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Godínez-Pérez CM, Loza A, Hurtado JM, Gutiérrez-Ríos RM. The benzoyl-CoA pathway serves as a genomic marker to identify the oxygen requirements in the degradation of aromatic hydrocarbons. Front Microbiol 2024; 14:1308626. [PMID: 38264488 PMCID: PMC10803450 DOI: 10.3389/fmicb.2023.1308626] [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: 10/06/2023] [Accepted: 12/22/2023] [Indexed: 01/25/2024] Open
Abstract
The first step of anaerobic benzoate degradation is the formation of benzoyl-coenzyme A by benzoate-coenzyme A ligase (BCL). The anaerobic route is steered by benzoyl-CoA reductase, which promotes benzoyl-CoA breakdown, which is subsequently oxidized. In certain bacteria at low oxygen conditions, the aerobic metabolism of monoaromatic hydrocarbons occurs through the degradation Box pathway. These pathways have undergone experimental scrutiny in Alphaproteobacteria and Betaproteobacteria and have also been explored bioinformatically in representative Betaproteobacteria. However, there is a gap in our knowledge regarding the distribution of the benzoyl-CoA pathway and the evolutionary forces propelling its adaptation beyond that of representative bacteria. To address these questions, we used bioinformatic procedures to identify the BCLs and the lower pathways that transform benzoyl-CoA. These procedures included the identification of conserved motifs. As a result, we identified two motifs exclusive to BCLs, describing some of the catalytic properties of this enzyme. These motifs helped to discern BCLs from other aryl-CoA ligases effectively. The predicted BCLs and the enzymes of lower pathways were used as genomic markers for identifying aerobic, anaerobic, or hybrid catabolism, which we found widely distributed in Betaproteobacteria. Despite these enhancements, our approach failed to distinguish orthologs from a small cluster of paralogs exhibiting all the specified features to predict an ortholog. Nonetheless, the conducted phylogenetic analysis and the properties identified in the genomic context aided in formulating hypotheses about how this redundancy contributes to refining the catabolic strategy employed by these bacteria to degrade the substrates.
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Affiliation(s)
| | | | | | - Rosa-María Gutiérrez-Ríos
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Wang J, Xue N, Pan W, Tu R, Li S, Zhang Y, Mao Y, Liu Y, Cheng H, Guo Y, Yuan W, Ni X, Wang M. Repurposing conformational changes in ANL superfamily enzymes to rapidly generate biosensors for organic and amino acids. Nat Commun 2023; 14:6680. [PMID: 37865661 PMCID: PMC10590383 DOI: 10.1038/s41467-023-42431-y] [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: 05/04/2023] [Accepted: 10/10/2023] [Indexed: 10/23/2023] Open
Abstract
Biosensors are powerful tools for detecting, real-time imaging, and quantifying molecules, but rapidly constructing diverse genetically encoded biosensors remains challenging. Here, we report a method to rapidly convert enzymes into genetically encoded circularly permuted fluorescent protein-based indicators to detect organic acids (GECFINDER). ANL superfamily enzymes undergo hinge-mediated ligand-coupling domain movement during catalysis. We introduce a circularly permuted fluorescent protein into enzymes hinges, converting ligand-induced conformational changes into significant fluorescence signal changes. We obtain 11 GECFINDERs for detecting phenylalanine, glutamic acid and other acids. GECFINDER-Phe3 and GECFINDER-Glu can efficiently and accurately quantify target molecules in biological samples in vitro. This method simplifies amino acid quantification without requiring complex equipment, potentially serving as point-of-care testing tools for clinical applications in low-resource environments. We also develop a GECFINDER-enabled droplet-based microfluidic high-throughput screening method for obtaining high-yield industrial strains. Our method provides a foundation for using enzymes as untapped blueprint resources for biosensor design, creation, and application.
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Affiliation(s)
- Jin Wang
- University of Chinese Academy of Sciences, 100049, Beijing, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- Haihe Laboratory of Synthetic Biology, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, 300308, Tianjin, China
| | - Ning Xue
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- Haihe Laboratory of Synthetic Biology, 300308, Tianjin, China
- Tianjin University of Science & Technology, 300457, Tianjin, China
| | - Wenjia Pan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, 300308, Tianjin, China
| | - Ran Tu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- College of Environmental and Resources, Chongqing Technology and Business University, 400067, Chongqing, China
| | - Shixin Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- Tianjin University of Science & Technology, 300457, Tianjin, China
| | - Yue Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, 300308, Tianjin, China
| | - Yufeng Mao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, 300308, Tianjin, China
| | - Ye Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, 300308, Tianjin, China
| | - Haijiao Cheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, 300308, Tianjin, China
| | - Yanmei Guo
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, 300308, Tianjin, China
| | - Wei Yuan
- University of Chinese Academy of Sciences, 100049, Beijing, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, 300308, Tianjin, China
| | - Xiaomeng Ni
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China
| | - Meng Wang
- University of Chinese Academy of Sciences, 100049, Beijing, China.
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 300308, Tianjin, China.
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, 300308, Tianjin, China.
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Jiang X, Wei W, Cui Y, Song W, Li Y, Chen X, Gao C, Liu J, Guo L, Liu L, Wu J. A Multi-Enzyme Cascade for Efficient Production of Pyrrolidone from l-Glutamate. Appl Environ Microbiol 2023; 89:e0001323. [PMID: 36951578 PMCID: PMC10132116 DOI: 10.1128/aem.00013-23] [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: 01/04/2023] [Accepted: 02/17/2023] [Indexed: 03/24/2023] Open
Abstract
Pyrrolidone is a high value-added monomer and an important active drug intermediate. However, the efficient enzymatic synthesis of pyrrolidone remains a challenge. Here, we developed and reconstructed a three-enzyme cascade pathway using Escherichia coli BL21(DE3) for the production of pyrrolidone from l-glutamate (l-Glu). The carnitine-CoA ligase from Escherichia coli (EcCaiC) at a low expression level and with a low activity is regarded as the rate-limiting enzyme. Here, we obtained the best EcCaiCF380M/N430D double mutant with a kcat/Km value 1.5 times higher than that of the wild type via mechanism-based protein engineering. For this, we (i) eliminated the steric hindrance of the loop ring to improve the precatalytic conformation of the adenylation intermediate and (ii) fixed the hinge region to stabilize the closed conformation of the enzyme. Furthermore, ribosome-binding site (RBS) optimization led to an increase in the expression level of EcCaiCF380M/N430D, which was then cloned into the plasmid pET-EcCaiCF380M/N430D-DegoPPK2. Finally, under optimal induction and transformation conditions, 16.62 g/L of pyrrolidone was generated from 30 g/L l-Glu (batch feeding) within 24 h with a molar conversion rate of 95.2% and the highest productivity ever obtained, to our knowledge (0.69 g/L/h). Our findings demonstrate a strategy that is potentially attractive for the industrial production of pyrrolidone. IMPORTANCE This study developed a three-enzyme cascade pathway for the production of pyrrolidone from l-Glu. The catalytic efficiency of carnitine CoA ligase from Escherichia coli (EcCaiC) was improved by mechanism-based protein engineering, and the titer of pyrrolidone was further increased by ribosome-binding site (RBS), induction conditions, and conversion conditions optimization. Finally, we efficiently produced pyrrolidone by one pot in vivo with 95.2% conversion and 0.69 g/L/h productivity. Our study provides a new possibility for the industrial production of enzymatic synthesis of pyrrolidone.
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Affiliation(s)
- Xuling Jiang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wanqing Wei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | | | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
| | - Yingying Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, China
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Li Y, He C, Dong F, Yuan S, Hu Z, Wang W. Performance of anaerobic digestion of phenol using exogenous hydrogen and granular activated carbon and analysis of microbial community. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:45077-45087. [PMID: 36701053 DOI: 10.1007/s11356-023-25275-3] [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: 09/15/2022] [Accepted: 01/08/2023] [Indexed: 06/17/2023]
Abstract
Anaerobic conversion rate of phenol to methane was low due to its biological toxicity. In this study, the coupling of granular activated carbon (GAC) and exogenous hydrogen (EH) could enhance greatly methane production of phenol anaerobic digestion, and the metagenomic was firstly used to analyze its potential mechanism. The results indicated that a mass of syntrophic acetate-oxidizing bacteria and hydrogen-utilizing methanogens were enriched on the GAC surface, and SAO-HM pathway has become the dominant pathway. The energy transfer analysis implied that the abundance of adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide (NADH) oxidase increased. Furthermore, direct interspecies electron transfer (DIET) was formed by promoting type IV e-pili between Methanobacterium and Syntrophus, thereby improving the interspecies electron transfer efficiency. The dominant SAO-HM pathway was induced and DIET was formed, which was the internal mechanism of the coupling of GAC and EH to enhance anaerobic biotransformation of phenol.
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Affiliation(s)
- Yongcun Li
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei, 230009, China
- Anhui Provincial Engineering Laboratory for Rural Water Environment and Resources, Hefei, 230009, China
- Anhui Province Key Laboratory of Industrial Wastewater and Environmental Treatment, Hefei, 230024, China
| | - Chunhua He
- Anhui Provincial Engineering Laboratory for Rural Water Environment and Resources, Hefei, 230009, China
- Anhui Province Key Laboratory of Industrial Wastewater and Environmental Treatment, Hefei, 230024, China
- Department of Municipal Engineering, School of Environment and Energy Engineering, Anhui JianZhu University, Hefei, 230009, China
| | - Fang Dong
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei, 230009, China
- Anhui Provincial Engineering Laboratory for Rural Water Environment and Resources, Hefei, 230009, China
- Anhui Province Key Laboratory of Industrial Wastewater and Environmental Treatment, Hefei, 230024, China
| | - Shoujun Yuan
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei, 230009, China
- Anhui Provincial Engineering Laboratory for Rural Water Environment and Resources, Hefei, 230009, China
- Anhui Province Key Laboratory of Industrial Wastewater and Environmental Treatment, Hefei, 230024, China
| | - Zhenhu Hu
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei, 230009, China
- Anhui Provincial Engineering Laboratory for Rural Water Environment and Resources, Hefei, 230009, China
- Anhui Province Key Laboratory of Industrial Wastewater and Environmental Treatment, Hefei, 230024, China
| | - Wei Wang
- Department of Municipal Engineering, School of Civil Engineering, Hefei University of Technology, Hefei, 230009, China.
- Anhui Provincial Engineering Laboratory for Rural Water Environment and Resources, Hefei, 230009, China.
- Anhui Province Key Laboratory of Industrial Wastewater and Environmental Treatment, Hefei, 230024, China.
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Jaroensuk J, Chuaboon L, Chaiyen P. Biochemical reactions for in vitro ATP production and their applications. MOLECULAR CATALYSIS 2023. [DOI: 10.1016/j.mcat.2023.112937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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