The Kinetic and Thermodynamic Aftermath of Horizontal Gene Transfer Governs Evolutionary Recovery

Abstract

Shared host cells can serve as melting pots for viral genomes, giving many phylogenies a web-like appearance due to horizontal gene transfer. However, not all virus families exhibit web-like phylogenies. Microviruses form three distinct clades, represented by φX174, G4, and α3. Here, we investigate protein-based barriers to horizontal gene transfer between clades. We transferred gene G, which encodes a structural protein, between φX174 and G4, and monitored the evolutionary recovery of the resulting chimeras. In both cases, particle assembly was the major barrier after gene transfer. The G4φXG chimera displayed a temperature-sensitive assembly defect that could easily be corrected through single mutations that promote productive assembly. Gene transfer in the other direction was more problematic. The initial φXG4G chimera required an exogenous supply of both the φX174 major spike G and DNA pilot H proteins. Elevated DNA pilot protein levels may be required to compensate for off-pathway reactions that may have become thermodynamically and/or kinetically favored when the foreign spike protein was present. After three targeted genetic selections, the foreign spike protein was productively integrated into the φX174 background. The first adaption involved a global decrease in gene expression. This was followed by modifications affecting key protein-protein interactions that govern assembly. Finally, gene expression was re-elevated. Although the first selection suppresses nonproductive reactions, subsequent selections promote productive assembly and ultimately viability. However, viable chimeric strains exhibited reduced fitness compared with wild-type. This chimera's path to recovery may partially explain how unusual recombinant viruses could persist long enough to naturally emerge.

Structural changes of tailless bacteriophage ΦX174 during penetration of bacterial cell walls

“…In time course experiments, most of the infectivity was lost during the first 5 min ( Fig. S1), consistent with the results of previous in vivo studies (17,19,20). Both native and LPS-treated ΦX174 particles…”

No Cost of Complexity in Bacteriophages Adapting to a Complex Environment

“…These early mutations initiated trajectories which led to higher end-point growth rates than three of the four wt lines. Sign epistasis has been well documented within the the genomes of microvirid bacteriophages (Sackman and Rokyta 2018;Rokyta et al 2011;Caudle et al 2014;Doore and Fane 2015), indicating that the fitness landscape is at least moderately rugged, and that the higher adaptive peaks reached by the ID8evol lines may have been inaccessible without the mutations fixed during the original growth adaptation of ID8, which would not have been as highly favored as the mutations fixed by the ID8wt lines because of their reduced fitness benefit in the context of two-trait selection (as seen by the fitness trajectories of the original growth adaptations of ID8 and NC28 in green on Figure 1 being significantly below those of their wt counterparts during the first 80 passages of adaptation).…”

“…These early mutations initiated trajectories which led 265 to higher end-point growth rates than three of the four wt lines. Sign epistasis has been 266 well documented within the the genomes of microvirid bacteriophages (Sackman and 267 Rokyta, 2018;Rokyta et al, 2011;Caudle et al, 2014;Doore and Fane, 2015), indicating 268 that the fitness landscape is at least moderately rugged, and that the higher adaptive (Tables 1; 2), has the third largest 278 effect on growth rate of any of the 24 unique first-step mutations previously identified 279 on the wild-type ID8 background, and was also the most commonly fixed first-step 280 mutation under growth-only selection (McGee et al, 2016). However, its deleterious 281 effect on decay rate results in only a modest total benefit to fitness under heat-shock 282 conditions, and it would therefore have been unlikely to fix early in the evolution of the 283 ID8wt lineages when mutations of larger synergistic effect were available.…”

Peer Review #3 of "Intergenic incompatibilities reduce fitness in hybrids of extremely closely related bacteriophages (v0.1)"

“…Epistasis has been implicated in the evolution of sexual reproduction (Otto and Gerstein, 2006), and an understanding of epistasis is essential to the field of personal genomics and to the unraveling of the genetic architectures of complex diseases (Moore and Williams, 2009;Green et al, 2010). Epistasis also poses a potential barrier to the evolutionary success of recombinant genomes (Kouyos et al, 2007;Sackman and Rokyta, 2013;Doore and Fane, 2015), and genic incompatibility, such as may be caused by epistasis, can enforce divergence between distinct lineages (Coyne and Orr, 2004). Horizontal gene transfer and recombination occur naturally in a wide array of viruses, including hepatitis E virus (Wang et al, 2010), hepatitis B virus (Lyons et al, 2012), and humam immunodeficiency virus (Motomura et al, 2008;Rigby et al, 2009;Ssemwanga et al, 2011), as well as in microvirid bacteriophages (Rokyta et al, 2006), and these processes may play a large role in microbial evolution and divergence (de la Cruz and Davis, 2000;Rokyta et al, 2006).…”