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PubMed1993

Nucleotide sequence and characterization of the traABCD region of IncI1 plasmid R64.

A 3.6-kb BglII-SmaI segment of the transfer region of IncI1 plasmid R64drd-11 was sequenced and characterized. Analysis of the DNA sequence indicated the presence of four genes, traA, traB, traC, and traD, in this region. The expression of the traB, traC, and traD genes was examined by maxicell experiments and that of the traA gene was examined by constructing the traA-lacZ fusion gene. The introduction of frameshift mutations into the four genes indicated that the traB and traC genes are essential for conjugal transfer in liquid medium and on a solid surface. Both were also required for the formation of the thin pilus, which is the receptor for phages I alpha and PR64FS. Upstream of the traA gene, a promoter sequence for sigma 70 of E. coli RNA polymerase was identified by S1 nuclease mapping and primer extension experiments.

Amino Acid Sequence↗
PubMedDate not supplied

HLA-G1 protein expression is not essential for fetal survival.

HLA-G is a nonclassical, class I HLA gene that is primarily expressed by fetal cells at the maternal-fetal interface and is thought to play a key role in the induction of tolerance in pregnancy. This paper reports the identification of a single base pair deletion at position 1597 (1597delC) in exon 3 (encoding the alpha2-domain) of HLA-G on 20 of 272 (7.4 per cent) African American chromosomes, three of 102 (2.9 per cent) Hispanic chromosomes, and none of 134 Caucasian chromosomes. This relatively common frameshift mutation results in amino acid substitutions in all of the residues in the second half of exon 3 including the conserved cysteine at codon 164. An adult individual was identified who was homozygous for this 'null' allele, and a first trimester placenta that was homozygous for 1597delC had no detectable HLA-G1 protein. These data indicate that expression of HLA-G1 protein is not essential for fetal survival.

Adult↗
PubMed1998

Hypermethylation can selectively silence individual p16ink4A alleles in neoplasia.

Inactivation of p16ink4A and other tumor suppressor genes has been associated with promoter region hypermethylation in neoplasia. However, direct proof for aberrant DNA methylation as an independent event for loss of gene function has been difficult to obtain. We addressed this question in the colon carcinoma cell line HCT116, which contains one allele of p16ink4A with a coding region frameshift mutation and one wild-type allele. Neither allele contains a mutation in the proximal promoter region. The promoter of the wild-type allele, but not the mutant allele, is hypermethylated, and only the mutant allele is expressed. Transcription from the methylated/wild-type allele was restored after cell treatment with the demethylating agent 5-aza-2'-deoxycytidine. Thus, in neoplastic cells, stable allele-specific loss of transcription may arise from aberrant methylation of a nonmutated promoter region, identifying hypermethylation as a direct mechanism for tumor suppressor gene inactivation.

Alleles↗
PubMed1999

Ambient pH signal transduction in Aspergillus: completion of gene characterization.

Completing the molecular analysis of the six pal genes of the ambient pH signal transduction pathway in Aspergillus nidulans, we report the characterization of palC and palH. The derived translation product of palH contains 760 amino acids with prediction of seven transmembrane domains in its N-terminal moiety. Remarkably, a palH frameshift mutant lacking just over half the PalH protein, including almost all of the long hydrophilic region C-terminal to the transmembrane domains, retains some PalH function. The palC-derived translation product contains 507 amino acids, and the null phenotype of a frameshift mutation indicates that at least one of the C-terminal 142 residues is essential for function. Uniquely among the A. nidulans pH-signalling pal genes, palC appears to have no Saccharomyces cerevisiae homologue, although it does have a Neurospora crassa expressed sequence tag homologue. In agreement with findings for the palA, palB and palI genes of this signalling pathway, levels of the palC and palH mRNAs do not appear to be pH regulated.

Amino Acid Sequence↗
PubMed2003

Mycobacterium bovis BCG vaccines exhibit defects in alanine and serine catabolism.

Mycobacterium bovis BCG is the only accepted vaccine for the prevention of tuberculosis (TB) in humans. BCG is a live vaccine, and induction of immunity to TB requires productive infection of the host by BCG. However, BCG is not a satisfactory vaccine, because it fails to protect against pulmonary TB in adults. In this study, we found that BCG strains cannot utilize many naturally occurring amino acids as the sole nitrogen source for growth. This defect is caused, at least partially, by the lack of functional metabolic enzymes. All BCG strains are unable to catabolize L-alanine or D-alanine due to a frameshift mutation in the L-alanine dehydrogenase gene (ald). Some BCG strains, such as BCG-Pasteur and BCG-Frappier, cannot catabolize L-serine, apparently due to inadequate expression of L-serine deaminase (sdaA). We also found that undegraded alanine and serine inhibit the growth of BCG through blockage of glutamine synthetase. These results suggest that BCG strains are limited in nitrogen metabolic capacity and predict defects that may restrict multiplication and persistence of the live vaccine within the host.

Alanine↗
PubMed2002

Integrated functional genomics approach for the design of patient-individual antitumor vaccines.

Our aim is to identify as many candidates as possible for tumor-associated T-cell epitopes in individual patients. First, we performed expression profiling of tumor and normal tissue to identify genes exclusively expressed or overexpressed in the tumor sample. Then, using mass spectrometry, we characterized up to 77 different MHC ligands from the same tumor sample. Several of the MHC ligands were derived from overexpressed gene products, one was derived from a proto-oncogene, and another was derived from a frameshift mutation. At least one was identified as an actual T-cell epitope. Thus, we could show that by combining these two analytic tools, it is possible to propose several candidates for peptide-based immunotherapy. We envision the use of this novel integrated functional genomics approach for the design of antitumor vaccines tailored to suit the needs of each patient.

Antigens, Neoplasm↗
PubMed2002

Genetics of mutagenesis in E. coli: various combinations of translesion polymerases (Pol II, IV and V) deal with lesion/sequence context diversity.

The biochemistry and genetics of translesion synthesis (TLS) and, as a consequence, of mutagenesis has recently received much attention in view of the discovery of novel DNA polymerases, most of which belong to the Y family. These distributive and low fidelity enzymes assist the progression of the high fidelity replication complex in the bypass of DNA lesions that normally hinder its progression. The present paper extends our previous observation that in Escherichia coli all three SOS-inducible DNA polymerases (Pol II, IV and V) are involved in TLS and mutagenesis. The genetic control of frameshift mutation pathways induced by N-2-acetylaminofluorene (AAF) adducts or by oxidative lesions induced by methylene blue and visible light is investigated. The data show various examples of mutation pathways with an absolute requirement for a specific combination of DNA polymerases and, in contrast, other examples where two DNA polymerases exhibit functional redundancy within the same pathway. We suggest that cells respond to the challenge of replicating DNA templates potentially containing a large diversity of DNA lesions by using a pool of accessory DNA polymerases with relaxed specificities that assist the high fidelity replicase.

2-Acetylaminofluorene↗
PubMed1991

Molecular characterization of the murinoglobulins.

Proteinase inhibitors of the alpha 2-macroglobulin (alpha 2M) type, although well characterized in vitro, still evade a precise description of their actual role in vivo. The main reason for this is the absence of any clinical evidence for the malfunctioning of alpha 2M in humans. Moreover, despite their ubiquitous presence in animals of very different taxa, animal models are notoriously absent in this field. With the advent of transgenic animals an important tool became available in this respect. As a first step in this direction we are analyzing at the molecular level all the members of this proteinase inhibitor family in the mouse. To retrieve related sequences we screened a mouse liver cDNA library with human alpha 2M cDNA. The sequences from two isolated clones partially coded for a protein with a high degree of sequence identity with human alpha 2M, rat alpha 2M, and rat alpha 1I3. Protein sequence data from the large and small subunits of mouse alpha 2M and of the protein isolated from mouse plasma allowed us to designate the clones as coding for murinoglobulin (MUG), an alpha 2M-related single-chain proteinase inhibitor. Rescreening resulted in the isolation of 24 clones, of which 21 were related or identical to the original MUG clones. Restriction analysis led to three groups of clones of which representative members were sequenced. Two highly homologous cDNA sequences were derived, coding for proteins that displayed the typical features of alpha 2M-type proteinase inhibitors: the overall size, the positions of a putative bait region and of the internal thiol ester, and the positional conservation of cysteine residues and putative asparagine-glycosylation sites. A third related member for which only one incomplete cDNA clone was obtained and sequenced, proved to be aberrant: the bait region contained what appeared to be an intron which escaped proper splicing. A second apparent intron was present at the 5' end of the cDNA while a frameshift mutation near the 3' end (insertion of a G) caused premature termination of the reading frame when compared to the other MUG sequences. These features were confirmed from an isolated genomic clone and extended at the genomic level: the corresponding gene, a transcriptionally weakly active pseudogene, contained the small intron but as part of a larger intron. The presence of suitable intron/exon splice sites show that a relatively small part of the intron is being introduced as an exon in the mRNA.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1995

Fate of the human immunodeficiency virus type 1 provirus in infected cells: a role for vpr.

We investigated the fate of human immunodeficiency virus type 1 (HIV-1) viral DNA in infected peripheral blood lymphocytes and immortalized T-cell lines by using a replication-defective HIV-1. We observed that integrated HIV-1 DNA and viral gene expression decrease over time. A frameshift mutation in vpr resulted in maintenance of the HIV-1 provirus and stable persistence of viral expression. Transfection of vpr together with the neomycin resistance gene in the absence of other viral genes decreased the formation of geneticin-resistant colonies, indicating either a cytotoxic or a cytostatic effect upon cells. Therefore, maintenance of HIV-1 infection within an infected proliferating population is due to two competing processes, the rate of viral spread and the degree of cell growth inhibition and/or death induced by Vpr.

Animals↗
PubMed2000

Molecular characterization of the vanD gene cluster and a novel insertion element in a vancomycin-resistant enterococcus isolated in Canada.

A single vanD-containing Enterococcus faecium strain (N97-330) was isolated in Canada. The vanD-containing region was cloned and sequenced. Although the proteins have more than 96% identity to a previously described vanD region in BM4339, the vanS(D) gene contains a frameshift mutation that leads to a predicted truncated protein. Furthermore, sequence analysis of the ddl gene revealed the presence of an IS982-like element (ISEfm1) which interrupted the D-Ala-D-Ala ligase. This suggested the constitutive expression of the vanD operon, which was confirmed. Pulsed-field gel electrophoresis fingerprinting demonstrated that BM4339 was not related to N97-330 (>15 band differences). Both strains contained multiple copies of the IS982-like element.

Amino Acid Sequence↗
PubMed2003

The adaptive imbalance in base excision-repair enzymes generates microsatellite instability in chronic inflammation.

Chronic infection and associated inflammation are key contributors to human carcinogenesis. Ulcerative colitis (UC) is an oxyradical overload disease and is characterized by free radical stress and colon cancer proneness. Here we examined tissues from noncancerous colons of ulcerative colitis patients to determine (a) the activity of two base excision-repair enzymes, AAG, the major 3-methyladenine DNA glycosylase, and APE1, the major apurinic site endonuclease; and (b) the prevalence of microsatellite instability (MSI). AAG and APE1 were significantly increased in UC colon epithelium undergoing elevated inflammation and MSI was positively correlated with their imbalanced enzymatic activities. These latter results were supported by mechanistic studies using yeast and human cell models in which overexpression of AAG and/or APE1 was associated with frameshift mutations and MSI. Our results are consistent with the hypothesis that the adaptive and imbalanced increase in AAG and APE1 is a novel mechanism contributing to MSI in patients with UC and may extend to chronic inflammatory or other diseases with MSI of unknown etiology.

Antigens, CD↗
PubMed2002

Distinct clinical features and outcomes of gastric cancers with microsatellite instability.

Microsatellite instability (MSI) is a hallmark of the DNA mismatch repair deficiency that is one of the pathways of gastric carcinogenesis. Clinicopathologic characteristics of MSI+ gastric cancers remain unclear. To determine the correlation between MSI status and clinical features, we analyzed 327 consecutive gastric cancers for the occurrence of MSI in the BAT-26 marker. Because it has been proven that MSI at BAT-26 reflects the MSI+ phenotype, cancers with alteration at BAT-26 were categorized as having the MSI+ phenotype. The expressions of hMLH1, hMSH2, p53, MUC1, MUC2, and CEA were evaluated immunohistochemically using the tissue array method. The MSI+ phenotype was found in 9.5% (31/327) of gastric cancers examined. MSI+ gastric cancers were significantly associated with older age, antral location, Borrmann's gross Type II, intestinal subtype, lower prevalence of lymph node metastasis, and lower pTNM stage (P <.05). By multivariate logistic regression, MSI+ gastric cancers had a lower prevalence of lymph node metastasis independent of tumor invasion (P <.001). MSI+ gastric cancers displayed frequent frameshift mutations of transforming growth factor-beta type II receptor (90.3%), BAX (61.3%), hMSH3 (38.7%), and E2F4 (61.3%) genes and diminished hMLH1 (24/31) or hMSH2 (4/31) expressions. The MSI+ phenotype correlated with patient survival in advanced gastric carcinoma (P =.046). In conclusion, MSI+ phenotype in gastric cancers was found to have distinct clinicopathologic characteristics and to be predictive of a favorable outcome in advanced carcinoma.

Adaptor Proteins, Signal Transducing↗
PubMed1996

Molecular characterization of a second mouse pancreatic polypeptide receptor and its inactivated human homologue.

The family of mammalian neuropeptide Y (NPY)/peptide YY (PYY)/pancreatic polypeptide (PP) receptors comprises several G protein-coupled receptors, i.e. Y1, Y2, and Y4/PP1. We now report cloning of a novel member of this family named PP2. The coding region of the mouse PP2 gene reveals no introns and predicts a seven transmembrane domain (TM) receptor of 371 amino acids. Percent identities of the mouse PP2 to mouse Y1, mouse Y4/PP1 and human Y2 receptors are 53, 42, and 31, respectively. The mouse PP2 receptor expressed in COS cells binds rat 125I-PP with high affinity, i.e. IC50 = 65 pM. Pharmacological characterization of 125I-PP binding shows a rank order of potency of PP >> PYY >/= NPY, which is similar to that of the mouse Y4/PP1 receptor. Mouse PP2 transcripts were not detectable by Northern analysis in adult tissues and in 11-, 15-, and 17-day-old embryos. However, a 9.8-kb PP2 transcript was detectable in 7-day-old mouse embryo, i.e. prior to the organogenesis of pancreas and the onset of PP production. We have also cloned the human homologue of PP2, which is a single copy gene and maps to human chromosome 5q31. Surprisingly, the human PP2 cDNAs and gene sequences display a single base deletion in the coding region. This frameshifting mutation predicts a truncated receptor of 290 amino acids without TM7. Transfection of COS-7 cells with several different human PP2 expression constructs failed to confirm any specific binding of 125I-PP, 125I-PYY, or 125I-NPY to cell membranes. These data suggest that in mouse there are at least two PP receptors, Y4/PP1 and PP2, whereas in humans, PP2 is either functionally inactive or it has acquired a PP-independent function.

Amino Acid Sequence↗
PubMed1995

Genetic instability within monotonous runs of CpG sequences in Escherichia coli.

Genetic information can be altered by base substitutions, frameshift mutations, and addition or deletion of nucleotides. Deletions represent an important class of genetic aberration occurring at DNA sequences where it is often possible to predict the existence of intermediates of mutation. Instability within tracts of repetitive sequence have recently been associated with several genetic disorders, including the so-called triplet repeat diseases and certain forms of colorectal cancers. In Escherichia coli, (GpC)n repetitive sequences have been shown to be deletion prone, but the precise mechanism of this mutagenic pathway is still unknown. We show here that interrupting the monotony of the (GpC)n run with an ApT or a GpT dinucleotide decreases the rate of deletions within these sequences. On the other hand, introducing purine-pyrimidine alternating sequences beside the GpC insert results in an increased rate of deletion. Two pathways can be envisioned: (1) (GpC)n tracts can be seen as potential Z-forming DNA sequences, and this unusual DNA structure can be processed by an unknown cellular mechanism to give rise to the observed deletions and (2) (GpC)n monotonous runs can be considered as a succession of direct or palindromic repeats, allowing formation of DNA structures that are known to participate to frameshift mutagenesis. The results presented in this article are discussed in the light of these two alternative pathways.

Base Sequence↗
PubMed2004

Determination of sediment mutagenicity and cytotoxicity in an area subjected to petrochemical contamination.

This study is an evaluation of the mutagenic and cytotoxic activity of sediments in Bom Jardim stream, one of the tributaries of the Cai River basin, Rio Grande do Sul, Brazil. This stream receives an indirect contribution of treated effluent from a petrochemical plant. The Salmonella/microsome assay, a microsuspension method, was used to evaluate moderately polar extracts of sediment samples at three points along the stream. The grain size analysis showed a lower mean content of fine particles in the principle face (front) of the complex, and this was also the sampling point with the lowest percentage of extracted organics. Low mutagenic activity was observed at the different sites studied, ranging from 3.3 to 8.3%; cytotoxic activity was more important in this area, ranging from 20 to 40%, adding up the results of assays in the presence and absence of external metabolism. In assays without S9mix there were more frequent mutagenic and cytotoxic responses, with frameshift mutations being the most frequent. The results also showed that there was a gradual, seasonal distribution of the responses as the stream mouth is reached, the most compromised points being in front of and downstream of the complex. Mutagenic and cytotoxic activity in sediment samples has proved important to determine environmental quality, despite the complexity of the chemical composition of the environmental matrix. Furthermore, use of the Salmonella assay to monitor mutagenesis and cytotoxicity helped identify the presence of pollutants. This assay is an important tool, aimed mainly at actions to preserve the genetic heritage of the fauna and flora affected by human activity and to improve environmental quality.

Brazil↗
PubMed2000

Nucleotide excision repair endonuclease genes in Drosophila melanogaster.

Nucleotide excision repair (NER) is the primary pathway for the removal of ultraviolet light-induced damage and bulky adducts from DNA in eukaryotes. During NER, the helix is unwound around the damaged site, and incisions are made on the 5' and 3' sides, to release an oligonucleotide carrying the lesion. Repair synthesis can then proceed, using the intact strand as a template. The incisions flanking the lesion are catalyzed by different structure-specific endonucleases. The 5' incision is made by a heterodimer of XPF and ERCC1 (Rad1p-Rad10p in Saccharomyces cerevisiae), and the 3' incision is made by XPG (Rad2p in S. cerevisiae). We previously showed that the Drosophila XPF homologue is encoded by the meiotic recombination gene mei-9. We report here the identification of the genes encoding the XPG and ERCC1 homologues (XPG(Dm) and ERCC1(Dm)). XPG(Dm) is encoded by the mus201 gene; we found frameshift mutations predicted to produce truncated XPG(Dm) proteins in each of two mus201 alleles. These mutations cause defects in nucleotide excision repair and hypersensitivity to alkylating agents and ultraviolet light, but do not cause hypersensitivity to ionizing radiation and do not impair viability or fertility. ERCC1(Dm) interacts strongly in a yeast two-hybrid assay with MEI-9, indicative of the presumed requirement for these polypeptides to dimerize to form the functional endonuclease. The Drosophila Ercc1 gene maps to polytene region 51D1-2. The nucleotide excision repair gene mus210 maps nearby (51E-F) but is distinct from Ercc1.

Alleles↗
PubMed1996

The viral ubiquitin gene of Autographa californica nuclear polyhedrosis virus is not essential for viral replication.

The baculovirus Autographa californica nuclear polyhedrosis virus (AcNPV) encodes a protein with significant homology to ubiquitin. To study the role of viral ubiquitin in infection, a recombinant virus was constructed with a frameshift mutation within the coding sequence of the viral ubiquitin gene, v-ubi. This recombinant, named Vubi-FS, was viable, indicating that viral ubiquitin is not essential for replication in tissue culture. However, the yields of infectious budded virus were decreased 5- to 10-fold in single step growth curves, and the production of total budded virions was reduced to a similar extent. The mutant virus particles contained the phospholipid-modified form of ubiquitin (Pt-Ub), and amino acid sequence analysis revealed that only host ubiquitin was packaged into virions. Together, these results suggest that viral ubiquitin is a nonessential protein that may confer a slight growth advantage under certain conditions.

Animals↗
PubMed1996

Sequence and analysis of the replication region of the Staphylococcus xylosus plasmid pSX267.

The region of the 29.5-kb plasmid pSX267 from Staphylococcus xylosus DSM 20267 that is required for autonomous replication in staphylococci was isolated on a 1.8-kb DNA fragment. The sequence analysis of the fragment yielded two open reading frames, repA and orf2, encoding proteins of 37.2 and 13.2 kDa, respectively. The deduced amino acid sequence of repA showed similarity to the replication initiator protein of plasmid pAD1 from Enterococcus faecalis, to two proteins of unknown function encoded by the E. faecalis plasmid pCF10 and the lactobacillus helveticus plasmid pLJ1, and surprisingly to the mouse interferon-response element binding factor 1. The repA gene of pSX267 is indispensable for replication suggesting that it encodes the replication initiator protein of pSX267. Introduction of a frameshift mutation into repA or deletion of 26 codons at its 3'-end resulted in nonreplicative plasmids. Removal of sequences required for repA expression also abolished replication. Complementation experiments with repA in trans identified the ori of pSX267 within the repA coding region. The second orf, which is located downstream of repA, could be deleted without affecting plasmid replication. It seems to be a nonfunctional remainder of a rolling circle plasmid of the pC194/pUB110 family, since its deduced amino acid sequence resembles the pC194/pUB110-type replication proteins. The minimal replicon of pSX267 defined so far comprises 1255 bp. Besides repA, no other plasmid-encoded gene is required to mediate replication in staphylococci.

Amino Acid Sequence↗