Genome-Wide Expression Analysis Indicates that FNR ofEscherichia coliK-12 Regulates a Large Number of Genes of Unknown Function

Abstract

The major regulator controlling the physiological switch between aerobic and anaerobic growth conditions in Escherichia coli is the DNA binding protein FNR. To identify genes controlled by FNR, we used Affymetrix Antisense GeneChips to compare global gene expression profiles from isogenic MG1655 wild-type and ⌬fnr strains grown in glucose minimal media under aerobic or anaerobic conditions. We found that 297 genes contained within 184 operons were regulated by FNR and/or by O 2 levels. The expression of many genes known to be involved in anaerobic respiration and fermentation was increased under anaerobic growth conditions, while that of genes involved in aerobic respiration and the tricarboxylic acid cycle were repressed as expected. The expression of nine operons associated with acid resistance was also increased under anaerobic growth conditions, which may reflect the production of acidic fermentation products. Ninety-one genes with no presently defined function were also altered in expression, including seven of the most highly anaerobically induced genes, six of which we found to be directly regulated by FNR. Classification of the 297 genes into eight groups by k-means clustering analysis indicated that genes with common gene expression patterns also had a strong functional relationship, providing clues for studying the function of unknown genes in each group. Six of the eight groups showed regulation by FNR; while some expression groups represent genes that are simply activated or repressed by FNR, others, such as those encoding functions for chemotaxis and motility, showed a more complex pattern of regulation. A computer search for FNR DNA binding sites within predicted promoter regions identified 63 new sites for 54 genes. We suggest that E. coli MG1655 has a larger metabolic potential under anaerobic conditions than has been previously recognized.

The RavA-ViaA Chaperone-Like System Interacts with and Modulates the Activity of the Fumarate Reductase Respiratory Complex

“…Though other transcription factors may also be responsible, the expression of RavA-ViaA during oxygen starvation was found to be primarily inducible by the transcriptional regulator Fnr, which also regulates the expression of the Frd complex as well as other proteins involved in anaerobiosis [29,41].Our finding of the regulation of the ravAviaA promoter by Fnr is consistent with a recent high throughput study based on a…”

“…ACCEPTED MANUSCRIPT 9 expression of a large number of genes during the transition from aerobiosis to anaerobiosis [28,29]. The co-expression of genes under Fnr control suggested that Fnr was also likely to regulate the expression of both ravA and viaA.…”

Transcriptional profiling of Corynebacterium glutamicum metabolism during organic acid production under oxygen deprivation conditions

“…In C. glutamicum, and again similar to what is observed in B. subtilis (Ye et al, 2000) and E. coli (Kang et al, 2005), numerous other genes are induced or repressed with changes in environmental conditions such as oxygen tension. Among the genes observed to be highly inducible in the last two species, beyond those genes involved in anaerobic respiration, carbon metabolism and electron transport, iron uptake, stress response and several hypothetical genes are also upregulated.…”

“…Among the genes observed to be highly inducible in the last two species, beyond those genes involved in anaerobic respiration, carbon metabolism and electron transport, iron uptake, stress response and several hypothetical genes are also upregulated. In B. subtilis and E. coli, the major regulator of the physiological switch between aerobic and anaerobic growth conditions is the DNA binding protein FNR (Gunsalus & Park, 1994;Kang et al, 2005;Pao et al, 1994;Ye et al, 2000). For example, in E. coli, 297 genes constituting 184 different operons are regulated by FNR and/or oxygen levels (Kang et al, 2005).…”

Functional Characterization of Crp/Fnr-Type Global Transcriptional Regulators in Desulfovibrio vulgaris Hildenborough

“…The characteristic structure of Crp/Fnr is a C-terminal helix-turn-helix (HTH) motif that fits the DNA major groove and an N-terminal nucleotide binding domain (34). This class of transcriptional factors is named after the first two representatives discovered in Escherichia coli, i.e., the Crp (cyclic AMP [cAMP] receptor protein) and Fnr (fumarate and nitrate reductase regulator protein) (4,21,24,27). Crp/Fnr regulators are generally classified into different subfamilies (e.g., CooA, Crp, Dnr, FixK, Fnr, HbaR, NnrR, etc.)…”