Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria.
BACKGROUND
Genomes of gram-positive bacteria encode many putative cell-surface proteins, of which the majority has no known function. From the rapidly increasing number of available genome sequences it has become apparent that many cell-surface proteins are conserved, and frequently encoded in gene clusters or operons, suggesting common functions, and interactions of multiple components.


RESULTS
A novel gene cluster encoding exclusively cell-surface proteins was identified, which is conserved in a subgroup of gram-positive bacteria. Each gene cluster generally has one copy of four new gene families called cscA, cscB, cscC and cscD. Clusters encoding these cell-surface proteins were found only in complete genomes of Lactobacillus plantarum, Lactobacillus sakei, Enterococcus faecalis, Listeria innocua, Listeria monocytogenes, Lactococcus lactis ssp lactis and Bacillus cereus and in incomplete genomes of L. lactis ssp cremoris, Lactobacillus casei, Enterococcus faecium, Pediococcus pentosaceus, Lactobacillius brevis, Oenococcus oeni, Leuconostoc mesenteroides, and Bacillus thuringiensis. These genes are neither present in the genomes of streptococci, staphylococci and clostridia, nor in the Lactobacillus acidophilus group, suggesting a niche-specific distribution, possibly relating to association with plants. All encoded proteins have a signal peptide for secretion by the Sec-dependent pathway, while some have cell-surface anchors, novel WxL domains, and putative domains for sugar binding and degradation. Transcriptome analysis in L. plantarum shows that the cscA-D genes are co-expressed, supporting their operon organization. Many gene clusters are significantly up-regulated in a glucose-grown, ccpA-mutant derivative of L. plantarum, suggesting catabolite control. This is supported by the presence of predicted CRE-sites upstream or inside the up-regulated cscA-D gene clusters.


CONCLUSIONS
We propose that the CscA, CscB, CscC and CscD proteins form cell-surface protein complexes and play a role in carbon source acquisition. Primary occurrence in plant-associated gram-positive bacteria suggests a possible role in degradation and utilization of plant oligo- or poly-saccharides.
Siezen
Roland
R
Wageningen Centre for Food Sciences (WCFS), Wageningen, The Netherlands. r.siezen@cmbi.ru.nl
Boekhorst
Jos
J
Muscariello
Lidia
L
Molenaar
Douwe
D
Renckens
Bernadet
B
Kleerebezem
Michiel
M
D000954:Antigens, Surface / Q000235:genetics* / Q000378:metabolism; D050260:Carbohydrate Metabolism / Q000235:genetics*; D002874:Chromosome Mapping; D017124:Conserved Sequence / Q000235:genetics*; D019143:Evolution, Molecular; D015870:Gene Expression; D005786:Gene Expression Regulation; D006094:Gram-Positive Bacteria / Q000235:genetics* / Q000378:metabolism; D048191:Lactiplantibacillus plantarum / Q000235:genetics* / Q000378:metabolism; D026901:Membrane Transport Proteins / Q000235:genetics / Q000378:metabolism; D008957:Models, Genetic; D005810:Multigene Family; D046912:Multiprotein Complexes / Q000235:genetics* / Q000378:metabolism; D009876:Operon / Q000235:genetics; D017434:Protein Structure, Tertiary; D012045:Regulatory Sequences, Nucleic Acid
D000954:Antigens, Surface; D026901:Membrane Transport Proteins; D046912:Multiprotein Complexes