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.

Telomerase is a ribonucleoprotein enzyme typically required for sustained cell proliferation. Although both telomerase activity and the telomerase catalytic protein component, TbTERT, have been identified in the eukaryotic pathogen Trypanosoma brucei, the RNA molecule that dictates telomere synthesis remains unknown. Here, we identify the RNA component of Trypanosoma brucei telomerase, TbTR, and provide phylogenetic and in vivo evidence for TbTR's native folding and activity. We show that TbTR is processed through trans-splicing, and is a capped transcript that interacts and copurifies with TbTERT in vivo. Deletion of TbTR caused progressive shortening of telomeres at a rate of 3-5 bp/population doubling (PD), which can be rescued by ectopic expression of a wild-type allele of TbTR in an apparent dose-dependent manner. Remarkably, introduction of mutations in the TbTR template domain resulted in corresponding mutant telomere sequences, demonstrating that telomere synthesis in T. brucei is dependent on TbTR. We also propose a secondary structure model for TbTR based on phylogenetic analysis and chemical probing experiments, thus defining TbTR domains that may have important functional implications in telomere synthesis. Identification and characterization of TbTR not only provide important insights into T. brucei telomere functions, which have been shown to play important roles in T. brucei pathogenesis, but also offer T. brucei as an attractive model system for studying telomerase biology in pathogenic protozoa and for comparative analysis of telomerase function with higher eukaryotes.

RhoGEFs are central controllers of small G-proteins in cells and are regulated by several mechanisms. There are at least 22 human RhoGEFs that contain SH3 domains, raising the possibility that, like several other enzymes, SH3 domains control the enzymatic activity of guanine nucleotide exchange factor (GEF) domains through intra-and/or intermolecular interactions. The structure of the N-terminal SH3 domain of Kalirin was solved using NMR spectroscopy, and it folds much like other SH3 domains. However, NMR chemical shift mapping experiments showed that this Kalirin SH3 domain is unique, containing novel cooperative binding site(s) for intramolecular PXXP ligands. Intramolecular Kalirin SH3 domain/ ligand interactions, as well as binding of the Kalirin SH3 domain to the adaptor protein Crk, inhibit the GEF activity of Kalirin. This study establishes a novel molecular mechanism whereby intramolecular and intermolecular Kalirin SH3 domain/ligand interactions modulate GEF activity, a regulatory mechanism that is likely used by other RhoGEF family members.There are ϳ69 RhoGEFs in the human genome that are expected to catalyze nucleotide exchange on ϳ22 Rho GTPases (1). As the major activators of the Rho GTPases, guanine nucleotide exchange factor (GEF) 2 proteins play important roles in cell signaling, rearrangement of the cytoskeleton, membrane trafficking, and translational regulation (2). The widespread effects of GEF domains dictate the need for tight regulation of activity, which is underscored by the observation that deregulation of RhoGEFs is associated with cellular transformation and mental retardation (1, 3).Most RhoGEFs are composed of tandem Dbl homology (DH) and pleckstrin homology (PH) domains. RhoGEFs are regulated by cellular localization, interaction of phosphoinositides with the PH domain, tyrosine phosphorylation, oligomerization, and other protein/protein interactions (2, 4 -8). Although the interaction of phosphoinositides with the PH domain seems to be a general mechanism for modulating GEF activity (5, 6, 9 -12), other regulatory mechanisms affect a subset of RhoGEFs. RhoGEFs often contain several domains that are involved in their localization, association with other proteins, and regulation of GEF activity.Approximately one-third (ϳ22) of the human RhoGEFs contain Src homology 3 (SH3) domains (see Fig. 1). The GEFs with SH3 domains can be grouped into three classes based on the number and arrangement of the domains: Group I, with SH3 domains located N-terminally to the DH and PH domains; Group II, with SH3 domains located C-terminally; and Group III, with multiple SH3 domains. Several pieces of data support the hypothesis that the SH3 domains regulate GEF activity. For example, the cellular transforming activity of Ost is inhibited by its SH3 domain (13), and the first SH3 domain of Trio is necessary for GEFmediated effects on neurite outgrowth (14).Regulation of RhoGEFs by SH3 domains could be through an inhibitory intramolecular SH3 domain/ligand association. Most SH3 domains bind to a conse...

SummaryAdhesion of human erythrocytes infected with the malaria parasite Plasmodium falciparum to host endothelium has been associated with severe forms of this disease. A number of endothelial receptors have been identified, and there is evidence that one of these, intercellular adhesion molecule-1 (ICAM-1), may play an important role in the pathology of cerebral malaria. Mutagenesis of domain 1 of ICAM-1, which is involved in parasite adhesion, shows that the binding sites for different parasite variants overlap to a large extent, but that there are subtle differences between them that correlate with their adhesive phenotypes. This suggests that the ability to bind to ICAM-1 has arisen from a common variant, but that subsequent changes have led to differences in binding avidity, which may affect pathogenesis. The definition of common binding determinants and the elucidation of links between ICAM-1 binding phenotype and disease will provide new leads in the design of therapeutic interventions.

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