Genomic Organization and Generation of Genetic Variability in the RHS (Retrotransposon Hot Spot) Protein Multigene Family in Trypanosoma cruzi

Abstract

Retrotransposon Hot Spot (RHS) is the most abundant gene family in Trypanosoma cruzi, with unknown function in this parasite. The aim of this work was to shed light on the organization and expression of RHS in T. cruzi. The diversity of the RHS protein family in T. cruzi was demonstrated by phylogenetic and recombination analyses. Transcribed sequences carrying the RHS domain were classified into ten distinct groups of monophyletic origin. We identified numerous recombination events among the RHS and traced the origins of the donors and target sequences. The transcribed RHS genes have a mosaic structure that may contain fragments of different RHS inserted in the target sequence. About 30% of RHS sequences are located in the subtelomere, a region very susceptible to recombination. The evolution of the RHS family has been marked by many events, including gene duplication by unequal mitotic crossing-over, homologous, as well as ectopic recombination, and gene conversion. The expression of RHS was analyzed by immunofluorescence and immunoblotting using anti-RHS antibodies. RHS proteins are evenly distributed in the nuclear region of T. cruzi replicative forms (amastigote and epimastigote), suggesting that they could be involved in the control of the chromatin structure and gene expression, as has been proposed for T. brucei.

From the origin and molecular diversity of the amastins, to the origin and diversity of intracellular parasitism from human Trypanosomatids

“…The evolution by genomic response depend of the environmental challenges response with different amounts of DNA. Finally in the case of the dangerous envrironmental challenges of the cell, the cells response with large syntheisis of DNA from the genomic response similar as retrotransposons [78][79]. As conclusion based in this analyseses the junk DNA, is immature DNA that remain in the genomes as evolutionary traces of the induction of the genomic response, form part of the large families of succesful proteins, this way is best form of create large families of proteins to resolve environmenetal challenges.…”

Genome plasticity driven by aneuploidy and loss of heterozygosity in Trypanosoma cruzi

“…However, the high number of hypothetical proteins complicates the understanding of the complete genomic organization of these segments (). RHS has been recently studied in T. cruzi and T. brucei where sequences have retrotransposon insertion sites in their 5′ coding region and coincide with large hemizygous regions and tandem amplification events [55, 56]. Unequal crossing-over between non-sister homologous chromatids with retrotransposons involved, could affect large segments of the genome and could serve as the explanation for the origins of the trisomic segments in chromosome 1, where one of the copies is deleted resulting in hemizygous, which has been demonstrated in T. brucei, where long regions of hemizygous segments affect VSG and other multigene families [57].…”

DNA Topoisomerase 3α Is Involved in Homologous Recombination Repair and Replication Stress Response in Trypanosoma cruzi

“…Since GC-rich regions have a propensity to form strong DNA secondary structures ( Zhao et al, 2017 ; Mao et al, 2018 ) and, in general, are associated with increased recombination rates ( Kiktev et al, 2018 ), mutations in this region could potentially not be resolved in the absence of TcTopo3α topoisomerase. The absence of a preferential loss of DGF-1 near replication origins ( Supplementary Figure 9 ), and the sub-telomeric localization of some DGF-1 and ∼30% or RHSs ( Bernardo et al, 2020 ) suggests that the DNA loss caused by MMS treatment was not associated with the start of DNA replication. In fact, structural instabilities in the DNA molecule that could not be resolved in the absence of the TcTopo3α could be “pushed” away from the replication origin by the DNA replication fork, until they find a highly structured region, such as DGF-1′s G-quadruplexes.…”