Exploring the genomic landscape of the GP63 family in Trypanosoma cruzi: Evolutionary dynamics and functional peculiarities

Members of the GP63 metalloprotease family play crucial roles in parasite-host interactions, immune evasion, and pathogenesis. Although it has been widely studied in Leishmania spp., less is known about its function and diversity in Trypanosoma cruzi. This study focuses on characterizing the complete repertoire of GP63 sequences in the T. cruzi genome, refining gene annotations, and exploring the evolutionary dynamics that shape the diversity of these proteins. Eleven GP63 groups were identified, which are sharply defined and have a higher intra- than inter-group sequence identity. These GP63 groups display some distinctive features. First, two groups lack an essential amino acid in the active site, indicating that they are enzymatically inactive. Second, GP63 groups show strong preference for different genomic compartments. Moreover, genes from groups located in the core genome compartment of T. cruzi, are often arranged as tandem arrays (of larger genomic fragments that generally include a SIRE retroposon), whereas genes from groups located in the disruptive compartment tend to be surrounded by genes encoding other surface proteins (such as MASP, mucins and trans-sialidases). Transcription patterns across different life cycle stages are not homogenous. Instead, some GP63 groups have higher mRNA levels in the infective trypomastigote stage, suggesting a potential role in host invasion. To get a wider picture of the evolutionary dynamics of these proteins, a phylogenetic analysis was conducted that included species representative of kinetoplastid diversity. It was found that 10 out of 11 GP63 T. cruzi groups are specific to the Trypanosoma genus, suggesting that the diversification of these subfamilies took place before speciation of the genus, followed by other species-specific expansions. Additionally, there are other GP63 groups that are absent in T. cruzi. Notably, the processes of expansion and diversification of GP63 in Leishmania is independent of that of trypanosomes. This suggests that these proteins may have evolved under species-specific selective (functional) pressures, resulting in unique amplifications in each parasite species.