Fig 1.
Distinct Clustering of GP63 into 11 Groups.
A) Phylogenetic analysis of amino acid sequences of the 96 GP63 genes from T. cruzi Dm28c, illustrating the division into 11 unique groups. B) Network visualization in Gephi of the pairwise identity distances among the 96 amino acid sequences of GP63 genes, where nodes symbolize genes (color coding matches the phylogeny in A), and the color of each edge indicates the level of identity. C) Identity matrix displaying average intra-group and inter-group amino acid identities, highlighting the distinctiveness of each group. D) Network visualization similar to B, with genes colored according to the genomic compartment to which they belong: green for the core compartment and pink for the disruptive compartment.
Fig 2.
GP63 Gene Environment Composition.
A) Diagram showing the average distance of GP63 genes with respect to their neighboring genes in the core (left) and disruptive (right) compartments. B) Analysis of the environment of GP63 genes within the core and the disruptive compartment illustrating the predominant genes found adjacent to each GP63 gene, focusing on the three genes upstream and downstream. C) Examples of GP63 gene environments in both compartments, with visuals sourced from http://bioinformatica.fcien.edu.uy/cruzi/browser/dm28c.500.php. For these examples, the contig and starting location of the depicted fragments are specified. Each region presents a schematic dotplot, showing the organization of the tandem repeats.
Fig 3.
Structure of GP63 Group proteins.
This figure provides a schematic overview of each GP63 group, depicting protein length, the location of the M8 domain, and the presence of signal peptides and GPI anchors. On the left side, each group is indicated and the number of sequences in each group is given in brackets. On the right side, the catalytic domain HEXXHXXG, the spacer to the subsequent histidine, and the conservation of the Met-turn are illustrated, along with all group-specific variations highlighted in red.
Fig 4.
Expression profiles at the ARNm levels in the different GP63 groups.
Each graph shows the expression profiles of the genes in each GP63 group. On the y-axis, expression levels are expressed in transcripts per million (tpm). Levels of expression were categorized as low, medium and high, and coloured differently. On the x-axis are the three stages of T. cruzi: Epimastigotes (E), Amastigotes (A) and Trypomastigotes (T). The black dots in each graph represent each individual gene. Statistical analysis of differential expression between stages was performed by one way ANOVA. *** represents a p-value <0.001.
Fig 5.
Phylogenetic Analysis of GP63 UTRs.
Phylogenetic analysis of the 5’UTRs (450nt) on the left and the 3’UTRs (700nt) on the right. Groups are differentiated by color coding, and labels include the name of the respective gene and group. UTRs that do not cluster with their respective groups are highlighted with a black arrow. Additionally, nodes are colored based on the genomic compartment to which they belong.
Fig 6.
Phylogenetic Analysis of representative GP63 Genes Across Kinetoplastids.
Phylogenetic analysis using PhyML (Maximum Likelihood method) based on the JTT model with gamma distribution and 100 bootstrap pseudoreplicates. It focuses on the entire GP63 amino acid sequences from representative genes of T. cruzi, T. cruzi marinkellei, T. rangeli, T. grayi, T. theileri, T. vivax, T. congolense, T. brucei, Leishmania major, L. braziliensis, Strigomonas culicis, and Bodo saltans.
Fig 7.
Global Phylogenetic Analysis of GP63 Genes Across Kinetoplastids.
Phylogenetic analysis of an enriched dataset of 282 sequences from a diverse array of kinetoplastids, i.e.,: T. cruzi, T. cruzi marinkellei, T. rangeli, T. grayi, T. theileri, T. vivax, T. congolense, T. brucei, L. major, L. braziliensis, Strigomonas culicis, and Bodo saltans. Pseudoreplicates support values above 75 are indicated at the respective nodes.