title: LAB-Secretome: a genome-scale comparative analysis of the predicted extracellular and surface-associated proteins of Lactic Acid Bacteria.
abstract: BACKGROUND
  In Lactic Acid Bacteria (LAB), the extracellular and surface-associated proteins can be involved in processes such as cell wall metabolism, degradation and uptake of nutrients, communication and binding to substrates or hosts. A genome-scale comparative study of these proteins (secretomes) can provide vast information towards the understanding of the molecular evolution, diversity, function and adaptation of LAB to their specific environmental niches.
  
  
  RESULTS
  We have performed an extensive prediction and comparison of the secretomes from 26 sequenced LAB genomes. A new approach to detect homolog clusters of secretome proteins (LaCOGs) was designed by integrating protein subcellular location prediction and homology clustering methods. The initial clusters were further adjusted semi-manually based on multiple sequence alignments, domain compositions, pseudogene analysis and biological function of the proteins. Ubiquitous protein families were identified, as well as species-specific, strain-specific, and niche-specific LaCOGs. Comparative analysis of protein subfamilies has shown that the distribution and functional specificity of LaCOGs could be used to explain many niche-specific phenotypes.A comprehensive and user-friendly database LAB-Secretome was constructed to store, visualize and update the extracellular proteins and LaCOGs http://www.cmbi.ru.nl/lab_secretome/. This database will be updated regularly when new bacterial genomes become available.
  
  
  CONCLUSIONS
  The LAB-Secretome database could be used to understand the evolution and adaptation of lactic acid bacteria to their environmental niches, to improve protein functional annotation and to serve as basis for targeted experimental studies.
authors.affiliation: Centre for Molecular and Biomolecular Informatics, Radboud University Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands. m.zhou@cmbi.ru.nl
authors.forename: Miaomiao
authors.initials: M
authors.lastname: Zhou
authors.forename: Daniel
authors.initials: D
authors.lastname: Theunissen
authors.forename: Michiel
authors.initials: M
authors.lastname: Wels
authors.forename: Roland J
authors.initials: RJ
authors.lastname: Siezen
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism*; D016000:Cluster Analysis; D030562:Databases, Protein; D005110:Extracellular Space / Q000378:metabolism*; D016680:Genome, Bacterial / Q000235:genetics*; D007777:Lactobacillaceae / Q000201:enzymology / Q000235:genetics* / Q000378:metabolism*; D008565:Membrane Proteins / Q000737:chemistry / Q000378:metabolism*; D016366:Open Reading Frames / Q000235:genetics; D017434:Protein Structure, Tertiary; D011544:Pseudogenes / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D013045:Species Specificity
chemical_list: D001426:Bacterial Proteins; D008565:Membrane Proteins