G. Flores-Rami´rez, R. Toman, Z. Sekeyova and L. SkultetyLaboratory for Diagnosis and Prevention of Rickettsial and Chlamydial Infections, Institute ofVirology, SAS, Bratislava, SlovakiaThe Gram-negative pathogen Coxiella burnetii isan obligate intracellular bacterium which growsonly within the phagolysosomes of eukaryotichost cells. The microbe is usually transmitted byaerosol and causes acute or chronic Q fever inhumans. It is well known that the outer mem-brane proteins (OMPs) play several importantroles in the host–parasite interactions of Gram-negative bacteria related to both pathogenesis andprotective immunity. In the present study, vari-ous bioinformatic tools and databases, togetherwith the mass spectrometry (MS) analyses, wereused to predict and to identify OMPs of C.burnetti,including the integral membrane proteins andlipoproteins (LPs) anchored to the outermembrane (OM) with an N-terminal lipid tail.The dataset of ORFs derived from the fullysequenced genome of C. burnetii strain Nine Mile I(RSA 493) [1] was processed for a subcellularlocalisation employing PSORTb (http://www.psort.org/psortb/index.html) with the Gram-neg-ative option. The results were compared with dataobtained from the Proteome Analyst PENCE data-base (http://www.cs.ualberta.ca/~bioinfo/PA/GOSUB) containing OMPs. The BOMP tool(http://www.bioinfo.no/tools/bomp) was usedto predict the presence of beta-barrels structures,and the TMBETA-SVM (tmbeta-svm.cbrc.jp) todiscriminate the OMPs from other folding typesof globular and membrane proteins. To predictLPs, the Lipo (http://services.cbu.uib.no/tools/lipo) tool, which detects LP sequences based on thelipobox region that is recognised by signal pepti-dase II, and the LipoP (http://www.cbs.dtu.dk/services/LipoP), which predicts LP signals pep-tides I and II in Gram-negative bacteria, have beenused. The results were further compared with thedata obtained from DOLOP database (http://www.mrc-lmb.cam.ac.uk/genomes/dolop) thatcontains LPs based on the lipobox present at theC-terminal end of the signal peptide. ORFpredicted as both OMP and LP was annotated asLP. In addition, the presence of any OMPs and LPsin the whole cell lysates of C.burnetiiRSA 493 wereconfirmed by MS techniques as describedpreviously [2].From the 2026 ORFs submitted to the bioinfor-matic tools, 160 ORFs including both low (onetool) and high confidence (at least two tools) werepredicted to be localised on the OM. Psortb,together with the PENCE database, has predicted34 OMPs, and BOMP, together with TMBETA-SVM, predicted 80 proteins with beta-barrelstructure related to OMP. Moreover, in total 46proteins were predicted as LPs, from which 33(71.73%) were predicted with a high confidence.It is noteworthy that 92% of all of them are basicproteins (pI higher than 8).Homology searches of predicted proteins sub-mitted to the Swiss-Prot database using the NCBIBLASTp tool (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi) and Pfam (http://www.pfam.sanger.ac.uk/) databases showed that the highconfidence predictions are homologous to thewell-characterised OMPs. Homologs of OM effluxproteins, components of bacterial type II, IIIand IV secretion systems, membrane proteinsinvolved in drug resistance, organic solventtolerance proteins, ATPases coupled to themembrane components, peptidoglycan associatedproteins, polysaccharide biosynthesis⁄exportproteins, endoglucanases, components of synthe-sis of lipid A, surface antigens and proteinsinvolved in sporulation have been predicted.Our analyses by various MS techniques re-vealed 21 predicted OMPs (Table 1) and 9 LPsanchored to the OM till now. Among them, thehypothetical components of the LolCDE trans-portation system, LolA, a carrier protein(CBU_1190) and LolB (CBU_1829), a lipoprotein-