Please use this identifier to cite or link to this item: http://hdl.handle.net/11189/4570
Title: Patterns of recombination in HIV-1M are influenced by selection disfavouring the survival of recombinants with disrupted genomic RNA and protein structures
Authors: Golden, Michael
Muhire, Brejnev M
Semegni, Yves
Martin, Darren P
Keywords: HIV-1M;Genomic RNA;Protein structures;DNA/RNA molecules
Issue Date: 2014
Publisher: Plos one
Source: Golden M, Muhire BM, Semegni Y, Martin DP (2014) Patterns of Recombination in HIV-1M Are Influenced by Selection Disfavouring the Survival of Recombinants with Disrupted Genomic RNA and Protein Structures. PLoS ONE 9(6): e100400.
Abstract: Genetic recombination is a major contributor to the ongoing diversification of HIV. It is clearly apparent that across the HIVgenome there are defined recombination hot and cold spots which tend to co-localise both with genomic secondary structures and with either inter-gene boundaries or intra-gene domain boundaries. There is also good evidence that most recombination breakpoints that are detectable within the genes of natural HIV recombinants are likely to be minimally disruptive of intra-protein amino acid contacts and that these breakpoints should therefore have little impact on protein folding. Here we further investigate the impact on patterns of genetic recombination in HIV of selection favouring the maintenance of functional RNA and protein structures. We confirm that chimaeric Gag p24, reverse transcriptase, integrase, gp120 and Nef proteins that are expressed by natural HIV-1 recombinants have significantly lower degrees of predicted folding disruption than randomly generated recombinants. Similarly, we use a novel single-stranded RNA folding disruption test to show that there is significant, albeit weak, evidence that natural HIV recombinants tend to have genomic secondary structures that more closely resemble parental structures than do randomly generated recombinants. These results are consistent with the hypothesis that natural selection has acted both in the short term to purge recombinants with disrupted RNA and protein folds, and in the longer term to modify the genome architecture of HIV to ensure that recombination prone sites correspond with those where recombination will be minimally deleterious.
URI: http://dx.doi.org/10.1371/journal.pone.0100400
http://hdl.handle.net/11189/4570
Appears in Collections:HWSci - Journal Articles (DHET subsidised)

Show full item record

Page view(s)

17
Last Week
0
Last month
0
checked on Oct 20, 2018

Download(s)

7
checked on Oct 20, 2018

Google ScholarTM

Check


This item is licensed under a Creative Commons License Creative Commons