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Yang L, Wang Y, Yu P, Ren S, Zhu Z, Jin Y, Yan J, Peng X, Chen L. Prophage-Related Gene VpaChn25_0724 Contributes to Cell Membrane Integrity and Growth of Vibrio parahaemolyticus CHN25. Front Cell Infect Microbiol 2020; 10:595709. [PMID: 33363055 PMCID: PMC7756092 DOI: 10.3389/fcimb.2020.595709] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/06/2020] [Indexed: 01/16/2023] Open
Abstract
Vibrio parahaemolyticus is a leading seafood-borne pathogen that can cause acute gastroenteritis and even death in humans. In aquatic ecosystems, phages constantly transform bacterial communities by horizontal gene transfer. Nevertheless, biological functions of prophage-related genes in V. parahaemolyticus remain to be fully unveiled. Herein, for the first time, we studied one such gene VpaChn25_0724 encoding an unknown hypothetical protein in V. parahaemolyticus CHN25. This gene deletion mutant ΔVpaChn25_0724 was constructed by homologous recombination, and its complementary mutant ΔVpaChn25_0724-com was also obtained. The ΔVpaChn25_0724 mutant exhibited a sever defect in growth and swimming motility particularly at lower temperatures. Biofilm formation and cytotoxicity capacity of V. parahaemolyticus CHN25 was significantly lowered in the absence of VpaChn25_0724. Comparative secretomic analysis revealed an increase in extracellular proteins of ΔVpaChn25_0724, which likely resulted from its damaged cell membrane. Comparison of transcriptome data showed twelve significantly altered metabolic pathways in ΔVpaChn25_0724, suggesting inactive transport and utilization of carbon sources, repressed energy production and membrane biogenesis in ΔVpaChn25_0724. Comparative transcriptomic analysis also revealed several remarkably down-regulated key regulators in bacterial gene regulatory networks linked to the observed phenotypic variations. Overall, the results here facilitate better understanding of biological significance of prophage-related genes remaining in V. parahaemolyticus.
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Affiliation(s)
- Lianzhi Yang
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, Shanghai, China.,College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yaping Wang
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, Shanghai, China.,College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Department of Internal Medicine, Virginia Commonwealth University/McGuire VA Medical Centre, Richmond, VA, United States
| | - Pan Yu
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, Shanghai, China.,College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Shunlin Ren
- Department of Internal Medicine, Virginia Commonwealth University/McGuire VA Medical Centre, Richmond, VA, United States
| | - Zhuoying Zhu
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, Shanghai, China.,College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yinzhe Jin
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, Shanghai, China.,College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Jizhou Yan
- College of Fishers and Life Science, Shanghai Ocean University, Shanghai, China
| | - Xu Peng
- Archaea Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture, Shanghai, China.,College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
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Yao P, Cui Y, Yu S, Du Y, Feng J, Wu Q, Zhu D. Efficient Biosynthesis of (R)- or (S)-2-Hydroxybutyrate froml-Threonine through a Synthetic Biology Approach. Adv Synth Catal 2016. [DOI: 10.1002/adsc.201600468] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Peiyuan Yao
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology; Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
| | - Yunfeng Cui
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology; Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
| | - Shanshan Yu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology; Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
| | - Yuncheng Du
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology; Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
| | - Jinhui Feng
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology; Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
| | - Qiaqing Wu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology; Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
| | - Dunming Zhu
- National Engineering Laboratory for Industrial Enzymes and Tianjin Engineering Research Center of Biocatalytic Technology; Tianjin Institute of Industrial Biotechnology; Chinese Academy of Sciences; 32 Xi Qi Dao, Tianjin Airport Economic Area Tianjin 300308 People's Republic of China
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Halophiles: biology, adaptation, and their role in decontamination of hypersaline environments. World J Microbiol Biotechnol 2016; 32:135. [PMID: 27344438 DOI: 10.1007/s11274-016-2081-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/07/2016] [Indexed: 10/21/2022]
Abstract
The unique cellular enzymatic machinery of halophilic microbes allows them to thrive in extreme saline environments. That these microorganisms can prosper in hypersaline environments has been correlated with the elevated acidic amino acid content in their proteins, which increase the negative protein surface potential. Because these microorganisms effectively use hydrocarbons as their sole carbon and energy sources, they may prove to be valuable bioremediation agents for the treatment of saline effluents and hypersaline waters contaminated with toxic compounds that are resistant to degradation. This review highlights the various strategies adopted by halophiles to compensate for their saline surroundings and includes descriptions of recent studies that have used these microorganisms for bioremediation of environments contaminated by petroleum hydrocarbons. The known halotolerant dehalogenase-producing microbes, their dehalogenation mechanisms, and how their proteins are stabilized is also reviewed. In view of their robustness in saline environments, efforts to document their full potential regarding remediation of contaminated hypersaline ecosystems merits further exploration.
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Yuan H, Liu D. Genetic evidence that Arabidopsis ALTERED ROOT ARCHITECTURE encodes a putative dehydrogenase involved in homoserine biosynthesis. PLANT CELL REPORTS 2014; 33:25-33. [PMID: 24101201 DOI: 10.1007/s00299-013-1509-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 09/11/2013] [Accepted: 09/20/2013] [Indexed: 06/02/2023]
Abstract
Genetic and molecular analysis of an Arabidopsis root development mutant identified a putative dehydrogenase gene involved in homoserine biosynthesis. In higher plants, homoserine (Hse) is derived from aspartate (Asp) and is an important intermediate for production of methionine (Met), threonine (Thr), and isoleucine (Ile). In Arabidopsis, six enzymes involved in the biosynthesis of Hse from Asp have been well characterized. It is not known, however, whether there exist other enzymes involved in this process. In this work, we characterized an Arabidopsis mutant, ara (altered root architecture), with a short primary root and an increased number of lateral roots. Genetic and molecular analysis indicated that the ARA gene encodes a protein with a D-isomer specific 2-hydroxyacid dehydrogenase domain. ARA is expressed in all plant organs and is localized in the cell periphery. The ara mutant phenotypes can be rescued by exogenously applied Hse, Met, Ile and 2-oxobutanoate. Based on the results presented here, we propose that the ARA protein may be a dehydrogenase involved in homoserine biosynthesis.
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Affiliation(s)
- Hui Yuan
- MOE Key Laboratory of Bioinformatics, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, People's Republic of China
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Janiak V, Petersen M, Zentgraf M, Klebe G, Heine A. Structure and substrate docking of a hydroxy(phenyl)pyruvate reductase from the higher plant Coleus blumei Benth. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:593-603. [PMID: 20445235 DOI: 10.1107/s0907444910006360] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 02/18/2010] [Indexed: 01/17/2023]
Abstract
Hydroxy(phenyl)pyruvate reductase [H(P)PR] belongs to the family of D-isomer-specific 2-hydroxyacid dehydrogenases and catalyzes the reduction of hydroxyphenylpyruvates as well as hydroxypyruvate and pyruvate to the corresponding lactates. Other non-aromatic substrates are also accepted. NADPH is the preferred cosubstrate. The crystal structure of the enzyme from Coleus blumei (Lamiaceae) has been determined at 1.47 A resolution. In addition to the apoenzyme, the structure of a complex with NADP(+) was determined at a resolution of 2.2 A. H(P)PR is a dimer with a molecular mass of 34 113 Da per subunit. The structure is similar to those of other members of the enzyme family and consists of two domains separated by a deep catalytic cleft. To gain insights into substrate binding, several compounds were docked into the cosubstrate complex structure using the program AutoDock. The results show two possible binding modes with similar docking energy. However, only binding mode A provides the necessary environment in the active centre for hydride and proton transfer during reduction, leading to the formation of the (R)-enantiomer of lactate and/or hydroxyphenyllactate.
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Affiliation(s)
- Verena Janiak
- Institut für Pharmazeutische Biologie, Philipps-Universität Marburg, Deutschhausstrasse 17A, 35037 Marburg, Germany
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Domenech J, Ferrer J. A new D-2-hydroxyacid dehydrogenase with dual coenzyme-specificity from Haloferax mediterranei, sequence analysis and heterologous overexpression. Biochim Biophys Acta Gen Subj 2006; 1760:1667-74. [PMID: 17049749 DOI: 10.1016/j.bbagen.2006.08.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2006] [Revised: 08/29/2006] [Accepted: 08/30/2006] [Indexed: 11/30/2022]
Abstract
A gene encoding a new D-2-hydroxyacid dehydrogenase (E.C. 1.1.1.) from the halophilic Archaeon Haloferax mediterranei has been sequenced, cloned and expressed in Escherichia coli cells with the inducible expression plasmid pET3a. The nucleotide sequence analysis showed an open reading frame of 927 bp which encodes a 308 amino acid protein. Multiple amino acid sequence alignments of the D-2-hydroxyacid dehydrogenase from H. mediterranei showed high homology with D-2-hydroxyacid dehydrogenases from different organisms and other enzymes of this family. Analysis of the amino acid sequence showed catalytic residues conserved in hydroxyacid dehydrogenases with d-stereospecificity. In the reductive reaction, the enzyme showed broad substrate specificity, although alpha-ketoisoleucine was the most favourable of all alpha-ketocarboxylic acids tested. Kinetic data revealed that this new D-2-hydroxyacid dehydrogenase from H. mediterranei exhibits dual coenzyme-specificity, using both NADPH and NADH as coenzymes. To date, all D-2-hydroxyacid dehydrogenases have been found to be NADH-dependent. Here, we report the first example of a D-2-hydroxyacid dehydrogenase with dual coenzyme-specificity.
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Affiliation(s)
- J Domenech
- Departamento de Agroquímica y Bioquímica, Division de Bioquímica, Facultad de Ciencias, Universidad de Alicante, Ap. 99, 03080 Alicante, Spain
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Cho BK, Park HY, Seo JH, Kinnera K, Lee BS, Kim BG. Enzymatic resolution for the preparation of enantiomerically enrichedD-?-heterocyclic alanine derivatives usingEscherichia coli aromaticL-amino acid transaminase. Biotechnol Bioeng 2004; 88:512-9. [PMID: 15459908 DOI: 10.1002/bit.20280] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
An enzymatic resolution was carried out for the preparation of enriched beta-heterocyclic D-alanine derivatives using Escherichia coli aromatic L-amino acid transaminase. The excess of pyrazole, imidazole, or 1,2,4-triazole reacted with methyl-2-acetamidoacrylate in acetonitrile in the presence of potassium carbonate at 60 degrees C, directly leading to make the potassium salt of the corresponding N-acetyl-beta-heterocyclic alanine derivatives. After the acidic deprotection of the N-acetyl group, 10 mM of racemic pyrazolylalanine, triazolylalanine, and imidazolylalanine were resolved to D-pyrazolylalanine, D-triazolylalanine, and D-imidazolylalanine with 46% (85% ee), 42% (72% ee), and 48% (95% ee) conversion yield in 18 h, respectively, using E. coli aromatic L-amino acid transaminase (EC 2.6.1.5). Although the three beta-heterocyclic L-alanine derivatives have similar molecular structures, they showed different reaction rates and enantioselectivities. The relative reactivities of the transaminase toward the beta-heterocyclic L-alanine derivatives could be explained by the relationship between the substrate binding energy (E, kcal/mol) to the enzyme active site and the distance (delta, A) from the nitrogen of alpha-amino group of the substrates to the C4' carbon of PLP-Lys258 Schiff base. As the ratio of the substrate binding energy (E) to the distance (delta) becomes indicative value of k(cat)/K(M) of the enzyme to the substrate, the relative reactivities of the beta-heterocyclic L-alanine derivatives were successfully correlated with E/delta, and the relationship was confirmed by our experiments.
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Affiliation(s)
- Byung-Kwan Cho
- School of Chemical Engineering and Institute of Molecular Biology and Genetics, Seoul National University, Seoul 151-742, Korea
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