Sunlight Ultraviolet and Bacterial DNA Base Ratios

Singer, Clifford E; Ames, Bruce N.

doi:10.1126/science.170.3960.822

Cited by 134 publications

(21 citation statements)

References 42 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Finally, we should remark that these results show not only the influence of T opt on genomic GC in prokaryotes, but also that it is not the only one influencing genome composition, as expected from other investigations [8,12,30,31]. Only when a factor becomes predominant, its effect on GC can be clearly seen.…”

Section: Resultsmentioning

confidence: 85%

“…The neutralist explanation was weakened by three observations: (i) that higher GC levels were found in bacteria exposed to UV light, this increase reducing the presence of TpT dinucleotides that could form dimers causing DNA replication problems [8]; (ii) that in some cases high GC levels of prokaryotes were associated with high growth temperatures [9][10][11] and with aerobiosis [12]; and (iii) that the compositional shifts associated with mutator mutations [5] were within the error limits of the ultracentrifugation approach used to detect them and only concerned ''hot spots'' [13]. Finally, when a pair of completely sequenced closely related bacteria (Corynebacterium efficiens and C. glutamicum) were compared, the positive relationship between T opt and GC level was striking [14].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Correlations between genomic GC levels and optimal growth temperatures in prokaryotes

et al. 2004

View full text Add to dashboard Cite

In prokaryotes, GC levels range from 25% to 75%, and T opt from %0°C to >100°C. When all species are considered together, no correlation is found between the two variables. Correlations are found, however, when Families of prokaryotes are analysed. Indeed, when Families comprising at least 10 species were studied (a set of 20 Families), positive correlations are found for 15 of them. Furthermore, a comparative analysis by independent contrasts made within the Families in order to control for phylogenetic non-independence showed qualitatively equivalent results. We conclude that T opt is one of the factors that influences genomic GC in prokaryotes.

show abstract

Section: Resultsmentioning

confidence: 85%

Section: Introductionmentioning

confidence: 99%

Correlations between genomic GC levels and optimal growth temperatures in prokaryotes

et al. 2004

View full text Add to dashboard Cite

show abstract

“…A generalized genomic acceleration of nucleotide substitutions in mutualistic species could reflect: a genetic bottleneck that took place in a highly genotypically variable population, leading to mutualist groups; deficient DNA repair systems (25); shorter generation time (26); reduced sexual reproduction (3) coupled with smaller population size (27); and an increase of mutagenic free radicals in the mycobiont caused by increased levels of oxygen, dessication, ionizing radiation, or UV-A and UV-B radiations between 320 and 380 nm (28)(29)(30) or UV radiation as a direct generalized selective force causing the formation of cyclobutane pyrimidine dimers (31,32). The results of this study point to the two latter hypotheses as the best explanations.…”

Section: Discussionmentioning

confidence: 99%

“…A second, nonexclusive scenario that could account for a general increase in rates of nucleotide substitutions invokes UV radiation as the selective force (31,32). Pyrimidine dimers are known to form after the interaction of UV radiation with DNA.…”

Section: Discussionmentioning

confidence: 99%

Accelerated evolution as a consequence of transitions to mutualism

Lutzoni

Pagel²

1997

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

121

102

View full text Add to dashboard Cite

Differential rates of nucleotide substitutions among taxa are a common observation in molecular phylogenetic studies, yet links between rates of DNA evolution and traits or behaviors of organisms have proved elusive. Likelihood ratio testing is used here for the first time to evaluate specific hypotheses that account for the induction of shifts in rates of DNA evolution. A molecular phylogenetic investigation of mutualist (lichen-forming fungi and fungi associated with liverworts) and nonmutualist fungi revealed four independent transitions to mutualism. We demonstrate a highly significant association between mutualism and increased rates of nucleotide substitutions in nuclear ribosomal DNA, and we demonstrate that a transition to mutualism preceded the rate acceleration of nuclear ribosomal DNA in these lineages. Our results suggest that the increased rate of evolution after the adoption of a mutualist lifestyle is generalized across the genome of these mutualist fungi.Mutualistic associations between fungi and photoautotrophic organisms (lichens and mycorrhizae) are almost ubiquitous in nature (1, 2). These symbiotic associations are concentrated in specific groups of fungi and are often tied to the diversification of at least one of the symbionts, suggesting that mutualism plays a major role in the evolution of most plants and in more than one-fifth of all known fungi (2-6). To study prerequisite conditions for, and evolutionary consequences of, a transition to mutualism in fungal lineages, a model system was developed (7) consisting of a group of closely related lichen-forming and nonmutualistic species of the mushroom genus Omphalina Quél. (Fig. 1a-d).Faster rates of nucleotide substitutions have been observed in endosymbiotic bacteria associated with aphids compared with free-living bacteria (8, 9). Mitochondria in fungi and animals also are reported to evolve faster than related bacteria (10). From these observations, it is tempting to conclude that accelerated rates of nucleotide substitutions resulted from an evolutionary transition to a symbiotic state. This conclusion is dependent on the sampling of free-living and symbiotic taxa, as well as on the extent of nucleotide sequence sampling. Both factors have a direct effect on the degree of confidence associated with a given phylogenetic tree and estimates of rates of nucleotide substitutions. Moreover, because nucleotide sequences contain phylogenetic structure, pairwise sequence comparisons are not independent, and thus a simple 2 test of association may overestimate the true strength of any association between evolutionary rates and symbiosis (11-13). Tests that take account of phylogenetic relationships are required for a better understanding of the factors causing shifts in rates of DNA evolution. Here we investigate, using a phylogenetically based maximum likelihood procedure, the association between transitions to mutualism and shifts in rates of nucleotide substitutions, as well as their relative order of occurrence, in a group of free-li...

show abstract

“…One of the first hypotheses proposed that exposure to thymine dimer‐inducing UV radiation in sunlight would selectively favor low thymine content (i.e., high GC content), supported by a positive association between qualitative assessments of UV exposure (e.g., “high” for aerobes) and GC content (Singer and Ames, ). Because UV selection cannot account for low GC content (the absence of selection for high GC content should result in an equilibrium GC around 50%), the authors proposed an additional (unknown) selective agent that operated only in the absence of sunlight.…”

Section: Selection Imposed By Environmental Factorsmentioning

confidence: 99%

The evolution of bacterial DNA base composition

Agashe

Shankar

2014

J Exp Zool Pt B

View full text Add to dashboard Cite

Bacterial genomes exhibit a large amount of variation in their base composition, which ranges from 13% to 75% GC. The evolution and maintenance of this variation has proved to be an enduring puzzle despite decades of theoretical and empirical work. We present an overview of various aspects of this problem, focusing on results from a diverse set of recent studies that use whole-genome sequencing in combination with bioinformatic, phylogenetic, molecular biological, and experimental evolution approaches. We propose that analysis of within-genome variance in GC content is also important to understand how genome-wide base composition has evolved. We close with a discussion of open questions and fruitful avenues of inquiry that may bring us closer to understanding the evolutionary dynamics of bacterial DNA base composition.

show abstract

Sunlight Ultraviolet and Bacterial DNA Base Ratios

Cited by 134 publications

References 42 publications

Correlations between genomic GC levels and optimal growth temperatures in prokaryotes

Correlations between genomic GC levels and optimal growth temperatures in prokaryotes

Accelerated evolution as a consequence of transitions to mutualism

The evolution of bacterial DNA base composition

Contact Info

Product

Resources

About