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This project is a part of a larger effort to uncover non-coding RNAs (e.g. microRNAs).  microRNAs, a subset of the small interfering RNAs (siRNAs) which serve as a guide for RNA interference (RNAi), are responsible for the regulation of gene expression during plant and animal development.  In 1993, the first miRNA, lin-4, was discovered in Caenorhabditis elegans.  By cloning the gene locus, Lee et al. discovered that lin-4 did not produce a protein-coding mRNA, but a 22 nucleotide non-coding RNA (ncRNA).  This miRNA functions to regulate the expression of lin-14 mRNA by binding to the 3’ UTR.  It wasn’t until 2000 with the discovery of let-7, a miRNA that targets lin-41 and hbl-1 in a functionally similar manner, that miRNA was established as a key element of gene regulatory networks (12).

In plant and animal cells, miRNAs originate in the nucleus as Pri-miRNA. A 20-22 nt segment is removed from the pre-miRNA hairpin either by an RNase III, DICER, in the cytoplasm, as is seen in animals, or by the RNase III enzyme DICER-LIKE 1 (DCL1) in the nucleus, in the case of plants.  The double-stranded miRNA is then split by a helicase into two separate strands, one of which is preferentially loaded into the RNA-induced silencing complex (RISC) (12).

RNAi has been discovered in several protozoan parasites, the first being Trypanosoma brucei by Ngo et al. in 1998.  It was shown that trypanosomes possess a mechanism to degrade mRNA through direct contact with double-stranded RNA (dsRNA), much like exists in C. elegans.  This is not generally the case in apicomplexan parasites.  Although one report has been published stating that RNAi may exist in Toxoplasma gondii, the same can not be said for other apicomplexa, such as Plasmodium falciparum, where such machinery does not exist.  Database searches for consensus domain sequences of Dicer, Piwi, PAZ, or RdRp showed no sign of target gene candidates.  Additionally, reports demonstrating loss of protein function as a result of small siRNA-like particles do not show any evidence that the small RNA sequences are indeed siRNAs. As a result, the presence of a functioning RNAi pathway in P. falciparum is a debatable topic (15).

Table 1. Experimental status of siRNA & microRNA in protozoan parasites
(Note: Reference numbers refer to source in the References section)

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