Relative Contributions Of Mutation Research Articles

Proteome-Wide Structural Computations Provide Insights into Empirical Amino Acid Substitution Matrices

The relative contribution of mutation and selection to the amino acid substitution rates observed in empirical matrices is unclear. Herein, we present a neutral continuous fitness-stability model, inspired by the Arrhenius law (qij=aije-ΔΔGij). The model postulates that the rate of amino acid substitution (i→j) is determined by the product of a pre-exponential factor, which is influenced by the genetic code structure, and an exponential term reflecting the relative fitness of the amino acid substitutions. To assess the validity of our model, we computed changes in stability of 14,094 proteins, for which 137,073,638 in silico mutants were analyzed. These site-specific data were summarized into a 20 square matrix, whose entries, ΔΔGij, were obtained after averaging through all the sites in all the proteins. We found a significant positive correlation between these energy values and the disease-causing potential of each substitution, suggesting that the exponential term accurately summarizes the fitness effect. A remarkable observation was that amino acids that were highly destabilizing when acting as the source, tended to have little effect when acting as the destination, and vice versa (source → destination). The Arrhenius model accurately reproduced the pattern of substitution rates collected in the empirical matrices, suggesting a relevant role for the genetic code structure and a tuning role for purifying selection exerted via protein stability.

The Mutation Landscape of Follicular Lymphoma and Chronic Lymphocytic Leukemia Reveals a Distinctive Frequency and Composition of Aid-Related Mutation Signatures

Introduction: Somatic mutations associated with distinctive types of cancer can be globally classified by the trinucleotide context of single nucleotide variants into mutational signatures. Distinct signatures can be attributed to underlying causative mechanisms such as UV irradiation or smoking. B-cell lymphomas have only been analyzed globally and carry a signature characterized by APOBEC activity (Alexandrov, 2014).The two most common indolent B-cell neoplasms, chronic lymphocytic leukemia (CLL) and follicular lymphoma (FL), are characterized by distinctive pathogenic processes, but mutagenesis caused by the APOBEC enzyme activation-induced cytosine deaminase (AID) may be shared by both malignancies. AID deaminates deoxycytidine to deoxyuridine, which is processed by DNA repair enzymes into a larger spectrum of point mutations and also DNA double-strand breaks. AID activity and subsequent DNA repair create two different mutation signatures: the canonical signature characterized by C>T/G transitions at RCY motifs and the non-canonical defined by A>C transversions at WAN motifs. More recently a third AID signature characterized by C>T transitions at RCG motifs has been associated with AID-mediated CpG-methylation dependent mutagenesis.We here investigate the hypothesis that AID mutational signatures contribute to the pathogenesis of FL, a lymphoma characterized by constitutional expression of AID, but also of CLL since high AID expression levels may account for a more aggressive disease, and a subset of CLL B-cells with AID expression display dissociation between class switch recombination and somatic hypermutation.Methods: We analyzed the mutational landscape in whole exome sequencing data from 31 FL and 24 CLL cases. Somatic variants were called by comparison of tumor and germline DNA with an in-house developed pipeline. The relative contribution of mutations at canonical and non-canonical AID hotspot motifs was computed by direct quantification of variants occurring in known AID motifs. Student's t test was used for comparison between CLL and FL.Mutational signatures were defined according to the 96-base substitution model (Alexandrov, 2013) by an unsupervised machine learning approach, with a local implementation of the SomaticSignatures R package.Results: The frequency of C>T/G transitions at canonical AID hotspot was more prevalent in CLL (9.0%; 95% CI: 8.1-10.0%) than in FL (6.6%, 95% CI: 5.9-7.3%)(p<0.001). Likewise, A>C transversions at non-canonical AID sites were significantly more frequent in CLL (1.9%; 95% CI: 1.6-2.2%) as compared to FL (0.5%; 95% CI: 0.4-0.6%)(p<0.0001).In the unsupervised analysis of FL and CLL cases, 97.7% of the mutation spectrum variance was explained by only 5 signatures (Figure 1). In FL, the mutational landscape was dominated by a signature (S2) characterized by C>A transversions in the trinucleotide KCH context (40%, 95% CI: 33-36%). The second most frequent signature (S3; 22%, 95% CI: 15-30%) was characterized by C>T transitions in the context of a hybrid between the canonical AID and the CpG hotspot motifs (RCY/RCG).In contrast, the mutational landscape of CLL was dominated by a signature (S5; 42%, 95% CI: 34-49%) characterized by C>T transitions in the RCY motif and A>C transversions in the WAN context, consistent with an overlapping between the canonical and the non-canonical AID hotspots (Kasar, 2016).Conclusions: The mutational landscape of both CLL and FL seems to be strongly shaped by AID activity. In FL, AID-induced mutations are mainly restricted to canonical AID hotspots and CpG-methylation dependent mutagenesis sites. In strong contrast, both canonical and non-canonical AID motifs contributed to the mutational landscape of CLL. In addition, FL carries a high prevalence of C>A substitutions that are associated with exposure to polycyclic aromatic hydrocarbons that produce bulky DNA adducts followed by the nucleotide excision repair process. These compounds are present in several industrial processes (food products, beverages, tobacco) that have been suggested as occupational risk factors for follicular lymphomas (Mester, 2009).Overall, our data suggest a much stronger role of AID in CLL pathogenesis than hitherto appreciated. The differential contribution of canonical versus non-canonical AID activity points to different regulation of AID in CLL compared to FL and warrants further investigation. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

The variation among sites of protein structure divergence is shaped by mutation and scaled by selection

Protein structures do not evolve uniformly, but the degree of structure divergence varies among sites. The resulting site-dependent structure divergence patterns emerge from a process that involves mutation and selection, which may both, in principle, influence the emergent pattern. In contrast with sequence divergence patterns, which are known to be mainly determined by selection, the relative contributions of mutation and selection to structure divergence patterns is unclear. Here, studying 6 protein families with a mechanistic biophysical model of protein evolution, we untangle the effects of mutation and selection. We found that even in the absence of selection, structure divergence varies from site to site because the mutational sensitivity is not uniform. Selection scales the profile, increasing its amplitude, without changing its shape. This scaling effect follows from the similarity between mutational sensitivity and sequence variability profiles.

Clonality and recombination in the arctic plant Saxifraga cernua

The circumarctic clonal plant Saxifraga cernua reproduces efficiently via bulbils, largely depends on insects for pollination and appears to set seed very rarely. However, high levels of genotypic variation observed at small spatial scales in the arctic archipelago of Svalbard have been taken as evidence of occasional sexual reproduction. Here we assess the relative contributions of mutation and recombination to random amplified polymorphic DNA variation in four populations in East Greenland and re-analyse the Svalbard data. Greater variation due to recombination was predicted in Greenland than in Svalbard, because the higher summer temperatures and longer growing season likely increase the chances for sexual reproduction. Although we observed higher levels of genotypic diversity in Greenland than in Svalbard, matrix incompatibility and linkage disequilibrium measures provided no evidence of more sexuality, suggesting differences in glacial/postglacial history. The genetic structure and spatial distribution of clones suggest that clonal migration may increase variability in local populations, which is consistent with frequent large-scale migration in this species inferred from a circumarctic analysis of chloroplast DNA haplotypes. We conclude that a combination of somatic mutations and sexual reproduction has contributed to the observed patterns of genotypic diversity in the Greenland and Svalbard populations of S. cernua, and that sexual reproduction is important in maintaining genotypic diversity, despite the rarity of observations of seed setting. © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society, 2006, 152, 209–217.

Epigenetic regulation of immune escape genes in cancer

According to the concept of immune surveillance, the appearance of a tumor indicates that it has earlier evaded host defenses and subsequently must have escaped immunity to evolve into a full-blown cancer. Tumor escape mechanisms have focused mainly on mutations of immune and apoptotic pathway genes. However, data obtained over the past few years suggest that epigenetic silencing in cancer may be as frequent a cause of gene inactivation as are mutations. Here, we discuss the evidence that tumor immune evasion is mediated by non-mutational epigenetic events involving chromatin and that epigenetics collaborates with mutations in determining tumor progression. Since epigenetic changes are potentially reversible, the relative contribution of mutations and epigenetics, to the gene defects in any given tumor, may be a factor in determining the efficacy of treatments. We review new developments in basic chromatin mechanisms and in this context describe the rationale for the current use of epigenetic agents in cancer therapy and for a novel epigenetically generated tumor vaccine model. We emphasize that epigenetic cancer treatments are currently a 'blunt-sword' and suggest future directions for designing chromatin-based programs of potential value in the diagnosis and treatment of cancer.

Generality of the Structurally Constrained Protein Evolution model: assessment on representatives of the four main fold classes

The Structurally Constrained Protein Evolution (SCPE) model simulates protein evolution by introducing random mutations into the evolving sequences and selecting them against too much structural perturbation. Given a single protein structure, the SCPE model can be used to obtain a whole set of site-dependent amino acid substitution matrices. The set of SCPE substitution matrices for a given protein family can be seen as an independent-sites model of evolution for that family. Thus, these matrices can be compared with other substitution-matrix-based models of evolution. So far, SCPE has been tested only on left-handed parallel beta helix (LβH) proteins. Here, we address the question of generality by assessing the SCPE model on representatives of the four main classes of folds: α, β, α+β, and α/β. We compare with other models using the likelihood ratio test with parametric bootstrapping. We show that SCPE performs better than the popular JTT model for all cases considered. Furthermore, by considering the relative contributions of mutation and selection, we found that the key to the success of the SCPE model is the selection step.

Two aspects of DNA base composition: G+C content and translation-coupled deviation from intra-strand rule of A = T and G = C.

The relative contribution of mutation and selection to the G+C content of DNA was analyzed in bacterial species having widely different G+C contents. The analysis used two methods that were developed previously. The first method was to plot the average G+C content of a set of nucleotides against the G+C content of the third codon position for each gene. This method was used to present the G+C distribution of the third codon position and to assess the relative neutrality of a set of nucleotides to that of the G+C content of the third codon position. The second method was to plot the intrastrand bias of the third codon position from Parity Rule 2 (PR2), where A = T and G = C. It was found that whereas intragenomic distributions of the DNA G+C content of these bacteria are narrow in the majority of species, in some species the G+C content of the minor class of genes distributes over wider ranges than the major class of genes. On the other hand, ubiquitous PR2 biases are amino acid specific and independent of the G+C content of DNA, so that when averaged over the amino acids, the biases are small and not correlated with the DNA G+C content. Therefore, translation coupled PR2-biases are unlikely to explain the wide range of G+C contents among different species. Considering all data available, it was concluded that the amino acid-specific PR2 bias has only a minor effect, if any, on the average G+C content. In addition, PR2 bias patterns of different species show phylogenetic relationships, and the pattern can be as a taxal fingerprint.

Infrequent Mutation of p16INK4 in Sporadic Melanoma

Loss of heterozygosity of chromosome region 9p21 occurs commonly and early in sporadic melanoma, suggesting the involvement of a tumor suppressor gene at this locus in the pathogenesis of this neoplasm. Although germline mutations and deletions of the p16INK4 gene located at 9p21 have been reported in familial melanoma, the relative contributions of mutation and deletion in sporadic melanoma are at present unclear. In this study, we investigated 26 cases of sporadic cutaneous melanoma (14 of which demonstrated loss of heterozygosity at 9p21) for mutations of p16INK4. One tumor with allelic loss of 9p contained a CC-->TT mutation at codons 57/58, altering an arginine to a stop codon, consistent with bi-allelic inactivation of p16INK4 in this case. No mutations were identified in any of the other melanomas, or in one benign intradermal nevus with atypical features and two Spitz nevi that also showed loss of heterozygosity of 9p. The inactivation of both copies of p16INK4 in the one case of melanoma adds support to the theory that p16INK4 is important in the development of sporadic cutaneous melanoma, although allelic loss or other methods of inactivation of p16INK4 rather than point mutation appears to be numerically more important. The low frequency of mutation of p16INK4 in cases of sporadic melanoma with loss of heterozygosity of 9p is, however, also consistent with there being another tumor suppressor gene near this locus that is involved in some cases of sporadic melanoma.

On transition bias in mitochondrial genes of pocket gophers.

The relative contribution of mutation and purifying selection to transition bias has not been quantitatively assessed in mitochondrial protein genes. The observed transition/transversion (s/v) ratio is (micros Ps)/(microv Pv), where micros and microv denote mutation rate of transitions and transversions, respectively, and Ps and Pv denote fixation probabilities of transitions and transversions, respectively. Because selection against synonymous transitions can be assumed to be roughly equal to that against synonymous transversions, Ps/Pv approximately 1 at fourfold degenerate sites, so that the s/v ratio at fourfold degenerate sites is approximately micros/microv, which is a measure of mutational contribution to transition bias. Similarly, the s/v ratio at nondegenerate sites is also an estimate of micros/microv if we assume that selection against nonsynonymous transitions is roughly equal to that against nonsynonymous transversions. In two mitochondrial genes, cytochrome oxidase subunit I (COI) and cytochrome b (cyt-b) in pocket gophers, the s/v ratio is about two at nondegenerate and fourfold degenerate sites for both the COI and the cyt-b genes. This implies that mutation contribution to transition bias is relatively small. In contrast, the s/v ratio is much greater at twofold degenerate sites, being 48 for COI and 40 for cyt-b. Given that the micros/microv ratio is about 2, the Ps/Pv ratio at twofold degenerate sites must be on the order of 20 or greater. This suggests a great effect of purifying selection on transition bias in mitochondrial protein genes because transitions are synonymous and transversions are nonsynonymous at twofold degenerate sites in mammalian mitochondrial genes. We also found that nonsynonymous mutations at twofold degenerate sites are more neutral than nonsynonymous mutations at nondegenerate sites, and that the COI gene is subject to stronger purifying selection than is the cyt-b gene. A model is presented to integrate the effect of purifying selection, codon bias, DNA repair and GC content on s/v ratio of protein-coding genes.