title: Peptide signal molecules and bacteriocins in Gram-negative bacteria: a genome-wide in silico screening for peptides containing a double-glycine leader sequence and their cognate transporters.
abstract: Quorum sensing (QS) in Gram-negative bacteria is generally assumed to be mediated by N-acyl-homoserine lactone molecules while Gram-positive bacteria make use of signaling peptides. We analyzed the occurrence in Gram-negative bacteria of peptides and transporters that are involved in quorum sensing in Gram-positive bacteria. Many class II bacteriocins and inducing factors produced by lactic acid bacteria (LAB) and competence stimulating peptides (CSPs) synthesized by streptococci are processed by their cognate ABC-transporters during their secretion. During transport, a conserved leader sequence, termed the double-glycine motif (GG-motif), is cleaved off by the N-terminal domain of the transporter, which belongs to the Peptidase C39 protein family. Several peptides containing a GG-motif were recently described in Gram-negative bacteria (Trends Microbiol 2001;9:164-8). To screen for additional putative GG-motif containing peptides, an in silico strategy based on MEME, HMMER2.2 and Wise2 was designed. Using a curated training set, a motif model of the leader peptide was built and used to screen over 120 fully sequenced bacterial genomes. The screening methodology was applied at the nucleotide level as probably many small peptide genes have not been annotated and may be absent from the non-redundant databases. It was found that 33% of the screened genomes of Gram-negative bacteria contained one or more transporters carrying a Peptidase C39 domain, compared to 44% of the genomes of Gram-positive bacteria. The transporters can be subdivided into four classes on the basis of their domain organization. Genes coding for putative peptides containing 23-142 amino acids and a GG-motif were found in close association with genes coding for Peptidase C39 domain containing proteins. These peptides show structural similarity to bacteriocins and peptide pheromones of Gram-positive bacteria. The possibility of signal transduction based on peptide signaling in Gram-negative bacteria is discussed.
authors.affiliation: Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium.
authors.forename: G
authors.initials: G
authors.lastname: Dirix
authors.forename: P
authors.initials: P
authors.lastname: Monsieurs
authors.forename: B
authors.initials: B
authors.lastname: Dombrecht
authors.forename: R
authors.initials: R
authors.lastname: Daniels
authors.forename: K
authors.initials: K
authors.lastname: Marchal
authors.forename: J
authors.initials: J
authors.lastname: Vanderleyden
authors.forename: J
authors.initials: J
authors.lastname: Michiels
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000096:biosynthesis; D001430:Bacteriocins / Q000737:chemistry* / Q000378:metabolism; D001692:Biological Transport; D002450:Cell Communication; D019295:Computational Biology; D016680:Genome, Bacterial; D005998:Glycine / Q000737:chemistry*; D006090:Gram-Negative Bacteria / Q000502:physiology*; D008954:Models, Biological; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry*; D010802:Phylogeny; D010957:Plasmids / Q000378:metabolism; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D015398:Signal Transduction; D012984:Software
chemical_list: D001426:Bacterial Proteins; D001430:Bacteriocins; D010455:Peptides; C002836:subtilin; D005998:Glycine