Conserved associations between G-quadruplex-forming DNA motifs and virulence gene families in malaria parasites

Abstract

Background: The Plasmodium genus of malaria parasites encodes several families of antigen-encoding genes. These genes tend to be hyper-variable, highly recombinogenic and variantly expressed. The best-characterized family is the var genes, exclusively found in the Laveranian subgenus of malaria parasites infecting humans and great apes. Var genes encode major virulence factors involved in immune evasion and the maintenance of chronic infections. In the human parasite P. falciparum, var gene recombination and diversification appear to be promoted by G-quadruplex (G4) DNA motifs, which are strongly associated with var genes in P. falciparum. Here, we investigated how this association might have evolved across Plasmodium speciesboth Laverania and also more distantly related species which lack vars but encode other, more ancient variant gene families. Results: The association between var genes and G4-forming motifs was conserved across Laverania, spanning~1 million years of evolutionary time, with suggestive evidence for evolution of the association occurring within this subgenus. In rodent malaria species, G4-forming motifs were somewhat associated with pir genes, but this was not conserved in the Laverania, nor did we find a strong association of these motifs with any gene family in a second outgroup of avian malaria parasites. Secondly, we compared two different G4 prediction algorithms in their performance on extremely A/T-rich Plasmodium genomes, and also compared these predictions with experimental data from G4-seq, a DNA sequencing method for identifying G4-forming motifs. We found a surprising lack of concordance between the two algorithms and also between the algorithms and G4-seq data. Conclusions: G4-forming motifs are uniquely strongly associated with Plasmodium var genes, suggesting a particular role for G4s in recombination and diversification of these genes. Secondly, in the A/T-rich genomes of Plasmodium species, the choice of prediction algorithm may be particularly influential when studying G4s in these important protozoan pathogens.

In-Depth Bioinformatic Analyses of Nidovirales Including Human SARS-CoV-2, SARS-CoV, MERS-CoV Viruses Suggest Important Roles of Non-canonical Nucleic Acid Structures in Their Lifecycles

“…Moreover, our analyses suggest that G-quadruplexes have been evolutionally eliminated in some genomes of Nidovirales. This is quite surprising, considering that G-quadruplexes have been found in all evolutionary groups, including such CG low-level organisms as Saccharomyces cerevisiae (Bartas et al, 2019;Brázda et al, 2019;Singh and Lakhanpaul, 2019;Gage and Merrick, 2020). In fact, it could be an evolutionary advantage not to present G-quadruplex in viral genome because a number of cellular proteins interact with G-quadruplexes (Brázda et al, 2014;Mishra et al, 2016) and therefore the presence of G-quadruplex in viral genome could serve as a structure recognized by the innate immune system (Unterholzner et al, 2010;Hároníková et al, 2016;Voter et al, 2020).…”

G-quadruplex RNA motifs influence gene expression in the malaria parasitePlasmodium falciparum

“…PF3D7_0500800 mature parasite-infected erythrocyte surface antigen Other P.fa genes 10 (0) 5 (4) 14 (0) 11 (5) (which was not certified by peer review) is the author/funder. All rights reserved.…”

“…It is classically formed from four tracts of at least three guanines found in close proximity on the same strand: these are arranged as three or more quartets stacked on top of one another 7 . The requisite guanine density is a rare feature in A/T-biased genomes, but the existence of G-quadruplexes has nevertheless been predicted in the P. falciparum genome by searching for the consensus sequence (G 3 N x ) 4 4,5,8 . Only ~100 PQSs are found outside the inherently-G-rich telomeres: this is approximately one per 300kb of the non-telomeric genome, compared to an average of one per kb in the human genome 9 .…”

Identifying and validating the presence of Guanine-Quadruplexes (G4) within the blood fluke parasite Schistosoma mansoni

“…In P . falciparum , a species with a particularly AT rich genome, putative quadruplex forming sequences (PQS) are found within VAR genes as well as in telomeric regions [ 11 , 15 , 18 ]. In T .…”