Journal of Microbiology

Journal Article

Regulatory role of cysteines in (2R, 3R)-butanediol dehydrogenase BdhA of Bacillus velezensis strain GH1-13: Yunhee Choi , Yong-Hak Kim; J. Microbiol. 2022;60(4):411-418. Published online March 14, 2022; DOI: https://doi.org/10.1007/s12275-022-2018-y

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Bacillus velezensis strain GH1-13 contains a (2R,3R)-butanediol dehydrogenase (R-BDH) BdhA which converts acetoin to R-BD reversibly, however, little is known about its regulatory cysteine and biological significance. We performed sitedirected mutation of three cysteines in BdhA. The C37S mutant had no enzyme activity and the C34S and C177S mutants differed from each other and wild type (WT). After zinc affinity chromatography, 1 mM ZnCl2 treatment resulted in a 3-fold enhancement of the WT activity, but reduced activity of the C34S mutant by more than 2 folds compared to the untreated ones. However, ZnCl2 treatment did not affect the activity of the C177S mutant. Most of the double and triple mutant proteins (C34S/C37S, C34S/C177S, C37S/C177S, and C34S/C37S/C177S) were aggregated in zinc resins, likely due to the decreased protein stability. All of the purified WT and single mutant proteins increased multiple intermolecular disulfide bonds in the presence of H2O2 as the buffer pH decreased from 7.5 to 5.5, whereas an intramolecular disulfide bond of cysteine 177 and another cysteine in the CGIC motif region was likely formed at pH higher than pKa of 7.5. When pH varied, WT and its C34S or C177S mutants reduced acetoin to R-BD at the optimum pH 5.5 and oxidized R-BD to acetoin at the optimum pH 10. This study demonstrated that cysteine residues in BdhA play a regulatory role for the production of acetoin and R-BD depending on pH as well as metal binding and oxidative stress.

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Significantly enhanced specific activity of Bacillus subtilis (2,3)-butanediol dehydrogenase through computer-aided refinement of its substrate-binding pocket
Bochun Hu, Xiaoqi Xi, Fugang Xiao, Xiaomeng Bai, Yuanyuan Gong, Yifan Li, Xueqin Qiao, Cunduo Tang, Jihong Huang
International Journal of Biological Macromolecules.2024; 281: 136443. CrossRef
Structural and enzymatic characterization of Bacillus subtilis R,R-2,3-butanediol dehydrogenase
Xiaofei Wang, Lingyun Jia, Fangling Ji
Biochimica et Biophysica Acta (BBA) - General Subjects.2023; 1867(4): 130326. CrossRef
Engineering a BsBDHA substrate-binding pocket entrance for the improvement in catalytic performance toward (R)-phenyl-1,2-ethanediol based on the computer-aided design
Bo-Chun Hu, Meng-Ran Li, Ying-Ying Li, Xin-Shuang Yuan, Yu-Ye Hu, Fu-Gang Xiao
Biochemical Engineering Journal.2023; 194: 108907. CrossRef

Research Support, Non-U.S. Gov'ts

Dimethyl sulfoxide reduction by a hyperhermophilic archaeon Thermococcus onnurineus NA1 via a cysteine-cystine redox shuttle: Ae Ran Choi , Min-Sik Kim , Sung Gyun Kang , Hyun Sook Lee; J. Microbiol. 2016;54(1):31-38. Published online January 5, 2016; DOI: https://doi.org/10.1007/s12275-016-5574-1

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Abstract

A variety of microbes grow by respiration with dimethyl sulfoxide (DMSO) as an electron acceptor, and several distinct DMSO respiratory systems, consisting of electron carriers and a terminal DMSO reductase, have been characterized. The heterotrophic growth of a hyperthermophilic archaeon Thermococcus onnurineus NA1 was enhanced by the addition of DMSO, but the archaeon was not capable of reducing DMSO to DMS directly using a DMSO reductase. Instead, the archaeon reduced DMSO via a cysteine-cystine redox shuttle through a mechanism whereby cystine is microbially reduced to cysteine, which is then reoxidized by DMSO reduction. A thioredoxin reductase-protein disulfide oxidoreductase redox couple was identified to have intracellular cystine-reducing activity, permitting recycle of cysteine. This study presents the first example of DMSO reduction via an electron shuttle. Several Thermococcales species also exhibited enhanced growth coupled with DMSO reduction, probably by disposing of excess reducing power rather than conserving energy.

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Heavy Metal-Resistant Biohybrid System Boosts Dissimilatory Nitrate Reduction to Ammonium for Agronomic Sustainability
Jialin Chi, Shiyin Wu, Liping Fang, Kai Liu, Shaochen Huang, Wenjun Zhang, Fangbai Li
ACS Sustainable Chemistry & Engineering.2024; 12(44): 16444. CrossRef
Phenotypic and genomic characterization of Bathyarchaeum tardum gen. nov., sp. nov., a cultivated representative of the archaeal class Bathyarchaeia
Maria A. Khomyakova, Alexander Y. Merkel, Dana D. Mamiy, Alexandra A. Klyukina, Alexander I. Slobodkin
Frontiers in Microbiology.2023;[Epub] CrossRef
Direct Electron Transfer between the frhAGB -Encoded Hydrogenase and Thioredoxin Reductase in the Nonmethanogenic Archaeon Thermococcus onnurineus NA1
Hae-Chang Jung, Jae Kyu Lim, Tae-Jun Yang, Sung Gyun Kang, Hyun Sook Lee, Haruyuki Atomi
Applied and Environmental Microbiology.2020;[Epub] CrossRef
A peroxiredoxin of Thermus thermophilus HB27: Biochemical characterization of a new player in the antioxidant defence
Gabriella Fiorentino, Patrizia Contursi, Giovanni Gallo, Simonetta Bartolucci, Danila Limauro
International Journal of Biological Macromolecules.2020; 153: 608. CrossRef
A Reexamination of Thioredoxin Reductase from Thermoplasma acidophilum, a Thermoacidophilic Euryarchaeon, Identifies It as an NADH-Dependent Enzyme
Dwi Susanti, Usha Loganathan, Austin Compton, Biswarup Mukhopadhyay
ACS Omega.2017; 2(8): 4180. CrossRef
Redox regulation of SurR by protein disulfide oxidoreductase in Thermococcus onnurineus NA1
Jae Kyu Lim, Hae-Chang Jung, Sung Gyun Kang, Hyun Sook Lee
Extremophiles.2017; 21(3): 491. CrossRef
Exploring membrane respiratory chains
Bruno C. Marreiros, Filipa Calisto, Paulo J. Castro, Afonso M. Duarte, Filipa V. Sena, Andreia F. Silva, Filipe M. Sousa, Miguel Teixeira, Patrícia N. Refojo, Manuela M. Pereira
Biochimica et Biophysica Acta (BBA) - Bioenergetics.2016; 1857(8): 1039. CrossRef

Structural basis for the ATP-independent proteolytic activity of LonB proteases and reclassification of their AAA+ modules: Young Jun An , Jung-Hyun Na , Myung-Il Kim , Sun-Shin Cha; J. Microbiol. 2015;53(10):711-717. Published online October 2, 2015; DOI: https://doi.org/10.1007/s12275-015-5417-5

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Abstract

Lon proteases degrade defective or denature proteins as well as some folded proteins for the control of cellular protein quality. There are two types of Lon proteases, LonA and LonB. Each consists of two functional components: a protease component and an ATPase associated with various cellular activities (AAA+ module). Here, we report the 2.03 Å-resolution crystal structure of the isolated AAA+ module (iAAA+ module) of LonB from Thermococcus onnurineus NA1 (TonLonB). The iAAA+ module, having no bound nucleotide, adopts a conformation virtually identical to the ADP-bound conformation of AAA+ modules in the hexameric structure of TonLonB; this provides insights into the ATP-independent proteolytic activity observed in a LonB protease. Structural comparison of AAA+ modules between LonA and LonB revealed that the AAA+ modules of Lon proteases are separated into two distinct clades depending on their structural features. The AAA+ module of LonB belongs to the ‘H2 & Ins1 insert clade (HINS clade)’ defined for the first time in this study, while the AAA+ module of LonA is a member of the HCLR clade.

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Unique Structural Fold of LonBA Protease from Bacillus subtilis, a Member of a Newly Identified Subfamily of Lon Proteases
Alla Gustchina, Mi Li, Anna G. Andrianova, Arsen M. Kudzhaev, George T. Lountos, Bartosz Sekula, Scott Cherry, Joseph E. Tropea, Ivan V. Smirnov, Alexander Wlodawer, Tatyana V. Rotanova
International Journal of Molecular Sciences.2022; 23(19): 11425. CrossRef
Structure and the Mode of Activity of Lon Proteases from Diverse Organisms
Alexander Wlodawer, Bartosz Sekula, Alla Gustchina, Tatyana V. Rotanova
Journal of Molecular Biology.2022; 434(7): 167504. CrossRef
Proteolytic systems of archaea: slicing, dicing, and mincing in the extreme
Nicholas P. Robinson, Julie A. Maupin-Furlow
Emerging Topics in Life Sciences.2018; 2(4): 561. CrossRef

Characterization of Thermostable Deblocking Aminopeptidases of Archaeon Thermococcus onnurineus NA1 by Proteomic and Biochemical Approaches: Yeol Gyun Lee , Sun-Hee Leem , Young-Ho Chung , Seung Il Kim; J. Microbiol. 2012;50(5):792-797. Published online November 4, 2012; DOI: https://doi.org/10.1007/s12275-012-2461-2

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Abstract: Thermococcus onnurineus NA1 is a hyperthermophilic archaeon that grows optimally at >80°C. The deblocking aminopeptidase (DAP) (TNA1-DAP1) encoded in Ton_1032 of T. onnurineus NA1 is considered a major DAP. However, four genes encoding putative DAP have been identified from a genomic analysis of T. onnurineus NA1. A proteomic analysis revealed that all four DAPs were differentially induced in YPS culture medium and, particularly, two DAPs (TNA1-DAP1 and TNA1-DAP2) were dominantly expressed in T. onnurineus NA1. The biochemical properties and enzyme activity of DAPs induced in an E. coli expression system suggested that the two major DAPs play complementary roles in T. onnurineus NA1.

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