Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis.
As the genomes of more eukaryotic pathogens are sequenced, understanding how molecular differences between parasite and host might be exploited to provide new therapies has become a major focus. Central to cell function are RNA-containing complexes involved in gene expression, such as the ribosome, the spliceosome, snoRNAs, RNase P, and telomerase, among others. In this article we identify by comparative genomics and validate by RNA analysis numerous previously unknown structural RNAs encoded by the Plasmodium falciparum genome, including the telomerase RNA, U3, 31 snoRNAs, as well as previously predicted spliceosomal snRNAs, SRP RNA, MRP RNA, and RNAse P RNA. Furthermore, we identify six new RNA coding genes of unknown function. To investigate the relationships of the RNA coding genes to other genomic features in related parasites, we developed a genome browser for P. falciparum (http://areslab.ucsc.edu/cgi-bin/hgGateway). Additional experiments provide evidence supporting the prediction that snoRNAs guide methylation of a specific position on U4 snRNA, as well as predicting an snRNA promoter element particular to Plasmodium sp. These findings should allow detailed structural comparisons between the RNA components of the gene expression machinery of the parasite and its vertebrate hosts.
Chakrabarti
Kausik
K
Department of Molecular, Cell and Developmental Biology, Center for Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.
Pearson
Michael
M
Grate
Leslie
L
Sterne-Weiler
Timothy
T
Deans
Jonathan
J
Donohue
John Paul
JP
Ares
Manuel
M
D000818:Animals; D020029:Base Pairing; D001483:Base Sequence; D018503:Genome, Protozoan; D023281:Genomics; D006801:Humans; D008288:Malaria / Q000469:parasitology; D008745:Methylation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010963:Plasmodium falciparum / Q000235:genetics* / Q000378:metabolism; D012313:RNA / Q000737:chemistry / Q000378:metabolism; D016053:RNA, Protozoan / Q000737:chemistry*; D012335:RNA, Ribosomal / Q000737:chemistry / Q000378:metabolism; D012342:RNA, Small Nuclear / Q000737:chemistry; D020537:RNA, Small Nucleolar / Q000737:chemistry / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry / Q000378:metabolism; D017381:Spliceosomes; D019098:Telomerase / Q000737:chemistry / Q000378:metabolism
D016053:RNA, Protozoan; D012335:RNA, Ribosomal; D012342:RNA, Small Nuclear; D020537:RNA, Small Nucleolar; C117378:RNA, U3 small nucleolar; C422952:telomerase RNA; D012313:RNA; D012343:RNA, Transfer; D019098:Telomerase