Prediction Of Hydrogenosomal Proteins In Trichomonas Vaginalis And The Evolution Of Presequence

Hydrogenosome is known as anaerobic mitochondria, which produces ATP and molecular hydrogen. It was firstly isolated, purified and biochemically characterized in early 1970s in anaerobic flagellate Tritrichomonas foetus. Recent studies have demonstrated a common origin of mitochondria and hydrogenosome. Mitochondrial proteins have been revealed by various molecular and genetic approaches, as well as the proteomics methods and in silico prediction. In hydrogenosome, however, limited by pure culture and organelle purifying, its components and biochemical pathways were poorly understood. Only forteen hydrogenosomal proteins and their presequences have been verifed experimentally to date, while another 300 proteins were identified with hydrogenosomal protein-like presequences. Although different tools have been used in subcellular sublocation prediction and worked well on identification of mitochondrial-proteins, it is not reasonable to use them directly to predict hydrogenosomal proteins in genome-wide screening as their difference in N-terminal sequence.In this study, we developed a new method HdPred to carry out the prediction of hydrogenosomal proteins in Trichomonas vaginalis. HdPred was performed based on the knowledge of hydrogenosome evolution. Alphabet indexing and approximate pattern search were used for identification of new hydrogenosomal proteins under the simple rules about the biological features of the mitochondrial/hydrogenosomal presequence. In total, seventy proteins were predicted hydrogenosomal sublocation by HdPred method. Independent approaches were used to evaluate the result, and about 50% of them were validated by proteomics methods or predicted by other tools with high probability. Function category revealed that HdPred result has collected eight proteins involved in energy production and conversion (8/70), which stressed angain that ATP production was the main function of mitochondria-related orgalle. Prediction of presequence was also evaluated and the results from HdPred were believed with higher accuracy. Thus we believed that well performance of HdPred on prediction of hydrogenosomal proteins could provided an acceptable collection for further studies.Presequences play an important role . in protein imported into mitochondria-related organelle. Its variod origin has been revealed in mitochondria, however, little about it was known about hydrogenosomal proteins. In the present study, the author reviewed different origin ways of mitochondrial presequence which were concluded into two groups, exogenous acquirement and spontaneous origin. The author also studied the presequence of three hydrogenosomal Hsp60 proteins. Results from comparative analysis to the homologs inα-proteobacteria indicated the exogenous acquirement of their presequences. Moreover, presequence acquirement was observed as an independent process in other protozoal species. Further analysis revealed that these three Hsp60 proteins were not origin from chromosomal or segmental duplication, and the author believed that their presequences were acquired by gene duplication.