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Wu Y, Zhu M, Ouyang X, Qi X, Guo Z, Yuan Y, Dang Z, Yin H. Integrated transcriptomics and metabolomics analyses reveal the aerobic biodegradation and molecular mechanisms of 2,3',4,4',5-pentachlorodiphenyl (PCB 118) in Methylorubrum sp. ZY-1. CHEMOSPHERE 2024; 356:141921. [PMID: 38588902 DOI: 10.1016/j.chemosphere.2024.141921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/18/2024] [Accepted: 04/04/2024] [Indexed: 04/10/2024]
Abstract
2,3',4,4',5-pentachlorodiphenyl (PCB 118), a highly representative PCB congener, has been frequently detected in various environments, garnering much attention across the scientific community. The degradation of highly chlorinated PCBs by aerobic microorganisms is challenging due to their hydrophobicity and persistence. Herein, the biodegradation and adaptation mechanisms of Methylorubrum sp. ZY-1 to PCB 118 were comprehensively investigated using an integrative approach that combined degradation performance, product identification, metabolomic and transcriptomic analyses. The results indicated that the highest degradation efficiency of 0.5 mg L-1 PCB 118 reached 75.66% after seven days of inoculation when the bacteria dosage was 1.0 g L-1 at pH 7.0. A total of eleven products were identified during the degradation process, including low chlorinated PCBs, hydroxylated PCBs, and ring-opening products, suggesting that strain ZY-1 degraded PCB 118 through dechlorination, hydroxylation, and ring-opening pathways. Metabolomic analysis demonstrated that the energy supply and redox metabolism of strain ZY-1 was disturbed with exposure to PCB 118. To counteract this environmental stress, strain ZY-1 adjusted both the fatty acid synthesis and purine metabolism. The analysis of transcriptomics disclosed that multiple intracellular and extracellular oxidoreductases (e.g., monooxygenase, alpha/beta hydrolase and cytochrome P450) participated in the degradation of PCB 118. Besides, active efflux of PCB 118 and its degradation intermediates mediated by multiple transporters (e.g., MFS transporter and ABC transporter ATP-binding protein) might enhance bacterial resistance against these substances. These discoveries provided the inaugural insights into the biotransformation of strain ZY-1 to PCB 118 stress, illustrating its potential in the remediation of contaminated environments.
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Affiliation(s)
- Yuxuan Wu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Minghan Zhu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Xiaofang Ouyang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Xin Qi
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Zhanyu Guo
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Yibo Yuan
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou, 510006, China
| | - Hua Yin
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China; Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Solid Wastes Pollution Control and Recycling, Guangzhou, 510006, China.
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2
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Kremer M, Schulze S, Eisenbruch N, Nagel F, Vogt R, Berndt L, Dörre B, Palm GJ, Hoppen J, Girbardt B, Albrecht D, Sievers S, Delcea M, Baumann U, Schnetz K, Lammers M. Bacteria employ lysine acetylation of transcriptional regulators to adapt gene expression to cellular metabolism. Nat Commun 2024; 15:1674. [PMID: 38395951 PMCID: PMC10891134 DOI: 10.1038/s41467-024-46039-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
The Escherichia coli TetR-related transcriptional regulator RutR is involved in the coordination of pyrimidine and purine metabolism. Here we report that lysine acetylation modulates RutR function. Applying the genetic code expansion concept, we produced site-specifically lysine-acetylated RutR proteins. The crystal structure of lysine-acetylated RutR reveals how acetylation switches off RutR-DNA-binding. We apply the genetic code expansion concept in E. coli in vivo revealing the consequences of RutR acetylation on the transcriptional level. We propose a model in which RutR acetylation follows different kinetic profiles either reacting non-enzymatically with acetyl-phosphate or enzymatically catalysed by the lysine acetyltransferases PatZ/YfiQ and YiaC. The NAD+-dependent sirtuin deacetylase CobB reverses enzymatic and non-enzymatic acetylation of RutR playing a dual regulatory and detoxifying role. By detecting cellular acetyl-CoA, NAD+ and acetyl-phosphate, bacteria apply lysine acetylation of transcriptional regulators to sense the cellular metabolic state directly adjusting gene expression to changing environmental conditions.
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Affiliation(s)
- Magdalena Kremer
- Institute of Biochemistry, University of Cologne, Zülpicher Straße 47, 50674, Cologne, Germany
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Sabrina Schulze
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Nadja Eisenbruch
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Felix Nagel
- Institute of Biochemistry, Department of Biophysical Chemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Robert Vogt
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Leona Berndt
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Babett Dörre
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Gottfried J Palm
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Jens Hoppen
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Britta Girbardt
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Dirk Albrecht
- Institute of Microbiology, Department of Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany
| | - Susanne Sievers
- Institute of Microbiology, Department of Microbial Physiology and Molecular Biology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489, Greifswald, Germany
| | - Mihaela Delcea
- Institute of Biochemistry, Department of Biophysical Chemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - Ulrich Baumann
- Institute of Biochemistry, University of Cologne, Zülpicher Straße 47, 50674, Cologne, Germany
| | - Karin Schnetz
- Institute for Genetics, University of Cologne Zülpicher Straße 47a, 50674, Cologne, Germany
| | - Michael Lammers
- Institute of Biochemistry, Department of Synthetic and Structural Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany.
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3
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Zhou S, Zhu R, Niu X, Zhao Y, Deng Y. Metabolic engineering of Paracoccus denitrificans for dual degradation of sulfamethoxazole and ammonia nitrogen. Microbiol Spectr 2023; 11:e0014623. [PMID: 37732744 PMCID: PMC10581052 DOI: 10.1128/spectrum.00146-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 07/21/2023] [Indexed: 09/22/2023] Open
Abstract
Sulfamethoxazole (SMX), as one of the most widely used sulfonamide antibiotics, has been frequently detected in the aqueous environment, posing potential risks to the environment and human health. Although microbial degradation methods have been widely applied, some issues remain, including low degradation efficiency and poor environmental adaptability. In this regard, constructing efficient degrading bacteria by metabolic engineering is an ideal solution to these challenges. In this study, we used Paracoccus denitrificans DYTN-1, a superior nitrogen removal environment strain, as chassis to construct an SMX degradation pathway, obtaining a new bacteria for simultaneous degradation of SMX and removal of ammonia nitrogen. In doing this, we first identified and characterized four native promoters of P. denitrificans DYTN-1 with gradient strength to control the expression of the SMX degradation pathway. After degradation pathway expression level optimization and FMN reductase optimization, SMX degradation efficiency was significantly improved. The constructed P. d-pIAB4-PCS-sutR strain exhibited superior co-degradation of SMX and ammonia nitrogen contaminants with degradation rates of 44% and 71%, respectively. This study could pave the way for SMX degradation engineered strain design and evolution of environmental bioremediation. IMPORTANCE The abuse of sulfamethoxazole (SMX) had led to an increased accumulation in the environment, resulting in the disruption of the structure of microbial communities, further disrupting the bio-degradation process of other pollutants, such as ammonia nitrogen. To solve this challenge, we first identified and characterized four native promoters of Paracoccus denitrificans DYTN-1 with gradient strength to control the expression of the SMX degradation pathway. Then SMX degradation efficiency was significantly improved with degradation pathway expression level optimization and FMN reductase optimization. Finally, the superior nitrogen removal environment strain, P. denitrificans DYTN-1, obtained an SMX degradation function. This pioneering study of metabolic engineering to enhance the SMX degradation in microorganisms could pave the way for designing the engineered strains of SMX and nitrogen co-degradation and the environmental bioremediation.
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Affiliation(s)
- Shenghu Zhou
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Rongrong Zhu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiaoqian Niu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yunying Zhao
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yu Deng
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, Jiangsu, China
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4
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Tong Y, Wei Y, Ju Y, Li P, Zhang Y, Li L, Gao L, Liu S, Liu D, Hu Y, Li Z, Yu H, Luo Y, Wang J, Wang Y, Zhang Y. Anaerobic purinolytic enzymes enable dietary purine clearance by engineered gut bacteria. Cell Chem Biol 2023; 30:1104-1114.e7. [PMID: 37164019 DOI: 10.1016/j.chembiol.2023.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/08/2023] [Accepted: 04/17/2023] [Indexed: 05/12/2023]
Abstract
Uric acid, the end product of purine degradation, causes hyperuricemia and gout, afflicting hundreds of millions of people. The debilitating effects of gout are exacerbated by dietary purine intake, and thus a potential therapeutic strategy is to enhance purine degradation in the gut microbiome. Aerobic purine degradation involves oxidative dearomatization of uric acid catalyzed by the O2-dependent uricase. The enzymes involved in purine degradation in strictly anaerobic bacteria remain unknown. Here we report the identification and characterization of these enzymes, which include four hydrolases belonging to different enzyme families, and a prenyl-flavin mononucleotide-dependent decarboxylase. Introduction of the first two hydrolases to Escherichia coli Nissle 1917 enabled its anaerobic growth on xanthine as the sole nitrogen source. Oral supplementation of these engineered probiotics ameliorated hyperuricemia in a Drosophila melanogaster model, including the formation of renal uric acid stones and a shortened lifespan, providing a route toward the development of purinolytic probiotics.
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Affiliation(s)
- Yang Tong
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Department of Chemistry, Tianjin University, Tianjin 300072, P.R. China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A∗STAR), Singapore 138669, Singapore
| | - Yingjie Ju
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Peishan Li
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yumin Zhang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300192, P.R. China
| | - Liqin Li
- Tianjin Speerise Challenge Biotechnology Co., Ltd., Zhangjiawo Industrial Park, No. 16 Huiyuan Road, Zhangjiawo Town, Xiqing District, Tianjin 300380, China
| | - Lujuan Gao
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Shengnan Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Dazhi Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Meining Pharma Inc, 2-401-1, Bldg 8, Huiying Industrial Park, No. 86 West Zhonghuan Road, Tianjin Pilot Free Trade Zone, Tianjin 300308, China
| | - Yiling Hu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Zhi Li
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Hongbin Yu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yunzi Luo
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jian Wang
- Tianjin Speerise Challenge Biotechnology Co., Ltd., Zhangjiawo Industrial Park, No. 16 Huiyuan Road, Zhangjiawo Town, Xiqing District, Tianjin 300380, China
| | - Yiwen Wang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Department of Chemistry, Tianjin University, Tianjin 300072, P.R. China.
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5
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Zhang X, Xin J, Wang Z, Wu W, Liu Y, Min Z, Xin Y, Liu B, He J, Zhang X, Xu X. Structural basis of a bi-functional malonyl-CoA reductase (MCR) from the photosynthetic green non-sulfur bacterium Roseiflexus castenholzii. mBio 2023; 14:e0323322. [PMID: 37278533 PMCID: PMC10470521 DOI: 10.1128/mbio.03233-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 04/10/2023] [Indexed: 06/07/2023] Open
Abstract
Malonyl-CoA reductase (MCR) is a NADPH-dependent bi-functional enzyme that performs alcohol dehydrogenase and aldehyde dehydrogenase (CoA-acylating) activities in the N- and C-terminal fragments, respectively. It catalyzes the two-step reduction of malonyl-CoA to 3-hydroxypropionate (3-HP), a key reaction in the autotrophic CO2 fixation cycles of Chloroflexaceae green non-sulfur bacteria and the archaea Crenarchaeota. However, the structural basis underlying substrate selection, coordination, and the subsequent catalytic reactions of full-length MCR is largely unknown. For the first time, we here determined the structure of full-length MCR from the photosynthetic green non-sulfur bacterium Roseiflexus castenholzii (RfxMCR) at 3.35 Å resolution. Furthermore, we determined the crystal structures of the N- and C-terminal fragments bound with reaction intermediates NADP+ and malonate semialdehyde (MSA) at 2.0 Å and 2.3 Å, respectively, and elucidated the catalytic mechanisms using a combination of molecular dynamics simulations and enzymatic analyses. Full-length RfxMCR was a homodimer of two cross-interlocked subunits, each containing four tandemly arranged short-chain dehydrogenase/reductase (SDR) domains. Only the catalytic domains SDR1 and SDR3 incorporated additional secondary structures that changed with NADP+-MSA binding. The substrate, malonyl-CoA, was immobilized in the substrate-binding pocket of SDR3 through coordination with Arg1164 and Arg799 of SDR4 and the extra domain, respectively. Malonyl-CoA was successively reduced through protonation by the Tyr743-Arg746 pair in SDR3 and the catalytic triad (Thr165-Tyr178-Lys182) in SDR1 after nucleophilic attack from NADPH hydrides. IMPORTANCE The bi-functional MCR catalyzes NADPH-dependent reduction of malonyl-CoA to 3-HP, an important metabolic intermediate and platform chemical, from biomass. The individual MCR-N and MCR-C fragments, which contain the alcohol dehydrogenase and aldehyde dehydrogenase (CoA-acylating) activities, respectively, have previously been structurally investigated and reconstructed into a malonyl-CoA pathway for the biosynthetic production of 3-HP. However, no structural information for full-length MCR has been available to illustrate the catalytic mechanism of this enzyme, which greatly limits our capacity to increase the 3-HP yield of recombinant strains. Here, we report the cryo-electron microscopy structure of full-length MCR for the first time and elucidate the mechanisms underlying substrate selection, coordination, and catalysis in the bi-functional MCR. These findings provide a structural and mechanistic basis for enzyme engineering and biosynthetic applications of the 3-HP carbon fixation pathways.
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Affiliation(s)
- Xin Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and the Affiliated Hospital, Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
- Photosynthesis Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Jiyu Xin
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and the Affiliated Hospital, Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Zhiguo Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and the Affiliated Hospital, Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Wenping Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and the Affiliated Hospital, Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Yutong Liu
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Zhenzhen Min
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and the Affiliated Hospital, Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Yueyong Xin
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and the Affiliated Hospital, Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Bing Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and the Affiliated Hospital, Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Jun He
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xingwei Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and the Affiliated Hospital, Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
| | - Xiaoling Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and the Affiliated Hospital, Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Hangzhou Normal University, Hangzhou, China
- Photosynthesis Research Center, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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6
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Sonnleitner E, Bassani F, Cianciulli Sesso A, Brear P, Lilic B, Davidovski L, Resch A, Luisi BF, Moll I, Bläsi U. Catabolite repression control protein antagonist, a novel player in Pseudomonas aeruginosa carbon catabolite repression control. Front Microbiol 2023; 14:1195558. [PMID: 37250041 PMCID: PMC10213629 DOI: 10.3389/fmicb.2023.1195558] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/18/2023] [Indexed: 05/31/2023] Open
Abstract
In the opportunistic human pathogen Pseudomonas aeruginosa (Pae), carbon catabolite repression (CCR) orchestrates the hierarchical utilization of N and C sources, and impacts virulence, antibiotic resistance and biofilm development. During CCR, the RNA chaperone Hfq and the catabolite repression control protein Crc form assemblies on target mRNAs that impede translation of proteins involved in uptake and catabolism of less preferred C sources. After exhaustion of the preferred C-source, translational repression of target genes is relieved by the regulatory RNA CrcZ, which binds to and acts as a decoy for Hfq. Here, we asked whether Crc action can be modulated to relieve CCR after exhaustion of a preferred carbon source. As Crc does not bind to RNA per se, we endeavored to identify an interacting protein. In vivo co-purification studies, co-immunoprecipitation and biophysical assays revealed that Crc binds to Pae strain O1 protein PA1677. Our structural studies support bioinformatics analyzes showing that PA1677 belongs to the isochorismatase-like superfamily. Ectopic expression of PA1677 resulted in de-repression of Hfq/Crc controlled target genes, while in the absence of the protein, an extended lag phase is observed during diauxic growth on a preferred and a non-preferred carbon source. This observations indicate that PA1677 acts as an antagonist of Crc that favors synthesis of proteins required to metabolize non-preferred carbon sources. We present a working model wherein PA1677 diminishes the formation of productive Hfq/Crc repressive complexes on target mRNAs by titrating Crc. Accordingly, we propose the name CrcA (catabolite repression control protein antagonist) for PA1677.
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Affiliation(s)
- Elisabeth Sonnleitner
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Center of Molecular Biology, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Flavia Bassani
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Center of Molecular Biology, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Anastasia Cianciulli Sesso
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Center of Molecular Biology, Vienna Biocenter, University of Vienna, Vienna, Austria
- Vienna BioCenter PhD Program, a doctoral School of the University of Vienna and Medical University of Vienna, Max Perutz Labs, Center of Molecular Biology, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Branislav Lilic
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Center of Molecular Biology, Vienna Biocenter, University of Vienna, Vienna, Austria
- Vienna BioCenter PhD Program, a doctoral School of the University of Vienna and Medical University of Vienna, Max Perutz Labs, Center of Molecular Biology, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Lovro Davidovski
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Center of Molecular Biology, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Armin Resch
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Center of Molecular Biology, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Ben F. Luisi
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Isabella Moll
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Center of Molecular Biology, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Center of Molecular Biology, Vienna Biocenter, University of Vienna, Vienna, Austria
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7
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Fulton RL, Downs DM. Modulators of a robust and efficient metabolism: Perspective and insights from the Rid superfamily of proteins. Adv Microb Physiol 2023; 83:117-179. [PMID: 37507158 PMCID: PMC10642521 DOI: 10.1016/bs.ampbs.2023.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Metabolism is an integrated network of biochemical pathways that assemble to generate the robust, responsive physiologies of microorganisms. Despite decades of fundamental studies on metabolic processes and pathways, our understanding of the nuance and complexity of metabolism remains incomplete. The ability to predict and model metabolic network structure, and its influence on cellular fitness, is complicated by the persistence of genes of unknown function, even in the best-studied model organisms. This review describes the definition and continuing study of the Rid superfamily of proteins. These studies are presented with a perspective that illustrates how metabolic complexity can complicate the assignment of function to uncharacterized genes. The Rid superfamily of proteins has been divided into eight subfamilies, including the well-studied RidA subfamily. Aside from the RidA proteins, which are present in all domains of life and prevent metabolic stress, most members of the Rid superfamily have no demonstrated physiological role. Recent progress on functional assignment supports the hypothesis that, overall, proteins in the Rid superfamily modulate metabolic processes to ensure optimal organismal fitness.
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Affiliation(s)
- Ronnie L Fulton
- Department of Microbiology, University of Georgia, Athens, GA, United States
| | - Diana M Downs
- Department of Microbiology, University of Georgia, Athens, GA, United States.
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8
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Busch MR, Rajendran C, Sterner R. Structural and Functional Characterization of the Ureidoacrylate Amidohydrolase RutB from Escherichia coli. Biochemistry 2023; 62:863-872. [PMID: 36599150 DOI: 10.1021/acs.biochem.2c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We present a detailed structure-function analysis of the ureidoacrylate amidohydrolase RutB from Eschericha coli, which is an essential enzyme of the Rut pathway for pyrimidine utilization. Crystals of selenomethionine-labeled RutB were produced, which allowed us to determine the first structure of the enzyme at a resolution of 1.9 Å and to identify it as a new member of the isochorismatase-like hydrolase family. RutB was co-crystallized with the substrate analogue ureidopropionate, revealing the mode of substrate binding. Mutation of residues constituting the catalytic triad (D24A, D24N, K133A, C166A, C166S, C166T, C166Y) resulted in complete inactivation of RutB, whereas mutation of other residues close to the active site (Y29F, Y35F, N72A, W74A, W74F, E80A, E80D, S92A, S92T, S92Y, Q105A, Y136A, Y136F) leads to distinct changes of the turnover number (kcat) and/or the Michaelis constant (KM). The results of our structural and mutational studies allowed us to assign specific functions to individual residues and to formulate a plausible reaction mechanism for RutB.
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Affiliation(s)
- Markus R Busch
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Chitra Rajendran
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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9
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Nie M, Li K, Li Z. β-Alanine Metabolism Leads to Increased Extracellular pH during the Heterotrophic Ammonia Oxidation of Pseudomonas putida Y-9. Microorganisms 2023; 11:microorganisms11020356. [PMID: 36838321 PMCID: PMC9963543 DOI: 10.3390/microorganisms11020356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 01/20/2023] [Accepted: 01/20/2023] [Indexed: 02/04/2023] Open
Abstract
The mechanisms underlying the increase in external pH caused by heterotrophic nitrification and aerobic denitrification microorganisms during ammonia oxidation were unclear. This work demonstrated that after culturing Pseudomonas putida Y-9 for 60 h in a medium with ammonium nitrogen as the sole nitrogen source at an initial pH of 7.20, the pH value increased to 9.21. GC-TOF-MS analysis was used to compare the significantly regulated metabolites and related metabolic pathways between different time points. The results showed that the consumption of H+ in the conversion of malonic acid to 3-hydroxypropionic acid in the β-alanine metabolic pathway was the main reason for the increase in pH. RT-qPCR confirmed that the functional gene ydfG dominated the consumption of H+. This study provides new research ideas for the change of external pH caused by bacterial metabolism and further expands the understanding of the interaction between bacteria and the environment.
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Affiliation(s)
- Ming Nie
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, College of Resources and Environment, Southwest University, Chongqing 400716, China
| | - Kaili Li
- School of Chemical Engineering, University of Queensland, Brisbane 4072, Australia
| | - Zhenlun Li
- Chongqing Key Laboratory of Soil Multiscale Interfacial Process, College of Resources and Environment, Southwest University, Chongqing 400716, China
- Correspondence: ; Tel.: +86-138-8337-2713
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10
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Koch NG, Baumann T, Nickling JH, Dziegielewski A, Budisa N. Engineered bacterial host for genetic encoding of physiologically stable protein nitration. Front Mol Biosci 2022; 9:992748. [PMID: 36353730 PMCID: PMC9638147 DOI: 10.3389/fmolb.2022.992748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/16/2022] [Indexed: 11/23/2022] Open
Abstract
Across scales, many biological phenomena, such as protein folding or bioadhesion and cohesion, rely on synergistic effects of different amino acid side chains at multiple positions in the protein sequence. These are often fine-tuned by post-translational modifications that introduce additional chemical properties. Several PTMs can now be genetically encoded and precisely installed at single and multiple sites by genetic code expansion. Protein nitration is a PTM of particular interest because it has been associated with several diseases. However, even when these nitro groups are directly incorporated into proteins, they are often physiologically reduced during or shortly after protein production. We have solved this problem by using an engineered Escherichia coli host strain. Six genes that are associated with nitroreductase activity were removed from the genome in a simple and robust manner. The result is a bacterial expression host that can stably produce proteins and peptides containing nitro groups, especially when these are amenable to modification. To demonstrate the applicability of this strain, we used this host for several applications. One of these was the multisite incorporation of a photocaged 3,4-dihydroxyphenylalanine derivative into Elastin-Like Polypeptides. For this non-canonical amino acid and several other photocaged ncAAs, the nitro group is critical for photocleavability. Accordingly, our approach also enhances the production of biomolecules containing photocaged tyrosine in the form of ortho-nitrobenzyl-tyrosine. We envision our engineered host as an efficient tool for the production of custom designed proteins, peptides or biomaterials for various applications ranging from research in cell biology to large-scale production in biotechnology.
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Affiliation(s)
- Nikolaj G. Koch
- Bioanalytics Group, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Tobias Baumann
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Jessica H. Nickling
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Anna Dziegielewski
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
| | - Nediljko Budisa
- Biocatalysis Group, Institute of Chemistry, Technische Universität Berlin, Berlin, Germany
- Chemical Synthetic Biology Group, Department of Chemistry, University of Manitoba, Winnipeg, MB, Canada
- *Correspondence: Nediljko Budisa,
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11
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Li ZW, Wang JH. Analysis of the functional gene of degrading BDE-47 by Acinetobacter pittii GB-2 based on transcriptome sequencing. Gene 2022; 844:146826. [PMID: 35998843 DOI: 10.1016/j.gene.2022.146826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 07/06/2022] [Accepted: 08/16/2022] [Indexed: 11/19/2022]
Abstract
2,2',4,4'-tetrabrominated diphenyl ether (BDE-47) is one of the most widely distributed PBDEs. BDE-47 is also the most abundant in organisms and the most toxic to humans and animals. Herein, we have studied the pathway of BDE-47 degradation and gene involvement in Acinetobacter pittii GB-2. This degradation is dominated by hydroxylation, resulting in hydroxylated products 6-OH-BDE-47, 5-OH-BDE-47 and 2'-OH-BDE-28, and bromophenol products 2,4-DBP and 4-BP. Transcriptome sequencing results showed 359 differentially expressed genes (DEGs) induced by BDE-47, of which 159 were up-regulated and 200 were down-regulated. The up-regulated ones were mainly related to substance transport, degradation and cell stress. From these results, we suggest that 1,2-dioxygenase, phenol hydroxylase and monooxygenase are involved in BDE-47 degradation. The function of AntA gene was identified by constructing a prokaryotic expression vector. Our study contributes to understanding how the metabolism of strain GB-2 changes under BDE-47 stress conditions, and sheds light on the mechanism of BDE-47 degradation.
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Affiliation(s)
- Zi-Wei Li
- School of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Ji-Hua Wang
- School of Life Science and Technology, Harbin Normal University, Harbin 150025, China.
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12
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Ouyang Q, Pang Y, Yuan C, Tan H, Li X, Chen G. Theoretical investigation on the reaction mechanism of UTP cyclohydrolase. Phys Chem Chem Phys 2022; 24:17641-17653. [PMID: 35833743 DOI: 10.1039/d2cp01740g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nucleoside triphosphate cyclohydrolase (UrcA) is a critical enzyme of the uracil catabolism pathway that catalyses the two-step hydrolysis of uridine triphosphate (UTP). Although the recently resolved X-ray structure of UrcA in complex with substrate analogue dUTP provided insights into the structural characteristics of the enzyme, the detailed catalytic mechanism, including how the reaction intermediate accomplishes conformational conversion in the active centre, remains unclear. In this study, extensive DFT calculations and MD simulations were performed to investigate the catalytic reaction process of UrcA. This study shows that the first hydrolytic reactions in UrcA follow a three-step mechanism, while the second hydrolytic reaction follows a two-step mechanism. Glu392 plays a critical role in deprotonating the lytic water in both hydrolytic reactions. The rate-limiting step of the first hydrolytic reaction lies in the cleavage of the uracil ring, in which an extraneous water molecule bridges the proton transfer from C6-OH to N1 to enable the reaction to go through a six-membered transition state with relatively low steric tension. In the second hydrolytic reaction, Glu392 abstracts protons from the lytic water and directly transfers them to the nitrogen atom of the cleaved C4-N3 bond so that the hydrolytic reaction is no longer rate-limited by the C-N bond cleavage step. MD simulations show that the reaction intermediate experiences spontaneous conformation overturn in the active site of UrcA under the assistance of the hydrogen bond interaction from Tyr307 to place its C4-N3 bond alongside the Zn2+ centre of the enzyme to trigger the second hydrolytic reaction.
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Affiliation(s)
- Qingwen Ouyang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Yunjie Pang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Chang Yuan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Hongwei Tan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Xichen Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
| | - Guangju Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China.
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13
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Converting the E. coli Isochorismatase Nicotinamidase into γ-Lactamase. Microbiol Spectr 2022; 10:e0098521. [PMID: 35171012 PMCID: PMC8849098 DOI: 10.1128/spectrum.00985-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nicotinamidase (Nic) (E.C.3.5.1.19) is a representative protein of the isochorismatase superfamily from Escherichia coli. Despite showing no (+) γ-lactamase activity, its active site constellations (ASCs) are very similar to those of two other known (+) γ-lactamases (Mhpg and RutB), indicating that it could be a latent (+) γ-lactamase. In this study, the primary sequences of the five representative proteins of the isochorismatase superfamily from E. coli were aligned, and a "lid"-like unit of a six-residue loop (112GENPLV117) was established. The Nic protein was converted to a (+) γ-lactamase by eliminating the loop. A conversion mechanism was proposed in which a more compact binding pocket is formed after lid deletion. In addition, the "shrunk" binding pocket stabilized the small substrate and the catalysis intermediate, which triggered catalysis. Moreover, we identified another latent (+) γ-lactamase in the E. coli isochorismatase superfamily and successfully converted it into an active (+) γ-lactamase. In summary, the isochorismatase superfamily is potentially a good candidate for obtaining novel (+) γ-lactamases. IMPORTANCE γ-Lactamases are important enzymatic catalysts in preparing optically pure γ-lactam enantiomers, which are high-value chiral intermediates. Different studies have presumed that the isochorismatase superfamily is a candidate to obtain novel (+) γ-lactamases. By engineering its substrate entrance tunnel, Nic, a representative protein of the isochorismatase superfamily, is converted to a (+) γ-lactamase. Tunnel engineering has proven effective in enhancing enzyme promiscuity. Therefore, the latent or active γ-lactamase activities of the isochorismatase superfamily members indicate their evolutionary path positions.
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14
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Sharma VK, Akavaram S, Bayles DO. Genomewide transcriptional response of Escherichia coli O157:H7 to norepinephrine. BMC Genomics 2022; 23:107. [PMID: 35135480 PMCID: PMC8822769 DOI: 10.1186/s12864-021-08167-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/10/2021] [Indexed: 01/18/2023] Open
Abstract
Background Chemical signaling between a mammalian host and intestinal microbes is health and maintenance of ‘healthy’ intestinal microbiota. Escherichia coli O157:H7 can hijack host- and microbiota-produced chemical signals for survival in a harsh and nutritionally competitive gastrointestinal environment and for intestinal colonization. Norepinephrine (NE) produced by sympathetic neurons of the enteric nervous system has been shown in vitro to induce expression of genes controlling E. coli O157:H7 swimming motility, acid resistance, and adherence to epithelial cells. A previous study used a microarray approach to identify differentially expressed genes in E. coli O157:H7 strain EDL933 in response to NE. To elucidate a comprehensive transcriptional response to NE, we performed RNA-Seq on rRNA-depleted RNA of E. coli O157:H7 strain NADC 6564, an isolate of a foodborne E. coli O157:H7 strain 86–24. The reads generated by RNA-Seq were mapped to NADC 6564 genome using HiSat2. The mapped reads were quantified by htseq-count against the genome of strain NADC 6564. The differentially expressed genes were identified by analyzing quantified reads by DESeq2. Results Of the 585 differentially expressed genes (≥ 2.0-fold; p < 0.05), many encoded pathways promoting ability of E. coli O157:H7 strain NADC 6564 to colonize intestines of carrier animals and to produce disease in an incidental human host through increased adherence to epithelial cells and production of Shiga toxins. In addition, NE exposure also induced the expression of genes encoding pathways conferring prolonged survival at extreme acidity, controlling influx/efflux of specific nutrients/metabolites, and modulating tolerance to various stressors. A correlation was also observed between the EvgS/EvgA signal transduction system and the ability of bacterial cells to survive exposure to high acidity for several hours. Many genes involved in nitrogen, sulfur, and amino acid uptake were upregulated while genes linked to iron (Fe3+) acquisition and transport were downregulated. Conclusion The availability of physiological levels of NE in gastrointestinal tract could serve as an important cue for E. coli O157:H7 to engineer its virulence, stress, and metabolic pathways for colonization in reservoir animals, such as cattle, causing illness in humans, and surviving outside of a host. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08167-z.
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Affiliation(s)
- Vijay K Sharma
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, ARS-USDA, Ames, IA, 50010, USA.
| | - Suryatej Akavaram
- Food Safety and Enteric Pathogens Research Unit, National Animal Disease Center, ARS-USDA, Ames, IA, 50010, USA.,Current address: 4302 TX-332, Freeport, TX, 77541, USA
| | - Darrell O Bayles
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, ARS-USDA, Ames, IA, 50010, USA
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15
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Beard DK, Bristol S, Cosby K, Davis A, Manning C, Perry L, Snapp L, Toy A, Wheeler K, Young J, Staker B, Arakaki TL, Abendroth J, Subrahamanian S, Edwards TE, Myler PJ, Asojo OA. Crystal structure of a hypothetical protein from Giardia lamblia. Acta Crystallogr F Struct Biol Commun 2022; 78:59-65. [PMID: 35102894 PMCID: PMC8805217 DOI: 10.1107/s2053230x21013595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/23/2021] [Indexed: 11/17/2022] Open
Abstract
Giardiasis is the most prevalent diarrheal disease globally and affects humans and animals. It is a significant problem in developing countries, the number one cause of travelers' diarrhea and affects children and immunocompromised individuals, especially HIV-infected individuals. Giardiasis is treated with antibiotics (tinidazole and metronidazole) that are also used for other infections such as trichomoniasis. The ongoing search for new therapeutics for giardiasis includes characterizing the structure and function of proteins from the causative protozoan Giardia lamblia. These proteins include hypothetical proteins that share 30% sequence identity or less with proteins of known structure. Here, the atomic resolution structure of a 15.6 kDa protein was determined by molecular replacement. The structure has the two-layer αβ-sandwich topology observed in the prototypical endoribonucleases L-PSPs (liver perchloric acid-soluble proteins) with conserved allosteric active sites containing small molecules from the crystallization solution. This article is an educational collaboration between Hampton University and the Seattle Structural Genomics Center for Infectious Disease.
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Affiliation(s)
- Dylan K. Beard
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Seonna Bristol
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Kayla Cosby
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Amber Davis
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Courtney Manning
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Lionel Perry
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Lauren Snapp
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Arian Toy
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Kayla Wheeler
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Jeremy Young
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
| | - Bart Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | | | - Jan Abendroth
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
| | - Sandhya Subrahamanian
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Thomas E. Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, Washington, USA
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Peter J. Myler
- Center for Infectious Disease Research, formerly Seattle Biomedical Research Institute, 307 Westlake Avenue North Suite 500, Seattle, WA 98109, USA
| | - Oluwatoyin A. Asojo
- Department of Chemistry and Biochemistry, Hampton University, 100 William R. Harvey Way, Hampton, VA 23668, USA
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16
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Van Houdt R, Vandecraen J, Heylen W, Leys N, Monsieurs P, Provoost A, Aertsen A. Phenotypic and Genetic Characterization of Temperature-Induced Mutagenesis and Mortality in Cupriavidus metallidurans. Front Microbiol 2021; 12:698330. [PMID: 34305863 PMCID: PMC8299993 DOI: 10.3389/fmicb.2021.698330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/11/2021] [Indexed: 11/26/2022] Open
Abstract
Cupriavidus metallidurans strains display a decreased viability when incubated in rich medium at a temperature of 37°C compared to their normal growth temperature of 30°C, a phenomenon coined “temperature-induced mortality and mutagenesis” (TIMM). To scrutinize this aberrant phenotype further, the contributions of specific inducers and protective agents were determined. Different growth media, including lysogeny broth (LB) and Schatz, and components, including casamino acids, in particular amino acids (proline, cysteine, glycine, glutamine, leucine, histidine and phenylalanine) and ammonium, were found to induce TIMM at 37°C. Sorbitol was found to counteract TIMM. Furthermore, although TIMM is well conserved within the C. metallidurans species, multiple and strain-specific TIMM inducers exist. Twenty-nine percent of the TIMM survivors inherited resistance to TIMM. Whole-genome sequencing of two resistant derivatives revealed an important role of an uncharacterized oxidoreductase, indicating putative metabolic poisoning when grown in high-concentration nitrogen-containing media at 37°C.
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Affiliation(s)
- Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Joachim Vandecraen
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium.,Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Wietse Heylen
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Natalie Leys
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Pieter Monsieurs
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Ann Provoost
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Abram Aertsen
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
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17
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Zhang H, Wei Y, Lin L, Liu J, Chu R, Cao P, Ang EL, Zhao H, Yuchi Z, Zhang Y. Structural and Biochemical Investigation of UTP Cyclohydrolase. ACS Catal 2021. [DOI: 10.1021/acscatal.1c02252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Haibin Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #01-01, Singapore 138669
| | - Lianyun Lin
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Jiayi Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Ruoxing Chu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Peng Cao
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ee Lui Ang
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #01-01, Singapore 138669
| | - Huimin Zhao
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #01-01, Singapore 138669
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Zhiguang Yuchi
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
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18
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Rid Enhances the 6-Hydroxypseudooxynicotine Dehydrogenase Reaction in Nicotine Degradation by Agrobacterium tumefaciens S33. Appl Environ Microbiol 2021; 87:AEM.02769-20. [PMID: 33514517 DOI: 10.1128/aem.02769-20] [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: 11/11/2020] [Accepted: 01/17/2021] [Indexed: 02/03/2023] Open
Abstract
Agrobacterium tumefaciens S33 degrades nicotine through a hybrid of the pyridine and pyrrolidine pathways. The oxidation of 6-hydroxypseudooxynicotine to 6-hydroxy-3-succinoyl-semialdehyde-pyridine by 6-hydroxypseudooxynicotine dehydrogenase (Pno) is an important step in the breakdown of the N-heterocycle in this pathway. Although Pno has been characterized, the reaction is not fully understood; what is known is that it starts at a high speed followed by a rapid drop in the reaction rate, leading to the formation of a very small amount of product. In this study, we speculated that an unstable imine intermediate that is toxic with regard to the metabolism is produced in the reaction. We found that a Rid protein (designated Rid-NC) encoded by a gene in the nicotine-degrading gene cluster enhanced the reaction. Rid is a widely distributed family of small proteins with various functions, and some subfamilies have deaminase activity to eliminate the toxicity of the reactive intermediate, imine. Biochemical analyses showed that Rid-NC relieved the toxicity of the presumed imine intermediate produced in the Pno reaction and that, in the presence of Rid-NC, Pno maintained a high level of activity and the amount of the reaction product was increase by at least 5-fold. Disruption of the rid-NC gene led to slower growth of strain S33 on nicotine. The mechanism of Rid-NC-mediated detoxification of the imine intermediate was discussed. A phylogenetic analysis indicated that Rid-NC belongs to the rarely studied Rid6 subfamily. These results further our understanding of the biochemical mechanism of nicotine degradation and provide new insights into the function of the Rid6 subfamily proteins.IMPORTANCE Rid is a family of proteins that participate in metabolite damage repair and is widely distributed in different organisms. In this study, we found that Rid-NC, which belongs to the Rid6 subfamily, promoted the 6-hydroxypseudooxynicotine dehydrogenase (Pno) reaction in the hybrid of the pyridine and pyrrolidine pathways for nicotine degradation by Agrobacterium tumefaciens S33. Rid-NC hydrolyzed the presumed reactive imine intermediate produced in the reaction to remove its toxicity on Pno. The finding furthers our understanding of the metabolic process of the toxic N-heterocyclic aromatic compounds in microorganisms. This study demonstrated that the Rid family of proteins also functions in the metabolism of N-heterocyclic aromatic alkaloids, in addition to the amino acid metabolism, and that Rid6-subfamily proteins also have deaminase activity, similar to the RidA subfamily. The ability of reactive imines to damage a non-pyridoxal-5'-phosphate-dependent enzyme was reported. This study provides new insights into the function of the Rid family of proteins.
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Buckner BA, Lato AM, Campagna SR, Downs DM. The Rid family member RutC of Escherichia coli is a 3-aminoacrylate deaminase. J Biol Chem 2021; 296:100651. [PMID: 33839153 PMCID: PMC8113886 DOI: 10.1016/j.jbc.2021.100651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 12/23/2022] Open
Abstract
The Rid protein family (PF14588, IPR006175) is divided into nine subfamilies, of which only the RidA subfamily has been characterized biochemically. RutC, the founding member of one subfamily, is encoded in the pyrimidine utilization (rut) operon that encodes a pathway that allows Escherichia coli to use uracil as a sole nitrogen source. Results reported herein demonstrate that RutC has 3-aminoacrylate deaminase activity and facilitates one of the reactions previously presumed to occur spontaneously in vivo. RutC was active with several enamine-imine substrates, showing similarities and differences in substrate specificity with the canonical member of the Rid superfamily, Salmonella enterica RidA. Under standard laboratory conditions, a Rut pathway lacking RutC generates sufficient nitrogen from uracil for growth of E. coli. These results support a revised model of the Rut pathway and provide evidence that Rid proteins may modulate metabolic fitness, rather than catalyzing essential functions.
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Affiliation(s)
- Brandi A Buckner
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Ashley M Lato
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, USA
| | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, USA
| | - Diana M Downs
- Department of Microbiology, University of Georgia, Athens, Georgia, USA.
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20
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New structural insights into bacterial sulfoacetaldehyde and taurine metabolism. Biochem J 2020; 477:1367-1371. [PMID: 32322897 DOI: 10.1042/bcj20200079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 01/17/2023]
Abstract
In last year's issue 4 of Biochemical Journal, Zhou et al. (Biochem J. 476, 733-746) kinetically and structurally characterized the reductase IsfD from Klebsiella oxytoca that catalyzes the reversible reduction in sulfoacetaldehyde to the corresponding alcohol isethionate. This is a key step in detoxification of the carbonyl intermediate formed in bacterial nitrogen assimilation from the α-aminoalkanesulfonic acid taurine. In 2019, the work on sulfoacetaldehyde reductase IsfD was the exciting start to a quite remarkable series of articles dealing with structural elucidation of proteins involved in taurine metabolism as well as the discovery of novel degradation pathways in bacteria.
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21
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Tian Y, Gui W, Rimal B, Koo I, Smith PB, Nichols RG, Cai J, Liu Q, Patterson AD. Metabolic impact of persistent organic pollutants on gut microbiota. Gut Microbes 2020; 12:1-16. [PMID: 33295235 PMCID: PMC7734116 DOI: 10.1080/19490976.2020.1848209] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Emerging evidence supports that exposure to persistent organic pollutants (POPs) can impact the interaction between the gut microbiota and host. Recent efforts have characterized the relationship between gut microbiota and environment pollutants suggesting additional research is needed to understand potential new avenues for toxicity. Here, we systematically examined the direct effects of POPs including 2,3,7,8-tetrachlorodibenzofuran (TCDF), 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), and polychlorinated biphenyls (PCB-123 and PCB-156) on the microbiota using metatranscriptomics and NMR- and mass spectrometry-based metabolomics combined with flow cytometry and growth rate measurements (OD600). This study demonstrated that (1) POPs directly and rapidly affect isolated cecal bacterial global metabolism that is associated with significant decreases in microbial metabolic activity; (2) significant changes in cecal bacterial gene expression related to tricarboxylic acid (TCA) cycle as well as carbon metabolism, carbon fixation, pyruvate metabolism, and protein export were observed following most POP exposure; (3) six individual bacterial species show variation in lipid metabolism in response to POP exposure; and (4) PCB-153 (non-coplanar)has a greater impact on bacteria than PCB-126 (coplanar) at the metabolic and transcriptional levels. These data provide new insights into the direct role of POPs on gut microbiota and begins to establish possible microbial toxicity endpoints which may help to inform risk assessment.
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Affiliation(s)
- Yuan Tian
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Wei Gui
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Bipin Rimal
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Imhoi Koo
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Philip B. Smith
- Huck Institutes of the Life Sciences, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Robert G. Nichols
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Jingwei Cai
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Qing Liu
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Andrew D. Patterson
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA, USA,CONTACT Andrew D. Patterson Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, PA16802, USA
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22
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Irons JL, Hodge-Hanson K, Downs DM. RidA Proteins Protect against Metabolic Damage by Reactive Intermediates. Microbiol Mol Biol Rev 2020; 84:e00024-20. [PMID: 32669283 PMCID: PMC7373157 DOI: 10.1128/mmbr.00024-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The Rid (YjgF/YER057c/UK114) protein superfamily was first defined by sequence homology with available protein sequences from bacteria, archaea, and eukaryotes (L. Parsons, N. Bonander, E. Eisenstein, M. Gilson, et al., Biochemistry 42:80-89, 2003, https://doi.org/10.1021/bi020541w). The archetypal subfamily, RidA (reactive intermediate deaminase A), is found in all domains of life, with the vast majority of free-living organisms carrying at least one RidA homolog. In over 2 decades, close to 100 reports have implicated Rid family members in cellular processes in prokaryotes, yeast, plants, and mammals. Functional roles have been proposed for Rid enzymes in amino acid biosynthesis, plant root development and nutrient acquisition, cellular respiration, and carcinogenesis. Despite the wealth of literature and over a dozen high-resolution structures of different RidA enzymes, their biochemical function remained elusive for decades. The function of the RidA protein was elucidated in a bacterial model system despite (i) a minimal phenotype of ridA mutants, (ii) the enzyme catalyzing a reaction believed to occur spontaneously, and (iii) confusing literature on the pleiotropic effects of RidA homologs in prokaryotes and eukaryotes. Subsequent work provided the physiological framework to support the RidA paradigm in Salmonella enterica by linking the phenotypes of mutants lacking ridA to the accumulation of the reactive metabolite 2-aminoacrylate (2AA), which damaged metabolic enzymes. Conservation of enamine/imine deaminase activity of RidA enzymes from all domains raises the likelihood that, despite the diverse phenotypes, the consequences when RidA is absent are due to accumulated 2AA (or a similar reactive enamine) and the diversity of metabolic phenotypes can be attributed to differences in metabolic network architecture. The discovery of the RidA paradigm in S. enterica laid a foundation for assessing the role of Rid enzymes in diverse organisms and contributed fundamental lessons on metabolic network evolution and diversity in microbes. This review describes the studies that defined the conserved function of RidA, the paradigm of enamine stress in S. enterica, and emerging studies that explore how this paradigm differs in other organisms. We focus primarily on the RidA subfamily, while remarking on our current understanding of the other Rid subfamilies. Finally, we describe the current status of the field and pose questions that will drive future studies on this widely conserved protein family to provide fundamental new metabolic information.
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Affiliation(s)
- Jessica L Irons
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | | | - Diana M Downs
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
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23
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A Pathway for Degradation of Uracil to Acetyl Coenzyme A in Bacillus megaterium. Appl Environ Microbiol 2020; 86:AEM.02837-19. [PMID: 31953335 DOI: 10.1128/aem.02837-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/10/2020] [Indexed: 11/20/2022] Open
Abstract
Bacteria utilize diverse biochemical pathways for the degradation of the pyrimidine ring. The function of the pathways studied to date has been the release of nitrogen for assimilation. The most widespread of these pathways is the reductive pyrimidine catabolic pathway, which converts uracil into ammonia, carbon dioxide, and β-alanine. Here, we report the characterization of a β-alanine:pyruvate aminotransferase (PydD2) and an NAD+-dependent malonic semialdehyde dehydrogenase (MSDH) from a reductive pyrimidine catabolism gene cluster in Bacillus megaterium Together, these enzymes convert β-alanine into acetyl coenzyme A (acetyl-CoA), a key intermediate in carbon and energy metabolism. We demonstrate the growth of B. megaterium in defined medium with uracil as its sole carbon and energy source. Homologs of PydD2 and MSDH are found in association with reductive pyrimidine pathway genes in many Gram-positive bacteria in the order Bacillales Our study provides a basis for further investigations of the utilization of pyrimidines as a carbon and energy source by bacteria.IMPORTANCE Pyrimidine has wide occurrence in natural environments, where bacteria use it as a nitrogen and carbon source for growth. Detailed biochemical pathways have been investigated with focus mainly on nitrogen assimilation in the past decades. Here, we report the discovery and characterization of two important enzymes, PydD2 and MSDH, which constitute an extension for the reductive pyrimidine catabolic pathway. These two enzymes, prevalent in Bacillales based on our bioinformatics studies, allow stepwise conversion of β-alanine, a previous "end product" of the reductive pyrimidine degradation pathway, to acetyl-CoA as carbon and energy source.
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24
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Son HF, Kim S, Seo H, Hong J, Lee D, Jin KS, Park S, Kim KJ. Structural insight into bi-functional malonyl-CoA reductase. Environ Microbiol 2019; 22:752-765. [PMID: 31814251 DOI: 10.1111/1462-2920.14885] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/23/2019] [Accepted: 12/04/2019] [Indexed: 11/27/2022]
Abstract
The bi-functional malonyl-CoA reductase is a key enzyme of the 3-hydroxypropionate bi-cycle for bacterial CO2 fixation, catalysing the reduction of malonyl-CoA to malonate semialdehyde and further reduction to 3-hydroxypropionate. Here, we report the crystal structure and the full-length architecture of malonyl-CoA reductase from Porphyrobacter dokdonensis. The malonyl-CoA reductase monomer of 1230 amino acids consists of four tandemly arranged short-chain dehydrogenases/reductases, with two catalytic and two non-catalytic short-chain dehydrogenases/reductases, and forms a homodimer through paring contact of two malonyl-CoA reductase monomers. The complex structures with its cofactors and substrates revealed that the malonyl-CoA substrate site is formed by the cooperation of two short-chain dehydrogenases/reductases and one novel extra domain, while only one catalytic short-chain dehydrogenase/reductase contributes to the formation of the malonic semialdehyde-binding site. The phylogenetic and structural analyses also suggest that the bacterial bi-functional malonyl-CoA has a structural origin that is completely different from the archaeal mono-functional malonyl-CoA and malonic semialdehyde reductase, and thereby constitute an efficient enzyme.
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Affiliation(s)
- Hyeoncheol Francis Son
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daegu, South Korea
| | - Sangwoo Kim
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daegu, South Korea
| | - Hogyun Seo
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daegu, South Korea
| | - Jiyeon Hong
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daegu, South Korea
| | - Donghoon Lee
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daegu, South Korea
| | - Kyeong Sik Jin
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, South Korea
| | - Sunghoon Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Kyung-Jin Kim
- School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daegu, South Korea
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25
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Yin J, Wei Y, Liu D, Hu Y, Lu Q, Ang EL, Zhao H, Zhang Y. An extended bacterial reductive pyrimidine degradation pathway that enables nitrogen release from β-alanine. J Biol Chem 2019; 294:15662-15671. [PMID: 31455636 DOI: 10.1074/jbc.ra119.010406] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/26/2019] [Indexed: 11/06/2022] Open
Abstract
The reductive pyrimidine catabolic pathway is the most widespread pathway for pyrimidine degradation in bacteria, enabling assimilation of nitrogen for growth. This pathway, which has been studied in several bacteria including Escherichia coli B, releases only one utilizable nitrogen atom from each molecule of uracil, whereas the other nitrogen atom remains trapped in the end product β-alanine. Here, we report the biochemical characterization of a β-alanine:2-oxoglutarate aminotransferase (PydD) and an NAD(P)H-dependent malonic semialdehyde reductase (PydE) from a pyrimidine degradation gene cluster in the bacterium Lysinibacillus massiliensis Together, these two enzymes converted β-alanine into 3-hydroxypropionate (3-HP) and generated glutamate, thereby making the second nitrogen from the pyrimidine ring available for assimilation. Using bioinformatics analyses, we found that PydDE homologs are associated with reductive pyrimidine pathway genes in many Gram-positive bacteria in the classes Bacilli and Clostridia. We demonstrate that Bacillus smithii grows in a defined medium with uracil or uridine as its sole nitrogen source and detected the accumulation of 3-HP as a waste product. Our findings extend the reductive pyrimidine catabolic pathway and expand the diversity of enzymes involved in bacterial pyrimidine degradation.
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Affiliation(s)
- Jinyu Yin
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yifeng Wei
- Metabolic Engineering Research Laboratory, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Dazhi Liu
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yiling Hu
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Qiang Lu
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Ee Lui Ang
- Metabolic Engineering Research Laboratory, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Huimin Zhao
- Metabolic Engineering Research Laboratory, Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore .,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
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26
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Hong LTT, Hachiya T, Hase S, Shiwa Y, Yoshikawa H, Sakakibara Y, Nguyen SLT, Kimura K. Poly-γ-glutamic acid production of Bacillus subtilis (natto) in the absence of DegQ: A gain-of-function mutation in yabJ gene. J Biosci Bioeng 2019; 128:690-696. [PMID: 31272833 DOI: 10.1016/j.jbiosc.2019.05.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 05/21/2019] [Accepted: 05/27/2019] [Indexed: 02/06/2023]
Abstract
Poly-γ-glutamic acid (γPGA) production by Bacillus subtilis is regulated by the quorum sensing system where DegQ transmits the cell density signal to a DNA-binding protein DegU. A mutation suppressing the γPGA-negative phenotype of degQ gene knock-out mutant (ΔdegQ) was identified through whole genome sequencing. The mutation conferred an amino acid substitution of Ser103 to phenylalanine (S103F) in yabJ that belongs to the highly conserved YjgF/YER057c/UK114 family. Genetic experiments including LacZ-fusion assay of γPGA synthetic operon confirmed that the suppressor mutation (yabJS103F) was responsible for the recovery of γPGA production. The yabJ itself was not essential for the γPGA production and the mutant allele enabled γPGA production of the ΔdegQ strain even in the presence of wild type yabJ. Thus, yabJS103F was a dominant positive allele. degU-lacZ fusion gene was hyper-expressed in cells carrying the yabJS103F, but disruption of yabJ did not affect the transcription level of the degU-lacZ. These observations suggested that YabJ acquired a function to stimulate expression of degU by the S103F mutation which is involved in the regulation of γPGA synthesis.
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Affiliation(s)
- Le Thi Thu Hong
- Food Research Institute, National Agriculture and Food Research Organization (NFRI/NARO), Tsukuba, Ibaraki 305-8642, Japan
| | - Tsuyoshi Hachiya
- Department of Bioscience and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Sumitaka Hase
- Department of Bioscience and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Yuh Shiwa
- Department of Molecular Microbiology, Tokyo University of Agriculture, Setagaya, Tokyo 156-8502, Japan
| | - Hirofumi Yoshikawa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya, Tokyo 156-8502, Japan; Department of Bioscience, Tokyo University of Agriculture, Setagaya, Tokyo 156-8502, Japan
| | - Yasubumi Sakakibara
- Department of Bioscience and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Sy Le Thanh Nguyen
- Food Research Institute, National Agriculture and Food Research Organization (NFRI/NARO), Tsukuba, Ibaraki 305-8642, Japan
| | - Keitarou Kimura
- Food Research Institute, National Agriculture and Food Research Organization (NFRI/NARO), Tsukuba, Ibaraki 305-8642, Japan.
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27
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Comparative genome analysis reveals niche-specific genome expansion in Acinetobacter baumannii strains. PLoS One 2019; 14:e0218204. [PMID: 31194814 PMCID: PMC6563999 DOI: 10.1371/journal.pone.0218204] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/28/2019] [Indexed: 12/11/2022] Open
Abstract
The nosocomial pathogen Acinetobacter baumannii acquired clinical significance due to the rapid development of its multi-drug resistant (MDR) phenotype. A. baumannii strains have the ability to colonize several ecological niches including soil, water, and animals, including humans. They also survive under extremely harsh environmental conditions thriving on rare and recalcitrant carbon compounds. However, the molecular basis behind such extreme adaptability of A. baumannii is unknown. We have therefore determined the complete genome sequence of A. baumannii DS002, which was isolated from agricultural soils, and compared it with 78 complete genome sequences of A. baumannii strains having complete information on the source of their isolation. Interestingly, the genome of A. baumannii DS002 showed high similarity to the genome of A. baumannii SDF isolated from the body louse. The environmental and clinical strains, which do not share a monophyletic origin, showed the existence of a strain-specific unique gene pool that supports niche-specific survival. The strains isolated from infected samples contained a genetic repertoire with a unique gene pool coding for iron acquisition machinery, particularly those required for the biosynthesis of acinetobactin. Interestingly, these strains also contained genes required for biofilm formation. However, such gene sets were either partially or completely missing in the environmental isolates, which instead harbored genes required for alternate carbon catabolism and a TonB-dependent transport system involved in the acquisition of iron via siderophores or xenosiderophores.
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Jessop‐Fabre MM, Dahlin J, Biron MB, Stovicek V, Ebert BE, Blank LM, Budin I, Keasling JD, Borodina I. The Transcriptome and Flux Profiling of Crabtree‐Negative Hydroxy Acid‐Producing Strains ofSaccharomyces cerevisiaeReveals Changes in the Central Carbon Metabolism. Biotechnol J 2019; 14:e1900013. [DOI: 10.1002/biot.201900013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/21/2019] [Indexed: 01/28/2023]
Affiliation(s)
- Mathew M. Jessop‐Fabre
- The Novo Nordisk Foundation for BiosustainabilityTechnical University of Denmark Building 220 2800 Kongens Lyngby Denmark
| | - Jonathan Dahlin
- The Novo Nordisk Foundation for BiosustainabilityTechnical University of Denmark Building 220 2800 Kongens Lyngby Denmark
| | - Mathias B. Biron
- The Novo Nordisk Foundation for BiosustainabilityTechnical University of Denmark Building 220 2800 Kongens Lyngby Denmark
| | - Vratislav Stovicek
- The Novo Nordisk Foundation for BiosustainabilityTechnical University of Denmark Building 220 2800 Kongens Lyngby Denmark
| | - Birgitta E. Ebert
- Institute of Applied MicrobiologyRWTH Aachen University Worringer Weg 1 52074 Aachen Germany
| | - Lars M. Blank
- Institute of Applied MicrobiologyRWTH Aachen University Worringer Weg 1 52074 Aachen Germany
| | - Itay Budin
- Department of Chemical and Biomolecular EngineeringUniversity of California Berkeley CA 94720 USA
- Department of BioengineeringUniversity of California Berkeley CA 94720 USA
| | - Jay D. Keasling
- The Novo Nordisk Foundation for BiosustainabilityTechnical University of Denmark Building 220 2800 Kongens Lyngby Denmark
- Joint BioEnergy Institute Emeryville CA 94608 USA
- Biological Systems & Engineering DivisionLawrence Berkeley National Laboratory Berkeley CA 94720 USA
- Department of Chemical and Biomolecular EngineeringUniversity of California Berkeley CA 94720 USA
- Department of BioengineeringUniversity of California Berkeley CA 94720 USA
| | - Irina Borodina
- The Novo Nordisk Foundation for BiosustainabilityTechnical University of Denmark Building 220 2800 Kongens Lyngby Denmark
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29
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Zhu K, Li G, Wei R, Mao Y, Zhao Y, He A, Bai Z, Deng Y. Systematic analysis of the effects of different nitrogen source and ICDH knockout on glycolate synthesis in Escherichia coli. J Biol Eng 2019; 13:30. [PMID: 30988698 PMCID: PMC6449901 DOI: 10.1186/s13036-019-0159-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/26/2019] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Glycolate is an important α-hydroxy carboxylic acid widely used in industrial and consumer applications. The production of glycolate from glucose in Escherichia coli is generally carried out by glycolysis and glyoxylate shunt pathways, followed by reduction to glycolate. Glycolate accumulation was significantly affected by nitrogen sources and isocitrate dehydrogenase (ICDH), which influenced carbon flux distribution between the tricarboxylic acid (TCA) cycle and the glyoxylate shunt, however, the mechanism was unclear. RESULTS Herein, we used RNA-Seq to explore the effects of nitrogen sources and ICDH knockout on glycolate production. The Mgly534 strain and the Mgly624 strain (with the ICDH deletion in Mgly534), displaying different phenotypes on organic nitrogen sources, were also adopted for the exploration. Though the growth of Mgly534 was improved on organic nitrogen sources, glycolate production decreased and acetate accumulated, while Mgly624 achieved a balance between cell growth and glycolate production, reaching 0.81 g glycolate/OD (2.6-fold higher than Mgly534). To further study Mgly624, the significant changed genes related to N-regulation, oxidative stress response and iron transport were analyzed. Glutamate and serine were found to increase the biomass and productivity respectively. Meanwhile, overexpressing the arginine transport gene argT accelerated the cell growth rate and increased the biomass. Further, the presence of Fe2+ also speeded up the cells growth and compensated for the lack of reducing equivalents. CONCLUSION Our studies identified that ICDH knockout strain was more suitable for glycolate production. RNA-Seq provided a better understanding of the ICDH knockout on cellular physiology and glycolate production.
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Affiliation(s)
- Kangjia Zhu
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
- School of Biotechnology, Jiangnan University, 1800 Lihu Rd, Wuxi, 214122 Jiangsu China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Guohui Li
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
- School of Biotechnology, Jiangnan University, 1800 Lihu Rd, Wuxi, 214122 Jiangsu China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Ren Wei
- Institute of Biochemistry, Leipzig University, Johannisallee 23, D-04103 Leipzig, Germany
| | - Yin Mao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
- School of Biotechnology, Jiangnan University, 1800 Lihu Rd, Wuxi, 214122 Jiangsu China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Yunying Zhao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
- School of Biotechnology, Jiangnan University, 1800 Lihu Rd, Wuxi, 214122 Jiangsu China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Aiyong He
- Jiangsu Key Laboratory for Biomass-based Energy and Enzyme Technology, Huaiyin Normal University, Huaian, 223300 China
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
- School of Biotechnology, Jiangnan University, 1800 Lihu Rd, Wuxi, 214122 Jiangsu China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, 214122 Jiangsu China
- School of Biotechnology, Jiangnan University, 1800 Lihu Rd, Wuxi, 214122 Jiangsu China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122 Jiangsu China
- Jiangsu Key Laboratory for Biomass-based Energy and Enzyme Technology, Huaiyin Normal University, Huaian, 223300 China
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30
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Biochemical and structural investigation of sulfoacetaldehyde reductase from Klebsiella oxytoca. Biochem J 2019; 476:733-746. [PMID: 30718306 DOI: 10.1042/bcj20190005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 01/25/2019] [Accepted: 02/01/2019] [Indexed: 11/17/2022]
Abstract
Sulfoacetaldehyde reductase (IsfD) is a member of the short-chain dehydrogenase/reductase (SDR) family, involved in nitrogen assimilation from aminoethylsulfonate (taurine) in certain environmental and human commensal bacteria. IsfD catalyzes the reversible NADPH-dependent reduction of sulfoacetaldehyde, which is generated by transamination of taurine, forming hydroxyethylsulfonate (isethionate) as a waste product. In the present study, the crystal structure of Klebsiella oxytoca IsfD in a ternary complex with NADPH and isethionate was solved at 2.8 Å, revealing residues important for substrate binding. IsfD forms a homotetramer in both crystal and solution states, with the C-terminal tail of each subunit interacting with the C-terminal tail of the diagonally opposite subunit, forming an antiparallel β sheet that constitutes part of the substrate-binding site. The sulfonate group of isethionate is stabilized by a hydrogen bond network formed by the residues Y148, R195, Q244 and a water molecule. In addition, F249 from the diagonal subunit restrains the conformation of Y148 to further stabilize the orientation of the sulfonate group. Mutation of any of these four residues into alanine resulted in a complete loss of catalytic activity for isethionate oxidation. Biochemical investigations of the substrate scope of IsfD, and bioinformatics analysis of IsfD homologs, suggest that IsfD is related to the promiscuous 3-hydroxyacid dehydrogenases with diverse metabolic functions.
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Arenas-López C, Locker J, Orol D, Walter F, Busche T, Kalinowski J, Minton NP, Kovács K, Winzer K. The genetic basis of 3-hydroxypropanoate metabolism in Cupriavidus necator H16. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:150. [PMID: 31236137 PMCID: PMC6572756 DOI: 10.1186/s13068-019-1489-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 06/07/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND 3-Hydroxypropionic acid (3-HP) is a promising platform chemical with various industrial applications. Several metabolic routes to produce 3-HP from organic substrates such as sugars or glycerol have been implemented in yeast, enterobacterial species and other microorganisms. In this study, the native 3-HP metabolism of Cupriavidus necator was investigated and manipulated as it represents a promising chassis for the production of 3-HP and other fatty acid derivatives from CO2 and H2. RESULTS When testing C. necator for its tolerance towards 3-HP, it was noted that it could utilise the compound as the sole source of carbon and energy, a highly undesirable trait in the context of biological 3-HP production which required elimination. Inactivation of the methylcitrate pathway needed for propionate utilisation did not affect the organism's ability to grow on 3-HP. Putative genes involved in 3-HP degradation were identified by bioinformatics means and confirmed by transcriptomic analyses, the latter revealing considerably increased expression in the presence of 3-HP. Genes identified in this manner encoded three putative (methyl)malonate semialdehyde dehydrogenases (mmsA1, mmsA2 and mmsA3) and two putative dehydrogenases (hpdH and hbdH). These genes, which are part of three separate mmsA operons, were inactivated through deletion of the entire coding region, either singly or in various combinations, to engineer strains unable to grow on 3-HP. Whilst inactivation of single genes or double deletions could only delay but not abolish growth, a triple ∆mmsA1∆mmsA2∆mmsA3 knock-out strain was unable utilise 3-HP as the sole source of carbon and energy. Under the used conditions this strain was also unable to co-metabolise 3-HP alongside other carbon and energy sources such as fructose and CO2/H2. Further analysis suggested primary roles for the different mmsA operons in the utilisation of β-alanine generating substrates (mmsA1), degradation of 3-HP (mmsA2), and breakdown of valine (mmsA3). CONCLUSIONS Three different (methyl)malonate semialdehyde dehydrogenases contribute to 3-HP breakdown in C. necator H16. The created triple ∆mmsA1∆mmsA2∆mmsA3 knock-out strain represents an ideal chassis for autotrophic 3-HP production.
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Affiliation(s)
- Christian Arenas-López
- BBSRC/EPSCR Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Jessica Locker
- BBSRC/EPSCR Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Diego Orol
- BBSRC/EPSCR Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Frederik Walter
- BBSRC/EPSCR Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Nigel P. Minton
- BBSRC/EPSCR Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Katalin Kovács
- BBSRC/EPSCR Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Klaus Winzer
- BBSRC/EPSCR Synthetic Biology Research Centre (SBRC), School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD UK
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32
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Stoffer-Bittner AJ, Alexander CR, Dingman DW, Mourad GS, Schultes NP. Functional characterization of the uracil transporter from honeybee pathogen Paenibacillus larvae. Microb Pathog 2018; 124:305-310. [DOI: 10.1016/j.micpath.2018.08.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 08/25/2018] [Indexed: 11/30/2022]
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33
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Pontrelli S, Fricke RCB, Teoh ST, Laviña WA, Putri SP, Fitz-Gibbon S, Chung M, Pellegrini M, Fukusaki E, Liao JC. Metabolic repair through emergence of new pathways in Escherichia coli. Nat Chem Biol 2018; 14:1005-1009. [DOI: 10.1038/s41589-018-0149-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/13/2018] [Indexed: 01/12/2023]
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34
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Liu S, Du MZ, Wen QF, Kang J, Dong C, Xiong L, Huang J, Guo FB. Comprehensive exploration of the enzymes catalysing oxygen-involved reactions and COGs relevant to bacterial oxygen utilization. Environ Microbiol 2018; 20:3836-3850. [PMID: 30187624 DOI: 10.1111/1462-2920.14399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 08/31/2018] [Indexed: 12/12/2022]
Abstract
To better understand the mechanisms of bacterial adaptation in oxygen environments, we explored the aerobic living-associated genes in bacteria by comparing Clusters of Orthologous Groups of proteins' (COGs) frequencies and gene expression analyses and 38 COGs were detected at significantly higher frequencies (p-value less than 1e-6) in aerobes than in anaerobes. Differential expression analyses between two conditions further narrowed the prediction to 27 aerobe-specific COGs. Then, we annotated the enzymes associated with these COGs. Literature review revealed that 14 COGs contained enzymes catalysing oxygen-involved reactions or products involved in aerobic pathways, suggesting their important roles for survival in aerobic environments. Additionally, protein-protein interaction analyses and step length comparisons of metabolic networks suggested that the other 13 COGs may function relevantly with the 14 enzymes-corresponding COGs, indicating that these genes may be highly associated with oxygen utilization. Phylogenetic and evolutionary analyses showed that the 27 COGs did not have similar trees, and all suffered purifying selection pressures. The divergent times of species containing or lacking aerobic COGs validated that the appearing time of oxygen-utilizing gene was approximately 2.80 Gyr ago. In addition to help better understand oxygen adaption, our method may be extended to identify genes relevant to other living environments.
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Affiliation(s)
- Shuo Liu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Meng-Ze Du
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Qing-Feng Wen
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Juanjuan Kang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Chuan Dong
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Lifeng Xiong
- Department of Microbiology, University of Hong Kong, Special Administrative Region, Hong Kong, 999077, China
| | - Jian Huang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Feng-Biao Guo
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
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Aguilar C, Martínez-Batallar G, Flores N, Moreno-Avitia F, Encarnación S, Escalante A, Bolívar F. Analysis of differentially upregulated proteins in ptsHIcrr - and rppH - mutants in Escherichia coli during an adaptive laboratory evolution experiment. Appl Microbiol Biotechnol 2018; 102:10193-10208. [PMID: 30284012 DOI: 10.1007/s00253-018-9397-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/10/2018] [Accepted: 09/13/2018] [Indexed: 11/25/2022]
Abstract
The previous deletion of the cytoplasmic components of the phosphotransferase system (PTS) in Escherichia coli JM101 resulted in the PTS- derivative strain PB11 with severely impaired growth capability in glucose as the sole carbon source. Previous adaptive laboratory evolution (ALE) experiment led to select a fast-growing strain named PB12 from PB11. Comparative genome analysis of PB12 showed a chromosomal deletion, which result in the loss of several genes including rppH which codes for the RNA pyrophosphohydrolase RppH, involved in the preparation of hundreds of mRNAs for further degradation by RNase E. Previous inactivation of rppH in PB11 (PB11rppH-) improved significantly its growing capabilities and increased several mRNAs respect its parental strain PB11. These previous results led to propose to the PB11rppH- mutant as an intermediate between PB11 and PB12 strains merged during the early ALE experiment. In this contribution, we report the metabolic response to the PTS- and rppH- mutations in the deep of a proteomic approach to understanding the relevance of rppH- phenotype during an ALE experiment. Differentially upregulated proteins between the wild-type JM101/PB11, PB11/PB11rppH-, and PB11/PB12 comparisons led to identifying 45 proteins between strain comparisons. Downregulated or upregulated proteins in PB11rppH- were found expressed at an intermediate level with respect to PB11 and PB12. Many of these proteins were found involved in non-previously metabolic traits reported in the study of the PTS- strains, including glucose, amino acids, ribose transport; amino acid biosynthesis; NAD biosynthesis/salvage pathway, biosynthesis of Ac-CoA precursors; detoxification and degradation pathways; stress response; protein synthesis; and possible mutator activities between comparisons. No changes were found in the expression of galactose permease GalP, previously proposed as the primary glucose transporter in the absence of PTS selected by the PTS- derivatives during the ALE experiment. This result suggests that the evolving PTS- population selected other transporters such as LamB, MglB, and ManX instead of GalP for glucose uptake during the early ALE experiment. Analysis of the biological relevance of the metabolic traits developed by the studied strains provided valuable information to understand the relevance of the rppH- mutation in the PTS- background during an ALE experiment as a strategy for the selection of valuable phenotypes for metabolic engineering purposes.
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Affiliation(s)
- César Aguilar
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Gabriel Martínez-Batallar
- Programa de Genómica Funcional de Procariontes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Noemí Flores
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Cuernavaca, Morelos, Mexico
| | - Fabián Moreno-Avitia
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Cuernavaca, Morelos, Mexico
| | - Sergio Encarnación
- Programa de Genómica Funcional de Procariontes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Adelfo Escalante
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Cuernavaca, Morelos, Mexico.
| | - Francisco Bolívar
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, UNAM, Cuernavaca, Morelos, Mexico.,Member of El Colegio Nacional, Ciudad de México, México
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36
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Stoffer‐Bittner AJ, Alexander CR, Dingman DW, Mourad GS, Schultes NP. The solute transport and binding profile of a novel nucleobase cation symporter 2 from the honeybee pathogen Paenibacillus larvae. FEBS Open Bio 2018; 8:1322-1331. [PMID: 30087835 PMCID: PMC6070649 DOI: 10.1002/2211-5463.12488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 06/22/2018] [Accepted: 06/24/2018] [Indexed: 11/29/2022] Open
Abstract
Here, we report that a novel nucleobase cation symporter 2 encoded in the genome of the honeybee bacterial pathogen Paenibacillus larvae reveals high levels of amino acid sequence similarity to the Escherichia coli and Bacillus subtilis uric acid and xanthine transporters. This transporter is named P. larvae uric acid permease-like protein (PlUacP). Even though PlUacP displays overall amino acid sequence similarities, has common secondary structures, and shares functional motifs and functionally important amino acids with E. coli xanthine and uric acid transporters, these commonalities are insufficient to assign transport function to PlUacP. The solute transport and binding profile of PlUacP was determined by radiolabeled uptake experiments via heterologous expression in nucleobase transporter-deficient Saccharomyces cerevisiae strains. PlUacP transports the purines adenine and guanine and the pyrimidine uracil. Hypoxanthine, xanthine, and cytosine are not transported by PlUacP, but, along with uric acid, bind in a competitive manner. PlUacP has strong affinity for adenine Km 7.04 ± 0.18 μm, and as with other bacterial and plant NCS2 proteins, PlUacP function is inhibited by the proton disruptor carbonyl cyanide m-chlorophenylhydrazone. The solute transport and binding profile identifies PlUacP as a novel nucleobase transporter.
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Affiliation(s)
| | | | - Douglas W. Dingman
- Department of EntomologyThe Connecticut Agricultural Experiment StationNew HavenCTUSA
| | - George S. Mourad
- Department of BiologyIndiana University‐Purdue University Fort WayneINUSA
| | - Neil P. Schultes
- Department of Plant Pathology & EcologyThe Connecticut Agricultural Experiment StationNew HavenCTUSA
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37
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Copp JN, Akiva E, Babbitt PC, Tokuriki N. Revealing Unexplored Sequence-Function Space Using Sequence Similarity Networks. Biochemistry 2018; 57:4651-4662. [PMID: 30052428 DOI: 10.1021/acs.biochem.8b00473] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The rapidly expanding number of protein sequences found in public databases can improve our understanding of how protein functions evolve. However, our current knowledge of protein function likely represents a small fraction of the diverse repertoire that exists in nature. Integrative computational methods can facilitate the discovery of new protein functions and enzymatic reactions through the observation and investigation of the complex sequence-structure-function relationships within protein superfamilies. Here, we highlight the use of sequence similarity networks (SSNs) to identify previously unexplored sequence and function space. We exemplify this approach using the nitroreductase (NTR) superfamily. We demonstrate that SSN investigations can provide a rapid and effective means to classify groups of proteins, therefore exposing experimentally unexplored sequences that may exhibit novel functionality. Integration of such approaches with systematic experimental characterization will expand our understanding of the functional diversity of enzymes and their associated physiological roles.
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Affiliation(s)
- Janine N Copp
- Michael Smith Laboratories , University of British Columbia , 2185 East Mall , Vancouver , British Columbia V6T 1Z4 , Canada
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences , University of California , San Francisco , California 94158 , United States.,Quantitative Biosciences Institute , University of California , San Francisco , California 94143 , United States
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences , University of California , San Francisco , California 94158 , United States.,Quantitative Biosciences Institute , University of California , San Francisco , California 94143 , United States
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories , University of British Columbia , 2185 East Mall , Vancouver , British Columbia V6T 1Z4 , Canada
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38
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An Escherichia coli Nitrogen Starvation Response Is Important for Mutualistic Coexistence with Rhodopseudomonas palustris. Appl Environ Microbiol 2018; 84:AEM.00404-18. [PMID: 29728387 DOI: 10.1128/aem.00404-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 04/28/2018] [Indexed: 02/04/2023] Open
Abstract
Microbial mutualistic cross-feeding interactions are ubiquitous and can drive important community functions. Engaging in cross-feeding undoubtedly affects the physiology and metabolism of individual species involved. However, the nature in which an individual species' physiology is influenced by cross-feeding and the importance of those physiological changes for the mutualism have received little attention. We previously developed a genetically tractable coculture to study bacterial mutualisms. The coculture consists of fermentative Escherichia coli and phototrophic Rhodopseudomonas palustris In this coculture, E. coli anaerobically ferments sugars into excreted organic acids as a carbon source for R. palustris In return, a genetically engineered R. palustris strain constitutively converts N2 into NH4+, providing E. coli with essential nitrogen. Using transcriptome sequencing (RNA-seq) and proteomics, we identified transcript and protein levels that differ in each partner when grown in coculture versus monoculture. When in coculture with R. palustris, E. coli gene expression changes resembled a nitrogen starvation response under the control of the transcriptional regulator NtrC. By genetically disrupting E. coli NtrC, we determined that a nitrogen starvation response is important for a stable coexistence, especially at low R. palustris NH4+ excretion levels. Destabilization of the nitrogen starvation regulatory network resulted in variable growth trends and, in some cases, extinction. Our results highlight that alternative physiological states can be important for survival within cooperative cross-feeding relationships.IMPORTANCE Mutualistic cross-feeding between microbes within multispecies communities is widespread. Studying how mutualistic interactions influence the physiology of each species involved is important for understanding how mutualisms function and persist in both natural and applied settings. Using a bacterial mutualism consisting of Rhodopseudomonas palustris and Escherichia coli growing cooperatively through bidirectional nutrient exchange, we determined that an E. coli nitrogen starvation response is important for maintaining a stable coexistence. The lack of an E. coli nitrogen starvation response ultimately destabilized the mutualism and, in some cases, led to community collapse after serial transfers. Our findings thus inform on the potential necessity of an alternative physiological state for mutualistic coexistence with another species compared to the physiology of species grown in isolation.
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39
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Botou M, Lazou P, Papakostas K, Lambrinidis G, Evangelidis T, Mikros E, Frillingos S. Insight on specificity of uracil permeases of the NAT/NCS2 family from analysis of the transporter encoded in the pyrimidine utilization operon ofEscherichia coli. Mol Microbiol 2018; 108:204-219. [DOI: 10.1111/mmi.13931] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Maria Botou
- Laboratory of Biological Chemistry Department of Medicine School of Health Sciences; University of Ioannina; Ioannina Greece
| | - Panayiota Lazou
- Laboratory of Biological Chemistry Department of Medicine School of Health Sciences; University of Ioannina; Ioannina Greece
| | - Konstantinos Papakostas
- Laboratory of Biological Chemistry Department of Medicine School of Health Sciences; University of Ioannina; Ioannina Greece
| | - George Lambrinidis
- Division of Pharmaceutical Chemistry Department of Pharmacy School of Health Sciences; National and Kapodistrian University of Athens; Athens Greece
| | - Thomas Evangelidis
- Division of Pharmaceutical Chemistry Department of Pharmacy School of Health Sciences; National and Kapodistrian University of Athens; Athens Greece
| | - Emmanuel Mikros
- Division of Pharmaceutical Chemistry Department of Pharmacy School of Health Sciences; National and Kapodistrian University of Athens; Athens Greece
| | - Stathis Frillingos
- Laboratory of Biological Chemistry Department of Medicine School of Health Sciences; University of Ioannina; Ioannina Greece
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40
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Esquirol L, Peat TS, Wilding M, Lucent D, French NG, Hartley CJ, Newman J, Scott C. Structural and biochemical characterization of the biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841. PLoS One 2018; 13:e0192736. [PMID: 29425231 PMCID: PMC5806882 DOI: 10.1371/journal.pone.0192736] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 01/29/2018] [Indexed: 11/24/2022] Open
Abstract
Biuret deamination is an essential step in cyanuric acid mineralization. In the well-studied atrazine degrading bacterium Pseudomonas sp. strain ADP, the amidase AtzE catalyzes this step. However, Rhizobium leguminosarum bv. viciae 3841 uses an unrelated cysteine hydrolase, BiuH, instead. Herein, structures of BiuH, BiuH with bound inhibitor and variants of BiuH are reported. The substrate is bound in the active site by a hydrogen bonding network that imparts high substrate specificity. The structure of the inactive Cys175Ser BiuH variant with substrate bound in the active site revealed that an active site cysteine (Cys175), aspartic acid (Asp36) and lysine (Lys142) form a catalytic triad, which is consistent with biochemical studies of BiuH variants. Finally, molecular dynamics simulations highlighted the presence of three channels from the active site to the enzyme surface: a persistent tunnel gated by residues Val218 and Gln215 forming a potential substrate channel and two smaller channels formed by Val28 and a mobile loop (including residues Phe41, Tyr47 and Met51) that may serve as channels for co-product (ammonia) or co-substrate (water).
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Affiliation(s)
- Lygie Esquirol
- CSIRO Biocatalysis and Synthetic Biology, Canberra, Australian Capital Territory, Australia
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Thomas S. Peat
- CSIRO Biomedical Manufacturing, Parkville, Melbourne, Victoria, Australia
| | - Matthew Wilding
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
- CSIRO Biomedical Manufacturing, Parkville, Melbourne, Victoria, Australia
| | - Del Lucent
- Department of Electrical Engineering and Physics, Wilkes University, Wilkes-Barre, Pennsylvania, United States of America
| | - Nigel G. French
- CSIRO Biocatalysis and Synthetic Biology, Canberra, Australian Capital Territory, Australia
| | - Carol J. Hartley
- CSIRO Biocatalysis and Synthetic Biology, Canberra, Australian Capital Territory, Australia
| | - Janet Newman
- CSIRO Biomedical Manufacturing, Parkville, Melbourne, Victoria, Australia
| | - Colin Scott
- CSIRO Biocatalysis and Synthetic Biology, Canberra, Australian Capital Territory, Australia
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41
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Alexander CR, Dingman DW, Schultes NP, Mourad GS. The solute transport profile of two Aza-guanine transporters from the Honey bee pathogen Paenibacillus larvae. FEMS Microbiol Lett 2018; 365:4828326. [DOI: 10.1093/femsle/fny018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/26/2018] [Indexed: 01/05/2023] Open
Affiliation(s)
- Candace R Alexander
- Department of Biology, Indiana University-Purdue University Fort Wayne, 2101 East Coliseum Blvd., Fort Wayne, IN 46805, USA
| | - Douglas W Dingman
- Department of Entomology, The Connecticut Agricultural Experiment Station, 123 Huntington St, New Haven, CT 06511, USA
| | - Neil P Schultes
- Department of Plant Pathology & Ecology, The Connecticut Agricultural Experiment Station, 123 Huntington St, New Haven, CT 06511, USA
| | - George S Mourad
- Department of Biology, Indiana University-Purdue University Fort Wayne, 2101 East Coliseum Blvd., Fort Wayne, IN 46805, USA
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42
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A Novel Aerobic Degradation Pathway for Thiobencarb Is Initiated by the TmoAB Two-Component Flavin Mononucleotide-Dependent Monooxygenase System in Acidovorax sp. Strain T1. Appl Environ Microbiol 2017; 83:AEM.01490-17. [PMID: 28939603 DOI: 10.1128/aem.01490-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/13/2017] [Indexed: 11/20/2022] Open
Abstract
Thiobencarb is a thiocarbamate herbicide used in rice paddies worldwide. Microbial degradation plays a crucial role in the dissipation of thiobencarb in the environment. However, the physiological and genetic mechanisms underlying thiobencarb degradation remain unknown. In this study, a novel thiobencarb degradation pathway was proposed in Acidovorax sp. strain T1. Thiobencarb was oxidized and cleaved at the C-S bond, generating diethylcarbamothioic S-acid and 4-chlorobenzaldehyde (4CDA). 4CDA was then oxidized to 4-chlorobenzoic acid (4CBA) and hydrolytically dechlorinated to 4-hydroxybenzoic acid (4HBA). The identification of catabolic genes suggested further hydroxylation to protocatechuic acid (PCA) and finally degradation through the protocatechuate 4,5-dioxygenase pathway. A novel two-component monooxygenase system identified in the strain, TmoAB, was responsible for the initial catabolic reaction. TmoA shared 28 to 32% identity with the oxygenase components of pyrimidine monooxygenase from Agrobacterium fabrum, alkanesulfonate monooxygenase from Pseudomonas savastanoi, and dibenzothiophene monooxygenase from Rhodococcus sp. TmoB shared 25 to 37% identity with reported flavin reductases and oxidized NADH but not NADPH. TmoAB is a flavin mononucleotide (FMN)-dependent monooxygenase and catalyzed the C-S bond cleavage of thiobencarb. Introduction of tmoAB into cells of the thiobencarb degradation-deficient mutant T1m restored its ability to degrade and utilize thiobencarb. A dehydrogenase gene, tmoC, was located 7,129 bp downstream of tmoAB, and its transcription was clearly induced by thiobencarb. The purified TmoC catalyzed the dehydrogenation of 4CDA to 4CBA using NAD+ as a cofactor. A gene cluster responsible for the complete 4CBA metabolic pathway was also cloned, and its involvement in thiobencarb degradation was preliminarily verified by transcriptional analysis.IMPORTANCE Microbial degradation is the main factor in thiobencarb dissipation in soil. In previous studies, thiobencarb was degraded initially via N-deethylation, sulfoxidation, hydroxylation, and dechlorination. However, enzymes and genes involved in the microbial degradation of thiobencarb have not been studied. This study revealed a new thiobencarb degradation pathway in Acidovorax sp. strain T1 and identified a novel two-component FMN-dependent monooxygenase system, TmoAB. Under TmoAB-mediated catalysis, thiobencarb was cleaved at the C-S bond, producing diethylcarbamothioic S-acid and 4CDA. Furthermore, the downstream degradation pathway of thiobencarb was proposed. Our study provides the physiological, biochemical, and genetic foundation of thiobencarb degradation in this microorganism.
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Saidi I, Fourcade F, Floner D, Soutrel I, Bellakhal N, Amrane A, Geneste F. Sulfamethazine removal by means of a combined process coupling an oxidation pretreatment and activated sludge culture - preliminary results. ENVIRONMENTAL TECHNOLOGY 2017; 38:2684-2690. [PMID: 27973980 DOI: 10.1080/09593330.2016.1273395] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A coupled electrochemical process and biological treatment was used to remove a biorecalcitrant antibiotic: sulfamethazine (SMT). The pretreatment was performed in a home-made flow cell involving graphite felt as a working electrode at potentials of 1 and 1.6 V/saturated calomel electrode (SCE); it was followed by a biological process involving activated sludge purchased from a local wastewater treatment plant. Activated sludge cultures of pretreated and non-pretreated SMT solution were carried out for 3 weeks, and different parameters were monitored, especially total organic carbon (TOC) and SMT concentrations. high-performance liquid chromatography results revealed that the target molecule was not assimilated by activated sludge. However, and confirming the improvement previously observed for the biological oxygen demand/chemical oxygen demand (BOD5/COD) ratio, from 0.08 before electrolysis to 0.58 after electrolysis, a pretreatment step in oxidation at 1.6 V/SCE led to a fast decrease of TOC during the subsequent biological treatment, since the mineralization yields increased from 10% for a non-pretreated SMT solution to 76.6% after electrolysis in oxidation (1.6 V/SCE), confirming the efficiency of coupling the electro-oxidation process with a biological treatment for the mineralization of SMT. Moreover, when the electrolysis was performed at 1 V/SCE, no biodegradation was observed, underlining the importance of the electrochemical pretreatment.
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Affiliation(s)
- Imen Saidi
- a Institut des Sciences Chimiques de Rennes , Université de Rennes 1, UMR-CNRS 6226 , Rennes , France
- c Unité de recherche de Catalyse d'Electrochimie de Nanomatériaux et leurs applications et de didactique CENAD , Institut National des Sciences Appliquées et de Technologie (INSAT) , Tunis Cedex , Tunisie
- d Institute of Chemical Sciences of Rennes, Université Européenne de Bretagne, 5 boulevard Laënnec , 35000 Rennes , France
| | - Florence Fourcade
- a Institut des Sciences Chimiques de Rennes , Université de Rennes 1, UMR-CNRS 6226 , Rennes , France
- b Ecole Nationale Supérieure de Chimie de Rennes, Université de Rennes 1, UMR-CNRS 6226 , Rennes , France
- d Institute of Chemical Sciences of Rennes, Université Européenne de Bretagne, 5 boulevard Laënnec , 35000 Rennes , France
| | - Didier Floner
- a Institut des Sciences Chimiques de Rennes , Université de Rennes 1, UMR-CNRS 6226 , Rennes , France
- d Institute of Chemical Sciences of Rennes, Université Européenne de Bretagne, 5 boulevard Laënnec , 35000 Rennes , France
| | - Isabelle Soutrel
- a Institut des Sciences Chimiques de Rennes , Université de Rennes 1, UMR-CNRS 6226 , Rennes , France
- b Ecole Nationale Supérieure de Chimie de Rennes, Université de Rennes 1, UMR-CNRS 6226 , Rennes , France
- d Institute of Chemical Sciences of Rennes, Université Européenne de Bretagne, 5 boulevard Laënnec , 35000 Rennes , France
| | - Nizar Bellakhal
- c Unité de recherche de Catalyse d'Electrochimie de Nanomatériaux et leurs applications et de didactique CENAD , Institut National des Sciences Appliquées et de Technologie (INSAT) , Tunis Cedex , Tunisie
| | - Abdeltif Amrane
- a Institut des Sciences Chimiques de Rennes , Université de Rennes 1, UMR-CNRS 6226 , Rennes , France
- b Ecole Nationale Supérieure de Chimie de Rennes, Université de Rennes 1, UMR-CNRS 6226 , Rennes , France
- d Institute of Chemical Sciences of Rennes, Université Européenne de Bretagne, 5 boulevard Laënnec , 35000 Rennes , France
| | - Florence Geneste
- a Institut des Sciences Chimiques de Rennes , Université de Rennes 1, UMR-CNRS 6226 , Rennes , France
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Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily. Proc Natl Acad Sci U S A 2017; 114:E9549-E9558. [PMID: 29078300 PMCID: PMC5692541 DOI: 10.1073/pnas.1706849114] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Functionally diverse enzyme superfamilies are sets of homologs that conserve a structural fold and mechanistic details but perform various distinct chemical reactions. What are the evolutionary routes by which ancestral proteins diverge to produce extant enzymes? We present an approach that combines experimental data with computational tools to trace these sequence–structure–function transitions in a model system, the functionally diverse flavin mononucleotide-dependent nitroreductases (NTRs). Our results suggest an evolutionary model in which contemporary NTR classes have diverged in a radial manner from a minimal flavin-binding scaffold via insertions at key positions and fixation of functional residues, yielding the reaction versatility of contemporary enzymes. These principles will facilitate rational design of NTRs and advance general approaches for delineating the emergence of functional diversity in enzyme superfamilies. Insight regarding how diverse enzymatic functions and reactions have evolved from ancestral scaffolds is fundamental to understanding chemical and evolutionary biology, and for the exploitation of enzymes for biotechnology. We undertook an extensive computational analysis using a unique and comprehensive combination of tools that include large-scale phylogenetic reconstruction to determine the sequence, structural, and functional relationships of the functionally diverse flavin mononucleotide-dependent nitroreductase (NTR) superfamily (>24,000 sequences from all domains of life, 54 structures, and >10 enzymatic functions). Our results suggest an evolutionary model in which contemporary subgroups of the superfamily have diverged in a radial manner from a minimal flavin-binding scaffold. We identified the structural design principle for this divergence: Insertions at key positions in the minimal scaffold that, combined with the fixation of key residues, have led to functional specialization. These results will aid future efforts to delineate the emergence of functional diversity in enzyme superfamilies, provide clues for functional inference for superfamily members of unknown function, and facilitate rational redesign of the NTR scaffold.
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Flavin-N5-oxide: A new, catalytic motif in flavoenzymology. Arch Biochem Biophys 2017; 632:4-10. [PMID: 28784589 DOI: 10.1016/j.abb.2017.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 11/22/2022]
Abstract
Flavin-N5-oxide is a recently discovered intermediate used by EncM (1,3-diketone oxidation), DszA (sulfone monooxygenase) and RutA (amide monooxygenase). This review describes the mechanism of these enzymes and proposes criteria for the identification of additional Flavin-N5-oxide dependent enzymes.
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Adak S, Begley TP. RutA-Catalyzed Oxidative Cleavage of the Uracil Amide Involves Formation of a Flavin-N5-oxide. Biochemistry 2017; 56:3708-3709. [PMID: 28661684 PMCID: PMC6040642 DOI: 10.1021/acs.biochem.7b00493] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
RutA is a novel flavoenzyme on the uracil catabolic pathway that catalyzes uracil ring opening by a unique amide oxidation reaction. Here we provide evidence that this reaction also involves the formation of a flavin-N5-oxide.
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Affiliation(s)
- Sanjoy Adak
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, 3255 TAMU, College Station, Texas 77843, United States
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Gipson AB, Morton KJ, Rhee RJ, Simo S, Clayton JA, Perrett ME, Binkley CG, Jensen EL, Oakes DL, Rouhier MF, Rouhier KA. Disruptions in valine degradation affect seed development and germination in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:1029-1039. [PMID: 28321931 PMCID: PMC5461199 DOI: 10.1111/tpj.13538] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 03/07/2017] [Accepted: 03/10/2017] [Indexed: 05/20/2023]
Abstract
We have functionally characterized the role of two putative mitochondrial enzymes in valine degradation using insertional mutants. Prior to this study, the relationship between branched-chain amino acid degradation (named for leucine, valine and isoleucine) and seed development was limited to leucine catabolism. Using a reverse genetics approach, we show that disruptions in the mitochondrial valine degradation pathway affect seed development and germination in Arabidopsis thaliana. A null mutant of 3-hydroxyisobutyryl-CoA hydrolase (CHY4, At4g31810) resulted in an embryo lethal phenotype, while a null mutant of methylmalonate semialdehyde dehydrogenase (MMSD, At2g14170) resulted in seeds with wrinkled coats, decreased storage reserves, elevated valine and leucine, and reduced germination rates. These data highlight the unique contributions CHY4 and MMSD make to the overall growth and viability of plants. It also increases our knowledge of the role branched-chain amino acid catabolism plays in seed development and amino acid homeostasis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Kerry A. Rouhier
- Kenyon College 200 N. College Rd, Gambier, OH 43022
- Doan University 1014 Boswell Ave, Crete, NE 68333
- Corresponding author: Kerry A. Rouhier, 200 N. College Rd, Gambier, OH 43022, USA tel: (740) 427-5359, fax: (740) 427-5731,
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Abstract
Genomic studies focus on key metabolites and pathways that, despite their obvious anthropocentric design, keep being 'predicted', while this is only finding again what is already known. As increasingly more genomes are sequenced, this lightpost effect may account at least in part for our failure to understand the function of a continuously growing number of genes. Core metabolism often goes astray, accidentally producing a variety of unexpected compounds. Catabolism of these forgotten metabolites makes an essential part of the functions coded in metagenomes. Here, I explore the fate of a limited number of those: compounds resulting from radical reactions and molecules derived from some reactive intermediates produced during normal metabolism. I try both to update investigators with the most recent literature and to uncover old articles that may open up new research avenues in the genome exploration of metabolism. This should allow us to foresee further developments in experimental genomics and genome annotation.
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Affiliation(s)
- Antoine Danchin
- Institute of Cardiometabolism and NutritionHôpital de la Pitié‐Salpêtrière47 Boulevard de l'HôpitalParis75013France
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David Y, Oh YH, Baylon MG, Baritugo KA, Joo JC, Chae CG, Kim YJ, Park SJ. Microbial Production of 3-Hydroxypropionic Acid. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807833.ch14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Yokimiko David
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Young Hoon Oh
- Industrial Biochemicals Research Group, Research Center for Biobased Chemistry; Division of Convergence Chemistry, Korea Research Institute of Chemical Technology; P.O. Box 107, 141 Gajeong-ro Yuseong-gu Daejeon 305-600 Republic of Korea
| | - Mary Grace Baylon
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Kei-Anne Baritugo
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Jeong Chan Joo
- Industrial Biochemicals Research Group, Research Center for Biobased Chemistry; Division of Convergence Chemistry, Korea Research Institute of Chemical Technology; P.O. Box 107, 141 Gajeong-ro Yuseong-gu Daejeon 305-600 Republic of Korea
| | - Cheol Gi Chae
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - You Jin Kim
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
| | - Si Jae Park
- Myongji University; Department of Environmental Engineering and Energy; 116 Myongji-ro, Cheoin-gu Yongin Gyeonggido 449-728 Republic of Korea
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Nguyen Le Minh P, de Cima S, Bervoets I, Maes D, Rubio V, Charlier D. Ligand binding specificity of RutR, a member of the TetR family of transcription regulators in Escherichia coli. FEBS Open Bio 2015; 5:76-84. [PMID: 25685666 PMCID: PMC4325133 DOI: 10.1016/j.fob.2015.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 01/14/2015] [Accepted: 01/14/2015] [Indexed: 02/01/2023] Open
Abstract
RutR, a TetR-family member in E. coli, exerts both positive and negative regulation. The crystal structure of the RutR mutant W167 protein without bound uracil is determined. Comparison of uracil-free and uracil-bound RutR reveal structural transitions. L74, W77, W167 and L78 are important for binding of the uracil effector. L78 is crucial for the specificity for uracil, preventing thymine binding.
RutR is a member of the large family of TetR transcriptional regulators in Escherichiacoli. It was originally discovered as the regulator of the rutABCDEFG operon encoding a novel pathway for pyrimidine utilization, but its highest affinity target is the control region of the carAB operon, encoding carbamoylphosphate synthase. Unlike most other TetR-like regulators, RutR exerts both positive and negative effects on promoter activity. Furthermore, RutR exhibits a very narrow ligand binding specificity, unlike the broad effector specificity that characterizes some of the well-studied multidrug resistance regulators of the family. Here we focus on ligand binding and ligand specificity of RutR. We construct single alanine substitution mutants of amino acid residues of the ligand-binding pocket, study their effect on in vitro DNA binding in absence and presence of potential ligands, and analyse their effect on positive regulation of the carP1 promoter and negative autoregulation in vivo. Although RutR structures have been determined previously, they were deposited in the Protein Data Bank without accompanying publications. All of them have uracil bound in the effector-binding site, representing the inactive form of the regulator. We determined the crystal structure of an unliganded mutant RutR protein and provide a structural basis for the use of uracil as sole effector molecule and the exclusion of the very similar thymine from the ligand-binding pocket.
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Affiliation(s)
- Phu Nguyen Le Minh
- Research Group of Microbiology, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussel, Belgium ; Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Cientificas (IBV-CSIC), Centro de Investigación Biomédicaen Red de Enfermedades Raras (CIBERER-ISCIII), C/Jaime Roig 11, E-46010 Valencia, Spain
| | - Sergio de Cima
- Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Cientificas (IBV-CSIC), Centro de Investigación Biomédicaen Red de Enfermedades Raras (CIBERER-ISCIII), C/Jaime Roig 11, E-46010 Valencia, Spain
| | - Indra Bervoets
- Research Group of Microbiology, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussel, Belgium
| | - Dominique Maes
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussel, Belgium
| | - Vicente Rubio
- Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Cientificas (IBV-CSIC), Centro de Investigación Biomédicaen Red de Enfermedades Raras (CIBERER-ISCIII), C/Jaime Roig 11, E-46010 Valencia, Spain
| | - Daniel Charlier
- Research Group of Microbiology, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussel, Belgium
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