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Chapter 25 : Evolution and Population Genetics of Bacterial Plasmids

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Abstract:

The distinction between plasmids and chromosomes has been blurred by the discovery of megaplasmids and small chromosomes through the use of pulsed-field gel electrophoresis. This chapter considers why plasmids have survived at all if they are not essential to their host and how they have evolved. Population genetics seeks to explain the evolution of species by considering the competition between individuals in a population and the effect that genetic differences have on this competition. An insight into the process can be gained from comparison of so-called operons of many self-transmissible bacterial plasmids of gram-negative bacteria. The function may be inserted diametrically opposite or it may occur close to the replicon. It may be, for example, that a location close to the region allows the genes to function better because partitioning of early replicated DNA is easier than for late replicated DNA. The selective pressure that promotes plasmid evolution does not work just at the level of competition between bacteria. It is widely accepted that to allow drift to occur requires gene duplication. However, for any other than an absolutely unit copy number plasmid, effective gene duplication is a way of life. The circumstances that place a premium on such evolution involve constantly changing physical/chemical and biological environments inherent to most microbial communities.

Citation: Thomas C. 2004. Evolution and Population Genetics of Bacterial Plasmids, p 509-528. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch25

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Figure 1

Evolution of microbial genomes. A number of authors have speculated on how bacterial genomes have evolved, for example, references 87, 106. The idea that the original genome may have consisted of multiple, relatively small, self-replicating molecules propagating beneficial traits fits with the diversity being discovered within the sequences of bacterial genomes. Integration would initially generate hybrids. Resolution to leave the bulk of the genes joined to the lower-copy-number and more stable replicon would be favored, the higher-copy-number replicon becoming free to develop as a plasmid. The process would repeat itself to increase the efficient transmission of genetic information

Citation: Thomas C. 2004. Evolution and Population Genetics of Bacterial Plasmids, p 509-528. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch25
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Image of Figure 2
Figure 2

The benefits of plasmid transfer. Conjugative transfer genes could benefit the host particularly when integrated into the chromosome. However, the genes themselves would not evolve so fast as if they spread to new hosts, which would be much more likely to occur if they were joined to a plasmid.

Citation: Thomas C. 2004. Evolution and Population Genetics of Bacterial Plasmids, p 509-528. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch25
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Figure 3

Variations in niche properties in space and time. A niche is often defined by more than one parameter. For example, the presence of an inhibitory substance may be constant while a second one, such as carbon source, may vary, perhaps in a cyclic way. Initially bacterium BI is well adapted, being both resistant (gene Rl) and able to utilize the carbon source due to catabolic genes CI. If resistance to the inhibitory substance is on a mobile element, then this can transfer to a new host (B2) that may be better able to use the second carbon source due to genes C2. Thus the mobile element provides the constant genetic trait in the niche.

Citation: Thomas C. 2004. Evolution and Population Genetics of Bacterial Plasmids, p 509-528. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch25
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Figure 4

Rearrangement of genes by excision and integration. (A) Examples of related operons are shown indicating related genes. The examples are selected to show how the same set of genes can appear in different, circular permutations of the same basic order. (B) A proposed explanation for the circular permutation, based on illegitimate excision to form a circle, followed by reintegration in a new location by a similar process, but with the site of integration lying between a different pair of genes. Each step is known to be possible, and the comparative order of genes in the operons provides the evidence that they have occurred.

Citation: Thomas C. 2004. Evolution and Population Genetics of Bacterial Plasmids, p 509-528. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch25
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Figure 5

Clustering of maintenance functions. A plasmid acquires a new stability function that provides an advantage in its present context. Once a plasmid has acquired a new beneficial trait, derivatives that have lost that trait will be disfavored relative to ones that retain it. Random deletions will tend to bring these maintenance functions closer together, and once the plasmid sectors are unequal, insertions will tend to occur in the longer arm. Occasionally the replicon will loop out on a small circle as in Fig. 1 , but only if it is able to carry with it the additional stability functions of the parent plasmid will it outcompete its larger parent.

Citation: Thomas C. 2004. Evolution and Population Genetics of Bacterial Plasmids, p 509-528. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch25
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Figure 6

Interplasmid competition driving plasmid evolution. (A) Cointegrate plasmids and evolution. Pairs of incompatible plasmids A1/A2 and B1/B2 compete equally between themselves. However, any cointegrate plasmid between an A and a B plasmid will immediately have an advantage over either parent, because it will have a backup replication system. (B) The drive to acquire multiple postsegregational killing systems. Two plasmids carrying the same postsegregational killing system will effectively neutralize the advantage of carrying such a system for the other plasmid, because loss of one plasmid will not result in loss of the antidote for the killer. Any plasmid that acquires a second postsegregational killing system will regain the advantage.

Citation: Thomas C. 2004. Evolution and Population Genetics of Bacterial Plasmids, p 509-528. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch25
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