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Results for “deleterious mutation”

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PubMed2005

Looking at structure, stability, and evolution of proteins through the principal eigenvector of contact matrices and hydrophobicity profiles.

We review and further develop an analytical model that describes how thermodynamic constraints on the stability of the native state influence protein evolution in a site-specific manner. To this end, we represent both protein sequences and protein structures as vectors: structures are represented by the principal eigenvector (PE) of the protein contact matrix, a quantity that resembles closely the effective connectivity of each site; sequences are represented through the "interactivity" of each amino acid type, using novel parameters that are correlated with hydropathy scales. These interactivity parameters are more strongly correlated than the other hydropathy scales that we examine with: (1) the change upon mutations of the unfolding free energy of proteins with two-states thermodynamics; (2) genomic properties as the genome-size and the genome-wide GC content; (3) the main eigenvectors of the substitution matrices. The evolutionary average of the interactivity vector correlates very strongly with the PE of a protein structure. Using this result, we derive an analytic expression for site-specific distributions of amino acids across protein families in the form of Boltzmann distributions whose "inverse temperature" is a function of the PE component. We show that our predictions are in agreement with site-specific amino acid distributions obtained from the Protein Data Bank, and we determine the mutational model that best fits the observed site-specific amino acid distributions. Interestingly, the optimal model almost minimizes the rate at which deleterious mutations are eliminated by natural selection.

Amino Acid Motifs↗

PubMed2003

Error thresholds and the constraints to RNA virus evolution.

RNA viruses are often thought of as possessing almost limitless adaptability as a result of their extreme mutation rates. However, high mutation rates also put a cap on the size of the viral genome by establishing an error threshold, beyond which lethal numbers of deleterious mutations accumulate. Herein, I argue that a lack of genomic space means that RNA viruses will be subject to important evolutionary constraints because specific sequences are required to encode multiple and often conflicting functions. Empirical evidence for these constraints, and how they limit viral adaptability, is now beginning to accumulate. Documenting the constraints to RNA virus evolution has important implications for predicting the emergence of new viruses and for improving therapeutic procedures.

Adaptation, Biological↗

PubMed1996

Significance of two point mutations present in each HEXB allele of patients with adult GM2 gangliosidosis (Sandhoff disease) homozygosity for the Ile207-->Val substitution is not associated with a clinical or biochemical phenotype.

The molecular defects in the HEXB gene encoding the common beta-subunit of lysosomal beta-hexosaminidase A (beta-Hex A, alpha beta) and beta-Hex B (beta beta) were investigated in a Portuguese family affected with late onset Sandhoff disease (GM2-gangliosidosis variant 0). This family comprised two unaffected daughters and three affected sibs who developed at about age 17 cerebellar ataxia and mental deficiency. Their parents were consanguineous and clinically asymptomatic. There was no detectable beta-Hex B activity and a profound reduction in the activity of beta-Hex A in the leukocytes and transformed lymphoid cell lines from the affected sibs. The expected intermediate values were observed in the parents as well as in one daughter and her children. Western analysis revealed the presence of reduced, but detectable amounts of mature beta-chain protein in cell lysates from the probands and intermediate levels in the parents. Nucleotide sequencing of amplified, reverse-transcribed beta-chain mRNA demonstrated the presence of two single point mutations: an A619 to G transition in exon 5 (Ile207-->Val), and a G1514 to A transition in exon 13 (Arg505-->Gln). Both of these two mutations have been previously linked to the adult form of Sandhoff disease in compound heterozygote patients. All three affected sibs were found to be homoallelic for both mutations. Interestingly, while the mother was heterozygous for each mutation, the father was homozygote for the A619-->G substitution and heterozygote for the G1514-->A transition. Since the father is homozygote for the A619-->G mutation but expresses a biochemical phenotype consistent with a carrier of Sandhoff disease and is clinically asymptomatic, this substitution is likely a neutral mutation. We confirmed this hypothesis by finding this transition present in 4 of 30 alleles from normal individuals. We conclude that homozygosity for the G1514-->A mutation is exclusively responsible for the adult form of Sandhoff disease in this family, and that the A619-->G substitution is not a deleterious mutation but rather a common HEXB polymorphism.

Adult↗

PubMed2006

Quantifying the genomic decay paradox due to Muller's ratchet in human mitochondrial DNA.

The observation of high mitochondrial mutation rates in human pedigrees has led to the question of how such an asexual genetic system can survive the accumulation of slightly deleterious mutations caused by Muller's ratchet. I define a null model to quantify in unprecedented detail the threat from extinction caused by Muller's ratchet. This model is general enough to explore the biological significance of Muller's ratchet in various species where its operation has been suspected. For increased precision over a wide range of parameter space I employ individual-based simulations run by evolution@home, the first global computing system for evolutionary biology. After compiling realistic values for the key parameters in human mitochondrial DNA (mtDNA) I find that a surprisingly large range of biologically realistic parameter combinations would lead to the extinction of the human line over a period of 20 million years - if accepted wisdom about mtDNA and Muller's ratchet is correct. The resulting genomic decay paradox complements a similar threat from extinction due to mutation accumulation in nuclear DNA and suggests evaluation of unconventional explanations for long-term persistence. A substantial list of potential solutions is given, including compensatory back mutations, mutation rate heterogeneity and occasional recombination in mtDNA. Future work will have to explore which of these actually solves the paradox. Nonetheless, the results presented here provide yet another reason to minimize anthropogenic increase of mutation rates.

Computer Simulation↗

PubMed2004

Are medullary breast cancers an indication for BRCA1 mutation screening? A mutation analysis of 42 cases of medullary breast cancer.

Recommended guidelines have limited breast cancer gene ( BRCA1 ) mutation testing to individuals with a personal or family history of early onset breast and/or ovarian cancer, and those with multiple affected close relatives. Such large breast cancer families are rare in the general population, limiting the clinical application of the BRCA1 discovery. Previous reports have suggested an association between medullary breast cancer and BRCA1 mutation carriers. To test the feasibility of using these rare histological subtypes as an alternative to epidemiological factors, 42 cases of medullary cancer unselected for family history were screened for BRCA1 point mutations and large exon rearrangements. The large majority (83%) of these patients did not have significant family of breast or ovarian cancer. Two deleterious mutations resulting in a premature stop codon, and one exon 13 duplication were found. All mutations were detected in patients with typical medullary cancer, who had family history of multiple breast and ovarian cancers. Our findings suggest that medullary breast cancers are not an indication for BRCA1 mutation screening in the absence of significant family risk factors.

Breast Neoplasms↗

PubMed2003

On the evolutionary advantage of fitness-associated recombination.

The adaptive value of recombination remains something of a puzzle. One of the basic problems is that recombination not only creates new and advantageous genetic combinations, but also breaks down existing good ones. A negative correlation between the fitness of an individual and its recombination rate would result in prolonged integrity of fitter genetic combinations while enabling less fit ones to produce new combinations. Such a correlation could be mediated by various factors, including stress responses, age, or direct DNA damage. For haploid population models, we show that an allele for such fitness-associated recombination (FAR) can spread both in asexual populations and in populations reproducing sexually at any uniform recombination rate. FAR also carries an advantage for the population as a whole, resulting in a higher average fitness at mutation-selection balance. These results are demonstrated in populations adapting to new environments as well as in well-adapted populations coping with deleterious mutations. Current experimental results providing evidence for the existence of FAR in nature are discussed.

Adaptation, Physiological↗

PubMed2000

The molecular basis of androgen insensitivity.

Androgen action is mediated in the peripheral target cell via the androgen receptor (AR). The AR is a nuclear transcription factor, combining a DNA-binding and a hormone-binding domain with a large transactivation unit. Androgen insensitivity syndrome (AIS) as the clinical entity of defective androgen action with variable phenotypes in 46,XY patients is caused by mutations of the X-chromosomal AR gene. Most variations in the AR gene are point mutations inhibiting either hormone or DNA binding. However, even within the same family, the phenotype for a given mutation can vary widely. Only few influential factors have been identified for the phenotypic diversity. For mutations affecting hormone binding, ligand concentration variability during fetal life may be an important influence on residual androgen action. A second factor is the occurrence of postzygotic de novo mutations, which are present at a high rate in single-case families. These somatic mutations lead to expression of both mutant and wild-type AR in a single patient and thus allow androgen action despite a deleterious mutation of the AR gene. Third, residual androgen response may be mediated by additional transcripts of the AR gene which are present in several cell types and can be affected in a different pattern by splice-site mutations. Whether differential expression of AR-interacting proteins has an influence on phenotype has not yet been proven. Moreover, little is known about the regulation of AR-dependent genes. Their identification is needed to understand post-AR action and, hence, androgenic control of sexual differentiation and maturation.

Androgen-Insensitivity Syndrome↗

PubMed1994

Mutations in steroid 21-hydroxylase (CYP21).

The inherited inability to synthesize cortisol is termed congenital adrenal hyperplasia. More than 90% of cases are caused by 21-hydroxylase deficiency. This syndrome is characterized by signs of androgen excess and often mineralocorticoid deficiency. Steroid 21-hydroxylase (P450c21) is a microsomal enzyme expressed in the adrenal gland that catalyzes conversion of 17-hydroxyprogesterone and progesterone to 11-deoxycortisol and deoxycorticosterone respectively. In man, this enzyme is encoded by the CYP21 (CYP21B) gene which is located in the HLA major histocompatibility complex along with a pseudogene, CYP21P (CYP21A). Mutations in CYP21 causing congenital adrenal hyperplasia are almost all generated by recombinations between CYP21 and CYP21P. These recombinations either delete CYP21 or transfer deleterious mutations from CYP21P to CYP21, a process termed apparent gene conversion. The degree of enzymatic compromise caused by each mutation is correlated with the clinical severity of the deficiency observed in patients carrying that mutation.

Adrenal Hyperplasia, Congenital↗

PubMed2004

Incontinentia pigmenti: a window to the role of NF-kappaB function.

Incontinentia pigmenti is an uncommon X-linked dominant genodermatosis primarily affecting females. Its hallmark is a unique skin eruption that presents in infancy along the lines of Blaschko and evolves through four stages: inflammatory, verrucous, hyperpigmented, and atrophic. Other persistent findings of the disease include alopecia and dental anomalies. In a minority of cases, serious ophthalmologic and neurological alterations may occur. Mutations in the NF-kappaB essential modulator (NEMO) that lead to an inability to activate the NF-kappaB pathway produce IP. Less deleterious mutations in NF-kappaB essential modulator give rise to hypohidrotic ectodermal dysplasia with immune deficiency in affected males, a related but distinct phenotype. These recent discoveries provide insight into the crucial role of NF-kappaB function in regulating the developmental, inflammatory, immune, and anti-apoptotic responses of the skin and other organs.

Diagnosis, Differential↗

PubMed2005

Prenatal diagnosis for severe methylenetetrahydrofolate reductase deficiency by linkage analysis and enzymatic assay.

Severe methylenetetrahydrofolate reductase (MTHFR) deficiency is characterized by varying degrees of developmental delay, motor and gait abnormalities, seizures, and thrombosis. Biochemical abnormalities include homocystinuria and hyperhomocysteinemia. Clinical severity correlates with MTHFR activity in cultured fibroblasts; activity can also be assayed in cultured amniocytes and chorionic villus cells (CVC). Forty-four private mutations have been identified, limiting the use of direct mutation detection for prenatal diagnosis. However, intragenic polymorphisms have been identified, making prenatal diagnosis by linkage analysis a possible option, even without knowledge of deleterious mutations. Prenatal diagnosis for severe MTHFR deficiency has been available by biochemical methodologies, but molecular genetic approaches have not yet been reported. We performed prenatal diagnosis for severe MTHFR deficiency in 11 at-risk pregnancies in seven families. A combined approach of linkage analysis and enzymatic assays was used in six pregnancies; linkage analysis alone was performed in one pregnancy. Linkage analysis for the 677C > T or 1298A > C polymorphisms predicted that all seven fetuses were unaffected. For six of these seven fetuses, enzymatic activities were also measured and demonstrated concordant results. Of the 10 pregnancies in which enzymatic assays were performed, activities in cultured amniocytes predicted six unaffected fetuses (1.4-7.1 nmol CHO/mg prot/h (U)) and one affected fetus (0.24 U [control 3.1-9.6 U]). Three pregnancies assessed via CVCs demonstrated two unaffected fetuses (3.6 and 7.7 U) and 1 affected fetus (0 U [control 4.5-7.8 U]). These values were compared to those of the probands (range = 0.02-0.7 U (control 2.4-11.7 U)) in cultured fibroblasts. Our findings suggest that linkage analysis for severe MTHFR deficiency can be a practical approach for prenatal diagnosis.

Clinical Enzyme Tests↗

PubMed2000

Mutators and sex in bacteria: conflict between adaptive strategies.

Bacterial mutation rates can increase and produce genetic novelty, as shown by in vitro and in silico experiments. Despite the cost due to a heavy deleterious mutation load, mutator alleles, which increase the mutation rate, can spread in asexual populations during adaptation because they remain associated with the rare favorable mutations they generate. This indirect selection for a genetic system generating diversity (second-order selection) is expected to be highly sensitive to changes in the dynamics of adaptation. Here we show by a simulation approach that even rare genetic exchanges, such as bacterial conjugation or transformation, can dramatically reduce the selection of mutators. Moreover, drift or competition between the processes of mutation and recombination in the course of adaptation reveal how second-order selection is unable to optimize the rate of generation of novelty.

Adaptation, Physiological↗

PubMed1999

Association of intron phases with conservation at splice site sequences and evolution of spliceosomal introns.

How exon-intron structures of eukaryotic genes evolved under various evolutionary forces remains unknown. The phases of spliceosomal introns (the placement of introns with respect to reading frame) provide an opportunity to approach this question. When a large number of nuclear introns in protein-coding genes were analyzed, it was found that most introns were of phase 0, which keeps codons intact. We found that the phase distribution of spliceosomal introns is strongly correlated with the sequence conservation of splice signals in exons; the relatively underrepresented phase 2 introns are associated with the lowest conservation, the relatively overrepresented phase 0 introns display the highest conservation, and phase 1 introns are intermediate. Given the detrimental effect of mutations in exon sequences near splice sites as found in molecular experiments, the underrepresentation of phase 2 introns may be the result of deleterious-mutation-driven intron loss, suggesting a possible genetic mechanism for the evolution of intron-exon structures.

Base Sequence↗

PubMed1999

Frameshift mutation of the STK11 gene in a sporadic gastrointestinal cancer with microsatellite instability.

Germline mutations of the STK11 gene lead to emergence of hamartomas in the gastrointestinal tract of patients with Peutz-Jeghers syndrome, who bear an increased risk of malignancies of the gastrointestinal tract, genital tract, and other organs. We analyzed 80 sporadic colorectal cancers, six small-intestinal cancers, and 40 gastric cancers for somatic mutations of STK11 by SSCP methods. Among them only one colorectal cancer, which showed a phenotype of microsatellite instability, was found to possess a deleterious mutation in this gene, a frameshift involving deletion of one base at codons 279-281. This region of the gene contains a mononucleotide-repeat sequence, CCCCCC. The other allele of STK11 had been lost in this tumor. If the STK11 gene is one of the mutational targets of microsatellite instability, its inactivation may be associated with tumor development in a small proportion of colorectal cancers.

AMP-Activated Protein Kinase Kinases↗

PubMed1993

Combinatorial mutagenesis of the lamB gene: residues 41 through 43, which are conserved in Escherichia coli outer membrane proteins, are informationally important in maltoporin structure and function.

A new strategy for combinatorial mutagenesis was developed and applied to residues 40 through 60 of LamB protein (maltoporin), with the aim of identifying amino acids important for LamB structure and function. The strategy involved a template containing a stop codon in the target sequence and a pool of random degenerate oligonucleotides covering the region. In vitro mutagenesis followed by selection for function (Dex+, ability to utilize dextrins) corrected the nonsense mutation and simultaneously forced incorporation of a random mutation(s) within the region. The relative importance of each residue within the target was indicated by the frequency and nature of neutral and deleterious mutations recovered at each position. Residues 41 through 43 in LamB accepted few neutral substitutions, whereas residues 55 through 57 were highly flexible in this regard. Consistent with this finding was that the majority of defective mutants were altered at residues 41 to 43. Characterization of these mutants indicated that the nature of residues 41 to 43 influenced the amount of stable protein in the outer membrane. These results, as well as the conserved nature of this stretch of residues among outer membrane proteins, suggest that residues 41 to 43 of LamB play an important role in the process of outer membrane localization.

Amino Acid Sequence↗

PubMed2000

Fast and efficient mutation detection method using multiplex PCR and cycle sequencing--application to haemophilia B.

A method using multiplex PCR followed by cycle-sequencing has been developed to detect mutations in the FIX gene. The procedure was evaluated in 45 severe or mild haemophilia B patients from 45 unrelated families. At least one deleterious mutation was identified in every haemophiliac demonstrating the efficiency of the method. Furthermore the described procedure offers many advantages compared to other screening detection methods: it is fast (less than 48 h), simple (partly automated) and of relatively low cost (it requires only one PCR).

Codon, Nonsense↗

PubMed2003

Mutations in the SDHB gene are associated with extra-adrenal and/or malignant phaeochromocytomas.

Germ-line mutations in the genes encoding succinate dehydrogenase complex subunits B (SDHB) and D (SDHD) have been reported in familial paragangliomas and apparently sporadic phaeochromocytomas (ASP), but the genotype-phenotype relationships of these mutations are unknown. Eighty-four patients (all but 2 followed up for 8.8 +/- 5.7 years) with ASP (57 with adrenal tumors, 27 with extra-adrenal, multiple, malignant, or recurrent tumors) were screened for the major susceptibility genes for phaeochromocytoma (RET, VHL, SDHD, and SDHB). Thirty-three tumors were available for molecular analysis, enzyme assays, and immunohistochemistry. No (0%) RET and 2 (2.4%) VHL mutations were detected. Only two coding single nucleotide polymorphisms in the SDHD gene (G12S and H50R) were found in 6 patients (7%). Conversely, six deleterious mutations in the SDHB gene were identified in 8 patients (9.5%). Ectopic site and recurrence or malignancy were strongly associated with SDHB mutations (7 of 8, 87%, versus 20 of 76, 26%; P = 0.001). Somatic DNA analysis indicated a loss of heterozygosity at chromosome 1p36 (SDHB locus) in 16 of 33 cases (48%). A loss of heterozygosity at the SDHB locus was found in all tumors with SDHB mutation, and assays of respiratory chain enzymes showed a complete loss of complex II catalytic activity. The vascular architecture of tumors with SDHB mutations displayed features typical of malignancy. These data strongly suggest that SDHB gene is a tumor suppressor gene and that the identification of germ-line mutations in SDHB gene in patients with ASPs should be considered as a high-risk factor for malignancy or recurrence.

Adrenal Gland Neoplasms↗

PubMed1998

A novel complex allele and two new point mutations in type 2 (acute neuronopathic) Gaucher disease.

Gaucher disease, the most prevalent inherited sphingolipidosis, is characterized by lipid laden histiocytes in the spleen, liver and bone marrow sinusoids of affected individuals. It results from deleterious mutations in the functional gene of glucocerebrosidase (acid beta-glucosidase, EC. 3.2.1.45) and is transmitted as an autosomal recessive trait. Three clinical forms of Gaucher disease have been described: Type 1 non-neuronopathic, type 2 acute neuronopathic, and type 3 subacute neuronopathic. In this report, we describe the identification and characterization of three novel mutations from two patients who died with type 2 Gaucher disease. Two heterozygous missense point mutations, one at cDNA nucleotide 238A (E41L) and the other at cDNA nucleotide 508T (R131C) were identified, both in the context of a cDNA nucleotide 1448C (L444P) mutation in the second allele. One of these L444P mutations was identified as a novel complex allele resulting from a crossover involving the glucocerebrosidase functional gene and pseudogene beginning between genomic nucleotides 5689 and 5723 and extending through the rest of the coding sequence. Based on the recent identification and sequence analysis of the metaxin gene and pseudogene contiguous with the glucocerebrosidase pseudogene and functional gene respectively, we have developed a PCR-based method for the analysis of the origin and extent of this recombination.

Adult↗

PubMed2000

The thermolabile variant 677C-->T can further reduce activity when expressed in cis with severe mutations for human methylenetetrahydrofolate reductase.

Methylenetetrahydrofolate reductase (MTHFR) catalyses the reduction of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate, a carbon donor for homocysteine remethylation to methionine. Severe MTHFR deficiency is associated with hyperhomocysteinemia and homocystinuria. These patients show a wide variety of neurological and vascular symptoms, with variable age of onset. Residual enzyme activity is usually less than 20% of control values, and correlates reasonably well with age of onset of symptoms. A milder deficiency of MTHFR, with 30%-50% residual enzyme activity and increased enzyme thermolability, has been described as a risk factor for vascular disease and for neural tube defects. In earlier work, we isolated the human cDNA for MTHFR, and reported 14 mutations in severe MTHFR deficiency, as well as a common 677C-->T missense mutation (Ala-->Val) that encodes the thermolabile MTHFR. This variant has also been observed in some patients with severe MTHFR deficiency, in cis with their severe mutations. We report here the in vitro expression of seven severe MTHFR mutations in a bacterial expression system; six of these were expressed in cis with the Val allele to mimic the situation in the patients. We show that three of these constructs have significantly reduced enzyme activity (<10% of control); the presence of the thermolabile variant in these patients in cis is unlikely to affect enzyme function since activity is already low. One mutation causes a dramatic increase in activity when it is expressed in cis with the Ala allele, but is associated with extreme lability when in cis with the Val allele. Three mutations cause moderate decreases in enzyme activity, with a further decrease in activity when they are in cis with the Val allele. We hypothesize that deleterious mutations which alter stability may be compromised to a greater degree when the thermolabile variant is present on the same allele.

Alanine↗