Impermanence of bacterial clones

Abstract

Bacteria reproduce asexually and pass on a single genome copied from the parent, a reproductive mode that assures the clonal descent of progeny; however, a truly clonal bacterial species is extremely rare. The signal of clonality can be interrupted by gene uptake and exchange, initiating homologous recombination that results in the unique sequence of one clone being incorporated into another. Because recombination occurs sporadically and on local scales, these events are often difficult to recognize, even when considering large samples of completely sequenced genomes. Moreover, several processes can produce the appearance of clonality in populations that undergo frequent recombination. The rates and consequences of recombination have been studied in Escherichia coli for over 40 y, and, during this time, there have been several shifting views of its clonal status, population structure, and rates of gene exchange. We reexamine the studies and retrace the evolution of the methods that have assessed the extent of DNA flux, largely focusing on its impact on the E. coli genome.clonality | homologous exchange | recombination | genome evolution | E. coli R eproduction by binary fission virtually guarantees the clonality of a bacterial lineage. Apart from mutations and other rare events that might modify chromosome integrity during replication, the primary sequence of DNA in all daughter and descendent cells remains identical, generation after generation after generation. Unlike animals, in which parthenogenetic forms are ecologically constrained and relatively short-lived over evolutionary timescales (1-3), asexually reproducing bacteria have persisted since the origin of cellular life and represent the most diverse and widespread organisms on the planet. Naturally, the vast diversity present in bacteria could have arisen solely by asexual means-there has certainly been sufficient time and large enough population sizes to allow for enormous numbers of mutations (and combinations of mutations) to be experienced. Moreover, it seems as though some of the most extraordinary innovations in the history of life have occurred without intervention of the sexual process (4). Bacteria as Clonal OrganismsDespite their obligatory asexual mode of reproduction, the clonality of bacterial lineages can be disrupted by sex, or at least by what we refer to as sex. In bacteria, sex is the inheritance of genetic material from any source aside from their one parent cell and can occur by any of several processes. Foreign DNA can be introduced by cell-to-cell contact, transmitted to the cell by an infectious agent, or acquired directly from the environment; and, therefore, genes can be obtained from organisms representing any domain of life, and even from entities (i.e., viruses and phages) that are not classified to any domain of life. Moreover, events of sex in bacteria occur without known regularity and usually constitute a very small portion of the genome. In fact, sexually acquired DNA need not involve recombination at all but can persist...

Is Predominant Clonal Evolution a Common Evolutionary Adaptation to Parasitism in Pathogenic Parasitic Protozoa, Fungi, Bacteria, and Viruses?

“…The MLEE A, B1, B2, D groups identified in the historical ECOR collection of strains by pioneer studies (Ochman and Selander, 1984;Whittam et al, 1983) have been fully corroborated, and their permanency as well, by many studies relying on various genetic markers (Chaudhuri and Henderson, 2012;Clermont et al, 2011;Denamur et al, 2010;Walk et al, 2009;Wirth et al, 2006). The fact that the rate of recombination in E. coli almost equals that of mutation (Bobay et al, 2015) has not prevented the long-term stability of a strong structuring into typical near-clades. WGS makes it possible to refine this picture and to uncover new near-clades, especially in environmental strains (Chaudhuri and Henderson, 2012;Luo et al, 2011).…”

“…However, this high rate of recombination 'does not destroy the clonal status of E. coli' (Bobay et al, 2015). These results on recombination versus mutation rates suggest that they have a poor predictive power regarding the actual population structure of the species considered.…”

“…However, some authors prefer to distinguish between 'strict' clonality (i.e., mitotic propagation) and other cases where recombination is restricted too. This is the case for 'unisexual reproduction' , selfing and inbreeding (Bobay et al, 2015;Rougeron et al, 2009Rougeron et al, , 2010. This is a matter of definition.…”

“…However, in general, the authors do not distinguish it from clonality. Nevertheless, Bobay et al (2015) consider that selfing in bacteria should be distinguished from mitotic clonality even if it do not make a difference on the apparent structure of the population. With respect to applied research, restrained recombination is the most important parameter to consider for strain typing (molecular epidemiology) and tracing of genes of interest.…”

In the light of evolution IX: Clonal reproduction: Alternatives to sex

“…It is about bacteria that the "clone concept" was first elaborated at the dawn of molecular population genetics during the era of isoenzymes. Louis-Marie Bobay, Charles Traverse, and Howard Ochman (18) emphasize that limited recombination events in bacteria are very difficult to detect, even with large samples and advanced techniques, such as wholegenome sequencing. Their paper focuses on Escherichia coli, a model for bacterial population genetics for more than 40 y.…”