Authors: Huanting Liu, James H Naismith

BACKGROUND

Mutagenesis plays an essential role in molecular biology and biochemistry. It has also been used in enzymology and protein science to generate proteins which are more tractable for biophysical techniques. The ability to quickly and specifically mutate a residue(s) in protein is important for mechanistic and functional studies. Although many site-directed mutagenesis methods have been developed, a simple, quick and multi-applicable method is still desirable.

RESULTS

We have developed a site-directed plasmid mutagenesis protocol that preserved the simple one step procedure of the QuikChange site-directed mutagenesis but enhanced its efficiency and extended its capability for multi-site mutagenesis. This modified protocol used a new primer design that promoted primer-template annealing by eliminating primer dimerization and also permitted the newly synthesized DNA to be used as the template in subsequent amplification cycles. These two factors we believe are the main reasons for the enhanced amplification efficiency and for its applications in multi-site mutagenesis.

CONCLUSION

Our modified protocol significantly increased the efficiency of single mutation and also allowed facile large single insertions, deletions/truncations and multiple mutations in a single experiment, an option incompatible with the standard QuikChange. Furthermore the new protocol required significantly less parental DNA which facilitated the DpnI digestion after the PCR amplification and enhanced the overall efficiency and reliability. Using our protocol, we generated single site, multiple single-site mutations and a combined insertion/deletion mutations. The results demonstrated that this new protocol imposed no additional reagent costs (beyond basic QuikChange) but increased the overall success rates.

Topics: DNA Primers; Mutagenesis, Insertional; Mutagenesis, Site-Directed; Plasmids; Polymerase Chain Reaction; Sequence Deletion

PubMed: 19055817
DOI: 10.1186/1472-6750-8-91

Authors: Hope Woods, Dominic L Schiano, Jonathan I Aguirre...

In-frame deletion mutations can result in disease. The impact of these mutations on protein structure and subsequent functional changes remain understudied, partially due to the lack of comprehensive datasets including a structural readout. In addition, the recent breakthrough in structure prediction through deep learning demands an update of computational deletion mutation prediction. In this study, we deleted individually every residue of a small α-helical sterile alpha motif domain and investigated the structural and thermodynamic changes using 2D NMR spectroscopy and differential scanning fluorimetry. Then, we tested computational protocols to model and classify observed deletion mutants. We show a method using AlphaFold2 followed by RosettaRelax performs the best overall. In addition, a metric containing pLDDT values and Rosetta ΔΔG is most reliable in classifying tolerated deletion mutations. We further test this method on other datasets and show they hold for proteins known to harbor disease-causing deletion mutations.

Topics: Proteins; Mutation; Computer Simulation; Sequence Deletion; Magnetic Resonance Spectroscopy; Computational Biology

PubMed: 37119820
DOI: 10.1016/j.str.2023.04.005

Authors: Tetsuya Akaishi

The evolutional process of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) development remains inconclusive. This study compared the genome sequences of severe acute respiratory syndrome coronavirus (SARS-CoV), bat coronavirus RaTG13, and SARS-CoV-2. In total, the genomes of SARS-CoV-2 and RaTG13 were 77.9% and 77.7% identical to the genome of SARS-CoV, respectively. A total of 3.6% (1,068 bases) of the SARS-CoV-2 genome was derived from insertion and/or deletion (indel) mutations, and 18.6% (5,548 bases) was from point mutations from the genome of SARS-CoV. At least 35 indel sites were confirmed in the genome of SARS-CoV-2, in which 17 were with ≥10 consecutive bases long. Ten of these relatively long indels were located in the spike (S) gene, five in nonstructural protein 3 (Nsp3) gene of open reading frame (ORF) 1a, and one in ORF8 and noncoding region. Seventeen (48.6%) of the 35 indels were based on insertion-and-deletion mutations with exchanged gene sequences of 7-325 consecutive bases. Almost the complete ORF8 gene was replaced by a single 325 consecutive base-long indel. The distribution of these indels was roughly in accordance with the distribution of the rate of point mutation rate around the indels. The genome sequence of SARS-CoV-2 was 96.0% identical to that of RaTG13. There was no long insertion-and-deletion mutation between the genomes of RaTG13 and SARS-CoV-2. The findings of the uneven distribution of multiple indels and the presence of multiple long insertion-and-deletion mutations with exchanged consecutive base sequences in the viral genome may provide insights into SARS-CoV-2 development. The developmental mechanism of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains inconclusive. This study compared the base sequence one-by-one between severe acute respiratory syndrome coronavirus (SARS-CoV) or bat coronavirus RaTG13 and SARS-CoV-2. The genomes of SARS-CoV-2 and RaTG13 were 77.9% and 77.7% identical to the genome of SARS-CoV, respectively. Seventeen of the 35 sites with insertion and/or deletion mutations between SARS-CoV-2 and SARS-CoV were based on insertion-and-deletion mutations with the replacement of 7-325 consecutive bases. Most of these long insertion-and-deletion sites were concentrated in the nonstructural protein 3 (Nsp3) gene of open reading frame (ORF) 1a, S1 domain of the spike protein, and ORF8 genes. Such long insertion-and-deletion mutations were not observed between the genomes of RaTG13 and SARS-CoV-2. The presence of multiple long insertion-and-deletion mutations in the genome of SARS-CoV-2 and their uneven distributions may provide further insights into the development of the virus.

Topics: Animals; COVID-19; Chiroptera; Genome, Viral; Phylogeny; SARS-CoV-2; Sequence Deletion

PubMed: 35658573
DOI: 10.1128/spectrum.00716-22

Review

Authors: Diederik W D Kuster, Sakthivel Sadayappan

Hypertrophic cardiomyopathy (HCM) is the most common form of inherited cardiac disease and the leading cause of sudden cardiac death in young people. HCM is caused by mutations in genes encoding contractile proteins. Cardiac myosin binding protein-C (cMyBP-C) is a thick filament contractile protein that regulates sarcomere organization and cardiac contractility. About 200 different mutations in the cMyBP-C gene (MYBPC3) have thus far been reported as causing HCM. Among them, a 25 base pair deletion in the branch point of intron 32 of MYBPC3 is widespread, particularly affecting people of South Asian descent, with 4% of this population carrying the mutation. This polymorphic mutation results in skipping of exon 33 and a reading frame shift, which, in turn, replaces the last 65 amino acids of the C-terminal C10 domain of cMyBP-C with a novel sequence of 58 residues (cMyBP-C(C10mut)). Carriers of the 25 base pair deletion mutation are at increased risk of developing cardiomyopathy and heart failure. Because of the high prevalence of this mutation in certain populations, genetic screening of at-risk groups might be beneficial. Scientifically, the functional consequences of C-terminal mutations and the precise mechanisms leading to HCM should be defined using induced pluripotent stem cells and engineered heart tissue in vitro or mouse models in vivo. Most importantly, therapeutic strategies that include pharmacology, gene repair, and gene therapy should be developed to prevent the adverse clinical effects of cMyBP-C(C10mut). This review article aims to examine the effects of cMyBP-C(C10mut) on cardiac function, emphasizing the need for the development of genetic testing and expanded therapeutic strategies.

Topics: Amino Acid Sequence; Animals; Asian People; Cardiomyopathy, Hypertrophic; Carrier Proteins; Frameshift Mutation; Humans; Myocardial Contraction; Sequence Deletion

PubMed: 24327208
DOI: 10.1007/s00424-013-1417-7

Authors: Allen Herbst, Steven J Prior, Cathy C Lee...

Mitochondrial DNA (mtDNA) quality and quantity relate to two hallmarks of aging-genomic instability and mitochondrial dysfunction. Physical performance relies on mitochondrial integrity and declines with age, yet the interactions between mtDNA quantity, quality, and physical performance are unclear. Using a validated digital PCR assay specific for mtDNA deletions, we tested the hypothesis that skeletal muscle mtDNA deletion mutation frequency (i.e., a measure of mtDNA quality) or mtDNA copy number predicts physical performance in older adults. Total DNA was isolated from vastus lateralis muscle biopsies and used to quantitate mtDNA copy number and mtDNA deletion frequency by digital PCR. The biopsies were obtained from a cross-sectional cohort of 53 adults aged 50 to 86 years. Before the biopsy procedure, physical performance measurements were collected, including VO, modified physical performance test score, 6-min walk distance, gait speed, grip strength, and total lean and leg mass. Linear regression models were used to evaluate the relationships between age, sex, and the outcomes. We found that mtDNA deletion mutation frequency increased exponentially with advancing age. On average from ages 50 to 86, deletion frequency increased from 0.008 to 0.15%, an 18-fold increase. Females may have lower deletion frequencies than males at older ages. We also measured declines in VO and mtDNA copy number with age in both sexes. The mtDNA deletion frequency measured from single skeletal muscle biopsies predicted 13.3% of the variation in VO. Copy number explained 22.6% of the variation in mtDNA deletion frequency and 10.4% of the lean mass variation. We found predictive relationships between age, mtDNA deletion mutation frequency, mtDNA copy number, and physical performance. These data are consistent with a role for mitochondrial function and genome integrity in maintaining physical performance with age. Analyses of mtDNA quality and quantity in larger cohorts and longitudinal studies could extend our understanding of the importance of mitochondrial DNA in human aging and longevity.

Topics: Aged; Aged, 80 and over; Cross-Sectional Studies; DNA Copy Number Variations; DNA, Mitochondrial; Female; Humans; Male; Middle Aged; Mitochondria; Muscle, Skeletal; Physical Functional Performance; Sequence Deletion

PubMed: 33740224
DOI: 10.1007/s11357-021-00351-z

Authors: Tetsuya Akaishi, Kei Fujiwara

The insertion/deletion (indel) mutation profiles of SARS-CoV-2 variants, including Omicron, remain unclear. We compared whole-genome sequences from various lineages and used preserved indels to infer the ancestral relationships between different lineages. Thirteen indel patterns from twelve sites were seen in ≥ 2 sequences; six of these sites were located in the N-terminal domain of the viral spike gene. Preserved indels in the coding regions were also identified in the non-structural protein 3 (Nsp3), Nsp6, and nucleocapsid genes. Seven of the thirteen indel patterns were specific to the Omicron variants, four of which were observed in BA.1, making it the most mutated variant. Other preserved indels observed in the Omicron variants were also seen in Alpha and/or Gamma, but not Delta, suggesting that Omicron is phylogenetically more proximal to Alpha. We demonstrated distinct profiles of preserved indels among SARS-CoV-2 variants and sublineages, suggesting the importance of indels in viral evolution.

Topics: Humans; SARS-CoV-2; COVID-19; Gamma Rays; Sequence Deletion

PubMed: 37000302
DOI: 10.1007/s00203-023-03493-0

Review

Authors: Sung-Pin Fan, Ni-Chung Lee, Chin-Hsien Lin...

BACKGROUND/PURPOSE

Type 1 sialidosis is a rare autosomal recessive lysosomal storage disease caused by Neuraminidase 1 (NEU1) gene mutations. We report a type 1 sialidosis patient with a novel deletion mutation in NEU1 and compared the phenotypes within different ethnicities.

METHODS

Targeted next generation sequencing and segregation analysis were performed to identify the causative gene mutation of the index patient. The clinical and electrophysiological characteristics of the patient were compared to those reported in previous studies of type 1 sialidosis from 1996 to 2019.

RESULTS

A 16-year-old boy presented with progressive onset of seizure, myoclonus, and ataxia since 5 years of age. Targeted next generation sequencing revealed the pathogenic missense variant c.544A>G (p.Ser182Gly) and the novel c.314_352del (p.A106_G118del) deletion in NEU1 in a compound heterozygote state. The leukocyte neuraminidase activity was significantly decreased (0.0323 nmol/mg protein/hour, normal reference: 0.326 ± 0.095 nmol/mg protein/hour). A total of 46 patients were identified in 18 reports from the literature. The most common symptoms were myoclonus (100%), followed by ataxia (88.3%) and seizure (72.5%). Notably, impaired cognition (50.0% vs. 21.7%, P = 0.04) and cherry-red spots (61.1% vs. 40.7%, P = 0.02) were less frequently reported in Asian patients than in Caucasian patients. Abnormal somatosensory evoked potentials with giant cortical waves and prolonged visual evoked potential latency were found consistently in Asian and Caucasian patients, and could be a surrogate marker of early diagnosis.

CONCLUSION

Our findings suggest a distinct phenotype of infrequent cherry-red spots and abnormal evoked potentials in Asian patients with type 1 sialidosis.

Topics: Adolescent; Humans; Male; Mucolipidoses; Mutation, Missense; Myoclonus; Neuraminidase; Phenotype; Seizures; Sequence Deletion

PubMed: 31371146
DOI: 10.1016/j.jfma.2019.07.017

Authors: Sun Jin Choi, In Sun Song, Ok Hee Ryu...

A 4 base-pair deletion mutation in the Distal-less 3 (DLX3) gene is etiologic for Tricho-Dento-Osseous syndrome (TDO). A cardinal feature of TDO is an increased thickness and density of bone. We tested the effects of the DLX3 gene mutation responsible for TDO on the osteoblastic differentiation of preosteoblastic MC3T3E1 cells and multipontent mesenchymal C2C12 cells. Differential expression analysis of C2C12 cells transfected with wild type DLX3 or mutant DLX3 was performed and desmin gene expression, an early myoblastic differentiation marker in mesenchymal cells, was evaluated by RT-PCR, western blot analysis, and desmin promoter transcriptional activity. Transfection of wild type DLX3 into MC3T3E1 and C2C12 cells increased alkaline phosphatase-2 activity, mineral deposition, and promoter activities of the osteocalcin and type 1 collagen genes compared to empty vector transfected cells. Transfection of mutant DLX3 into these cells further enhanced alkaline phosphatase activity, mineral deposition, and osteocalcin promoter activities, but did not further enhance type 1 collagen promoter activity. Transfection of mutant DLX3 into C2C12 cells markedly down regulated desmin gene expression, and protein expression of desmin and MyoD, while increasing protein expression of osterix and Runx2. These results demonstrate that the DLX3 deletion mutation associated with TDO enhances mesenchymal cell differentiation to an osteoblastic lineage rather than a myoblastic lineage by changing the fate of mesenchymal cells. This DLX3 mutation also accelerates the differentiation of osteoprogenitor cells to osteoblasts at later stages of osteogenesis.

Topics: Animals; Cell Differentiation; Collagen Type I; DNA, Complementary; Down-Regulation; Genes, Homeobox; Homeodomain Proteins; Mice; MyoD Protein; Osteoblasts; Osteocalcin; Osteogenesis; Promoter Regions, Genetic; Protein Binding; Sequence Deletion; Transcription Factors; Up-Regulation

PubMed: 17950683
DOI: 10.1016/j.bone.2007.08.047

Authors: Sheng Cui, Yoo Jin Shin, Eun Jeong Ko...

Human-induced pluripotent stem cell lines (hiPSCs) derived from the peripheral blood mononuclear cells (PBMCs) of a woman (CMCi007-A) and her son (CMCi006-A) diagnosed with Fabry disease (FD) caused by the frameshift deletion mutation c.969delC in the alpha-galactosidase A (GLA) gene were generated. These hiPSCs showed typical human embryonic stem cell-like morphology and expressed pluripotency-associated markers, and directly differentiated into all three germ-layers. Karyotyping showed normal 46, XY (CMCi006-A) and 46, XX (CMCi007-A). In summary, we generated novel patient-specific hiPSC lines from both a female and male containing the same mutation, which may provide additional insight into the pathophysiology of FD.

Topics: Fabry Disease; Female; Humans; Induced Pluripotent Stem Cells; Leukocytes, Mononuclear; Male; Mutation; Sequence Deletion; alpha-Galactosidase

PubMed: 33545641
DOI: 10.1016/j.scr.2021.102214

Meta-Analysis

Authors: Chao Wang, Zhaowei Teng, Yun Zhu...

BACKGROUND

Hepatocellular carcinoma (HCC) is the most common liver cancer, leading to many cancer-related deaths worldwide. Several studies have shown an association between pre-S deletion mutation of hepatitis B virus (HBV) and HCC risk, but the results remain conflicting. We aimed to verify HBV pre-S deletion mutations in relation to the risk of HCC.

MATERIAL AND METHODS

We searched the commonly used electronic databases for relevant studies of this association among the Asian population until September 30th, 2014. Odds ratios (ORs) with 95% confidence intervals (CIs) were employed to calculate the association.

RESULTS

A total of 17 case-control studies were screened out, including 2837 HBV-infected patients, of whom 1246 had HCC. The results showed that the frequency of pre-S deletion of HBV in patients with HCC was higher than that in patients without HCC (35.7% vs. 11.5%), indicating the prevalence of this mutation in patients with HCC. Statistically significant correlations were observed for pre-S deletion mutation and risk of HCC in a random-effects model (OR=3.90, 95% CI=2.80-5.44, P<0.00001). This association was also found in Chinese populations (OR=4.84, 95% CI=2.86-8.20, P<0.00001).

CONCLUSIONS

Our data indicate that HBV pre-S deletion mutations might be associated with HCC risk. Their oncogenic role may be important in studying the potential mechanism of HBV hepatocarcinogenesis.

Topics: Adult; Asian People; Carcinoma, Hepatocellular; Genetic Association Studies; Genetic Predisposition to Disease; Hepatitis B virus; Humans; Liver Neoplasms; Middle Aged; Publication Bias; Risk Factors; Sequence Deletion

PubMed: 25868851
DOI: 10.12659/MSM.894058