Uncovering Pseudogenes and Intergenic Protein-coding Sequences in TriTryps’ Genomes

Abstract

Trypanosomatids belong to a remarkable group of unicellular, parasitic organisms of the order Kinetoplastida, an early diverging branch of the phylogenetic tree of eukaryotes, exhibiting intriguing biological characteristics affecting gene expression (intronless polycistronic transcription, trans-splicing, and RNA editing), metabolism, surface molecules, and organelles (compartmentalization of glycolysis, variation of the surface molecules, and unique mitochondrial DNA), cell biology and life cycle (phagocytic vacuoles evasion, and intricate patterns of cell morphogenesis). With numerous genomic-scale data of several trypanosomatids becoming available since 2005 (genomes, transcriptomes, and proteomes), the scientific community can further investigate the mechanisms underlying these unusual features and address other unexplored phenomena possibly revealing biological aspects of the early evolution of eukaryotes. One fundamental aspect comprises the processes and mechanisms involved in the acquisition and loss of genes throughout the evolutionary history of these primitive microorganisms. Here, we present a comprehensive in silico analysis of pseudogenes in three major representatives of this group: Leishmania major, Trypanosoma brucei, and Trypanosoma cruzi. Pseudogenes, DNA segments originating from altered genes that lost their original function, are genomic relics that can offer an essential record of the evolutionary history of functional genes, as well as clues about the dynamics and evolution of hosting genomes. Scanning these genomes with functional proteins as proxies to reveal intergenic regions with protein-coding features, relying on a customized threshold to distinguish statistically and biologically significant sequence similarities, and reassembling remnant sequences from their debris, we found thousands of pseudogenes and hundreds of open reading frames (ORFs), with particular characteristics in each trypanosomatid: mutation profile, number, content, density, codon bias, average size, single- or multi-copy gene origin, number and type of mutations, putative primitive function, and transcriptional activity. These features suggest a common process of pseudogene formation, different patterns of pseudogene evolution and extant biological functions, and/or distinct genome organization undertaken by those parasites during evolution, as well as different evolutionary and/or selective pressures acting on distinct lineages.

Exploring the Genomic Landscape of the GP63 family inTrypanosoma cruzi: Evolutionary Dynamics and Functional Peculiarities

“…Concerning pseudogenes, it is important to bear in mind that many sequences classified as pseudogenes may actually represent remnant fragments of the same former functional GP63 gene that underwent pseudogenization, as already reported for most trypanosomatid genes (19). In fact, among the 281 sequences previously classified as pseudogenes, 63 are observed in pairs or groups, either juxtaposed, overlapping, or separated by short distances.…”

Genomic surveillance: a potential shortcut for effective Chagas disease management

“…These are intergenic regions displaying protein-coding features, resembling known functional protein(s), bearing substitution(s) and/or insertion(s)/deletion(s) disrupting their open reading frames, which are remnants of the processes of acquisition and gene loss throughout the parasite’s evolutionary history. 50 Surface protein sequence diversity enables immune evasion during infection and represent a major challenge in the development of vaccines. 51 Also, variations in gene copy number and in the size of chromosomes have already been reported, 43 , 52 including in cells that presumably had a clonal relationship, as they were artificially cultured in mammalian epithelial cells.…”