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.

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.

The retinoid-X receptor gene from the freshwater prawn Macrobrachium nipponense: cloning, expression pattern and different responses of two splice variants during the molting cycle

Crustaceana ◽  
2013 ◽  
Vol 86 (13-14) ◽  
pp. 1586-1604 ◽  
Author(s):  
Huaishun Shen ◽  
Xin Zhou ◽  
Aixu Bai ◽  
Xiufang Ren
Keyword(s):  
Amino Acid ◽  
Developmental Stages ◽  
Splice Variants ◽  
Retinoid X Receptor ◽  
Full Length ◽  
Freshwater Prawn ◽  
Molting Cycle ◽  
Macrobrachium Nipponense ◽  
Acid Protein ◽  
Amino Acid Protein

The retinoid-X receptor (RXR) is among the most conserved members of the nuclear receptor superfamily and is widely studied in vertebrate and invertebrate families. RXR plays an important role in regulation of molting and/or metamorphosis, development and reproduction. We cloned the full-length cDNA sequence of the RXR from the freshwater prawn Macrobrachium nipponense (De Haan, 1849) (MnRXR) and investigated the expression profile of MnRXR in different developmental stages of embryos, in different tissues and in the molting cycle. Two MnRXR splice variants were identified: One, MnRXR-L, the full length of which was 2472 bp, encoded a 449-amino-acid protein; the second, MnRXR-S, the full length of which was 1832 bp, encoded a 420-amino-acid protein, in which the first 29 amino-acid residues of MnRXR-L were absent. MnRXR was observed in all developmental stages of embryos and had the highest expression level in the embryonised-zoea stage, it was highly expressed in hepatopancreas, gill and intestine among the ten tissues examined. The expression of MnRXR was rapidly up-regulated in the premolt stage and rapidly down-regulated after molting. Moreover, of the two MnRXR splice variants, only MnRXR-S was induced during the molting cycle, suggesting that the two splice variants play different roles in the molting cycle.

scholarly journals Detection of ALDH3B2 in Human Placenta

2019 ◽  
Vol 20 (24) ◽  
pp. 6292
Author(s):  
Sylwia Michorowska ◽  
Joanna Giebułtowicz ◽  
Renata Wolinowska ◽  
Anna Konopka ◽  
Anna Wilkaniec ◽  
...  
Keyword(s):  
Western Blot ◽  
Human Placenta ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Premature Termination Codon ◽  
Full Length ◽  
Start Codon ◽  
Phosphorylation Sites ◽  
Putative Open Reading Frame ◽  
Healthy Human

Aldehyde dehydrogenase 3B2 (ALDH3B2) gene contains a premature termination codon, which can be skipped or suppressed resulting in full-length protein expression. Alternatively, the longest putative open reading frame starting with the second in-frame start codon would encode short isoform. No unequivocal evidence of ALDH3B2 expression in healthy human tissues is available. The aim of this study was to confirm its expression in human placenta characterized by the highest ALDH3B2 mRNA abundance. ALDH3B2 DNA and mRNA were sequenced. The expression was investigated using western blot. The identity of the protein was confirmed using mass spectrometry (MS). The predicted tertiary and quaternary structures, subcellular localization, and phosphorylation sites were assessed using bioinformatic analyses. All DNA and mRNA isolates contained the premature stop codon. In western blot analyses, bands corresponding to the mass of full-length protein were detected. MS analysis led to the identification of two unique peptides, one of which is encoded by the nucleotide sequence located upstream the second start codon. Bioinformatic analyses suggest cytoplasmic localization and several phosphorylation sites. Despite premature stop codon in DNA and mRNA sequences, full-length ALDH3B2 was found. It can be formed as a result of premature stop codon readthrough, complex phenomenon enabling stop codon circumvention.

scholarly journals ε-Tubulin Is an Essential Component of the Centriole

2002 ◽  
Vol 13 (11) ◽  
pp. 3859-3869 ◽  
Author(s):  
Susan K. Dutcher ◽  
Naomi S. Morrissette ◽  
Andrea M. Preble ◽  
Craig Rackley ◽  
John Stanga
Keyword(s):  
Basal Body ◽  
Positional Cloning ◽  
Stop Codon ◽  
Polyclonal Antibodies ◽  
Premature Stop Codon ◽  
Full Length ◽  
Basal Bodies ◽  
Cleavage Furrow ◽  
Essential Component ◽  
Flagellar Assembly

Centrioles and basal bodies are cylinders composed of nine triplet microtubule blades that play essential roles in the centrosome and in flagellar assembly. Chlamydomonas cells with thebld2-1 mutation fail to assemble doublet and triplet microtubules and have defects in cleavage furrow placement and meiosis. Using positional cloning, we have walked 720 kb and identified a 13.2-kb fragment that contains ε-tubulin and rescues the Bld2 defects. The bld2-1 allele has a premature stop codon and intragenic revertants replace the stop codon with glutamine, glutamate, or lysine. Polyclonal antibodies to ε-tubulin show peripheral labeling of full-length basal bodies and centrioles. Thus, ε-tubulin is encoded by the BLD2 allele and ε-tubulin plays a role in basal body/centriole morphogenesis.

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 G418-mediated ribosomal read-through of a nonsense mutation causing autosomal recessive proximal renal tubular acidosis

2008 ◽  
Vol 295 (3) ◽  
pp. F633-F641 ◽  
Author(s):  
Rustam Azimov ◽  
Natalia Abuladze ◽  
Pakan Sassani ◽  
Debra Newman ◽  
Liyo Kao ◽  
...  
Keyword(s):  
Renal Tubular Acidosis ◽  
Autosomal Recessive ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Immunoblot Analysis ◽  
Full Length ◽  
Aminoglycoside Resistance ◽  
Proximal Renal Tubular Acidosis ◽  
Renal Tubular

Autosomal recessive proximal renal tubular acidosis is caused by mutations in the SLC4A4 gene encoding the electrogenic sodium bicarbonate cotransporter NBCe1-A. The mutations that have been characterized thus far result in premature truncation, mistargeting, or decreased function of the cotransporter. Despite bicarbonate treatment to correct the metabolic acidosis, extrarenal manifestations persist, including glaucoma, cataracts, corneal opacification, and mental retardation. Currently, there are no known therapeutic approaches that can specifically target mutant NBCe1-A proteins. In the present study, we tested the hypothesis that the NBCe1-A-Q29X mutation can be rescued in vitro by treatment with aminoglycoside antibiotics, which are known for their ability to suppress premature stop codons. As a model system, we cloned the NBCe1-A-Q29X mutant into a vector lacking an aminoglycoside resistance gene and transfected the mutant cotransporter in HEK293-H cells. Cells transfected with the NBCe1-A-Q29X mutant failed to express the cotransporter because of the premature stop codon. Treatment of the cells with G418 significantly increased the expression of the full-length cotransporter, as assessed by immunoblot analysis. Furthermore, immunocytochemical studies demonstrated that G418 treatment induced cotransporter expression on the plasma membrane whereas in the absence of G418, NBCe1-A-Q29X was not expressed. In HEK293-H cells transfected with the NBCe1-A-Q29X mutant not treated with G418, NBCe1-A-mediated flux was not detectable. In contrast, in cells transfected with the NBCe1-A-Q29X mutant, G418 treatment induced Na+- and HCO3−-dependent transport that did not differ from wild-type NBCe1-A function. G418 treatment in mock-transfected cells was without effect. In conclusion, G418 induces ribosomal read-through of the NBCe1-A-Q29X mutation in HEK293-H cells. These findings represent the first evidence that in the presence of the NBCe1-A-Q29X mutation that causes proximal renal tubular acidosis, full-length functional NBCe1-A protein can be produced. Our results provide the first demonstration of a mutation in NBCe1-A that has been treated in a targeted and specific manner.

Ectopic Transcript Analysis Indicates that Allelic Exclusion is an Important Cause of Type I Protein C Deficiency in Patients with Nonsense and Frameshift Mutations in the PROC Gene

1996 ◽  
Vol 75 (06) ◽  
pp. 870-876 ◽  
Author(s):  
José Manuel Soria ◽  
Lutz-Peter Berg ◽  
Jordi Fontcuberta ◽  
Vijay V Kakkar ◽  
Xavier Estivill ◽  
...  
Keyword(s):  
Splice Site ◽  
Protein C ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Allelic Exclusion ◽  
Polymorphism Analysis ◽  
Type I ◽  
Protein C Deficiency ◽  
Nonsense Mutations ◽  
Stop Codons

SummaryNonsense mutations, deletions and splice site mutations are a common cause of type I protein C deficiency. Either directly or indirectly by altering the reading frame, these' lesions generate or may generate premature stop codons and could therefore be expected to result in premature termination of translation. In this study, the possibility that such mutations could instead exert their pathological effects at an earlier stage in the expression pathway, through “allelic exclusion” at the RNA level, was investigated. Protein C (PROC) mRNA was analysed in seven Spanish type I protein C deficient patients heterozygous for two nonsense mutations, a 7bp deletion, a 2bp insertion and three splice site mutations. Ectopic RNA transcripts from patient and control lymphocytes were analysed by RT-PCR and direct sequencing of amplified PROC cDNA fragments. The nonsense mutations and the deletion were absent from the cDNAs indicating that only mRNA derived from the normal allele had been expressed. Similarly for the splice site mutations, only normal PROC cDNAs were obtained. In one case, exclusion of the mutated allele could be confirmed by polymorphism analysis. In contrast to these six mutations, the 2 bp insertion was not associated with loss of mRNA from the mutated allele. In this case, cDNA analysis revealed the absence of 19 bases from the PROC mRNA consistent with the generation and utilization of a cryptic splice site 3’ to the site of mutation, which would result in a frameshift and a premature stop codon. It is concluded that allelic exclusion is a common causative mechanism in those cases of type I protein C deficiency which result from mutations that introduce premature stop codons

Effect of Turmeric and Ginger on Lipid Profile in Male Rats Exposed to Oxidative Stress

2019 ◽  
Vol 10 (01) ◽  
Author(s):  
Eman A. Al-Rekabi ◽  
Dheyaa K. Alomer ◽  
Rana Talib Al-Muswie ◽  
Khalid G. Al-Fartosi
Keyword(s):  
Oxidative Stress ◽  
Hydrogen Peroxide ◽  
Drinking Water ◽  
Lipid Profile ◽  
Low Density Lipoprotein ◽  
Density Lipoprotein ◽  
Male Rats ◽  
Control Group ◽  
Very Low Density Lipoprotein ◽  
Low Density

The present study aimed to investigate the effect of turmeric and ginger on lipid profile of male rats exposed to oxidative stress induced by hydrogen peroxide H2O2 at a concentration of 1% given with consumed drinking water to male rats. Methods: 200 mg/kg from turmeric and ginger were used, and the animals were treatment for 30 days. Results: the results showed a significant increase in cholesterol, triglycerides, low density lipoprotein (LDL), very low density lipoprotein (VLDL), whereas it explained a significant decrease in high density lipoprotein (HDL) of male rats exposed to oxidative stress when compared with control group. the results showed a significant decrease in cholesterol, triglycerides, (LDL), (VLDL), whereas it explained a significant increase in (HDL) of rats treated with turmeric and ginger at dose 200 mg/kg when compared with male rats exposed to oxidative stress.

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