Mapping of VSG similarities in Trypanosoma brucei

Abstract

The protozoan parasite Trypanosoma brucei switches its variant surface glycoprotein (VSG) to subvert its mammalian hosts’ immune responses. The T. brucei genome contains as many as 1600 VSG genes (VSGs), but most are silent noncoding pseudogenes. Only one functional VSG, located in a telomere-linked expression site, is transcribed at a time. Silent VSGs are copied into a VSG expression site through gene conversion. Truncated gene conversion events can generate new mosaic VSGs with segments of sequence identity to other VSGs. To examine the VSG family sub-structure within which these events occur, we combined the available VSG sequences and annotations with scripted BLAST searches to map the relationships among VSGs in the T. brucei genome. Clusters of related VSGs were visualized in 2- and 3-dimensions for different N- and C-terminal regions. Five types of N-termini (N1 – N5) were observed, within which gene recombinational events are likely to occur, often with fully-coding ‘functional’ or ‘atypical’ VSGs centrally located between more dissimilar VSGs. Members of types N1, N3 and N4 are most closely related in the middle of the N-terminal region, whereas type N2 members are more similar near the N-terminus. Some preference occurs in pairing between specific N- and C- terminal types. Statistical analyses indicated no overall tendency for more related VSGs to be located closer in the genome than less related VSGs, although exceptions were noted. Many potential mosaic gene formation events within each N-terminal type were identified, contrasted by only one possible mosaic gene formation between N-terminal types (N1 and N2). These data suggest that mosaic gene formation is a major contributor to the overall VSG diversity, even though gene recombinational events between members of different N-terminal types occur only rarely.

Transcriptome Profiling of Trypanosoma brucei Development in the Tsetse Fly Vector Glossina morsitans

“…The invariant surface glycoproteins have been described more than 20 years ago [36] and although it was recently shown that a bloodstream stage-specific ISG75 family mediates suramin uptake [37], these invariant proteins remain poorly characterized and it is not known what role, if any, they play during the trypanosome development cycle. Atypical VSGs are another family of poorly characterized surface proteins and they were named atypical, because they lack cysteine residues in the C terminus [38]. Finally, the salivary gland CSP data set revealed four up-regulated transcripts encoding hypothetical proteins with predicted GPI anchors (Tb927.7.360, Tb927.7.380, Tb927.7.400, Tb927.7.420), that we previously showed by RT-PCR to be up-regulated in trypanosomes residing in salivary glands [16, 39].…”

Recombination-driven generation of the largest pathogen repository of antigen variants in the protozoan Trypanosoma cruzi

“…For gene families such as TcTS containing thousands of members, such methods are not possible. Alternatively, BLAST algorithms can be used to find local sequence matches between different family members [ 31 ] or phylogenetic incompatibility distribution can be used as an index to estimate recombination activity [ 13 ] and such methods have been applied to document recombination events in the T. brucei VSG gene family. However, such alternative methods, unlike the classical recombination analysis, cannot ensure both statistical support and the search-comprehensiveness of recombination events.…”

Computational approaches to the study of human trypanosomatid infections

“…animation of the clustered BLAST analysis graph. 70 Using an even less stringent E-value of E < 1e-02, the separation between five N-terminal types is clearly observed. The video figure S1 published by Weirather et al 70 also illustrates additional features, such as the possibility of subgroups within the N1 cluster.…”

“…These 3D visualizations reveal substructures not easily visualized in the 2D graphs. 70 2.2.10. Detection of mosaic genes BLAST hits between functional VSGs and other VSGs were used to illustrate regions of possible mosaic gene formation.…”

“…Types C4 and C6 are not readily discernable ( Figure 4A, C). Viewing the clustering in a 3D animation provides better visual resolution of the C2 type; 70 however, the high degree of similarity among most of the C-terminal types and thus the dense graph of BLAST hits among types precludes resolution of all but the most different types. Interestingly, some small sets of VSG sequences coding for C-terminal domains did not cluster with any other known types.…”