IHF Is Required for the Transcriptional Regulation of the Desulfovibrio vulgaris Hildenborough orp Operons

Abstract

Transcriptional activation of σ54-dependent promoters is usually tightly regulated in response to environmental cues. The high abundance of potential σ54-dependent promoters in the anaerobe bacteria, Desulfovibrio vulgaris Hildenborough, reflects the high versatility of this bacteria suggesting that σ54 factor is the nexus of a large regulatory network. Understanding the key players of σ54-regulation in this organism is therefore essential to gain insights into the adaptation to anaerobiosis. Recently, the D. vulgaris orp genes, specifically found in anaerobe bacteria, have been shown to be transcribed by the RNA polymerase coupled to the σ54 alternative sigma factor. In this study, using in vitro binding experiments and in vivo reporter fusion assays in the Escherichia coli heterologous host, we showed that the expression of the divergent orp promoters is strongly dependent on the integration host factor IHF. Bioinformatic and mutational analysis coupled to reporter fusion activities and mobility shift assays identified two functional IHF binding site sequences located between the orp1 and orp2 promoters. We further determined that the D. vulgaris DVU0396 (IHFα) and DVU1864 (IHFβ) subunits are required to control the expression of the orp operons suggesting that they form a functionally active IHF heterodimer. Interestingly results obtained from the in vivo inactivation of DVU0396, which is required for orp operons transcription, suggest that several functionally IHF active homodimer or heterodimer are present in D. vulgaris.

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

“…Although the sequences shared only 30% identity, the structures were superimposable (Cort, Yee, Edwards, Arrowsmith, & Kennedy, 2000). A similar domain was found to be encoded in three members of a divergent set of co-regulated genes in D. vulgaris (Fiévet, Cascales, Valette, Dolla, & Aubert, 2014;Fiévet et al, 2011). Further exploration showed that proteins with this COG shared homology with a protein from D. gigas that had been described earlier as the "orange protein" (ORP) (George et al, 2000).…”

Specialization of the Reiterated Copies of the Heterodimeric Integration Host Factor Genes in Geobacter sulfurreducens

“…These results suggest that the gene duplication present in the Deltaproteobacteria is very ancient but occurred after the separation of the Gamma and Deltaproteobacteria lineages. D. vulgaris H is the only Deltaproteobacteria in which the role of IHF has been studied; in this organism, IHF participates in the expression of the orp genes involved in cell division ( Fiévet et al, 2014 ).…”

“…The canonical structure of IHF consists of two paralogous subunits, IHFα and IHFβ, encoded by the unlinked ihfA and ihfB genes ( Haluzi et al, 1991 ; Weisberg et al, 1996 ). Among other roles, IHF is required for the activation of genes transcribed by RpoN-containing RNA polymerase ( Cannon et al, 1990 ; Hoover et al, 1990 ; de Lorenzo et al, 1991 ), including those participating in nitrogen fixation in Klebsiella pneumoniae , alginate synthesis in Pseudomonas aeruginosa , regulation of flagella genes in Caulobacter crescentus , toluene degradation in Pseudomonas putida , and cell division in Desulfovibrio vulgaris Hildenborough ( Cannon et al, 1990 ; Santero et al, 1992 ; Calb et al, 1996 ; Delic-Attree et al, 1996 ; Muir and Gober, 2005 ; Fiévet et al, 2014 ). Upon binding, IHF bends the DNA, promoting the interaction between the bound upstream activator, EBP with the RpoN-RNA polymerase ( Morett and Segovia, 1993 ).…”

“…So far, IHF contribution has been evaluated only in bacterial species whose genome encodes a single copy of each IHF gene subunit ( ihfA and ihfB ). However, in some Deltaproteobacteria, including Geobacter sulfurreducens , multiple copies of these genes have been detected ( Fiévet et al, 2014 ).…”

The bacterial MrpORP is a novel Mrp/NBP35 protein involved in iron-sulfur biogenesis

“…The ORP complex is made of 5 proteins named Orp3 (DVU2103), Orp4 (DVU2104), Orp5 (DVU2105), Orp8 (DVU2108) and Orp9 (DVU2109), putatively involved in cell division 19 . The genes coding for ORP proteins are clustered into two divergent operons whose expression is controled from a σ 54 -dependent promoter 19,20 . Most of the ORP proteins are predicted to be metal binding proteins.…”