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Zhang Z, Huo J, Velo J, Zhou H, Flaherty A, Saier MH. Comprehensive Characterization of fucAO Operon Activation in Escherichia coli. Int J Mol Sci 2024; 25:3946. [PMID: 38612757 PMCID: PMC11011485 DOI: 10.3390/ijms25073946] [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: 02/14/2024] [Revised: 03/26/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
Wildtype Escherichia coli cells cannot grow on L-1,2-propanediol, as the fucAO operon within the fucose (fuc) regulon is thought to be silent in the absence of L-fucose. Little information is available concerning the transcriptional regulation of this operon. Here, we first confirm that fucAO operon expression is highly inducible by fucose and is primarily attributable to the upstream operon promoter, while the fucO promoter within the 3'-end of fucA is weak and uninducible. Using 5'RACE, we identify the actual transcriptional start site (TSS) of the main fucAO operon promoter, refuting the originally proposed TSS. Several lines of evidence are provided showing that the fucAO locus is within a transcriptionally repressed region on the chromosome. Operon activation is dependent on FucR and Crp but not SrsR. Two Crp-cAMP binding sites previously found in the regulatory region are validated, where the upstream site plays a more critical role than the downstream site in operon activation. Furthermore, two FucR binding sites are identified, where the downstream site near the first Crp site is more important than the upstream site. Operon transcription relies on Crp-cAMP to a greater degree than on FucR. Our data strongly suggest that FucR mainly functions to facilitate the binding of Crp to its upstream site, which in turn activates the fucAO promoter by efficiently recruiting RNA polymerase.
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Affiliation(s)
- Zhongge Zhang
- Department of Molecular Biology, School of Biological Sciences, University of California at San Diego, 9500 Gilman Dr, La Jolla, CA 92093-0116, USA; (J.H.); (J.V.); (A.F.)
| | | | | | | | | | - Milton H. Saier
- Department of Molecular Biology, School of Biological Sciences, University of California at San Diego, 9500 Gilman Dr, La Jolla, CA 92093-0116, USA; (J.H.); (J.V.); (A.F.)
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Skorokhodova AY, Gulevich AY, Debabov VG. Engineering Escherichia coli for efficient aerobic conversion of glucose to fumaric acid. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2022; 33:e00703. [PMID: 35145886 PMCID: PMC8801760 DOI: 10.1016/j.btre.2022.e00703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/09/2022] [Accepted: 01/16/2022] [Indexed: 12/16/2022]
Abstract
Escherichia coli was engineered for efficient aerobic conversion of glucose to fumaric acid. A novel design for biosynthesis of the target product through the modified TCA cycle rather than via glyoxylate shunt, implying oxaloacetate formation from pyruvate and artificial channelling of 2-ketoglutarate towards succinic acid via succinate semialdehyde formation, was implemented. The main fumarases were inactivated in the core strain MSG1.0 (∆ackA-pta, ∆poxB, ∆ldhA, ∆adhE, ∆ptsG, PL-glk, Ptac-galP) by the deletion of the fumA, fumB, and fumC genes. The Bacillus subtilis pycA gene was expressed in the strain to ensure pyruvate to oxaloacetate conversion. The Mycobacterium tuberculosis kgd gene was expressed to enable succinate semialdehyde formation. The resulting strain was able to convert glucose to fumaric acid with a yield of 0.86 mol/mol, amounting to 86% of the theoretical maximum. The results demonstrated the high potential of the implemented strategy for development of efficient strains for bio-based fumaric acid production.
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Affiliation(s)
- Alexandra Yu. Skorokhodova
- Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2. Leninsky Ave., Moscow 119071, Russia
| | - Andrey Yu. Gulevich
- Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2. Leninsky Ave., Moscow 119071, Russia
| | - Vladimir G. Debabov
- Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2. Leninsky Ave., Moscow 119071, Russia
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Tafur Rangel AE, Ríos W, Mejía D, Ojeda C, Carlson R, Gómez Ramírez JM, González Barrios AF. In silico Design for Systems-Based Metabolic Engineering for the Bioconversion of Valuable Compounds From Industrial By-Products. Front Genet 2021; 12:633073. [PMID: 33868371 PMCID: PMC8044919 DOI: 10.3389/fgene.2021.633073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/23/2021] [Indexed: 11/13/2022] Open
Abstract
Selecting appropriate metabolic engineering targets to build efficient cell factories maximizing the bioconversion of industrial by-products to valuable compounds taking into account time restrictions is a significant challenge in industrial biotechnology. Microbial metabolism engineering following a rational design has been widely studied. However, it is a cost-, time-, and laborious-intensive process because of the cell network complexity; thus, it is important to use tools that allow predicting gene deletions. An in silico experiment was performed to model and understand the metabolic engineering effects on the cell factory considering a second complexity level by transcriptomics data integration. In this study, a systems-based metabolic engineering target prediction was used to increase glycerol bioconversion to succinic acid based on Escherichia coli. Transcriptomics analysis suggests insights on how to increase cell glycerol utilization to further design efficient cell factories. Three E. coli models were used: a core model, a second model based on the integration of transcriptomics data obtained from growth in an optimized culture media, and a third one obtained after integration of transcriptomics data from adaptive laboratory evolution (ALE) experiments. A total of 2,402 strains were obtained with fumarase and pyruvate dehydrogenase being frequently predicted for all the models, suggesting these reactions as essential to increase succinic acid production. Finally, based on using flux balance analysis (FBA) results for all the mutants predicted, a machine learning method was developed to predict new mutants as well as to propose optimal metabolic engineering targets and mutants based on the measurement of the importance of each knockout's (feature's) contribution. Glycerol has become an interesting carbon source for industrial processes due to biodiesel business growth since it has shown promising results in terms of biomass/substrate yields. The combination of transcriptome, systems metabolic modeling, and machine learning analyses revealed the versatility of computational models to predict key metabolic engineering targets in a less cost-, time-, and laborious-intensive process. These data provide a platform to improve the prediction of metabolic engineering targets to design efficient cell factories. Our results may also work as a guide and platform for the selection/engineering of microorganisms for the production of interesting chemical compounds.
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Affiliation(s)
- Albert Enrique Tafur Rangel
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
- Grupo de Investigación CINBIOS, Department of Microbiology, Universidad Popular del Cesar, Valledupar, Colombia
| | - Wendy Ríos
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Daisy Mejía
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Carmen Ojeda
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Ross Carlson
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, United States
| | - Jorge Mario Gómez Ramírez
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Andrés Fernando González Barrios
- Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
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Yang CD, Huang HY, Shrestha S, Chen YH, Huang HD, Tseng CP. Large-Scale Functional Analysis of CRP-Mediated Feed-Forward Loops. Int J Mol Sci 2018; 19:ijms19082335. [PMID: 30096859 PMCID: PMC6121374 DOI: 10.3390/ijms19082335] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 07/23/2018] [Accepted: 08/02/2018] [Indexed: 11/16/2022] Open
Abstract
Feed-forward loops (FFLs) represent an important and basic network motif to understand specific biological functions. Cyclic-AMP (cAMP) receptor protein (CRP), a transcription factor (TF), mediates catabolite repression and regulates more than 400 genes in response to changes in intracellular concentrations of cAMP in Escherichia coli. CRP participates in some FFLs, such as araBAD and araFGH operons and adapts to fluctuating environmental nutrients, thereby enhancing the survivability of E. coli. Although computational simulations have been conducted to explore the potential functionality of FFLs, a comprehensive study on the functions of all structural types on the basis of in vivo data is lacking. Moreover, the regulatory role of CRP-mediated FFLs (CRP-FFLs) remains obscure. We identified 393 CRP-FFLs in E. coli using EcoCyc and RegulonDB. Dose⁻response genomic microarray of E. coli revealed dynamic gene expression of each target gene of CRP-FFLs in response to a range of cAMP dosages. All eight types of FFLs were present in CRP regulon with various expression patterns of each CRP-FFL, which were further divided into five functional groups. The microarray and reported regulatory relationships identified 202 CRP-FFLs that were directly regulated by CRP in these eight types of FFLs. Interestingly, 34% (147/432) of genes were directly regulated by CRP and CRP-regulated TFs, which indicates that these CRP-regulated genes were also regulated by other CRP-regulated TFs responding to environmental signals through CRP-FFLs. Furthermore, we applied gene ontology annotation to reveal the biological functions of CRP-FFLs.
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Affiliation(s)
- Chi-Dung Yang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan.
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli 350, Taiwan.
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan.
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China.
- School of Science and Engineering, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China.
| | - Hsi-Yuan Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan.
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China.
- School of Science and Engineering, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China.
- Department of Laboratory Medicine, China Medical University Hospital, Taichung 420, Taiwan.
| | - Sirjana Shrestha
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan.
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan.
| | - Yen-Hua Chen
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu 300, Taiwan.
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan.
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China.
- School of Science and Engineering, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China.
| | - Ching-Ping Tseng
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan.
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Li Y, Huang B, Wu H, Li Z, Ye Q, Zhang YHP. Production of Succinate from Acetate by Metabolically Engineered Escherichia coli. ACS Synth Biol 2016; 5:1299-1307. [PMID: 27088218 DOI: 10.1021/acssynbio.6b00052] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acetate, a major component of industrial biological wastewater and of lignocellulosic biomass hydrolysate, could potentially be a less costly alternative carbon source. Here we engineered Escherichia coli MG1655 strain for succinate production from acetate as the sole carbon source. Strategies of metabolic engineering included the blockage of the TCA cycle, redirection of the gluconeogenesis pathway, and enhancement of the glyoxylate shunt. The engineered strain MG03 featuring the deletion of genes: succinate dehydrogenase (sdhAB), isocitrate lyase regulator (iclR), and malic enzymes (maeB) accumulated 6.86 mM of succinate in 72 h. MG03(pTrc99a-gltA) overexpressing citrate synthase (gltA) accumulated 16.45 mM of succinate and the yield reached 0.46 mol/mol, about 92% of the maximum theoretical yield. Resting-cell was adopted for the conversion of acetate to succinate, and the highest concentration of succinate achieved 61.7 mM.
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Affiliation(s)
- Yunjie Li
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Bing Huang
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Hui Wu
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Zhimin Li
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qin Ye
- State
Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Y-H Percival Zhang
- Biological
Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, Virginia 24061, United States
- Tianjin
Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West seventh Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
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Yang CD, Chen YH, Huang HY, Huang HD, Tseng CP. CRP represses the CRISPR/Cas system in Escherichia coli: evidence that endogenous CRISPR spacers impede phage P1 replication. Mol Microbiol 2014; 92:1072-91. [PMID: 24720807 DOI: 10.1111/mmi.12614] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2014] [Indexed: 12/26/2022]
Abstract
The CRISPR/Cas system is an important aspect in bacterial immunology. The anti-phage activity of the CRISPR system has been established using synthetic CRISPR spacers, but in vivo studies of endogenous CRISPR spacers are relatively scarce. Here, we showed that bacteriophage P1 titre in Escherichia coli decreased in the glucose-containing medium compared with that in the absence of glucose. This glucose effect of E. coli against phage P1 infection disappeared in cse3 deletion mutants. The effect on the susceptibility to phage P1 was associated with cAMP receptor protein (CRP)-mediated repression of cas genes transcription and crRNA maturation. Analysis of the regulatory element in the cse1 promoter region revealed a novel CRP binding site, which overlapped with a LeuO binding site. Furthermore, the limited sequence identity between endogenous spacers and the phage P1 genome was necessary and sufficient for CRISPR-mediated repression of phage P1 replication. Trans-expression of the third and seventh spacers in the CRISPR I region or third and sixth spacers in the CRISPR II region effectively reduced phage P1 titres in the CRISPR deletion mutants. These results demonstrate a novel regulatory mechanism for cas repression by CRP and provide evidence that endogenous spacers can repress phage P1 replication in E. coli.
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Affiliation(s)
- Chi-Dung Yang
- Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu, 300, Taiwan
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Li Z, Nimtz M, Rinas U. The metabolic potential of Escherichia coli BL21 in defined and rich medium. Microb Cell Fact 2014; 13:45. [PMID: 24656150 PMCID: PMC4021462 DOI: 10.1186/1475-2859-13-45] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 03/14/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The proteome reflects the available cellular machinery to deal with nutrients and environmental challenges. The most common E. coli strain BL21 growing in different, commonly employed media was evaluated using a detailed quantitative proteome analysis. RESULTS The presence of preformed biomass precursor molecules in rich media such as Luria Bertani supported rapid growth concomitant to acetate formation and apparently unbalanced abundances of central metabolic pathway enzymes, e.g. high levels of lower glycolytic pathway enzymes as well as pyruvate dehydrogenase, and low levels of TCA cycle and high levels of the acetate forming enzymes Pta and AckA. The proteome of cells growing exponentially in glucose-supplemented mineral salt medium was dominated by enzymes of amino acid synthesis pathways, contained more balanced abundances of central metabolic pathway enzymes, and a lower portion of ribosomal and other translational proteins. Entry into stationary phase led to a reconstruction of the bacterial proteome by increasing e.g. the portion of proteins required for scavenging rare nutrients and general cell protection. This proteomic reconstruction during entry into stationary phase was more noticeable in cells growing in rich medium as they have a greater reservoir of recyclable proteins from the translational machinery. CONCLUSIONS The proteomic comparison of cells growing exponentially in different media reflected the antagonistic and competitive regulation of central metabolic pathways through the global transcriptional regulators Cra, Crp, and ArcA. For example, the proteome of cells growing exponentially in rich medium was consistent with a dominating role of phosphorylated ArcA most likely a result from limitations in reoxidizing reduced quinones in the respiratory chain under these growth conditions. The proteomic alterations of exponentially growing cells into stationary phase cells were consistent with stringent-like and stationary phase responses and a dominating control through DksA-ppGpp and RpoS.
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Affiliation(s)
| | | | - Ursula Rinas
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, D-38124 Braunschweig, Germany.
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Biochemical similarities and differences between the catalytic [4Fe-4S] cluster containing fumarases FumA and FumB from Escherichia coli. PLoS One 2013; 8:e55549. [PMID: 23405168 PMCID: PMC3565967 DOI: 10.1371/journal.pone.0055549] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 01/02/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The highly homologous [4Fe-4S] containing fumarases FumA and FumB, sharing 90% amino acid sequence identity, from Escherichia coli are differentially regulated, which suggests a difference in their physiological function. The ratio of FumB over FumA expression levels increases by one to two orders of magnitude upon change from aerobic to anaerobic growth conditions. METHODOLOGY/PRINCIPAL FINDINGS To understand this difference in terms of structure-function relations, catalytic and thermodynamic properties were determined for the two enzymes obtained from homologous overexpression systems. FumA and FumB are essentially identical in their Michaelis-Menten kinetics of the reversible fumarate to L-malate conversion; however, FumB has a significantly greater catalytic efficiency for the conversion of D-tartrate to oxaloacetate consistent with the requirement of the fumB gene for growth on D-tartrate. Reduction potentials of the [4Fe-4S](2+) Lewis acid active centre were determined in mediated bulk titrations in the presence of added substrate and were found to be approximately -290 mV for both FumA and FumB. CONCLUSIONS/SIGNIFICANCE This study contradicts previously published claims that FumA and FumB exhibit different catalytic preferences for the natural substrates L-malate and fumarate. FumA and FumB differ significantly only in the catalytic efficiency for the conversion of D-tartrate, a supposedly non-natural substrate. The reduction potential of the substrate-bound [4Fe-4S] active centre is, contrary to previously reported values, close to the cellular redox potential.
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