Correlations between genomic GC levels and optimal growth temperatures in prokaryotes

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

doi:10.1016/j.febslet.2004.07.056

Cited by 121 publications

(108 citation statements)

References 25 publications

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“…This contradicts the correlation between genomic GC content and the optimal growth temperature in prokaryotes [41,42]. When the environmental temperature rises in the spring and C. sinensis stroma germinates, the AT-biased mutants (AB067744 and AB067740 genotypes) and the inversely orientated GC-biased mutant (EF378610 genotype) in the stroma may not manifest the psychrophilic phenotype like their counterpart (the AB067721 genotype).…”

Section: Discussionmentioning

confidence: 55%

Maturational Alteration of Oppositely Orientated rDNA and Differential Proliferation of GC- and AT-biased Genotypes of Ophiocordyceps sinensis and Paecilomyces hepiali in Natural Cordyceps sinensis

Zhu¹,

Gao²,

Li³

et al. 2010

Am. J. Biomed. Sci.

165

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Multiple reports have detailed the simultaneous detection of ribosomal DNA (rDNA) of Paecilomyces hepiali (Ph), Hirsutella sinensis and two genotypes of Ophiocordyceps sinensis (Os) from Cordyceps sinensis (Cs), and the altered phenotypes and chemical components of Cs during Cs maturation. In this study, we observed an increase in the biomass of Ph and two moieties of Os rDNA during Cs maturation. The GCand AT-biased genotypes of transition mutations in the Cs stroma were confirmed using MassARRAY SNP genotyping. In premature Cs, the AT-biased genotypes were not expressed in the caterpillar, but highly predominated in the stroma. The GC bias was expressed in an opposite manner in the premature Cs compartments. The differential expression of GC-and AT-biased mutants was altered during Cs maturation. The increased biomass of the inverse-oriented Os rDNA of the GC-genotype was associated with a maturational increase in stroma height. We also report evidence of transversion mutations within Cs genes. The dynamic alterations of Ph and Os mutant gene expressions along with Cs maturation may play an essential role in Cs germination and maturation, the key elements of Cs life cycle, and result in the varied therapeutic potency of Cs.

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Section: Discussionmentioning

confidence: 55%

Maturational Alteration of Oppositely Orientated rDNA and Differential Proliferation of GC- and AT-biased Genotypes of Ophiocordyceps sinensis and Paecilomyces hepiali in Natural Cordyceps sinensis

Zhu¹,

Gao²,

Li³

et al. 2010

Am. J. Biomed. Sci.

165

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“…There are two different ways to interpret such a deviation from equilibrium, one based on selection of compositional strand bias and the other on shifting mutational spectra. Selection for nucleotide composition has been proposed in a variety of cases: varying availability of nucleotides in different ecological niches (Rocha and Danchin 2002;Foerstner et al 2005) and differences in metabolism (Naya et al 2002;Rocha and Danchin 2002) and temperature (Musto et al 2004). If G was more adaptive than C in the leading strand (or the reverse on the lagging strand), this would have the advantage of explaining why GC skews are always of the same type, independently of the substitution spectra.…”

Section: Discussionmentioning

confidence: 99%

Similar compositional biases are caused by very different mutational effects

Rocha¹,

Touchon²,

Feil³

2006

Genome Res.

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Compositional replication strand bias, commonly referred to as GC skew, is present in many genomes of prokaryotes, eukaryotes, and viruses. Although cytosine deamination in ssDNA (resulting in C→T changes on the leading strand) is often invoked as its major cause, the precise contributions of this and other substitution types are currently unknown. It is also unclear if the underlying mutational asymmetries are the same among taxa, are stable over time, or how closely the observed biases are to mutational equilibrium. We analyzed nearly neutral sites of seven taxa each with between three and six complete bacterial genomes, and inferred the substitution spectra of fourfold degenerate positions in nonhighly expressed genes. Using a bootstrap procedure, we extracted compositional biases associated with replication and identified the significant asymmetries. Although all taxa showed an overrepresentation of G relative to C on the leading strand (and imbalances between A and T), widely variable substitution asymmetries are noted. Surprisingly, all substitution types show significant asymmetry in at least one taxon, but none were universally biased in all taxa. Notably, in the two most biased genomes, A→G, rather than C→T, shapes the compositional bias. Given the variability in these biases, we propose that the process is multifactorial. Finally, we also find that most genomes are not at compositional equilibrium, and suggest that mutational-based heterotachy is deeply imprinted in the history of biological macromolecules. This shows that similar compositional biases associated with the same essential well-conserved process, replication, do not reflect similar mutational processes in different genomes, and that caution is required in inferring the roles of specific mutational biases on the basis of contemporary patterns of sequence composition.[Supplemental material is available online at www.genome.org.]The study of genome composition made direct and important contributions to our understanding of DNA structure and evolution well before complete genome sequences were available (Chargaff 1950;Sueoka 1962). Since then, many studies have attempted to infer mutational scenarios to account for compositional deviations such as asymmetric nucleotide composition on the two strands of replication. A major difficulty arises from the fact that 12 different substitutions are possible between the four nucleotides in DNA. Because very different sets of mutations may lead to similar compositional biases, it is usually a very speculative exercise to infer the grounds of the relevant mutational asymmetries just by analyzing compositional deviations. Since many different chemical attacks and repair mechanisms affect DNA mutations (Friedberg et al. 1995), it is even more difficult to unravel the biological basis of the mutational biases. The usual processes of inference also implicitly assume that compositional deviations reflect the current mutational biases affecting genomes. However, compositional deviations accumulate through milli...

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“…This selectionist explanation was supported (i) by the similar genome changes occurring in the independent lines of mammals and birds; (ii) by the decreases of CpG doublets and methylcytosine, which are correlated with increasing body temperatures in vertebrates ranging from Antarctic fishes to mammals (72)(73)(74)(75)(76); (iii) by the variable compositional heterogeneity and methylation levels (intermediate between those of fishes/amphibians and mammals/birds) of the genomes from reptiles (51,47,77), which are known to have different body temperatures and thermal regulations; (iv) by the mammalian-like isochore organization of the genomes of subtropical and tropical insects (Drosophila, Anopheles) (78,79); and (v) by the increase of GC levels that accompanies the increase in optimal growth temperatures in many families of prokaryotes (80).…”

Section: Compositional Evolution: Genome Phenotypes and The Transitimentioning

confidence: 99%

The neoselectionist theory of genome evolution

Bernardi

2007

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

Self Cite

124

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The vertebrate genome is a mosaic of GC-poor and GC-rich isochores, megabase-sized DNA regions of fairly homogeneous base composition that differ in relative amount, gene density, gene expression, replication timing, and recombination frequency. At the emergence of warm-blooded vertebrates, the gene-rich, moderately GC-rich isochores of the cold-blooded ancestors underwent a GC increase. This increase was similar in mammals and birds and was maintained during the evolution of mammalian and avian orders. Neither the GC increase nor its conservation can be accounted for by the random fixation of neutral or nearly neutral single-nucleotide changes (i.e., the vast majority of nucleotide substitutions) or by a biased gene conversion process occurring at random genome locations. Both phenomena can be explained, however, by the neoselectionist theory of genome evolution that is presented here. This theory fully accepts Ohta's nearly neutral view of point mutations but proposes in addition (i) that the AT-biased mutational input present in vertebrates pushes some DNA regions below a certain GC threshold; (ii) that these lower GC levels cause regional changes in chromatin structure that lead to deleterious effects on replication and transcription; and (iii) that the carriers of these changes undergo negative (purifying) selection, the final result being a compositional conservation of the original isochore pattern in the surviving population. Negative selection may also largely explain the GC increase accompanying the emergence of warm-blooded vertebrates. In conclusion, the neoselectionist theory not only provides a solution to the neutralist/selectionist debate but also introduces an epigenomic component in genome evolution.base composition ͉ isochores ͉ nearly neutral theory ͉ neutral theory

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Correlations between genomic GC levels and optimal growth temperatures in prokaryotes

Cited by 121 publications

References 25 publications

Maturational Alteration of Oppositely Orientated rDNA and Differential Proliferation of GC- and AT-biased Genotypes of Ophiocordyceps sinensis and Paecilomyces hepiali in Natural Cordyceps sinensis

Maturational Alteration of Oppositely Orientated rDNA and Differential Proliferation of GC- and AT-biased Genotypes of Ophiocordyceps sinensis and Paecilomyces hepiali in Natural Cordyceps sinensis

Similar compositional biases are caused by very different mutational effects

The neoselectionist theory of genome evolution

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