Abstract
The rpoB and rpoC genes of eubacteria and archaea, coding respectively for the beta- and beta'-like subunits of DNA-dependent RNA polymerase, are organized in an operon with rpoB always preceding rpoC. The genome sequence of the gastric pathogen Helicobacter pylori (strain 26695) revealed homologs of two genes in one continuous open reading frame that potentially could encode one 2890-amino acid-long beta-beta' fusion protein. Here, we show that this open reading frame does in fact encode a fused beta-beta' polypeptide. In addition, we establish by DNA sequencing that rpoB and rpoC are also fused in each of four other unrelated strains of H. pylori, as well as in Helicobacter felis, another member of the same genus. In contrast, the rpoB and rpoC genes are separate in two members of the related genus Campylobacter (Campylobacter jejuni and Campylobacter fetus) and encode separate RNA polymerase subunits. The Campylobacter genes are also unusual in overlapping one another rather than being separated by a spacer as in other Gram-negative bacteria. We propose that the unique organization of rpoB and rpoC in H. pylori may contribute to its ability to colonize the human gastric mucosa.
Highlights
The rpoB and rpoC genes of eubacteria and archaea, coding respectively for the - and -like subunits of DNA-dependent RNA polymerase, are organized in an operon with rpoB always preceding rpoC
RpoBC Genes Are Fused in Helicobacter but Not in Campylobacter—Two primers that target the rpoB-rpoC junction and that are complimentary to highly conserved sequences in the 3Ј end of the rpoB portion and the 5Ј end of the rpoC portion of the H. pylori 26695 rpoBC gene were used for PCR amplification with genomic DNA from the following organisms: H. pylori strains Hp1 [14], J-166 [15], SS1 [16], and NCTC11638 [17]; an isolate of Helicobacter felis; and isolates of two different Campylobacter species: C. jejuni, strain H840, and C. fetus [13]
Because no proteins in H. pylori lysates that would comigrate with separate RNAP  and Ј subunits were detected, the fused subunit is probably not extensively proteolyzed; it is likely to be the only source of RNAP  and Ј in the cell, as is the case for an E. coli strain with a -Ј fusion RNAP that we had engineered to study holoenzyme topology and assembly [9]
Summary
The genome sequence of the gastric pathogen Helicobacter pylori (strain 26695) revealed homologs of two genes in one continuous open reading frame that potentially could encode one 2890-amino acid-long - fusion protein. We establish by DNA sequencing that rpoB and rpoC are fused in each of four other unrelated strains of H. pylori, as well as in Helicobacter felis, another member of the same genus. The genome sequence of the gastric pathogen Helicobacter pylori (strain 26695) revealed one continuous open reading frame containing the homologs of rpoB and rpoC, potentially encoding one fused 2890-amino acid-long -Ј polypeptide [8]. We suggest that the -Ј tethering in Helicobacter might (i) be an accident of evolution because of a frameshift mutation in an ancestor that, like current Campylobacters, contained overlapping but separate rpoB and rpoC genes or (ii) help gastric organisms cope with their acidand urea-rich niche.
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