Weaver, K. E., Kwong, S. M., Firth, N. & Francia, M. V. (2009).The RepA_N replicons of Gram-positive bacteria: a family of broadly distributed but narrow host range plasmids. Plasmid 61, 94–109.
Considering the rate at which sequence databases, and therefore our knowledge of existing plasmids, are growing, it is becoming increasingly important to organize and categorize plasmids into relevant groups. Proper organization of known plasmids would allow us to unravel evolutionary histories and make more efficient the process of integrating our current knowledge. In this article, Weaver et. al. propose to create a family of plasmids characterized by RepA_N, a highly conserved domain in the initiator protein.
Unlike most other plasmid classification systems, this family is not based upon the incompatibility of two plasmids due to similar replication machineryc. Indeed, many of the plasmids within the RepA_N family can stably coexist within a single host bacterium (Kwong et. al. 2008). Rather, the determining characteristic of this plasmid is this conserved initiator protein domain. Phylogenies based on RepA_N matched those of each plasmid’s hosts. What’s more, members of this family are narrow host range plasmids but are found in a diverse range of low G+C gram-positive bacteria (Firth et al., 2000). This suggests that RepA_N family plasmids were present in ancestral gram-positive bacteria of low G+C content and then proceeded to diverge with individual hosts at an early split in the host evolution.
When compared to phylogenies based on other protein domains the modular nature of plasmid evolution becomes apparent. Phylogenies based on RepB, for instance, do not match with host phylogenies or those of RepA_N. RepB is just one among many examples of how plasmids can acquire complete, functional units of DNA from various sources throughout their evolutionary histories. The authors site the specific examples of the replication, partition, and conjugative components of RepA_N plasmids as evolving by “shuffling” between various other plasmids that are found within the same host. Again, RepA_N serves as a good classification marker in that it is conserved within each host and matches its host’s phylogeny.
This article touched on several points that bear particular attention. To begin, the authors point out that this sort of a study cannot be effective without a certain volume of raw data in sequence databases, which was not feasible even a few years ago but is now available and growing. Secondly, with such data evolutionary histories of plasmids and their coevolution with their bacterial hosts can be elucidated and that such information is vital to our understanding of why plasmids are distributed as they are today (e.g., how a family of plasmids can be both broadly distributed and only stably transferred to and maintained in a narrow host range). Finally, this study provides several excellent examples of the modular nature of plasmid evolution. Hopefully in the future available information on previously uncharacterized plasmids will continue to grow and will continue to be organized such that more such evolutionary insights may be made in the future.
Kwong, S.M., Lim, R., LeBard, R.J., Skurray, R.A., Firth, N., 2008. Analysis of the pSK1 replicon, a prototype from the staphylococcal multiresistance plasmid family. Microbiology 154, 3084–3094.
Firth, N., Apisiridej, S., Berg, T., O’Rourke, B.A., Curnock, S., Dyke, K.G.H., Skurray, R.A., 2000. Replication of staphylococcal multiresistance plasmids. J. Bacteriol. 182, 2170–2178.
Department of Biological Sciences
University of Idaho