Comparative genomics of gene-family size in closely related bacteria

Pushker, Ravindra; Mira, Álex; Rodrı́guez-Valera, Francisco

doi:10.1186/gb-2004-5-4-r27

Cited by 61 publications

(54 citation statements)

References 42 publications

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“…Smaller genomes, such as those found in intracellular parasites and endosymbionts, were previously shown to have smaller families [30], [31]. Our results reveal that Reduced genomes had smaller families than could be expected if they followed the same trend as the FL genomes, in particular, they had a significantly higher number of singletons, i.e.…”

Section: Resultssupporting

confidence: 48%

Loss of Genetic Redundancy in Reductive Genome Evolution

2011

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Biological systems evolved to be functionally robust in uncertain environments, but also highly adaptable. Such robustness is partly achieved by genetic redundancy, where the failure of a specific component through mutation or environmental challenge can be compensated by duplicate components capable of performing, to a limited extent, the same function. Highly variable environments require very robust systems. Conversely, predictable environments should not place a high selective value on robustness. Here we test this hypothesis by investigating the evolutionary dynamics of genetic redundancy in extremely reduced genomes, found mostly in intracellular parasites and endosymbionts. By combining data analysis with simulations of genome evolution we show that in the extensive gene loss suffered by reduced genomes there is a selective drive to keep the diversity of protein families while sacrificing paralogy. We show that this is not a by-product of the known drivers of genome reduction and that there is very limited convergence to a common core of families, indicating that the repertoire of protein families in reduced genomes is the result of historical contingency and niche-specific adaptations. We propose that our observations reflect a loss of genetic redundancy due to a decreased selection for robustness in a predictable environment.

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Section: Resultssupporting

confidence: 48%

Loss of Genetic Redundancy in Reductive Genome Evolution

2011

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“…CP000113). (12,13), and global studies have borne out the importance of duplications in bacteria (14,15).…”

Section: Resultsmentioning

confidence: 99%

Evolution of sensory complexity recorded in a myxobacterial genome

Goldman

Nierman

Kaiser

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

412

483

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Myxobacteria are single-celled, but social, eubacterial predators. Upon starvation they build multicellular fruiting bodies using a developmental program that progressively changes the pattern of cell movement and the repertoire of genes expressed. Development terminates with spore differentiation and is coordinated by both diffusible and cell-bound signals. The growth and development of Myxococcus xanthus is regulated by the integration of multiple signals from outside the cells with physiological signals from within. A collection of M. xanthus cells behaves, in many respects, like a multicellular organism. For these reasons M. xanthus offers unparalleled access to a regulatory network that controls development and that organizes cell movement on surfaces. The genome of M. xanthus is large (9.14 Mb), considerably larger than the other sequenced δ-proteobacteria. We suggest that gene duplication and divergence were major contributors to genomic expansion from its progenitor. More than 1,500 duplications specific to the myxobacterial lineage were identified, representing >15% of the total genes. Genes were not duplicated at random; rather, genes for cell–cell signaling, small molecule sensing, and integrative transcription control were amplified selectively. Families of genes encoding the production of secondary metabolites are overrepresented in the genome but may have been received by horizontal gene transfer and are likely to be important for predation.

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“…This is a remarkable example of xenologous gene replacement (28) in the case of coding for ubiquitous functions.…”

Section: Discussionmentioning

confidence: 99%

Degradation of nanoRNA is performed by multiple redundant RNases in Bacillus subtilis

Fang

Zeisberg

Condon

et al. 2009

Nucleic Acids Research

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Escherichia coli possesses only one essential oligoribonuclease (Orn), an enzyme that can degrade oligoribonucleotides of five residues and shorter in length (nanoRNA). Firmicutes including Bacillus subtilis do not have an Orn homolog. We had previously identified YtqI (NrnA) as functional analog of Orn in B. subtilis. Screening a genomic library from B. subtilis for genes that can complement a conditional orn mutant, we identify here YngD (NrnB) as a second nanoRNase in B. subtilis. Like NrnA, NrnB is a member of the DHH/DHHA1 protein family of phosphoesterases. NrnB degrades nanoRNA 5-mers in vitro similarily to Orn. Low expression levels of NrnB are sufficient for orn complementation. YhaM, a known RNase present in B. subtilis, degrades nanoRNA efficiently in vitro but requires high levels of expression for only partial complementation of the orn– strain. A triple mutant (nrnA–, nrnB–, yhaM–) in B. subtilis is viable and shows almost no impairment in growth. Lastly, RNase J1 seems also to have some 5′-to-3′ exoribonuclease activity on nanoRNA and thus can potentially finish degradation of RNA. We conclude that, unlike in E. coli, degradation of nanoRNA is performed in a redundant fashion in B. subtilis.

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Comparative genomics of gene-family size in closely related bacteria

Cited by 61 publications

References 42 publications

Loss of Genetic Redundancy in Reductive Genome Evolution

Loss of Genetic Redundancy in Reductive Genome Evolution

Evolution of sensory complexity recorded in a myxobacterial genome

Degradation of nanoRNA is performed by multiple redundant RNases in Bacillus subtilis

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