Mutation rate and genome reduction in endosymbiotic and free-living bacteria

Université de Lyon, Centre National de la Recherche Scientifique, UMR5558, Laboratoire de Biométrie et Biologie évolutive, Villeurbanne Cedex, 69622, France.
Genetica (Impact Factor: 1.75). 12/2007; 134(2):205-10. DOI: 10.1007/s10709-007-9226-6
Source: PubMed

ABSTRACT Genome reduction has been considered the hallmark of endosymbiotic bacteria, such as endocellular mutualists or obligatory pathogens until it was found exactly the same in several free-living bacteria. In endosymbiotic bacteria genome reduction is mainly attributed to degenerative processes due to small population size. These cannot affect the free-living bacteria with reduced genomes because they are known to have very large population sizes. It has been proposed that selection for simplification drove genome reduction in these free-living bacteria. For at least one of them (Prochlorococcus), genome reduction is associated with accelerated evolution and we suggest an alternative hypothesis based on increase in mutation rate as the primary cause of genome reduction in free-living bacteria.

Download full-text


Available from: Gabriel Marais, Aug 22, 2015
  • Source
    • "Consistent with this model (Moran 2002), both the AT content (.60%) and the nucleotide substitution rate of the Paulinella plastid genomes are relatively elevated (Nowack et al. 2008; Yoon et al. 2009). The assumption that a subset of endosymbiont genes have little or no consequences for host fitness would explain why the size of endosymbiont genomes is significantly reduced over short evolutionary periods (Marais et al. 2008; Moran et al. 2009). In Paulinella, we observe that the relative distribution of plastid gene losses in FK01 and M0880/a (i.e., 39/27, respectively, vs. the null expectation of 33/33) is consistent with genetic drift as the underlying explanation (Fisher's exact test, P 5 0.382). "
  • Source
    • "Comparative genomics studies have shown that different clades possess distinct gene complements and that one of the functional categories that was most differentiated between ecotypes was DNA replication, recombination and repair (Kettler et al. 2007; Partensky & Garczarek 2010). It has been suggested that the loss of genes involved in the repair of GC to AT transversions in some genotypes may have caused them to become 'mutators', i.e. cells with an increased mutation rate (Marais et al. 2008). This type of transversion appears to have occurred at least twice during evolution, once before the differentiation of LLI-III ecotypes and a second time before the differentiation of HL ecotypes (Partensky & Garczarek 2010). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Environmental (ecological) genomics aims to understand the genetic basis of relationships between organisms and their abiotic and biotic environments. It is a rapidly progressing field of research largely due to recent advances in the speed and volume of genomic data being produced by next generation sequencing (NGS) technologies. Building on information generated by NGS-based approaches, functional genomic methodologies are being applied to identify and characterize genes and gene systems of both environmental and evolutionary relevance. Marine photosynthetic organisms (MPOs) were poorly represented amongst the early genomic models, but this situation is changing rapidly. Here we provide an overview of the recent advances in the application of ecological genomic approaches to both prokaryotic and eukaryotic MPOs. We describe how these approaches are being used to explore the biology and ecology of marine cyanobacteria and algae, particularly with regard to their functions in a broad range of marine ecosystems. Specifically, we review the ecological and evolutionary insights gained from whole genome and transcriptome sequencing projects applied to MPOs and illustrate how their genomes are yielding information on the specific features of these organisms.
    Molecular Ecology 02/2013; 22(3):867-907. DOI:10.1111/mec.12000 · 6.49 Impact Factor
  • Source
    • "Alternatively, because genome size is correlated with cell size, genome reduction may have occurred in the process of evolving a small cell volume, which may be advantageous in avoiding predation by bacterivores and/or increasing surface-to-volume ratio for uptake of scarce nutrients (Giovannoni et al. 2005; Yooseph et al. 2010). As a nonselective alternative, it has been proposed that gene loss in Prochlorococcus has resulted from an increased mutation rate (Marais et al. 2008). However, reported evidence of an increased rate of nonsynonymous substitution in Prochlorococcus (Dufresne et al. 2005) may also be explained by inefficient purifying selection, perhaps implying that effective population sizes of these bacteria are not as large as has been supposed. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Several isolates of the marine cyanobacterial genus Prochlorococcus have smaller genome sizes than those of the closely related genus Synechococcus. In order to test whether loss of protein-coding genes has contributed to genome size reduction in Prochlorococcus, we reconstructed events of gene family evolution over a strongly supported phylogeny of 12 Prochlorococcus genomes and 9 Synechococcus genomes. Significantly, more events both of loss of paralogs within gene families and of loss of entire gene families occurred in Prochlorococcus than in Synechococcus. The number of nonancestral gene families in genomes of both genera was positively correlated with the extent of genomic islands (GIs), consistent with the hypothesis that horizontal gene transfer (HGT) is associated with GIs. However, even when only isolates with comparable extents of GIs were compared, significantly more events of gene family loss and of paralog loss were seen in Prochlorococcus than in Synechococcus, implying that HGT is not the primary reason for the genome size difference between the two genera.
    Molecular Biology and Evolution 04/2011; 28(10):2751-60. DOI:10.1093/molbev/msr081 · 14.31 Impact Factor
Show more