An integrated approach to understand apicomplexan metabolism from their genomes
© Shanmugasundram et al; licensee BioMed Central Ltd. 2014
Published: 11 February 2014
The Apicomplexa is a large phylum of intracellular parasites that show great diversity and adaptability in the various ecological niches they occupy. They are the causative agents of human and animal infections including malaria, toxoplasmosis and theileriosis, which have a huge economic and social impact. A number of apicomplexan genomes have been sequenced and are publicly available. However, the prediction of gene models and annotation of gene functions remains challenging.
We have utilised an approach called ‘metabolic reconstruction’, in which genes are systematically assigned to functions within pathways/networks [1–4]. Functional annotation and metabolic reconstruction was carried out using a semi-automatic approach, integrating genomic information with biochemical evidence from the literature. The functions were automatically assigned using a sequence similarity-based approach and protein motif information. Experimental evidence was also accommodated in the confirmation of functions and the grouping of genes into metabolic pathways.
A survey of the data available for the different apicomplexan genomes in LAMP. The analysis is updated from the survey table published in the previous publication 
No of metabolic pathways
No of unique enzymesa
No of missing enzymesb
No of reactionsc
Total no of metabolitesd
No of metabolites from hoste
No of end metabolites to host or of unknown fatef
The carefully annotated metabolic pathways and the comparative analysis of metabolism for eight apicomplexan species are publicly available for the research community in the LAMP database (http://www.llamp.net). This has improved the functional annotation immensely and led to identification of putative drug targets. The hyperlinks for LAMP metabolic pathway annotations are available from the respective gene pages of the T. gondii primary database, ToxoDB (release 9) , enabling a wider reach for LAMP.
LAMP web database was already published in the database issue of Nucleic acids research (January 2013). LAMP is indirectly funded through several grants from Biotechnology and Biological Sciences Research Council. Travel expenses of AS to the ISCB Student Council Symposium was funded from the BBSRC DTG studentship awarded to the University of Liverpool.
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