Evolvability of an RNA virus is determined by its mutational neighbourhood

Novel enzyme activities and functional plasticity revealed by recombining highly homologous enzymes

BACKGROUND

Directed evolution by DNA shuffling has been used to modify physical and catalytic properties of biological systems. We have shuffled two highly homologous triazine hydrolases and conducted an exploration of the substrate specificities of the resulting enzymes to acquire a better understanding of the possible distributions of novel functions in sequence space.

RESULTS

Both parental enzymes and a library of 1600 variant triazine hydrolases were screened against a synthetic library of 15 triazines. The shuffled library contained enzymes with up to 150-fold greater transformation rates than either parent. It also contained enzymes that hydrolyzed five of eight triazines that were not substrates for either starting enzyme.

CONCLUSIONS

Permutation of nine amino acid differences resulted in a set of enzymes with surprisingly diverse patterns of reactions catalyzed. The functional richness of this small area of sequence space may aid our understanding of both natural and artificial evolution.

Evolution of digital organisms at high mutation rates leads to survival of the flattest

Darwinian evolution favours genotypes with high replication rates, a process called 'survival of the fittest'. However, knowing the replication rate of each individual genotype may not suffice to predict the eventual survivor, even in an asexual population. According to quasi-species theory, selection favours the cloud of genotypes, interconnected by mutation, whose average replication rate is highest. Here we confirm this prediction using digital organisms that self-replicate, mutate and evolve. Forty pairs of populations were derived from 40 different ancestors in identical selective environments, except that one of each pair experienced a 4-fold higher mutation rate. In 12 cases, the dominant genotype that evolved at the lower mutation rate achieved a replication rate >1.5-fold faster than its counterpart. We allowed each of these disparate pairs to compete across a range of mutation rates. In each case, as mutation rate was increased, the outcome of competition switched to favour the genotype with the lower replication rate. These genotypes, although they occupied lower fitness peaks, were located in flatter regions of the fitness surface and were therefore more robust with respect to mutations.

Evolution of the Old World Arenaviridae and their rodent hosts: generalized host-transfer or association by descent?

Ten scenarios optimizing the number of cospeciation events between the phylogenies of the Old World Arenaviridae (OWA) and their murine hosts are tested while attempting to answer the following questions. Does the coevolutionary model explain their respective distribution? What kind of evolutionary events could have most frequently contributed to the horizontal and/or vertical transmission of the OWA? How to define secondary hosts and to interpret their existence in the evolutionary process? Where are the geographical origins of the OWA? All scenarios support the "diffuse coevolution" hypothesis previously proposed for the OWA, in which parallel phylogeny and/or host switches on closely related hosts can be considered as the most common mechanisms of transmission. The scenarios allow defining more precisely the concepts of principal and secondary hosts. Such scenarios also suggest that the diversity of the viruses and their rodent hosts could be higher than currently expected and that cophylogeny could have been underestimated. The "diffuse coevolution" hypothesis permits to interpret the transfer of the viruses to distant hosts as a result of a disturbance in their regular mode of dispersion, which could match with the periods of emergence as human parasites. The comparison of the viral phylogeny with the host cladogram also suggests that the viruses parasitized the Murinae before several lineages became distinct and spread in Africa. This supposes that the origin of the arenaviruses has to be found out of Africa.

Evolution: towards a genetical theory of adaptation

The population genetic basis for adaptation has remained obscure despite a longstanding body of theory. Microbial selection experiments are beginning to provide some answers.

Perspective: reverse evolution

For some time, the reversibility of evolution was primarily discussed in terms of comparative patterns. Only recently has this problem been studied using experimental evolution over shorter evolutionary time frames. This has raised questions of definition, experimental procedure, and the hypotheses being tested. Experimental evolution has provided evidence for multiple population genetic mechanisms in reverse evolution, including pleiotropy and mutation accumulation. It has also pointed to genetic factors that might prevent reverse evolution, such as a lack of genetic variability, epistasis, and differential genotype-by-environment interactions. The main focus of this perspective is on laboratory studies and their relevance to the genetics of reverse evolution. We discuss reverse evolution experiments with Drosophila, bacterial, and viral populations. Field studies of the reverse evolution of melanism in the peppered moth are also reviewed.

Variability and genetic structure of plant virus populations

Populations of plant viruses, like all other living beings, are genetically heterogeneous, a property long recognized in plant virology. Only recently have the processes resulting in genetic variation and diversity in virus populations and genetic structure been analyzed quantitatively. The subject of this review is the analysis of genetic variation, its quantification in plant virus populations, and what factors and processes determine the genetic structure of these populations and its temporal change. The high potential for genetic variation in plant viruses, through either mutation or genetic exchange by recombination or reassortment of genomic segments, need not necessarily result in high diversity of virus populations. Selection by factors such as the interaction of the virus with host plants and vectors and random genetic drift may in fact reduce genetic diversity in populations. There is evidence that negative selection results in virus-encoded proteins being not more variable than those of their hosts and vectors. Evidence suggests that small population diversity, and genetic stability, is the rule. Populations of plant viruses often consist of a few genetic variants and many infrequent variants. Their distribution may provide evidence of a population that is undifferentiated, differentiated by factors such as location, host plant, or time, or that fluctuates randomly in composition, depending on the virus.