haikou 570288, China
| | - Yinhe Zhang
- College of Tropical Crops, Hainan University, Haikou 570288, China
| | - Yuntong Zhang
- College of Tropical Crops, Hainan University, Haikou 570288, China
| | - Muhammad Azhar Hussain
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 570288, China
| | - Fawei Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Xinquan Yang
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, China
| | - Haiyan Li
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 570288, China
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Tasnim A, Jahan I, Azim T, Karmoker D, Seraj ZI. Paired growth of cultivated and halophytic wild rice under salt stress induces bacterial endophytes and gene expression responses. FRONTIERS IN PLANT SCIENCE 2023; 14:1244743. [PMID: 37746015 PMCID: PMC10516563 DOI: 10.3389/fpls.2023.1244743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/17/2023] [Indexed: 09/26/2023]
Abstract
Introduction Utilizing salt-affected marginal lands in coastal regions can help meet the growing demand for rice. We explored a nature-based solution involving wild halophytic rice (O. coarctata, Oc) and commercial rice BRRI Dhan 67 (O. sativa, Os) grown in close proximity to each other under salt stress. Methods This was to investigate whether a paired planting strategy could help complement rice growth and yield under stress. We also investigated the gene expression and endophytic bacterial profiles of both Os and Oc in unpaired and paired conditions without and with salt. Results Paired plants exhibited lower salt damage indicators such as smaller reduction in plant height, electrolyte leakage and chlorophyll loss, as well as higher K+/Na+ ratio under saline stress. Some of the 39 endophytic bacteria in the mutualism experiment were unique to Oc and transferred to Os when paired. Differentially expressed genes in leaves of paired Os versus unpaired Os were 1097 (994 up-regulated, 101 down-regulated) without salt and 893 (763 up-regulated, 130 down-regulated) under salt stress. The presence of Oc plants under salt stress influenced major biological processes in Os, including oxidative stress; chitinase activity; phenylalanine catabolic process and response to ABA. Protein binding and serine/threonine kinase activity were primarily affected in molecular function. The downregulated WRKY transcription factor 22 in paired conditions under salt stress played a role in the MAPK signaling pathway, reducing respiratory cell death. The upregulated auxin-responsive protein IAA18 gene, involved in hormone signaling and cell enlargement, was present only in paired plants. Discussion Our findings therefore, offer insights into developing more effective cultivation strategies for sustainable rice production.
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Wang X, Komatsu S. Subcellular Proteomics to Elucidate Soybean Response to Abiotic Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:2865. [PMID: 37571018 PMCID: PMC10421527 DOI: 10.3390/plants12152865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/13/2023]
Abstract
Climate change jeopardizes soybean production by declining seed yield and quality. In this review, the morphophysiological alterations of soybean in response to abiotic stress are summarized, followed by illustrations of cellular metabolisms and regulatory mechanisms to organellar stress based on subcellular proteomics. This highlights the communications associated with reactive oxygen species scavenging, molecular chaperones, and phytohormone signals among subcellular compartments. Given the complexity of climate change and the limitations of plants in coping with multiple abiotic stresses, a generic response to environmental constraints is proposed between calcium and abscisic acid signals in subcellular organelles. This review summarizes the findings of subcellular proteomics in stressed soybean and discusses the future prospects of subcellular proteomics for promoting the improvement of climate-tolerant crops.
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Affiliation(s)
- Xin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China;
| | - Setsuko Komatsu
- Faculty of Environmental and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
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Wang H, Cheng X, Yin D, Chen D, Luo C, Liu H, Huang C. Advances in the Research on Plant WRKY Transcription Factors Responsive to External Stresses. Curr Issues Mol Biol 2023; 45:2861-2880. [PMID: 37185711 PMCID: PMC10136515 DOI: 10.3390/cimb45040187] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/20/2023] [Accepted: 03/23/2023] [Indexed: 04/05/2023] Open
Abstract
The WRKY transcription factors are a class of transcriptional regulators that are ubiquitous in plants, wherein they play key roles in various physiological activities, including responses to stress. Specifically, WRKY transcription factors mediate plant responses to biotic and abiotic stresses through the binding of their conserved domain to the W-box element of the target gene promoter and the subsequent activation or inhibition of transcription (self-regulation or cross-regulation). In this review, the progress in the research on the regulatory effects of WRKY transcription factors on plant responses to external stresses is summarized, with a particular focus on the structural characteristics, classifications, biological functions, effects on plant secondary metabolism, regulatory networks, and other aspects of WRKY transcription factors. Future research and prospects in this field are also proposed.
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Affiliation(s)
- Hongli Wang
- College of Ecology, Shanghai Institute of Technology, Shanghai 201418, China
| | - Xi Cheng
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Dongmei Yin
- College of Ecology, Shanghai Institute of Technology, Shanghai 201418, China
| | - Dongliang Chen
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Chang Luo
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Hua Liu
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Conglin Huang
- Beijing Engineering Research Center of Functional Floriculture, Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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