Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the Chlamydiae

Abstract

Background: Chlamydiae are obligate intracellular bacteria comprising some of the most important bacterial pathogens of animals and humans. Although chlamydial outer membrane proteins play a key role for attachment to and entry into host cells, only few have been described so far. We developed a comprehensive, multiphasic in silico approach, including the calculation of clusters of orthologues, to predict outer membrane proteins using conservative criteria. We tested this approach using Escherichia coli (positive control) and Bacillus subtilis (negative control), and applied it to five chlamydial species; Chlamydia trachomatis, Chlamydia muridarum, Chlamydia (a.k.a. Chlamydophila) pneumoniae, Chlamydia (a.k.a. Chlamydophila) caviae, and Protochlamydia amoebophila.

Results: In total, 312 chlamydial outer membrane proteins and lipoproteins in 88 orthologous clusters were identified, including 238 proteins not previously recognized to be located in the outer membrane. Analysis of their taxonomic distribution revealed an evolutionary conservation among Chlamydiae, Verrucomicrobia, Lentisphaerae and Planctomycetes as well as lifestyle-dependent conservation of the chlamydial outer membrane protein composition.

Conclusion: This analysis suggested a correlation between the outer membrane protein composition and the host range of chlamydiae and revealed a common set of outer membrane proteins shared by these intracellular bacteria. The collection of predicted chlamydial outer membrane proteins is available at the online database pCOMP http://www.microbial-ecology.net/pcomp and might provide future guidance in the quest for anti-chlamydial vaccines.

Figure 1

The approach to identify chlamydial outer membrane proteins applied in this study. The individual steps used to identify chlamydial outer membrane proteins are indicated. Further details on the prediction approach on the level of individual genomes are given in Figure 2. Protein reclassification is described in more detail in additional file 1: Supporting Information, Figure S1. Annotated prediction results are available in the pCOMP database http://www.microbial-ecology.net/pcomp and in additional file 1: Supporting Information, Table S3.

Figure 2

Prediction of outer membrane proteins. All proteins from the five chlamydial proteomes of C. caviae GPIC, C. trachomatis D/UW-3/CX, C. muridarum Nigg, C. pneumoniae AR39 and P. amoebophila UWE25 as well as E. coli K12 and B. subtilis subsp. subtilis were subjected to the prediction approach for the identification of outer membrane proteins. Solid green lines indicate subsets of proteins included in further analysis; solid red lines indicate protein subsets excluded from further analysis; dashed black lines indicate negative result obtained with the respective prediction programs. Total numbers of proteins for all five chlamydial organisms and E. coli, respectively, are shown.

Figure 3

Taxonomic distribution of the 88 chlamydial outer membrane clusters. The Venn diagram shows the numbers of clusters that contain at least one protein from the Chlamydiaceae, the Parachlamydiaceae or other bacteria, and the respective intersections.