DNA cytosine methylation and heat-induced deamination

Ehrlich, Melanie; Norris, Kyle F.; Wang, Richard Y.; Kuo, Kenneth C.; Gehrke, Charles W.

doi:10.1007/bf01116426

Cited by 166 publications

(113 citation statements)

References 31 publications

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“…The selectionist hypothesis was (i) apparently weakened by the observation that hyperthermophiles exhibited low GC levels, a point later understood, however, as due to the avoidance of C which can be deaminated at high temperatures [15], and (ii) apparently disposed off by the investigations of Galtier and Lobry [16] and Hurst and Merchant [17] who reported no correlation between T opt and GC (or GC 3 ). This was interpreted not only as a strong evidence against the thermodynamic hypothesis in prokaryotes, but also as a disproval of the same hypothesis in vertebrates [17][18][19].…”

Section: Introductionmentioning

confidence: 99%

Correlations between genomic GC levels and optimal growth temperatures in prokaryotes

et al. 2004

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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.

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Section: Introductionmentioning

confidence: 99%

Correlations between genomic GC levels and optimal growth temperatures in prokaryotes

et al. 2004

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“…This water-mediated reaction can also occur spontaneously (as alluded above), though enzymatic deamination occurs at much faster rates especially on unprotected ssDNA substrates. [15] With the exception of AID, these genes were all named after APOBEC1 as a result of sequence homology indicating a shared lineage of inter-and intra-chromosomal gene duplication events. However, this nomenclature is misnomeric as APOBEC1 is the only family member whose gene product carries out apolipoprotein B mRNA editing.…”

Section: The Apobec Familymentioning

confidence: 99%

APOBEC3B: Pathological consequences of an innate immune DNA mutator

Burns¹,

Leonard²,

Harris³

2015

Biomed J

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Cancer is a disease that results from alterations in the cellular genome. Several recent studies have identified mutational signatures that implicate a variety of mutagenic processes in cancer, a major one of which is explained by the enzymatic activity of the DNA cytosine deaminase, APOBEC3B. As a deaminase, APOBEC3B converts cytosines to uracils in single-stranded DNA. Failure to properly repair these uracil lesions can result in a diverse array of mutations. For instance, DNA uracils can template the insertion of complementary adenines leading to C-to-T transition mutations. DNA uracils can also be converted into abasic sites that, depending upon the DNA polymerase recruited to bypass this lesion in the template strand, can lead to adenine insertion and C-to-T mutations as well as cytosine insertion and C-to-G transversion mutations. Finally, DNA uracils can also be converted into DNA breaks that may precipitate some types of larger chromosomal aberrations observed in cancer. These studies cumulatively demonstrate that APOBEC3B is a major source of genetic heterogeneity in several human cancers and, as such, this enzyme may prove to be a critical diagnostic and therapeutic target. (Biomed J 2015;38:102-110)

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“…The overall accuracy and error spectrum of a DNA polymerase are determined mainly by three parameters: the nucleotide selectivity of its active site, its mismatch extension capacity, and its proofreading ability (Beard & Wilson, 1998Joyce & Benkovic, 2004). Yet, natural and exogenous sources of DNA damage result in a variety of DNA modifications, the most common including nucleobase oxidation (Nakabeppu et al, 2007), alkylation (Drabløs et al, 2004) and deamination (Ehrlich et al, 1986;Kow, 2002;Labet et al, 2008). 60 evolution would not be possible.…”

Section: Introductionmentioning

confidence: 99%