Breaking the Stereo Barrier of Amino Acid Attachment to tRNA by a Single Nucleotide

2005 ◽  
Vol 348 (3) ◽  
pp. 513-521 ◽  
Author(s):  
Svetlana Shitivelband ◽  
Ya-Ming Hou
Keyword(s):  
Author(s):  
Yi Sun ◽  
Haiyan Mao ◽  
Xiuyu Lou ◽  
Xinying Wang ◽  
Yin Chen ◽  
...  

AbstractThere have been five waves of influenza A (H7N9) epidemics in Zhejiang Province between 2013 and 2017. Although the epidemiological characteristics of the five waves have been reported, the molecular genetics aspects, including the phylogeny, evolution, and mutation of hemagglutinin (HA), have not been systematically investigated. A total of 154 H7N9 samples from Zhejiang Province were collected between 2013 and 2017 and sequenced using an Ion Torrent Personal Genome Machine. The starting dates of the waves were 16 March 2013, 1 July 2013, 1 July 2014, 1 July 2015, and 1 July 2016. Single-nucleotide polymorphisms (SNPs) and amino acid mutations were counted after the HA sequences were aligned. The evolution of H7N9 matched the temporal order of the five waves, among which wave 3 played an important role. The 55 SNPs and 14 amino acid mutations with high frequency identified among the five waves revealed the dynamic occurrence of mutation in the process of viral dissemination. Wave 3 contributed greatly to the subsequent epidemic of waves 4 and 5 of H7N9. Compared with wave 1, wave 5 was characterized by more mutations, including A143V and R148K, two mutations that have been reported to weaken the immune response. In addition, some amino acid mutations were observed in wave 5 that led to more lineages. It is necessary to strengthen the surveillance of subsequent H7N9 influenza outbreaks.


Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2454
Author(s):  
Marta Budziszewska ◽  
Przemysław Wieczorek

Tomato torrado virus (ToTV) induces severe systemic necrosis in Solanum lycopersicum. This work aimed at describing the genetic variability of necrosis-inducing ToTV-Wal’17 collected in 2017, derived from the ToTV-Wal’03 after long-term passages in plants. Sequence analyses of the ToTV-Wal’17 indicated twenty-eight single nucleotide substitutions in coding sequence of both RNAs, twelve of which resulted in amino acid changes in viral polyproteins. Moreover the sequencing data revealed that the 3’UTR of ToTV-Wal’17 RNA1 was 394 nts shorter in comparison to Wal’03. The performed sequence analyses revealed that 3’UTR of RNA1 of ToTV-Wal’17 is the most divergent across all previously described European isolates.


2004 ◽  
Vol 78 (4) ◽  
pp. 2029-2036 ◽  
Author(s):  
Josephine M. McAuliffe ◽  
Sonja R. Surman ◽  
Jason T. Newman ◽  
Jeffrey M. Riggs ◽  
Peter L. Collins ◽  
...  

ABSTRACT The Y942H and L992F temperature-sensitive (ts) and attenuating amino acid substitution mutations, previously identified in the L polymerase of the HPIV3cp45 vaccine candidate, were introduced into homologous positions of the L polymerase of recombinant human parainfluenza virus type 1 (rHPIV1). In rHPIV1, the Y942H mutation specified the ts phenotype in vitro and the attenuation (att) phenotype in hamsters, whereas the L992F mutation specified neither phenotype. Each of these codon mutations was generated by a single nucleotide substitution and therefore had the potential to readily revert to a codon specifying the wild-type amino acid residue. We introduced alternative amino acid assignments at codon 942 or 992 as a strategy to increase genetic stability and to generate mutants that exhibit a range of attenuation. Twenty-three recombinants with codon substitutions at position 942 or 992 of the L protein were viable. One highly ts and att mutant, the Y942A virus, which had a difference of three nucleotides from the codon encoding a wild-type tyrosine, also possessed a high level of genetic and phenotypic stability upon serial passage in vitro at restrictive temperatures compared to that of the parent Y942H virus, which possessed a single nucleotide substitution. We obtained mutants with substitutions at position 992 that, in contrast to the L992F virus, possessed the ts and att phenotypes. These findings identify the use of alternative codon substitution mutations as a method that can be used to generate candidate vaccine viruses with increased genetic stability and/or a modified level of attenuation.


2020 ◽  
Author(s):  
Da Kuang ◽  
Jochen Weile ◽  
Nishka Kishore ◽  
Alan F. Rubin ◽  
Stanley Fields ◽  
...  

AbstractSummaryMultiplexed assays of variant effect (MAVEs) are capable of experimentally testing all possible single nucleotide or amino acid variants in selected genomic regions, generating ‘variant effect maps’, which provide biochemical insight and functional evidence to enable more rapid and accurate clinical interpretation of human variation. Because the international community applying MAVE approaches is growing rapidly, we developed the online MaveRegistry platform to catalyze collaboration, reduce redundant efforts, allow stakeholders to nominate targets, and enable tracking and sharing of progress on ongoing MAVE projects.Availability and implementationhttps://[email protected]


2018 ◽  
Vol 98 (4) ◽  
pp. 881-888 ◽  
Author(s):  
Masum Akond ◽  
Jiazheng Yuan ◽  
Shiming Liu ◽  
Stella K. Kantartzi ◽  
Khalid Meksem ◽  
...  

Improving seed composition and quality, including protein, oil, fatty acid, and amino acid contents, is an important goal of soybean farmers and breeders. The aim of this study was to map the quantitative trait loci (QTL) underlying the contents of protein, oil, fatty acids, and amino acids with 1510 single nucleotide polymorphism (SNP) markers using the ‘Hamilton’ × ‘Spencer’ recombinant inbred line population (H × S; n = 93). A total of 13 QTL for the traits studied have been mapped on 3 chromosomes (Chr.) of the soybean genome. Three major QTL have been mapped to a 7–13 cM region on Chr. 6. One major QTL for oil content (qOIL001) explained approximately 76% of the total phenotypic variation in this population; the second major QTL for amino acid alanine (Ala; qALA001) explained approximately 74% of the total variation in Ala content; moreover, two major QTL for palmitic acid (qPAL001 and qPAL002) were identified on Chr. 6 and explained approximately 21% of the phenotypic variation in this population. The SNP markers flanking the QTL identified here will be very useful for soybean breeders to develop and select soybean lines with higher seed composition qualities using marker-assisted selection.


Author(s):  
Zahraa Isam ◽  
Rabab Omran ◽  
Ammad Hassan Mahmood

  Objective: The calcium-sensing receptor (CASR) is a G-protein-coupled receptor that is mainly expressed in the parathyroid and the kidneys where it regulates parathyroid hormone secretion and renal tubular calcium reabsorption. Inactivating and activating CASR gene due to mutations severally caused hypercalcemia or hypocalcemia disorders. The aim of the study was to investigate the risk factor of CASR rs1801725 (Ala986Ser) patients with renal disease.Method: The blood samples were collected from 100 patients and divided into two groups, each one containing 50 samples; chronic kidney disease and end-stage renal disease, who admitted Merjan Teaching Hospital in Babylon Province, Iraq, from February to July 2016. In addition, healthy persons as a control group (50 samples). Genotyping of CASR single-nucleotide polymorphisms (SNP) was performed using a polymerase chain reaction technique, followed by single-strand conformation polymorphism. Accordingly, these DNA polymorphisms were confirmed using DNA sequencing.Results: The conformational haplotypes of CASR, exon7 NCBI Primer3plus reference were obtained in three patterns, including two, three, and four bands, due to the presence SNPs within the studied region. These SNPs leads to change three amino acid residues of CASR, including amino acid substitutions were Ala 128→ Ser 128, Leu 155→Tye 155, and Leu 156→ Ser 156 that may affect or modified the tertiary structure of the receptor, subsequently the function like the affinity to calcium ion may be effected.Conclusion: These results suggest that the variants of CASR SNP, namely, rs1801725 might be involved in susceptibility to kidney stone disease.


1993 ◽  
Vol 70 (04) ◽  
pp. 636-641 ◽  
Author(s):  
Masaru Ido ◽  
Michiaki Ohiwa ◽  
Tatsuya Hayashi ◽  
Junji Nishioka ◽  
Tsuyoshi Hatada ◽  
...  

SummaryWe report genetic abnormalities of protein C gene in a male infant who developed neonatal purpura fulminans. DNA-sequence analysis of all exons in protein C gene in this family revealed two mutations. The first abnormality, derived from the mother, was a deletion of one of four consecutive G at nucleotide number 10758 in exon IX which would result in a frame shift mutation and completely change amino acid sequence from Gly381 in the carboxyl-terminal region of protein C. The second abnormality, derived from the father, was a single nucleotide mutation from G to A in the codon (GAG to AAG) at nucleotide number 2977 in exon III, which would result in a substitution of Lys for γ-carboxyglutamic acid (Gla)26. This change would be responsible for the reduced immunological protein C levels of the patient and the father, estimated by a monoclonal antibody which recognizes the Gla-domain in a Ca2+-dependent manner (3.8% and 57%, respectively). Partially purified abnormal protein C from the father’s plasma showed a normal amidolytic activity and a change in the electrophoretic mobility. We detected the above mutations in his family members using two methods; one was a creation of new restriction enzyme sites using mutagenic primers and the other was single nucleotide primer extension. Both methods are rapid and useful for the diagnosis of prenatal protein C abnormalities.


Blood ◽  
1988 ◽  
Vol 72 (5) ◽  
pp. 1817-1821 ◽  
Author(s):  
SL Thein ◽  
DA Lane

Abstract Antithrombin III (ATIII) Northwick Park is caused by a single amino acid substitution, Arg 393---Cys and antithrombin III Glasgow is caused by Arg 393----His. Examination of the genetic code and the sequence of normal antithrombin III revealed that these amino acid substitutions could arise from the substitution of either two nucleotides or a single nucleotide at codon 393 of the antithrombin III gene. In two families, detection of the ATIII variants by genetic linkage analysis was not possible owing to lack of informative RFLP markers. Consequently, we synthesized two 22-base-long oligonucleotides specific for the single- base substitutions in the region of codon 393 and demonstrated by oligonucleotide hybridization that the molecular defect of ATIII Northwick Park is caused by the CGT----TGT mutation at codon 393 and that ATIII Glasgow is caused by the CGT----CAT mutation at codon 393. These oligonucleotide probes should prove useful as an alternative method for early detection of the ATIII variants.


2005 ◽  
Vol 187 (2) ◽  
pp. 707-715 ◽  
Author(s):  
Kumaran S. Ramamurthi ◽  
Olaf Schneewind

ABSTRACT Yersinia spp. inject virulence proteins called Yops into the cytosol of target eukaryotic cells in an effort to evade phagocytic killing via a dedicated protein-sorting pathway termed type III secretion. Previous studies have proposed that, unlike other protein translocation mechanisms, Yops are not recognized as substrates for secretion via a solely proteinaceous signal. Rather, at least some of this information may be encoded within yop mRNA. Herein, we report that the first seven codons of yopE, when fused to the reporter protein neomycin phosphotransferase (Npt), are sufficient for the secretion of YopE1-7-Npt when type III secretion is induced in vitro. Systematic mutagenesis of yopE codons 1 to 7 reveals that, like yopQ, codons 2, 3, 5, and 7 are sensitive to mutagenesis, thereby defining the first empirical similarity between the secretion signals of two type III secreted substrates. Like that of yopQ, the secretion signal of yopE exhibits a bipartite nature. This is manifested by the ability of codons 8 to 15 to suppress point mutations in the minimal secretion signal that change the amino acid specificities of particular codons or that induce alterations in the reading frame. Further, we have identified a single nucleotide position in codon 3 that, when mutated, conserves the predicted amino acid sequence of the YopE1-7-Npt but abrogates secretion of the reporter protein. When introduced into the context of the full-length yopE gene, the single-nucleotide mutation reduces the type III injection of YopE into HeLa cells, even though the predicted amino acid sequence remains the same. Thus, yopE mRNA appears to encode a property that mediates the type III injection of YopE.


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