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- 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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Abstract
- 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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Citations
Citations to this article as recorded by
- 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
- Significantly enhanced specific activity of Bacillus subtilis (2,3)-butanediol dehydrogenase through computer-aided refinement of its substrate-binding pocket
- Changpingibacter yushuensis gen. nov., sp. nov., isolated from fluvial sediment in Qinghai Tibet Plateau of China
- Yifan Jiao , Sihui Zhang , Jing Yang , Xin-He Lai , Kui Dong , Yanpeng Cheng , Mingchao Xu , Wentao Zhu , Shan Lu , Dong Jin , Ji Pu , Ying Huang , Liyun Liu , Suping Wang , Jianguo Xu
- J. Microbiol. 2022;60(2):147-155. Published online January 7, 2022
- DOI: https://doi.org/10.1007/s12275-022-1199-8
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Abstract
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Two facultatively anaerobic, short rod-shaped, non-motile,
Gram-stain-positive, unknown bacterial strains (JY-X040T
and JY-X174) were isolated from fluvial sediments of Tongtian
River in Yushu Tibetan Autonomous Prefecture, Qinghai
province, China. Cells formed translucent, gray, round and
convex colonies, with a diameter of less than 0.5 mm after 5
days of incubation at 30°C on brain heart infusion-5% sheep
blood agar. The 16S rRNA gene sequence similarity between
strain JY-X040T and Fudania jinshanensis 313T is 93.87%.
In the four phylogenetic trees constructed based on the 16S
rRNA gene and 423 core genes, the two isolates form an independent
branch, phylogenetically closest to F. jinshanensis
313T, but could not be classified as a member of the genus
Fudania or any other genus of the family Arcanobacteriaceae.
The DNA G + C content of strain JY-X040T was 57.8%. Calculation
results
of average nucleotide identity, digital DNADNA hybridization value and amino acid identity between strain JY-X040T and F. jinshanensis 313T are 69.9%, 22.9%, and 64.1%. The major cellular fatty acids were C16:0 (23%) and C18:1ω9c (22%). The cell-wall peptidoglycan type was A5α (L-Lys-L-Ala-L-Lys-D-Glu). The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and four unidentified components. The whole-cell sugars contained rhamnose and ribose. MK-10(H4) was the sole respiratory quinone. The minimum inhibitory concentration of streptomycin was 32 μg/ml. All physiological, biochemical, chemotaxonomic and genomic characteristics support that strains JY-X040T and JY-X174 represent members of a novel species in a new genus, Changpingibacter yushuensis gen. nov., sp. nov. The type strain is JY-X040T (GDMCC 1.1996T = KCTC 49514T). -
Citations
Citations to this article as recorded by- Metagenomic and Culturomics Analysis of Microbial Communities within Surface Sediments and the Prevalence of Antibiotic Resistance Genes in a Pristine River: The Zaqu River in the Lancang River Source Region, China
Yi Yan, Jialiang Xu, Wenmin Huang, Yufeng Fan, Zhenpeng Li, Mingkai Tian, Jinsheng Ma, Xin Lu, Jian Liang
Microorganisms.2024; 12(5): 911. CrossRef - Bacterial diversity in arboreal ant nesting spaces is linked to colony developmental stage
Maximilian Nepel, Veronika E. Mayer, Veronica Barrajon-Santos, Dagmar Woebken
Communications Biology.2023;[Epub] CrossRef
- Metagenomic and Culturomics Analysis of Microbial Communities within Surface Sediments and the Prevalence of Antibiotic Resistance Genes in a Pristine River: The Zaqu River in the Lancang River Source Region, China
- Natronorubrum halophilum sp. nov. isolated from two inland salt lakes
- Cong-Qi Tao , Yi Ding , Yang-Jie Zhao , Heng-Lin Cui
- J. Microbiol. 2020;58(2):105-112. Published online January 29, 2020
- DOI: https://doi.org/10.1007/s12275-020-9514-8
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Abstract
- Two halophilic archaeal strains, SHR37T and NEN6, were isolated from salt lakes located in the Tibet and Xinjiang regions of China. The two strains were found to form a single cluster (99.9% and 99.3% similarity, respectively) separating them from the six current members of Natronorubrum (94.7– 96.9% and 86.1–90.8% similarity, respectively) on the basis of the 16S rRNA and rpoB gene sequence similarities and phylogenetic analysis. Diverse phenotypic characteristics differentiate strains SHR37T and NEN6 from current Natronorubrum members. Their polar lipids are C20C20 and C20C25 glycerol diether derivatives of PG, PGP-Me, and a major glycolipid chromatographically identical to disulfated mannosyl glucosyl diether (S2-DGD). Four minor unidentified glycolipids are also present. The OrthoANI and in silico DDH values of the two strains were 97.3% and 76.1%, respectively, which were much higher than the threshold values proposed as a species boundary (ANI 95–96% and in silico DDH 70%), which revealed that the two strains represent one species; the two values (ANI 79.0–81.9% and in silico DDH 23.5– 25.7%) of the strains examined in this study and the current members of Natronorubrum are much lower than the recommended threshold values, suggesting that strains SHR37T and NEN6 represent a genomically different species of Natronorubrum. These results showed that strains SHR37T (= CGMCC 1.15233T = JCM 30845T) and NEN6 (= CGMCC 1.17161) represent a novel species of Natronorubrum, for which the name Natronorubrum halophilum sp. nov. is proposed.
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Citations
Citations to this article as recorded by- Genome-based taxonomy of genera Haloarcula and Halomicroarcula, and description of six novel species of Haloarcula
Xue Ma, Yao Hu, Xin-Xin Li, Shun Tan, Mu Cheng, Jing Hou, Heng-Lin Cui
Extremophiles.2024;[Epub] CrossRef - Genome-based classification of the family Haloferacaceae and description of five novel species of Halobaculum
Shun Tan, Ling-Rui Zhu, Qing-Ke Zhang, Xin-Yue Dong, Jing Hou, Heng-Lin Cui
Extremophiles.2024;[Epub] CrossRef - Halobacterium yunchengense sp. nov., Natronomonas amylolytica sp. nov., Halorientalis halophila sp. nov., Halobellus salinisoli sp. nov., halophilic archaea isolated from a saline lake and inland saline soil
Ling Cui, Yao Hu, Xin-Xin Li, Xue Ma, Mu Cheng, Shun Tan, Jing Hou, Heng-Lin Cui
Extremophiles.2024;[Epub] CrossRef - Prokaryotic Community Structure, Abundances, and Potential Ecological Functions in a Mars Analog Salt Lake
Wenqi Cai, Ke Yu, Wanting Yang, Rong Mu, Chunang Lian, Luhua Xie, Yan Yan, Shibin Liao, Fan Wang
Astrobiology.2023; 23(5): 550. CrossRef - Halocatena marina sp. nov., a novel filamentous halophilic archaeon isolated from marine tidal flat and emended description of the genus Halocatena
Zhang-Ping Wu, Xi-Wen Zheng, Ya-Ping Sun, Bei-Bei Wang, Jing Hou, Heng-Lin Cui
Extremophiles.2023;[Epub] CrossRef -
Halomicroarcula laminariae sp. nov. and Halomicroarcula marina sp. nov., extremely halophilic archaea isolated from salted brown alga Laminaria and coastal saline-alkali lands
Xue Ma, Yao Hu, Xin-Xin Li, Shun Tan, Mu Cheng, Jing Hou, Heng-Lin Cui
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef - Natrinema caseinilyticum sp. nov., Natrinema gelatinilyticum sp. nov., Natrinema marinum sp. nov., Natrinema zhouii sp. nov., extremely halophilic archaea isolated from marine environments and a salt mine
Yao Hu, Xue Ma, Xin-Xin Li, Shun Tan, Mu Cheng, Jing Hou, Heng-Lin Cui
Extremophiles.2023;[Epub] CrossRef -
Halobacterium wangiae sp. nov. and Halobacterium zhouii sp. nov., two extremely halophilic archaea isolated from sediment of a salt lake and saline soil of an inland saltern
Bei-Bei Wang, Chen-Xi Bao, Ya-Ping Sun, Jing Hou, Heng-Lin Cui
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef -
Halocatena salina sp. nov., a filamentous halophilic archaeon isolated from Aiding Salt Lake
Zhang-Ping Wu, Xi-Wen Zheng, Ya-Ping Sun, Bei-Bei Wang, Jing Hou, Heng-Lin Cui
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef - Correlating bacterial and archaeal community with efficiency of a coking wastewater treatment plant employing anaerobic-anoxic-oxic process in coal industry
Qiaoying Ban, Liguo Zhang, Jianzheng Li
Chemosphere.2022; 286: 131724. CrossRef - Isolation and characterization of tick-borne Roseomonas haemaphysalidis sp. nov. and rodent-borne Roseomonas marmotae sp. nov.
Wentao Zhu, Juan Zhou, Shan Lu, Jing Yang, Xin-He Lai, Dong Jin, Ji Pu, Yuyuan Huang, Liyun Liu, Zhenjun Li, Jianguo Xu
Journal of Microbiology.2022; 60(2): 137. CrossRef - Haloprofundus salilacus sp. nov., Haloprofundus halobius sp. nov. and Haloprofundus salinisoli sp. nov.: three extremely halophilic archaea isolated from salt lake and saline soil
Si-Ya Li, Yu-Jie Xin, Chen-Xi Bao, Jing Hou, Heng-Lin Cui
Extremophiles.2022;[Epub] CrossRef - Natronorubrum halalkaliphilum sp. nov., a haloalkaliphilic archaeon isolated from soda lake in Inner Mongolia Autonomous Region, China
Qiong Xue, Dahe Zhao, Zhenqiang Zuo, Jian Zhou, Hua Xiang
Archives of Microbiology.2021; 203(5): 2335. CrossRef - Phylogenomics of Haloarchaea: The Controversy of the Genera Natrinema-Haloterrigena
Rafael R. de la Haba, Hiroaki Minegishi, Masahiro Kamekura, Yasuhiro Shimane, Antonio Ventosa
Frontiers in Microbiology.2021;[Epub] CrossRef -
Salinadaptatus halalkaliphilus gen. nov., sp. nov., a haloalkaliphilic archaeon isolated from salt pond in Inner Mongolia Autonomous Region, China
Qiong Xue, Zhenqiang Zuo, Heng Zhou, Jian Zhou, Shengjie Zhang, Jing Han, Dahe Zhao, Hua Xiang
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef - Cultivation of halophilic archaea (class Halobacteria) from thalassohaline and athalassohaline environments
Heng-Lin Cui, Mike L. Dyall-Smith
Marine Life Science & Technology.2021; 3(2): 243. CrossRef - List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology.2020; 70(5): 2960. CrossRef
- Genome-based taxonomy of genera Haloarcula and Halomicroarcula, and description of six novel species of Haloarcula
- Oxygen-mediated growth enhancement of an obligate anaerobic archaeon Thermococcus onnurineus NA1
- Seong Hyuk Lee , Hwan Youn , Sung Gyun Kang , Hyun Sook Lee
- J. Microbiol. 2019;57(2):138-142. Published online January 31, 2019
- DOI: https://doi.org/10.1007/s12275-019-8592-y
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Abstract
- Thermococcus onnurineus NA1, an obligate anaerobic hyperthermophilic archaeon, showed variable oxygen (O2) sensitivity depending on the types of substrate employed as an energy source. Unexpectedly, the culture with yeast extract as a sole energy source showed enhanced growth by 2-fold in the presence of O2. Genome-wide transcriptome analysis revealed the upregulation of several antioxidant-related genes encoding thioredoxin peroxidase (TON_0862), rubrerythrin (TON_0864), rubrerythrin-related protein (TON_0873), NAD(P)H rubredoxin oxidoreductase (TON_0865), or thioredoxin reductase (TON_1603), which can couple the detoxification of reactive oxygen species with the regeneration of NAD(P)+ from NAD(P)H. We present a plausible mechanism by which O2 serves to maintain the intracellular redox balance. This study demonstrates an unusual strategy of an obligate anaerobe underlying O2-mediated growth enhancement despite not having heme-based or cytochrome-type proteins.
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Citations
Citations to this article as recorded by- How low can they go? Aerobic respiration by microorganisms under apparent anoxia
Jasmine S Berg, Soeren Ahmerkamp, Petra Pjevac, Bela Hausmann, Jana Milucka, Marcel M M Kuypers
FEMS Microbiology Reviews.2022;[Epub] CrossRef - Reductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii
David Moreira, Yvan Zivanovic, Ana I. López-Archilla, Miguel Iniesto, Purificación López-García
Nature Communications.2021;[Epub] CrossRef
- How low can they go? Aerobic respiration by microorganisms under apparent anoxia
Research Support, Non-U.S. Gov't
- Halorubrum cibi sp. nov., an Extremely Halophilic Archaeon from Salt-Fermented Seafood
- Seong Woon Roh , Jin-Woo Bae
- J. Microbiol. 2009;47(2):162-166. Published online May 2, 2009
- DOI: https://doi.org/10.1007/s12275-009-0016-y
- 36 View
- 0 Download
- 21 Crossref
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Abstract
- Strain B31T is a Gram-staining-negative, motile, and extremely halophilic archaeon that was isolated from salt-fermented seafood. Its morphology, physiology, biochemical features, and 16S rRNA gene sequence were determined. Phylogenetic analysis of its 16S rRNA gene sequence and composition of its major polar lipids placed this archaeon in the genus Halorubrum of the family Halobacteriaceae. Strain B31T showed 97.3, 97.2, and 96.9% 16S rRNA similarity to the type strains of Halorubrum alkaliphilum, Hrr. tibetense, and Hrr. vacuolatum, respectively. Its major polar lipids were phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me) and sulfated diglycosyl diether (S-DGD). Genomic DNA from strain B31T has a 61.7 mol% G+C content. Analysis of 16S rRNA gene sequences, as well as physiological and biochemical tests, identified genotypic and phenotypic differences between strain B31T and other Halorubrum species. The type strain of the novel species is B31T (=JCM 15757T =DSM 19504T).
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Citations
Citations to this article as recorded by- Tissue-like multicellular development triggered by mechanical compression in archaea
Theopi Rados, Olivia S. Leland, Pedro Escudeiro, John Mallon, Katherine Andre, Ido Caspy, Andriko von Kügelgen, Elad Stolovicki, Sinead Nguyen, Inés Lucía Patop, L. Thiberio Rangel, Sebastian Kadener, Lars D. Renner, Vera Thiel, Yoav Soen, Tanmay A. M. Bh
Science.2025; 388(6742): 109. CrossRef - Halophilic microbes and mineral compositions in salts associated to fermentation and quality of fermented radish
Niu Haiyue, Zhang Jianming, Zhang Chengcheng, Xin Xiaoting, Liu Daqun
LWT.2024; 193: 115746. CrossRef - Archaeal lipids
Tomáš Řezanka, Lucie Kyselová, Denis J. Murphy
Progress in Lipid Research.2023; 91: 101237. CrossRef - Comparative Genomics of Halobacterium salinarum Strains Isolated from Salted Foods Reveals Protechnological Genes for Food Applications
Alessandra Fontana, Irene Falasconi, Paolo Bellassi, Elisabetta Fanfoni, Edoardo Puglisi, Lorenzo Morelli
Microorganisms.2023; 11(3): 587. CrossRef -
Jeotgalibaca ciconiae sp. nov., isolated from the faeces of an Oriental stork
So-Yeon Lee, Woorim Kang, Pil Soo Kim, Hyun Sik Kim, Hojun Sung, Na-Ri Shin, Ji-Hyun Yun, Jae-Yun Lee, June-Young Lee, Mi-Ja Jung, Yun-Seok Jeong, Euon Jung Tak, Jeong Eun Han, Dong-Wook Hyun, Myung-Suk Kang, Ki-Eun Lee, Byoung-Hee Lee, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2020; 70(5): 3247. CrossRef - Undibacterium piscinae sp. nov., isolated from Korean shiner intestine
So-Yeon Lee, Woorim Kang, Pil Soo Kim, Hyun Sik Kim, Hojun Sung, Na-Ri Shin, Tae Woong Whon, Ji-Hyun Yun, Jae-Yun Lee, June-Young Lee, Mi-Ja Jung, Yun-Seok Jeong, Euon Jung Tak, Jeong Eun Han, Dong-Wook Hyun, Myung-Suk Kang, Ki-Eun Lee, Byoung-Hee Lee, Ji
International Journal of Systematic and Evolutionary Microbiology.2019; 69(10): 3148. CrossRef - Halorubrum aethiopicum sp. nov., an extremely halophilic archaeon isolated from commercial rock salt
Ashagrie Gibtan, Hye Seon Song, Joon Yong Kim, Yeon Bee Kim, Nakyeong Park, Kyounghee Park, Sang-Jae Lee, Joseph Kwon, Seong Woon Roh, Han-Seung Lee
International Journal of Systematic and Evolutionary Microbiology.2018; 68(1): 416. CrossRef - Systematics of haloarchaea and biotechnological potential of their hydrolytic enzymes
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Microbiology.2017; 163(5): 623. CrossRef - Halorubrum halodurans sp. nov., an extremely halophilic archaeon isolated from a hypersaline lake
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Aquatic Biosystems.2012;[Epub] CrossRef -
Halorubrum aquaticum sp. nov., an archaeon isolated from hypersaline lakes
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International Journal of Microbiology.2011; 2011: 1. CrossRef - Salinarchaeum laminariae gen. nov., sp. nov.: a new member of the family Halobacteriaceae isolated from salted brown alga Laminaria
Heng-Lin Cui, Xin Yang, Yun-Zhuang Mou
Extremophiles.2011; 15(6): 625. CrossRef -
Complete Genome Sequence of
Halalkalicoccus jeotgali
B3
T
, an Extremely Halophilic Archaeon
Seong Woon Roh, Young-Do Nam, Seong-Hyeuk Nam, Sang-Haeng Choi, Hong-Seog Park, Jin-Woo Bae
Journal of Bacteriology.2010; 192(17): 4528. CrossRef - Haladaptatus cibarius sp. nov., an extremely halophilic archaeon from seafood, and emended description of the genus Haladaptatus
Seong Woon Roh, Myung-Lip Lee, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology.2010; 60(5): 1187. CrossRef - List of new names and new combinations previously effectively, but not validly, published
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY.2009; 59(9): 2129. CrossRef
- Tissue-like multicellular development triggered by mechanical compression in archaea
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