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Chen Y, Ke W, Qin H, Chen S, Qin L, Yang Y, Yu H, Tan Y. Effect of dithiocyano-methane on hexose monophosphate pathway in the respiratory metabolism of Escherichia coli. AMB Express 2020; 10:205. [PMID: 33175252 PMCID: PMC7658277 DOI: 10.1186/s13568-020-01142-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/02/2020] [Indexed: 11/17/2022] Open
Abstract
This paper studied the inhibitory effects of dithiocyano-methane (DM) on the glucose decomposition pathway in the respiratory metabolism of Escherichia coli. We investigated the effects of DM on the activities of key enzymes (ATPase and glucose-6-phosphate dehydrogenase, G6PDH), the levels of key product (nicotinamide adenosine denucleotide hydro-phosphoric acid, NADPH), and gene expression in the hexose monophosphate pathway (HMP). The results showed that the minimum inhibitory concentration (MIC) and the minimum bactericide concentration (MBC) of DM against the tested strains were 5.86 mg/L and 11.72 mg/L, respectively. Bacteria exposed to DM at MIC demonstrated an increase in bacterial ATPase and G6PDH activities, NADPH levels, and gene expression in the HMP pathway compared to bacteria in the control group, which could be interpreted as a behavioral response to stress introduced by DM. However, DM at a lethal concentration of 10 × MIC affected glucose decomposition by inhibiting mainly the HMP pathway in E. coli.
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Shaw JA, Henard CA, Liu L, Dieckman LM, Vázquez-Torres A, Bourret TJ. Salmonella enterica serovar Typhimurium has three transketolase enzymes contributing to the pentose phosphate pathway. J Biol Chem 2018; 293:11271-11282. [PMID: 29848552 DOI: 10.1074/jbc.ra118.003661] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/23/2018] [Indexed: 11/06/2022] Open
Abstract
The genus Salmonella is responsible for many illnesses in humans and other vertebrate animals. We report here that Salmonella enterica serovar Typhimurium harbors three transketolases that support the non-oxidative branch of the pentose phosphate pathway. BLAST analysis identified two genes, STM14_2885 and STM14_2886, that together encode a putative transketolase (TktC) with 46-47% similarity to the known TktA and TktB isoforms. Assessing the mRNA and protein expression for each of the three transketolases, we determined that all are expressed in WT cells and regulated to varying extents by the alternative sigma factor RpoS. Enzyme assays with lysates from WT and transketolase-knockout strains established that TktA is responsible for >88% of the transketolase activity in WT cells. We purified recombinant forms of each isoenzyme to assess the kinetics for canonical transketolase reactions. TktA and TktB had comparable values for Vmax (539-1362 μm NADH consumed/s), Km (80-739 μm), and catalytic efficiency (1.02 × 108-1.06 × 109 m-1/s) for each substrate tested. The recombinant form of TktC had lower Km values (23-120 μm), whereas the Vmax (7.8-16 μm NADH consumed/s) and catalytic efficiency (5.58 × 106 to 6.07 × 108 m-1/s) were 10-100-fold lower. Using a murine model of Salmonella infection, we showed that a strain lacking all three transketolases is avirulent in C57BL/6 mice. These data provide evidence that S Typhimurium possesses three transketolases that contribute to pathogenesis.
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Affiliation(s)
- Jeff A Shaw
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska 68178
| | - Calvin A Henard
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado 80011
| | - Lin Liu
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado 80011
| | - Lynne M Dieckman
- Department of Chemistry, Creighton University, Omaha, Nebraska 68178
| | - Andrés Vázquez-Torres
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado 80011; Veterans Affairs Eastern Colorado Health Care System, Denver, Colorado 80220
| | - Travis J Bourret
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, Nebraska 68178.
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Golubeva LI, Shupletsov MS, Mashko SV. Metabolic Flux Analysis Using 13C Isotopes (13C-MFA). 1. Experimental Basis of the Method and the Present State of Investigations. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683817070031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Dumpala PR, Lawrence ML, Karsi A. Identification of Differentially Regulated Edwardsiella ictaluri Proteins During Catfish Serum Treatment. JOURNAL OF AQUATIC ANIMAL HEALTH 2018; 30:50-56. [PMID: 29595885 DOI: 10.1002/aah.10007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 11/20/2017] [Indexed: 06/08/2023]
Abstract
Edwardsiella ictaluri is a facultative, intracellular, gram-negative bacterium that causes enteric septicemia of catfish (ESC). Edwardsiella ictaluri is known to be resistant to defense mechanisms present in catfish serum, which might aid in its use of a host's bloodstream to become septicemic. However, the precise mechanisms of the survival of E. ictaluri in host serum are not known. Analysis of the response of E. ictaluri to the host serum treatment at a proteomic level might aid in the elucidation of its adaptation mechanisms against defense mechanisms present in catfish serum. Thus, the objective of this study was to identify differentially regulated proteins of E. ictaluri upon exposure to naïve catfish serum. Two-dimensional difference gel electrophoresis (2D-DIGE) followed by in-gel trypsin digestion and MALDI-TOF/TOF analysis were used for identification of differentially expressed E. ictaluri proteins. A total of 19 differentially regulated proteins (7 up- and 12 downregulated) were identified. Among those were four putative immunogenic proteins, two chaperones and eight proteins involved in the translational process, two nucleic acid degradation and integration proteins, two intermediary metabolism proteins, and one iron-ion-binding protein. Further research focusing on the functions of these differentially expressed proteins may reveal their roles in host adaptation by E. ictaluri.
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Affiliation(s)
- Pradeep R Dumpala
- The Rogosin Institute-Xenia Division, 740 Birch Road, Xenia, Ohio, 45385, USA
| | - Mark L Lawrence
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, 39762, USA
| | - Attila Karsi
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, Mississippi, 39762, USA
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Maravić A, Cvjetan S, Konta M, Ladouce R, Martín FA. Proteomic response of β-lactamases-producing Enterobacter cloacae complex strain to cefotaxime-induced stress. Pathog Dis 2016; 74:ftw045. [PMID: 27162211 DOI: 10.1093/femspd/ftw045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2016] [Indexed: 11/14/2022] Open
Abstract
Bacteria of the Enterobacter cloacae complex are among the ten most common pathogens causing nosocomial infections in the USA. Consequently, increased resistance to β-lactam antibiotics, particularly expanded-spectrum cephalosporins like cefotaxime (CTX), poses a serious threat. Differential In-Gel Electrophoresis (DIGE), followed by LC-MS/MS analysis and bioinformatics tools, was employed to investigate the survival mechanisms of a multidrug-resistant E. hormaechei subsp. steigerwaltii 51 carrying several β-lactamase-encoding genes, including the 'pandemic' blaCTX-M-15 After exposing the strain with sub-minimal inhibitory concentration (MIC) of CTX, a total of 1072 spots from the whole-cell proteome were detected, out of which 35 were differentially expressed (P ≤ 0.05, fold change ≥1.5). Almost 50% of these proteins were involved in cell metabolism and energy production, and then cell wall organization/virulence, stress response and transport. This is the first study investigating the whole-cell proteomic response related to the survival of β-lactamases-producing strain, belonging to the E. cloacae complex when exposed to β-lactam antibiotic. Our data support the theory of a multifactorial synergistic effect of diverse proteomic changes occurring in bacterial cells during antibiotic exposure, depicting the complexity of β-lactam resistance and giving us an insight in the key pathways mediating the antibiotic resistance in this emerging opportunistic pathogen.
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Affiliation(s)
- Ana Maravić
- Department of Biology, Faculty of Science, University of Split, Teslina 12, 21000 Split, Croatia
| | - Svjetlana Cvjetan
- Department of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia Mediterranean Institute for Life Sciences, Meštovićevo šetalište 45, 21000 Split, Croatia
| | - Marina Konta
- Mediterranean Institute for Life Sciences, Meštovićevo šetalište 45, 21000 Split, Croatia
| | - Romain Ladouce
- Mediterranean Institute for Life Sciences, Meštovićevo šetalište 45, 21000 Split, Croatia
| | - Fernando A Martín
- Mediterranean Institute for Life Sciences, Meštovićevo šetalište 45, 21000 Split, Croatia
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Vimala A, Harinarayanan R. Transketolase activity modulates glycerol-3-phosphate levels inEscherichia coli. Mol Microbiol 2016; 100:263-77. [DOI: 10.1111/mmi.13317] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2015] [Indexed: 11/30/2022]
Affiliation(s)
- A. Vimala
- Laboratory of Bacterial Genetics; Center for DNA Fingerprinting and Diagnostics; Hyderabad 500 001 India
| | - R. Harinarayanan
- Laboratory of Bacterial Genetics; Center for DNA Fingerprinting and Diagnostics; Hyderabad 500 001 India
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Du Z, Nandakumar R, Nickerson KW, Li X. Proteomic adaptations to starvation prepare Escherichia coli for disinfection tolerance. WATER RESEARCH 2015; 69:110-119. [PMID: 25463932 PMCID: PMC4351261 DOI: 10.1016/j.watres.2014.11.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 11/10/2014] [Accepted: 11/12/2014] [Indexed: 05/10/2023]
Abstract
Despite the low nutrient level and constant presence of secondary disinfectants, bacterial re-growth still occurs in drinking water distribution systems. The molecular mechanisms that starved bacteria use to survive low-level chlorine-based disinfectants are not well understood. The objective of this study is to investigate these molecular mechanisms at the protein level that prepare starved cells for disinfection tolerance. Two commonly used secondary disinfectants chlorine and monochloramine, both at 1 mg/L, were used in this study. The proteomes of normal and starved Escherichia coli (K12 MG1655) cells were studied using quantitative proteomics. Over 60-min disinfection, starved cells showed significantly higher disinfection tolerance than normal cells based on the inactivation curves for both chlorine and monochloramine. Proteomic analyses suggest that starvation may prepare cells for the oxidative stress that chlorine-based disinfection will cause by affecting glutathione metabolism. In addition, proteins involved in stress regulation and stress responses were among the ones up-regulated under both starvation and chlorine/monochloramine disinfection. By comparing the fold changes under different conditions, it is suggested that starvation prepares E. coli for disinfection tolerance by increasing the expression of enzymes that can help cells survive chlorine/monochloramine disinfection. Protein co-expression analyses show that proteins in glycolysis and pentose phosphate pathway that were up-regulated under starvation are also involved in disinfection tolerance. Finally, the production and detoxification of methylglyoxal may be involved in the chlorine-based disinfection and cell defense mechanisms.
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Affiliation(s)
- Zhe Du
- Department of Civil Engineering, University of Nebraska-Lincoln, USA
| | - Renu Nandakumar
- Proteomics and Metabolomics Core Facility, Redox Biology Center, Department of Biochemistry, University of Nebraska-Lincoln, USA
| | | | - Xu Li
- Department of Civil Engineering, University of Nebraska-Lincoln, USA.
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Yoshida M, Tsuru S, Hirata N, Seno S, Matsuda H, Ying BW, Yomo T. Directed evolution of cell size in Escherichia coli. BMC Evol Biol 2014; 14:257. [PMID: 25514845 PMCID: PMC4279887 DOI: 10.1186/s12862-014-0257-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 11/27/2014] [Indexed: 11/16/2022] Open
Abstract
Background In bacteria, cell size affects chromosome replication, the assembly of division machinery, cell wall synthesis, membrane synthesis and ultimately growth rate. In addition, cell size can also be a target for Darwinian evolution for protection from predators. This strong coupling of cell size and growth, however, could lead to the introduction of growth defects after size evolution. An important question remains: can bacterial cell size change and/or evolve without imposing a growth burden? Results The directed evolution of particular cell sizes, without a growth burden, was tested with a laboratory Escherichia coli strain. Cells of defined size ranges were collected by a cell sorter and were subsequently cultured. This selection-propagation cycle was repeated, and significant changes in cell size were detected within 400 generations. In addition, the width of the size distribution was altered. The changes in cell size were unaccompanied by a growth burden. Whole genome sequencing revealed that only a few mutations in genes related to membrane synthesis conferred the size evolution. Conclusions In conclusion, bacterial cell size could evolve, through a few mutations, without growth reduction. The size evolution without growth reduction suggests a rapid evolutionary change to diverse cell sizes in bacterial survival strategies. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0257-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mari Yoshida
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Saburo Tsuru
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Naoko Hirata
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Shigeto Seno
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Hideo Matsuda
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Bei-Wen Ying
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
| | - Tetsuya Yomo
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,Graduate School of Frontier Biosciences, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Agency (JST), Suita, Osaka, 565-0871, Japan. .,Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.
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Shimizu K. Metabolic Regulation of a Bacterial Cell System with Emphasis on Escherichia coli Metabolism. ISRN BIOCHEMISTRY 2013; 2013:645983. [PMID: 25937963 PMCID: PMC4393010 DOI: 10.1155/2013/645983] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 10/25/2012] [Indexed: 12/19/2022]
Abstract
It is quite important to understand the overall metabolic regulation mechanism of bacterial cells such as Escherichia coli from both science (such as biochemistry) and engineering (such as metabolic engineering) points of view. Here, an attempt was made to clarify the overall metabolic regulation mechanism by focusing on the roles of global regulators which detect the culture or growth condition and manipulate a set of metabolic pathways by modulating the related gene expressions. For this, it was considered how the cell responds to a variety of culture environments such as carbon (catabolite regulation), nitrogen, and phosphate limitations, as well as the effects of oxygen level, pH (acid shock), temperature (heat shock), and nutrient starvation.
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Affiliation(s)
- Kazuyuki Shimizu
- Kyushu Institute of Technology, Fukuoka, Iizuka 820-8502, Japan
- Institute of Advanced Bioscience, Keio University, Yamagata, Tsuruoka 997-0017, Japan
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Tuntufye HN, Gwakisa PS, Goddeeris BM. In silico analysis of tkt1 from avian pathogenic Escherichia coli and its virulence evaluation in chickens. Res Microbiol 2013; 164:310-8. [PMID: 23376541 DOI: 10.1016/j.resmic.2013.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 11/19/2012] [Indexed: 12/13/2022]
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) contain tktA and tktB which code for transketolases involved in the pentose phosphate pathway. Recent studies demonstrated that a third gene coding for transketolase 1 (tkt1) was located in a pathogenicity island of avian and human ExPEC belonging to phylogenetic group B2. In the present study, in silico analysis of tkt1 revealed 68% and 69% identity with tktA and tktB, respectively, of ExPEC and 68% identity with tktA and tktB of E. coli MG1655. The translated tkt1 shared 69% and 68% identity with TktA and TktB proteins, respectively, of ExPEC and E. coli MG1655. Phylogenetically, it is shown that the three genes (tktA, tktB and tkt1) cluster in three different clades. Further analysis suggests that tkt1 has been acquired though horizontal gene transfer from plant-associated bacteria within the family Enterobacteriaceae. Virulence studies were performed in order to evaluate whether tkt1 played a role in avian pathogenic E. coli CH2 virulence in chickens. The evaluation revealed that mutant virulence was slightly lower based on LD50 when compared to the wild type during infection of chickens, but there were no significant differences when the two strains were compared based on the number of deaths and lesion scores.
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Affiliation(s)
- Huruma Nelwike Tuntufye
- Department of Biosystems, Faculty of Bioscience Engineering, University of Leuven (KU Leuven), Kasteelpark Arenberg 30, B-3001 Heverlee, Belgium.
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Singh P, Batth TS, Juminaga D, Dahl RH, Keasling JD, Adams PD, Petzold CJ. Application of targeted proteomics to metabolically engineered Escherichia coli. Proteomics 2012; 12:1289-99. [PMID: 22577029 DOI: 10.1002/pmic.201100482] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 12/13/2011] [Indexed: 11/09/2022]
Abstract
As synthetic biology matures to compete with chemical transformation of commodity and high-value compounds, a wide variety of well-characterized biological parts are needed to facilitate system design. Protein quantification based on selected-reaction monitoring (SRM) mass spectrometry compliments metabolite and transcript analysis for system characterization and optimizing flux through engineered pathways. By using SRM quantification, we assayed red fluorescent protein (RFP) expressed from plasmids containing several inducible and constitutive promoters and subsequently assessed protein production from the same promoters driving expression of eight mevalonate pathway proteins in Escherichia coli. For each of the promoter systems, the protein level for the first gene in the operon followed that of RFP, however, the levels of proteins produced from genes farther from the promoter were much less consistent. Second, we used targeted proteomics to characterize tyrosine biosynthesis pathway proteins after removal of native regulation. The changes were not expected to cause significant impact on protein levels, yet significant variation in protein abundance was observed and tyrosine production for these strains spanned a range from less than 1 mg/L to greater than 250 mg/L. Overall, our results underscore the importance of targeted proteomics for determining accurate protein levels in engineered systems and fine-tuning metabolic pathways.
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Affiliation(s)
- Pragya Singh
- Joint BioEnergy Institute, Emeryville, CA 94608, USA
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12
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Toward systematic metabolic engineering based on the analysis of metabolic regulation by the integration of different levels of information. Biochem Eng J 2009. [DOI: 10.1016/j.bej.2009.06.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Harinarayanan R, Murphy H, Cashel M. Synthetic growth phenotypes of Escherichia coli lacking ppGpp and transketolase A (tktA) are due to ppGpp-mediated transcriptional regulation of tktB. Mol Microbiol 2008; 69:882-94. [PMID: 18532980 DOI: 10.1111/j.1365-2958.2008.06317.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Many physiological adjustments to nutrient changes involve ppGpp. Recent attempts to deduce ppGpp regulatory effects using proteomics or gene profiling can rigorously identify proteins or transcripts, but the functional significance is often unclear. Using a random screen for synthetic lethals we found a ppGpp-dependent functional pathway that operates through transketolase B (TktB), and which is 'buffered' in wildtype strain by the presence of an isozyme, transketolase A (TktA). Transketolase activity is required in cells to make erythrose-4-phosphate, a precursor of aromatic amino acids and vitamins. By studying tktB-dependent nutritional requirements as well as measuring activities using PtalA-tktB'-lacZ transcriptional reporter fusion, we show positive transcriptional regulation of the talA-tktB operon by ppGpp. Our results show the existence of RpoS-dependent and RpoS-independent modes of positive regulation by ppGpp. Both routes of activation are magnified by elevating ppGpp levels with a spoT mutation (spoT-R39A) defective in hydrolase but not synthetase activity or with the stringent suppressor mutations rpoB-A532Delta or rpoB-T563P in the absence of ppGpp.
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Affiliation(s)
- Rajendran Harinarayanan
- Laboratory of Molecular Genetics, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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Lintner RE, Mishra PK, Srivastava P, Martinez-Vaz BM, Khodursky AB, Blumenthal RM. Limited functional conservation of a global regulator among related bacterial genera: Lrp in Escherichia, Proteus and Vibrio. BMC Microbiol 2008; 8:60. [PMID: 18405378 PMCID: PMC2374795 DOI: 10.1186/1471-2180-8-60] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Accepted: 04/11/2008] [Indexed: 02/03/2023] Open
Abstract
Background Bacterial genome sequences are being determined rapidly, but few species are physiologically well characterized. Predicting regulation from genome sequences usually involves extrapolation from better-studied bacteria, using the hypothesis that a conserved regulator, conserved target gene, and predicted regulator-binding site in the target promoter imply conserved regulation between the two species. However many compared organisms are ecologically and physiologically diverse, and the limits of extrapolation have not been well tested. In E. coli K-12 the leucine-responsive regulatory protein (Lrp) affects expression of ~400 genes. Proteus mirabilis and Vibrio cholerae have highly-conserved lrp orthologs (98% and 92% identity to E. coli lrp). The functional equivalence of Lrp from these related species was assessed. Results Heterologous Lrp regulated gltB, livK and lrp transcriptional fusions in an E. coli background in the same general way as the native Lrp, though with significant differences in extent. Microarray analysis of these strains revealed that the heterologous Lrp proteins significantly influence only about half of the genes affected by native Lrp. In P. mirabilis, heterologous Lrp restored swarming, though with some pattern differences. P. mirabilis produced substantially more Lrp than E. coli or V. cholerae under some conditions. Lrp regulation of target gene orthologs differed among the three native hosts. Strikingly, while Lrp negatively regulates its own gene in E. coli, and was shown to do so even more strongly in P. mirabilis, Lrp appears to activate its own gene in V. cholerae. Conclusion The overall similarity of regulatory effects of the Lrp orthologs supports the use of extrapolation between related strains for general purposes. However this study also revealed intrinsic differences even between orthologous regulators sharing >90% overall identity, and 100% identity for the DNA-binding helix-turn-helix motif, as well as differences in the amounts of those regulators. These results suggest that predicting regulation of specific target genes based on genome sequence comparisons alone should be done on a conservative basis.
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Affiliation(s)
- Robert E Lintner
- Department of Medical Microbiology and Immunology, University of Toledo Health Sciences Center, Toledo, OH 43614-2598, USA.
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Rahman M, Shimizu K. Altered acetate metabolism and biomass production in several Escherichia coli mutants lacking rpoS-dependent metabolic pathway genes. MOLECULAR BIOSYSTEMS 2007; 4:160-9. [PMID: 18213409 DOI: 10.1039/b712023k] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The stress responsive sigma factor RpoS regulates the expression of tktB and talAgenes of the non-oxidative pentose phosphate (PP) pathway, and fumCand acnA genes of the TCA cycle at the stationary phase of growth. In the present study, batch cultivations were performed using tktB, talA, fumC or acnA-knockout mutants of Escherichia coli to observe the metabolic changes at different phases of growth compared to the wild type strain. Although the specific growth rates of the mutants were similar to the wild type, acetate yield was nearly half in all mutants except the acnA mutant. Altered acetate yield in the mutants was also accompanied by variations in the biomass yield. While the biomass yield in both the tktB and talA mutants was increased by 13.8%, biomass was 5.5% and 13.8% lower in the fumC and acnA mutants, respectively. Upregulation of global regulators such as rpoS and soxRS, the acs, aceA, aceB genes, and several TCA cycle genes such as fumC, acnA and sucA, is consistent with higher acetate consumption and biomass yield in the tktB and talA mutants. On the other hand, the fumC and acnA mutants, with their impaired TCA cycles, were unable to utilize acetate for biomass production in spite of the higher expression of rpoS and soxRS.
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Affiliation(s)
- Mahbuba Rahman
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and System Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
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Domain F, Bina XR, Levy SB. Retracted: Transketolase A, an enzyme in central metabolism, derepresses themarRABmultiple antibiotic resistance operon ofEscherichia coliby interaction with MarR. Mol Microbiol 2007; 66:383-94. [PMID: 17850260 DOI: 10.1111/j.1365-2958.2007.05928.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Escherichia coli marRAB operon specifies two regulatory proteins, MarR (which represses) and MarA (which activates expression of the operon). The latter controls expression of multiple other chromosomal genes implicated in cell physiology, multiple drug resistance and virulence. Using randomly cloned E. coli DNA fragments in the bacterial adenylate cyclase two-hybrid system, we found that transketolase A (TktA) interacts with MarR. Purified (6H)-TktA immobilized on NiNTA resin-bound MarR. Overexpression or deletion of tktA showed that TktA interfered with MarR repression of the marRAB operon. Deletion of tktA increased antibiotic and oxidative stress susceptibilities, while its overexpression decreased them. Hydrogen peroxide induced tktA at 1 h treatment, while an increase in marRAB expression occurred only after 3 h exposure. This increase was dependent on the presence of tktA. Two MarR mutations which eliminated MarR binding to the marRAB operator and one which decreased dimerization of MarR had no effect on MarR interaction with TktA in the two-hybrid system. However, the interaction was disrupted by one of the three tested superrepressor mutant MarR proteins known to increase MarR binding to DNA. TktA inhibition of repression by MarR demonstrates a previously unrecognized level of control of the expression of marRAB operon.
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Affiliation(s)
- Francis Domain
- Center for Adaptation Genetics and Drug Resistance, Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA
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