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Zhang S, Yan C, Lu T, Fan Y, Ren Y, Zhao J, Shan X, Guan Y, Song P, Li D, Hu H. New insights into molecular features of the genome-wide AOX family and their responses to various stresses in common wheat (Triticum aestivum L.). Gene 2023; 888:147756. [PMID: 37659597 DOI: 10.1016/j.gene.2023.147756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 08/22/2023] [Accepted: 08/31/2023] [Indexed: 09/04/2023]
Abstract
Alternative oxidase (AOX) is an important terminal oxidase involved in the alternative oxidation pathway in plants, which is closely related to various biotic and abiotic stress responses. However, a comprehensive research on AOX gene family of wheat is still lacking. In this study, the members of wheat AOX (TaAOX) family were identified, and their molecular characteristics and gene expression patterns were systematically investigated. Seventeen TaAOX genes were identified from Chinese Spring (CS) genome, which were mapped on 7 chromosomes and mainly clustered on the long arm's distal end of the second homologous groups. Phylogenetic analysis showed that TaAOX genes were classified into four subgroups (Ia, Ib, Ic, and Id), and the Ia subgroup possessed the most members. Tandem duplication and segmental duplication events were found during the evolution of TaAOX genes and they were affected by purifying selection demonstrated by Ka/Ks analysis. The exon numbers of this family gene varied greatly from 1 to 9. Except for Ta3BSAOX14, all the proteins encoded by the other 16 TaAOX genes contained the amino acid residues of the key active sites in the AOX domain (cd01053). The expression patterns of TaAOX genes in various tissues and under abiotic and biotic stresses were analyzed using public transcriptome data, furthermore, qRT-PCR analysis was performed for some selected TaAOX genes, and the results suggested that most members of this gene family play an important role in response to different stresses in common wheat. Our results provide basic information and valuable reference for further exploring the gene function of TaAOX family by using gene editing, RNAi, VIGS, and other technologies.
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Affiliation(s)
- Shengli Zhang
- School of Life Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China; Henan Engineering Research Center of Crop Genome Editing, Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, Henan, China.
| | - Cuiping Yan
- School of Life Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China; Henan Engineering Research Center of Crop Genome Editing, Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, Henan, China
| | - Tairui Lu
- School of Life Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China; Henan Engineering Research Center of Crop Genome Editing, Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, Henan, China
| | - Yuchao Fan
- School of Life Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China; Henan Engineering Research Center of Crop Genome Editing, Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, Henan, China
| | - Yueming Ren
- School of Life Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China; Henan Engineering Research Center of Crop Genome Editing, Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, Henan, China
| | - Jishun Zhao
- School of Life Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China; Henan Engineering Research Center of Crop Genome Editing, Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, Henan, China
| | - Xiaojing Shan
- School of Life Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China; Henan Engineering Research Center of Crop Genome Editing, Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, Henan, China
| | - Yuanyuan Guan
- School of Life Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China; Henan Engineering Research Center of Crop Genome Editing, Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, Henan, China
| | - Puwen Song
- School of Life Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China; Henan Engineering Research Center of Crop Genome Editing, Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, Henan, China
| | - Dongfang Li
- School of Resource and Environmental Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Haiyan Hu
- School of Life Sciences, Henan Institute of Science and Technology, Xinxiang, Henan, China; Henan Engineering Research Center of Crop Genome Editing, Henan Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, Henan, China
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Zhao X, Qu D, Wang L, Gao Y, An N, Wang A, Li Y, Yang J, Wu F, Su H. Genome-wide identification of cysteine-rich receptor-like kinases in sweet cherry reveals that PaCRK1 enhances sweet cherry resistance to salt stress. Plant Cell Rep 2022; 41:2037-2088. [PMID: 35904590 DOI: 10.1007/s00299-022-02907-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Forty PaCRKs have been identified from sweet cherry and overexpression PaCRK1 in sweet cherry enhances its resistance to salt stress. Cysteine-rich receptor-like kinases (CRKs), a large subgroup of the receptor-like kinases, play an important role in plant development and stress response. However, knowledge about CRKs and its function against adverse environmental stresses in sweet cherry were lacking. In this study, 40 PaCRKs were identified from sweet cherry (Prunus avium) genome database. Phylogenetic analysis indicated that PaCRKs could be classified into six subgroups. Transcriptome analysis showed that the expression levels of most PaCRKs were changed under external environmental stresses. Functional study showed that PaCRK1 overexpression could enhance Arabidopsis and sweet cherry tolerance to salt stress. Moreover, biochemical analysis showed that PaCRK1 increased salt tolerance of sweet cherry by regulating the expression of antioxidation-related genes and their enzyme activities. This study provides a comprehensive understanding of PaCRKs in sweet cherry and elucidates the potential role of PaCRKs in response to various environmental stimuli.
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Affiliation(s)
- Xiaohui Zhao
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Dehui Qu
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Lei Wang
- College of Life Sciences, Ludong University, Yantai, 264025, China
| | - Yuanhui Gao
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Ningning An
- Yantai Laishan Garden Construction and Maintenance Center, Yantai, 264003, China
| | - Aiping Wang
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Yaxin Li
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Jingjing Yang
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Fanlin Wu
- School of Agriculture, Ludong University, Yantai, 264025, China.
| | - Hongyan Su
- School of Agriculture, Ludong University, Yantai, 264025, China.
- The Institute of Ecological Garden, Ludong University, Yantai, 264025, China.
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Brew-Appiah RAT, Peracchi LM, Sanguinet KA. Never the Two Shall Mix: Robust Indel Markers to Ensure the Fidelity of Two Pivotal and Closely-Related Accessions of Brachypodium distachyon. Plants (Basel) 2019; 8:plants8060153. [PMID: 31174296 PMCID: PMC6630600 DOI: 10.3390/plants8060153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 05/30/2019] [Accepted: 06/05/2019] [Indexed: 11/25/2022]
Abstract
Brachypodium distachyon is an established model for monocotyledonous plants. Numerous markers intended for gene discovery and population genetics have been designed. However to date, very few indel markers with larger and easily scored length polymorphism differences, that distinguish between the two morphologically similar and highly utilized B. distachyon accessions, Bd21, the reference genome accession, and Bd21-3, the transformation-optimal accession, are publically available. In this study, 22 indel markers were designed and utilized to produce length polymorphism differences of 150 bp or more, for easy discrimination between Bd21 and Bd21-3. When tested on four other B. distachyon accessions, one case of multiallelism was observed. It was also shown that the markers could be used to determine homozygosity and heterozygosity at specific loci in a Bd21 x Bd3-1 F2 population. The work done in this study allows researchers to maintain the fidelity of Bd21 and Bd21-3 stocks for both transgenic and nontransgenic studies. It also provides markers that can be utilized in conjunction with others already available for further research on population genetics, gene discovery and gene characterization, all of which are necessary for the relevance of B. distachyon as a model species.
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Affiliation(s)
- Rhoda A T Brew-Appiah
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
| | - Luigi M Peracchi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
| | - Karen A Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
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Ebiloma GU, Balogun EO, Cueto-Díaz EJ, de Koning HP, Dardonville C. Alternative oxidase inhibitors: Mitochondrion-targeting as a strategy for new drugs against pathogenic parasites and fungi. Med Res Rev 2019; 39:1553-1602. [PMID: 30693533 DOI: 10.1002/med.21560] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/07/2018] [Accepted: 12/08/2018] [Indexed: 12/11/2022]
Abstract
The alternative oxidase (AOX) is a ubiquitous terminal oxidase of plants and many fungi, catalyzing the four-electron reduction of oxygen to water alongside the cytochrome-based electron transfer chain. Unlike the classical electron transfer chain, however, the activity of AOX does not generate adenosine triphosphate but has functions such as thermogenesis and stress response. As it lacks a mammalian counterpart, it has been investigated intensely in pathogenic fungi. However, it is in African trypanosomes, which lack cytochrome-based respiration in their infective stages, that trypanosome alternative oxidase (TAO) plays the central and essential role in their energy metabolism. TAO was validated as a drug target decades ago and among the first inhibitors to be identified was salicylhydroxamic acid (SHAM), which produced the expected trypanocidal effects, especially when potentiated by coadministration with glycerol to inhibit anaerobic energy metabolism as well. However, the efficacy of this combination was too low to be of practical clinical use. The antibiotic ascofuranone (AF) proved a much stronger TAO inhibitor and was able to cure Trypanosoma vivax infections in mice without glycerol and at much lower doses, providing an important proof of concept milestone. Systematic efforts to improve the SHAM and AF scaffolds, aided with the elucidation of the TAO crystal structure, provided detailed structure-activity relationship information and reinvigorated the drug discovery effort. Recently, the coupling of mitochondrion-targeting lipophilic cations to TAO inhibitors has dramatically improved drug targeting and trypanocidal activity while retaining target protein potency. These developments appear to have finally signposted the way to preclinical development of TAO inhibitors.
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Affiliation(s)
- Godwin U Ebiloma
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan.,Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Emmanuel O Balogun
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria.,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | | | - Harry P de Koning
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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Quezada EH, García GX, Arthikala MK, Melappa G, Lara M, Nanjareddy K. Cysteine-Rich Receptor-Like Kinase Gene Family Identification in the Phaseolus Genome and Comparative Analysis of Their Expression Profiles Specific to Mycorrhizal and Rhizobial Symbiosis. Genes (Basel) 2019; 10:genes10010059. [PMID: 30658517 PMCID: PMC6356535 DOI: 10.3390/genes10010059] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/06/2019] [Accepted: 01/09/2019] [Indexed: 01/03/2023] Open
Abstract
Receptor-like kinases (RLKs) are conserved upstream signaling molecules that regulate several biological processes, including plant development and stress adaptation. Cysteine (C)-rich receptor-like kinases (CRKs) are an important class of RLK that play vital roles in disease resistance and cell death in plants. Genome-wide analyses of CRK genes have been carried out in Arabidopsis and rice, while functional characterization of some CRKs has been carried out in wheat and tomato in addition to Arabidopsis. A comprehensive analysis of the CRK gene family in leguminous crops has not yet been conducted, and our understanding of their roles in symbiosis is rather limited. Here, we report the comprehensive analysis of the PhaseolusCRK gene family, including identification, sequence similarity, phylogeny, chromosomal localization, gene structures, transcript expression profiles, and in silico promoter analysis. Forty-six CRK homologs were identified and phylogenetically clustered into five groups. Expression analysis suggests that PvCRK genes are differentially expressed in both vegetative and reproductive tissues. Further, transcriptomic analysis revealed that shared and unique CRK genes were upregulated during arbuscular mycorrhizal and rhizobial symbiosis. Overall, the systematic analysis of the PvCRK gene family provides valuable information for further studies on the biological roles of CRKs in various Phaseolus tissues during diverse biological processes, including Phaseolus-mycorrhiza/rhizobia symbiosis.
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Affiliation(s)
- Elsa-Herminia Quezada
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León-Universidad Nacional Autónoma de México (UNAM), C.P. 37684 León, Mexico.
| | - Gabriel-Xicoténcatl García
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León-Universidad Nacional Autónoma de México (UNAM), C.P. 37684 León, Mexico.
| | - Manoj-Kumar Arthikala
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León-Universidad Nacional Autónoma de México (UNAM), C.P. 37684 León, Mexico.
| | - Govindappa Melappa
- Department of Biotechnology, Dayananda Sagar College of Engineering, Shavige Malleshwara Hills, Kumaraswamy Layout, Bengaluru 560 078, India.
| | - Miguel Lara
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), C.P. 62271 Cuernavaca, Mexico.
| | - Kalpana Nanjareddy
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León-Universidad Nacional Autónoma de México (UNAM), C.P. 37684 León, Mexico.
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Brew-Appiah RAT, Sanguinet KA. Considerations of AOX Functionality Revealed by Critical Motifs and Unique Domains. Int J Mol Sci 2018; 19:ijms19102972. [PMID: 30274246 PMCID: PMC6213860 DOI: 10.3390/ijms19102972] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 09/14/2018] [Accepted: 09/28/2018] [Indexed: 12/28/2022] Open
Abstract
An understanding of the genes and mechanisms regulating environmental stress in crops is critical for boosting agricultural yield and safeguarding food security. Under adverse conditions, response pathways are activated for tolerance or resistance. In multiple species, the alternative oxidase (AOX) genes encode proteins which help in this process. Recently, this gene family has been extensively investigated in the vital crop plants, wheat, barley and rice. Cumulatively, these three species and/or their wild ancestors contain the genes for AOX1a, AOX1c, AOX1e, and AOX1d, and common patterns in the protein isoforms have been documented. Here, we add more information on these trends by emphasizing motifs that could affect expression, and by utilizing the most recent discoveries from the AOX isoform in Trypanosoma brucei to highlight clade-dependent biases. The new perspectives may have implications on how the AOX gene family has evolved and functions in monocots. The common or divergent amino acid substitutions between these grasses and the parasite are noted, and the potential effects of these changes are discussed. There is the hope that the insights gained will inform the way future AOX research is performed in monocots, in order to optimize crop production for food, feed, and fuel.
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Affiliation(s)
- Rhoda A T Brew-Appiah
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
| | - Karen A Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
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