Identification and characterization of the caiF gene encoding a potential transcriptional activator of carnitine metabolism in Escherichia coli

Eichler, Knut; Buchet, Anne; Lemke, Rainer; Kleber, Hans‐Peter; Mandrand‐Berthelot, Marie‐Andrée

doi:10.1128/jb.178.5.1248-1257.1996

Cited by 47 publications

(70 citation statements)

References 35 publications

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“…Besides autoregulation, it has been noticed in many cases (Dickson et al 1975;Eichler et al 1996;Palacios and Escalante-Semerena 2000;Torres et al 2003) that TFs and the genes they regulate are near each other in the genome. Both phenomena imply a distance constraint between the TF and its closest binding site in the genome.…”

Section: Resultsmentioning

confidence: 99%

Making connections between novel transcription factors and their DNA motifs

Tan¹,

McCue²,

Stormo³

2005

Genome Res.

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The key components of a transcriptional regulatory network are the connections between trans-acting transcription factors and cis-acting DNA-binding sites. In spite of several decades of intense research, only a fraction of the estimated ∼300 transcription factors in Escherichia coli have been linked to some of their binding sites in the genome. In this paper, we present a computational method to connect novel transcription factors and DNA motifs in E. coli. Our method uses three types of mutually independent information, two of which are gleaned by comparative analysis of multiple genomes and the third one derived from similarities of transcription-factor-DNA-binding-site interactions. The different types of information are combined to calculate the probability of a given transcription-factor-DNA-motif pair being a true pair. Tested on a study set of transcription factors and their DNA motifs, our method has a prediction accuracy of 59% for the top predictions and 85% for the top three predictions. When applied to 99 novel transcription factors and 70 novel DNA motifs, our method predicted 64 transcription-factor-DNA-motif pairs. Supporting evidence for some of the predicted pairs is presented. Functional annotations are made for 23 novel transcription factors based on the predicted transcription-factor-DNA-motif connections.

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Section: Resultsmentioning

confidence: 99%

Making connections between novel transcription factors and their DNA motifs

Tan¹,

McCue²,

Stormo³

2005

Genome Res.

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“…The lack of binding in vitro may be the result of different situations, including the possibility that GrlA may become inactive upon purification or that it requires another factor for DNA binding. Correlating with the second possibility, it has been shown that CaiF, the only characterized homologue of GrlA, binds more efficiently to the intergenic cai-fix regulatory region when CRP is present (3) and also counteracts H-NS repression (15). Furthermore, IHF has been shown to be essential for ler expression in EPEC (19) and for pCRler-cat fusion expression in E. coli K-12 (unpublished results), making it a candidate for acting synergistically with GrlA to activate ler expression.…”

Section: Discussionmentioning

confidence: 99%

“…The closest GrlA homologue is the putative product of an uncharacterized gene found in different Salmonella enterica serotypes. In addition, GrlA is 23% identical to CaiF, a regulatory protein responsible for the carnitine-dependent induction of the cai and fix E. coli operons under anaerobic conditions and the best-characterized member of this novel family of transcriptional regulators (15). A motif search of GrlA has also revealed the presence of a putative helix-turn-helix DNA binding motif at its N-terminal domain, where most of the similarity with CaiF and the Salmonella GrlA homologue (Sgh) is found (12).…”

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confidence: 99%

A Positive Regulatory Loop Controls Expression of the Locus of Enterocyte Effacement-Encoded Regulators Ler and GrlA

et al. 2005

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The formation of attaching and effacing (A/E) lesions on intestinal epithelial cells is an essential step in the pathogenesis of human enteropathogenic and enterohemorrhagic Escherichia coli and of the mouse pathogen Citrobacter rodentium. The genes required for the development of the A/E phenotype are located within a pathogenicity island known as the locus of enterocyte effacement (LEE). The LEE-encoded transcriptional regulators Ler, an H-NS-like protein, and GrlA, a member of a novel family of transcriptional activators, positively control the expression of the genes located in the LEE and their corresponding virulence. In this study, we used C. rodentium as a model to study the mechanisms controlling the expression of Ler and GrlA. By deletion analysis of the ler and grlRA regulatory regions and complementation experiments, negative and positive cis-acting regulatory motifs were identified that are essential for the regulation of both genes. This analysis confirmed that GrlA is required for the activation of ler, but it also showed that Ler is required for the expression of grlRA, revealing a novel regulatory loop controlling the optimal expression of virulence genes in A/E pathogens. Furthermore, our results indicate that Ler and GrlA induce the expression of each other by, at least in part, counteracting the repression mediated by H-NS. However, whereas GrlA is still required for the optimal expression of ler even in the absence of H-NS, Ler is not needed for the expression of grlRA in the absence of H-NS. This type of transcriptional positive regulatory loop represents a novel mechanism in pathogenic bacteria that is likely required to maintain an appropriate spatiotemporal transcriptional response during infection.Enteropathogenic Escherichia coli (EPEC), enterohemorrhagic E. coli (EHEC), and Citrobacter rodentium belong to a family of bacterial pathogens causing a destructive lesion of the intestinal enterocyte, called the attaching and effacing (A/E) lesion, as well as gastrointestinal disorders in infected hosts (reviewed in references 28 and 33). EPEC is an important etiological agent of childhood diarrhea in developing countries, whereas EHEC is the cause of frequent outbreaks of food and water poisoning in the developed world. In addition to causing diarrhea, an EHEC infection can result in severe complications, such as hemorrhagic colitis and hemolytic-uremic syndrome (reviewed in reference 33). Due to the specificity of EPEC and EHEC for human hosts, a corresponding small-animal infection model does not exist. Thus, most of the current models to explain EHEC and EPEC pathogen-host interactions, such as those for A/E lesion formation, have been developed based on in vitro studies performed with infected cultured epithelial cells. In recent years, C. rodentium has become accepted as a representative infection system to study the mechanisms leading to the production of the A/E lesion and A/E-associated pathogenesis (12, 13, 47).The A/E lesion is characterized by a localized loss of microvilli from ...

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“…In addition, it has been proposed that a positively controlled caiF gene, 3V adjacent region to the cai operon, acts as a specific transcriptional regulator for carnitine metabolism (Eichler et al, 1996). This pathway is detectable not only in cells previously grown anaerobically but also in some species, such as E. coli ATCC 25922 and DSM 8828, P. vulgaris, and P. mirabilis, grown under aerobiosis in the presence of inducers such as D,L (-)-carnitine mixture or crotonobetaine (Cánovas et al, 2002;Elssner et al, 2000;Kleber, 1997;Obón et al, 1999).…”

Section: E Coli Carnitine Metabolismmentioning

confidence: 99%

“…Genetic studies have been conducted to elucidate carnitine metabolism in E. coli O44 K74 (Kleber, 1997). Two divergent structural operons, caiTABCDE and fixABCX, are coexpressed, the former being responsible for the enzymes of carnitine metabolism and the latter being required to provide electrons for carnitine reduction (Eichler et al, 1996;Walt and Kahn, 2002). Although the pathway/genome database of E. coli is available (Karp et al, 2002), if the cell biochemistry and physiology to optimize this bioprocess is to be understood, it will be necessary to decipher the links, quantify the kinetics, and determine the regulatory structure of the metabolic pathways involved in the different scenarios, such as the reactor type used and the cell either in the growing or resting state.…”

Section: Introductionmentioning

confidence: 99%

Link between primary and secondary metabolism in the biotransformation of trimethylammonium compounds by escherichia coli

Cánovas

Bernal

Torroglosa

et al. 2003

Biotech & Bioengineering

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The aim of this work was to understand the steps controlling the process of biotransformation of trimethylamonium compounds into L(-)-carnitine by Escherichia coli and the link between the central carbon or primary and the secondary metabolism expressed. Thus, the enzyme activities involved in the biotransformation process of crotonobetaine into L(-)-carnitine (crotonobetaine hydration reaction and crotonobetaine reduction reaction), in the synthesis of acetyl-CoA (pyruvate dehydrogenase, acetyl-CoA synthetase, and ATP:acetate phosphotransferase) and in the distribution of metabolites for the tricarboxylic acid (isocitrate dehydrogenase) and glyoxylate (isocitrate lyase) cycles, were followed in batch with both growing and resting cells and during continuous cell growth in stirred-tank and high-cell-density membrane reactors. In addition, the levels of carnitine, crotonobetaine, gamma-butyrobetaine, ATP, NADH/NAD(+), and acetyl-CoA/CoA ratios were measured to determine how metabolic fluxes were distributed in the catabolic system. The results provide the first experimental evidence demonstrating the important role of the glyoxylate shunt during biotransformation of resting cells and the need for high levels of ATP to maintain metabolite transport and biotransformation (2.1 to 16.0 mmol L cellular/mmol ATP L reactor h). Moreover, the results obtained for the pool of acetyl-CoA/CoA indicate that it also correlated with the biotransformation process. The main metabolic pathway operating during cell growth in the high cell-density membrane reactor was that related to isocitrate dehydrogenase (during start-up) and isocitrate lyase (during steady-state operation), together with phosphotransacetylase and acetyl-CoA synthetase. More importantly, the link between central carbon and L(-)-carnitine metabolism at the level of the ATP pool was also confirmed.

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Identification and characterization of the caiF gene encoding a potential transcriptional activator of carnitine metabolism in Escherichia coli

Cited by 47 publications

References 35 publications

Making connections between novel transcription factors and their DNA motifs

Making connections between novel transcription factors and their DNA motifs

A Positive Regulatory Loop Controls Expression of the Locus of Enterocyte Effacement-Encoded Regulators Ler and GrlA

Link between primary and secondary metabolism in the biotransformation of trimethylammonium compounds by escherichia coli

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