Comparison of the protein-coding gene content of Chlamydia trachomatis and Protochlamydia amoebophila using a Raspberry Pi computer

James F Robson, Daniel Barker

Research output: Contribution to journalArticlepeer-review

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 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 widespectrum drugs against Chlamydiae.
Original languageEnglish
Article number561
JournalBMC Research Notes
Volume8
Issue number561
DOIs
Publication statusPublished - 13 Oct 2015

Keywords

  • Chlamydia
  • Protochlamydia
  • Chlamydiae
  • Parasite
  • Endosymbiont
  • Bioinformatics
  • Comparative genomics
  • Protein families
  • Raspberry Pi

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