Functional and structural segregation of overlapping helices in HIV-1

Abstract

Overlapping coding regions balance selective forces between multiple genes. One possible division of nucleotide sequence is that the predominant selective force on a particular nucleotide can be attributed to just one gene. While this arrangement has been observed in regions in which one gene is structured and the other is disordered, we sought to explore how overlapping genes balance constraints when both protein products are structured over the same sequence. We use a combination of sequence analysis, functional assays and selection experiments to examine an overlapped region in HIV-1 that encodes helical regions in both Env and Rev. We find that functional segregation occurs even in this overlap, with each protein spacing its functional residues in a manner that allows a mutable non-binding face of one helix to encode important functional residues on a charged face in the other helix. Additionally, our experiments reveal novel and critical functional residues in Env and have implications for the therapeutic targeting of HIV-1.

Highly Similar Average Collateral Effect of Synonymous Mutations Across Alternative Reading Frames: A Potential Role In Evolvability

“…Evolutionary constraint in OLGs has not yet been studied in much detail for specific gene pairs, apart from the case of overlapping genes in HIV-1. In this virus it has been shown first that constrained regions of overlapping genes in a pair are organized so as not to overlap (79) and second that even when domains do overlap, functionally constrained residues in one protein are encoded overlapping more mutable codons in the other protein (80). Further, constraint can be conceived either negatively or positively.…”

Rev-Rev Response Element Activity Selection Bias at the HIV Transmission Bottleneck

“…Previous work by Frankel et al has demonstrated that functional regions of rev are segregated from functional regions of the overlying tat and env genes, permitting mutations that affect the activity of one protein at a time (35,36). RRE activity is similarly robust to nonsynonymous changes in Env, as the functional consequence of these mutations can be compensated by additional synonymous changes in other portions of the RRE (37,38).…”

Single-molecule epitranscriptomic analysis of full-length HIV-1 RNAs reveals functional roles of site-specific m6As

“…The A8079G mutation is situated in the overlapping region of rev and env genes, designed to be a silent mutation for Rev but inducing the substitution of glutamine with glycine at position 771 in Env. We selected this mutation because this amino acid substitution was shown to only moderately reduce HIV-1 fitness in vitro 89 . A8975C and A8989T are located in the 3′ UTR (U3) of the HIV-1 RNAs.…”