Identifying novel cell cycle proteins in Apicomplexa parasites through co-expression decision analysis.
Hypothetical proteins comprise roughly half of the predicted gene complement of Toxoplasma gondii and Plasmodium falciparum and represent the largest class of uniquely functioning proteins in these parasites. Following the idea that functional relationships can be informed by the timing of gene expression, we devised a strategy to identify the core set of apicomplexan cell division cycling genes with important roles in parasite division, which includes many uncharacterized proteins. We assembled an expanded list of orthologs from the T. gondii and P. falciparum genome sequences (2781 putative orthologs), compared their mRNA profiles during synchronous replication, and sorted the resulting set of dual cell cycle regulated orthologs (744 total) into protein pairs conserved across many eukaryotic families versus those unique to the Apicomplexa. The analysis identified more than 100 ortholog gene pairs with unknown function in T. gondii and P. falciparum that displayed co-conserved mRNA abundance, dynamics of cyclical expression and similar peak timing that spanned the complete division cycle in each parasite. The unknown cyclical mRNAs encoded a diverse set of proteins with a wide range of mass and showed a remarkable conservation in the internal organization of ordered versus disordered structural domains. A representative sample of cyclical unknown genes (16 total) was epitope tagged in T. gondii tachyzoites yielding the discovery of new protein constituents of the parasite inner membrane complex, key mitotic structures and invasion organelles. These results demonstrate the utility of using gene expression timing and dynamic profile to identify proteins with unique roles in Apicomplexa biology.
Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America.
Carrie L
CL
Butler
Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America.
Olivier
O
Lucas
National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, United States of America.
Stefan
S
Wuchty
Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America.
Bin
B
Xue
Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States of America.
Vladimir N
VN
Uversky
Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida, United States of America; Florida Center for Drug Discovery and Innovation, University of South Florida, Tampa, Florida, United States of America.
Michael
M
White
D018797:Cell Cycle Proteins / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology; D017124:Conserved Sequence / Q000235:genetics; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000235:genetics*; D053263:Gene Regulatory Networks / Q000235:genetics; D008856:Microscopy, Fluorescence; D010963:Plasmodium falciparum / Q000235:genetics*; D015800:Protozoan Proteins / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D014122:Toxoplasma / Q000235:genetics*; D020798:Two-Hybrid System Techniques
D018797:Cell Cycle Proteins; D015800:Protozoan Proteins; D012333:RNA, Messenger