Identification and functional characterization of cis-regulatory elements in the apicomplexan parasite Toxoplasma gondii.
BACKGROUND
Toxoplasma gondii is a member of the phylum Apicomplexa, which consists entirely of parasitic organisms that cause several diseases of veterinary and human importance. Fundamental mechanisms of gene regulation in this group of protistan parasites remain largely uncharacterized. Owing to their medical and veterinary importance, genome sequences are available for several apicomplexan parasites. Their genome sequences reveal an apparent paucity of known transcription factors and the absence of canonical cis-regulatory elements. We have approached the question of gene regulation from a sequence perspective by mining the genomic sequence data to identify putative cis-regulatory elements using a de novo approach.


RESULTS
We have identified putative cis-regulatory elements present upstream of functionally related groups of genes and subsequently characterized the function of some of these conserved elements using reporter assays in the parasite. We show a sequence-specific role in gene-expression for seven out of eight identified elements.


CONCLUSIONS
This work demonstrates the power of pure sequence analysis in the absence of expression data or a priori knowledge of regulatory elements in eukaryotic organisms with compact genomes.
Mullapudi
Nandita
N
Department of Genetics, University of Georgia, East Green Street, Athens, Georgia 30602, USA. mnandita@gmail.com
Joseph
Sandeep J
SJ
Kissinger
Jessica C
JC
D000465:Algorithms; D000818:Animals; D030541:Databases, Genetic; D005786:Gene Expression Regulation; D018503:Genome, Protozoan; D006019:Glycolysis / Q000235:genetics; D008156:Luciferases / Q000235:genetics / Q000378:metabolism; D009154:Mutation; D011401:Promoter Regions, Genetic / Q000235:genetics; D015800:Protozoan Proteins / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D012269:Ribosomal Proteins / Q000235:genetics; D014122:Toxoplasma / Q000235:genetics*; D014162:Transfection
D015800:Protozoan Proteins; D012269:Ribosomal Proteins; D008156:Luciferases