Factors affecting transcriptional regulation of the formate-hydrogen-lyase pathway of Escherichia coli

Birkmann, A; Zinoni, F; Sawers, R. Gary; Böck, August

doi:10.1007/bf00429646

Cited by 100 publications

(85 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Under anaerobic conditions, E. coli synthesizes some or all of the three HYD isoenzymes, depending on the growth medium (5,44). HYD 2 catalyzes the oxidation of hydrogen, while HYD 3 and 1 are responsible for production and recycling of hydrogen during fermentative growth, respectively.…”

Section: Resultsmentioning

confidence: 99%

Osmotic repression of anaerobic metabolic systems in Escherichia coli

Gouesbet

Abaibou

et al. 1993

J Bacteriol

View full text Add to dashboard Cite

The influence of the osmolarity of the growth medium on anaerobic fermentation and nitrate respiratory pathways was analyzed. The levels of several enzymes, including formate dehydrogenase, hydrogenase, and nitrate reductase, plus a nickel uptake system were examined, as was the expression of the corresponding structural and regulatory genes. While some functions appear to be only moderately affected by an increase in osmolarity, others were found to vary considerably. An increase in the osmolarity of the medium inhibits both fermentation and anaerobic respiratory pathways, though in a more dramatic fashion for the former. fnr expression is affected by osmolarity, but the repression of anaerobic gene expression was shown to be independent of FNR regulatory protein, at least for hyd-17 andfdhF. This repression could be mediated by the intracellular concentration of potassium and is reversed by glycine betaine.

show abstract

Section: Resultsmentioning

confidence: 99%

Osmotic repression of anaerobic metabolic systems in Escherichia coli

Gouesbet

Abaibou

et al. 1993

J Bacteriol

View full text Add to dashboard Cite

show abstract

“…Theoretically, maximum flux through Equation 1 would result in four formic acid molecules per glucose, a twofold yield increase compared to PFL-catalyzed reactions associated with mixed acid fermentation in E. coli (Birkmann et al 1987). This may have important biotechnological applications for biofuel production.…”

Section: Pathway Analysis Of C1 Metabolism In Yeastmentioning

confidence: 99%

“…Formic acid is used commercially as a preservative in animal feed and has a potential use as a precursor to hydrogen, since it is one of only a few biological molecules with sufficient reducing potential (Milliken and May 2007). The main pathway for biohydrogen production during mixed acid fermentation in Escherichia coli proceeds through a formic acid intermediate: a product of the reaction catalyzed by pyruvate formate lyase (PFL) (EC 2.3.1.54) (Birkmann et al 1987).…”

mentioning

confidence: 99%

Systems-Level Engineering of Nonfermentative Metabolism in Yeast

Kennedy

Boyle²,

Waks

et al. 2009

Genetics

View full text Add to dashboard Cite

We designed and experimentally validated an in silico gene deletion strategy for engineering endogenous one-carbon (C1) metabolism in yeast. We used constraint-based metabolic modeling and computer-aided gene knockout simulations to identify five genes (ALT2, FDH1, FDH2, FUM1, and ZWF1), which, when deleted in combination, predicted formic acid secretion in Saccharomyces cerevisiae under aerobic growth conditions. Once constructed, the quintuple mutant strain showed the predicted increase in formic acid secretion relative to a formate dehydrogenase mutant ( fdh1 fdh2), while formic acid secretion in wild-type yeast was undetectable. Gene expression and physiological data generated post hoc identified a retrograde response to mitochondrial deficiency, which was confirmed by showing Rtg1-dependent NADH accumulation in the engineered yeast strain. Formal pathway analysis combined with gene expression data suggested specific modes of regulation that govern C1 metabolic flux in yeast. Specifically, we identified coordinated transcriptional regulation of C1 pathway enzymes and a positive flux control coefficient for the branch point enzyme 3-phosphoglycerate dehydrogenase (PGDH).Together, these results demonstrate that constraint-based models can identify seemingly unrelated mutations, which interact at a systems level across subcellular compartments to modulate flux through nonfermentative metabolic pathways.

show abstract

“…Several factors regulate FHL complex synthesis (22,125). Low pH and formate induce its synthesis, while oxygen, nitrate, and glucose repress it (138).…”

Section: -Dependent Genes That Are Not Involved In Nitrogen Metabolismentioning

confidence: 99%

Metabolic Context and Possible Physiological Themes of ς⁵⁴-Dependent Genes inEscherichia coli

Reitzer

Schneider

2001

Microbiol Mol Biol Rev

253

300

View full text Add to dashboard Cite

SUMMARY ς54 has several features that distinguish it from other sigma factors in Escherichia coli: it is not homologous to other ς subunits, ς54-dependent expression absolutely requires an activator, and the activator binding sites can be far from the transcription start site. A rationale for these properties has not been readily apparent, in part because of an inability to assign a common physiological function for ς54-dependent genes. Surveys of ς54-dependent genes from a variety of organisms suggest that the products of these genes are often involved in nitrogen assimilation; however, many are not. Such broad surveys inevitably remove the ς54-dependent genes from a potentially coherent metabolic context. To address this concern, we consider the function and metabolic context of ς54-dependent genes primarily from a single organism, Escherichia coli, in which a reasonably complete list of ς54-dependent genes has been identified by computer analysis combined with a DNA microarray analysis of nitrogen limitation-induced genes. E. coli appears to have approximately 30 ς54-dependent operons, and about half are involved in nitrogen assimilation and metabolism. A possible physiological relationship between ς54-dependent genes may be based on the fact that nitrogen assimilation consumes energy and intermediates of central metabolism. The products of the ς54-dependent genes that are not involved in nitrogen metabolism may prevent depletion of metabolites and energy resources in certain environments or partially neutralize adverse conditions. Such a relationship may limit the number of physiological themes of ς54-dependent genes within a single organism and may partially account for the unique features of ς54 and ς54-dependent gene expression.

show abstract

Factors affecting transcriptional regulation of the formate-hydrogen-lyase pathway of Escherichia coli

Cited by 100 publications

References 46 publications

Osmotic repression of anaerobic metabolic systems in Escherichia coli

Osmotic repression of anaerobic metabolic systems in Escherichia coli

Systems-Level Engineering of Nonfermentative Metabolism in Yeast

Metabolic Context and Possible Physiological Themes of ς⁵⁴-Dependent Genes inEscherichia coli

Contact Info

Product

Resources

About

Factors affecting transcriptional regulation of the formate-hydrogen-lyase pathway of Escherichia coli

Cited by 100 publications

References 46 publications

Osmotic repression of anaerobic metabolic systems in Escherichia coli

Osmotic repression of anaerobic metabolic systems in Escherichia coli

Systems-Level Engineering of Nonfermentative Metabolism in Yeast

Metabolic Context and Possible Physiological Themes of ς54-Dependent Genes inEscherichia coli

Contact Info

Product

Resources

About

Metabolic Context and Possible Physiological Themes of ς⁵⁴-Dependent Genes inEscherichia coli