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Ma K, Xue B, Chu R, Zheng Y, Sharma S, Jiang L, Hu M, Xie Y, Hu Y, Tao T, Zhou Y, Liu D, Li Z, Yang Q, Chen Y, Wu S, Tong Y, Robinson RC, Yew WS, Jin X, Liu Y, Zhao H, Ang EL, Wei Y, Zhang Y. A Widespread Radical-Mediated Glycolysis Pathway. J Am Chem Soc 2024; 146:26187-26197. [PMID: 39283600 DOI: 10.1021/jacs.4c07718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
Glycyl radical enzymes (GREs) catalyze mechanistically diverse radical-mediated reactions, playing important roles in the metabolism of anaerobic bacteria. The model bacterium Escherichia coli MG1655 contains two GREs of unknown function, YbiW and PflD, which are widespread among human intestinal bacteria. Here, we report that YbiW and PflD catalyze ring-opening C-O cleavage of 1,5-anhydroglucitol-6-phosphate (AG6P) and 1,5-anhydromannitol-6-phosphate (AM6P), respectively. The product of both enzymes, 1-deoxy-fructose-6-phosphate (DF6P), is then cleaved by the aldolases FsaA or FsaB to form glyceraldehyde-3-phosphate (G3P) and hydroxyacetone (HA), which are then reduced by the NADH-dependent dehydrogenase GldA to form 1,2-propanediol (1,2-PDO). Crystal structures of YbiW and PflD in complex with their substrates provided insights into the mechanism of radical-mediated C-O cleavage. This "anhydroglycolysis" pathway enables anaerobic growth of E. coli on 1,5-anhydroglucitol (AG) and 1,5-anhydromannitol (AM), and we probe the feasibility of harnessing this pathway for the production of 1,2-PDO, a highly demanded chiral chemical feedstock, from inexpensive starch. Discovery of the anhydroglycolysis pathway expands the known catalytic repertoire of GREs, clarifies the hitherto unknown physiological functions of the well-studied enzymes FsaA, FsaB, and GldA, and demonstrates how enzyme discovery efforts can cast light on prevalent yet overlooked metabolites in the microbiome.
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Affiliation(s)
- Kailiang Ma
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Faculty of Medicine, 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
| | - Bo Xue
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, Singapore 117456, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Ruoxing Chu
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yuchun Zheng
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Shishir Sharma
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Li Jiang
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Min Hu
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yiren Xie
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yiling Hu
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Tiantian Tao
- School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, China
| | - Yan Zhou
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Dazhi Liu
- New Cornerstone Science Laboratory, 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
| | - Zhi Li
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Qiaoyu Yang
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Yiwei Chen
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Songgu Wu
- School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin 300072, China
| | - Yang Tong
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Robert C Robinson
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Wen Shan Yew
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, Singapore 117456, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Xinghua Jin
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China
| | - Yanhong Liu
- Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Ee Lui Ang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos, Singapore 138669, Singapore
| | - Yan Zhang
- New Cornerstone Science Laboratory, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Faculty of Medicine, 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
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Carbon-Negative Synthetic Biology for Biomaterial Production from CO2 (CNSB), Campus for Research Excellence and Technological Enterprise (CREATE), 1 CREATE Way, Singapore 138602, Singapore
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Taylor ZA, Chen P, Noeparvar P, Pham DN, Walker AR, Kitten T, Zeng L. Glycerol metabolism contributes to competition by oral streptococci through production of hydrogen peroxide. J Bacteriol 2024; 206:e0022724. [PMID: 39171915 PMCID: PMC11411925 DOI: 10.1128/jb.00227-24] [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: 06/10/2024] [Accepted: 07/10/2024] [Indexed: 08/23/2024] Open
Abstract
As a biological byproduct from both humans and microbes, glycerol's contribution to microbial homeostasis in the oral cavity remains understudied. In this study, we examined glycerol metabolism by Streptococcus sanguinis, a commensal associated with oral health. Genetic mutants of glucose-PTS enzyme II (manL), glycerol metabolism (glp and dha pathways), and transcriptional regulators were characterized with regard to glycerol catabolism, growth, production of hydrogen peroxide (H2O2), transcription, and competition with Streptococcus mutans. Biochemical assays identified the glp pathway as a novel source for H2O2 production by S. sanguinis that is independent of pyruvate oxidase (SpxB). Genetic analysis indicated that the glp pathway requires glycerol and a transcriptional regulator, GlpR, for expression and is negatively regulated by PTS, but not the catabolite control protein, CcpA. Conversely, deletion of either manL or ccpA increased the expression of spxB and a second, H2O2-non-producing glycerol metabolic pathway (dha), indicative of a mode of regulation consistent with conventional carbon catabolite repression (CCR). In a plate-based antagonism assay and competition assays performed with planktonic and biofilm-grown cells, glycerol greatly benefited the competitive fitness of S. sanguinis against S. mutans. The glp pathway appears to be conserved in several commensal streptococci and actively expressed in caries-free plaque samples. Our study suggests that glycerol metabolism plays a more significant role in the ecology of the oral cavity than previously understood. Commensal streptococci, though not able to use glycerol as a sole carbohydrate source for growth, benefit from the catabolism of glycerol through production of both ATP and H2O2. IMPORTANCE Glycerol is an abundant carbohydrate in the oral cavity. However, little is understood regarding the metabolism of glycerol by commensal streptococci, some of the most abundant oral bacteria. This was in part because most streptococci cannot grow on glycerol as the sole carbon source. In this study, we show that Streptococcus sanguinis, a commensal associated with dental health, can degrade glycerol for persistence and competition through two pathways, one of which generates hydrogen peroxide at levels capable of inhibiting Streptococcus mutans. Preliminary studies suggest that several additional commensal streptococci are also able to catabolize glycerol, and glycerol-related genes are actively expressed in human dental plaque samples. Our findings reveal the potential of glycerol to significantly impact microbial homeostasis, which warrants further exploration.
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Affiliation(s)
- Zachary A Taylor
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Ping Chen
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Payam Noeparvar
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Danniel N Pham
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Alejandro R Walker
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
| | - Todd Kitten
- Philips Institute for Oral Health Research, Virginia Commonwealth University School of Dentistry, Richmond, Virginia, USA
| | - Lin Zeng
- Department of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USA
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Taylor ZA, Chen P, Noeparvar P, Pham DN, Walker AR, Kitten T, Zeng L. Glycerol Metabolism Contributes to Competition by Oral Streptococci through Production of Hydrogen Peroxide. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.598274. [PMID: 38979179 PMCID: PMC11230354 DOI: 10.1101/2024.06.28.598274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
As a biological byproduct from both humans and microbes, glycerol's contribution to microbial homeostasis in the oral cavity remains understudied. Here we examined glycerol metabolism by Streptococcus sanguinis, a commensal associated with oral health. Genetic mutants of glucose-PTS enzyme II ( manL ), glycerol metabolism ( glp and dha pathways), and transcriptional regulators were characterized with regard to glycerol catabolism, growth, production of hydrogen peroxide (H 2 O 2 ), transcription, and competition with Streptococcus mutans . Biochemical assays identified the glp pathway as a novel source of H 2 O 2 production by S. sanguinis that is independent of pyruvate oxidase (SpxB). Genetic analysis indicated that the glp pathway requires glycerol and a transcriptional regulator, GlpR, for expression and is negatively regulated by PTS, but not the catabolite control protein, CcpA. Conversely, deletion of either manL or ccpA increased expression of spxB and a second, H 2 O 2 -non-producing glycerol metabolic pathway ( dha ), indicative of a mode of regulation consistent with conventional carbon catabolite repression (CCR). In a plate-based antagonism assay and competition assays performed with planktonic and biofilm-grown cells, glycerol greatly benefited the competitive fitness of S. sanguinis against S. mutans. The glp pathway appears to be conserved in several commensal streptococci and actively expressed in caries-free plaque samples. Our study suggests that glycerol metabolism plays a more significant role in the ecology of the oral cavity than previously understood. Commensal streptococci, though not able to use glycerol as a sole carbohydrate for growth, benefit from catabolism of glycerol through production of both ATP and H 2 O 2 . Importance Glycerol is an abundant carbohydrate found in oral cavity, both due to biological activities of humans and microbes, and as a common ingredient of foods and health care products. However, very little is understood regarding the metabolism of glycerol by some of the most abundant oral bacteria, commensal streptococci. This was in part because most streptococci cannot grow on glycerol as the sole carbon source. Here we show that Streptococcus sanguinis , an oral commensal associated with dental health, can degrade glycerol for persistence and competition through two independent pathways, one of which generates hydrogen peroxide at levels capable of inhibiting a dental pathobiont, Streptococcus mutans . Preliminary studies suggest that several other commensal streptococci are also able to catabolize glycerol, and glycerol-related genes are being actively expressed in human dental plaque samples. Our findings reveal the potential of glycerol to significantly impact microbial homeostasis which warrants further exploration.
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Zhang K, Li M, Wang J, Huang G, Ma K, Peng J, Lin H, Zhang C, Wang H, Zhan T, Sun Z, Zhang X. Optimizing enzyme properties to enhance dihydroxyacetone production via methylglyoxal biosensor development. Microb Cell Fact 2024; 23:153. [PMID: 38796416 PMCID: PMC11127321 DOI: 10.1186/s12934-024-02393-2] [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: 02/10/2024] [Accepted: 04/16/2024] [Indexed: 05/28/2024] Open
Abstract
BACKGROUND Dihydroxyacetone (DHA) stands as a crucial chemical material extensively utilized in the cosmetics industry. DHA production through the dephosphorylation of dihydroxyacetone phosphate, an intermediate product of the glycolysis pathway in Escherichia coli, presents a prospective alternative for industrial production. However, insights into the pivotal enzyme, dihydroxyacetone phosphate dephosphorylase (HdpA), remain limited for informed engineering. Consequently, the development of an efficient tool for high-throughput screening of HdpA hypermutants becomes imperative. RESULTS This study introduces a methylglyoxal biosensor, based on the formaldehyde-responding regulator FrmR, for the selection of HdpA. Initial modifications involved the insertion of the FrmR binding site upstream of the -35 region and into the spacer region between the -10 and -35 regions of the constitutive promoter J23110. Although the hybrid promoter retained constitutive expression, expression of FrmR led to complete repression. The addition of 350 μM methylglyoxal promptly alleviated FrmR inhibition, enhancing promoter activity by more than 40-fold. The methylglyoxal biosensor system exhibited a gradual increase in fluorescence intensity with methylglyoxal concentrations ranging from 10 to 500 μM. Notably, the biosensor system responded to methylglyoxal spontaneously converted from added DHA, facilitating the separation of DHA producing and non-producing strains through flow cytometry sorting. Subsequently, the methylglyoxal biosensor was successfully applied to screen a library of HdpA mutants, identifying two strains harboring specific mutants 267G > T and D110G/G151C that showed improved DHA production by 68% and 114%, respectively. Expressing of these two HdpA mutants directly in a DHA-producing strain also increased DHA production from 1.45 to 1.92 and 2.29 g/L, respectively, demonstrating the enhanced enzyme properties of the HdpA mutants. CONCLUSIONS The methylglyoxal biosensor offers a novel strategy for constructing genetically encoded biosensors and serves as a robust platform for indirectly determining DHA levels by responding to methylglyoxal. This property enables efficiently screening of HdpA hypermutants to enhance DHA production.
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Affiliation(s)
- Kaibo Zhang
- School of Chemistry and Life Science, Changchun University of Technology, Changchun, 130012, Jilin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Mengying Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- College of Biotechnology, Tianjin University of Sciences and Technology, Tianjin, 300457, China
| | - Jinsheng Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Guozhong Huang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
| | - Kang Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- College of Biotechnology, Tianjin University of Sciences and Technology, Tianjin, 300457, China
| | - Jiani Peng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- Bioengineering College, Chongqing University, Chongqing, 400044, China
| | - Haoyue Lin
- School of Chemistry and Life Science, Changchun University of Technology, Changchun, 130012, Jilin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Chunjie Zhang
- School of Chemistry and Life Science, Changchun University of Technology, Changchun, 130012, Jilin, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Honglei Wang
- School of Chemistry and Life Science, Changchun University of Technology, Changchun, 130012, Jilin, China.
| | - Tao Zhan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Zhe Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China.
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Chen Z, Niu C, Wei L, Huang Z, Ran S. Genome-wide analysis of acid tolerance genes of Enterococcus faecalis with RNA-seq and Tn-seq. BMC Genomics 2024; 25:261. [PMID: 38454321 PMCID: PMC10921730 DOI: 10.1186/s12864-024-10162-z] [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: 12/05/2023] [Accepted: 02/26/2024] [Indexed: 03/09/2024] Open
Abstract
Enterococcus faecalis, a formidable nosocomial and community-acquired opportunistic pathogen, can persist a wide range of extreme environments, including low pH and nutrient deficiency. Clarifying the survival mechanism of E. faecalis in low-pH conditions is the key to combating the infectious diseases caused by E. faecalis. In this study, we combined transcriptome profiling (RNA-seq) and transposon insertion sequencing (TIS) to comprehensively understand the genes that confer these features on E. faecalis. The metadata showed that genes whose products are involved in cation transportation and amino acid biosynthesis were predominantly differentially expressed under acid conditions. The products of genes such as opp1C and copY reduced the hydrion concentration in the cell, whereas those of gldA2, gnd2, ubiD, and ubiD2 mainly participated in amino metabolism, increasing matters to neutralize excess acid. These, together with the folE and hexB genes, which are involved in mismatch repair, form a network of E. faecalis genes necessary for its survival under acid conditions.
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Affiliation(s)
- Zhanyi Chen
- Department of Endodontics and Operative Dentistry, Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Chenguang Niu
- Department of Endodontics and Operative Dentistry, Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Lifan Wei
- Department of Endodontics and Operative Dentistry, Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
- Nucleic acid drug Research and Development Institute, CSPC, Shanghai, China
| | - Zhengwei Huang
- Department of Endodontics and Operative Dentistry, Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China
| | - Shujun Ran
- Department of Endodontics and Operative Dentistry, Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- National Clinical Research Center for Oral Diseases, Shanghai, China.
- Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, China.
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Luna-Bulbarela A, Romero-Gutiérrez MT, Tinoco-Valencia R, Ortiz E, Martínez-Romero ME, Galindo E, Serrano-Carreón L. Response of Bacillus velezensis 83 to interaction with Colletotrichum gloeosporioides resembles a Greek phalanx-style formation: A stress resistant phenotype with antibiosis capacity. Microbiol Res 2024; 280:127592. [PMID: 38199003 DOI: 10.1016/j.micres.2023.127592] [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: 10/13/2023] [Revised: 12/06/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024]
Abstract
Plant growth-promoting rhizobacteria, such as Bacillus spp., establish beneficial associations with plants and may inhibit the growth of phytopathogenic fungi. However, these bacteria are subject to multiple biotic stimuli from their competitors, causing stress and modifying their development. This work is a study of an in vitro interaction between two model microorganisms of socioeconomic relevance, using population dynamics and transcriptomic approaches. Co-cultures of Bacillus velezensis 83 with the phytopathogenic fungus Colletotrichum gloeosporioides 09 were performed to evaluate the metabolic response of the bacteria under conditions of non-nutritional limitation. The bacterial response was associated with the induction of a stress-resistant phenotype, characterized by a lower specific growth rate, but with antimicrobial production capacity. About 12% of co-cultured B. velezensis 83 coding sequences were differentially expressed, including the up-regulation of the general stress response (sigB regulon), and the down-regulation of alternative carbon sources catabolism (glucose preference). Defense strategies in B. velezensis are a determining factor in order to preserve the long-term viability of its population. Mostly, the presence of the fungus does not affect the expression of antibiosis genes, except for those corresponding to surfactin/bacillomycin D production. Indeed, the up-regulation of antibiosis genes expression is associated with bacterial growth, regardless of the presence of the fungus. This behavior in B. velezensis 83 resembles the strategy used by the classical Greek phalanx formation: by sacrificing growth rate and metabolic versatility, resources can be redistributed to defense (stress resistant phenotype) while maintaining the attack (antibiosis capacity). The presented results are the first characterization of the molecular phenotype at the transcriptome level of a biological control agent under biotic stress caused by a phytopathogen without nutrient limitation.
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Affiliation(s)
- Agustín Luna-Bulbarela
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad #2001, Col. Chamilpa, CP 62210 Cuernavaca, Morelos, Mexico; Agro&Biotecnia S. de R.L. de C.V., Limones 8, Amate Redondo, 62334 Cuernavaca, Morelos, Mexico
| | - María Teresa Romero-Gutiérrez
- Technological Innovation Department, Tlajomulco University Center, University of Guadalajara, 45641 Tlajomulco de Zúñiga, Jalisco, Mexico; Translational Bioengineering Department, Exact Sciences and Engineering University Center, Universidad de Guadalajara, Blvd. Marcelino García Barragán #1421, 44430 Guadalajara, Jalisco, Mexico
| | - Raunel Tinoco-Valencia
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad #2001, Col. Chamilpa, CP 62210 Cuernavaca, Morelos, Mexico
| | - Ernesto Ortiz
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad #2001, Col. Chamilpa, CP 62210 Cuernavaca, Morelos, Mexico
| | - María Esperanza Martínez-Romero
- Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, CP 62210 Cuernavaca, Morelos, Mexico
| | - Enrique Galindo
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad #2001, Col. Chamilpa, CP 62210 Cuernavaca, Morelos, Mexico; Agro&Biotecnia S. de R.L. de C.V., Limones 8, Amate Redondo, 62334 Cuernavaca, Morelos, Mexico
| | - Leobardo Serrano-Carreón
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad #2001, Col. Chamilpa, CP 62210 Cuernavaca, Morelos, Mexico; Agro&Biotecnia S. de R.L. de C.V., Limones 8, Amate Redondo, 62334 Cuernavaca, Morelos, Mexico.
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Li J, Wang R, Liu Y, Miao X. Role of ERA protein in enhancing glyceroglycolipid synthesis and phosphate starvation tolerance in Synechococcus elongatus PCC 7942. Biochim Biophys Acta Mol Cell Biol Lipids 2024; 1869:159431. [PMID: 37977490 DOI: 10.1016/j.bbalip.2023.159431] [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: 06/15/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Glyceroglycolipids are the primary thylakoid membrane lipids in cyanobacteria. Their diverse bioactivities have led to extensive utilization in the biomedical industry. In this study, we elucidated the role of ERA (E. coli Ras-like protein) in augmenting glyceroglycolipid synthesis and bolstering stress resilience in Synechococcus elongatus PCC 7942 during phosphate starvation. Notably, the ERA overexpression strain (ERA OE) outperformed the wild-type (WT) strain under phosphate-starved conditions, displaying an average 13.9 % increase in biomass over WT during the entire growth period, peaking at 0.185 g L-1 of dry cell weight on day 6. Lipidomic analysis using UHPLC-MS/MS techniques revealed that ERA OE exhibited a higher total glyceroglycolipid content compared to WT under phosphate starvation, representing a 7.95 % increase over WT and constituting a maximum of 5.07 % of dry cell weight on day 6. Transcriptomic analysis identified a significant up-regulation of the gldA gene (encoding glycerol dehydrogenase) involved in glycerolipid metabolism due to overexpression of ERA during phosphate starvation. These findings suggest a potential mechanism by which ERA regulates glyceroglycolipid synthesis through the up-regulation of GldA, thereby enhancing phosphate starvation tolerance in S. elongatus PCC 7942. Furthermore, lipidomic analysis revealed that ERA facilitated the production of glyceroglycolipid molecules containing C16:1 and C18:1 fatty acids. Additionally, ERA redirected lipid flux and promoted glyceroglycolipid accumulation while attenuating triacylglycerol production under phosphate starvation. This study represents the first demonstration of pivotal role of ERA in enhancing glyceroglycolipid synthesis and phosphate starvation tolerance in cyanobacteria, offering new insights into the effective utilization of glyceroglycolipids in various applications.
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Affiliation(s)
- Junhao Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Rui Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuhong Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoling Miao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China; Biomass Energy Research Center, Shanghai Jiao Tong University, Shanghai 200240, China.
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8
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Hassa J, Tubbesing TJ, Maus I, Heyer R, Benndorf D, Effenberger M, Henke C, Osterholz B, Beckstette M, Pühler A, Sczyrba A, Schlüter A. Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics. Microorganisms 2023; 11:2412. [PMID: 37894070 PMCID: PMC10608942 DOI: 10.3390/microorganisms11102412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
The current focus on renewable energy in global policy highlights the importance of methane production from biomass through anaerobic digestion (AD). To improve biomass digestion while ensuring overall process stability, microbiome-based management strategies become more important. In this study, metagenomes and metaproteomes were used for metagenomically assembled genome (MAG)-centric analyses to investigate a full-scale biogas plant consisting of three differentially operated digesters. Microbial communities were analyzed regarding their taxonomic composition, functional potential, as well as functions expressed on the proteome level. Different abundances of genes and enzymes related to the biogas process could be mostly attributed to different process parameters. Individual MAGs exhibiting different abundances in the digesters were studied in detail, and their roles in the hydrolysis, acidogenesis and acetogenesis steps of anaerobic digestion could be assigned. Methanoculleus thermohydrogenotrophicum was an active hydrogenotrophic methanogen in all three digesters, whereas Methanothermobacter wolfeii was more prevalent at higher process temperatures. Further analysis focused on MAGs, which were abundant in all digesters, indicating their potential to ensure biogas process stability. The most prevalent MAG belonged to the class Limnochordia; this MAG was ubiquitous in all three digesters and exhibited activity in numerous pathways related to different steps of AD.
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Affiliation(s)
- Julia Hassa
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
| | - Tom Jonas Tubbesing
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Irena Maus
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
| | - Robert Heyer
- Multidimensional Omics Data Analyses Group, Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Bunsen-Kirchhoff-Straße 11, Dortmund 44139, Germany
- Multidimensional Omics Data Analyses Group, Faculty of Technology, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Dirk Benndorf
- Biosciences and Process Engineering, Anhalt University of Applied Sciences, Bernburger Straße 55, Postfach 1458, 06366 Köthen, Germany
- Bioprocess Engineering, Otto von Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106 Magdeburg, Germany
| | - Mathias Effenberger
- Bavarian State Research Center for Agriculture, Institute for Agricultural Engineering and Animal Husbandry, Vöttinger Straße 36, 85354 Freising, Germany
| | - Christian Henke
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Benedikt Osterholz
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Michael Beckstette
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Alfred Pühler
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
| | - Alexander Sczyrba
- Computational Metagenomics Group, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (T.J.T.)
| | - Andreas Schlüter
- Genome Research of Industrial Microorganisms, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615 Bielefeld, Germany; (J.H.)
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9
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Li HK, Zhi X, Vieira A, Whitwell HJ, Schricker A, Jauneikaite E, Li H, Yosef A, Andrew I, Game L, Turner CE, Lamagni T, Coelho J, Sriskandan S. Characterization of emergent toxigenic M1 UK Streptococcus pyogenes and associated sublineages. Microb Genom 2023; 9:mgen000994. [PMID: 37093716 PMCID: PMC10210942 DOI: 10.1099/mgen.0.000994] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/23/2023] [Indexed: 04/25/2023] Open
Abstract
Streptococcus pyogenes genotype emm1 is a successful, globally distributed epidemic clone that is regarded as inherently virulent. An emm1 sublineage, M1UK, that produces increased levels of SpeA toxin was associated with increased scarlet fever and invasive infections in England in 2015/2016. Defined by 27 SNPs in the core genome, M1UK is now dominant in England. To more fully characterize M1UK, we undertook comparative transcriptomic and proteomic analyses of M1UK and contemporary non-M1UK emm1 strains (M1global). Just seven genes were differentially expressed by M1UK compared with contemporary M1global strains. In addition to speA, five genes in the operon that includes glycerol dehydrogenase were upregulated in M1UK (gldA, mipB/talC, pflD, and phosphotransferase system IIC and IIB components), while aquaporin (glpF2) was downregulated. M1UK strains have a stop codon in gldA. Deletion of gldA in M1global abrogated glycerol dehydrogenase activity, and recapitulated upregulation of gene expression within the operon that includes gldA, consistent with a feedback effect. Phylogenetic analysis identified two intermediate emm1 sublineages in England comprising 13/27 (M113SNPs) and 23/27 SNPs (M123SNPs), respectively, that had failed to expand in the population. Proteomic analysis of invasive strains from the four phylogenetic emm1 groups highlighted sublineage-specific changes in carbohydrate metabolism, protein synthesis and protein processing; upregulation of SpeA was not observed in chemically defined medium. In rich broth, however, expression of SpeA was upregulated ~10-fold in both M123SNPs and M1UK sublineages, compared with M113SNPs and M1global. We conclude that stepwise accumulation of SNPs led to the emergence of M1UK. While increased expression of SpeA is a key indicator of M1UK and undoubtedly important, M1UK strains have outcompeted M123SNPs and other emm types that produce similar or more superantigen toxin. We speculate that an accumulation of adaptive SNPs has contributed to a wider fitness advantage in M1UK on an inherently successful emm1 streptococcal background.
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Affiliation(s)
- Ho Kwong Li
- Department of Infectious Disease, Imperial College London, London, UK
- MRC Centre for Molecular Bacteriology & Infection (CMBI), Imperial College London, London, UK
| | - Xiangyun Zhi
- Department of Infectious Disease, Imperial College London, London, UK
- MRC Centre for Molecular Bacteriology & Infection (CMBI), Imperial College London, London, UK
| | - Ana Vieira
- Department of Infectious Disease, Imperial College London, London, UK
- MRC Centre for Molecular Bacteriology & Infection (CMBI), Imperial College London, London, UK
| | - Harry J. Whitwell
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Amelia Schricker
- UK Dementia Research Institute, Department of Brain Sciences, Imperial College London, London, UK
| | - Elita Jauneikaite
- NIHR Health Protection Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
- School of Public Health, Imperial College London, London, UK
| | - Hanqi Li
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ahmed Yosef
- Department of Infectious Disease, Imperial College London, London, UK
| | - Ivan Andrew
- Genomics Facility, UKRI-MRC London Institute for Medical Sciences (LMS), Imperial College London, London, UK
| | - Laurence Game
- Genomics Facility, UKRI-MRC London Institute for Medical Sciences (LMS), Imperial College London, London, UK
| | - Claire E. Turner
- The Florey Institute, School of Biosciences, University of Sheffield, South Yorkshire, UK
| | - Theresa Lamagni
- NIHR Health Protection Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
- Centre for Infections, UK Health Security Agency, London, UK
| | - Juliana Coelho
- NIHR Health Protection Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
- Centre for Infections, UK Health Security Agency, London, UK
| | - Shiranee Sriskandan
- Department of Infectious Disease, Imperial College London, London, UK
- MRC Centre for Molecular Bacteriology & Infection (CMBI), Imperial College London, London, UK
- NIHR Health Protection Unit in Healthcare-associated Infection and Antimicrobial Resistance, Imperial College London, London, UK
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10
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Escobedo-Hinojosa W, Vila MA, Wissner JL, Härterich N, Horz P, Iglesias C, Hauer B. Exploring the substrate scope of glycerol dehydrogenase GldA from E. coli BW25113 towards cis-dihydrocatechol derivatives. J Biotechnol 2023; 366:19-24. [PMID: 36870480 DOI: 10.1016/j.jbiotec.2023.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
Glycerol dehydrogenase (GldA) from Escherichia coli BW25113, naturally catalyzes the oxidation of glycerol to dihydroxyacetone. It is known that GldA exhibits promiscuity towards short-chain C2-C4 alcohols. However, there are no reports regarding the substrate scope of GldA towards larger substrates. Herein we demonstrate that GldA can accept bulkier C6-C8 alcohols than previously anticipated. Overexpression of the gldA gene in the knockout background, E. coli BW25113 ΔgldA, was strikingly effective converting 2 mM of the compounds: cis-dihydrocatetechol, cis-(1 S,2 R)- 3-methylcyclohexa-3,5-diene-1,2-diol and cis-(1 S,2 R)- 3-ethylcyclohexa-3,5-diene-1,2-diol, into 2.04 ± 0.21 mM of catechol, 0.62 ± 0.11 mM 3-methylcatechol, and 0.16 ± 0.02 mM 3-ethylcatechol, respectively. In-silico studies on the active site of GldA enlightened the decrease in product formation as the steric substrate demand increased. These results are of high interests for E. coli-based cell factories expressing Rieske non-heme iron dioxygenases, producing cis-dihydrocatechols, since such sough-after valuable products can be immediately degraded by GldA, substantially hampering the expected performance of the recombinant platform.
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Affiliation(s)
- Wendy Escobedo-Hinojosa
- Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Puerto de abrigo s/n, 97356 Sisal, Yucatán, Mexico
| | - María Agustina Vila
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Química Orgánica y Departamento de Biociencias, Facultad de Química Universidad de la República, Av General Flores 2124, CP 11800 Montevideo, Uruguay
| | - Julian L Wissner
- Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Puerto de abrigo s/n, 97356 Sisal, Yucatán, Mexico; Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Natalie Härterich
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Philip Horz
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - César Iglesias
- Laboratorio de Biocatálisis y Biotransformaciones, Departamento de Química Orgánica y Departamento de Biociencias, Facultad de Química Universidad de la República, Av General Flores 2124, CP 11800 Montevideo, Uruguay
| | - Bernhard Hauer
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
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11
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An extended catalogue of ncRNAs in Streptomyces coelicolor reporting abundant tmRNA, RNase-P RNA and RNA fragments derived from pre-ribosomal RNA leader sequences. Arch Microbiol 2022; 204:582. [PMID: 36042049 DOI: 10.1007/s00203-022-03203-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/05/2022] [Accepted: 08/18/2022] [Indexed: 11/02/2022]
Abstract
Streptomyces coelicolor is a model organism for studying streptomycetes. This genus possesses relevant medical and economical roles, because it produces many biologically active metabolites of pharmaceutical interest, including the majority of commercialized antibiotics. In this bioinformatic study, the transcriptome of S. coelicolor has been analyzed to identify novel RNA species and quantify the expression of both annotated and novel transcripts in solid and liquid growth medium cultures at different times. The major characteristics disclosed in this study are: (i) the diffuse antisense transcription; (ii) the great abundance of transfer-messenger RNAs (tmRNA); (iii) the abundance of rnpB transcripts, paramount for the RNase-P complex; and (iv) the presence of abundant fragments derived from pre-ribosomal RNA leader sequences of unknown biological function. Overall, this study extends the catalogue of ncRNAs in S. coelicolor and suggests an important role of non-coding transcription in the regulation of biologically active molecule production.
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12
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Kovács SC, Szappanos B, Tengölics R, Notebaart RA, Papp B. Underground metabolism as a rich reservoir for pathway engineering. Bioinformatics 2022; 38:3070-3077. [PMID: 35441658 PMCID: PMC9154287 DOI: 10.1093/bioinformatics/btac282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 11/25/2022] Open
Abstract
Motivation Bioproduction of value-added compounds is frequently achieved by utilizing enzymes from other species. However, expression of such heterologous enzymes can be detrimental due to unexpected interactions within the host cell. Recently, an alternative strategy emerged, which relies on recruiting side activities of host enzymes to establish new biosynthetic pathways. Although such low-level ‘underground’ enzyme activities are prevalent, it remains poorly explored whether they may serve as an important reservoir for pathway engineering. Results Here, we use genome-scale modeling to estimate the theoretical potential of underground reactions for engineering novel biosynthetic pathways in Escherichia coli. We found that biochemical reactions contributed by underground enzyme activities often enhance the in silico production of compounds with industrial importance, including several cases where underground activities are indispensable for production. Most of these new capabilities can be achieved by the addition of one or two underground reactions to the native network, suggesting that only a few side activities need to be enhanced during implementation. Remarkably, we find that the contribution of underground reactions to the production of value-added compounds is comparable to that of heterologous reactions, underscoring their biotechnological potential. Taken together, our genome-wide study demonstrates that exploiting underground enzyme activities could be a promising addition to the toolbox of industrial strain development. Availability and implementation The data and scripts underlying this article are available on GitHub at https://github.com/pappb/Kovacs-et-al-Underground-metabolism. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Szabolcs Cselgő Kovács
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary.,Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Balázs Szappanos
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary.,Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary.,Department of Biotechnology, University of Szeged, Szeged, Hungary
| | - Roland Tengölics
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary.,Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Richard A Notebaart
- Food Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Balázs Papp
- HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary.,Biological Research Centre, Institute of Biochemistry, Synthetic and Systems Biology Unit, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
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13
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Systems metabolic engineering of Corynebacterium glutamicum for high-level production of 1,3-propanediol from glucose and xylose. Metab Eng 2022; 70:79-88. [PMID: 35038553 DOI: 10.1016/j.ymben.2022.01.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/14/2021] [Accepted: 01/12/2022] [Indexed: 01/02/2023]
Abstract
Corynebacterium glutamicum is a versatile chassis which has been widely used to produce various amino acids and organic acids. In this study, we report the development of an efficient C. glutamicum strain to produce 1,3-propanediol (1,3-PDO) from glucose and xylose by systems metabolic engineering approaches, including (1) construction and optimization of two different glycerol synthesis modules; (2) combining glycerol and 1,3-PDO synthesis modules; (3) reducing 3-hydroxypropionate accumulation by clarifying a mechanism involving 1,3-PDO re-consumption; (4) reducing the accumulation of toxic 3-hydroxypropionaldehyde by pathway engineering; (5) engineering NADPH generation pathway and anaplerotic pathway. The final engineered strain can efficiently produce 1,3-PDO from glucose with a titer of 110.4 g/L, a yield of 0.42 g/g glucose, and a productivity of 2.30 g/L/h in fed-batch fermentation. By further introducing an optimized xylose metabolism module, the engineered strain can simultaneously utilize glucose and xylose to produce 1,3-PDO with a titer of 98.2 g/L and a yield of 0.38 g/g sugars. This result demonstrates that C. glutamicum is a potential chassis for the industrial production of 1,3-PDO from abundant lignocellulosic feedstocks.
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14
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Miguez AM, Zhang Y, Piorino F, Styczynski MP. Metabolic Dynamics in Escherichia coli-Based Cell-Free Systems. ACS Synth Biol 2021; 10:2252-2265. [PMID: 34478281 PMCID: PMC9807262 DOI: 10.1021/acssynbio.1c00167] [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] [Indexed: 01/04/2023]
Abstract
The field of metabolic engineering has yielded remarkable accomplishments in using cells to produce valuable molecules, and cell-free expression (CFE) systems have the potential to push the field even further. However, CFE systems still face some outstanding challenges, including endogenous metabolic activity that is poorly understood yet has a significant impact on CFE productivity. Here, we use metabolomics to characterize the temporal metabolic changes in CFE systems and their constituent components, including significant metabolic activity in central carbon and amino acid metabolism. We find that while changing the reaction starting state via lysate preincubation impacts protein production, it has a comparatively small impact on metabolic state. We also demonstrate that changes to lysate preparation have a larger effect on protein yield and temporal metabolic profiles, though general metabolic trends are conserved. Finally, while we improve protein production through targeted supplementation of metabolic enzymes, we show that the endogenous metabolic activity is fairly resilient to these enzymatic perturbations. Overall, this work highlights the robust nature of CFE reaction metabolism as well as the importance of understanding the complex interdependence of metabolites and proteins in CFE systems to guide optimization efforts.
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15
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Functional Analysis of Deoxyhexose Sugar Utilization in Escherichia coli Reveals Fermentative Metabolism under Aerobic Conditions. Appl Environ Microbiol 2021; 87:e0071921. [PMID: 34047632 DOI: 10.1128/aem.00719-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
l-Rhamnose and l-fucose are the two main 6-deoxyhexoses Escherichia coli can use as carbon and energy sources. Deoxyhexose metabolism leads to the formation of lactaldehyde, whose fate depends on oxygen availability. Under anaerobic conditions, lactaldehyde is reduced to 1,2-propanediol, whereas under aerobic conditions, it should be oxidized into lactate and then channeled into the central metabolism. However, although this all-or-nothing view is accepted in the literature, it seems overly simplistic since propanediol is also reported to be present in the culture medium during aerobic growth on l-fucose. To clarify the functioning of 6-deoxyhexose sugar metabolism, a quantitative metabolic analysis was performed to determine extra- and intracellular fluxes in E. coli K-12 MG1655 (a laboratory strain) and in E. coli Nissle 1917 (a human commensal strain) during anaerobic and aerobic growth on l-rhamnose and l-fucose. As expected, lactaldehyde is fully reduced to 1,2-propanediol under anoxic conditions, allowing complete reoxidation of the NADH produced by glyceraldehyde-3-phosphate-dehydrogenase. We also found that net ATP synthesis is ensured by acetate production. More surprisingly, lactaldehyde is also primarily reduced into 1,2-propanediol under aerobic conditions. For growth on l-fucose, 13C-metabolic flux analysis revealed a large excess of available energy, highlighting the need to better characterize ATP utilization processes. The probiotic E. coli Nissle 1917 strain exhibits similar metabolic traits, indicating that they are not the result of the K-12 strain's prolonged laboratory use. IMPORTANCE E. coli's ability to survive in, grow in, and colonize the gastrointestinal tract stems from its use of partially digested food and hydrolyzed glycosylated proteins (mucins) from the intestinal mucus layer as substrates. These include l-fucose and l-rhamnose, two 6-deoxyhexose sugars, whose catabolic pathways have been established by genetic and biochemical studies. However, the functioning of these pathways has only partially been elucidated. Our quantitative metabolic analysis provides a comprehensive picture of 6-deoxyhexose sugar metabolism in E. coli under anaerobic and aerobic conditions. We found that 1,2-propanediol is a major by-product under both conditions, revealing the key role of fermentative pathways in 6-deoxyhexose sugar metabolism. This metabolic trait is shared by both E. coli strains studied here, a laboratory strain and a probiotic strain. Our findings add to our understanding of E. coli's metabolism and of its functioning in the bacterium's natural environment.
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16
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Zhan C, Li X, Yang Y, Nielsen J, Bai Z, Chen Y. Strategies and challenges with the microbial conversion of methanol to high-value chemicals. Biotechnol Bioeng 2021; 118:3655-3668. [PMID: 34133022 DOI: 10.1002/bit.27862] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 05/25/2021] [Accepted: 06/10/2021] [Indexed: 01/03/2023]
Abstract
As alternatives to traditional fermentation substrates, methanol (CH3 OH), carbon dioxide (CO2 ) and methane (CH4 ) represent promising one-carbon (C1) sources that are readily available at low-cost and share similar metabolic pathway. Of these C1 compounds, methanol is used as a carbon and energy source by native methylotrophs, and can be obtained from CO2 and CH4 by chemical catalysis. Therefore, constructing and rewiring methanol utilization pathways may enable the use of one-carbon sources for microbial fermentations. Recent bioengineering efforts have shown that both native and nonnative methylotrophic organisms can be engineered to convert methanol, together with other carbon sources, into biofuels and other commodity chemicals. However, many challenges remain and must be overcome before industrial-scale bioprocessing can be established using these engineered cell refineries. Here, we provide a comprehensive summary and comparison of methanol metabolic pathways from different methylotrophs, followed by a review of recent progress in engineering methanol metabolic pathways in vitro and in vivo to produce chemicals. We discuss the major challenges associated with establishing efficient methanol metabolic pathways in microbial cells, and propose improved designs for future engineering.
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Affiliation(s)
- Chunjun Zhan
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Xiaowei Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Yankun Yang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden.,BioInnovation Institute, Copenhagen N, Denmark
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, China.,The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
| | - Yun Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
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17
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Du GF, Yin XF, Yang DH, He QY, Sun X. Proteomic Investigation of the Antibacterial Mechanism of trans-Cinnamaldehyde against Escherichia coli. J Proteome Res 2021; 20:2319-2328. [PMID: 33749271 DOI: 10.1021/acs.jproteome.0c00847] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Trans-Cinnamaldehyde (TC) is a widely used food additive, known for its sterilization, disinfection, and antiseptic properties. However, its antibacterial mechanism is not completely understood. In this study, quantitative proteomics was performed to investigate differentially expressed proteins (DEPs) in Escherichia coli in response to TC treatment. Bioinformatics analysis suggested aldehyde toxicity, acid stress, oxidative stress, interference of carbohydrate metabolism, energy metabolism, and protein translation as the bactericidal mechanism. E. coli BW25113ΔyqhD, ΔgldA, ΔbetB, ΔtktB, ΔgadA, ΔgadB, ΔgadC, and Δrmf were used to investigate the functions of DEPs through biochemical methods. The present study revealed that TC exerts its antibacterial effects by inducing the toxicity of its aldehyde group producing acid stress. These findings will contribute to the application of TC in the antibacterial field.
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Affiliation(s)
- Gao-Fei Du
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou 510632, China.,Medical Technology School, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Xing-Feng Yin
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou 510632, China
| | - Dong-Hong Yang
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou 510632, China
| | - Qing-Yu He
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou 510632, China
| | - Xuesong Sun
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou 510632, China
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18
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Opening a Novel Biosynthetic Pathway to Dihydroxyacetone and Glycerol in Escherichia coli Mutants through Expression of a Gene Variant ( fsaAA129S) for Fructose 6-Phosphate Aldolase. Int J Mol Sci 2020; 21:ijms21249625. [PMID: 33348713 PMCID: PMC7767278 DOI: 10.3390/ijms21249625] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/05/2020] [Accepted: 12/15/2020] [Indexed: 01/19/2023] Open
Abstract
Phosphofructokinase (PFK) plays a pivotal role in glycolysis. By deletion of the genes pfkA, pfkB (encoding the two PFK isoenzymes), and zwf (glucose 6-phosphate dehydrogenase) in Escherichia coli K-12, a mutant strain (GL3) with a complete block in glucose catabolism was created. Introduction of plasmid-borne copies of the fsaA wild type gene (encoding E. coli fructose 6-phosphate aldolase, FSAA) did not allow a bypass by splitting fructose 6-phosphate (F6P) into dihydroxyacetone (DHA) and glyceraldehyde 3-phosphate (G3P). Although FSAA enzyme activity was detected, growth on glucose was not reestablished. A mutant allele encoding for FSAA with an amino acid exchange (Ala129Ser) which showed increased catalytic efficiency for F6P, allowed growth on glucose with a µ of about 0.12 h−1. A GL3 derivative with a chromosomally integrated copy of fsaAA129S (GL4) grew with 0.05 h−1 on glucose. A mutant strain from GL4 where dhaKLM genes were deleted (GL5) excreted DHA. By deletion of the gene glpK (glycerol kinase) and overexpression of gldA (of glycerol dehydrogenase), a strain (GL7) was created which showed glycerol formation (21.8 mM; yield approximately 70% of the theoretically maximal value) as main end product when grown on glucose. A new-to-nature pathway from glucose to glycerol was created.
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Rohwerder T, Rohde MT, Jehmlich N, Purswani J. Actinobacterial Degradation of 2-Hydroxyisobutyric Acid Proceeds via Acetone and Formyl-CoA by Employing a Thiamine-Dependent Lyase Reaction. Front Microbiol 2020; 11:691. [PMID: 32351493 PMCID: PMC7176365 DOI: 10.3389/fmicb.2020.00691] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/25/2020] [Indexed: 11/13/2022] Open
Abstract
The tertiary branched short-chain 2-hydroxyisobutyric acid (2-HIBA) has been associated with several metabolic diseases and lysine 2-hydroxyisobutyrylation seems to be a common eukaryotic as well as prokaryotic post-translational modification in proteins. In contrast, the underlying 2-HIBA metabolism has thus far only been detected in a few microorganisms, such as the betaproteobacterium Aquincola tertiaricarbonis L108 and the Bacillus group bacterium Kyrpidia tusciae DSM 2912. In these strains, 2-HIBA can be specifically activated to the corresponding CoA thioester by the 2-HIBA-CoA ligase (HCL) and is then isomerized to 3-hydroxybutyryl-CoA in a reversible and B12-dependent mutase reaction. Here, we demonstrate that the actinobacterial strain Actinomycetospora chiangmaiensis DSM 45062 degrades 2-HIBA and also its precursor 2-methylpropane-1,2-diol via acetone and formic acid by employing a thiamine pyrophosphate-dependent lyase. The corresponding gene is located directly upstream of hcl, which has previously been found only in operonic association with the 2-hydroxyisobutyryl-CoA mutase genes in other bacteria. Heterologous expression of the lyase gene from DSM 45062 in E. coli established a 2-hydroxyisobutyryl-CoA lyase activity in the latter. In line with this, analysis of the DSM 45062 proteome reveals a strong induction of the lyase-HCL gene cluster on 2-HIBA. Acetone is likely degraded via hydroxylation to acetol catalyzed by a MimABCD-related binuclear iron monooxygenase and formic acid appears to be oxidized to CO2 by selenium-dependent dehydrogenases. The presence of the lyase-HCL gene cluster in isoprene-degrading Rhodococcus strains and Pseudonocardia associated with tropical leafcutter ant species points to a role in degradation of biogenic short-chain ketones and highly branched organic compounds.
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Affiliation(s)
- Thore Rohwerder
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Maria-Teresa Rohde
- Institut für Chemie - Biophysikalische Chemie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Jessica Purswani
- Institute of Water Research, University of Granada, Granada, Spain
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Lindner SN, Aslan S, Müller A, Hoffart E, Behrens P, Edlich-Muth C, Blombach B, Bar-Even A. A synthetic glycerol assimilation pathway demonstrates biochemical constraints of cellular metabolism. FEBS J 2019; 287:160-172. [PMID: 31436884 DOI: 10.1111/febs.15048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/06/2019] [Accepted: 08/20/2019] [Indexed: 11/28/2022]
Abstract
The engineering of synthetic metabolic routes can provide valuable lessons on the roles of different biochemical constraints in shaping pathway activity. In this study, we designed and engineered a novel glycerol assimilation pathway in Escherichia coli. While the synthetic pathway was based only on well-characterized endogenous reactions, we were not able to establish robust growth using standard concentrations of glycerol. Long-term evolution failed to improve growth via the pathway, indicating that this limitation was not regulatory but rather relates to fundamental aspects of cellular metabolism. We show that the activity of the synthetic pathway is fully controlled by three key physicochemical constraints: thermodynamics, kinetics and metabolite toxicity. Overcoming a thermodynamic barrier at the beginning of the pathway requires high glycerol concentrations. A kinetic barrier leads to a Monod-like growth dependency on substrate concentration, but with a very high substrate saturation constant. Finally, the flat thermodynamic profile of the pathway enforces a pseudoequilibrium between glycerol and the reactive intermediate dihydroxyacetone, which inhibits growth when the feedstock concentration surpasses 1000 mm. Overall, this study serves to demonstrate the use of synthetic biology to elucidate key design principles of cellular metabolism.
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Affiliation(s)
- Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Selçuk Aslan
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Alexandra Müller
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Eugenia Hoffart
- Institute of Biochemical Engineering, University of Stuttgart, Germany
| | - Patrick Behrens
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Bastian Blombach
- Institute of Biochemical Engineering, University of Stuttgart, Germany.,Microbial Biotechnology, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Straubing, Germany
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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Chemical and Metabolic Controls on Dihydroxyacetone Metabolism Lead to Suboptimal Growth of Escherichia coli. Appl Environ Microbiol 2019; 85:AEM.00768-19. [PMID: 31126940 PMCID: PMC6643234 DOI: 10.1128/aem.00768-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/11/2019] [Indexed: 12/26/2022] Open
Abstract
DHA is an attractive triose molecule with a wide range of applications, notably in cosmetics and the food and pharmaceutical industries. DHA is found in many species, from microorganisms to humans, and can be used by Escherichia coli as a growth substrate. However, knowledge about the mechanisms and regulation of this process is currently lacking, motivating our investigation of DHA metabolism in E. coli. We show that under aerobic conditions, E. coli growth on DHA is far from optimal and is hindered by chemical, hierarchical, and possibly allosteric constraints. We show that optimal growth on DHA can be restored by releasing the hierarchical constraint. These results improve our understanding of DHA metabolism and are likely to help unlock biotechnological applications involving DHA as an intermediate, such as the bioconversion of glycerol or C1 substrates into value-added chemicals. In this work, we shed light on the metabolism of dihydroxyacetone (DHA), a versatile, ubiquitous, and important intermediate for various chemicals in industry, by analyzing its metabolism at the system level in Escherichia coli. Using constraint-based modeling, we show that the growth of E. coli on DHA is suboptimal and identify the potential causes. Nuclear magnetic resonance analysis shows that DHA is degraded nonenzymatically into substrates known to be unfavorable to high growth rates. Transcriptomic analysis reveals that DHA promotes genes involved in biofilm formation, which may reduce the bacterial growth rate. Functional analysis of the genes involved in DHA metabolism proves that under the aerobic conditions used in this study, DHA is mainly assimilated via the dihydroxyacetone kinase pathway. In addition, these results show that the alternative routes of DHA assimilation (i.e., the glycerol and fructose-6-phosphate aldolase pathways) are not fully activated under our conditions because of anaerobically mediated hierarchical control. These pathways are therefore certainly unable to sustain fluxes as high as the ones predicted in silico for optimal aerobic growth on DHA. Overexpressing some of the genes in these pathways releases these constraints and restores the predicted optimal growth on DHA. IMPORTANCE DHA is an attractive triose molecule with a wide range of applications, notably in cosmetics and the food and pharmaceutical industries. DHA is found in many species, from microorganisms to humans, and can be used by Escherichia coli as a growth substrate. However, knowledge about the mechanisms and regulation of this process is currently lacking, motivating our investigation of DHA metabolism in E. coli. We show that under aerobic conditions, E. coli growth on DHA is far from optimal and is hindered by chemical, hierarchical, and possibly allosteric constraints. We show that optimal growth on DHA can be restored by releasing the hierarchical constraint. These results improve our understanding of DHA metabolism and are likely to help unlock biotechnological applications involving DHA as an intermediate, such as the bioconversion of glycerol or C1 substrates into value-added chemicals.
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22
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Glycerol metabolism and its regulation in lactic acid bacteria. Appl Microbiol Biotechnol 2019; 103:5079-5093. [DOI: 10.1007/s00253-019-09830-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/02/2019] [Accepted: 04/04/2019] [Indexed: 01/09/2023]
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Zhang J, Nanjaraj Urs AN, Lin L, Zhou Y, Hu Y, Hua G, Gao Q, Yuchi Z, Zhang Y. Structure of glycerol dehydrogenase (GldA) from Escherichia coli. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2019; 75:176-183. [PMID: 30839292 DOI: 10.1107/s2053230x19000037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 01/02/2019] [Indexed: 11/10/2022]
Abstract
Escherichia coli (strain K-12, substrain MG1655) glycerol dehydrogenase (GldA) is required to catalyze the first step in fermentative glycerol metabolism. The protein was expressed and purified to homogeneity using a simple combination of heat-shock and chromatographic methods. The high yield of the protein (∼250 mg per litre of culture) allows large-scale production for potential industrial applications. Purified GldA exhibited a homogeneous tetrameric state (∼161 kDa) in solution and relatively high thermostability (Tm = 65.6°C). Sitting-drop sparse-matrix screens were used for protein crystallization. An optimized condition with ammonium sulfate (2 M) provided crystals suitable for diffraction, and a binary structure containing glycerol in the active site was solved at 2.8 Å resolution. Each GldA monomer consists of nine β-strands, thirteen α-helices, two 310-helices and several loops organized into two domains, the N- and C-terminal domains; the active site is located in a deep cleft between the two domains. The N-terminal domain contains a classic Rossmann fold for NAD+ binding. The O1 and O2 atoms of glycerol serve as ligands for the tetrahedrally coordinated Zn2+ ion. The orientation of the glycerol within the active site is mainly stabilized by van der Waals and electrostatic interactions with the benzyl ring of Phe245. Computer modeling suggests that the glycerol molecule is sandwiched by the Zn2+ and NAD+ ions. Based on this, the mechanism for the relaxed substrate specificity of this enzyme is also discussed.
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Affiliation(s)
- Jun Zhang
- The Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Ankanahalli N Nanjaraj Urs
- 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, People's Republic of China
| | - Lianyun Lin
- 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, People's Republic of China
| | - Yan Zhou
- 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, People's Republic of 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, People's Republic of China
| | - Gaoqun Hua
- 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, People's Republic of China
| | - Qiang Gao
- The Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Zhiguang Yuchi
- 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, People's Republic of China
| | - 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, People's Republic of China
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Metcalf KJ, Slininger Lee MF, Jakobson CM, Tullman-Ercek D. An estimate is worth about a thousand experiments: using order-of-magnitude estimates to identify cellular engineering targets. Microb Cell Fact 2018; 17:135. [PMID: 30165868 PMCID: PMC6117934 DOI: 10.1186/s12934-018-0979-7] [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: 05/29/2018] [Accepted: 08/21/2018] [Indexed: 11/10/2022] Open
Abstract
Biotechnological processes use microbes to convert abundant molecules, such as glucose, into high-value products, such as pharmaceuticals, commodity and fine chemicals, and energy. However, from the outset of the development of a new bioprocess, it is difficult to determine the feasibility, expected yields, and targets for engineering. In this review, we describe a methodology that uses rough estimates to assess the feasibility of a process, approximate the expected product titer of a biological system, and identify variables to manipulate in order to achieve the desired performance. This methodology uses estimates from literature and biological intuition, and can be applied in the early stages of a project to help plan future engineering. We highlight recent literature examples, as well as two case studies from our own work, to demonstrate the use and power of rough estimates. Describing and predicting biological function using estimates guides the research and development phase of new bioprocesses and is a useful first step to understand and build a new microbial factory.
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Affiliation(s)
- Kevin James Metcalf
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA. .,Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.
| | - Marilyn F Slininger Lee
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.,U.S. Army Edgewood Chemical Biological Center, Gunpowder, MD, 21010, USA
| | - Christopher Matthew Jakobson
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.,Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
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25
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Toxicity of dihydroxyacetone is exerted through the formation of methylglyoxal in Saccharomyces cerevisiae: effects on actin polarity and nuclear division. Biochem J 2018; 475:2637-2652. [DOI: 10.1042/bcj20180234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/12/2018] [Accepted: 07/20/2018] [Indexed: 01/21/2023]
Abstract
Dihydroxyacetone (DHA) is the smallest ketotriose, and it is utilized by many organisms as an energy source. However, at higher concentrations, DHA becomes toxic towards several organisms including the budding yeast Saccharomyces cerevisiae. In the present study, we show that DHA toxicity is due to its spontaneous conversion to methylglyoxal (MG) within yeast cells. A mutant defective in MG-metabolizing enzymes (glo1Δgre2Δgre3Δ) exhibited higher susceptibility to DHA. Intracellular MG levels increased following the treatment of glo1Δgre2Δgre3Δ cells with DHA. We previously reported that MG depolarized the actin cytoskeleton and changed vacuolar morphology. We herein demonstrated the depolarization of actin and morphological changes in vacuoles following a treatment with DHA. Furthermore, we found that both MG and DHA caused the morphological change in nucleus, and inhibited the nuclear division. Our results suggest that the conversion of DHA to MG is a dominant contributor to its cytotoxicity.
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26
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Chae TU, Choi SY, Ryu JY, Lee SY. Production of ethylene glycol from xylose by metabolically engineeredEscherichia coli. AIChE J 2018. [DOI: 10.1002/aic.16339] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Tong Un Chae
- Dept. of Chemical and Biomolecular Engineering (BK21 Plus Program); BioProcess Engineering Research Center; Korea Advanced Institute of Science and Technology; Daejeon 34141 Republic of Korea
| | - So Young Choi
- Dept. of Chemical and Biomolecular Engineering (BK21 Plus Program); BioProcess Engineering Research Center; Korea Advanced Institute of Science and Technology; Daejeon 34141 Republic of Korea
| | - Jae Yong Ryu
- Dept. of Chemical and Biomolecular Engineering (BK21 Plus Program); Bioinformatics Research Center; Korea Advanced Institute of Science and Technology; Daejeon 34141 Republic of Korea
| | - Sang Yup Lee
- Dept. of Chemical and Biomolecular Engineering (BK21 Plus Program); BioProcess Engineering Research Center; Bioinformatics Research Center; Korea Advanced Institute of Science and Technology; Daejeon 34141 Republic of Korea
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Trinchieri V, Laghi L, Vitali B, Parolin C, Giusti I, Capobianco D, Mastromarino P, De Simone C. Efficacy and Safety of a Multistrain Probiotic Formulation Depends from Manufacturing. Front Immunol 2017; 8:1474. [PMID: 29163538 PMCID: PMC5681494 DOI: 10.3389/fimmu.2017.01474] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/20/2017] [Indexed: 12/12/2022] Open
Abstract
Background Variability in probiotics manufacturing may affect their properties, with potential implications for their efficacy and safety. This is of particular concern with probiotic products destined for use in patients with serious medical conditions, including human immunodeficiency virus (HIV) infection. The purpose of the study was to carry out a series of experiments comparing the properties of the US-made probiotic formulation originally commercialized under the brand name VSL#3®, with those of the Italian-made formulation now commercialized under the same name. The US-made formulation has previously shown beneficial effects at the intestinal and neurological levels in HIV-infected subjects as well as in patients with inflammatory bowel diseases and hepatic encephalopathy. Methods Eleven subjects receiving combined antiretroviral therapy for HIV-1 were treated for 6 months with the US-made VSL#3 formulation. At baseline and 6 months, T-cells were analyzed for phenotype and activation markers, and fecal samples were analyzed for bifidobacteria, lactobacilli, and their metabolites. The fecal metabolome was assessed using 1H-NMR spectroscopy. Production of metabolites of interest by bacteria obtained from sachets of the two formulations was compared in vitro and their effects on a rat intestinal epithelial cell line (IEC-6) were assessed. Particular attention was paid to the metabolite 1,3-dihydroxyacetone (DHA). Results At 6 months, fecal samples showed a significant increase in the specific bacterial genera contained in the probiotic supplement. Immune activation was reduced as shown by a significant reduction in the percentage of CD4+CD38+HLA-DR+ T-cells at 6 months. Fecal concentrations of DHA decreased significantly. In vitro, significant differences in the production and metabolism of DHA were found between bacteria from the US-made and Italian-made formulations: the US-made formulation was able to metabolize DHA whereas the bacteria in the Italian-made formulation were producing DHA. DHA reduced the viability of Streptococcus thermophilus, reduced IEC-6 cell viability in a dose-dependent manner, and also led to a lower rate of repair to scratched IEC-6 cell monolayer. Conclusion Our data, in conjunction with previously published findings, confirm that the new Italian-made formulation of VSL#3® is different from the previous US-made VSL#3 and therefore its efficacy and safety in HIV-infected subjects is still unproven.
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Affiliation(s)
- Vito Trinchieri
- Department of Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - Luca Laghi
- Department of Agricultural and Food Sciences, Interdepartmental Centre for Agri-Food Industrial Research, University of Bologna, Cesena, Italy
| | - Beatrice Vitali
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Carola Parolin
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Ilaria Giusti
- Department of Life, Health and Environmental Sciences, University of L'Aquila, Piazzale S. Tommasi, Coppito, Italy
| | - Daniela Capobianco
- Department of Public Health and Infectious Diseases, Sapienza University, Rome, Italy
| | - Paola Mastromarino
- Department of Public Health and Infectious Disease, Section of Microbiology, Sapienza University Rome, Rome, Italy
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Bacterial Responses to Glyoxal and Methylglyoxal: Reactive Electrophilic Species. Int J Mol Sci 2017; 18:ijms18010169. [PMID: 28106725 PMCID: PMC5297802 DOI: 10.3390/ijms18010169] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 11/29/2022] Open
Abstract
Glyoxal (GO) and methylglyoxal (MG), belonging to α-oxoaldehydes, are produced by organisms from bacteria to humans by glucose oxidation, lipid peroxidation, and DNA oxidation. Since glyoxals contain two adjacent reactive carbonyl groups, they are referred to as reactive electrophilic species (RES), and are damaging to proteins and nucleotides. Therefore, glyoxals cause various diseases in humans, such as diabetes and neurodegenerative diseases, from which all living organisms need to be protected. Although the glyoxalase system has been known for some time, details on how glyoxals are sensed and detoxified in the cell have not been fully elucidated, and are only beginning to be uncovered. In this review, we will summarize the current knowledge on bacterial responses to glyoxal, and specifically focus on the glyoxal-associated regulators YqhC and NemR, as well as their detoxification mediated by glutathione (GSH)-dependent/independent glyoxalases and NAD(P)H-dependent reductases. Furthermore, we will address questions and future directions.
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29
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Liang K, Shen CR. Selection of an endogenous 2,3-butanediol pathway in Escherichia coli by fermentative redox balance. Metab Eng 2016; 39:181-191. [PMID: 27931827 DOI: 10.1016/j.ymben.2016.11.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/24/2016] [Accepted: 11/30/2016] [Indexed: 01/01/2023]
Abstract
Fermentative redox balance has long been utilized as a metabolic evolution platform to improve efficiency of NADH-dependent pathways. However, such system relies on the complete recycling of NADH and may become limited when the target pathway results in excess NADH stoichiometrically. In this study, endogenous capability of Escherichia coli for 2,3-butanediol (2,3-BD) synthesis was explored using the anaerobic selection platform based on redox balance. To address the issue of NADH excess associated with the 2,3-BD pathway, we devised a substrate-decoupled system where a pathway intermediate is externally supplied in addition to the carbon source to decouple NADH recycling ratio from the intrinsic pathway stoichiometry. In this case, feeding of the 2,3-BD precursor acetoin effectively restored anaerobic growth of the mixed-acid fermentation mutant that remained otherwise inhibited even in the presence of a functional 2,3-BD pathway. Using established 2,3-BD dehydrogenases as model enzyme, we verified that the redox-based selection system is responsive to NADPH-dependent reactions but with lower sensitivity. Based on this substrate-decoupled selection scheme, we successfully identified the glycerol/1,2-propanediol dehydrogenase (Ec-GldA) as the major enzyme responsible for the acetoin reducing activity (kcat/Km≈0.4mM-1s-1) observed in E. coli. Significant shift of 2,3-BD configuration upon withdrawal of the heterologous acetolactate decarboxylase revealed that the endogenous synthesis of acetoin occurs via diacetyl. Among the predicted diacetyl reductase in E. coli, Ec-UcpA displayed the most significant activity towards diacetyl reduction into acetoin (Vmax≈6U/mg). The final strain demonstrated a meso-2,3-BD production titer of 3g/L without introduction of foreign genes. The substrate-decoupled selection system allows redox balance regardless of the pathway stoichiometry thus enables segmented optimization of different reductive pathways through enzyme bioprospecting and metabolic evolution.
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Affiliation(s)
- Keming Liang
- Department of Chemical Engineering, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Claire R Shen
- Department of Chemical Engineering, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan.
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Metabolic pathway optimization for biosynthesis of 1,2,4-butanetriol from xylose by engineered Escherichia coli. Enzyme Microb Technol 2016; 93-94:51-58. [DOI: 10.1016/j.enzmictec.2016.07.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/16/2016] [Accepted: 07/18/2016] [Indexed: 12/22/2022]
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31
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Richter C, Krumrey M, Klaue K, Mahrwald R. Cascade Reactions of Unprotected Ketoses with Ketones - A Stereoselective Access to C-Glycosides. European J Org Chem 2016. [DOI: 10.1002/ejoc.201601058] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Celin Richter
- Humboldt University; Department of Chemistry; Brook-Taylor Str. 2 12489 Berlin Germany
| | - Michael Krumrey
- Humboldt University; Department of Chemistry; Brook-Taylor Str. 2 12489 Berlin Germany
| | - Kristin Klaue
- Humboldt University; Department of Chemistry; Brook-Taylor Str. 2 12489 Berlin Germany
| | - Rainer Mahrwald
- Humboldt University; Department of Chemistry; Brook-Taylor Str. 2 12489 Berlin Germany
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32
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Chin YW, Seo N, Kim JH, Seo JH. Metabolic engineering of Escherichia coli to produce 2'-fucosyllactose via salvage pathway of guanosine 5'-diphosphate (GDP)-l-fucose. Biotechnol Bioeng 2016; 113:2443-52. [PMID: 27217241 DOI: 10.1002/bit.26015] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 04/20/2016] [Accepted: 05/15/2016] [Indexed: 12/24/2022]
Abstract
2'-Fucosyllactose (2-FL) is one of the key oligosaccharides in human milk. In the present study, the salvage guanosine 5'-diphosphate (GDP)-l-fucose biosynthetic pathway from fucose was employed in engineered Escherichia coli BL21star(DE3) for efficient production of 2-FL. Introduction of the fkp gene coding for fucokinase/GDP-l-fucose pyrophosphorylase (Fkp) from Bacteroides fragilis and the fucT2 gene encoding α-1,2-fucosyltransferase from Helicobacter pylori allows the engineered E. coli to produce 2-FL from fucose, lactose and glycerol. To enhance the lactose flux to 2-FL production, the attenuated, and deleted mutants of β-galactosidase were employed. Moreover, the 2-FL yield and productivity were further improved by deletion of the fucI-fucK gene cluster coding for fucose isomerase (FucI) and fuculose kinase (FucK). Finally, fed-batch fermentation of engineered E. coli BL21star(DE3) deleting lacZ and fucI-fucK, and expressing fkp and fucT2 resulted in 23.1 g/L of extracellular concentration of 2-FL and 0.39 g/L/h productivity. Biotechnol. Bioeng. 2016;113: 2443-2452. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Young-Wook Chin
- Department of Agricultural Biotechnology and Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea
| | - Nari Seo
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
| | - Jae-Han Kim
- Department of Food and Nutrition, Chungnam National University, Daejeon, Republic of Korea
| | - Jin-Ho Seo
- Department of Agricultural Biotechnology and Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea.
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Häuslein I, Manske C, Goebel W, Eisenreich W, Hilbi H. Pathway analysis using13C-glycerol and other carbon tracers reveals a bipartite metabolism ofLegionella pneumophila. Mol Microbiol 2016; 100:229-46. [DOI: 10.1111/mmi.13313] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Ina Häuslein
- Lehrstuhl für Biochemie, Technische Universität München; Munich Germany
| | - Christian Manske
- Max von Pettenkofer Institut, Ludwig-Maximilians Universität; Munich Germany
| | - Werner Goebel
- Max von Pettenkofer Institut, Ludwig-Maximilians Universität; Munich Germany
| | | | - Hubert Hilbi
- Max von Pettenkofer Institut, Ludwig-Maximilians Universität; Munich Germany
- Institute of Medical Microbiology, University of Zürich; Switzerland
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Jain VK, Tear CJY, Lim CY. Dihydroxyacetone production in an engineered Escherichia coli through expression of Corynebacterium glutamicum dihydroxyacetone phosphate dephosphorylase. Enzyme Microb Technol 2016; 86:39-44. [PMID: 26992791 DOI: 10.1016/j.enzmictec.2016.01.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/27/2016] [Accepted: 01/28/2016] [Indexed: 11/18/2022]
Abstract
Dihydroxyacetone (DHA) has several industrial applications such as a tanning agent in tanning lotions in the cosmetic industry; its production via microbial fermentation would present a more sustainable option for the future. Here we genetically engineered Escherichia coli (E. coli) for DHA production from glucose. Deletion of E. coli triose phosphate isomerase (tpiA) gene was carried out to accumulate dihydroxyacetone phosphate (DHAP), for use as the main intermediate or precursor for DHA production. The accumulated DHAP was then converted to DHA through the heterologous expression of Corynebacterium glutamicum DHAP dephosphorylase (cghdpA) gene. To conserve DHAP exclusively for DHA production we removed methylglyoxal synthase (mgsA) gene in the ΔtpiA strain. This drastically improved DHA production from 0.83g/l (0.06g DHA/g glucose) in the ΔtpiA strain bearing cghdpA to 5.84g/l (0.41g DHA/g glucose) in the ΔtpiAΔmgsA double mutant containing the same gene. To limit the conversion of intracellular DHA to glycerol, glycerol dehydrogenase (gldA) gene was further knocked out resulting in a ΔtpiAΔmgsAΔgldA triple mutant. This triple mutant expressing the cghdpA gene produced 6.60g/l of DHA at 87% of the maximum theoretical yield. In summary, we demonstrated an efficient system for DHA production in genetically engineered E. coli strain.
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Affiliation(s)
- Vishist Kumar Jain
- Industrial Biotechnology Division, Institute of Chemical & Engineering Sciences, Agency for Science, Technology and Research (A-STAR), 1, Pesek Road, Jurong Island 627833, Singapore.
| | - Crystal Jing Ying Tear
- Industrial Biotechnology Division, Institute of Chemical & Engineering Sciences, Agency for Science, Technology and Research (A-STAR), 1, Pesek Road, Jurong Island 627833, Singapore
| | - Chan Yuen Lim
- Industrial Biotechnology Division, Institute of Chemical & Engineering Sciences, Agency for Science, Technology and Research (A-STAR), 1, Pesek Road, Jurong Island 627833, Singapore
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Alkim C, Cam Y, Trichez D, Auriol C, Spina L, Vax A, Bartolo F, Besse P, François JM, Walther T. Optimization of ethylene glycol production from (D)-xylose via a synthetic pathway implemented in Escherichia coli. Microb Cell Fact 2015; 14:127. [PMID: 26336892 PMCID: PMC4559361 DOI: 10.1186/s12934-015-0312-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 08/04/2015] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Ethylene glycol (EG) is a bulk chemical that is mainly used as an anti-freezing agent and a raw material in the synthesis of plastics. Production of commercial EG currently exclusively relies on chemical synthesis using fossil resources. Biochemical production of ethylene glycol from renewable resources may be more sustainable. RESULTS Herein, a synthetic pathway is described that produces EG in Escherichia coli through the action of (D)-xylose isomerase, (D)-xylulose-1-kinase, (D)-xylulose-1-phosphate aldolase, and glycolaldehyde reductase. These reactions were successively catalyzed by the endogenous xylose isomerase (XylA), the heterologously expressed human hexokinase (Khk-C) and aldolase (Aldo-B), and an endogenous glycolaldehyde reductase activity, respectively, which we showed to be encoded by yqhD. The production strain was optimized by deleting the genes encoding for (D)-xylulose-5 kinase (xylB) and glycolaldehyde dehydrogenase (aldA), and by overexpressing the candidate glycolaldehyde reductases YqhD, GldA, and FucO. The strain overproducing FucO was the best EG producer reaching a molar yield of 0.94 in shake flasks, and accumulating 20 g/L EG with a molar yield and productivity of 0.91 and 0.37 g/(L.h), respectively, in a controlled bioreactor under aerobic conditions. CONCLUSIONS We have demonstrated the feasibility to produce EG from (D)-xylose via a synthetic pathway in E. coli at approximately 90 % of the theoretical yield.
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Affiliation(s)
- Ceren Alkim
- INSA, UPS, INP, LISBP, Université de Toulouse, 135 Avenue de Rangueil, 31077, Toulouse, France. .,UMR792 Ingénierie des Systèmes Biologiques et des Procédés (LISBP), INRA, Toulouse, France. .,CNRS, UMR5504, Toulouse, France. .,TWB, 3 rue Ariane, 31520, Ramonville-St. Agnes, France.
| | - Yvan Cam
- INSA, UPS, INP, LISBP, Université de Toulouse, 135 Avenue de Rangueil, 31077, Toulouse, France. .,UMR792 Ingénierie des Systèmes Biologiques et des Procédés (LISBP), INRA, Toulouse, France. .,CNRS, UMR5504, Toulouse, France. .,TWB, 3 rue Ariane, 31520, Ramonville-St. Agnes, France.
| | - Debora Trichez
- INSA, UPS, INP, LISBP, Université de Toulouse, 135 Avenue de Rangueil, 31077, Toulouse, France. .,UMR792 Ingénierie des Systèmes Biologiques et des Procédés (LISBP), INRA, Toulouse, France. .,CNRS, UMR5504, Toulouse, France.
| | - Clément Auriol
- INSA, UPS, INP, LISBP, Université de Toulouse, 135 Avenue de Rangueil, 31077, Toulouse, France. .,UMR792 Ingénierie des Systèmes Biologiques et des Procédés (LISBP), INRA, Toulouse, France. .,CNRS, UMR5504, Toulouse, France. .,TWB, 3 rue Ariane, 31520, Ramonville-St. Agnes, France.
| | - Lucie Spina
- INSA, UPS, INP, LISBP, Université de Toulouse, 135 Avenue de Rangueil, 31077, Toulouse, France. .,UMR792 Ingénierie des Systèmes Biologiques et des Procédés (LISBP), INRA, Toulouse, France. .,CNRS, UMR5504, Toulouse, France.
| | - Amélie Vax
- INSA, UPS, INP, LISBP, Université de Toulouse, 135 Avenue de Rangueil, 31077, Toulouse, France. .,UMR792 Ingénierie des Systèmes Biologiques et des Procédés (LISBP), INRA, Toulouse, France. .,CNRS, UMR5504, Toulouse, France.
| | - François Bartolo
- UMR CNRS 5219, Institut de Mathématiques de Toulouse, INSA, Université de Toulouse, Toulouse, France.
| | - Philippe Besse
- UMR CNRS 5219, Institut de Mathématiques de Toulouse, INSA, Université de Toulouse, Toulouse, France.
| | - Jean Marie François
- INSA, UPS, INP, LISBP, Université de Toulouse, 135 Avenue de Rangueil, 31077, Toulouse, France. .,UMR792 Ingénierie des Systèmes Biologiques et des Procédés (LISBP), INRA, Toulouse, France. .,CNRS, UMR5504, Toulouse, France. .,TWB, 3 rue Ariane, 31520, Ramonville-St. Agnes, France.
| | - Thomas Walther
- INSA, UPS, INP, LISBP, Université de Toulouse, 135 Avenue de Rangueil, 31077, Toulouse, France. .,UMR792 Ingénierie des Systèmes Biologiques et des Procédés (LISBP), INRA, Toulouse, France. .,CNRS, UMR5504, Toulouse, France. .,TWB, 3 rue Ariane, 31520, Ramonville-St. Agnes, France.
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Siebert D, Wendisch VF. Metabolic pathway engineering for production of 1,2-propanediol and 1-propanol by Corynebacterium glutamicum. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:91. [PMID: 26110019 PMCID: PMC4478622 DOI: 10.1186/s13068-015-0269-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/05/2015] [Indexed: 05/03/2023]
Abstract
BACKGROUND Production of the versatile bulk chemical 1,2-propanediol and the potential biofuel 1-propanol is still dependent on petroleum, but some approaches to establish bio-based production from renewable feed stocks and to avoid toxic intermediates have been described. The biotechnological workhorse Corynebacterium glutamicum has also been shown to be able to overproduce 1,2-propanediol by metabolic engineering. Additionally, C. glutamicum has previously been engineered for production of the biofuels ethanol and isobutanol but not for 1-propanol. RESULTS In this study, the improved production of 1,2-propanediol by C. glutamicum is presented. The product yield of a C. glutamicum strain expressing the heterologous genes gldA and mgsA from Escherichia coli that encode methylglyoxal synthase gene and glycerol dehydrogenase, respectively, was improved by additional expression of alcohol dehydrogenase gene yqhD from E. coli leading to a yield of 0.131 mol/mol glucose. Deletion of the endogenous genes hdpA and ldh encoding dihydroxyacetone phosphate phosphatase and lactate dehydrogenase, respectively, prevented formation of glycerol and lactate as by-products and improved the yield to 0.343 mol/mol glucose. To construct a 1-propanol producer, the operon ppdABC from Klebsiella oxytoca encoding diol dehydratase was expressed in the improved 1,2-propanediol producing strain ending up with 12 mM 1-propanol and up to 60 mM unconverted 1,2-propanediol. Thus, B12-dependent diol dehydratase activity may be limiting 1-propanol production. CONCLUSIONS Production of 1,2-propanediol by C. glutamicum was improved by metabolic engineering targeting endogenous enzymes. Furthermore, to the best of our knowledge, production of 1-propanol by recombinant C. glutamicum was demonstrated for the first time.
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Affiliation(s)
- Daniel Siebert
- Chair of Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Volker F. Wendisch
- Chair of Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
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Ex uno plures: clonal reinforcement drives evolution of a simple microbial community. PLoS Genet 2014; 10:e1004430. [PMID: 24968217 PMCID: PMC4072538 DOI: 10.1371/journal.pgen.1004430] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 04/24/2014] [Indexed: 11/19/2022] Open
Abstract
A major goal of genetics is to define the relationship between phenotype and genotype, while a major goal of ecology is to identify the rules that govern community assembly. Achieving these goals by analyzing natural systems can be difficult, as selective pressures create dynamic fitness landscapes that vary in both space and time. Laboratory experimental evolution offers the benefit of controlling variables that shape fitness landscapes, helping to achieve both goals. We previously showed that a clonal population of E. coli experimentally evolved under continuous glucose limitation gives rise to a genetically diverse community consisting of one clone, CV103, that best scavenges but incompletely utilizes the limiting resource, and others, CV101 and CV116, that consume its overflow metabolites. Because this community can be disassembled and reassembled, and involves cooperative interactions that are stable over time, its genetic diversity is sustained by clonal reinforcement rather than by clonal interference. To understand the genetic factors that produce this outcome, and to illuminate the community's underlying physiology, we sequenced the genomes of ancestral and evolved clones. We identified ancestral mutations in intermediary metabolism that may have predisposed the evolution of metabolic interdependence. Phylogenetic reconstruction indicates that the lineages that gave rise to this community diverged early, as CV103 shares only one Single Nucleotide Polymorphism with the other evolved clones. Underlying CV103's phenotype we identified a set of mutations that likely enhance glucose scavenging and maintain redox balance, but may do so at the expense of carbon excreted in overflow metabolites. Because these overflow metabolites serve as growth substrates that are differentially accessible to the other community members, and because the scavenging lineage shares only one SNP with these other clones, we conclude that this lineage likely served as an “engine” generating diversity by creating new metabolic niches, but not the occupants themselves. The variability of natural systems makes it difficult to deduce how organisms' genotypes manifest as phenotypes, and how communities of interacting organisms arise. Using laboratory experimental evolution we can control this variation. We previously showed that a population of E. coli that originated from a single clone and was cultured in the presence of a single limiting resource, evolves into a stable, three-membered community, wherein one clone excretes metabolites that the others utilize as carbon sources. To discern the genetic factors at work in producing this outcome and to illuminate the community's physiology, we sequenced the genomes of the ancestral and evolved clones. We identified in the ancestor mutations that may have predisposed evolution of cross-feeding. We found that the lineages which gave rise to the community diverged early on, and that the numerically dominant lineage that best scavenges limiting glucose does so as a result of adaptive mutations that enhance glucose uptake but favor fermentative over respiratory pathways, resulting in overflow metabolites. Because this clone produces secondary resources that sustain other community members, and because it shares with them only one mutation, we conclude that it is an “engine” generating diversity by creating new niches, but not the occupants themselves.
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Metabolic engineering of Escherichia coli to enhance hydrogen production from glycerol. Appl Microbiol Biotechnol 2014; 98:4757-70. [PMID: 24615384 DOI: 10.1007/s00253-014-5600-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/05/2014] [Accepted: 02/06/2014] [Indexed: 12/20/2022]
Abstract
Glycerol is an attractive carbon source for biofuel production since it is cheap and abundant due to the increasing demand for renewable and clean energy sources, which includes production of biodiesel. This research aims to enhance hydrogen production by Escherichia coli from glycerol by manipulating its metabolic pathways via targeted deletions. Since our past strain, which had been engineered for producing hydrogen from glucose, was not suitable for producing hydrogen from glycerol, we rescreened 14 genes related to hydrogen production and glycerol metabolism. We found that 10 single knockouts are beneficial for enhanced hydrogen production from glycerol, namely, frdC (encoding for furmarate reductase), ldhA (lactate dehydrogenase), fdnG (formate dehydrogenase), ppc (phosphoenolpyruvate carboxylase), narG (nitrate reductase), focA (formate transporter), hyaB (the large subunit of hydrogenase 1), aceE (pyruvate dehydrogenase), mgsA (methylglyoxal synthase), and hycA (a regulator of the transcriptional regulator FhlA). On that basis, we created multiple knockout strains via successive P1 transductions. Simultaneous knockouts of frdC, ldhA, fdnG, ppc, narG, mgsA, and hycA created the best strain that produced 5-fold higher hydrogen and had a 5-fold higher hydrogen yield than the parent strain. The engineered strain also reached the theoretical maximum yield of 1 mol H2/mol glycerol after 48 h. Under low partial pressure fermentation, the strain grew over 2-fold faster, indicating faster utilization of glycerol and production of hydrogen. By combining metabolic engineering and low partial pressure fermentation, hydrogen production from glycerol was enhanced significantly.
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Engineering NAD+ availability for Escherichia coli whole-cell biocatalysis: a case study for dihydroxyacetone production. Microb Cell Fact 2013; 12:103. [PMID: 24209782 PMCID: PMC3831814 DOI: 10.1186/1475-2859-12-103] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 11/05/2013] [Indexed: 01/29/2023] Open
Abstract
Background Whole-cell redox biocatalysis has been intensively explored for the production of valuable compounds because excellent selectivity is routinely achieved. Although the cellular cofactor level, redox state and the corresponding enzymatic activity are expected to have major effects on the performance of the biocatalysts, our ability remains limited to predict the outcome upon variation of those factors as well as the relationship among them. Results In order to investigate the effects of cofactor availability on whole-cell redox biocatalysis, we devised recombinant Escherichia coli strains for the production of dihydroxyacetone (DHA) catalyzed by the NAD+-dependent glycerol dehydrogenase (GldA). In this model system, a water-forming NAD+ oxidase (NOX) and a NAD+ transporter (NTT4) were also co-expressed for cofactor regeneration and extracellular NAD+ uptake, respectively. We found that cellular cofactor level, NAD+/NADH ratio and NOX activity were not only strain-dependent, but also growth condition-dependent, leading to significant differences in specific DHA titer among different whole-cell biocatalysts. The host E. coli DH5α had the highest DHA specific titer of 0.81 g/gDCW with the highest NAD+/NADH ratio of 6.7 and NOX activity of 3900 U. The biocatalyst had a higher activity when induced with IPTG at 37°C for 8 h compared with those at 30°C for 8 h and 18 h. When cells were transformed with the ntt4 gene, feeding NAD+ during the cell culture stage increased cellular NAD(H) level by 1.44 fold and DHA specific titer by 1.58 fold to 2.13 g/gDCW. Supplementing NAD+ during the biotransformation stage was also beneficial to cellular NAD(H) level and DHA production, and the highest DHA productivity reached 0.76 g/gDCW/h. Cellular NAD(H) level, NAD+/NADH ratio, and NOX and GldA activity dropped over time during the biotransformation process. Conclusions High NAD+/NADH ratio driving by NOX was very important for DHA production. Once cofactor was efficiently cycled, high cellular NAD(H) level was also beneficial for whole-cell redox biocatalysis. Our results indicated that NAD+ transporter could be applied to manipulate redox cofactor level for biocatalysis. Moreover, we suggested that genetically designed redox transformation should be carefully profiled for further optimizing whole-cell biocatalysis.
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Soellner S, Rahnert M, Siemann-Herzberg M, Takors R, Altenbuchner J. Evolution of pyruvate kinase-deficient Escherichia coli mutants enables glycerol-based cell growth and succinate production. J Appl Microbiol 2013; 115:1368-78. [PMID: 23957584 DOI: 10.1111/jam.12333] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 08/09/2013] [Accepted: 08/13/2013] [Indexed: 11/28/2022]
Abstract
AIMS The aim of this study was to engineer Escherichia coli strains that efficiently produce succinate from glycerol under anaerobic conditions after an aerobic growth phase. METHODS AND RESULTS We constructed E. coli strain ss195 with deletions of pykA and pykF, which resulted in slow growth on glycerol as sole carbon source. This growth defect was overcome by the selection of fast-growing mutants. Whole-genome resequencing of the evolved mutant ss251 identified the mutation A595S in PEP carboxylase (Ppc). Reverse metabolic engineering by introducing the wild-type allele revealed that this mutation is crucial for the described phenotype. Strain ss251 and derivatives thereof produced succinate with high yields above 80% mol mol(-1) from glycerol under nongrowth conditions. CONCLUSIONS The results show that during the aerobic growth of ss251, the formation of pyruvate proceeds via the proposed POMP pathway, starting with the carboxylation of PEP by Ppc. The resulting oxaloacetate is reduced by malate dehydrogenase (Mdh) to malate, which is then decarboxylated back to pyruvate by a malic enzyme (MaeA or MaeB). Mutation of ppc is crucial for fast growth of pykAF mutants on glycerol. SIGNIFICANCE AND IMPACT OF STUDY An E. coli mutant that is capable of achieving high yields of succinate (a top valued-added chemical) from glycerol (an abundant carbon source) was constructed. The identified ppc mutation could be applied to other production strains that require strong PEP carboxylation fluxes.
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Affiliation(s)
- S Soellner
- Institut für Industrielle Genetik, Universität Stuttgart, Stuttgart, Germany
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Riemer SA, Rex R, Schomburg D. A metabolite-centric view on flux distributions in genome-scale metabolic models. BMC SYSTEMS BIOLOGY 2013; 7:33. [PMID: 23587327 PMCID: PMC3644240 DOI: 10.1186/1752-0509-7-33] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 04/03/2013] [Indexed: 11/18/2022]
Abstract
Background Genome-scale metabolic models are important tools in systems biology. They permit the in-silico prediction of cellular phenotypes via mathematical optimisation procedures, most importantly flux balance analysis. Current studies on metabolic models mostly consider reaction fluxes in isolation. Based on a recently proposed metabolite-centric approach, we here describe a set of methods that enable the analysis and interpretation of flux distributions in an integrated metabolite-centric view. We demonstrate how this framework can be used for the refinement of genome-scale metabolic models. Results We applied the metabolite-centric view developed here to the most recent metabolic reconstruction of Escherichia coli. By compiling the balance sheets of a small number of currency metabolites, we were able to fully characterise the energy metabolism as predicted by the model and to identify a possibility for model refinement in NADPH metabolism. Selected branch points were examined in detail in order to demonstrate how a metabolite-centric view allows identifying functional roles of metabolites. Fructose 6-phosphate aldolase and the sedoheptulose bisphosphate bypass were identified as enzymatic reactions that can carry high fluxes in the model but are unlikely to exhibit significant activity in vivo. Performing a metabolite essentiality analysis, unconstrained import and export of iron ions could be identified as potentially problematic for the quality of model predictions. Conclusions The system-wide analysis of split ratios and branch points allows a much deeper insight into the metabolic network than reaction-centric analyses. Extending an earlier metabolite-centric approach, the methods introduced here establish an integrated metabolite-centric framework for the interpretation of flux distributions in genome-scale metabolic networks that can complement the classical reaction-centric framework. Analysing fluxes and their metabolic context simultaneously opens the door to systems biological interpretations that are not apparent from isolated reaction fluxes. Particularly powerful demonstrations of this are the analyses of the complete metabolic contexts of energy metabolism and the folate-dependent one-carbon pool presented in this work. Finally, a metabolite-centric view on flux distributions can guide the refinement of metabolic reconstructions for specific growth scenarios.
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Affiliation(s)
- S Alexander Riemer
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig, Germany
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Cintolesi A, Clomburg JM, Rigou V, Zygourakis K, Gonzalez R. Quantitative analysis of the fermentative metabolism of glycerol in Escherichia coli. Biotechnol Bioeng 2011; 109:187-98. [DOI: 10.1002/bit.23309] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 08/09/2011] [Accepted: 08/12/2011] [Indexed: 11/11/2022]
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Clomburg JM, Gonzalez R. Metabolic engineering of Escherichia coli for the production of 1,2-propanediol from glycerol. Biotechnol Bioeng 2010; 108:867-79. [DOI: 10.1002/bit.22993] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Revised: 10/11/2010] [Accepted: 10/15/2010] [Indexed: 11/07/2022]
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Shiloach J, Reshamwala S, Noronha SB, Negrete A. Analyzing metabolic variations in different bacterial strains, historical perspectives and current trends – example E. coli. Curr Opin Biotechnol 2010; 21:21-6. [DOI: 10.1016/j.copbio.2010.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 01/06/2010] [Indexed: 10/19/2022]
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de Figueiredo LF, Podhorski A, Rubio A, Kaleta C, Beasley JE, Schuster S, Planes FJ. Computing the shortest elementary flux modes in genome-scale metabolic networks. ACTA ACUST UNITED AC 2009; 25:3158-65. [PMID: 19793869 DOI: 10.1093/bioinformatics/btp564] [Citation(s) in RCA: 164] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
MOTIVATION Elementary flux modes (EFMs) represent a key concept to analyze metabolic networks from a pathway-oriented perspective. In spite of considerable work in this field, the computation of the full set of elementary flux modes in large-scale metabolic networks still constitutes a challenging issue due to its underlying combinatorial complexity. RESULTS In this article, we illustrate that the full set of EFMs can be enumerated in increasing order of number of reactions via integer linear programming. In this light, we present a novel procedure to efficiently determine the K-shortest EFMs in large-scale metabolic networks. Our method was applied to find the K-shortest EFMs that produce lysine in the genome-scale metabolic networks of Escherichia coli and Corynebacterium glutamicum. A detailed analysis of the biological significance of the K-shortest EFMs was conducted, finding that glucose catabolism, ammonium assimilation, lysine anabolism and cofactor balancing were correctly predicted. The work presented here represents an important step forward in the analysis and computation of EFMs for large-scale metabolic networks, where traditional methods fail for networks of even moderate size. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Gonçalves AT, Marçal D, Carrondo MA, Enguita FJ. Crystallization and preliminary X-ray characterization of a glycerol dehydrogenase from the human pathogen Salmonella enterica serovar Typhimurium. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:698-701. [PMID: 19574643 PMCID: PMC2705638 DOI: 10.1107/s1744309109020296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 05/27/2009] [Indexed: 11/10/2022]
Abstract
Glycerol dehydrogenase (GldA) encoded by the STM4108 gene (gldA) has been related to the synthesis of HilA, a major transcriptional regulator that is responsible for the expression of invasion genes in the human pathogen Salmonella enterica serovar Typhimurium. Single colourless crystals were obtained from a recombinant preparation of GldA overexpressed in Escherichia coli. They belonged to space group P222(1), with unit-cell parameters a = 127.0, b = 160.1, c = 665.2 A. The crystals contained a very large number of molecules in the asymmetric unit, probably 30-35. Diffraction data were collected to 3.5 A resolution using synchrotron radiation at the European Synchrotron Radiation Facility.
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Affiliation(s)
- A. T. Gonçalves
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras, Portugal
| | - D. Marçal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras, Portugal
| | - M. A. Carrondo
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Avenida da República, Apartado 127, 2781-901 Oeiras, Portugal
| | - F. J. Enguita
- Cell Biology Unit, Institute of Molecular Medicine, Faculty of Medicine, University of Lisbon, 1649-028 Lisbon, Portugal
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Rühle T, Hemschemeier A, Melis A, Happe T. A novel screening protocol for the isolation of hydrogen producing Chlamydomonas reinhardtii strains. BMC PLANT BIOLOGY 2008; 8:107. [PMID: 18928519 PMCID: PMC2576467 DOI: 10.1186/1471-2229-8-107] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Accepted: 10/17/2008] [Indexed: 05/21/2023]
Abstract
BACKGROUND Sealed Chlamydomonas reinhardtii cultures evolve significant amounts of hydrogen gas under conditions of sulfur depletion. However, the eukaryotic green alga goes through drastic metabolic changes during this nutritional stress resulting in cell growth inhibition and eventually cell death. This study aimed at isolating C. reinhardtii transformants which produce hydrogen under normal growth conditions to allow a continuous hydrogen metabolism without the stressful impact of nutrient deprivation. RESULTS To achieve a steady photobiological hydrogen production, a screening protocol was designed to identify C. reinhardtii DNA insertional mutagenesis transformants with an attenuated photosynthesis to respiration capacity ratio (P/R ratio). The screening protocol entails a new and fast method for mutant strain selection altered in their oxygen production/consumption balance. Out of 9000 transformants, four strains with P/R ratios varying from virtually zero to three were isolated. Strain apr1 was found to have a slightly higher respiration rate and a significantly lower photosynthesis rate than the wild type. Sealed cultures of apr1 became anaerobic in normal growth medium (TAP) under moderate light conditions and induced [FeFe]-hydrogenase activity, yet without significant hydrogen gas evolution. However, Calvin-Benson cycle inactivation of anaerobically adapted apr1 cells in the light led to a 2-3-fold higher in vivo hydrogen production than previously reported for the sulfur-deprived C. reinhardtii wild type. CONCLUSION Attenuated P/R capacity ratio in microalgal mutants constitutes a platform for achieving steady state photobiological hydrogen production. Using this platform, algal hydrogen metabolism can be analyzed without applying nutritional stress. Furthermore, these strains promise to be useful for biotechnological hydrogen generation, since high in vivo hydrogen production rates are achievable under normal growth conditions, when the photosynthesis to respiration capacity ratio is lowered in parallel to down regulated assimilative pathways.
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Affiliation(s)
- Thilo Rühle
- Fakultät für Biologie und Biotechnologie, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Anja Hemschemeier
- Fakultät für Biologie und Biotechnologie, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Anastasios Melis
- Department of Plant and Microbial Biology, University of California, Berkeley, California, 94720-3102, USA
| | - Thomas Happe
- Fakultät für Biologie und Biotechnologie, Lehrstuhl für Biochemie der Pflanzen, AG Photobiotechnologie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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