May 20, 2007

Size and shape in the genomes of actinomycetes

A new genome sequence of an antibiotic-producing actinomycete has been recently published in Nature Biotechnology. This seems to me a good excuse to highlight some peculiar aspects of genome evolution in this group of bacteria.

The mentioned microorganism is Saccharopolyspora erythraea, known as an industrial source for erythromycin. The size of the genome, 8.2 Mbp (Mbp = megabasepairs = million base pairs), is similar to that of Streptomyces coelicolor (8.7 Mbp) and Streptomyces avermitilis (9 Mbp). These are some of the largest genomes in bacteria, although much smaller genomes are found in other actinomycetes. An example of the latter is Bifidobacterium adolescentis, with only 2.1 Mbp (not to mention the obligate parasite Tropheryma whipplei, the causative agent of Whipple's disease, with a tiny 0.9-Mbp genome).

In the Sac. erythraea chromosome, the majority of conserved, essential genes are contained in a region extending either side of the origin of replication (the "core"). This genome organization consisting of core and "non-core" regions is also found in streptomycetes. The non-core region (3.8 Mbp in Sac. erythraea) includes most of the genes coding for conditionally adaptive functions, such as production of secondary metabolites (although the genes for erythromycin synthesis happen to be located in the core).

What about shape? Most bacteria possess a circular chromosome, which is the case of Sac. erythraea and the majority of actinomycetes. On the other hand, at least some species of Streptomyces and Rhodococcus contain linear chromosomes. Given that actinomycetes more closely related to Rhodococcus (such as Nocardia) possess circular chromosomes, linearization may have occurred more than once during the evolution of this group of bacteria. Remarkably, genomic instability is frequently found in Streptomyces: the non-core region of the chromosome contains transposable elements and is prone to undergo rearrangements and deletions. This leads to large-scale variations, even among genomes of the same species. When the telomeres are lost, a circular chromosome results, and there are examples of the co-existence of linear and circular forms for a particular strain. It has been proposed that linear chromosomes arose from the recombination of linear plasmids with circular chromosomes, and that linear plasmids evolved from bacteriophages.

(Figure: Schematic representation of Saccharopolyspora erythraea chromosome. Reprinted by permission from Macmillan Publishers Ltd: Nat. Biotechnol. 25: 447-453, copyright 2007).

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