A New, Expressed Multigene Family Containing a Hot Spot for Insertion of Retroelements Is Associated with Polymorphic Subtelomeric Regions of <i>Trypanosoma brucei</i>

<jats:title>ABSTRACT</jats:title> <jats:p> We describe a novel gene family that forms clusters in subtelomeric regions of <jats:italic>Trypanosoma brucei</jats:italic> chromosomes and partially accounts for the observed clustering of retrotransposons. The <jats:italic>ingi</jats:italic> and ribosomal inserted mobile element (RIME) non-LTR retrotransposons share 250 bp at both extremities and are the most abundant putatively mobile elements, with about 500 copies per haploid genome. From cDNA clones and subsequently in the <jats:italic>T. brucei</jats:italic> genomic DNA databases, we identified 52 homologous gene and pseudogene sequences, 16 of which contain a RIME and/or <jats:italic>ingi</jats:italic> retrotransposon inserted at exactly the same relative position. Here these genes are called the <jats:italic>RHS</jats:italic> family, for retrotransposon hot spot. Comparison of the protein sequences encoded by <jats:italic>RHS</jats:italic> genes (21 copies) and pseudogenes (24 copies) revealed a conserved central region containing an ATP/GTP-binding motif and the RIME/ <jats:italic>ingi</jats:italic> insertion site. The RHS proteins share between 13 and 96% identity, and six subfamilies, <jats:italic>RHS1</jats:italic> to <jats:italic>RHS6</jats:italic> , can be defined on the basis of their divergent C-terminal domains. Immunofluorescence and Western blot analyses using RHS subfamily-specific immune sera show that RHS proteins are constitutively expressed and occur mainly in the nucleus. Analysis of Genome Survey Sequence databases indicated that the <jats:italic>Trypanosoma brucei</jats:italic> diploid genome contains about 280 <jats:italic>RHS</jats:italic> (pseudo)-genes. Among the 52 identified <jats:italic>RHS</jats:italic> (pseudo)genes, 48 copies are in three <jats:italic>RHS</jats:italic> clusters located in subtelomeric regions of chromosomes Ia and II and adjacent to the active bloodstream form expression site in <jats:italic>T. brucei</jats:italic> strain TREU927/4 GUTat10.1. <jats:italic>RHS</jats:italic> genes comprise the remaining sequence of the size-polymorphic “repetitive region” described for <jats:italic>T. brucei</jats:italic> chromosome I, and a homologous gene family is present in the <jats:italic>Trypanosoma cruzi</jats:italic> genome. </jats:p>