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: 1.4). 12/2007; 134(2):205-10. DOI: 10.1007/s10709-007-9226-6
Source: PubMed


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
  • Source
    • "Shading indicates larger mean proteome size or higher mean genome GC content, for a particular gene. ocean bacterium Candidatus Pelagibacter ubique, discussed above, and the Prochlorococcus cyanobacteria, which have also undergone reductions in cell size, P and loss of DNA repair genes (Rocap et al. 2003; Dufresne et al. 2005; Marais et al. 2008; Partensky and Garczarek 2010). Cell and genome size reduction are also observed in open ocean picoeukaryotes such as Ostreococcus tauri (the smallest freeliving eukaryote) and Micromonas species, which also have strong genome AT biases (Derelle et al. 2006; Worden et al. 2009). "
    [Show abstract] [Hide abstract]
    ABSTRACT: The concept of a "proteomic constraint" proposes that DNA repair capacity is positively correlated with the information content of a genome, which can be approximated to the size of the proteome (P). This in turn implies that DNA repair genes are more likely to be present in genomes with larger values of P. This stands in contrast to the common assumption that informational genes have a core function and so are evenly distributed across organisms. We examined the presence/absence of 18 DNA repair genes in bacterial genomes. A positive relationship between gene presence and P was observed for 17 genes in the total dataset, and 16 genes when only nonintracellular bacteria were examined. A marked reduction of DNA repair genes was observed in intracellular bacteria, consistent with their reduced value of P. We also examined archaeal and DNA virus genomes, and show that the presence of DNA repair genes is likewise related to a larger value of P. In addition, the products of the bacterial genes mutY, vsr, and ndk, involved in the correction of GC/AT mutations, are strongly associated with reduced genome GC content. We therefore propose that a reduction in information content leads to a loss of DNA repair genes and indirectly to a reduction in genome GC content in bacteria by exposure to the underlying AT mutation bias. The reduction in P may also indirectly lead to the increase in substitution rates observed in intracellular bacteria via loss of DNA repair genes. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail:
    Full-text · Article · Aug 2015 · Journal of Heredity
  • 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). "

    Full-text · Dataset · Aug 2013
  • 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.
    Full-text · Article · Feb 2013 · Molecular Ecology
Show more