Molecular Mechanisms of Recombination Restriction in the Envelope Gene of the Human Immunodeficiency Virus

Abstract

The ability of pathogens to escape the host's immune response is crucial for the establishment of persistent infections and can influence virulence. Recombination has been observed to contribute to this process by generating novel genetic variants. Although distinctive recombination patterns have been described in many viral pathogens, little is known about the influence of biases in the recombination process itself relative to selective forces acting on newly formed recombinants. Understanding these influences is important for determining how recombination contributes to pathogen genome and proteome evolution. Most previous research on recombination-driven protein evolution has focused on relatively simple proteins, usually in the context of directed evolution experiments. Here, we study recombination in the envelope gene of HIV-1 between primary isolates belonging to subtypes that recombine naturally in the HIV/AIDS pandemic. By characterizing the early steps in the generation of recombinants, we provide novel insights into the evolutionary forces that shape recombination patterns within viral populations. Specifically, we show that the combined effects of mechanistic processes that determine the locations of recombination breakpoints across the HIV-1 envelope gene, and purifying selection acting against dysfunctional recombinants, can explain almost the entire distribution of breakpoints found within this gene in nature. These constraints account for the surprising paucity of recombination breakpoints found in infected individuals within this highly variable gene. Thus, the apparent randomness of HIV evolution via recombination may in fact be relatively more predictable than anticipated. In addition, the dominance of purifying selection in localized areas of the HIV genome defines regions where functional constraints on recombinants appear particularly strong, pointing to vulnerable aspects of HIV biology.

Identifying Recombination Hot Spots in the HIV-1 Genome

“…Surprisingly, the gag hot/cold spots identified in our study match closely with those identified by analyzing patient sequences (6,9,61). This is surprising, because regions of sequence similarity are presumed to drive intersubtype recombination, and one would not expect to see the impact of local recombination hot spots after so many confounding factors, such as selection for functional proteins, drug resistance, or selection from the immune system (9,62). One of the most comprehensive studies, by Simon-Loriere and colleagues, analyzed sequences retrieved from the Los Alamos National Laboratory HIV sequence database (http://www.hiv.lanl.gov) and provides evidence of recombination (9).…”

“…This is surprising, because regions of sequence similarity are presumed to drive intersubtype recombination, and one would not expect to see the impact of local recombination hot spots after so many confounding factors, such as selection for functional proteins, drug resistance, or selection from the immune system (9,62). One of the most comprehensive studies, by Simon-Loriere and colleagues, analyzed sequences retrieved from the Los Alamos National Laboratory HIV sequence database (http://www.hiv.lanl.gov) and provides evidence of recombination (9). Their study identified two hot spots and one cold spot in the capsid of gag, corresponding to our regions G H 5 to G H 8, G H 12 and G H 13, and G H 9 and G H 10.…”

“…Recombination occurs much more frequently than mutation and is a powerful force that influences the evolution of the HIV-1 genome (for a review, see reference 4). Investigations into locations of inter/intrasubtype recombination indicate that sequence identity is sufficient to explain most breakpoint locations (6)(7)(8)(9). This is unsurprising, as sequence similarity between genomic partners is a strict requirement for efficient recombination (7,(10)(11)(12).…”

Emergent gene order in a model of modular polyketide synthases

“…Our goal here has been less to investigate the conditions favoring recombination, which is itself an interesting question discussed by many authors (25), but to examine a possible evolutionary connection between recombination and genomic architecture. The latter is particularly interesting in the case of strong interactions between genes, also known as physiological epistasis (26), which through interplay with recombination can create selective pressure for modularity in gene arrangement (27,28). The PKS system (and our simplified model of it) represent an interesting special case of epistasis associated with the requirement for multiple coadapted synthases inherent in the biosynthetic architecture.…”

HIV-1 Nucleocapsid Protein Increases Strand Transfer Recombination by Promoting Dimeric G-quartet Formation

“…Features such as genomic structures of viral RNA, genome similarity, viral and host protein factors, and selection pressures on maintaining RNA elements and viral proteins all contribute to the potential of recombination in HIV-1 (11)(12)(13)(14). A prominent hotspot for recombination was mapped previously by our group using a cell culture-based system to a 112-nt region surrounding the HIV-1 gag start codon.…”