Genomic GC level, optimal growth temperature, and genome size in prokaryotes

Musto, Héctor; Naya, Hugo; Zavala, Alejandro; Romero, Héctor; Álvarez-Valín, Fernando; Bernardi, Giorgio

doi:10.1016/j.bbrc.2006.06.054

Cited by 127 publications

(103 citation statements)

References 14 publications

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“…This view was bolstered by sequence information showing that the base compositional differences among bacteria were most pronounced at synonymous and noncoding positions, sites that are thought to be under the least selective constraints (5). Furthermore, repeated attempts to link genomic base composition with an environmental factor or other selective processes have met with limited success (6)(7)(8)(9)(10).…”

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confidence: 99%

A selective force favoring increased G+C content in bacterial genes

Raghavan

Kelkar

Ochman

2012

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

116

131

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Bacteria display considerable variation in their overall base compositions, which range from 13% to over 75% G+C. This variation in genomic base compositions has long been considered to be a strictly neutral character, due solely to differences in the mutational process; however, recent sequence comparisons indicate that mutational input alone cannot produce the observed base compositions, implying a role for natural selection. Because bacterial genomes have high gene content, forces that operate on the base composition of individual genes could help shape the overall genomic base composition. To explore this possibility, we tested whether genes that encode the same protein but vary only in their base compositions at synonymous sites have effects on bacterial fitness. Escherichia coli strains harboring G+C-rich versions of genes display higher growth rates, indicating that despite a pervasive mutational bias toward A+T, a selective force, independent of adaptive codon use, is driving genes toward higher G+C contents.bacterial adaptation | genome evolution | mutational patterns

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confidence: 99%

A selective force favoring increased G+C content in bacterial genes

Raghavan

Kelkar

Ochman

2012

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

116

131

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“…Finally, a GC bias could be introduced by selection. Several theories emphasizing the role of selection in affecting genomic GC content have been suggested (16)(17)(18)(19)(20)(21). Not surprisingly, given the complexities of bacterial ecology, none of these theories provides a universal explanation regarding the nature of those putative selective forces to explain the advantage of a high or low GC content.…”

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confidence: 99%

Whole-genome mutational biases in bacteria

Lind

Andersson

2008

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

181

158

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A fundamental biological question is what forces shape the guanine plus cytosine (GC) content of genomes. We studied the specificity and rate of different mutational biases in real time in the bacterium Salmonella typhimurium under conditions of strongly reduced selection and in the absence of the major DNA repair systems involved in repairing common spontaneous mutations caused by oxidized and deaminated DNA bases. The mutational spectrum was determined by whole-genome sequencing of two S. typhimurium mutants that were serially passaged for 5,000 generations. Analysis of 943 identified base pair substitutions showed that 91% were GC-to-TA transversions and 7% were GC-to-AT transitions, commonly associated with 8-oxoG-and deaminationinduced damages, respectively. Other types of base pair substitutions constituted the remaining 2% of the mutations. With regard to mutational biases, there was a significant increase in C-to-T transitions on the nontranscribed strand, and for highly expressed genes, C/G-to-T mutations were more common than expected; however, no significant mutational bias with regard to leading and lagging strands of replication or chromosome position were found. These results suggest that, based on the experimentally determined mutational rates and specificities, a bacterial genome lacking the relevant DNA repair systems could, as a consequence of these underlying mutational biases, very rapidly reduce its GC content.dna repair ͉ experimental evolution ͉ gc bias ͉ mutation spectra ͉ Salmonella typhimurium A central question in evolutionary genomics is what mechanisms cause the variation observed in DNA base composition between and within genomes and how rapidly and by what mechanisms these biases might change in response to, for example, altered ecology and genetic constitution of the organism. The large range in guanine plus cytosine (GC) content among bacterial species is well established, varying between at least 17% and 75% GC, with an even larger variation in the third codon position (1). Within a genome, GC content usually is quite homogeneous and has a strong phylogenetic signal, but despite this overall homogeneity, there frequently exist strand-specific biases between the two strands of DNA such that the average nucleotide composition deviates from the theoretically expected A ϭ T and G ϭ C within each strand. Thus, most bacterial chromosomes are relatively strongly enriched in G over C and in T over A and are slightly depleted in GϩC in weakly selected positions in the leading strand compared with in the lagging strand (2). In addition, highly transcribed genes appear to show a G and T skew on the nontranscribed strand compared with poorly transcribed genes (3).Although the causes of these biases remain unclear, the biases can be expected to arise at least at three different levels. First, there might exist an underlying bias in the mutation pressure caused by unavoidable spontaneous DNA damage, such as deamination of C3U and 5-meC3T (4, 5) or oxidation of G to form 7,8-dihydro-8-oxoG (8-...

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“…Differences in GC contents between host genome DNA and horizontally transferred DNA regions Genome size and GC content are weakly correlated in bacteria and archaea (Bentley and Parkhill, 2004;Musto et al, 2006;Mitchell, 2007;Suzuki et al, 2008;Guo et al, 2009;Nishida, 2012). The genomes of obligate host-associated bacteria are short and low GC content (Moran, 2002;Klasson and Andersson, 2004;McCutcheon and Moran, 2012), with exception of Candidatus Hodgkinia cicadicola (McCutcheon et al, 2009;Van Leuven and McCutcheon, 2012).…”

Section: Number Of Organismsmentioning

confidence: 99%

Genome DNA Sequence Variation, Evolution, and Function in Bacteria and Archaea

Nishida

2013

Current Issues in Molecular Biology

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Comparative genomics has revealed that variations in bacterial and archaeal genome DNA sequences cannot be explained by only neutral mutations. Virus resistance and plasmid distribution systems have resulted in changes in bacterial and archaeal genome sequences during evolution. The restriction-modification system, a virus resistance system, leads to avoidance of palindromic DNA sequences in genomes. Clustered, regularly interspaced, short palindromic repeats (CRISPRs) found in genomes represent yet another virus resistance system. Comparative genomics has shown that bacteria and archaea have failed to gain any DNA with GC content higher than the GC content of their chromosomes. Thus, horizontally transferred DNA regions have lower GC content than the host chromosomal DNA does. Some nucleoid-associated proteins bind DNA regions with low GC content and inhibit the expression of genes contained in those regions. This form of gene repression is another type of virus resistance system. On the other hand, bacteria and archaea have used plasmids to gain additional genes. Virus resistance systems influence plasmid distribution. Interestingly, the restrictionmodification system and nucleoid-associated protein genes have been distributed via plasmids. Thus, GC content and genomic signatures do not reflect bacterial and archaeal evolutionary relationships.

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Genomic GC level, optimal growth temperature, and genome size in prokaryotes

Cited by 127 publications

References 14 publications

A selective force favoring increased G+C content in bacterial genes

A selective force favoring increased G+C content in bacterial genes

Whole-genome mutational biases in bacteria

Genome DNA Sequence Variation, Evolution, and Function in Bacteria and Archaea

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