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Internal Deletions (internal + deletion)
Selected AbstractsA Rox1-independent hypoxic pathway in yeast.MOLECULAR MICROBIOLOGY, Issue 4 2000Antagonistic action of the repressor Ord, activator Yap1 for hypoxic expression of the SRP1/TIR1 gene Hypoxic SRP1/TIR1 gene expression depends on the absence of haem but is independent of Rox1-mediated repression. We have found a new hypoxic pathway involving an antagonistic interaction between the Ixr1/Ord1 repressor and the Yap1 factor, a transcriptional activator involved in oxidative stress response. Here, we show that Ord1 repressed SRP1 gene expression under normoxia and hypoxia, whereas Yap1 activated it. Ord1 and Yap1 have been shown to bind the SRP1 promoter in a region extending from ,299 to ,156 bp upstream of the start codon. A typical AP-1 responsive element lying from ,247 to ,240 bp allows Yap1 binding. Internal deletion of sequences within the SRP1 promoter were introduced. Two regions were characterized at positions ,299/,251 and ,218/,156 that, once removed, resulted in a constitutive expression of SRP1 in a wild-type strain under normoxic conditions. Deletion of both these two sequences allowed the bypass of YAP1 requirement in a ,yap1 strain, whereas these two internal deletions did not yield increased expression in a ,ord1 strain compared with the full-length promoter. Both a single ,ord1 mutant and a doubly disrupted ,yap1 ,ord1 strain yielded normoxic constitutive SRP1 expression and increased hypoxic SRP1 induction, thereby demonstrating that ord1 is epistatic to yap1. Thus, Yap1 is not directly involved in SRP1 induction by hypoxia, but is necessary to counteract the Ord1 effect. [source] Characterization of a human alternatively spliced truncated reduced folate carrier increasing folate accumulation in parental leukemia cellsFEBS JOURNAL, Issue 3 2000Stavit Drori Human CEM-7A cells established by gradual deprivation of leucovorin from the growth medium, display 100-fold overexpression of methotrexate transport activity. We found that this was associated with 10-fold reduced folate carrier gene amplification and 50-fold overexpression of both the principal 3 kb reduced folate carrier transcript and, surprisingly, a novel truncated 2 kb reduced folate carrier mRNA poorly expressed in parental CEM cells. The molecular basis for the generation of this truncated reduced folate carrier transcript and its potential functional role in folate accumulation were studied. Reduced folate carrier genomic and cDNA sequencing revealed that the truncated transcript had an internal deletion of 987 nucleotides which was a result of an alternative splicing utilizing a cryptic acceptor splice site within exon 6. This deletion consisted of the 3,-most 480 nucleotides of the reduced folate carrier ORF and the following 507 nucleotides of the 3,-UTR. These resulted in a truncated reduced folate carrier protein, which lacks the C-terminal 160 amino acids, but instead contains 58 new C-terminal amino acids obtained from reading through the 3,-UTR. Consequently, a truncated reduced folate carrier protein is generated that lacks the 12th transmembrane domain and contains a new and much shorter C-terminus predicted to reside at the extracellular face. Western analysis with plasma-membrane fraction from CEM-7A cells revealed marked overexpression of both a broadly migrating , 65,90 kDa native reduced folate carrier and a , 40,45 kDa truncated reduced folate carrier, the core molecular masses of which were confirmed by in vitro translation. However, unlike the native reduced folate carrier, the truncated reduced folate carrier protein failed to bind the affinity labels NHS-[3H]MTX and NHS-[3H]folic acid. Stable transfection of the truncated reduced folate carrier cDNA into mouse L1210 leukemia cells: increased folate accumulation, decreased their leucovorin and folic acid growth requirements, and increased their sensitivity to methotrexate. This constitutes the first documentation of an expressed alternatively spliced truncated reduced folate carrier that, when coexpressed along with the native carrier, augments folate accumulation and consequently decreases the cellular folate growth requirement. The possible mechanisms by which the truncated reduced folate carrier may increase folate accumulation and/or metabolism in cells coexpressing the truncated and native reduced folate carrier are discussed. [source] The mosquito ribonucleotide reductase R2 gene: ultraviolet light induces expression of a novel R2 variant with an internal amino acid deletionINSECT MOLECULAR BIOLOGY, Issue 3 2004G. Jayachandran Abstract Using RT-PCR, we examined expression of the ribonucleotide reductase R2 subunit (RNR-R2) in Aedes albopictus mosquito cells after treatment with ultraviolet light (UV). In control cells, a predominant band at 1.2 kb corresponded to the full-length cDNA. A smaller 650 bp band was unique to UV-treated cells. Sequence analysis showed that the 650 bp band encoded a protein with an internal deletion of 179 amino acids, relative to Ae. albopictus RNR-R2. The N-terminal twenty amino acids were identical between AalRNR-R2 and Aal,R2; downstream of the deletion, the proteins differed at only four residues. In Aal,R2, the internal deletion spanned five residues critical to RNR-R2 enzymatic activity, including a key tyrosine residue that generates an essential free radical. The full-length 46 kDa and truncated 25 kDa RNR-R2 proteins were shown to be expressed on Western blots, and to differ in their subcellular localization. Similarly, expression of the two proteins was differentially regulated during the cell cycle, and expression of Aal,R2 predominated after UV treatment. Aal,R2 resembled a human RNR-R2 variant called p53R2, which was induced by agents that damage DNA. As was the case with p53R2 and its antisense RNA, levels of Aal,R2 were diminished after treatment of mosquito cells with RNAi corresponding to p53 from Drosophila melanogaster. Examination of the AalRNR-R2 homologue in the Anopheles gambiae genome suggested that Aal,R2 resulted from precise splicing between Exons 1, 4 and 5, eliminating Exons 2 and 3. The likelihood that Aal,R2 is a non-enzymatic, functional participant in DNA metabolism is suggested by enhancement of DNA repair in an in vitro system and by the presence of a similar gene (rnr4) in yeast. [source] Molecular diversity of the genetic loci responsible for lipopolysaccharide core oligosaccharide assembly within the genus SalmonellaMOLECULAR MICROBIOLOGY, Issue 5 2002Natalia A. Kaniuk Summary The waa locus on the chromosome of Salmonella enterica encodes enzymes involved in the assembly of the core oligosaccharide region of the lipopolysaccharide (LPS) molecule. To date, there are two known core structures in Salmonella, represented by serovars Typhimurium (subspecies I) and Arizonae (subspecies IIIA). The waa locus for serovar Typhimurium has been characterized. Here, the corresponding locus from serovar Arizonae is described, and the molecular basis for the distinctive structures is established. Eleven of the 13 open reading frames (ORFs) are shared by the two loci and encode conserved proteins of known function. Two polymorphic regions distinguish the waa loci. One involves the waaK gene, the product of which adds a terminal ,-1,2-linked N -acetylglucosamine residue that characterizes the serovar Typhimurium core oligosaccharide. There is an extensive internal deletion within waaK of serovar Arizonae. The serovar Arizonae locus contains a novel ORF (waaH) between the waaB and waaP genes. Structural analyses and in vitro glycosyltransferase assays identified WaaH as the UDP-glucose:(glucosyl) LPS ,-1,2-glucosyltransferase responsible for the addition of the characteristic terminal glucose residue found in serovar Arizonae. Isolates comprising the Salmonella Reference Collections, SARC (representing the eight subspecies of S. enterica) and SARB (representing subspecies I), were examined to assess the distribution of the waa locus polymorphic regions in natural populations. These comparative studies identified additional waa locus polymorphisms, shedding light on the genetic basis for diversity in the LPS core oligosaccharides of Salmonella isolates and identifying potential sources of further novel LPS structures. [source] Functional characterization of PGRP-LC1 of Anopheles gambiae through deletion and RNA interferenceINSECT SCIENCE, Issue 6 2009Yang Chen Abstract, Peptidoglycan recognition proteins (PGRP) play an important role in innate immunity in insects through the activation of the Imd pathway, which has been shown to be required in the antibacterial response in insects and in the limitation of the number of Plasmodium berghei oocysts developing in mosquito midgut. The LC1 gene of the PRGP family in Anopheles gambiae produces many products through alternative splicing. In this work, we demonstrate that PGRP-LC1a alone is sufficient to activate the Imd pathway in the A. gambiae L3,5 cell line through a combination of terminal or internal deletions, and RNA interference against endogenous PGRP-LC products. In the absence of endogenous PGRP-LC proteins, the integrity of the cytoplasmic domain is necessary for LC1a function, while that of the extracellular domain is not. Moreover, the shorter the extracellular domain, the higher the activity for LC1a. However, the removal of either the cytoplasmic or the extracellular PGRP-binding domain has little impact on the activity of LC1a in the presence of endogenous PGRP-LC proteins. [source] Defective human T-cell leukaemia virus type 1 (HTLV-1) genomes: No evidence in serologically indeterminate german blood donors but new type detected in established cell linesJOURNAL OF MEDICAL VIROLOGY, Issue 1 2002V.A. Morozov Abstract Individuals reactive in antibody screening tests (ELISA) and with one or more reactions to HTLV-1 proteins on Western blotting, but lacking the criteria of a confirmed HTLV infection, are not exceptional in regions with a low prevalence of HTLV-1/-2 infections. PCR analysis of these indeterminate samples, using "diagnostic" pol and tax sets of primers, give negative results. However, expression of HTLV-1 defective proviruses with internal deletions undetectable by PCR with diagnostic primers could have taken place. Seven German HTLV-1 ELISA-reactive blood donors, who showed reactivity also in Western blots against several viral proteins, and twenty haemophiliacs, were examined by nested PCR and/or PCR/Southern hybridisation with primers designed for detection of HTLV-1 defective proviruses. No HTLV-1-specific amplification products were obtained. However, HTLV-1 defective proviruses with large internal deletions were detected in four out of five cell lines established from symptomatic HTLV-1 cases and two in HUT-102 cells. In two amplicons, short inverted rRNA sequences between gag and env fragments of HTLV-1 defective proviruses were revealed. These results do not exclude the presence of defective HTLV-1 proviruses in individuals with indeterminate serology although this is unlikely. J. Med. Virol. 66:102,106, 2002. © 2002 Wiley-Liss, Inc. [source] A Rox1-independent hypoxic pathway in yeast.MOLECULAR MICROBIOLOGY, Issue 4 2000Antagonistic action of the repressor Ord, activator Yap1 for hypoxic expression of the SRP1/TIR1 gene Hypoxic SRP1/TIR1 gene expression depends on the absence of haem but is independent of Rox1-mediated repression. We have found a new hypoxic pathway involving an antagonistic interaction between the Ixr1/Ord1 repressor and the Yap1 factor, a transcriptional activator involved in oxidative stress response. Here, we show that Ord1 repressed SRP1 gene expression under normoxia and hypoxia, whereas Yap1 activated it. Ord1 and Yap1 have been shown to bind the SRP1 promoter in a region extending from ,299 to ,156 bp upstream of the start codon. A typical AP-1 responsive element lying from ,247 to ,240 bp allows Yap1 binding. Internal deletion of sequences within the SRP1 promoter were introduced. Two regions were characterized at positions ,299/,251 and ,218/,156 that, once removed, resulted in a constitutive expression of SRP1 in a wild-type strain under normoxic conditions. Deletion of both these two sequences allowed the bypass of YAP1 requirement in a ,yap1 strain, whereas these two internal deletions did not yield increased expression in a ,ord1 strain compared with the full-length promoter. Both a single ,ord1 mutant and a doubly disrupted ,yap1 ,ord1 strain yielded normoxic constitutive SRP1 expression and increased hypoxic SRP1 induction, thereby demonstrating that ord1 is epistatic to yap1. Thus, Yap1 is not directly involved in SRP1 induction by hypoxia, but is necessary to counteract the Ord1 effect. [source] New multiplex PCR method for the detection of Clostridium difficile toxin A (tcdA) and toxin B (tcdB) and the binary toxin (cdtA/cdtB) genes applied to a Danish strain collectionCLINICAL MICROBIOLOGY AND INFECTION, Issue 11 2008S. Persson Abstract Isolates of Clostridium difficile from 159 hospitalized Danish patients (2005) were analysed by a new 5-plex PCR method targeting the toxin genes tcdA, tcdB, cdtA and cdtB, and 16S rDNA as an internal positive control. Additionally, the toxin-regulating gene tcdC was partially sequenced by a new sequencing-based method that revealed genetic changes that may render the gene product inactive. Finally tcdA was analysed using a previously published method for the detection of internal deletions. The 5-plex PCR revealed four different toxin gene profiles: 36 tcdA+, tcdB+, cdtA+/cdtB+; one tcdA+, tcdB,, cdtA+/cdtB+; 98 tcdA+, tcdB+, cdtA,/cdtB,; and 24 non-toxigenic tcdA,, tcdB,, cdtA,/cdtB,. Deletion studies revealed that 26 strains contained a c. 700-bp deletion in tcdA, and 39 strains contained at least one possible inactivation feature in tcdC. The prevalence of the binary toxin genes was 23%. All strains with the tcdA+, tcdB+, cdtA+/cdtB+ profile were investigated by PCR ribotyping, and this revealed eight different ribotypes, none of which were 027. The 5-plex PCR method offers a one-step, rapid and specific screening method for C. difficile toxin genes. This toxin gene profiling, together with deletion studies in tcdA and tcdC, may allow an evaluation of the pathogenic potential of C. difficile. [source] | ||||||||||