An Allele of
            <i>gyrA</i>
            Prevents
            <i>Salmonella enterica</i>
            Serovar Typhimurium from Using Succinate as a Carbon Source

Schmitz, George E.; Downs, Diana M.

doi:10.1128/jb.188.8.3126-3129.2006

Cited by 4 publications

(5 citation statements)

References 31 publications

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“…A mutant allele of the essential gene gyrA , which encodes part of the DNA gyrase complex, was identified by a positive selection for metabolic function. Further analysis showed that the variant protein resulted in reduced negative supercoiling [69] and changed expression of almost every gene tested. No single gene could be identified as the cause of the phenotype.…”

Section: Increased Accumulation Of Pra Identifies New Metabolic Linksmentioning

confidence: 99%

Thiamine biosynthesis can be used to dissect metabolic integration

Koenigsknecht

Downs

2010

Trends in Microbiology

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The emergence of systems biology has reemphasized the advantages of understanding biological processes with a global perspective. One biological process amenable to global approaches is microbial metabolism. This review describes a model system that contributes to the goals of systems biology by experimentally defining metabolic integration found in a bacterial cell and thus providing data needed for implementation and interpretation of systems approaches. We have taken a largely unbiased in vivo approach centered on thiamine biosynthesis to identify new metabolic components and connections and explore uncharacterized paradigms of the integration amongst them. This article summarizes recent results from this approach that include the identification of the function of unknown genes, connections between cofactors biosynthesis and thiamine biosynthesis, and how metabolites from one biosynthetic pathway can be used in thiamine biosynthesis.

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Section: Increased Accumulation Of Pra Identifies New Metabolic Linksmentioning

confidence: 99%

Thiamine biosynthesis can be used to dissect metabolic integration

Koenigsknecht

Downs

2010

Trends in Microbiology

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“…It was noted that the growth rate of the sgrR1-carrying strain with thiamine was less than the growth rate of the parental strain (0.33 Ϯ 0.01 h Ϫ1 ). This result suggested that the suppressing mutations carried a fitness cost to the strains on glucose medium, a result not atypical when the metabolic network is remodeled to compensate for a perturbation or to generate a new function (40)(41)(42)(43)(44).…”

Section: Resultsmentioning

confidence: 89%

Induction of the Sugar-Phosphate Stress Response Allows Saccharomyces cerevisiae 2-Methyl-4-Amino-5-Hydroxymethylpyrimidine Phosphate Synthase To Function in Salmonella enterica

2015

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Thiamine pyrophosphate is a required cofactor for all forms of life. The pyrimidine moiety of thiamine, 2-methyl-4-amino-5-hydroxymethylpyrimidine phosphate (HMP-P), is synthesized by different mechanisms in bacteria and plants compared to fungi. In this study, Salmonella enterica was used as a host to probe requirements for activity of the yeast HMP-P synthase, Thi5p. Thi5p synthesizes HMP-P from histidine and pyridoxal-5-phosphate and was reported to use a backbone histidine as the substrate, which would mean that it was a single-turnover enzyme. Heterologous expression of Thi5p did not complement an S. enterica HMP-P auxotroph during growth with glucose as the sole carbon source. Genetic analyses described here showed that Thi5p was activated in S. enterica by alleles of sgrR that induced the sugar-phosphate stress response. Deletion of ptsG (encodes enzyme IICB [EIICB] of the phosphotransferase system [PTS]) also allowed function of Thi5p and required sgrR but not sgrS. This result suggested that the role of sgrS in activation of Thi5p was to decrease PtsG activity. In total, the data herein supported the hypothesis that one mechanism to activate Thi5p in S. enterica grown on minimal medium containing glucose (minimal glucose medium) required decreased PtsG activity and an unidentified gene regulated by SgrR. IMPORTANCEThis work describes a metabolic link between the sugar-phosphate stress response and the yeast thiamine biosynthetic enzyme Thi5p when heterologously expressed in Salmonella enterica during growth on minimal glucose medium. Suppressor analysis (i) identified a mutant class of the regulator SgrR that activate sugar-phosphate stress response constitutively and (ii) determined that Thi5p is conditionally active in S. enterica. These results emphasized the power of genetic systems in model organisms to uncover enzyme function and underlying metabolic network structure.T hiamine pyrophosphate (TPP) is a cofactor for many central metabolic enzymes and is required at low levels by all organisms. Humans require dietary intake of thiamine, which is biosynthesized by a variety of plants, bacteria, and fungi. TPP is composed of two independently synthesized moieties, 5-(2-hydroxyethyl)-4-methylthiazole phosphate (THZ-P) and 2-methyl-4-amino-5-hydroxymethylpyrimidine phosphate (HMP-P). In bacteria and plants, the first steps of the HMP-P biosynthesis pathway are shared with purine biosynthesis (Fig. 1) (1-3). In these organisms, the radical S-adenosylmethionine (SAM) enzyme ThiC catalyzes an intramolecular rearrangement of the purine intermediate 5-aminoimidazole ribotide (AIR) to the pyrimidine HMP-P (4, 5).In contrast, fungi do not contain a ThiC homolog; under aerobic conditions, HMP-P is synthesized by the Thi5p enzyme family. In vivo labeling in yeast implicated histidine and pyridoxine as precursors to HMP-P biosynthesis under aerobic conditions ( , and other species have between zero and five copies of this gene (9). Genetic analysis in S. cerevisiae demonstrated that the four enzymes are f...

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“…For instance, microarray studies monitoring expression of genes by mutation or environmental perturbation require a change in expression greater than twofold to be considered relevant. This cutoff reflects a technical rather than a biological definition of relevance because changes in expression and/or activity of less than twofold can have significant consequences on metabolism (18,35,86,125).…”

Section: Genomic/bioinformatics Approachesmentioning

confidence: 99%

“…The integrated nature of complex systems allows perturbations in one area to radiate and possibly amplify their effect in other areas distant from the site of initial impact (66a). Small changes in gene expression, flux distribution, or enzyme activity exert largemagnitude changes on the growth phenotype (i.e., metabolism) of the organism (35,40,58,86,125). These examples emphasize the need to probe a phenotype without a bias for the magnitude of change that caused the effect.…”

Section: Small-flux Changes Can Be Amplifiedmentioning

confidence: 99%

“…Such mutations can change a phenotype by altering the function of a protein or, alternatively, causing metabolic rerouting. When selecting for suppression of a defect, one can find examples in which the suppressing mutation directly mediates a change (i.e., an altered enzymatic activity that can provide a missing product) (115), or a mutation that indirectly mediates the suppression (i.e., a change in a global gene expression that compensates on a system-wide level) (35,125). Often a repeating cycle of isolating gain-and loss-offunction mutations can result in significant metabolic insight.…”

Section: Expanding Our Understanding Of the Network Through Suppressomentioning

confidence: 99%

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Understanding Microbial Metabolism

Downs

2006

Annu. Rev. Microbiol.

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Metabolism encompasses the biochemical basis of life and as such spans all biological disciplines. Many decades of basic research, primarily in microbes, have resulted in extensive characterization of metabolic components and regulatory paradigms. With this basic knowledge in hand and the technologies currently available, it has become feasible to move toward an understanding of microbial metabolism as a system rather than as a collection of component parts. Insight into the system will be generated by continued efforts to rigorously define metabolic components combined with renewed efforts to discover components and connections using in vivo-driven approaches. On the tail of a detailed understanding of components and connections that comprise metabolism will come the ability to generate a comprehensive mathematical model that describes the system. While microbes provide the logical organism for this work, the value of such a model would span biological disciplines. Described herein are approaches that can provide insight into metabolism and caveats of their use. The goal of this review is to emphasize that in silico, in vitro, and in vivo approaches must be used in combination to achieve a full understanding of microbial metabolism.

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An Allele of gyrA Prevents Salmonella enterica Serovar Typhimurium from Using Succinate as a Carbon Source

Cited by 4 publications

References 31 publications

Thiamine biosynthesis can be used to dissect metabolic integration

Thiamine biosynthesis can be used to dissect metabolic integration

Induction of the Sugar-Phosphate Stress Response Allows Saccharomyces cerevisiae 2-Methyl-4-Amino-5-Hydroxymethylpyrimidine Phosphate Synthase To Function in Salmonella enterica

Understanding Microbial Metabolism

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