Comparison of the protein-coding gene content of Chlamydia trachomatis and Protochlamydia amoebophila using a Raspberry Pi computer. (December 2015)

• Record Type: Journal Article
• Authors: Robson, James; Barker, Daniel
• Is Part Of: BMC research notes. Volume 8:Number 1(2015)
• Page Start: 1
• Page End: 6
• Publication Date: 2015-12
• Subjects: Chlamydia -- Protochlamydia -- Chlamydiae -- Parasite -- Endosymbiont -- Bioinformatics -- Comparative genomics -- Protein families -- Raspberry Pi; Medicine -- Periodicals; Biology -- Periodicals; 610.5
• DOI: 10.1186/s13104-015-1476-2
• Languages: English
• ISSNs: 1756-0500

Abstract

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 CandidatusProtochlamydia 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 andP. amoebophila, and their members counted. Examples include nine multi-protein families unique toC. trachomatis, 132 multi-protein families unique toP. amoebophila and one family with multiple copies in both. Most families unique toC. 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 toP. 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 inC. trachomatis, suggesting importance for host evasion. The tyrosine transport protein family is shared between both species, with four proteins inC. trachomatis and two inP. amoebophila. Shared protein families could provide a starting point for discovery of wide-spectrum drugs against Chlamydiae.