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Chen Y, Li Y, Luo G, Luo C, Xiao Z, Lu Y, Xiang Z, Hou Z, Xiao Q, Zhou Y, Tang Q. Gene identification, expression analysis, and molecular docking of SAT and OASTL in the metabolic pathway of selenium in Cardamine hupingshanensis. PLANT CELL REPORTS 2024; 43:148. [PMID: 38775862 PMCID: PMC11111505 DOI: 10.1007/s00299-024-03227-6] [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: 02/21/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
KEY MESSAGE Identification of selenium stress-responsive expression and molecular docking of serine acetyltransferase (SAT) and O-acetyl serine (thiol) lyase (OASTL) in Cardamine hupingshanensis. A complex coupled with serine acetyltransferase (SAT) and O-acetyl serine (thiol) lyase (OASTL) is the key enzyme that catalyzes selenocysteine (Sec) synthesis in plants. The functions of SAT and OASTL genes were identified in some plants, but it is still unclear whether SAT and OASTL are involved in the selenium metabolic pathway in Cardamine hupingshanensis. In this study, genome-wide identification and comparative analysis of ChSATs and ChOASTLs were performed. The eight ChSAT genes were divided into three branches, and the thirteen ChOASTL genes were divided into four branches by phylogenetic analysis and sequence alignment, indicating the evolutionary conservation of the gene structure and its association with other plant species. qRT-PCR analysis showed that the ChSAT and ChOASTL genes were differentially expressed in different tissues under various selenium levels, suggesting their important roles in Sec synthesis. The ChSAT1;2 and ChOASTLA1;2 were silenced by the VIGS system to investigate their involvement in selenium metabolites in C. hupingshanensis. The findings contribute to understanding the gene functions of ChSATs and ChOASTLs in the selenium stress and provide a reference for further exploration of the selenium metabolic pathway in plants.
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Affiliation(s)
- Yushan Chen
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Hubei Minzu University, Enshi, 44500, China
- Hubei Key Laboratory of Selenium Resource Research and Biological Application, Hubei Minzu University, Enshi, 44500, China
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, 44500, China
| | - Yao Li
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, 44500, China
| | - Guoqiang Luo
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, 44500, China
| | - Cihang Luo
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, 44500, China
| | - Zhijing Xiao
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, 44500, China
| | - Yanke Lu
- Hubei Key Laboratory of Selenium Resource Research and Biological Application, Hubei Minzu University, Enshi, 44500, China
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, 44500, China
| | - Zhixin Xiang
- Hubei Key Laboratory of Selenium Resource Research and Biological Application, Hubei Minzu University, Enshi, 44500, China
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, 44500, China
| | - Zhi Hou
- Hubei Key Laboratory of Selenium Resource Research and Biological Application, Hubei Minzu University, Enshi, 44500, China
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, 44500, China
| | - Qiang Xiao
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Hubei Minzu University, Enshi, 44500, China
- College of Forestry and Horticulture, Hubei Minzu University, Enshi, 44500, China
| | - Yifeng Zhou
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Hubei Minzu University, Enshi, 44500, China.
- Hubei Key Laboratory of Selenium Resource Research and Biological Application, Hubei Minzu University, Enshi, 44500, China.
- College of Biological and Food Engineering, Hubei Minzu University, Enshi, 44500, China.
| | - Qiaoyu Tang
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Hubei Minzu University, Enshi, 44500, China.
- College of Forestry and Horticulture, Hubei Minzu University, Enshi, 44500, China.
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Verma D, Gupta V. New insights into the structure and function of an emerging drug target CysE. 3 Biotech 2021; 11:373. [PMID: 34367865 DOI: 10.1007/s13205-021-02891-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 06/09/2021] [Indexed: 11/24/2022] Open
Abstract
The antimicrobial resistant strains of several pathogens are major culprits of hospital-acquired nosocomial infections. An active and urgent action is necessary against these pathogens for the development of unique therapeutics. The cysteine biosynthetic pathway or genes (that are absent in humans) involved in the production of L-cysteine appear to be an attractive target for developing novel antibiotics. CysE, a Serine Acetyltransferase (SAT), catalyzes the first step of cysteine synthesis and is reported to be essential for the survival of persistence in several microbes including Mycobacterium tuberculosis. Structure determination provides fundamental insight into structure and function of protein and aid in drug design/discovery efforts. This review focuses on the overview of current knowledge of structure function, regulatory mechanism, and potential inhibitors (active site as well as allosteric site) of CysE. Despite having conserved structure, slight modification in CysE structure lead to altered the regulatory mechanism and hence affects the cysteine production. Due to its possible role in virulence and vital metabolism of pathogens makes it a potential target in the quest to develop novel therapeutics to treat multi-drug-resistant bacteria.
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Affiliation(s)
- Deepali Verma
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida, Uttar Pradesh 201309 India
| | - Vibha Gupta
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, Noida, Uttar Pradesh 201309 India
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Zhao Z, Li S, Ji C, Zhou Y, Li C, Wang W. Genetic Variation of the Serine Acetyltransferase Gene Family for Sulfur Assimilation in Maize. Genes (Basel) 2021; 12:437. [PMID: 33808582 PMCID: PMC8003530 DOI: 10.3390/genes12030437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 11/28/2022] Open
Abstract
Improving sulfur assimilation in maize kernels is essential due to humans and animals' inability to synthesize methionine. Serine acetyltransferase (SAT) is a critical enzyme that controls cystine biosynthesis in plants. In this study, all SAT gene members were genome-wide characterized by using a sequence homology search. The RNA-seq quantification indicates that they are highly expressed in leaves, other than root and seeds, consistent with their biological functions in sulfur assimilation. With the recently released 25 genomes of nested association mapping (NAM) founders representing the diverse maize stock, we had the opportunity to investigate the SAT genetic variation comprehensively. The abundant transposon insertions into SAT genes indicate their driving power in terms of gene structure and genome evolution. We found that the transposon insertion into exons could change SAT gene transcription, whereas there was no significant correlation between transposable element (TE) insertion into introns and their gene expression, indicating that other regulatory elements such as promoters could also be involved. Understanding the SAT gene structure, gene expression and genetic variation involved in natural selection and species adaption could precisely guide genetic engineering to manipulate sulfur assimilation in maize and to improve nutritional quality.
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Affiliation(s)
- Zhixuan Zhao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (Z.Z.); (S.L.)
| | - Shuai Li
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (Z.Z.); (S.L.)
| | - Chen Ji
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; (C.J.); (Y.Z.); (C.L.)
| | - Yong Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; (C.J.); (Y.Z.); (C.L.)
| | - Changsheng Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; (C.J.); (Y.Z.); (C.L.)
| | - Wenqin Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (Z.Z.); (S.L.)
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Molecular characterization of Hsf1 as a master regulator of heat shock response in the thermotolerant methylotrophic yeast Ogataea parapolymorpha. J Microbiol 2021; 59:151-163. [PMID: 33527316 DOI: 10.1007/s12275-021-0646-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 10/22/2022]
Abstract
Ogataea parapolymorpha (Hansenula polymorpha DL-1) is a thermotolerant methylotrophic yeast with biotechnological applications. Here, O. parapolymorpha genes whose expression is induced in response to heat shock were identified by transcriptome analysis and shown to possess heat shock elements (HSEs) in their promoters. The function of O. parapolymorpha HSF1 encoding a putative heat shock transcription factor 1 (OpHsf1) was characterized in the context of heat stress response. Despite exhibiting low sequence identity (26%) to its Saccharomyces cerevisiae homolog, OpHsf1 harbors conserved domains including a DNA binding domain (DBD), domains involved in trimerization (TRI), transcriptional activation (AR1, AR2), transcriptional repression (CE2), and a C-terminal modulator (CTM) domain. OpHSF1 could complement the temperature sensitive (Ts) phenotype of a S. cerevisiae hsf1 mutant. An O. parapolymorpha strain with an H221R mutation in the DBD domain of OpHsf1 exhibited significantly retarded growth and a Ts phenotype. Intriguingly, the expression of heat-shock-protein-coding genes harboring HSEs was significantly decreased in the H221R mutant strain, even under non-stress conditions, indicating the importance of the DBD for the basal growth of O. parapolymorpha. Notably, even though the deletion of C-terminal domains (ΔCE2, ΔAR2, ΔCTM) of OpHsf1 destroyed complementation of the growth defect of the S. cerevisiae hsf1 strain, the C-terminal domains were shown to be dispensable in O. parapolymorpha. Overexpression of OpHsf1 in S. cerevisiae increased resistance to transient heat shock, supporting the idea that OpHsf1 could be useful in the development of heat-shock-resistant yeast host strains.
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Magalhães J, Franko N, Raboni S, Annunziato G, Tammela P, Bruno A, Bettati S, Mozzarelli A, Pieroni M, Campanini B, Costantino G. Inhibition of Nonessential Bacterial Targets: Discovery of a Novel Serine O-Acetyltransferase Inhibitor. ACS Med Chem Lett 2020; 11:790-797. [PMID: 32435386 DOI: 10.1021/acsmedchemlett.9b00627] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/13/2020] [Indexed: 11/29/2022] Open
Abstract
In ϒ-proteobacteria and Actinomycetales, cysteine biosynthetic enzymes are indispensable during persistence and become dispensable during growth or acute infection. The biosynthetic machinery required to convert inorganic sulfur into cysteine is absent in mammals; therefore, it is a suitable drug target. We searched for inhibitors of Salmonella serine acetyltransferase (SAT), the enzyme that catalyzes the rate-limiting step of l-cysteine biosynthesis. The virtual screening of three ChemDiv focused libraries containing 91 243 compounds was performed to identify potential SAT inhibitors. Scaffold similarity and the analysis of the overall physicochemical properties allowed the selection of 73 compounds that were purchased and evaluated on the recombinant enzyme. Six compounds displaying an IC50 <100 μM were identified via an indirect assay using Ellman's reagent and then tested on a Gram-negative model organism, with one of them being able to interfere with bacterial growth via SAT inhibition.
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Affiliation(s)
| | | | | | | | - Päivi Tammela
- Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, P.O. Box 56 (Viikinkaari 5 E), Helsinki FI-00014, Finland
| | | | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy
- National Institute of Biostructures and Biosystems, 00136 Rome, Italy
- Institute of Biophysics, CNR, 56124 Pisa, Italy
| | - Andrea Mozzarelli
- National Institute of Biostructures and Biosystems, 00136 Rome, Italy
- Institute of Biophysics, CNR, 56124 Pisa, Italy
| | - Marco Pieroni
- Centro Interdipartimentale “Biopharmanet-tec”, Università degli Studi di Parma, 43124 Parma, Italy
| | | | - Gabriele Costantino
- Centro Interdipartimentale “Biopharmanet-tec”, Università degli Studi di Parma, 43124 Parma, Italy
- Centro Interdipartimentale Misure (CIM) ‘G. Casnati’, University of Parma, 43124 Parma, Italy
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Sharma S, Ahmed M, Akhter Y. Fungal acetyltransferases structures, mechanisms and inhibitors: A review. Int J Biol Macromol 2019; 157:626-640. [PMID: 31786301 DOI: 10.1016/j.ijbiomac.2019.11.214] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 12/31/2022]
Abstract
Acetylation of proteins is vital and mediate many processes within the cells like protein interactions, intercellular localization, protein stability, transcriptional regulation, enzyme activity and many more. Acetylation, an evolutionarily conserved process, attracted more attention due to its key regulatory role in many cellular processes and its effect on proteome and metabolome. In eukaryotes, protein acetylation also contribute to the epigenetic regulation of gene expression. Acetylation involves the transfer of acetyl group from donor acetyl coenzyme A to a suitable acceptor molecule and the reaction is catalyzed by acetyltransferase enzymes. The review focuses on current understanding of different acetyltransferase families: their discovery, structure and catalytic mechanism in fungal species. Fungal acetyltransferases use divergent catalytic mechanisms and carry out catalysis in a substrate-specific manner. The studies have explored different fungal acetyltransferases in relation to secondary metabolite production and the fungal pathogenesis. Although, the functions and catalytic mechanism of acetyltransferases are well known, however further enhanced knowledge may improve their utilization in various applications of biotechnology.
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Affiliation(s)
- Shikha Sharma
- School of Earth and Environmental Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, Himachal Pradesh 176206, India
| | - Mushtaq Ahmed
- School of Earth and Environmental Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, Himachal Pradesh 176206, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, VidyaVihar, Raebareli Road, Lucknow, Uttar Pradesh 226025, India.
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Yoo SJ, Sohn MJ, Jeong DM, Kang HA. Short bZIP homologue of sulfur regulator Met4 from Ogataea parapolymorpha does not depend on DNA-binding cofactors for activating genes in sulfur starvation. Environ Microbiol 2019; 22:310-328. [PMID: 31680403 DOI: 10.1111/1462-2920.14849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 11/28/2022]
Abstract
The acquisition of sulfur from environment and its assimilation is essential for fungal growth and activities. Here, we describe novel features of the regulatory network of sulfur metabolism in Ogataea parapolymorpha, a thermotolerant methylotrophic yeast with high resistance to harsh environmental conditions. A short bZIP protein (OpMet4p) of O. parapolymorpha, displaying the combined structural characteristics of yeast and filamentous fungal Met4 homologues, plays a key role as a master regulator of cell homeostasis during sulfur limitation, but also its function is required for the tolerance of various stresses. Domain swapping analysis, combined with deletion analysis of the regulatory domains and genes encoding OpCbf1p, OpMet28p, and OpMet32p, indicated that OpMet4p does not require the interaction with these DNA-binding cofactors to induce the expression of sulfur genes, unlike the Saccharomyces cerevisiae Met4p. ChIP analysis confirmed the notion that OpMet4p, which contains a canonical bZIP domain, can bind the target DNA in the absence of cofactors, similar to homologues in other filamentous fungi. Collectively, the identified unique features of the O. parapolymorpha regulatory network, as the first report on the sulfur regulation by a short yeast Met4 homologue, provide insights into conservation and divergence of the sulfur regulatory networks among diverse ascomycetous fungi.
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Affiliation(s)
- Su Jin Yoo
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul, 06974, Korea
| | - Min Jeong Sohn
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul, 06974, Korea
| | - Da Min Jeong
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul, 06974, Korea
| | - Hyun Ah Kang
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul, 06974, Korea
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Takagi H. Metabolic regulatory mechanisms and physiological roles of functional amino acids and their applications in yeast. Biosci Biotechnol Biochem 2019; 83:1449-1462. [PMID: 30712454 DOI: 10.1080/09168451.2019.1576500] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In yeast, amino acid metabolism and its regulatory mechanisms vary under different growth environments by regulating anabolic and catabolic processes, including uptake and export, and the metabolic styles form a complicated but robust network. There is also crosstalk with various metabolic pathways, products and signal molecules. The elucidation of metabolic regulatory mechanisms and physiological roles is important fundamental research for understanding life phenomenon. In terms of industrial application, the control of amino acid composition and content is expected to contribute to an improvement in productivity, and to add to the value of fermented foods, alcoholic beverages, bioethanol, and other valuable compounds (proteins and amino acids, etc.). This review article mainly describes our research in constructing yeast strains with high functionality, focused on the metabolic regulatory mechanisms and physiological roles of "functional amino acids", such as l-proline, l-arginine, l-leucine, l-valine, l-cysteine, and l-methionine, found in yeast.
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Affiliation(s)
- Hiroshi Takagi
- a Division of Biological Science, Graduate School of Science and Technology , Nara Institute of Science and Technology , Nara , Japan
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