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Zhou M, Wu J, Wu L, Sun X, Chen C, Huang L. The utilization of N-acetylgalactosamine and its effect on the metabolism of amino acids in Erysipelotrichaceae strain. BMC Microbiol 2024; 24:397. [PMID: 39379811 PMCID: PMC11462708 DOI: 10.1186/s12866-024-03505-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: 05/01/2024] [Accepted: 09/06/2024] [Indexed: 10/10/2024] Open
Abstract
BACKGROUND The metabolism of gut microbiota produces bioactive metabolites that modulate host physiology and promote self-growth. Erysipelotrichaceae is one of the most common anaerobic microorganism families in the gut, which has been discovered to play a vital role in host metabolic disorders and inflammatory diseases. Our previous study found that N-acetylgalactosamine (GalNAc) in caecal content of pigs significantly affected the abundance of Erysipelotrichaceae strains. However, it remains unknown how GalNAc feeding in vitro culture affects the expression levels of genes in the GalNAc metabolic pathway and the concentrations of intermediate metabolites in the Erysipelotrichaceae strain. Whether GalNAc feeding should influence the metabolism of other nutrients, such as amino acids, remains unrevealed. RESULTS In this study, whole-genome sequence, transcriptome, and metabolome data were analyzed to assess the utilization of a Erysipelotrichaceae strain on GalNAc. The results showed the presence of a complete GalNAc catabolism pathway in the genome of this Erysipelotrichaceae strain. GalNAc feeding to this Erysipelotrichaceae strain significantly changed the expression levels of genes involved in glycolysis and tricarboxylic acid (TCA) cycle. Meanwhile, the concentrations of lactate, pyruvate, citrate, succinate and malate from the glycolysis and TCA cycle were significantly increased. In addition, transcriptome analysis indicated that the genes involved in the metabolism of amino acids were affected by GalNAc, including lysA (a gene involved in lysine biosynthesis) that was significantly down-regulated. The intracellular concentrations of 14 amino acids in the Erysipelotrichaceae strain were significantly increased after feeding GalNAc. CONCLUSIONS Our findings comfirmed and extended our previous works that demonstrated the utilization of GalNAc by Erysipelotrichaceae strain, and explained the possible mechanism of GalNAc affecting the abundance of Erysipelotrichaceae strain in vitro.
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Affiliation(s)
- Mengqing Zhou
- National Key Laboratory of Pig Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, PR China
| | - Jinyuan Wu
- National Key Laboratory of Pig Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, PR China
| | - Lin Wu
- National Key Laboratory of Pig Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, PR China
| | - Xiao Sun
- National Key Laboratory of Pig Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, PR China
| | - Congying Chen
- National Key Laboratory of Pig Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, PR China.
| | - Lusheng Huang
- National Key Laboratory of Pig Genetic Improvement and Germplasm Innovation, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, PR China.
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Hanson BS, Hailemariam A, Yang Y, Mohamed F, Donati GL, Baker D, Sacchettini J, Cai JJ, Subashchandrabose S. Identification of a copper-responsive small molecule inhibitor of uropathogenic Escherichia coli. J Bacteriol 2024; 206:e0011224. [PMID: 38856220 PMCID: PMC11270900 DOI: 10.1128/jb.00112-24] [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: 03/14/2024] [Accepted: 05/10/2024] [Indexed: 06/11/2024] Open
Abstract
Urinary tract infections (UTIs) are a major global health problem and are caused predominantly by uropathogenic Escherichia coli (UPEC). UTIs are a leading cause of prescription antimicrobial use. Incessant increase in antimicrobial resistance in UPEC and other uropathogens poses a serious threat to the current treatment practices. Copper is an effector of nutritional immunity that impedes the growth of pathogens during infection. We hypothesized that copper would augment the toxicity of select small molecules against bacterial pathogens. We conducted a small molecule screening campaign with a library of 51,098 molecules to detect hits that inhibit a UPEC ΔtolC mutant in a copper-dependent manner. A molecule, denoted as E. coli inhibitor or ECIN, was identified as a copper-responsive inhibitor of wild-type UPEC strains. Our gene expression and metal content analysis results demonstrate that ECIN works in concert with copper to exacerbate Cu toxicity in UPEC. ECIN has a broad spectrum of activity against pathogens of medical and veterinary significance including Acinetobacter baumannii, Pseudomonas aeruginosa, and methicillin-resistant Staphylococcus aureus. Subinhibitory levels of ECIN eliminate UPEC biofilm formation. Transcriptome analysis of UPEC treated with ECIN reveals induction of multiple stress response systems. Furthermore, we demonstrate that L-cysteine rescues the growth of UPEC exposed to ECIN. In summary, we report the identification and characterization of a novel copper-responsive small molecule inhibitor of UPEC.IMPORTANCEUrinary tract infection (UTI) is a ubiquitous infectious condition affecting millions of people annually. Uropathogenic Escherichia coli (UPEC) is the predominant etiological agent of UTI. However, UTIs are becoming increasingly difficult to resolve with antimicrobials due to increased antimicrobial resistance in UPEC and other uropathogens. Here, we report the identification and characterization of a novel copper-responsive small molecule inhibitor of UPEC. In addition to E. coli, this small molecule also inhibits pathogens of medical and veterinary significance including Acinetobacter baumannii, Pseudomonas aeruginosa, and methicillin-resistant Staphylococcus aureus.
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Affiliation(s)
- Braden S Hanson
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Amanuel Hailemariam
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas, USA
| | - Yongjian Yang
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Faras Mohamed
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - George L Donati
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Dwight Baker
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas, USA
| | - James Sacchettini
- Department of Biochemistry and Biophysics, College of Agriculture and Life Sciences, Texas A&M University, College Station, Texas, USA
| | - James J Cai
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
| | - Sargurunathan Subashchandrabose
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, USA
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van ‘t Hof M, Mohite OS, Monk JM, Weber T, Palsson BO, Sommer MOA. High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917. BMC Bioinformatics 2022; 23:566. [PMID: 36585633 PMCID: PMC9801561 DOI: 10.1186/s12859-022-05108-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 12/12/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Escherichia coli Nissle 1917 (EcN) is a probiotic bacterium used to treat various gastrointestinal diseases. EcN is increasingly being used as a chassis for the engineering of advanced microbiome therapeutics. To aid in future engineering efforts, our aim was to construct an updated metabolic model of EcN with extended secondary metabolite representation. RESULTS An updated high-quality genome-scale metabolic model of EcN, iHM1533, was developed based on comparison with 55 E. coli/Shigella reference GEMs and manual curation, including expanded secondary metabolite pathways (enterobactin, salmochelins, aerobactin, yersiniabactin, and colibactin). The model was validated and improved using phenotype microarray data, resulting in an 82.3% accuracy in predicting growth phenotypes on various nutrition sources. Flux variability analysis with previously published 13C fluxomics data validated prediction of the internal central carbon fluxes. A standardised test suite called Memote assessed the quality of iHM1533 to have an overall score of 89%. The model was applied by using constraint-based flux analysis to predict targets for optimisation of secondary metabolite production. Modelling predicted design targets from across amino acid metabolism, carbon metabolism, and other subsystems that are common or unique for influencing the production of various secondary metabolites. CONCLUSION iHM1533 represents a well-annotated metabolic model of EcN with extended secondary metabolite representation. Phenotype characterisation and the iHM1533 model provide a better understanding of the metabolic capabilities of EcN and will help future metabolic engineering efforts.
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Affiliation(s)
- Max van ‘t Hof
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Omkar S. Mohite
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Jonathan M. Monk
- grid.266100.30000 0001 2107 4242Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Tilmann Weber
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Bernhard O. Palsson
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark ,grid.266100.30000 0001 2107 4242Department of Bioengineering, University of California San Diego, La Jolla, CA 92093 USA
| | - Morten O. A. Sommer
- grid.5170.30000 0001 2181 8870The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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4
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Kim HJ, Jeong H, Lee SJ. Glucose Transport through N-Acetylgalactosamine Phosphotransferase System in Escherichia coli C Strain. J Microbiol Biotechnol 2022; 32:1047-1053. [PMID: 35791075 PMCID: PMC9628945 DOI: 10.4014/jmb.2205.05059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 12/15/2022]
Abstract
When ptsG, a glucose-specific phosphotransferase system (PTS) component, is deleted in Escherichia coli, growth can be severely poor because of the lack of efficient glucose transport. We discovered a new PTS transport system that could transport glucose through the growth-coupled experimental evolution of ptsG-deficient E. coli C strain under anaerobic conditions. Genome sequencing revealed mutations in agaR, which encodes a repressor of N-acetylgalactosamine (Aga) PTS expression in evolved progeny strains. RT-qPCR analysis showed that the expression of Aga PTS gene increased because of the loss-of-function of agaR. We confirmed the efficient Aga PTS-mediated glucose uptake by genetic complementation and anaerobic fermentation. We discussed the discovery of new glucose transporter in terms of different genetic backgrounds of E. coli strains, and the relationship between the pattern of mixed-acids fermentation and glucose transport rate.
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Affiliation(s)
- Hyun Ju Kim
- Department of Systems Biotechnology and Institute of Microbiomics, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Haeyoung Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology and Institute of Microbiomics, Chung-Ang University, Anseong 17546, Republic of Korea,Corresponding author Phone: +82-31-670-3356 E-mail:
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5
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Wu J, Liu M, Zhou M, Wu L, Yang H, Huang L, Chen C. Isolation and genomic characterization of five novel strains of Erysipelotrichaceae from commercial pigs. BMC Microbiol 2021; 21:125. [PMID: 33888068 PMCID: PMC8063399 DOI: 10.1186/s12866-021-02193-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/07/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Members of the Erysipelotrichaceae family have a high abundance in the intestinal tract of mammals, and have been reported to be associated with host metabolic disorders and inflammatory diseases. In our previous study, we found that the abundance of Erysipelotrichaceae strains in the cecum was associated with the concentration of N-acetylgalactosamine (GalNAc). However, only a few members of Erysipelotrichaceae have been isolated and cultured, and their main characteristics, genomic information and the functional capacity of carbohydrate metabolism remain unknown. RESULTS In this study, we tested 10 different kinds of commercially available media and successfully isolated five Erysipelotrichaceae strains from healthy porcine feces. The five isolates were Gram-positive, and their colonies on Gifu anaerobic medium (GAM) or modified GAM were approximately 0.25-1.0 mm in diameter, and they were circular, white, convex, moist, translucent, and contained colony margins. These isolates were subjected to Oxford Nanopore and Illumina whole-genome sequencing, genome assembly, and annotation. Based on whole-genome sequences, the five strains belong to Erysipelotrichaceae bacterium OH741_COT-311, Eubacterium sp. AM28-29, and Faecalitalea cylindroides. The GC content of the five strains ranged from 34.1 to 37.37%. Functional annotation based on the Kyoto encyclopedia of genes and genomes pathways revealed tens to hundreds of strain-specific proteins among different strains, and even between the strains showing high 16S rRNA gene sequence identity. Prediction analysis of carbohydrate metabolism revealed different capacities for metabolizing carbohydrate substrates among Erysipelotrichaceae strains. We identified that genes related to the GalNAc metabolism pathway were enriched in the genomes of all five isolates and 16 Erysipelotrichaceae strains downloaded from GenBank, suggesting the importance of GalNAc metabolism in Erysipelotrichaceae strains. Polysaccharide utilization loci (PUL) analysis revealed that the strains of Erysipelotrichaceae may have the ability to utilize plant polysaccharides. CONCLUSIONS The present study not only reports the successful isolation of novel Erysipelotrichaceae strains that enrich the cultured strains of Erysipelotrichaceae, but also provided the genome information of Erysipelotrichaceae strains for further studying the function roles of Erysipelotrichaceae in host phenotypes.
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Affiliation(s)
- Jinyuan Wu
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, 330045, People's Republic of China.
| | - Min Liu
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, 330045, People's Republic of China
| | - Mengqing Zhou
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, 330045, People's Republic of China
| | - Lin Wu
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, 330045, People's Republic of China
| | - Hui Yang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, 330045, People's Republic of China
| | - Lusheng Huang
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, 330045, People's Republic of China
| | - Congying Chen
- National Key Laboratory for Swine genetic improvement and production technology, Ministry of Science and Technology of China, Jiangxi Agricultural University, NanChang, Jiangxi Province, 330045, People's Republic of China.
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Hasan I, Rahman SN, Islam MM, Ghosh SK, Mamun MR, Uddin MB, Shaha RK, Kabir SR. A N-acetyl-D-galactosamine-binding lectin from Amaranthus gangeticus seeds inhibits biofilm formation and Ehrlich ascites carcinoma cell growth in vivo in mice. Int J Biol Macromol 2021; 181:928-936. [PMID: 33878355 DOI: 10.1016/j.ijbiomac.2021.04.052] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 11/29/2022]
Abstract
AGL, a 15-kDa lectin from Amaranthus gangeticus seeds was isolated using ion-exchange and gel filtration chromatography. AGL contained 8.55% of neutral sugar and became specifically inhibited by N-acetyl-D-galactosamine. Hemagglutination activity of the lectin was maximum over the pH range of 4.0-6.0 and temperatures of 30-60 °C though it lost the activity when treated with urea and EDTA. With an LC50 value of 250 μg/ml, AGL showed mild toxicity against Artemia nauplii. It inhibited the growth of pathogenic bacteria like Shigella boydii, Shigella dysenteriae and Staphylococcus aureus when treated for 8 and 16 h, respectively, but lost the antibacterial activity during a 24 h treatment. AGL could not inhibit the growth of Escherichia coli and mitogenic growth (7.0-9.0%) was observed instead. AGL inhibited 37.14%, 65.71% and 82.85% of biofilm formation of Escherichia coli at the concentrations of 250, 500 and 1000 μg/ml, respectively. Marked inhibition of the proliferation of Ehrlich ascites carcinoma cells was determined when treated with various doses of AGL. AGL inhibited 65.89% and 81.25% of the in vivo growth of EAC cells in mice at the doses of 2.0 and 4.0 mg/kg/day, respectively. Significant alteration of the expression of apoptosis related genes Fas, NF-kB and MAPK were observed.
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Affiliation(s)
- Imtiaj Hasan
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Sharif Nasibur Rahman
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md Mahenur Islam
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Sourov Kumar Ghosh
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Mizanur Rahman Mamun
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md Belal Uddin
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Ranajit Kumar Shaha
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Syed Rashel Kabir
- Department of Biochemistry and Molecular Biology, Faculty of Science, University of Rajshahi, Rajshahi 6205, Bangladesh.
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7
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Norsigian CJ, Danhof HA, Brand CK, Oezguen N, Midani FS, Palsson BO, Savidge TC, Britton RA, Spinler JK, Monk JM. Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence. NPJ Syst Biol Appl 2020; 6:31. [PMID: 33082337 PMCID: PMC7576604 DOI: 10.1038/s41540-020-00151-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 08/26/2020] [Indexed: 12/15/2022] Open
Abstract
Hospital acquired Clostridioides (Clostridium) difficile infection is exacerbated by the continued evolution of C. difficile strains, a phenomenon studied by multiple laboratories using stock cultures specific to each laboratory. Intralaboratory evolution of strains contributes to interlaboratory variation in experimental results adding to the challenges of scientific rigor and reproducibility. To explore how microevolution of C. difficile within laboratories influences the metabolic capacity of an organism, three different laboratory stock isolates of the C. difficile 630 reference strain were whole-genome sequenced and profiled in over 180 nutrient environments using phenotypic microarrays. The results identified differences in growth dynamics for 32 carbon sources including trehalose, fructose, and mannose. An updated genome-scale model for C. difficile 630 was constructed and used to contextualize the 28 unique mutations observed between the stock cultures. The integration of phenotypic screens with model predictions identified pathways enabling catabolism of ethanolamine, salicin, arbutin, and N-acetyl-galactosamine that differentiated individual C. difficile 630 laboratory isolates. The reconstruction was used as a framework to analyze the core-genome of 415 publicly available C. difficile genomes and identify areas of metabolism prone to evolution within the species. Genes encoding enzymes and transporters involved in starch metabolism and iron acquisition were more variable while C. difficile distinct metabolic functions like Stickland fermentation were more consistent. A substitution in the trehalose PTS system was identified with potential implications in strain virulence. Thus, pairing genome-scale models with large-scale physiological and genomic data enables a mechanistic framework for studying the evolution of pathogens within microenvironments and will lead to predictive modeling to combat pathogen emergence.
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Affiliation(s)
- Charles J Norsigian
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Heather A Danhof
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.,Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Colleen K Brand
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.,Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Numan Oezguen
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Firas S Midani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.,Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Tor C Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Robert A Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.,Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer K Spinler
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Jonathan M Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
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Kohlmeier MG, White CE, Fowler JE, Finan TM, Oresnik IJ. Galactitol catabolism in Sinorhizobium meliloti is dependent on a chromosomally encoded sorbitol dehydrogenase and a pSymB-encoded operon necessary for tagatose catabolism. Mol Genet Genomics 2019; 294:739-755. [DOI: 10.1007/s00438-019-01545-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/08/2019] [Indexed: 01/22/2023]
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9
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Na H, Kim Y, Kim D, Yoon H, Ryu S. Transcriptomic Analysis of Shiga Toxin-Producing Escherichia coli FORC_035 Reveals the Essential Role of Iron Acquisition for Survival in Canola Sprouts and Water Dropwort. Front Microbiol 2018; 9:2397. [PMID: 30349522 PMCID: PMC6186786 DOI: 10.3389/fmicb.2018.02397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 09/19/2018] [Indexed: 12/03/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) is a foodborne pathogen that poses a serious threat to humans. Although EHEC is problematic mainly in food products containing meat, recent studies have revealed that many EHEC-associated foodborne outbreaks were attributable to spoiled produce such as sprouts and green leafy vegetables. To understand how EHEC adapts to the environment in fresh produce, we exposed the EHEC isolate FORC_035 to canola spouts (Brassica napus) and water dropwort (Oenanthe javanica) and profiled the transcriptome of this pathogen at 1 and 3 h after incubation with the plant materials. Transcriptome analysis revealed that the expression of genes associated with iron uptake were down-regulated during adaptation to plant tissues. A mutant strain lacking entB, presumably defective in enterobactin biosynthesis, had growth defects in co-culture with water dropwort, and the defective phenotype was complemented by the addition of ferric ion. Furthermore, gallium treatment to block iron uptake inhibited bacterial growth on water dropwort and also hampered biofilm formation. Taken together, these results indicate that iron uptake is essential for the fitness of EHEC in plants and that gallium can be used to prevent the growth of this pathogen in fresh produce.
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Affiliation(s)
- Hongjun Na
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Yeonkyung Kim
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Dajeong Kim
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Hyunjin Yoon
- Department of Molecular Science and Technology, Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, South Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Center for Food and Bioconvergence, Seoul National University, Seoul, South Korea
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10
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Clarke TH, Brinkac LM, Inman JM, Sutton G, Fouts DE. PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes. BMC Bioinformatics 2018; 19:246. [PMID: 29945570 PMCID: PMC6020400 DOI: 10.1186/s12859-018-2250-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 06/14/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacterial pan-genomes, comprised of conserved and variable genes across multiple sequenced bacterial genomes, allow for identification of genomic regions that are phylogenetically discriminating or functionally important. Pan-genomes consist of large amounts of data, which can restrict researchers ability to locate and analyze these regions. Multiple software packages are available to visualize pan-genomes, but currently their ability to address these concerns are limited by using only pre-computed data sets, prioritizing core over variable gene clusters, or by not accounting for pan-chromosome positioning in the viewer. RESULTS We introduce PanACEA (Pan-genome Atlas with Chromosome Explorer and Analyzer), which utilizes locally-computed interactive web-pages to view ordered pan-genome data. It consists of multi-tiered, hierarchical display pages that extend from pan-chromosomes to both core and variable regions to single genes. Regions and genes are functionally annotated to allow for rapid searching and visual identification of regions of interest with the option that user-supplied genomic phylogenies and metadata can be incorporated. PanACEA's memory and time requirements are within the capacities of standard laptops. The capability of PanACEA as a research tool is demonstrated by highlighting a variable region important in differentiating strains of Enterobacter hormaechei. CONCLUSIONS PanACEA can rapidly translate the results of pan-chromosome programs into an intuitive and interactive visual representation. It will empower researchers to visually explore and identify regions of the pan-chromosome that are most biologically interesting, and to obtain publication quality images of these regions.
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Affiliation(s)
| | - Lauren M Brinkac
- J. Craig Venter Institute, Rockville, MD, 20850, USA
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, 4000, South Africa
| | - Jason M Inman
- J. Craig Venter Institute, Rockville, MD, 20850, USA
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11
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Sutton GG, Brinkac LM, Clarke TH, Fouts DE. Enterobacterhormaechei subsp. hoffmannii subsp. nov., Enterobacter hormaechei subsp. xiangfangensis comb. nov., Enterobacter roggenkampii sp. nov., and Enterobacter muelleri is a later heterotypic synonym of Enterobacter asburiae based on computational analysis of sequenced Enterobacter genomes. F1000Res 2018; 7:521. [PMID: 30430006 PMCID: PMC6097438 DOI: 10.12688/f1000research.14566.2] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/27/2018] [Indexed: 12/22/2022] Open
Abstract
Background: The predominant species in clinical Enterobacter isolates is E. hormaechei. Many articles, clinicians, and GenBank submissions misname these strains as E. cloacae. The lack of sequenced type strains or named species/subspecies for some clades in the E. cloacae complex complicate the issue. Methods: The genomes of the type strains for Enterobacter hormaechei subsp. oharae, E. hormaechei subsp. steigerwaltii, and E. xiangfangensis, and two strains from Hoffmann clusters III and IV of the E. cloacae complex were sequenced. These genomes, the E. hormaechei subsp. hormaechei type strain, and other available Enterobacter type strains were analysed in conjunction with all extant Enterobacter genomes in NCBI's RefSeq using Average Nucleotide Identity (ANI). Results: There were five recognizable subspecies of E. hormaechei: E. hormaechei subsp. hoffmannii subsp. nov., E. hormaechei subsp. xiangfangensis comb. nov., and the three previously known subspecies. One of the strains sequenced from the E. cloacae complex was not a novel E. hormaechei subspecies but rather a member of a clade of a novel species: E. roggenkampii sp. nov.. E. muelleri was determined to be a later heterotypic synonym of E. asburiae which should take precedence. Conclusion: The phylogeny of the Enterobacter genus, particularly the cloacae complex, was re-evaluated based on the type strain genome sequences and all other available Enterobacter genomes in RefSeq.
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Sutton GG, Brinkac LM, Clarke TH, Fouts DE. Enterobacterhormaechei subsp. hoffmannii subsp. nov., Enterobacter hormaechei subsp. xiangfangensis comb. nov., Enterobacter roggenkampii sp. nov., and Enterobacter muelleri is a later heterotypic synonym of Enterobacter asburiae based on computational analysis of sequenced Enterobacter genomes. F1000Res 2018; 7:521. [PMID: 30430006 PMCID: PMC6097438 DOI: 10.12688/f1000research.14566.1] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/25/2018] [Indexed: 07/24/2023] Open
Abstract
Background: The predominant species in clinical Enterobacter isolates is E. hormaechei. Many articles, clinicians, and GenBank submissions misname these strains as E. cloacae. The lack of sequenced type strains or named species/subspecies for some clades in the E. cloacae complex complicate the issue. Methods: The genomes of the type strains for Enterobacter hormaechei subsp. oharae, E. hormaechei subsp. steigerwaltii, and E. xiangfangensis, and two strains from Hoffmann clusters III and IV of the E. cloacae complex were sequenced. These genomes, the E. hormaechei subsp. hormaechei type strain, and other available Enterobacter type strains were analysed in conjunction with all extant Enterobacter genomes in NCBI's RefSeq using Average Nucleotide Identity (ANI). Results: There were five recognizable subspecies of E. hormaechei: E. hormaechei subsp. hoffmannii subsp. nov., E. hormaechei subsp. xiangfangensis comb. nov., and the three previously known subspecies. One of the strains sequenced from the E. cloacae complex was not a novel E. hormaechei subspecies but rather a member of a clade of a novel species: E. roggenkampii sp. nov.. E. muelleri was determined to be a later heterotypic synonym of E. asburiae which should take precedence. Conclusion: The phylogeny of the Enterobacter genus, particularly the cloacae complex, was re-evaluated based on the type strain genome sequences and all other available Enterobacter genomes in RefSeq.
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Comprehensive Genome Analysis of Carbapenemase-Producing Enterobacter spp.: New Insights into Phylogeny, Population Structure, and Resistance Mechanisms. mBio 2016; 7:mBio.02093-16. [PMID: 27965456 PMCID: PMC5156309 DOI: 10.1128/mbio.02093-16] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Knowledge regarding the genomic structure of Enterobacter spp., the second most prevalent carbapenemase-producing Enterobacteriaceae, remains limited. Here we sequenced 97 clinical Enterobacter species isolates that were both carbapenem susceptible and resistant from various geographic regions to decipher the molecular origins of carbapenem resistance and to understand the changing phylogeny of these emerging and drug-resistant pathogens. Of the carbapenem-resistant isolates, 30 possessed blaKPC-2, 40 had blaKPC-3, 2 had blaKPC-4, and 2 had blaNDM-1. Twenty-three isolates were carbapenem susceptible. Six genomes were sequenced to completion, and their sizes ranged from 4.6 to 5.1 Mbp. Phylogenomic analysis placed 96 of these genomes, 351 additional Enterobacter genomes downloaded from NCBI GenBank, and six newly sequenced type strains into 19 phylogenomic groups—18 groups (A to R) in the Enterobacter cloacae complex and Enterobacter aerogenes. Diverse mechanisms underlying the molecular evolutionary trajectory of these drug-resistant Enterobacter spp. were revealed, including the acquisition of an antibiotic resistance plasmid, followed by clonal spread, horizontal transfer of blaKPC-harboring plasmids between different phylogenomic groups, and repeated transposition of the blaKPC gene among different plasmid backbones. Group A, which comprises multilocus sequence type 171 (ST171), was the most commonly identified (23% of isolates). Genomic analysis showed that ST171 isolates evolved from a common ancestor and formed two different major clusters; each acquiring unique blaKPC-harboring plasmids, followed by clonal expansion. The data presented here represent the first comprehensive study of phylogenomic interrogation and the relationship between antibiotic resistance and plasmid discrimination among carbapenem-resistant Enterobacter spp., demonstrating the genetic diversity and complexity of the molecular mechanisms driving antibiotic resistance in this genus. Enterobacter spp., especially carbapenemase-producing Enterobacter spp., have emerged as a clinically significant cause of nosocomial infections. However, only limited information is available on the distribution of carbapenem resistance across this genus. Augmenting this problem is an erroneous identification of Enterobacter strains because of ambiguous typing methods and imprecise taxonomy. In this study, we used a whole-genome-based comparative phylogenetic approach to (i) revisit and redefine the genus Enterobacter and (ii) unravel the emergence and evolution of the Klebsiella pneumoniae carbapenemase-harboring Enterobacter spp. Using genomic analysis of 447 sequenced strains, we developed an improved understanding of the species designations within this complex genus and identified the diverse mechanisms driving the molecular evolution of carbapenem resistance. The findings in this study provide a solid genomic framework that will serve as an important resource in the future development of molecular diagnostics and in supporting drug discovery programs.
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Afzal M, Shafeeq S, Ahmed H, Kuipers OP. N-acetylgalatosamine-Mediated Regulation of the aga Operon by AgaR in Streptococcus pneumoniae. Front Cell Infect Microbiol 2016; 6:101. [PMID: 27672623 PMCID: PMC5018945 DOI: 10.3389/fcimb.2016.00101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 08/29/2016] [Indexed: 11/14/2022] Open
Abstract
Here, we analyze the transcriptomic response of Streptococcus pneumoniae D39 to N-acetylgalactosamine (NAGa). Transcriptome comparison of S. pneumoniae D39 grown in NAGaM17 (0.5% NAGa + M17) to that grown in GM17 (0.5% Glucose + M17) revealed the elevated expression of various carbon metabolic genes/operons, including a PTS operon (denoted here as the aga operon), which is putatively involved in NAGa transport and utilization, in the presence of NAGa. We further studied the role of a GntR-family transcriptional regulator (denoted here as AgaR) in the regulation of aga operon. Our transcriptome and RT-PCR data suggest the role of AgaR as a transcriptional repressor of the aga operon. We predicted a 20-bp operator site of AagR (5′-ATAATTAATATAACAACAAA-3′) in the promoter region of the aga operon (PbgaC), which was further verified by mutating the AgaR operator site in the respective promoter. The role of CcpA in the additional regulation of the aga operon was elucidated by further transcriptome analyses and confirmed by quantitative RT-PCR.
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Affiliation(s)
- Muhammad Afzal
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningen, Netherlands; Department of Bioinformatics and Biotechnology, Government College University FaisalabadFaisalabad, Pakistan
| | - Sulman Shafeeq
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet Stockholm, Sweden
| | - Hifza Ahmed
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Groningen, Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen Groningen, Netherlands
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Zhang H, Ravcheev DA, Hu D, Zhang F, Gong X, Hao L, Cao M, Rodionov DA, Wang C, Feng Y. Two novel regulators of N-acetyl-galactosamine utilization pathway and distinct roles in bacterial infections. Microbiologyopen 2015; 4:983-1000. [PMID: 26540018 PMCID: PMC4694137 DOI: 10.1002/mbo3.307] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 09/21/2015] [Accepted: 09/28/2015] [Indexed: 12/19/2022] Open
Abstract
Bacterial pathogens can exploit metabolic pathways to facilitate their successful infection cycles, but little is known about roles of d‐galactosamine (GalN)/N‐acetyl‐d‐galactosamine (GalNAc) catabolism pathway in bacterial pathogenesis. Here, we report the genomic reconstruction of GalN/GalNAc utilization pathway in Streptococci and the diversified aga regulons. We delineated two new paralogous AgaR regulators for the GalN/GalNAc catabolism pathway. The electrophoretic mobility shift assays experiment demonstrated that AgaR2 (AgaR1) binds the predicted palindromes, and the combined in vivo data from reverse transcription quantitative polymerase chain reaction and RNA‐seq suggested that AgaR2 (not AgaR1) can effectively repress the transcription of the target genes. Removal of agaR2 (not agaR1) from Streptococcus suis 05ZYH33 augments significantly the abilities of both adherence to Hep‐2 cells and anti‐phagocytosis against RAW264.7 macrophage. As anticipated, the dysfunction in AgaR2‐mediated regulation of S. suis impairs its pathogenicity in experimental models of both mice and piglets. Our finding discovered two novel regulators specific for GalN/GalNAc catabolism and assigned them distinct roles into bacterial infections. To the best of our knowledge, it might represent a first paradigm that links the GalN/GalNAc catabolism pathway to bacterial pathogenesis.
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Affiliation(s)
- Huimin Zhang
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
| | - Dmitry A Ravcheev
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, L-4360, Luxembourg
| | - Dan Hu
- Department of Epidemiology, Research Institute for Medicine of Nanjing Command, Nanjing, 210002, China
| | - Fengyu Zhang
- Department of Epidemiology, Research Institute for Medicine of Nanjing Command, Nanjing, 210002, China
| | - Xiufang Gong
- Department of Epidemiology, Research Institute for Medicine of Nanjing Command, Nanjing, 210002, China
| | - Lina Hao
- Department of Epidemiology, Research Institute for Medicine of Nanjing Command, Nanjing, 210002, China
| | - Min Cao
- Department of Epidemiology, Research Institute for Medicine of Nanjing Command, Nanjing, 210002, China
| | - Dmitry A Rodionov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127994, Russia
| | - Changjun Wang
- Department of Epidemiology, Research Institute for Medicine of Nanjing Command, Nanjing, 210002, China
| | - Youjun Feng
- Department of Medical Microbiology and Parasitology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310058, China
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Wichelecki DJ, Vetting MW, Chou L, Al-Obaidi N, Bouvier JT, Almo SC, Gerlt JA. ATP-binding Cassette (ABC) Transport System Solute-binding Protein-guided Identification of Novel d-Altritol and Galactitol Catabolic Pathways in Agrobacterium tumefaciens C58. J Biol Chem 2015; 290:28963-76. [PMID: 26472925 DOI: 10.1074/jbc.m115.686857] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Indexed: 01/27/2023] Open
Abstract
Innovations in the discovery of the functions of uncharacterized proteins/enzymes have become increasingly important as advances in sequencing technology flood protein databases with an exponentially growing number of open reading frames. This study documents one such innovation developed by the Enzyme Function Initiative (EFI; U54GM093342), the use of solute-binding proteins for transport systems to identify novel metabolic pathways. In a previous study, this strategy was applied to the tripartite ATP-independent periplasmic transporters. Here, we apply this strategy to the ATP-binding cassette transporters and report the discovery of novel catabolic pathways for d-altritol and galactitol in Agrobacterium tumefaciens C58. These efforts resulted in the description of three novel enzymatic reactions as follows: 1) oxidation of d-altritol to d-tagatose via a dehydrogenase in Pfam family PF00107, a previously unknown reaction; 2) phosphorylation of d-tagatose to d-tagatose 6-phosphate via a kinase in Pfam family PF00294, a previously orphan EC number; and 3) epimerization of d-tagatose 6-phosphate C-4 to d-fructose 6-phosphate via a member of Pfam family PF08013, another previously unknown reaction. The epimerization reaction catalyzed by a member of PF08013 is especially noteworthy, because the functions of members of PF08013 have been unknown. These discoveries were assisted by the following two synergistic bioinformatics web tools made available by the Enzyme Function Initiative: the EFI-Enzyme Similarity Tool and the EFI-Genome Neighborhood Tool.
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Affiliation(s)
- Daniel J Wichelecki
- From the Departments of Biochemistry and Chemistry and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 and
| | - Matthew W Vetting
- the Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Liyushang Chou
- From the Departments of Biochemistry and Chemistry and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 and
| | - Nawar Al-Obaidi
- the Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Jason T Bouvier
- From the Departments of Biochemistry and Chemistry and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 and
| | - Steven C Almo
- the Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - John A Gerlt
- From the Departments of Biochemistry and Chemistry and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 and
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Lengeler JW. PTS 50: Past, Present and Future, or Diauxie Revisited. J Mol Microbiol Biotechnol 2015; 25:79-93. [DOI: 10.1159/000369809] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
<b><i>Past:</i></b> The title ‘PTS 50 or The PTS after 50 years' relies on the first description in 1964 of the phosphoenolpyruvate-dependent carbohydrate:phosphotransferase system (PTS) by Kundig, Gosh and Roseman [Proc Natl Acad Sci USA 1964;52:1067-1074]. The system comprised proteins named Enzyme I, HPr and Enzymes II, as part of a novel PTS for carbohydrates in Gram-negative and Gram-positive bacteria, whose ‘biological significance remained unclear'. In contrast, studies which would eventually lead to the discovery of the central role of the PTS in bacterial metabolism had been published since before 1942. They are primarily linked to names like Epps and Gale, J. Monod, Cohn and Horibata, and B. Magasanik, and to phenomena like ‘glucose effects', ‘diauxie', ‘catabolite repression' and carbohydrate transport. <b><i>Present:</i></b> The pioneering work from Roseman's group initiated a flood of publications. The extraordinary progress from 1964 to this day in the qualitative and in vitro description of the genes and enzymes of the PTS, and of its multiple roles in global cellular control through ‘inducer exclusion', gene induction and ‘catabolite repression', in cellular growth, in cell differentiation and in chemotaxis, as well as the differences of its functions between Gram-positive and Gram-negative bacteria, was one theme of the meeting and will not be treated in detail here. <b><i>Future:</i></b> At the 1988 Paris meeting entitled ‘The PTS after 25 years', Saul Roseman predicted that ‘we must describe these interactions [of the PTS components] in a quantitative way [under] in vivo conditions'. I will present some results obtained by our group during recent years on the old phenomenon of diauxie by means of very fast and quantitative tests, measured in vivo, and obtained from cultures of isogenic mutant strains growing under chemostat conditions. The results begin to hint at the problems relating to future PTS research, but also to the ‘true science' of Roseman.
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Tran KT, Maeda T, Sanchez-Torres V, Wood TK. Beneficial knockouts in Escherichia coli for producing hydrogen from glycerol. Appl Microbiol Biotechnol 2015; 99:2573-81. [DOI: 10.1007/s00253-014-6338-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 12/12/2014] [Accepted: 12/14/2014] [Indexed: 12/28/2022]
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Metabolism of sialic acid by Bifidobacterium breve UCC2003. Appl Environ Microbiol 2014; 80:4414-26. [PMID: 24814790 DOI: 10.1128/aem.01114-14] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Bifidobacteria constitute a specific group of commensal bacteria that inhabit the gastrointestinal tracts of humans and other mammals. Bifidobacterium breve UCC2003 has previously been shown to utilize several plant-derived carbohydrates that include cellodextrins, starch, and galactan. In the present study, we investigated the ability of this strain to utilize the mucin- and human milk oligosaccharide (HMO)-derived carbohydrate sialic acid. Using a combination of transcriptomic and functional genomic approaches, we identified a gene cluster dedicated to the uptake and metabolism of sialic acid. Furthermore, we demonstrate that B. breve UCC2003 can cross feed on sialic acid derived from the metabolism of 3'-sialyllactose, an abundant HMO, by another infant gut bifidobacterial strain, Bifidobacterium bifidum PRL2010.
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20
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Hu Z, Patel IR, Mukherjee A. Genetic analysis of the roles of agaA, agaI, and agaS genes in the N-acetyl-D-galactosamine and D-galactosamine catabolic pathways in Escherichia coli strains O157:H7 and C. BMC Microbiol 2013; 13:94. [PMID: 23634833 PMCID: PMC3668189 DOI: 10.1186/1471-2180-13-94] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 04/24/2013] [Indexed: 11/30/2022] Open
Abstract
Background The catabolic pathways of N-acetyl-D-galactosamine (Aga) and D-galactosamine (Gam) in E. coli were proposed from bioinformatic analysis of the aga/gam regulon in E. coli K-12 and later from studies using E. coli C. Of the thirteen genes in this cluster, the roles of agaA, agaI, and agaS predicted to code for Aga-6-P-deacetylase, Gam-6-P deaminase/isomerase, and ketose-aldolase isomerase, respectively, have not been experimentally tested. Here we study their roles in Aga and Gam utilization in E. coli O157:H7 and in E. coli C. Results Knockout mutants in agaA, agaI, and agaS were constructed to test their roles in Aga and Gam utilization. Knockout mutants in the N-acetylglucosamine (GlcNAc) pathway genes nagA and nagB coding for GlcNAc-6-P deacetylase and glucosamine-6-P deaminase/isomerase, respectively, and double knockout mutants ΔagaA ΔnagA and ∆agaI ∆nagB were also constructed to investigate if there is any interplay of these enzymes between the Aga/Gam and the GlcNAc pathways. It is shown that Aga utilization was unaffected in ΔagaA mutants but ΔagaA ΔnagA mutants were blocked in Aga and GlcNAc utilization. E. coli C ΔnagA could not grow on GlcNAc but could grow when the aga/gam regulon was constitutively expressed. Complementation of ΔagaA ΔnagA mutants with either agaA or nagA resulted in growth on both Aga and GlcNAc. It was also found that ΔagaI, ΔnagB, and ∆agaI ΔnagB mutants were unaffected in utilization of Aga and Gam. Importantly, ΔagaS mutants were blocked in Aga and Gam utilization. Expression analysis of relevant genes in these strains with different genetic backgrounds by real time RT-PCR supported these observations. Conclusions Aga utilization was not affected in ΔagaA mutants because nagA was expressed and substituted for agaA. Complementation of ΔagaA ΔnagA mutants with either agaA or nagA also showed that both agaA and nagA can substitute for each other. The ∆agaI, ∆nagB, and ∆agaI ∆nagB mutants were not affected in Aga and Gam utilization indicating that neither agaI nor nagB is involved in the deamination and isomerization of Gam-6-P. We propose that agaS codes for Gam-6-P deaminase/isomerase in the Aga/Gam pathway.
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Affiliation(s)
- Zonglin Hu
- Division of Molecular Biology, Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U,S, Food and Drug Administration, Laurel, MD 20708, USA
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21
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Moe KM, Porcellato D, Skeie S. Metabolism of milk fat globule membrane components by nonstarter lactic acid bacteria isolated from cheese. J Dairy Sci 2012. [PMID: 23182353 DOI: 10.3168/jds.2012-5497] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The objective of this study was to investigate how components present in the milk fat globule membrane (MFGM) may be used for growth and survival by cheese-ripening lactobacilli. This was achieved by analyzing metabolites produced during incubation on appropriate media. The lactobacilli investigated were able to utilize components from the MFGM throughout a 24-d incubation period. We observed an apparent connection between the higher proteolytic activity of Lactobacillus paracasei INF448 and its ability to grow in the MFGM media after depletion of readily available sugars. All the studied strains produced large amounts of acetate when grown on an acylated aminosugar, presumably from deacetylation of the monosaccharides. Growth of Lb. plantarum INF15D on D-galactose resulted in a metabolic shift, expressed as different fates of the produced pyruvate, compared with growth on the other monosaccharides. For Lb. plantarum INF15D, the presence of D-galactose also seemed to initiate degradation of some amino acids known to take part in energy production, specifically Arg and Tyr.
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Affiliation(s)
- K M Moe
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, PO Box 5003, NO-1432 Ås, Norway.
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Leyn SA, Gao F, Yang C, Rodionov DA. N-acetylgalactosamine utilization pathway and regulon in proteobacteria: genomic reconstruction and experimental characterization in Shewanella. J Biol Chem 2012; 287:28047-56. [PMID: 22711537 DOI: 10.1074/jbc.m112.382333] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We used a comparative genomics approach to reconstruct the N-acetyl-d-galactosamine (GalNAc) and galactosamine (GalN) utilization pathways and transcriptional regulons in Proteobacteria. The reconstructed GalNAc/GalN utilization pathways include multiple novel genes with specific functional roles. Most of the pathway variations were attributed to the amino sugar transport, phosphorylation, and deacetylation steps, whereas the downstream catabolic enzymes in the pathway were largely conserved. The predicted GalNAc kinase AgaK, the novel variant of GalNAc-6-phosphate deacetylase AgaA(II) and the GalN-6-phosphate deaminase AgaS from Shewanella sp. ANA-3 were validated in vitro using individual enzymatic assays and reconstitution of the three-step pathway. By using genetic techniques, we confirmed that AgaS but not AgaI functions as the main GalN-6-P deaminase in the GalNAc/GalN utilization pathway in Escherichia coli. Regulons controlled by AgaR repressors were reconstructed by bioinformatics in most proteobacterial genomes encoding GalNAc pathways. Candidate AgaR-binding motifs share a common sequence with consensus CTTTC that was found in multiple copies and arrangements in regulatory regions of aga genes. This study provides comprehensive insights into the common and distinctive features of the GalNAc/GalN catabolism and its regulation in diverse Proteobacteria.
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Affiliation(s)
- Semen A Leyn
- Sanford-Burnham Medical Research Institute, La Jolla, California 92037, USA
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Pan JY, Wu H, Liu X, Li PP, Li H, Wang SY, Peng XX. Complexome of Escherichia coli cytosolic proteins under normal native conditions. MOLECULAR BIOSYSTEMS 2011; 7:2651-63. [PMID: 21717022 DOI: 10.1039/c1mb05103b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The interactions between proteins are important for the majority of biological functions and the interacting proteins are usually assembled into a complex. Knowing a set of protein complexes of a cell (complexome) is, therefore, essential for a better understanding and global view of cell functions. To visualize and identify the protein complexome of E. coli K-12 under normal native conditions on a proteome-wide scale, we developed an integrated proteomic platform with the combination of 2-D native/SDS-PAGE-based proteomics with co-immunoprecipitation, far-Western blotting, His-tag affinity purification and functional analysis, and used it to investigate the E. coli cytosolic complexome. A total of 24 distinct heteromeric and 8 homomeric protein complexes were identified. These complexes mainly contributed to glycolysis/gluconeogenesis, bioinformation processing, and cellular processes. Of the 24 hetereomeric complexes, 16 were reported for the first time, and 2 known complexes contained novel components that have not been reported previously based on DIP database search. Among them, RpoC-RpsA-Tig-GroL was found to be involved in transcriptional and co-translational folding, and EF-G-TufA-Tsf-RpsA linked a protein synthesis site with protein translational elongation factors. This systematic proteome analysis provides new insights into E. coli molecular systems biology.
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Affiliation(s)
- Jian-Yi Pan
- Lab of proteomics, School of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, People's Republic of China
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Archer CT, Kim JF, Jeong H, Park JH, Vickers CE, Lee SY, Nielsen LK. The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli. BMC Genomics 2011; 12:9. [PMID: 21208457 PMCID: PMC3032704 DOI: 10.1186/1471-2164-12-9] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 01/06/2011] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Escherichia coli is a model prokaryote, an important pathogen, and a key organism for industrial biotechnology. E. coli W (ATCC 9637), one of four strains designated as safe for laboratory purposes, has not been sequenced. E. coli W is a fast-growing strain and is the only safe strain that can utilize sucrose as a carbon source. Lifecycle analysis has demonstrated that sucrose from sugarcane is a preferred carbon source for industrial bioprocesses. RESULTS We have sequenced and annotated the genome of E. coli W. The chromosome is 4,900,968 bp and encodes 4,764 ORFs. Two plasmids, pRK1 (102,536 bp) and pRK2 (5,360 bp), are also present. W has unique features relative to other sequenced laboratory strains (K-12, B and Crooks): it has a larger genome and belongs to phylogroup B1 rather than A. W also grows on a much broader range of carbon sources than does K-12. A genome-scale reconstruction was developed and validated in order to interrogate metabolic properties. CONCLUSIONS The genome of W is more similar to commensal and pathogenic B1 strains than phylogroup A strains, and therefore has greater utility for comparative analyses with these strains. W should therefore be the strain of choice, or 'type strain' for group B1 comparative analyses. The genome annotation and tools created here are expected to allow further utilization and development of E. coli W as an industrial organism for sucrose-based bioprocesses. Refinements in our E. coli metabolic reconstruction allow it to more accurately define E. coli metabolism relative to previous models.
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Affiliation(s)
- Colin T Archer
- Australian Institute for Bioengineering and Nanotechnology, Cnr Cooper and College Rds, The University of Queensland, St Lucia, Queensland 4072 Australia
| | - Jihyun F Kim
- Industrial Biotechnology and Bioenergy Research Center, Korea Research Institute of Bioscience and Biotechnology, 111 Gwahangno, Yuseong-gu, Daejeon, Korea
| | - Haeyoung Jeong
- Industrial Biotechnology and Bioenergy Research Center, Korea Research Institute of Bioscience and Biotechnology, 111 Gwahangno, Yuseong-gu, Daejeon, Korea
| | - Jin Hwan Park
- Department of Chemical and Biomolecular Engineering (BK21 program) and Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, KAIST, 335 Gwahangno, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology, Cnr Cooper and College Rds, The University of Queensland, St Lucia, Queensland 4072 Australia
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering (BK21 program) and Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, KAIST, 335 Gwahangno, Yuseong-gu, Daejeon 305-701, Republic of Korea
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology, Cnr Cooper and College Rds, The University of Queensland, St Lucia, Queensland 4072 Australia
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Garces F, Fernández FJ, Gómez AM, Pérez-Luque R, Campos E, Prohens R, Aguilar J, Baldomà L, Coll M, Badía J, Vega MC. Quaternary structural transitions in the DeoR-type repressor UlaR control transcriptional readout from the L-ascorbate utilization regulon in Escherichia coli. Biochemistry 2008; 47:11424-33. [PMID: 18844374 DOI: 10.1021/bi800748x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
UlaR is a DNA binding protein of the DeoR family of eubacterial transcriptional repressors which maintains the utilization of the L-ascorbate ula regulon in a repressed state. The availability of L-ascorbate in the growth medium releases UlaR-mediated repression on the ula regulon, thereby activating transcription. The molecular details of this induction by L-ascorbate have remained elusive to date. Here we have identified L-ascorbate 6-phosphate as a direct effector of UlaR; using a combination of site-directed mutagenesis, gel retardation, isothermal titration calorimetry, and analytical ultracentrifugation studies, we have identified the key amino acid residues that mediate L-ascorbate 6-phosphate binding and constructed the first model of regulation of a DeoR family member, establishing the basis of the ula regulon transcription control by UlaR. In this model, specific quaternary rearrangements of the DeoR-type repressor are the molecular underpinning of the activating and repressing forms. A DNA-bound UlaR tetramer establishes repression, whereas an L-ascorbate-6-phosphate-induced breakdown of the tetrameric configuration in favor of an UlaR dimeric state results in dissociation of UlaR from DNA and allows transcription of ulaG and ula ABCDEF structural genes. Despite the fact that similar changes have been described for other unrelated repressor factors, this is the first report to demonstrate that specific oligomerization changes are responsible for the activating and repressing forms of a DeoR-type eubacterial transcriptional repressor.
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Affiliation(s)
- Fernando Garces
- Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, E-28040 Madrid, Spain
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26
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Mukherjee A, LeClerc J, Cebula T. Phenotypic Microarray Approaches to the Study of Prokaryotes. Genomics 2008. [DOI: 10.3109/9781420067064-16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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27
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Altered utilization of N-acetyl-D-galactosamine by Escherichia coli O157:H7 from the 2006 spinach outbreak. J Bacteriol 2007; 190:1710-7. [PMID: 18156259 DOI: 10.1128/jb.01737-07] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In silico analyses of previously sequenced strains of Escherichia coli O157:H7, EDL933 and Sakai, localized the gene cluster for the utilization of N-acetyl-D-galactosamine (Aga) and D-galactosamine (Gam). This gene cluster encodes the Aga phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) and other catabolic enzymes responsible for transport and catabolism of Aga. As the complete coding sequences for enzyme IIA (EIIA)(Aga/Gam), EIIB(Aga), EIIC(Aga), and EIID(Aga) of the Aga PTS are present, E. coli O157:H7 strains normally are able to utilize Aga as a sole carbon source. The Gam PTS complex, in contrast, lacks EIIC(Gam), and consequently, E. coli O157:H7 strains cannot utilize Gam. Phenotypic analyses of 120 independent isolates of E. coli O157:H7 from our culture collection revealed that the overwhelming majority (118/120) displayed the expected Aga+ Gam- phenotype. Yet, when 194 individual isolates, derived from a 2006 spinach-associated E. coli O157:H7 outbreak, were analyzed, all (194/194) displayed an Aga- Gam- phenotype. Comparison of aga/gam sequences from two spinach isolates with those of EDL933 and Sakai revealed a single nucleotide change (G:C-->A:T) in the agaF gene in the spinach-associated isolates. The base substitution in agaF, which encodes EIIA(Aga/Gam) of the PTS, changes a conserved glycine residue to serine (Gly91Ser). Pyrosequencing of this region showed that all spinach-associated E. coli O157:H7 isolates harbored this same G:C-->A:T substitution. Notably, when agaF+ was cloned into an expression vector and transformed into six spinach isolates, all (6/6) were able to grow on Aga, thus demonstrating that the Gly91Ser substitution underlies the Aga- phenotype in these isolates.
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Abstract
Operons are clusters of genes that are transcribed as a single message, and regulated by the same gene expression machinery. They are found primarily in prokaryotic genomes. Because genes in the same operon are likely to have related functions, identification of the operon structure is potentially useful for assigning gene function. We report the development and benchmarking of two different methods for detecting operons, based on an analysis of 42 fully sequenced prokaryotic organisms. The Gene Neighbor method (GNM) utilizes the relatively high conservation of gene order in operons, compared with genes in general. The Gene Gap Method (GGM) makes use of the relatively short gap between genes in operons compared with that otherwise found between adjacent genes. The methods have been benchmarked using KEGG pathway data and RegulonDB Escherichia coli operon data. With optimum parameters, the specificity of the GNM is 93% and the sensitivity is 70%. For the GGM, the specificity is 95% and the sensitivity is 68%. Together, the two methods have a sensitivity of 87.2%, while joint predictions have a sensitivity of 50% and a specificity of 98%. The methods are used to infer possible functions for some hypothetical genes in prokaryotic genomes. The methods have proven a useful addition to structure information in deriving protein function in a structural genomics project.
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Affiliation(s)
- Yongpan Yan
- Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA
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29
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Elgrably-Weiss M, Schlosser-Silverman E, Rosenshine I, Altuvia S. DeoT, a DeoR-type transcriptional regulator of multiple target genes. FEMS Microbiol Lett 2006; 254:141-8. [PMID: 16451192 DOI: 10.1111/j.1574-6968.2005.00020.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In this study, we investigated the genetic organization and function of Escherichia coli yciT, a gene predicted by computational methods to belong to the DeoR-type family of transcriptional regulators. We show that transcription of yciT (here denoted deoT for deoR-Type) initiates from a promoter located upstream of a putative open reading frame (denoted deoL for deoT Leader). We also show that DeoT acts as a global regulator, repressing the expression of a number of genes involved in a variety of metabolic pathways including transport of maltose, fatty acid beta-oxidation and peptide degradation.
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Affiliation(s)
- Maya Elgrably-Weiss
- Department of Molecular Genetics and Biotechnology, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
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30
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Tanaka T, Takahashi F, Fukui T, Fujiwara S, Atomi H, Imanaka T. Characterization of a novel glucosamine-6-phosphate deaminase from a hyperthermophilic archaeon. J Bacteriol 2005; 187:7038-44. [PMID: 16199574 PMCID: PMC1251617 DOI: 10.1128/jb.187.20.7038-7044.2005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A key step in amino sugar metabolism is the interconversion between fructose-6-phosphate (Fru6P) and glucosamine-6-phosphate (GlcN6P). This conversion is catalyzed in the catabolic and anabolic directions by GlcN6P deaminase and GlcN6P synthase, respectively, two enzymes that show no relationship with one another in terms of primary structure. In this study, we examined the catalytic properties and regulatory features of the glmD gene product (GlmD(Tk)) present within a chitin degradation gene cluster in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. Although the protein GlmD(Tk) was predicted as a probable sugar isomerase related to the C-terminal sugar isomerase domain of GlcN6P synthase, the recombinant GlmD(Tk) clearly exhibited GlcN6P deaminase activity, generating Fru6P and ammonia from GlcN6P. This enzyme also catalyzed the reverse reaction, the ammonia-dependent amination/isomerization of Fru6P to GlcN6P, whereas no GlcN6P synthase activity dependent on glutamine was observed. Kinetic analyses clarified the preference of this enzyme for the deaminase reaction rather than the reverse one, consistent with the catabolic function of GlmD(Tk). In T. kodakaraensis cells, glmD(Tk) was polycistronically transcribed together with upstream genes encoding an ABC transporter and a downstream exo-beta-glucosaminidase gene (glmA(Tk)) within the gene cluster, and their expression was induced by the chitin degradation intermediate, diacetylchitobiose. The results presented here indicate that GlmD(Tk) is actually a GlcN6P deaminase functioning in the entry of chitin-derived monosaccharides to glycolysis in this hyperthermophile. This enzyme is the first example of an archaeal GlcN6P deaminase and is a structurally novel type distinct from any previously known GlcN6P deaminase.
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Affiliation(s)
- Takeshi Tanaka
- Department of Synthetic and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
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31
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Ezquerro-Sáenz C, Ferrero MA, Revilla-Nuin B, López Velasco FF, Martínez-Blanco H, Rodríguez-Aparicio LB. Transport of N-acetyl-D-galactosamine in Escherichia coli K92: effect on acetyl-amino sugar metabolism and polysialic acid production. Biochimie 2005; 88:95-102. [PMID: 16040188 DOI: 10.1016/j.biochi.2005.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2005] [Accepted: 06/20/2005] [Indexed: 10/25/2022]
Abstract
The N-acetyl-D-galactosamine (GalNAc) transport system of Escherichia coli K92 was studied when the bacterium was grown in a chemically defined medium containing GalNAc as a carbon source. Kinetic measurements were carried out in vivo at 37 degrees C in 25 mM phosphate buffer, pH 7.0. Under these conditions, the uptake rate was linear for at least 3 min and the calculated Km for GalNAc was 3 microM. The transport system was strongly inhibited by sodium arsenate (70%), potassium cyanide (62%) and 2,4-dinitrophenol (75%). Analysis of bacterial GalNAc phosphotransferase activity revealed in vitro GalNAc phosphorylation activity only when phosphoenolpyruvate was present. These results strongly support the notion that GalNAc uptake depends on a specific phosphotransferase system. Study of activity regulation showed that N-acetylglucosamine and mannosamine specifically inhibit the transport of GalNAc in this bacterium. Analysis of expression revealed that the GalNAc transport system is specifically induced by GalNAc but not by N-acetylglucosamine (GlcNAc) or N-acetylmannosamine (ManNAc), two intimately related sugars. Moreover, full induction of GalNAc transport required the presence of both cAMP and GalNAc. Comparative studies revealed that E. coli K92 has developed a regulation mechanism that specifically induces the appropriate permease based on the presence of each respective phospho-amino sugar (GlcNAc, ManNAc and GalNAc). In this regulation system, GlcNAc is the preferred amino sugar as the carbon source. Finally, when E. coli K92 was grown using GalNAc, capsular polysialic acid production was strongly affected. The presence of intracellular phosphoderivative acetylamino sugars, generated by the action of the phosphotransferase transport system, can be responsible for this effect.
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Affiliation(s)
- C Ezquerro-Sáenz
- Departamento de Bioquímica y Biología Molecular, Universidad de León, Campus de Vegazana, 24007 León, Spain
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Cheek S, Ginalski K, Zhang H, Grishin NV. A comprehensive update of the sequence and structure classification of kinases. BMC STRUCTURAL BIOLOGY 2005; 5:6. [PMID: 15771780 PMCID: PMC1079889 DOI: 10.1186/1472-6807-5-6] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2005] [Accepted: 03/16/2005] [Indexed: 12/02/2022]
Abstract
Background A comprehensive update of the classification of all available kinases was carried out. This survey presents a complete global picture of this large functional class of proteins and confirms the soundness of our initial kinase classification scheme. Results The new survey found the total number of kinase sequences in the protein database has increased more than three-fold (from 17,310 to 59,402), and the number of determined kinase structures increased two-fold (from 359 to 702) in the past three years. However, the framework of the original two-tier classification scheme (in families and fold groups) remains sufficient to describe all available kinases. Overall, the kinase sequences were classified into 25 families of homologous proteins, wherein 22 families (~98.8% of all sequences) for which three-dimensional structures are known fall into 10 fold groups. These fold groups not only include some of the most widely spread proteins folds, such as the Rossmann-like fold, ferredoxin-like fold, TIM-barrel fold, and antiparallel β-barrel fold, but also all major classes (all α, all β, α+β, α/β) of protein structures. Fold predictions are made for remaining kinase families without a close homolog with solved structure. We also highlight two novel kinase structural folds, riboflavin kinase and dihydroxyacetone kinase, which have recently been characterized. Two protein families previously annotated as kinases are removed from the classification based on new experimental data. Conclusion Structural annotations of all kinase families are now revealed, including fold descriptions for all globular kinases, making this the first large functional class of proteins with a comprehensive structural annotation. Potential uses for this classification include deduction of protein function, structural fold, or enzymatic mechanism of poorly studied or newly discovered kinases based on proteins in the same family.
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Affiliation(s)
- Sara Cheek
- Department of Biochemistry, University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390, USA
| | - Krzysztof Ginalski
- Department of Biochemistry, University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390, USA
- Bioinformatics Laboratory, Interdisciplinary Centre for Mathematical and Computational Modelling Warsaw University, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Hong Zhang
- Department of Biochemistry, University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390, USA
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390, USA
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Lun S, Willson PJ. Putative mannose-specific phosphotransferase system component IID represses expression of suilysin in serotype 2 Streptococcus suis. Vet Microbiol 2004; 105:169-80. [PMID: 15708813 DOI: 10.1016/j.vetmic.2004.10.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2004] [Revised: 10/15/2004] [Accepted: 10/15/2004] [Indexed: 10/26/2022]
Abstract
In this study, we generated a genomic mutant library from a North American strain of serotype 2 Streptococcus suis using the pGh9:ISS1 transposition vector. Suilysin is the hemolysin made by S. suis. A hyper-hemolytic mutant was identified by screening for hemolytic phenotype using media with human blood. The hyper-hemolytic phenotype was characterised by a quantitative hemolysis microplate method. The use of green fluorescent protein (GFP) as a reporter also showed that suilysin gene expression was greater in the mutant. DNA sequence analysis of 3.8 kb surrounding the ISS1 insertion site revealed four open reading frames (ORFs) with three consecutive ORFs that belong to a putative mannose-specific phosphotransferase system (PTS). The S. suis gene homologous to mannose permease IID, manN, was interrupted by the transposon. A complementation test showed that manN repressed the expression of suilysin and the absence of manN was responsible for the hyper-hemolytic phenotype. However, both wild type and isogenic hyper-hemolytic mutant S. suis fermented mannose, glucose and lactose. Thus, despite its potential roles in carbohydrate transport, phosphorylation and metabolism, the manN homologue in the putative mannose-specific PTS regulates gene expression in S. suis.
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Affiliation(s)
- Shichun Lun
- 120 Veterinary Road, Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Sask., Canada S7N 5E3
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34
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Ray WK, Larson TJ. Application of AgaR repressor and dominant repressor variants for verification of a gene cluster involved in N-acetylgalactosamine metabolism in Escherichia coli K-12. Mol Microbiol 2004; 51:813-26. [PMID: 14731281 DOI: 10.1046/j.1365-2958.2003.03868.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The agaZVWEFASYBCDI gene cluster encodes the phosphotransferase systems and enzymes responsible for the uptake and metabolism of N-acetylgalactosamine and galactosamine in Escherichia coli. In some strains of E. coli, particularly the common K-12 strain, a portion of this cluster is missing because of a site-specific recombination event that occurred between sites in agaW and agaA. Strains that have undergone this recombination event have lost the ability to utilize either N-acetylgalactosamine or galactosamine as sole sources of carbon. Divergently transcribed from this gene cluster is the gene agaR encoding a transcriptional repressor belonging to the DeoR/GlpR family of transcriptional regulators. Promoters upstream of agaR, agaZ and agaS were characterized. All three promoters had elevated activity in the presence of N-acetylgalactosamine or galactosamine, were regulated in vivo by AgaR and possessed specific DNA-binding sites for AgaR upstream from the start sites of transcription as determined by DNase I footprinting. In vivo analysis and DNase I footprinting indicated that the promoter specific for agaZ also requires activation by cAMP-CRP. Previous work with GlpR and other members of the DeoR/GlpR family have identified highly conserved amino acid residues that function in DNA-binding or response to inducer. These residues of AgaR were targeted for site-directed mutagenesis and yielded variants of AgaR that were either negatively dominant or non-inducible. The apparent ability to produce negatively dominant and non-inducible variants of proteins of the DeoR/GlpR family of currently unknown function will likely facilitate screening for function.
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Affiliation(s)
- W Keith Ray
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
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35
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Wiegert T, Schumann W. Analysis of a DNA-binding motif of the Bacillus subtilis HrcA repressor protein. FEMS Microbiol Lett 2003; 223:101-6. [PMID: 12799007 DOI: 10.1016/s0378-1097(03)00350-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The hrcA gene of Bacillus subtilis encodes a transcriptional repressor protein which negatively controls the heat shock operons dnaK and groESL. Alignment of the HrcA protein with repressor proteins from the NCBI database revealed that it exhibits a striking homology near its N-terminal part with proteins of the DeoR family. This region contains a helix-turn-helix motif and has been shown to be involved in DNA binding. To investigate whether this is also true for the HrcA protein, three critical amino acid residues were changed within or adjacent to the recognition helix. While single amino acid replacements barely influenced the binding activity, alteration of two consecutive amino acid residues within the recognition helix completely abolished the binding activity. When this mutant hrcA allele was expressed together with the wild-type allele within the same cell, it conferred a dominant-negative phenotype to the cells underlining that these amino acid residues are crucial for specific DNA binding and that HrcA binds to DNA in an oligomeric form.
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Affiliation(s)
- Thomas Wiegert
- Institute of Genetics, University of Bayreuth, D-95440, Bayreuth, Germany.
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36
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Campos E, Aguilar J, Baldoma L, Badia J. The gene yjfQ encodes the repressor of the yjfR-X regulon (ula), which is involved in L-ascorbate metabolism in Escherichia coli. J Bacteriol 2002; 184:6065-8. [PMID: 12374842 PMCID: PMC135402 DOI: 10.1128/jb.184.21.6065-6068.2002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mutations in yjfQ allowed us to identify this gene as the regulator of the operon yjfS-X (ula operon), reported to be involved in L-ascorbate metabolism. Inactivation of this gene renders constitutive the expression of the ula operon, indicating that YjfQ acts as a repressor. We also demonstrate that this repressor regulates the nearby yjfR gene, which in this way constitutes a regulon with the ula operon.
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Affiliation(s)
- Evangelina Campos
- Department of Biochemistry, Faculty of Pharmacy, University of Barcelona, 08028 Barcelona, Spain
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37
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Hall DR, Bond CS, Leonard GA, Watt CI, Berry A, Hunter WN. Structure of tagatose-1,6-bisphosphate aldolase. Insight into chiral discrimination, mechanism, and specificity of class II aldolases. J Biol Chem 2002; 277:22018-24. [PMID: 11940603 DOI: 10.1074/jbc.m202464200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tagatose-1,6-bisphosphate aldolase (TBPA) is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phosphate to produce tagatose 1,6-bisphosphate. The high resolution (1.45 A) crystal structure of the Escherichia coli enzyme, encoded by the agaY gene, complexed with phosphoglycolohydroxamate (PGH) has been determined. Two subunits comprise the asymmetric unit, and a crystallographic 2-fold axis generates the functional tetramer. A complex network of hydrogen bonds position side chains in the active site that is occupied by two cations. An unusual Na+ binding site is created using a pi interaction with Tyr183 in addition to five oxygen ligands. The catalytic Zn2+ is five-coordinate using three histidine nitrogens and two PGH oxygens. Comparisons of TBPA with the related fructose-1,6-bisphosphate aldolase (FBPA) identifies common features with implications for the mechanism. Because the major product of the condensation catalyzed by the enzymes differs in the chirality at a single position, models of FBPA and TBPA with their cognate bisphosphate products provide insight into chiral discrimination by these aldolases. The TBPA active site is more open on one side than FBPA, and this contributes to a less specific enzyme. The availability of more space and a wider range of aldehyde partners used by TBPA together with the highly specific nature of FBPA suggest that TBPA might be a preferred enzyme to modify for use in biotransformation chemistry.
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Affiliation(s)
- David R Hall
- Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
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Gaurivaud P, Laigret F, Garnier M, Bové JM. Characterization of FruR as a putative activator of the fructose operon of Spiroplasma citri. FEMS Microbiol Lett 2001; 198:73-8. [PMID: 11325556 DOI: 10.1111/j.1574-6968.2001.tb10621.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The role of fruR, the first gene of the Spiroplasma citri fructose operon, was investigated. In vivo transcription of the fructose operon is greatly enhanced by the presence of fructose in the growth medium while glucose has no effect. When fruR is not expressed, transcription of the fructose operon is not stimulated by fructose, and fructose fermentation is decreased, indicating that FruR is an activator of the fructose operon. The promoter of the fructose operon was localized by primer extension, and a direct T-rich repeat was found to overlap the -35 box. This repeat could be the binding site of FruR. The presence of fructose in the culture medium also decreases the toxicity of methyl alpha-glucoside, however FruR is not involved in this regulation. This is the first description of transcription regulation of a mollicute operon.
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Affiliation(s)
- P Gaurivaud
- Laboratoire de Biologie Cellulaire et Moléculaire, Institut de Biologie Végétale Moléculaire, Institut National de la Recherche Agronomique and Université Victor Segalen Bordeaux 2, 33883 Cedex, Villenave d'Ornon, France.
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Saier MH. Phylogenetic approaches to the identification and characterization of protein families and superfamilies. MICROBIAL & COMPARATIVE GENOMICS 2001; 1:129-50. [PMID: 9689209 DOI: 10.1089/mcg.1996.1.129] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
With the advent of megabase genome sequencing, the need for computational analyses increases exponentially. Sequencing errors must be corrected, encoded proteins must be identified, functions must be assigned to these proteins, and distant phylogenetic relationships must be recognized in order to maximize the yield of information obtainable from genome sequencing projects. Both the computer and the human brain have their limitations, but using them in combination, the biologist can vastly extend his or her analytic capabilities. Computer techniques can be used to estimate protein structure, function, biogenesis, and evolution. In this review, the application of available computer programs to several protein families, particularly transport, receptor, and transcriptional regulatory protein families, illustrate our current capabilities and limitations. Although some multidomain protein families are evolutionarily homogeneous, others have mosaic origins. Evidence concerning the nature and frequency of occurrence of domain shuffling, splicing, fusion, deletion, and duplication during evolution of specific protein families is evaluated. It is shown that specific families of enzymes, receptors, transport proteins, and transcriptional regulatory proteins share a common evolutionary origin, frequently diverging in function because of domain splicing and ligation. Some large families arose gradually over evolutionary time, whereas others developed suddenly, due to bursts of intragenic or intergenic (or both) duplication events occurring over relatively short periods of time. It is argued that energy coupling to transport was a late occurrence, superimposed on preexisting mechanisms of solute facilitation. It is also shown that several transport protein families have evolved independently of each other, employing different routes, at different times in evolutionary history, to give topologically similar transmembrane protein complexes.
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Affiliation(s)
- M H Saier
- Department of Biology, University of California at San Diego, La Jolla, USA
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Reizer J, Paulsen IT, Reizer A, Titgemeyer F, Saier MH. Novel phosphotransferase system genes revealed by bacterial genome analysis: the complete complement of pts genes in mycoplasma genitalium. MICROBIAL & COMPARATIVE GENOMICS 2001; 1:151-64. [PMID: 9689210 DOI: 10.1089/mcg.1996.1.151] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete sequence of the Mycoplasma genitalium chromosome has recently been determined. We here report analyses of the genes encoding proteins of the phosphoenolpyruvate:sugar phosphotransferase system, PTS. These genes encode (1) Enzyme I, (2) HPr, (3) a glucose-specific Enzyme IICBA, (4) an inactive glucose-specific Enzyme IIB, lacking the active site cysteyl residue, and (5) a fructose-specific Enzyme IIABC. Some of the unique features of these genes and their enzyme products are as follows. (1) Each of the genes is encoded within a distinct operon. (2) Both Enzyme I and HPr have basic isoelectric points. (3) The glucose-specific Enzyme IIC bears a centrally located, hydrophilic, 200 amino acyl residue insert that lacks sequence similarity with any protein in the current database. (4) The fructose-specific Enzyme II has a domain order (IIABC), different from those of previously characterized fructose permeases, and its IIA domain more closely resembles the IIANtr protein of Escherichia coli than other fructose-specific IIA domains. The potential significance of these novel features is discussed.
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Affiliation(s)
- J Reizer
- Department of Biology, University of California at San Diego, La Jolla, USA
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41
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Collin M, Olsén A. Identification of conditionally expressed genes in Streptococcus pyogenes using RNA fingerprinting. FEMS Microbiol Lett 2001; 196:123-7. [PMID: 11267767 DOI: 10.1111/j.1574-6968.2001.tb10552.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
RNA fingerprinting using arbitrarily primed reverse transcription-polymerase chain reaction was employed on isolated RNA from Streptococcus pyogenes bacteria in order to identify genes that were regulated in response to environmental changes. When S. pyogenes was cultured under glucose-rich growth conditions a number of transcriptionally up-regulated products were identified, cloned and sequenced. Using the Streptococcal Genome Sequencing Project database and similarity searches against the GenBank database the corresponding genes encoding enzyme IIB and IIC component of a putative phosphotransferase system were identified. Thus, we show that RNA fingerprinting could be a useful tool to identify unknown genes in S. pyogenes that are expressed under certain environmental conditions.
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Affiliation(s)
- M Collin
- Section for Molecular Pathogenesis, Biomedical Center, Lund University, Floor B14, Tornavägen 10, SE-221 84 Lund, Sweden
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Kumar MJ, Jamaluddin MS, Natarajan K, Kaur D, Datta A. The inducible N-acetylglucosamine catabolic pathway gene cluster in Candida albicans: discrete N-acetylglucosamine-inducible factors interact at the promoter of NAG1. Proc Natl Acad Sci U S A 2000; 97:14218-23. [PMID: 11114181 PMCID: PMC18898 DOI: 10.1073/pnas.250452997] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The catabolic pathway of N-acetylglucosamine (GlcNAc) in Candida albicans is an important facet of its pathogenicity. One of the pathway genes, encoding glucosamine-6-phosphate deaminase (NAG1) is transcriptionally regulated by GlcNAc. Sequence analysis of a 4-kb genomic clone containing NAG1 indicates that this gene is part of a cluster containing two other genes of the GlcNAc catabolic pathway, i.e., DAC1, GlcNAc-6-phosphate deacetylase, and HXK1, hexokinase. All three genes are temporally and coordinately induced by GlcNAc suggesting a common regulatory mechanism for these genes. The NAG1 promoter is up-regulated when induced by GlcNAc in C. albicans but not in Saccharomyces cerevisiae. In vivo analysis of the deletion constructs delineated the minimal promoter to -130 bp and mapped two regions at -200 and -400 bp upstream of +1 (ATG) responsible for GlcNAc induction. Gel mobility-shift assays and "footprinting" (DNase protection method) analyses revealed two regions, 5'-GGAGCAAAAAAATGT 3' (-164 to -150, box A) and 5'-ACGGTGAGTTG 3' (-291 to -281, box B), that are recognized and bound by at least two inducible activator proteins directing the regulation of gene expression.
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Affiliation(s)
- M J Kumar
- Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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Gaurivaud P, Laigret F, Verdin E, Garnier M, Bové JM. Fructose operon mutants of Spiroplasma citri. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 9):2229-2236. [PMID: 10974110 DOI: 10.1099/00221287-146-9-2229] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Fructose-negative mutants of Spiroplasma citri wild-type strain GII-3 were selected by two methods. The first method is based on the selection of spontaneous xylitol-resistant mutants, xylitol being a toxic fructose analogue. Five such mutants were obtained, but only one, xyl3, was unable to use fructose and had no phosphoenolpuryvate:fructose phosphotransferase system (fructose-PTS) activity. Amplification and sequencing of the fructose permease gene of mutant xyl3 revealed the presence of an adenylic insertion leading to a truncated permease. The second method is based on inactivation of fruA and/or fruK by homologous recombination involving one crossing-over between the chromosomal genes and inactivated genes carried by replicative plasmids. Fructose-negative mutants were obtained at a frequency of about 10%. Fructose-PTS activity and 1-phosphofructokinase activity were not detected in four representative mutants that were characterized (H31, H45, E38 and E53). In strain H31, Southern blot analysis and PCR showed that the result of homologous recombination was, as expected, the presence in the chromosome of two mutated fruA-fruK copies with the plasmid sequence in between. Only the mutated copy, under control of the fructose operon promoter, was transcribed. This work describes for the first time the use of two methods to obtain fructose-auxotrophic mutants of S. citri. The method involving homologous recombination is a general procedure for gene disruption in S. citri.
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Affiliation(s)
- Patrice Gaurivaud
- Laboratoire de Biologie Cellulaire et Moléculaire, Institut de Biologie Végétale Moléculaire, Institut National de la Recherche Agronomique and Université Victor Segalen Bordeaux 2, Domaine de la Grande Ferrade, BP 81, 33883 Villenave d'Ornon cedex, France1
| | - Frédéric Laigret
- Laboratoire de Biologie Cellulaire et Moléculaire, Institut de Biologie Végétale Moléculaire, Institut National de la Recherche Agronomique and Université Victor Segalen Bordeaux 2, Domaine de la Grande Ferrade, BP 81, 33883 Villenave d'Ornon cedex, France1
| | - Eric Verdin
- Laboratoire de Biologie Cellulaire et Moléculaire, Institut de Biologie Végétale Moléculaire, Institut National de la Recherche Agronomique and Université Victor Segalen Bordeaux 2, Domaine de la Grande Ferrade, BP 81, 33883 Villenave d'Ornon cedex, France1
| | - Monique Garnier
- Laboratoire de Biologie Cellulaire et Moléculaire, Institut de Biologie Végétale Moléculaire, Institut National de la Recherche Agronomique and Université Victor Segalen Bordeaux 2, Domaine de la Grande Ferrade, BP 81, 33883 Villenave d'Ornon cedex, France1
| | - Joseph M Bové
- Laboratoire de Biologie Cellulaire et Moléculaire, Institut de Biologie Végétale Moléculaire, Institut National de la Recherche Agronomique and Université Victor Segalen Bordeaux 2, Domaine de la Grande Ferrade, BP 81, 33883 Villenave d'Ornon cedex, France1
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Gaurivaud P, Laigret F, Garnier M, Bove JM. Fructose utilization and pathogenicity of Spiroplasma citri: characterization of the fructose operon. Gene 2000; 252:61-9. [PMID: 10903438 DOI: 10.1016/s0378-1119(00)00230-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Transposon Tn4001 mutagenesis of Spiroplasma citri wild-type (wt) strain GII-3 led to the isolation and characterization of non-phytopathogenic mutant GMT 553. In this mutant, transposon Tn4001 is inserted within the first gene of the fructose operon. This operon comprises three genes. The first gene (fruR) codes for a putative transcriptional regulator protein belonging to the deoxyribonucleoside repressor (DeoR) family. Sequence similarities and functional complementation of mutant GMT 553 with different combinations of the wt genes of the fructose operon showed that the second gene (fruA) codes for the permease of the phosphoenolpyruvate:fructose phosphotransferase system (fructose PTS), and the third, fruK, for the 1-phosphofructokinase (1-PFK). Transcription of the fructose operon in wt strain GII-3 resulted in two messenger RNAs, one of 2.8kb and one of 3.8kb. Insertion of Tn4001 in the genome of mutant GMT 553 abolished transcription of the fructose operon, and resulted in the inability of this mutant to use fructose. Functional complementation experiments demonstrated that fructose utilization was restored with fruR-fruA-fruK, fruA-fruK or fruA only, but not with fruR or fruR-fruA. This is the first time that an operon for sugar utilization has been functionally characterized in the mollicutes.
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Affiliation(s)
- P Gaurivaud
- Laboratoire de Biologie Cellulaire et Moléculaire, Institut de Biologie Végétale Moléculaire, Institut National de la Recherche Agronomique, Université Victor Segalen Bordeaux 2, 71 avenue Edouard Bourleaux, Cedex, France
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Brinkkötter A, Klöss H, Alpert C, Lengeler JW. Pathways for the utilization of N-acetyl-galactosamine and galactosamine in Escherichia coli. Mol Microbiol 2000; 37:125-35. [PMID: 10931310 DOI: 10.1046/j.1365-2958.2000.01969.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Among enteric bacteria, the ability to grow on N-acetyl-galactosamine (GalNAc or Aga) and on D-galactosamine (GalN or Gam) differs. Thus, strains B, C and EC3132 of Escherichia coli are Aga+ Gam+ whereas E. coli K-12 is Aga- Gam-, similarly to Klebsiella pneumoniae KAY2026, Klebsiella oxytoca M5a1 and Salmonella typhimurium LT2. The former strains carry a complete aga/kba gene cluster at 70.5 min of their gene map. These genes encode an Aga-specific phosphotransferase system (PTS) or IIAga (agaVWE) and a GalN-specific PTS or IIGam (agaBCD). Both PTSs belong to the mannose-sorbose family, i.e. the IIB, IIC and IID domains are encoded by different genes, and they share a IIA domain (agaF). Furthermore, the genes encode an Aga6P-deacetylase (agaA), a GalN6P deaminase (agaI), a tagatose-bisphosphate aldolase comprising two different peptides (kbaYZ) and a putative isomerase (agaS), i.e. complete pathways for the transport and degradation of both amino sugars. The genes are organized in two adjacent operons (kbaZagaVWEFA and agaS kbaYagaBCDI) and controlled by a repressor AgaR. Its gene agaR is located upstream of kbaZ, and AgaR responds to GalNAc and GalN in the medium. All Aga- Gam- strains, however, carry a deletion covering genes agaW' EF 'A; consequently they lack active IIAga and IIGam PTSs, thus explaining their inability to grow on the two amino sugars. Remnants of a putative recombination site flank the deleted DNA in the various Aga- Gam- enteric bacteria. Derivatives with an Aga+ Gam- phenotype can be isolated from E. coli K-12. These retain the DeltaagaW' EF 'A deletion and carry suppressor mutations in the gat and nag genes for galactitol and N-acetyl-glucosamine metabolism, respectively, that allow growth on Aga but not on GalN.
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Affiliation(s)
- A Brinkkötter
- Universität Osnabrück, Fachbereich Biologie/Chemie, D-49069 Osnabrück, Germany
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Lortie LA, Pelletier M, Vadeboncoeur C, Frenette M. The gene encoding IIAB(Man)L in Streptococcus salivarius is part of a tetracistronic operon encoding a phosphoenolpyruvate: mannose/glucose phosphotransferase system. MICROBIOLOGY (READING, ENGLAND) 2000; 146 ( Pt 3):677-685. [PMID: 10746771 DOI: 10.1099/00221287-146-3-677] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Glucose and mannose are transported in streptococci by the mannose-PTS (phosphoenolpyruvate:mannose phosphotransferase system), which consists of a cytoplasmic IIAB protein, called IIAB(Man), and an uncharacterized membrane permease. This paper reports the characterization of the man operon encoding the specific components of the mannose-PTS of Streptococcus salivarius. The man operon was composed of four genes, manL, manM, manN and manO. These genes were transcribed from a canonical promoter (Pman) into a 3.6 kb polycistronic mRNA that contained a 5'-UTR (untranslated region). The predicted manL gene product encoded a 35.5 kDa protein and contained the amino acid sequences of the IIA and IIB phosphorylation sites already determined from purified S. salivarius IIAB(Man)L. Expression of manL in Escherichia coli generated a 35 kDa protein that reacted with anti-IIAB(Man)L antibodies. The predicted ManM protein had an estimated size of 27.2 kDa. ManM had similarity with IIC domains of the mannose-EII family, but did not possess the signature proposed for mannose-IIC proteins from Gram-negative bacteria. From multiple alignment analyses of sequences available in current databases, the following modified IIC(Man) signature is proposed: GX3G[DNH]X3G[LIVM]2XG2[STL][LT][EQ]. The deduced product of manN was a hydrophobic protein with a predicted molecular mass of 33.4 kDa. The ManN protein contained an amino acid sequence similar to the signature sequence of the IID domains of the mannose-EII family. manO encoded a 13.7 kDa protein. This gene was also transcribed as a monocistronic mRNA from a promoter located in the manN-manO intergenic region. A search of current databases revealed the presence of IIAB(Man)L, ManM, ManN and ManO orthologues in Streptococcus mutans, Streptococcus pyogenes, Streptococcus pneumoniae and Enterococcus faecalis. This work has elucidated the molecular structure of the mannose PTS in streptococci and enterococci, and demonstrated the presence of a putative regulatory protein (ManO) within the man operon.
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Affiliation(s)
- Louis-André Lortie
- Groupe de Recherche en Ecologie Buccale, Département de Biochimie et de Microbiologie, Faculté des Sciences et de Génie, and Faculté de Médecine Dentaire, Université Laval, Québec, Canada G1K 7P41
| | - Michel Pelletier
- Groupe de Recherche en Ecologie Buccale, Département de Biochimie et de Microbiologie, Faculté des Sciences et de Génie, and Faculté de Médecine Dentaire, Université Laval, Québec, Canada G1K 7P41
| | - Christian Vadeboncoeur
- Groupe de Recherche en Ecologie Buccale, Département de Biochimie et de Microbiologie, Faculté des Sciences et de Génie, and Faculté de Médecine Dentaire, Université Laval, Québec, Canada G1K 7P41
| | - Michel Frenette
- Groupe de Recherche en Ecologie Buccale, Département de Biochimie et de Microbiologie, Faculté des Sciences et de Génie, and Faculté de Médecine Dentaire, Université Laval, Québec, Canada G1K 7P41
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Zgiby SM, Thomson GJ, Qamar S, Berry A. Exploring substrate binding and discrimination in fructose1, 6-bisphosphate and tagatose 1,6-bisphosphate aldolases. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:1858-68. [PMID: 10712619 DOI: 10.1046/j.1432-1327.2000.01191.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Fructose 1,6-bisphosphate aldolase catalyses the reversible condensation of glycerone-P and glyceraldehyde 3-phosphate into fructose 1,6-bisphosphate. A recent structure of the Escherichia coli Class II fructose 1,6-bisphosphate aldolase [Hall, D.R., Leonard, G.A., Reed, C.D., Watt, C.I., Berry, A. & Hunter, W.N. (1999) J. Mol. Biol. 287, 383-394] in the presence of the transition state analogue phosphoglycolohydroxamate delineated the roles of individual amino acids in binding glycerone-P and in the initial proton abstraction steps of the mechanism. The X-ray structure has now been used, together with sequence alignments, site-directed mutagenesis and steady-state enzyme kinetics to extend these studies to map important residues in the binding of glyceraldehyde 3-phosphate. From these studies three residues (Asn35, Ser61 and Lys325) have been identified as important in catalysis. We show that mutation of Ser61 to alanine increases the Km value for fructose 1, 6-bisphosphate 16-fold and product inhibition studies indicate that this effect is manifested most strongly in the glyceraldehyde 3-phosphate binding pocket of the active site, demonstrating that Ser61 is involved in binding glyceraldehyde 3-phosphate. In contrast a S61T mutant had no effect on catalysis emphasizing the importance of an hydroxyl group for this role. Mutation of Asn35 (N35A) resulted in an enzyme with only 1.5% of the activity of the wild-type enzyme and different partial reactions indicate that this residue effects the binding of both triose substrates. Finally, mutation of Lys325 has a greater effect on catalysis than on binding, however, given the magnitude of the effects it is likely that it plays an indirect role in maintaining other critical residues in a catalytically competent conformation. Interestingly, despite its proximity to the active site and high sequence conservation, replacement of a fourth residue, Gln59 (Q59A) had no significant effect on the function of the enzyme. In a separate study to characterize the molecular basis of aldolase specificity, the agaY-encoded tagatose 1,6-bisphosphate aldolase of E. coli was cloned, expressed and kinetically characterized. Our studies showed that the two aldolases are highly discriminating between the diastereoisomers fructose bisphosphate and tagatose bisphosphate, each enzyme preferring its cognate substrate by a factor of 300-1500-fold. This produces an overall discrimination factor of almost 5 x 105 between the two enzymes. Using the X-ray structure of the fructose 1,6-bisphosphate aldolase and multiple sequence alignments, several residues were identified, which are highly conserved and are in the vicinity of the active site. These residues might potentially be important in substrate recognition. As a consequence, nine mutations were made in attempts to switch the specificity of the fructose 1,6-bisphosphate aldolase to that of the tagatose 1,6-bisphosphate aldolase and the effect on substrate discrimination was evaluated. Surprisingly, despite making multiple changes in the active site, many of which abolished fructose 1, 6-bisphosphate aldolase activity, no switch in specificity was observed. This highlights the complexity of enzyme catalysis in this family of enzymes, and points to the need for further structural studies before we fully understand the subtleties of the shaping of the active site for complementarity to the cognate substrate.
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Affiliation(s)
- S M Zgiby
- School of Biochemistry and Molecular Biology, University of Leeds, Leeds, UK
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Yebra MJ, Veyrat A, Santos MA, Pérez-Martínez G. Genetics of L-sorbose transport and metabolism in Lactobacillus casei. J Bacteriol 2000; 182:155-63. [PMID: 10613875 PMCID: PMC94252 DOI: 10.1128/jb.182.1.155-163.2000] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genes encoding L-sorbose metabolism of Lactobacillus casei ATCC 393 have been identified on a 6.8-kb chromosomal DNA fragment. Sequence analysis revealed seven complete genes and a partial open reading frame transcribed as two units. The deduced amino acid sequences of the first transcriptional unit (sorRE) showed high similarity to the transcriptional regulator and the L-sorbose-1-phosphate reductase of the sorbose (sor) operon from Klebsiella pneumoniae. The other genes are transcribed as one unit (sorFABCDG) in opposite direction to sorRE. The deduced peptide sequence of sorF showed homology with the D-sorbitol-6-phosphate dehydrogenase encoded in the sor operon from K. pneumoniae and sorABCD to components of the mannose phosphotransferase system (PTS) family but especially to domains EIIA, EIIB, EIIC and EIID of the phosphoenolpyruvate-dependent L-sorbose PTS from K. pneumoniae. Finally, the deduced amino acid sequence of a truncated gene (sorG) located downstream of sorD presented high similarity with ketose-1,6-bisphosphate aldolases. Results of studies on enzyme activities and transcriptional analysis revealed that the two gene clusters, sorRE and sorFABCDG, are induced by L-sorbose and subject to catabolite repression by D-glucose. Data indicating that the catabolite repression is mediated by components of the PTS elements and by CcpA, are presented. Results of sugar uptake assays in L. casei wild-type and sorBC mutant strains indicated that L-sorbose is taken up by L-sorbose-specific enzyme II and that L. casei contains an inducible D-fructose-specific PTS. Results of growth analysis of those strains and a man sorBC double mutant suggested that L-sorbose is probably also transported by the D-mannose PTS. We also present evidence, from studies on a sorR mutant, suggesting that the sorR gene encodes a positive regulator of the two sor operons. Sequence alignment of SorR, SorC (K. pneumoniae), and DeoR (Bacillus subtilis) revealed that they might constitute a new group of transcriptional regulators.
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Affiliation(s)
- M J Yebra
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, CSIC, 46100 Burjassot, Spain
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Plumbridge J. Expression of the phosphotransferase system both mediates and is mediated by Mlc regulation in Escherichia coli. Mol Microbiol 1999; 33:260-73. [PMID: 10411743 DOI: 10.1046/j.1365-2958.1999.01462.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The ptsHIcrr operon encodes the cytoplasmic components of the phosphotransferase system (PTS). It is expressed from two major promoters, of which the upstream promoter has previously been shown to be induced by glucose and to be dependent upon cAMP/CAP. This promoter is now shown to be repressed by Mlc. Mlc is a transcriptional regulator controlling, among others, the gene ptsG, encoding EIICBGlc, the glucose-specific transporter of the PTS. Transcription of ptsH p0 and ptsG are subject to the same regulatory pattern. In addition to induction by glucose and repression by Mlc, mutations in ptsHIcrr, which interrupt the PEP-dependent phosphate transfer through the soluble components of the PTS, lead to high expression of both ptsH and ptsG, while mutations inactivating EIIBCGlc are non-inducible. Mutations in mlc lead to high constitutive expression and are dominant, implying that Mlc is the ultimate regulator of ptsHI and ptsG expression. Growth on other PTS sugars, besides glucose, also induces ptsH and ptsG expression, suggesting that the target of Mlc regulation is the PTS. However, induction by these other sugars is only observed in the presence of ptsG+, thus confirming the importance of glucose and EIICBGlc in the regulation of the PTS. The ptsG22 mutation, although negative for glucose transport, shows a weak positive regulatory phenotype. The mutation has been sequenced and its effect on regulation investigated.
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Affiliation(s)
- J Plumbridge
- Institut de Biologie Physico-chimique (UPR9073), 13, rue Pierre et Marie Curie, 75005 Paris, France.
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50
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Lamrani S, Ranquet C, Gama MJ, Nakai H, Shapiro JA, Toussaint A, Maenhaut-Michel G. Starvation-induced Mucts62-mediated coding sequence fusion: a role for ClpXP, Lon, RpoS and Crp. Mol Microbiol 1999; 32:327-43. [PMID: 10231489 DOI: 10.1046/j.1365-2958.1999.01352.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The formation of araB-lacZ coding sequence fusions in Escherichia coli is a particular type of chromosomal rearrangement induced by Mucts62, a thermoinducible mutant of mutator phage Mu. Fusion formation is controlled by the host physiology. It only occurs after aerobic carbon starvation and requires the phage-encoded transposase pA, suggesting that these growth conditions trigger induction of the Mucts62 prophage. Here, we show that thermal induction of the prophage accelerated araB-lacZ fusion formation, confirming that derepression is a rate-limiting step in the fusion process. Nonetheless, starvation conditions remained essential to complete fusions, suggesting additional levels of physiological regulation. Using a transcriptional fusion indicator system in which the Mu early lytic promoter is fused to the reporter E. coli lacZ gene, we confirmed that the Mucts62 prophage was derepressed in stationary phase (S derepression) at low temperature. S derepression did not apply to prophages that expressed the Mu wild-type repressor. It depended upon the host ClpXP and Lon ATP-dependent proteases and the RpoS stationary phase-specific sigma factor, but not upon Crp. None of these four functions was required for thermal induction. Crp was required for fusion formation, but only when the Mucts62 prophage encoded the transposition/replication activating protein pB. Finally, we found that thermally induced cultures did not return to the repressed state when shifted back to low temperature and, hence, remained activated for accelerated fusion formation upon starvation. The maintenance of the derepressed state required the ClpXP and Lon host proteases and the prophage Ner-regulatory protein. These observations illustrate how the cts62 mutation in Mu repressor provides the prophage with a new way to respond to growth phase-specific regulatory signals and endows the host cell with a new potential for adaptation through the controlled use of the phage transposition machinery.
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Affiliation(s)
- S Lamrani
- Laboratoire de Génétique des Procaryotes, Département de Biologie Moléculaire, Université Libre de Bruxelles, 67 rue des Chevaux, B1640 Rhode St Genèse, Belgium
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