The B-hordein prolamin family of barley

Genome ◽  
2013 ◽  
Vol 56 (3) ◽  
pp. 179-185 ◽  
Author(s):  
Olin D. Anderson
Keyword(s):  
Stop Codon ◽  
Premature Stop Codon ◽  
In Silico Analysis ◽  
Gene Families ◽  
Full Length ◽  
C Terminus ◽  
Est Assembly ◽  
Silico Analysis ◽  
Total Ests ◽  
Relative Gene

The spectrum of B-hordein prolamins and genes in the single barley cultivar Barke is described from an in silico analysis of 1452 B-hordein ESTs and available genomic DNA. Eleven unique B-hordein proteins are derived from EST contigs. Ten contigs encode apparent full-length B-hordeins and the eleventh contains a premature stop codon that will lead to a truncated B-hordein. The 11 sequences are placed within the two previously described classes, i.e., the B1- and B3-type B-hordeins. The number of ESTs assigned to each sequence is used as an estimate of relative gene transcription and expression. Three of the sequences account for 79% of the total ESTs, with one sequence comprises 32% of the total ESTs and has a variant C-terminus caused by an undefined sequence change history near the 3′ coding terminus. The 70× difference in EST distribution among sequences points to the importance of understanding differential rates of expression within closely related gene families. Analysis of available genomic sequences confirms the EST assembly and reveals one full-length and two partial sequences of pseudogenes as evidenced by no matching ESTs for the sequences and premature stop codons and frame shifts.

scholarly journals A Novel Loss-of-Sclerostin Function Mutation in a First Egyptian Family with Sclerosteosis

2015 ◽  
Vol 2015 ◽  
pp. 1-8 ◽  
Author(s):  
Alaaeldin Fayez ◽  
Mona Aglan ◽  
Nora Esmaiel ◽  
Taher El Zanaty ◽  
Mohamed Abdel Kader ◽  
...  
Keyword(s):  
Bone Density ◽  
Autosomal Recessive ◽  
Frameshift Mutation ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
In Silico Analysis ◽  
Genomic Sequencing ◽  
Gene Coding ◽  
Autosomal Recessive Condition ◽  
Silico Analysis

Sclerosteosis is a rare autosomal recessive condition characterized by increased bone density. Mutations inSOSTgene coding for sclerostin are linked to sclerosteosis. Two Egyptian brothers with sclerosteosis and their apparently normal consanguineous parents were included in this study. Clinical evaluation and genomic sequencing of theSOSTgene were performed followed by in silico analysis of the resulting variation. A novel homozygous frameshift mutation in theSOSTgene, characterized as one nucleotide cytosine insertion that led to premature stop codon and loss of functional sclerostin, was identified in the two affected brothers. Their parents were heterozygous for the same mutation. To our knowledge this is the first Egyptian study of sclerosteosis andSOSTgene causing mutation.

scholarly journals CRISPR/Cas9-mediated mutation revealed cytoplasmic tail is dispensable for IZUMO1 function and male fertility

Reproduction ◽  
2016 ◽  
Vol 152 (6) ◽  
pp. 665-672 ◽  
Author(s):  
Samantha A M Young ◽  
Haruhiko Miyata ◽  
Yuhkoh Satouh ◽  
Masanaga Muto ◽  
Martin R Larsen ◽  
...  
Keyword(s):  
Amino Acid ◽  
Point Mutation ◽  
Male Fertility ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Cytoplasmic Tail ◽  
Binding Partner ◽  
C Terminus ◽  
Manipulation System

IZUMO1 is a protein found in the head of spermatozoa that has been identified as essential for sperm–egg fusion. Its binding partner in the egg has been discovered (JUNO); however, the roles of several domains within IZUMO1 remain unexplored. One such domain is the C-terminus, which undergoes major phosphorylation changes in the cytoplasmic portion of the protein during rat epididymal transit. However, the cytoplasmic tail of IZUMO1 in many species is highly variable, ranging from 55 to one amino acid. Therefore, to understand the role of the cytoplasmic tail of IZUMO1 in mouse, we utilised the gene manipulation system of CRISPR/Cas9 to generate a point mutation resulting in a premature stop codon, producing mice with truncated IZUMO1. Mice without the cytoplasmic tail of IZUMO1 showed normal fertility but decreased the amount of protein, indicating that whilst this region is important for the expression level of IZUMO1, it is dispensable for fertilisation in the mouse.

scholarly journals C-terminally truncated human O6-alkylguanine-DNA alkyltransferase retains activity

1992 ◽  
Vol 285 (3) ◽  
pp. 707-709 ◽  
Author(s):  
R H Elder ◽  
J Tumelty ◽  
K T Douglas ◽  
G P Margison ◽  
J A Rafferty
Keyword(s):  
Molecular Mass ◽  
Stop Codon ◽  
Full Length ◽  
Amino Acid Residues ◽  
Truncated Protein ◽  
Methylated Dna ◽  
Methyl Transfer ◽  
C Terminus ◽  
Calf Thymus ◽  
Dna Alkyltransferase

A cDNA encoding the human O6-alkylguanine-DNA alkyltransferase (ATase; EC 2.1.1.63; methylated-DNA: protein-cysteine methyltransferase) has been manipulated to generate a C-terminally deleted protein which retains full methyl-transfer activity. The elimination of 22 amino-acid residues from the C-terminus was achieved by endonuclease-SacI digestion of the 623 bp cDNA coding sequence and ligation of a SacI/HindIII linker containing an in-frame stop codon. The truncated protein was characterized by its reduced molecular mass in immunoblots probed with an antiserum against the full-length protein and by fluorography after incubation with [3H]methylated calf thymus DNA. The rate of methyl transfer was virtually identical for the full-length and truncated ATases. The construction of such a truncated, yet still functional, ATase, with a molecular mass of 19.7 kDa should facilitate a detailed n.m.r. structural study and help to determine the functional significance of the C-terminal domain of mammalian ATases.

Analysis of ZP1 gene reveals differences in zona pellucida composition in carnivores

2018 ◽  
Vol 30 (2) ◽  
pp. 272 ◽  
Author(s):  
C. Moros-Nicolás ◽  
A. Leza ◽  
P. Chevret ◽  
A. Guillén-Martínez ◽  
L. González-Brusi ◽  
...  
Keyword(s):  
Zona Pellucida ◽  
In Silico ◽  
Polar Bear ◽  
Acrosome Reaction ◽  
Stop Codon ◽  
In Silico Analysis ◽  
Weddell Seal ◽  
Fur Seal ◽  
The Antarctic ◽  
Silico Analysis

The zona pellucida (ZP) is an extracellular envelope that surrounds mammalian oocytes. This coat participates in the interaction between gametes, induction of the acrosome reaction, block of polyspermy and protection of the oviductal embryo. Previous studies suggested that carnivore ZP was formed by three glycoproteins (ZP2, ZP3 and ZP4), with ZP1 being a pseudogene. However, a recent study in the cat found that all four proteins were expressed. In the present study, in silico and molecular analyses were performed in several carnivores to clarify the ZP composition in this order of mammals. The in silico analysis demonstrated the presence of the ZP1 gene in five carnivores: cheetah, panda, polar bear, tiger and walrus, whereas in the Antarctic fur seal and the Weddell seal there was evidence of pseudogenisation. Molecular analysis showed the presence of four ZP transcripts in ferret ovaries (ZP1, ZP2, ZP3 and ZP4) and three in fox ovaries (ZP2, ZP3 and ZP4). Analysis of the fox ZP1 gene showed the presence of a stop codon. The results strongly suggest that all four ZP genes are expressed in most carnivores, whereas ZP1 pseudogenisation seems to have independently affected three families (Canidae, Otariidae and Phocidae) of the carnivore tree.

scholarly journals Identification of SNPs in rice GPAT genes and in silico analysis of their functional impact on GPAT proteins

2021 ◽  
Vol 49 (3) ◽  
pp. 12346
Author(s):  
Imran SAFDER ◽  
Gaoneng SHAO ◽  
Zhonghua SHENG ◽  
Peisong HU ◽  
Shaoqing TANG
Keyword(s):  
In Silico ◽  
Association Studies ◽  
Rice Genome ◽  
In Silico Analysis ◽  
Gene Families ◽  
Coding Region ◽  
Rice Varieties ◽  
Functional Impact ◽  
Functional Snps ◽  
Silico Analysis

SNPs are the most common nucleotide variations in the genome. Functional SNPs in the coding region, known as nonsynonymous SNPs (nsSNPs), change amino acid residues and affect protein function. Identifying functional SNPs is an uphill task as it is difficult to correlate between variation and phenotypes in association studies. Computational in silico analysis provides an opportunity to understand the SNPs functional impact to proteins and facilitate experimental approaches in understanding the relationship between the phenotype and genotype. Advancement in sequencing technologies contributed to sequencing thousands of genomes. As a result, many public databases have been designed incorporating this sequenced data to explore nucleotide variations. In this study, we explored functional SNPs in the rice GPAT family (as a model plant gene family), using 3000 Rice Genome Sequencing Project data. We identified 1056 SNPs, among hundred rice varieties in 26 GPAT genes, and filtered 98 nsSNPs. We further investigated the structural and functional impact of these nsSNPs using various computational tools and shortlisted 13 SNPs having high damaging effects on protein structure. We found that rice GPAT genes can be influenced by nsSNPs and they might have a major effect on regulation and function of GPAT genes. This information will be useful to understand the possible relationships between genetic mutation and phenotypic variation, and their functional implication on rice GPAT proteins. The study will also provide a computational pathway to identify SNPs in other rice gene families.

scholarly journals YPK9 and WHI2 Negatively Interact during Oxidative Stress

2021 ◽  
Vol 9 (12) ◽  
pp. 2584
Author(s):  
Florenal Joseph ◽  
Darach Miller ◽  
Oleg V. Evgrafov ◽  
William J. Chirico
Keyword(s):  
Oxidative Stress ◽  
Hydrogen Peroxide ◽  
Genetic Interaction ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Full Length ◽  
Deletion Strain ◽  
Acid Protein ◽  
Insight Into ◽  
Amino Acid Protein

Yeast PARK9 (YPK9) shares homology with human ATP13A2, which encodes a polyamine transporter implicated in juvenile forms of Parkinson’s disease. We used YPK9 to gain insight into how ATP13A2 affects cell growth and sensitivity to oxidative stress. Surprisingly, the YPK9 deletion strain from the Saccharomyces cerevisiae deletion collection (YKO) in wildtype BY4741 (mating type a) grew faster and was more resistant to hydrogen peroxide than a commercial, putative parental BY4741 wildtype strain (BY4741COM). In contrast, deleting YPK9 from BY4741COM rendered it very sensitive to hydrogen peroxide, suggesting its background is different from that of the deletion collection. Whole-genome sequencing revealed that BY4741COM and BY4741COMypk9∆ contain a novel premature stop codon near the 3′ end of WHI2 (WHI2G1324T), whereas the collection’s YPK9 deletion strain contains WHI2, which encodes a 486 amino acid protein, Whi2p. Replacing full-length WHI2 with the sequence coding for the predicted truncation (Whi2pE442*) rendered strains more sensitive to hydrogen peroxide, whereas the converse replacement rendered them more resistant. The sequences of WHI2 in 20 randomly chosen strains from the collection encode the full-length protein, indicating that the putative parental BY4741 WHI2G1324T strain’s genetic background differs from that of the deletion collection. Examination of WHI2 sequences in several commonly used wildtype S. cerevisiae strains and isolates revealed other Whi2p truncations that might yield altered phenotypes. Together, these results demonstrate a novel premature stop codon in WHI2 that renders yeast sensitive to hydrogen peroxide; they also reveal a negative genetic interaction between WHI2 and YPK9 in the presence of hydrogen peroxide in the BY4741 background.

Characterization of a Monoclonal Antibody, D73H, that Maps to a Highly Conserved Region on Fibrinogen Bβ Chain

2000 ◽  
Vol 84 (07) ◽  
pp. 43-48 ◽  
Author(s):  
B. J. Rybarczyk ◽  
M. Pereira ◽  
P. J. Simpson-Haidaris
Keyword(s):  
In Silico ◽  
Coiled Coil ◽  
In Silico Analysis ◽  
Antigenic Determinants ◽  
Human Fibrinogen ◽  
Western Blots ◽  
C Terminus ◽  
Probability Prediction ◽  
Silico Analysis

SummaryThe primary structure of fibrinogen is highly conserved across species, yet often times monoclonal antibodies produced against the fibrinogen of one species will not crossreact with the fibrinogen of another. Herein, we describe the production and characterization of murine MAb, D73H, raised against human fibrinogen. D73H crossreacts with a highly conserved epitope on the Bβ chain of fibrinogen from human, rat, bovine, guinea pig, and mouse. Western blotting revealed that D73H reacted with the Bβ chain of plasmin fragment D, localizing its epitope to Bβ134-461. A 7 kDa band was identified by D73H in Western blots of reduced fibrinogen CNBr-fragments. N-terminal sequencing mapped this fragment to Bβ243-253, further localizing the epitope to Bβ243-305. In silico analysis indicated that Bβ243-305 is predominantly hydrophilic, and surface probability prediction indicated three potential antigenic determinants corresponding to Bβ252-258, Bβ262-269, and Bβ279-286. Further in silico analysis of the crystal structure of fibrinogen fragment D-D indicated that Bβ262-269 (FGRKWDPY) is predominantly α-helical and located on the surface of the molecule adjacent to a bend imposed in the β chain at residue 260, which is near the junction between the rigid coiled-coil domain and the globular C-terminus. A synthetic peptide corresponding to Bβ261-272 competitively inhibited the binding of D73H to the Bβ chain of denatured intact fibrinogen and reduced and denatured Bβ chain in Western blots, experimentally proving the validity of these predictive algorithms. Together these data indicate that, although plasmin resistant, Bβ chain residues Bβ261-272 comprising the D73H epitope are highly conserved across species, surface exposed, and immunogenic.

scholarly journals Variation inListeria monocytogenesDose Responses in Relation to Subtypes Encoding a Full-Length or Truncated Internalin A

2010 ◽  
Vol 77 (4) ◽  
pp. 1171-1180 ◽  
Author(s):  
Yuhuan Chen ◽  
William H. Ross ◽  
Richard C. Whiting ◽  
Anna Van Stelten ◽  
Kendra K. Nightingale ◽  
...  
Keyword(s):  
Stop Codon ◽  
Premature Stop Codon ◽  
Intestinal Barrier ◽  
Full Length ◽  
Quantitative Evidence ◽  
Consumption Data ◽  
Genes Encoding ◽  
A Cell ◽  
Dose Responses ◽  
Internalin A

ABSTRACTInternalin A (InlA; encoded byinlA) facilitates the crossing of the intestinal barrier byListeria monocytogenes. Mutations leading to a premature stop codon (PMSC) ininlAand thus attenuated mammalian virulence have been reported. We recently characterized 502L. monocytogenesfood isolates from a retail survey and 507 human clinical isolates from multiple U.S. states with respect to the presence/absence ofinlAmutations. The objective of this study was to investigate the hypothesis that dose responses for human listeriosis vary betweenL. monocytogenesstrains with and those without a PMSC ininlA. Subtype-specific prevalence and concentration distributions in food, along with epidemiologic and consumption data, were input into established dose-response models to generate anrvalue (probability of a cell causing illness). Under the conservative assumption thatL. monocytogeneslevels at retail represent levels consumed, mean log10rvalues were −8.1 and −10.7 forL. monocytogenessubtypes with genes encoding a full-length and a truncated InlA, respectively.L. monocytogenescarrying a 5′ frameshift mutation in a homopolymeric tract showed a mean log10rvalue of −12.1. Confidence intervals for thervalues and their differences varied depending on subtypes. When the increase in concentration ofL. monocytogenessubtypes between retail and consumption was considered, mean log10rvalues were reduced to −10.4, −13.8, and −12.8 for the subtypes with genes encoding a full-length InlA, for the subtypes carrying a PMSC ininlA, and for allL. monocytogenesisolates regardless of subtype, respectively. Our study provides further quantitative evidence thatL. monocytogenessubtypes vary in abilities and relative likelihoods of causing human disease, which were mechanistically related to defined genetic markers.

scholarly journals Characterization of Two Novel Intronic Variants Affecting Splicing in FBN1-Related Disorders

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 442 ◽  
Author(s):  
Carmela Fusco ◽  
Silvia Morlino ◽  
Lucia Micale ◽  
Alessandro Ferraris ◽  
Paola Grammatico ◽  
...  
Keyword(s):  
Stop Codon ◽  
Premature Stop Codon ◽  
In Silico Analysis ◽  
Aortic Disease ◽  
High Rate ◽  
Functional Studies ◽  
Variants Of Unknown Significance ◽  
Wide Range ◽  
Fibrillin 1 ◽  
Intronic Variants

FBN1 encodes fibrillin 1, a key structural component of the extracellular matrix, and its variants are associated with a wide range of hereditary connective tissues disorders, such as Marfan syndrome (MFS) and mitral valve–aorta–skeleton–skin (MASS) syndrome. Interpretations of the genomic data and possible genotype–phenotype correlations in FBN1 are complicated by the high rate of intronic variants of unknown significance. Here, we report two unrelated individuals with the FBN1 deep intronic variants c.6872-24T>A and c.7571-12T>A, clinically associated with MFS and MASS syndrome, respectively. The individual carrying the c.6872-24T>A variant is positive for aortic disease. Both individuals lacked ectopia lentis. In silico analysis and subsequent mRNA study by RT-PCR demonstrated the effect of the identified variant on the splicing process in both cases. The c.6872-24T>A and c.7571-12T>A variants generate the retention of intronic nucleotides and lead to the introduction of a premature stop codon. This study enlarges the mutation spectrum of FBN1 and points out the importance of intronic sequence analysis and the need for integrative functional studies in FBN1 diagnostics.

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