Anders Norman, Lars H. Hansen and Soren Sorensen
Phil. Trans. R. Soc. B 2009 364: 2275-2289
Browsing the Internet for a recent review article talking generally about plasmids, I found an article written by the group of Prof. Sorensen from the University of Copenhagen in Denmark. The first surprise was the journal, which full title is Philosophical Transactions of The Royal Society B: Biological Sciences. The “Royal Society” sounds great and the journal is really good with the IF=5.9 (2008), but may be not very popular especially among molecular biologists now days. Philosophical Transactions B is divided into four cluster areas: Cell and Development, Health and Disease, Environment and Evolution, Neuroscience and Cognition. The leading theme of the August 2009 issue, where this review was published, was 'The network of life: genome beginnings and evolution'. Second, the title “…plasmids as vessels of the communal gene pool”: what does this really mean? The explanation can be found in the abstract. The authors point out that evolution of microorganisms is tightly linked to the environment in which they live and the communal (total) pool of genes within that environment. As conjugative plasmids play a major role in horizontal gene transfer (HGT) within and between different bacterial populations, the accessory genes carried by these plasmids belong to the pool of communal genes.
The review consists of seven main chapters. After a short introduction to the current bacterial evolution research based on single genomes or metagenomic DNA sequences, the authors propose some new terms (chapter 2) such as:
“supergenome” – the total pool of genes readily available to a prokaryotic organism within a particular setting;
“private pool” - which consists of the fixed and ‘idiosyncratic’ genes encoded on the chromosome of the prokaryote;
“communal pool” - which consists of genes encoded on mobile genetic elements (MGEs) and that are thus available to all permissive prokaryotes,
and discuss the relations of these new concepts to older terms like: core genome, which define the genes present in all strains of a prokaryotic species; dispensable genome (or flexible genome), which are genes present in some, but not all, strains of the same species; and pan genome—the sum of the former two.
The difference between these new and old terms is that the latter are related to a single species, while the new ones are more related to the population of microorganisms. Actually, I like the idea because it really reflects the natural state. As new DNA sequencing technologies enable us to analyze whole populations generating gigabytes/bases of information, it is better to treat this as a “supergenome-gene pool” than pan genome, especially since assembling single genomes out of this population is not an easy task and can generate many errors. On the other hand, the authors confine the communal pool to genes present on mobile genetics elements, which in my opinion is not really good as we know that the structure of these elements can be very unstable with almost continuous exchange between different genome parts (chapter 3).
I think that in ‘population genetics’/metagenomic kinds of studies based on current technology in DNA sequencing and analysis one really could concentrate on two things:
1) identification of species within the population based on 16SrDNA sequence;
2) supergenome analysis – presentation of all genes available within a population with their relative abundance – which will reflect the physiology of the analyzed population.
But back to the article; in chapter 4 and 5 –‘The tools of genetic mobility’ and ‘Mechanisms of, and barriers to, horizontal gene transfer’, the authors briefly describe different mobile elements and mechanisms that drive HGT. This leads us to the main part describing ‘The world of conjugative plasmids’, where in a few subchapters the authors describe origin of plasmids and its organization (with a description of plasmid modular structure) and discuss the role of conjugative plasmids in the cell. Finally, in the last part they talk about some methods used to study the communal gene pool and how these studies reflect on our understanding of bacterial evolution.
I found this article very well written and really interesting. It is a very current review article talking about horizontal gene transfer and conjugative plasmids with up-to-date references. Simple and relatively broad presentation of HGT and all the processes that lead to genetic exchange within microbial populations as well as a simple description of conjugative plasmids and their role in HGT make this review an ideal article as an introduction for students and researchers new to this field.
Jarek Krol PhD