scholarly journals Analysis of phage-resistant mechanisms inStaphylococcus aureusSA003 reveals a different binding mechanism for the closely related Twort-like phages ϕSA012 and ϕSA039

2018 ◽  
Author(s):  
Aa Haeruman Azam ◽  
Fumiya Hoshiga ◽  
Ippei Takeuchi ◽  
Kazuhiko Miyanaga ◽  
Yasunori Tanji
Keyword(s):  
Teichoic Acid ◽  
Point Mutations ◽  
In Silico Analysis ◽  
Close Relative ◽  
Phenotypic Change ◽  
Missense Mutations ◽  
Wild Type ◽  
Wall Teichoic Acid ◽  
Whole Genome Analysis ◽  
Specific Phage

ABSTRACTWe have previously generated strains ofStaphylococcus aureusSA003 resistant to its specific phage ϕSA012 through long-term coevolution experiment. However, the DNA mutations responsible for the phenotypic change of phage resistance are unknown. Whole-genome analysis revealed six genes that acquired unique point mutations: five missense mutations and one nonsense mutation. Moreover, one deletion, 1.779-bp, resulted in the deletion of the genes encoding glycosyltransferase, TarS, and iron-sulfure repair protein, ScdA. The deletion occurred from the second round of coculture (SA003R2) and remained through the last round. The ϕSA012 infection toward SA003R2 had decreased to 79.77±7.50% according to plating efficiency. Complementation of the phage-resistant strain by the wild-type allele showed two mutated host genes were linked to the inhibition of post-adsorption, and five genes were linked to phage adsorption of ϕSA012. Unlike ϕSA012, infection by ϕSA039, a close relative of ϕSA012, onto SA003R2 was impaired drastically. Complementation of SA003R2 by wild-typetarSrestores the infectivity of ϕSA039. Thus, we concluded that ϕSA039 requires β-GlcNAc in Wall Teichoic Acid (WTA) for its binding. In silico analysis of the ϕSA039 genome revealed that several proteins in the tail and baseplate region were different from ϕSA012; notably the partial deletion oforf96of ϕSA039, a homolog oforf99of ϕSA012.Orf100of ϕSA039, a homolog ofOrf103of ϕSA012, a previously reported receptor binding protein (RBP), had low similarity (86%) to that of ϕSA012. The difference in tail and baseplate proteins might be the factor for specificity difference between ϕSA012 and ϕSA039.

scholarly journals PLP1 Mutations in Patients with Multiple Sclerosis: Identification of a New Mutation and Potential Pathogenicity of the Mutations

2018 ◽  
Vol 7 (10) ◽  
pp. 342 ◽  
Author(s):  
Nancy Cloake ◽  
Jun Yan ◽  
Atefeh Aminian ◽  
Michael Pender ◽  
Judith Greer
Keyword(s):  
Multiple Sclerosis ◽  
Clinical Symptoms ◽  
Point Mutations ◽  
Human Leukocyte ◽  
In Silico Analysis ◽  
Proteolipid Protein ◽  
Wild Type ◽  
Exon 2 ◽  
Mutant Proteins ◽  
The Unfolded Protein Response

PLP1 is located on the X-chromosome and encodes myelin proteolipid protein (PLP), the most abundant protein in central nervous system myelin. Generally, point mutations in PLP1 result in X-linked dysmyelinating disorders, such as Pelizaeus-Merzbacher disease (PMD) or spastic paraplegia type 2 (SPG2). However, several case studies have identified patients with missense point mutations in PLP1 and clinical symptoms and signs compatible with a diagnosis of multiple sclerosis (MS). To investigate if PLP1 mutations occur relatively frequently in MS, we sequenced the coding regions of PLP1 in 22 female MS patients who had developed disease after the age of 40 and in 42 healthy women, and identified a missense mutation in exon 2 of PLP1 resulting in a Leu30Val mutation in the protein in one of the MS patients. mCherry-tagged plasmids containing wild type or mutant PLP1 sequences of PLP, including two known PMD/SPG2-related mutations as positive controls, were constructed and transfected into Cos-7 cells. In comparison with cells transfected with wild type PLP1, all mutations caused significant accumulation of PLP in the endoplasmic reticulum of the cells and induction of the unfolded protein response—a mechanism that leads to apoptosis of cells expressing mutant proteins. Additionally, in silico analysis of the binding of peptides containing the Leu30Val mutation to the human leukocyte antigen (HLA) molecules carried by the patient harboring this mutation suggested that the mutation could produce several novel immunogenic epitopes in this patient. These results support the idea that mutations in myelin-related genes could contribute to the development of MS in a small proportion of patients.

scholarly journals Lipoteichoic acid of Streptococcus oralis Uo5: a novel biochemical structure comprising an unusual phosphorylcholine substitution pattern compared to Streptococcus pneumoniae

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Nicolas Gisch ◽  
Dominik Schwudke ◽  
Simone Thomsen ◽  
Nathalie Heß ◽  
Regine Hakenbeck ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Teichoic Acid ◽  
Structural Complexity ◽  
Lipoteichoic Acid ◽  
Close Relative ◽  
Structural Variations ◽  
Wall Teichoic Acid ◽  
Substitution Pattern ◽  
Type Iv ◽  
Streptococcus Oralis

Abstract Members of the Mitis group of streptococci possess teichoic acids (TAs) as integral components of their cell wall that are unique among Gram-positive bacteria. Both, lipoteichoic (LTA) and wall teichoic acid, are formed by the same biosynthetic pathway, are of high complexity and contain phosphorylcholine (P-Cho) residues. These residues serve as anchors for choline-binding proteins (CBPs), some of which have been identified as virulence factors of the human pathogen Streptococcus pneumoniae. We investigated the LTA structure of its close relative Streptococcus oralis. Our analysis revealed that S. oralis Uo5 LTA has an overall architecture similar to pneumococcal LTA (pnLTA) and can be considered as a subtype of type IV LTA. Its structural complexity is even higher than that of pnLTA and its composition differs in number and type of carbohydrate moieties, inter-residue connectivities and especially the P-Cho substitution pattern. Here, we report the occurrence of a saccharide moiety substituted with two P-Cho residues, which is unique as yet in bacterial derived surface carbohydrates. Finally, we could link the observed important structural variations between S. oralis and S. pneumoniae LTA to the divergent enzymatic repertoire for their TA biosynthesis.

scholarly journals Structural and functional effects of hereditary hemolytic anemia-associated point mutations in the alpha spectrin tetramer site

Blood ◽  
2008 ◽  
Vol 111 (12) ◽  
pp. 5712-5720 ◽  
Author(s):  
Massimiliano Gaetani ◽  
Sara Mootien ◽  
Sandra Harper ◽  
Patrick G. Gallagher ◽  
David W. Speicher
Keyword(s):  
Clinical Symptoms ◽  
Point Mutations ◽  
Titration Calorimetry ◽  
Missense Mutations ◽  
Binding Affinities ◽  
Wild Type ◽  
Tetramer Binding ◽  
Structural And Functional Properties ◽  
Recombinant Peptides ◽  
Self Association

Abstract The most common hereditary elliptocytosis (HE) and hereditary pyropoikilocytosis (HPP) mutations are α-spectrin missense mutations in the dimer-tetramer self-association site. In this study, we systematically compared structural and functional properties of the 14 known HE/HPP mutations located in the α-spectrin tetramer binding site. All mutant α-spectrin recombinant peptides were well folded, stable structures, with only the R34W mutant exhibiting a slight structural destabilization. In contrast, binding affinities measured by isothermal titration calorimetry were greatly variable, ranging from no detectable binding observed for I24S, R28C, R28H, R28S, and R45S to approximately wild-type binding for R34W and K48R. Binding affinities for the other 7 mutants were reduced by approximately 10- to 100-fold relative to wild-type binding. Some sites, such as R28, were hot spots that were very sensitive to even relatively conservative substitutions, whereas other sites were only moderately perturbed by nonconservative substitutions. The R34W and K48R mutations were particularly intriguing mutations that apparently either destabilize tetramers through mechanisms not probed by the univalent tetramer binding assay or represent polymorphisms rather than the pathogenic mutations responsible for observed clinical symptoms. All α0 HE/HPP mutations studied here appear to exert their destabilizing effects through molecular recognition rather than structural mechanisms.

Abnormal WNT5A Signaling Causes Mandibular Hypoplasia in Robinow Syndrome

2017 ◽  
Vol 96 (11) ◽  
pp. 1265-1272 ◽  
Author(s):  
S. Hosseini-Farahabadi ◽  
S.J. Gignac ◽  
A. Danescu ◽  
K. Fu ◽  
J.M. Richman
Keyword(s):  
Cell Migration ◽  
Genetic Diseases ◽  
Adaptor Protein ◽  
In Silico Analysis ◽  
Missense Mutations ◽  
Loss Of Function ◽  
Wild Type ◽  
Mandibular Hypoplasia ◽  
Robinow Syndrome ◽  
The Impact

The study of rare genetic diseases provides valuable insights into human gene function. Here, we investigate dominant Robinow syndrome (RS), which affects the WNT5A signaling pathway. Autosomal dominant RS is caused by missense mutations in WNT5A or nonsense mutations in the adaptor protein DVL1 or DVL3. The recessive form of the disease is caused by loss-of-function mutations in the receptor ROR2. RS is characterized by hypertelorism, midface, and mandibular hypoplasia. Here, we focus on the missense mutations in WNT5A, since the impact on function is difficult to predict from in silico analysis. We used chicken embryo to express wild-type or 2 mutant versions of human WNT5A in the mandible and then examined the morphologic, cellular, and molecular effects. The 3 experimental viruses—wt WNT5A, WNT5AC83S, or WNT5AC182R—all caused shortening of the mandible on the injected side as compared with GFP controls. Although the phenotypes initially appeared similar, we uncovered specific disruption of chondrocyte polarity and shape, inhibition of cell migration, differences in target gene expression, and absence of JNK signaling only in the presence of mutant viruses. In addition, the missense mutations do not appear to block receptor binding, since in paracrine experiments, the mutant protein inhibits cell migration. In this study, we ruled out a straightforward gain or loss of function caused by the WNT5A missense mutations. Instead, the mutations are likely redirecting WNT signaling away from JNK-PCP toward other noncanonical pathways. We conclude that in RS, WNT5A missense mutations have dominant neomorphic effects that interfere with the function of the wild-type protein.

scholarly journals The mtDNA mutation spectrum in the PolG mutator mouse reveals germline and somatic selection

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Kendra D. Maclaine ◽  
Kevin A. Stebbings ◽  
Daniel A. Llano ◽  
Justin C. Havird
Keyword(s):  
Mitochondrial Gene ◽  
Point Mutations ◽  
Germline Mutations ◽  
Premature Aging ◽  
Missense Mutations ◽  
Wild Type ◽  
Mtdna Mutation ◽  
Mtdna Mutations ◽  
Strand Asymmetry ◽  
D Loop

Abstract Background Mitochondrial DNA (mtDNA) codes for products necessary for electron transport and mitochondrial gene translation. mtDNA mutations can lead to human disease and influence organismal fitness. The PolG mutator mouse lacks mtDNA proofreading function and rapidly accumulates mtDNA mutations, making it a model for examining the causes and consequences of mitochondrial mutations. Premature aging in PolG mice and their physiology have been examined in depth, but the location, frequency, and diversity of their mtDNA mutations remain understudied. Identifying the locations and spectra of mtDNA mutations in PolG mice can shed light on how selection shapes mtDNA, both within and across organisms. Results Here, we characterized somatic and germline mtDNA mutations in brain and liver tissue of PolG mice to quantify mutation count (number of unique mutations) and frequency (mutation prevalence). Overall, mtDNA mutation count and frequency were the lowest in the D-loop, where an mtDNA origin of replication is located, but otherwise uniform across the mitochondrial genome. Somatic mtDNA mutations have a higher mutation count than germline mutations. However, germline mutations maintain a higher frequency and were also more likely to be silent. Cytosine to thymine mutations characteristic of replication errors were the plurality of basepair changes, and missense C to T mutations primarily resulted in increased protein hydrophobicity. Unlike wild type mice, PolG mice do not appear to show strand asymmetry in mtDNA mutations. Indel mutations had a lower count and frequency than point mutations and tended to be short, frameshift deletions. Conclusions Our results provide strong evidence that purifying selection plays a major role in the mtDNA of PolG mice. Missense mutations were less likely to be passed down in the germline, and they were less likely to spread to high frequencies. The D-loop appears to have resistance to mutations, either through selection or as a by-product of replication processes. Missense mutations that decrease hydrophobicity also tend to be selected against, reflecting the membrane-bound nature of mtDNA-encoded proteins. The abundance of mutations from polymerase errors compared with reactive oxygen species (ROS) damage supports previous studies suggesting ROS plays a minimal role in exacerbating the PolG phenotype, but our findings on strand asymmetry provide discussion for the role of polymerase errors in wild type organisms. Our results provide further insight on how selection shapes mtDNA mutations and on the aging mechanisms in PolG mice.

scholarly journals Molecular insights into the role of genetic determinants of congenital hypothyroidism

2021 ◽  
Vol 19 (3) ◽  
pp. e29
Author(s):  
Yedukondalu Kollati ◽  
Radha Rama Devi Akella ◽  
Shaik Mohammad Naushad ◽  
Rajesh K. Patel ◽  
G. Bhanuprakash Reddy ◽  
...  
Keyword(s):  
Thyroid Hormones ◽  
Congenital Hypothyroidism ◽  
In Silico ◽  
In Silico Analysis ◽  
Thyroid Stimulating Hormone ◽  
Binding Energies ◽  
Thyroid Peroxidase ◽  
Transcriptional Level ◽  
Missense Mutations ◽  
Wild Type

In our previous studies, we have demonstrated the association of certain variants of the thyroid-stimulating hormone receptor (TSHR), thyroid peroxidase (TPO), and thyroglobulin (TG) genes with congenital hypothyroidism. Herein, we explored the mechanistic basis for this association using different in silico tools. The mRNA 3'-untranslated region (3'-UTR) plays key roles in gene expression at the post-transcriptional level. In TSHR variants (rs2268477, rs7144481, and rs17630128), the binding affinity of microRNAs (miRs) (hsa-miR-154-5p, hsa-miR-376a-2-5p, hsa-miR-3935, hsa-miR-4280, and hsa-miR-6858-3p) to the 3'-UTR is disrupted, affecting post-transcriptional gene regulation. TPO and TG are the two key proteins necessary for the biosynthesis of thyroid hormones in the presence of iodide and H2O2. Reduced stability of these proteins leads to aberrant biosynthesis of thyroid hormones. Compared to the wild-type TPO protein, the p.S398T variant was found to exhibit less stability and significant rearrangements of intra-atomic bonds affecting the stoichiometry and substrate binding (binding energies, ΔG of wild-type vs. mutant: ‒15 vs. ‒13.8 kcal/mol; and dissociation constant, Kd of wild-type vs. mutant: 7.2E-12 vs. 7.0E-11 M). The missense mutations p.G653D and p.R1999W on the TG protein showed altered ΔG (0.24 kcal/mol and 0.79 kcal/mol, respectively). In conclusion, an in silico analysis of TSHR genetic variants in the 3'-UTR showed that they alter the binding affinities of different miRs. The TPO protein structure and mutant protein complex (p.S398T) are less stable, with potentially deleterious effects. A structural and energy analysis showed that TG mutations (p.G653D and p.R1999W) reduce the stability of the TG protein and affect its structure-functional relationship.

scholarly journals Cell Wall Teichoic Acid Glycosylation inListeria monocytogenes Serotype 4b Requires gtcA, a Novel, Serogroup-Specific Gene

1999 ◽  
Vol 181 (2) ◽  
pp. 418-425 ◽  
Author(s):  
N. Promadej ◽  
F. Fiedler ◽  
P. Cossart ◽  
S. Dramsi ◽  
S. Kathariou
Keyword(s):  
Cell Wall ◽  
Marked Reduction ◽  
Teichoic Acid ◽  
Lipoteichoic Acid ◽  
Specific Gene ◽  
Specific Monoclonal Antibody ◽  
Wild Type ◽  
Wall Teichoic Acid ◽  
Insertional Inactivation ◽  
Serotype 4B

ABSTRACT We have identified a novel gene, gtcA, involved in the decoration of cell wall teichoic acid of Listeria monocytogenes serotype 4b with galactose and glucose. Insertional inactivation of gtcA brought about loss of reactivity with the serotype 4b-specific monoclonal antibody c74.22 and was accompanied by a complete lack of galactose and a marked reduction in the amounts of glucose on teichoic acid. Interestingly, the composition of membrane-associated lipoteichoic acid was not affected. Complementation of the mutants with the clonedgtcA in trans restored galactose and glucose on teichoic acid to wild-type levels. The complemented strains also recovered reactivity with c74.22. Within L. monocytogenes, sequences homologous to gtcA were found in all serogroup 4 isolates but not in strains of any other serotypes. In serotype 4b, gtcA appears to be the first member of a bicistronic operon which includes a gene with homology toBacillus subtilis rpmE, encoding ribosomal protein L31. In contrast to gtcA, the latter gene appears conserved among all screened serotypes of L. monocytogenes.

scholarly journals Packpred: Predicting the functional effect of missense mutations

2021 ◽  
Author(s):  
Kuan Pern Tan ◽  
Tejashree Rajaram Kanitkar ◽  
Kwoh Chee Keong ◽  
M.S. Madhusudhan
Keyword(s):  
Amino Acid ◽  
Single Point ◽  
Point Mutations ◽  
Substitution Matrix ◽  
Saturation Mutagenesis ◽  
Data Sets ◽  
Missense Mutations ◽  
Wild Type ◽  
Data Set ◽  
Functional Consequences

1.AbstractPredicting the functional consequences of single point mutations has relevance to protein function annotation and to clinical analysis/diagnosis. We developed and tested Packpred that makes use of a multi-body clique statistical potential in combination with a depth dependent amino acid substitution matrix (FADHM) and positional Shannon Entropy to predict the functional consequences of point mutations in proteins. Parameters were trained over a saturation mutagenesis data set of T4-lysozyme (1966 mutations). The method was tested over another saturation mutagenesis data set (CcdB; 1534 mutations) and the Missense3D data set (4099 mutations). The performance of Packpred was compared against those of six other contemporary methods. With MCC values of 0.42, 0.47 and 0.36 on the training and testing data sets respectively, Packpred outperforms all method in all data sets, with the exception of marginally underperforming to FADHM in the CcdB data set. On analyzing the results, we could build meta servers that chose best performing methods of wild type amino acids and for wild type-mutant amino acid pairs. This lead to an increase of MCC value of 0.40 and 0.51 for the two meta predictors respectively on the Missense3D data set. We conjecture that it is possible to improve accuracy with better meta predictors as among the 7 methods compared, at the least one method or another is able to correctly predict ∼99% of the data.

scholarly journals Neoantimon: a multifunctional R package for identification of tumor-specific neoantigens

2020 ◽  
Vol 36 (18) ◽  
pp. 4813-4816
Author(s):  
Takanori Hasegawa ◽  
Shuto Hayashi ◽  
Eigo Shimizu ◽  
Shinichi Mizuno ◽  
Atsushi Niida ◽  
...  
Keyword(s):  
Point Mutations ◽  
R Package ◽  
Missense Mutations ◽  
Wild Type ◽  
Structural Variants ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Additional Information ◽  
Histocompatibility Complex ◽  
Allele Specific

Abstract Summary It is known that some mutant peptides, such as those resulting from missense mutations and frameshift insertions, can bind to the major histocompatibility complex and be presented to antitumor T cells on the surface of a tumor cell. These peptides are termed neoantigen, and it is important to understand this process for cancer immunotherapy. Here, we introduce an R package termed Neoantimon that can predict a list of potential neoantigens from a variety of mutations, which include not only somatic point mutations but insertions, deletions and structural variants. Beyond the existing applications, Neoantimon is capable of attaching and reflecting several additional information, e.g. wild-type binding capability, allele specific RNA expression levels, single nucleotide polymorphism information and combinations of mutations to filter out infeasible peptides as neoantigen. Availability and implementation The R package is available at http://github/hase62/Neoantimon.

scholarly journals Packpred: Predicting the Functional Effect of Missense Mutations

2021 ◽  
Vol 8 ◽  
Author(s):  
Kuan Pern Tan ◽  
Tejashree Rajaram Kanitkar ◽  
Chee Keong Kwoh ◽  
Mallur Srivatsan Madhusudhan
Keyword(s):  
Amino Acid ◽  
Single Point ◽  
Point Mutations ◽  
Substitution Matrix ◽  
Saturation Mutagenesis ◽  
Data Sets ◽  
Missense Mutations ◽  
Wild Type ◽  
Data Set ◽  
Functional Consequences

Predicting the functional consequences of single point mutations has relevance to protein function annotation and to clinical analysis/diagnosis. We developed and tested Packpred that makes use of a multi-body clique statistical potential in combination with a depth-dependent amino acid substitution matrix (FADHM) and positional Shannon entropy to predict the functional consequences of point mutations in proteins. Parameters were trained over a saturation mutagenesis data set of T4-lysozyme (1,966 mutations). The method was tested over another saturation mutagenesis data set (CcdB; 1,534 mutations) and the Missense3D data set (4,099 mutations). The performance of Packpred was compared against those of six other contemporary methods. With MCC values of 0.42, 0.47, and 0.36 on the training and testing data sets, respectively, Packpred outperforms all methods in all data sets, with the exception of marginally underperforming in comparison to FADHM in the CcdB data set. A meta server analysis was performed that chose best performing methods of wild-type amino acids and for wild-type mutant amino acid pairs. This led to an increase in the MCC value of 0.40 and 0.51 for the two meta predictors, respectively, on the Missense3D data set. We conjecture that it is possible to improve accuracy with better meta predictors as among the seven methods compared, at least one method or another is able to correctly predict ∼99% of the data.

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