The secE gene of Helicobacter pylori

Abstract

Despite extensive annotation by two independent teams, the Helicobacter pylori genome appeared to lack a complete secretion machinery. The use of clinical isolates to substantiate in silico annotation is used here to identify the missing secE component of the major secretion machinery of Helicobacter pylori.

FIG. 1.

The nusG region in H. pylori. Four frames with putative CDSs are displayed in the tufB nusG region. The upper line is the prediction by GeneMark, and the lower line is the prediction by Glimmer. While Glimmer predicts a long CDS in the opposite strand, GeneMark predicts an excellent CDS between rmpG and nusG. The present work shows that this corresponds to the secE gene.

FIG. 2.

The H. pylori SecE gene and protein. The upper part is an alignment of the nucleotide sequences of several H. pylori isolates. Capital letters represent strains from the Hong Kong University Department of Medicine, and lowercase letters represent the sequences of the two model genomes, 26695 and J99 (http://genolist.pasteur.fr/PyloriGene). Boldface letters represent the codon specifying the most-conserved residues in SecE. Codons on a light grey background indicate the placement of mutations with conservation of the protein sequence, and codons in italics indicate mutations leading to conservative replacements. The lower part is an alignment of reference SecE protein sequences. The Escherichia coli sequence is truncated from its two amino-proximal transmembrane domains. Boldface letters represent highly conserved residues (in particular, residues making contact with SecY); letters in italics are conservative replacements (ASTPG, MLIV, DNEQ, RKH, FYW). In the sequence of SecE from H. pylori, conservative replacements are noted in parentheses. RBS, ribosome binding site; HP, H. pylori; CJ, Campylobacter jejuni; DR, Deinococcus radiodurans; EC, E. coli; BS, Bacillus subtilis.

FIG. 3.

The SecE protein in context. Phylogenetically conserved residues are in grey. Inverted colors correspond to the transmembrane segment of the protein. Stars correspond to residues encoded by synonymous codons in the various H. pylori isolates. The six variable residues are shown as indicated (e.g., K > E at the beginning of the protein).