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Comparative Study
, 8, 561

Comparison of the Protein-Coding Gene Content of Chlamydia Trachomatis and Protochlamydia Amoebophila Using a Raspberry Pi Computer

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Comparative Study

Comparison of the Protein-Coding Gene Content of Chlamydia Trachomatis and Protochlamydia Amoebophila Using a Raspberry Pi Computer

James F Robson et al. BMC Res Notes.

Abstract

Background: To demonstrate the bioinformatics capabilities of a low-cost computer, the Raspberry Pi, we present a comparison of the protein-coding gene content of two species in phylum Chlamydiae: Chlamydia trachomatis, a common sexually transmitted infection of humans, and Candidatus Protochlamydia amoebophila, a recently discovered amoebal endosymbiont. Identifying species-specific proteins and differences in protein families could provide insights into the unique phenotypes of the two species.

Results: Using a Raspberry Pi computer, sequence similarity-based protein families were predicted across the two species, C. trachomatis and P. amoebophila, and their members counted. Examples include nine multi-protein families unique to C. trachomatis, 132 multi-protein families unique to P. amoebophila and one family with multiple copies in both. Most families unique to C. trachomatis were polymorphic outer-membrane proteins. Additionally, multiple protein families lacking functional annotation were found. Predicted functional interactions suggest one of these families is involved with the exodeoxyribonuclease V complex.

Conclusion: The Raspberry Pi computer is adequate for a comparative genomics project of this scope. The protein families unique to P. amoebophila may provide a basis for investigating the host-endosymbiont interaction. However, additional species should be included; and further laboratory research is required to identify the functions of unknown or putative proteins. Multiple outer membrane proteins were found in C. trachomatis, suggesting importance for host evasion. The tyrosine transport protein family is shared between both species, with four proteins in C. trachomatis and two in P. amoebophila. Shared protein families could provide a starting point for discovery of wide-spectrum drugs against Chlamydiae.

Figures

Fig. 1
Fig. 1
Predicting functional interactions of unannotated proteins. To further investigate the function of the protein family whose members were all unannotated, Group 40 (Additional file 1), functional interactions were investigated using the STRING database. It was found that P. amoebophilia Q6MEA2 (a STRING ID pc0373) and C. trachomatis Q3KL42 (b STRING ID CTA_0708) both interact with the (putative) exodeoxyribonuclease V alpha chain with a high confidence score. Each query protein is in the centre of the interaction web and is coloured red. Grey dots in the key represent strength of evidence (darker is stronger). The sum of each distinct evidence type was used to generate the total score

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