Overcoming function annotation errors in the Gram-positive pathogen Streptococcus suis by a proteomics-driven approach

Abstract

Background: Annotation of protein-coding genes is a key step in sequencing projects. Protein functions are mainly assigned on the basis of the amino acid sequence alone by searching of homologous proteins. However, fully automated annotation processes often lead to wrong prediction of protein functions, and therefore time-intensive manual curation is often essential. Here we describe a fast and reliable way to correct function annotation in sequencing projects, focusing on surface proteomes. We use a proteomics approach, previously proven to be very powerful for identifying new vaccine candidates against Gram-positive pathogens. It consists of shaving the surface of intact cells with two proteases, the specific cleavage-site trypsin and the unspecific proteinase K, followed by LC/MS/MS analysis of the resulting peptides. The identified proteins are contrasted by computational analysis and their sequences are inspected to correct possible errors in function prediction.

Fhb, a Novel Factor H-Binding Surface Protein, Contributes to the Antiphagocytic Ability and Virulence of Streptococcus suis

“…Above all, Fhb was not likely to be, as in a previous genome annotation of Fhb (gene ID SSU05_0272), translation initiation factor 2 (IF2) in S. suis 05ZYH33. The process of overcoming function annotation errors in Streptococcus suis has been undertaken by a proteomics-driven approach in recent years (46).…”

Genomic organization, structure, regulation and pathogenic role of pilus constituents in major pathogenic Streptococci and Enterococci

“…The zoonosis pathogen, S. suis, is one such example where the presence of peritrichous fimbriae on the surface of negatively stained cells was first revealed by Jacques and colleagues using transmission electron microscopy (Jacques et al, 1990). More recently, 4 gene clusters encoding putative pilus-like structures were identified in S. suis, designated srtBCD and srtF, srtE and srtG, according to the type of class C sortases present in the respective locus (Fittipaldi et al, 2007;Rodriguez-Ortega et al, 2008;Takamatsu et al, 2009). The most prevalent cluster, srtF, was recently studied in detail by Fittipaldi et al (2010) and Garibaldi et al (2010).…”

A Pneumococcal Protein Array as a Platform to Discover Serodiagnostic Antigens Against Infection

“…Many of these were also identified in a high proportion of adult clinical isolates (22). Our results show the enrichment of LPXTG-cell wall proteins when compared with their predicted figures from the genome, as already demonstrated in previous works for this and other pathogens (20,21,48,49,(51)(52)(53)(54). We decided to include also some cytoplasmic proteins, as for some of them their surface localization and immunogenicity/protective activity, are described, like Eno (55,56) or GAPDH (57).…”

“…A successful approach to identify in a fast and reliable way the "surfome," i.e. the set of surface proteins, consists of "shaving" live cells with proteases, following LC/MS/MS analysis (20,48,49). When applied to a collection of strains or clinical isolates of a given species, it provides a very interesting overview of the presence, frequency, and abundance of the identified proteins throughout the studied population, which allows choosing good candidates for vaccine or diagnostic purposes.…”