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Manzoor MA, Sabir IA, Shah IH, Wang H, Yu Z, Rasool F, Mazhar MZ, Younas S, Abdullah M, Cai Y. Comprehensive Comparative Analysis of the GATA Transcription Factors in Four Rosaceae Species and Phytohormonal Response in Chinese Pear ( Pyrus bretschneideri) Fruit. Int J Mol Sci 2021; 22:12492. [PMID: 34830372 PMCID: PMC8618624 DOI: 10.3390/ijms222212492] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 12/16/2022] Open
Abstract
The GATA gene family is one of the most important transcription factors (TFs). It extensively exists in plants, contributes to diverse biological processes such as the development process, and responds to environmental stress. Although the GATA gene family has been comprehensively and systematically studied in many species, less is known about GATA genes in Chinese pears (Pyrus bretschneideri). In the current study, the GATA gene family in the four Rosaceae genomes was identified, its structural characteristics identified, and a comparative analysis of its properties was carried out. Ninety-two encoded GATA proteins were authenticated in the four Rosaceae genomes (Pyrus bretschneideri, Prunus avium, Prunus mume, and Prunus persica) and categorized into four subfamilies (Ⅰ-Ⅳ) according to phylogeny. The majority of GATA genes contained one to two introns and conserved motif composition analysis revealed their functional divergence. Whole-genome duplications (WGDs) and dispersed duplication (DSD) played a key role in the expansion of the GATA gene family. The microarray indicated that, among P. bretschneideri, P. avium, P. mume and P. persica, GATA duplicated regions were more conserved between Pyrus bretschneideri and Prunus persica with 32 orthologous genes pairs. The physicochemical parameters, duplication patterns, non-synonymous (ka), and synonymous mutation rate (ks) and GO annotation ontology were performed using different bioinformatics tools. cis-elements respond to various phytohormones, abiotic/biotic stress, and light-responsive were found in the promoter regions of GATA genes which were induced via stimuli. Furthermore, subcellular localization of the PbGATA22 gene product was investigated, showing that it was present in the nucleus of tobacco (Nicotiana tabacum) epidermal cells. Finally, in silico analysis was performed on various organs (bud, leaf, stem, ovary, petal, and sepal) and different developmental stages of fruit. Subsequently, the expression profiles of PbGATA genes were extensively expressed under exogenous hormonal treatments of SA (salicylic acid), MeJA (methyl jasmonate), and ABA (abscisic acid) indicating that play important role in hormone signaling pathways. A comprehensive analysis of GATA transcription factors was performed through systematic biological approaches and comparative genomics to establish a theoretical base for further structural and functional investigations in Rosaceae species.
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Affiliation(s)
- Muhammad Aamir Manzoor
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (M.A.M.); (H.W.); (Z.Y.)
| | - Irfan Ali Sabir
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (I.A.S.); (I.H.S.)
| | - Iftikhar Hussain Shah
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (I.A.S.); (I.H.S.)
| | - Han Wang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (M.A.M.); (H.W.); (Z.Y.)
| | - Zhao Yu
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (M.A.M.); (H.W.); (Z.Y.)
| | - Faiz Rasool
- Gulab Davi Education Institute, Lahore 200240, Pakistan;
| | - Muhammad Zaid Mazhar
- Department of Agriculture, University of Agriculture, Faisalabad 38000, Pakistan;
| | - Shoaib Younas
- Department of Food Science and Technology, University of Central Punjab, Lahore 200240, Pakistan;
| | - Muhammad Abdullah
- Queenland Alliance of Agriculture and Food Innovation, The University of Queensland, Brisbane 4072, Australia;
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (M.A.M.); (H.W.); (Z.Y.)
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González J, Castillo R, García-Campos MA, Noriega-Samaniego D, Escobar-Sánchez V, Romero-Aguilar L, Alba-Lois L, Segal-Kischinevzky C. Tolerance to Oxidative Stress in Budding Yeast by Heterologous Expression of Catalases A and T from Debaryomyces hansenii. Curr Microbiol 2020; 77:4000-4015. [PMID: 33064189 DOI: 10.1007/s00284-020-02237-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 10/01/2020] [Indexed: 01/24/2023]
Abstract
The function of catalases A and T from the budding yeast Saccharomyces cerevisiae (ScCta1 and ScCtt1) is to decompose hydrogen peroxide (H2O2) to mitigate oxidative stress. Catalase orthologs are widely found in yeast, suggesting that scavenging H2O2 is crucial to avoid the oxidative damage caused by reactive oxygen species (ROS). However, the function of catalase orthologs has not yet been experimentally characterized in vivo. Here, we heterologously expressed Debaryomyces hansenii DhCTA1 and DhCTT1 genes, encoding ScCta1 and ScCtt1 orthologs, respectively, in a S. cerevisiae acatalasemic strain (cta1Δ ctt1Δ). We performed a physiological analysis evaluating growth, catalase activity, and H2O2 tolerance of the strains grown with glucose or ethanol as carbon source, as well as under NaCl stress. We found that both genes complement the catalase function in S. cerevisiae. Particularly, the strain harboring DhCTT1 showed improved growth when ethanol was used as carbon source both in the absence or presence of salt stress. This phenotype is attributed to the high catalase activity of DhCtt1 detected at the exponential growth phase, which prevents intracellular ROS accumulation and confers oxidative stress resistance.
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Affiliation(s)
- James González
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Cd. Universitaria, 04510, Coyoacán, Ciudad de México, México
| | - Román Castillo
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Cd. Universitaria, 04510, Coyoacán, Ciudad de México, México
| | - Miguel Angel García-Campos
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Cd. Universitaria, 04510, Coyoacán, Ciudad de México, México
| | - Diego Noriega-Samaniego
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Cd. Universitaria, 04510, Coyoacán, Ciudad de México, México
| | - Viviana Escobar-Sánchez
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Cd. Universitaria, 04510, Coyoacán, Ciudad de México, México
| | - Lucero Romero-Aguilar
- Departamento de Bioquímica, Facultad de Medicina, Facultad de Medicina, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Cd. Universitaria, 04510, Coyoacán, Ciudad de México, México
| | - Luisa Alba-Lois
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Cd. Universitaria, 04510, Coyoacán, Ciudad de México, México
| | - Claudia Segal-Kischinevzky
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México. Avenida Universidad 3000, Cd. Universitaria, 04510, Coyoacán, Ciudad de México, México.
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Wei Y, Zhang SH. Abiostress resistance and cellulose degradation abilities of haloalkaliphilic fungi: applications for saline-alkaline remediation. Extremophiles 2017; 22:155-164. [PMID: 29290045 DOI: 10.1007/s00792-017-0986-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 12/08/2017] [Indexed: 01/02/2023]
Abstract
Soda saline-alkaline lands are significantly harmful to agriculture; thus, effective strategies to remediate such soil are urgently needed. Multiple negative factors exist in the community structure of saline-alkaline fields, among which the lack of fungal species diversity remains the most prominent problem. The haloalkaliphilic fungi are a unique group of extremophiles that grow optimally under conditions of extreme salinity and alkalinity; these fungi, which buffer salinity and alkalinity by absorbing and/or constraining salt ions, produce organic acids and/or macromolecules, secrete macromolecules such as cellulose degradation enzymes, and provide biomass that is beneficial for soil health. Considering that haloalkaliphilic fungi are a valuable genetic resource of resistance and degradation genes, these fungi are expected to be applied in biotechnology. Aspergillus glaucus exhibits high resistance to a variety of stressors and the ability to degrade crop straw; and it is a practical genetic tool that can be used to identify and validate genes involved in abiotic stress resistance and cellulose decomposition genes. This review will focus on the following aspects: isolation of extreme haloalkaliphilic fungi, fungal genes involved in salt and alkalinity resistance, macromolecule degrading enzymes, applications for genetic improvement of haloalkaliphilic fungi, and application of haloalkaliphilic fungi in saline-alkali soil mycoremediation.
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Affiliation(s)
- Yi Wei
- College of Plant Sciences, Jilin University, Changchun, 130062, People's Republic of China
| | - Shi-Hong Zhang
- College of Plant Sciences, Jilin University, Changchun, 130062, People's Republic of China.
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Castro DE, Murguía-Romero M, Thomé PE, Peña A, Calderón-Torres M. Putative 3-nitrotyrosine detoxifying genes identified in the yeast Debaryomyces hansenii : In silico search of regulatory sequences responsive to salt and nitrogen stress. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2017.06.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Applications of Haloalkaliphilic Fungi in Mycoremediation of Saline-Alkali Soil. Fungal Biol 2017. [DOI: 10.1007/978-3-319-68957-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Gupta P, Nutan KK, Singla-Pareek SL, Pareek A. Abiotic Stresses Cause Differential Regulation of Alternative Splice Forms of GATA Transcription Factor in Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:1944. [PMID: 29181013 PMCID: PMC5693882 DOI: 10.3389/fpls.2017.01944] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 10/30/2017] [Indexed: 05/05/2023]
Abstract
The GATA gene family is one of the most conserved families of transcription factors, playing a significant role in different aspects of cellular processes, in organisms ranging from fungi to angiosperms. GATA transcription factors are DNA-binding proteins, having a class IV zinc-finger motif CX2CX17-20CX2C followed by a highly basic region and are known to bind a consensus sequence WGATAR. In plants, GATAs are known to be involved in light-dependent gene regulation and nitrate assimilation. However, a comprehensive analysis of these GATA gene members has not yet been highlighted in rice when subjected to environmental stresses. In this study, we present an overview of the GATA gene family in rice (OsGATA) in terms of, their chromosomal distribution, domain architecture, and phylogeny. Our study has revealed the presence of 28 genes, encoding 35 putative GATA transcription factors belonging to seven subfamilies in the rice genome. Transcript abundance analysis in contrasting genotypes of rice-IR64 (salt sensitive) and Pokkali (salt tolerant), for individual GATA members indicated their differential expression in response to various abiotic stresses such as salinity, drought, and exogenous ABA. One of the members of subfamily VII-OsGATA23a, emerged as a multi-stress responsive transcription factor giving elevated expression levels in response to salinity and drought. ABA also induces expression of OsGATA23a by 35 and 55-folds in IR64 and Pokkali respectively. However, OsGATA23b, an alternative splice variant of OsGATA23 did not respond to above-mentioned stresses. Developmental regulation of the OsGATA genes based on a publicly available microarray database showed distinct expression patterns for most of the GATA members throughout different stages of rice development. Altogether, our results suggest inherent roles of diverse OsGATA factors in abiotic stress signaling and also throw some light on the tight regulation of the spliced variants of OsGATA genes in response to different environmental conditions.
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Affiliation(s)
- Priyanka Gupta
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Kamlesh K. Nutan
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sneh L. Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- *Correspondence: Ashwani Pareek
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Prista C, Michán C, Miranda IM, Ramos J. The halotolerant Debaryomyces hansenii, the Cinderella of non-conventional yeasts. Yeast 2016; 33:523-533. [PMID: 27279567 DOI: 10.1002/yea.3177] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 05/10/2016] [Accepted: 05/10/2016] [Indexed: 11/10/2022] Open
Abstract
Debaryomyces hansenii is a halotolerant yeast with a high biotechnological potential, particularly in the food industry. However, research in this yeast is limited by its molecular peculiarities. In this review we summarize the state of the art of research in this microorganisms, describing both pros and cons. We discuss (i) its halotolerance, (ii) the molecular factors involved in saline and osmotic stress, (iii) its high gene density and ambiguous CUG decoding, and (iv) its biotechnological and medical interests. We trust that all the bottlenecks in its study will soon be overcome and D. hansenii will become a fundamental organism for food biotechnological processes. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Catarina Prista
- LEAF - Research Centre Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, 1649-003, Portugal
| | - Carmen Michán
- Departamento de Bioquímica y Biología Molecular, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Isabel M Miranda
- Department of Microbiology, Faculty of Medicine, University of Porto, Porto, Portugal.,CINTESIS - Centre for Health Technology and Services Research, Faculty of Medicine of the University of Porto, Portugal
| | - José Ramos
- Departamento de Microbiología, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain.
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Zhang SH. The Genetic Basis of Abiotic Stress Resistance in Extremophilic Fungi: The Genes Cloning and Application. FUNGAL APPLICATIONS IN SUSTAINABLE ENVIRONMENTAL BIOTECHNOLOGY 2016. [DOI: 10.1007/978-3-319-42852-9_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Ment D, Alkan N, Luria N, Bi FC, Reuveni E, Fluhr R, Prusky D. A Role of AREB in the Regulation of PACC-Dependent Acid-Expressed-Genes and Pathogenicity of Colletotrichum gloeosporioides. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2015; 28:154-66. [PMID: 25317668 DOI: 10.1094/mpmi-09-14-0252-r] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Gene expression regulation by pH in filamentous fungi and yeasts is controlled by the PACC/RIM101 transcription factor. In Colletotrichum gloeosporioides, PACC is known to act as positive regulator of alkaline-expressed genes, and this regulation was shown to contribute to fungal pathogenicity. PACC is also a negative regulator of acid-expressed genes, however; the mechanism of downregulation of acid-expressed genes by PACC and their contribution to C. gloeosporioides pathogenicity is not well understood. RNA sequencing data analysis was employed to demonstrate that PACC transcription factor binding sites (TFBS) are significantly overrepresented in the promoter of PACC-upregulated, alkaline-expressed genes. In contrast, they are not overrepresented in the PACC-downregulated, acid-expressed genes. Instead, acid-expressed genes showed overrepresentation of AREB GATA TFBS in C. gloeosporioides and in homologs of five other ascomycetes genomes. The areB promoter contains PACC TFBS; its transcript was upregulated at pH 7 and repressed in ΔpacC. Furthermore, acid-expressed genes were found to be constitutively upregulated in ΔareB during alkalizing conditions. The areB mutants showed significantly reduced ammonia secretion and pathogenicity on tomato fruit. Present results indicate that PACC activates areB expression, thereby conditionally repressing acid-expressed genes and contributing critically to C. gloeosporioides pathogenicity.
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Current awareness on yeast. Yeast 2007. [DOI: 10.1002/yea.1325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Platara M, Ruiz A, Serrano R, Palomino A, Moreno F, Ariño J. The transcriptional response of the yeast Na(+)-ATPase ENA1 gene to alkaline stress involves three main signaling pathways. J Biol Chem 2006; 281:36632-42. [PMID: 17023428 DOI: 10.1074/jbc.m606483200] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Adaptive response of the yeast Saccharomyces cerevisiae to environmental alkalinization results in remodeling of gene expression. A key target is the gene ENA1, encoding a Na(+)-ATPase, whose induction by alkaline pH has been shown to involve calcineurin and the Rim101/Nrg1 pathway. Previous functional analysis of the ENA1 promoter revealed a calcineurin-independent pH responsive region (ARR2, 83 nucleotides). We restrict here this response to a small (42 nucleotides) ARR2 5.-region, named MCIR (minimum calcineurin independent response), which contains a MIG element, able to bind Mig1,2 repressors. High pH-induced response driven from this region was largely abolished in snf1 cells and moderately reduced in a rim101 strain. Cells lacking Mig1 or Mig2 repressors had a near wild type response, but the double mutant presented a high level of expression upon alkaline stress. Deletion of NRG1 (but not of NRG2) resulted in increased expression. Induction from the MCIR region was marginal in a quadruple mutant lacking Nrg1,2 and Mig1,2 repressors. In vitro band shift experiments demonstrated binding of Nrg1 to the 5. end of the ARR2 region. Furthermore, we show that Nrg1 binds in vivo around the MCIR region under standard growth conditions, and that binding is largely abolished after high pH stress. Therefore, the calcineurin-independent response of the ENA1 gene is under the regulation of Rim101 (through Nrg1) and Snf1 (through Nrg1 and Mig2). Accordingly, induction by alkaline stress of the entire ENA1 promoter in a snf1 rim101 mutant in the presence of the calcineurin inhibitor FK506 is completely abolished. Thus, the transcriptional response to alkaline stress of the ENA1 gene integrates three different signaling pathways.
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Affiliation(s)
- Maria Platara
- Department of Bioquímica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra 08193, Barcelona
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