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Nedd4.1-mediated ubiquitination and subsequent recruitment of Tsg101 ensure HTLV-1 Gag trafficking towards the multivesicular body pathway prior to virus budding.

One of the most exciting recent developments in the field of retroviruses is the finding that their Gag proteins hijack cellular proteins from the mutivesicular body (MVB) pathway during the budding process. The Gag proteins of oncoretroviruses possess a PPxY motif that recruits a ubiquitin ligase from the Nedd4 family, whereas those of the human immunodeficiency virus interact through a PTAP motif with Tsg101, a protein of the ESCRT-1 complex. It is currently assumed that Nedd4 and Tsg101 represent equivalent entry gates towards the same cellular process leading to budding, and that both partners are recruited to the plasma membrane where viral budding occurs. However, we report here that the budding of the human oncoretrovirus HTLV-1, the Gag proteins of which possess tandem PPPY/PTAP motifs, requires both Nedd4 and Tsg101. We show that Nedd4.1, but not Nedd4.2, is recruited by the PPPY motif of Gag and subsequently catalyzes Gag ubiquitination. We also demonstrate that Gag interacts first with Nedd4.1 at the plasma membrane and then with Tsg101 in late endosomes/MVBs. Consistently, we found that HTLV-1 particles mutated in the PPPY motif remain underneath the plasma membrane, blocked at an early step of the budding process, whereas PTAP-mutated viruses accumulate in intracellular vesicles, blocked at a later step. Our findings indicate that Nedd4.1 and Tsg101 act successively in the assembly process of HTLV-1 to ensure proper Gag trafficking through the endocytic pathway up to late endosomes where the late steps of retroviral release occur.

Amino Acid Motifs↗

IgM-producing chronic lymphocytic leukemia cells undergo immunoglobulin isotype-switching without acquiring somatic mutations.

The malignant B cells in chronic lymphocytic leukemia (CLL) typically express low-density membrane IgM or IgM/IgD. In vitro experiments have shown that the CLL cells can be induced to differentiate into cells that secrete immunoglobulin (Ig) and can occasionally undergo heavy (H) chain class switching. We now show that the CLL cells also undergo isotype-switching in vivo, since gamma and/or alpha H chain transcripts with identical FW3/CDR3/FW4 regions as the mu CLL transcripts were detected in all of the 13 investigated patients with IgM+ CLL. In most cases switching had occurred to alpha1 and gamma3, but CLL transcripts corresponding to the other gamma chain isotypes were also detected. In one case both the productively and nonproductively rearranged allele were found to undergo H chain class switching. CLL gamma transcripts were also present in surface IgG+ sorted B cells, demonstrating that a small subset of the CLL cells express membrane IgG. In addition, transcripts encoding secretary gamma2 and gamma3 H chains were detected in two cases, which suggests that some serum IgG could be produced by the leukemic clone. Analysis of sorted PBL showed that isotype-switching occurs in CLL cells that express the CD5 antigen. Finally, nucleotide sequence analysis showed that the mu, alpha, and gamma CLL transcripts are identical, demonstrating that the CLL cells do not accumulate somatic mutations in their variable region genes after the H chain class switching. These data provide in vivo evidence that isotype-switching is a frequent phenomenon in CLL, and indicate that a subset of the CLL lymphocytes progress to later stages of B cell differentiation.

Base Sequence↗

An algorithm for the study of DNA sequence evolution based on the genetic code.

Recent studies of the quantum-mechanical processes in the DNA molecule have seriously challenged the principle that mutations occur randomly. The proton tunneling mechanism causes tautomeric transitions in base pairs resulting in mutations during DNA replication. The meticulous study of the quantum-mechanical phenomena in DNA may reveal that the process of mutagenesis is not completely random. We are still far away from a complete quantum-mechanical model of DNA sequence mutagenesis because of the complexity of the processes and the complex three-dimensional structure of the molecule. In this paper we have developed a quantum-mechanical description of DNA evolution and, following its outline, we have constructed a classical model for DNA evolution assuming that some aspects of the quantum-mechanical processes have influenced the determination of the genetic code. Conversely, our model assumes that the genetic code provides information about the quantum-mechanical mechanisms of mutagenesis, as the current code is the product of an evolutionary process that tries to minimize the spurious consequences of mutagenesis. Based on this model we develop an algorithm that can be used to study the accumulation of mutations in a DNA sequence. The algorithm has a user-friendly interface and the user can change key parameters in order to study relevant hypotheses.

Algorithms↗

Genetic dissection of clonally inherited genomes of Poeciliopsis: II. Investigation of a silent carboxylesterase allele.

According to the ratchet mechanism hypothesis, deleterious mutations should accumulate in clonal genomes of unisexual fish of the genus Poeciliopsis. This study defines one such mutant, a silent carboxylesterase allele (ES-5 degrees) which is found in the heterozygous condition in a particular population of P. monacha-occidentalis. An antiserum to purified Poeciliopsis carboxylesterase cross-reacts with the gene product of the Es-5 degrees allele upon immunoelectrophoresis. This finding of cross-reacting material associated with the Es-5 degrees allele provides a useful marker for the breeding of a carboxylesterase deficient strain.

Alleles↗

Demethylation of 3-methylthymine in DNA by bacterial and human DNA dioxygenases.

Rare DNA lesions that are chemically stable and refractory to repair may add disproportionately to the accumulation of mutations in long lived cells. 3-Methylthymine is a minor lesion that is induced by DNA-methylating agents and for which no repair process has been described previously. Here we demonstrate that this lesion can be directly demethylated in vitro by bacterial and human DNA dioxygenases. The Escherichia coli AlkB and human ABH3 proteins repaired 3-methylthymine in both single-stranded and double-stranded polydeoxynucleotides, whereas the human ABH2 protein preferred a duplex substrate. Thus, the known substrates of these enzymes now include 3-methylthymine in DNA, as well as 1-methyladenine and 3-methylcytosine, which all have structurally similar sites of alkylation. Repair of 3-methylthymine by AlkB and ABH3 was optimal at pH 6, but inefficient. At physiological pH, 3-methylthymine, which is a minor methylated lesion, was more slowly repaired than the major lesion generated in single-stranded DNA, 3-methylcytosine. Our data suggest that 3-methylthymine residues in DNA will be repaired inefficiently in vivo and therefore may occur at a low steady-state level, but the residues should not gradually accumulate to high levels in long lived cells.

Adenine↗

Esophagogastric adenocarcinoma in an E1A/E1B transgenic model involves p53 disruption.

We studied tumorigenesis and p53 immunostaining in a murine transgenic model introducing E1A/E1B under the control of the mouse mammary tumor virus-long terminal repeat (MMTV-LTR) promoter in which adenocarcinoma occurs at the squamocolumnar junction in the foregut, predominantly in males, and at no other site. Mutations of p53 are frequent in human esophageal adenocarcinoma and the E1B gene product interferes with p53-mediated apoptosis, inhibiting tumor suppression at the G(1)/S checkpoint. Transgenic animals were generated utilizing a purified linear 6.7 kb fragment of plasmid DNA containing MMTV-LTR/E1A/E1B and were confirmed by dot blot hybridization of tail DNA to (32)P-labeled E1A/E1B probe and polymerase chain reaction (PCR) amplification of E1A. Transgenic and control animals were observed for morbidity and weight changes. Eleven of 45 animals were transgenic (24% efficiency) with an estimated 5 to 57 copies of the gene per genome. Profound weight loss (>20%) led to sacrifice or death of one of five females (at 12 weeks) and four of six males (at 16 to 17 weeks). Grossly visible tumors (2 to 10 mm) were noted in the forestomach at the visible margin between the proximal (squamous-lined) stomach and the distal glandular stomach. Histologic sections confirmed adenocarcinoma arising in each case at the squamocolumnar junction with glandular formation, pleomorphism, and frequent mitotic figures. Immunostaining was positive for p53 indicating accumulation of mutated or altered p53 protein. E1A/E1B transgenic animals developed macroscopic and microscopic adenocarcinoma at the squamocolumnar junction, which corresponds to adenocarcinoma at the human esophagogastric junction. Disruption of p53 was present in the transgenic model as in the human cancer.

Adenocarcinoma↗

Expression of the Arabidopsis abi1-1 mutant allele inhibits proteinase inhibitor wound-induction in tomato.

Abscisic acid (ABA) is an essential component in the wound signalling cascade. Increased levels of endogenous ABA were observed after wounding and shown to be a requisite for wound-induced expression of the proteinase inhibitor II genes. We have taken advantage of the dominant character of the Arabidopsis abi1-1 mutation, to investigate whether ABl1 has a function in ABA signalling in response to wounding. Transgenic tomato plants carrying copies of either the wild-type ABI1 or the mutant abi1-1 alleles were obtained and assayed for wound-induction of the pin2 or LAP genes. While normal levels of gene induction were observed in the transgenic ABI1 plants, the abi1-1 transformants displayed a severe wilty phenotype and reduced seed dormancy. Expression of the abi1-1 dominant mutation blocked accumulation of the drought-induced TAS14 and LE25 mRNAs in response to ABA, as well as ABA- and wound-induced expression of the defense-associated pin2 and LAP transcripts. MeJA-induction of the pin2 and LAP mRNAs, on the contrary, was not affected in the abi1-1 transformants. These results indicate that abi1-1 inhibits wound-induced expression of the pin2 and LAP transcripts by blocking ABA-induction of these genes. This implicates ABI1 in wound-signalling and suggests that a common early ABA signalling pathway may function in the responses to wounding and water stress.

Alleles↗

Analysis for heterozygosity of protein S mRNA: application to genetic screening and family studies in hereditary protein S deficiency.

We genetically screened patients with hereditary protein S deficiency for heterozygosity of protein S mRNA using PCR-RFLP for Pro626 polymorphism. All patients who showed hemizygous state of protein S mRNA, characterized by markedly decreased levels of one allele, had a phenotype of type I protein S deficiency. A putative mutation, such as a nonsense or splice site mutation, in the silent alleles may have affected the mutated mRNA metabolism and reduced the mutated mRNA accumulation, and consequently resulted in type I protein S deficiency in these patients. We also applied this mRNA-based analysis to family studies in hereditary protein S deficiency. In a family with type I protein S deficiency, all affected individuals showed a loss of one allele at the mRNA level and the silent allele cosegregated with the disease phenotype. Detection of hemizygous expression of protein S mRNA provided direct evidence for type I protein S deficiency without further precise genetic analysis. Our findings indicate that this mRNA-based analysis can be a useful strategy for genetic screening and family studies in hereditary protein S deficiency.

Codon↗

Stem cell relationships and the origin of gastrointestinal cancer.

Gastrointestinal stem cells have the capacity for long-term self-replication and the ability to give rise to all other epithelial cell lineages. These properties make them essential since they maintain tissue homeostasis by regulating cell turnover depending on the current demand. However, they are also important players in the earliest stages of gastric and colonic cancer, as they form a target for mutations to accumulate and lead to the development of the malignant phenotype. Due to the lack of reliable markers, gastrointestinal stem cells are difficult to define and characterise. This limits the knowledge about their number and position within the gastric gland and the intestinal crypt, respectively, and consequently about the clonal structure of these units. Therefore, the morphological events of early gastrointestinal carcinoma formation and expansion are hotly debated. In this review we summarize the properties of gastrointestinal stem cells and illuminate their role in the development of the earliest lesions in the gastric and colonic mucosa. We also resume current opinions about the morphological pathways and the clonality of these neoplasias and the subsequent mechanism of spread within the adjacent tissues.

Cell Division↗

Further characterization and validation of gpt delta transgenic mice for quantifying somatic mutations in vivo.

The utility of any mutation assay depends on its characteristics, which are best discovered using model mutagens. To this end, we report further on the characteristics of the lambda-based gpt delta transgenic assay first described by Nohmi et al. ([1996]: Environ Mol Mutagen 28:465-470). Our studies show that the gpt transgene responds similarly to other transgenic loci, specifically lacZ and cII, after treatment with acute doses of N-ethyl-N-nitrosourea (ENU). Because genetic neutrality is an important factor in the design of treatment protocols for mutagenicity testing, as well as for valid comparisons between different tissues and treatments, a time-course study was conducted. The results indicate that the gpt transgene, like cII and lacZ, is genetically neutral in vivo. The sensitivities of the loci are also equivalent, as evidenced by spontaneous mutant frequency data and dose- response curves after acute treatment with 50, 150, or 250 mg/kg ENU. The results are interesting in light of transgenic target size and location and of host genetic background differences. Based on these studies, protocols developed for other transgenic assays should be suitable for the gpt delta. Additionally, a comparison of the gpt and an endogenous locus, Dlb-1, within the small intestine of chronically treated animals (94 microg/mL ENU in drinking water daily) shows differential accumulation of mutations at the loci during chronic exposure. The results further support the existence of preferential repair at endogenous, expressed genes relative to transgenes.

Animals↗

Spontaneous mutations at aprt locus in a mammalian cell line defective in mismatch recognition.

Clone B is a CHO cell line that shows a moderate mutator phenotype as a consequence of a defect in mismatch recognition. To identify the classes of mutation that accumulate spontaneously in a functional gene, we isolated and sequenced 54 clone B spontaneous mutants at the adenine phosphoribosyltransferase gene. This spectrum was compared to 42 mutants collected in the parental cells. Rates of AT-->TA transversions and frameshifts were strikingly increased in clone B (almost eight- and sixfold, respectively). Minor increases were also observed for GC-->TA transversions and GC-->AT transition rates. Frameshifts occurred in repeated sequences, and a large proportion were losses of 2 bases occurring in dinucleotide runs of a type similar to microsatellite sequences. AT-->TA transversions clustered in regions of secondary structure and their formation might be explained by slippage-mediated mechanisms. These data indicate that an important function of mismatch recognition is in repair of extrahelical bases generated by misalignment during DNA replication.

Adenine Phosphoribosyltransferase↗

Lineage-specific selection in human mtDNA: lack of polymorphisms in a segment of MTND5 gene in haplogroup J.

Human mitochondrial DNA (mtDNA) is a nonrecombining genome that codes for 13 subunits of the mitochondrial oxidative phosphorylation system, 2 rRNAs, and 22 tRNAs. Mutations have accumulated sequentially in mtDNA lineages that diverged tens of thousands of years ago. The genes in mtDNA are subject to different functional constraints and are therefore expected to evolve at different rates, but the rank order of these rates should be the same in all lineages of a phylogeny. Previous studies have indicated, however, that specific regions of mtDNA may have experienced different histories of selection in different lineages, possibly because of lineage-specific interactions or environmental factors such as climate. We report here on a survey for lineage-specific patterns of nucleotide polymorphism in human mtDNA. We calculated molecular polymorphism indices and neutrality tests for classes of functional sites and genes in 837 human mtDNA sequences, compared the results between continent-specific mtDNA lineages, and used two sliding window methods to identify differences in the patterns of polymorphism between haplogroups. A general correlation between nucleotide position and the level of nucleotide polymorphism was identified in the coding region of the mitochondrial genome. Nucleotide diversity in the protein-coding sequence of mtDNA was generally not much higher than that found for many genes in nuclear DNA. A comparison of nonsynonymous/synonymous rate ratios in the 13 protein-coding genes suggested differences in the relative levels of selection between haplogroups, including the European haplogroup clusters. Interestingly, a segment of the MTND5 gene was found to be almost void of segregating sites and nonsynonymous mutations in haplogroup J, which has been associated with susceptibility to certain complex diseases. Our results suggest that there are haplogroup-specific differences in the intensity of selection against particular regions of the mitochondrial genome, indicating that some mutations may be non-neutral within specific phylogenetic lineages but neutral within others.

DNA, Mitochondrial↗

Spontaneous and ethyl methanesulfonate-induced mutations controlling viability in Drosophila melanogaster. III. Heterozygous effect of polygenic mutations.

Spontaneous and EMS-induced mutations were accumulated for several generations on the second chromosome of Drosophila melanogaster by keeping this chromosome heterozygous under conditions of minimal natural selection. This article reports studies of heterozygous effects of these mutants.--Both lethal and mildly deleterious mutants have a deleterious heterozygous effect. There was no discernible difference between heterozygotes in which all the mutants were on one chromosome and those where the mutants were distributed over both homologs; thus the coupling-repulsion effect of MUKAI and YAMAZAKI (1964, 1968) is not confirmed. The spontaneous polygenic mutants have a dominance of 0.4 to 0.5, and the same value is found at very low EMS doses. However, the value at higher EMS doses is only about half as high. Since the low doses have a large fraction of spontaneous mutants, the dominance of EMS mutants is less, in the range 0.1 to 0.3, but still larger than for lethals.

Animals↗

Mutated p53 protein expression and proliferative activity in advanced gastric cancer.

BACKGROUND/AIMS: When the DNA of cells is damaged, wild-type p53 protein induces the expression of p21 (Waf1/Cip1/Sdi1), and regulates the progression of the cell cycle by inducing G1 arrest. Thus, wild type p53 or p21 protein negatively regulates cancer cell proliferation. However, in tumor with loss of expression of functional wild-type p53 protein by mutation or allelic deletion of the gene for p53, whether the proliferative activity of cancer cells might be accelerated or not is unclear. In this study, we investigated the correlation between the level of expression of mutated p53 protein and the proliferative activity of cancer cells in advanced gastric cancer. METHODOLOGY: Ninety-seven samples from patients with gastric cancer that had invaded the serosa without lymph node metastasis (t3, n0, stage II) were investigated by immunohistochemical staining with a monoclonal antibody against p53 and against p21, and with the monoclonal antibody Ki-67. DNA ploidy patterns were analyzed by flow cytometry. The immunoreactivity against p53 and the proliferative activity of cancer cells were scored in terms of a labeling index (LI; percentage of immunostained cells) in each case. Moreover, the prognostic values for 93 surviving patients were evaluated by univariate and multivariate analysis. RESULTS: The mean p53 LI was 24% (range: 0-82.4%) and the mean Ki-67 LI was 23.1% (range: 0-70.7%) in 97 tumors. The expression of p21 protein was detected in 30 of 97 tumors (30.9%) and DNA aneuploidy was detected in 36 of 97 tumors (37.1%). There was significant correlation between the p53 LI and the Ki-67 LI (r = 0.61, t = 7.456, p < 0.001) in 97 tumors. Although, no significant difference was detected, the mean p53 LI (18.3%) of 30 tumors with expression of p21 protein was lower than that of 67 tumors without expression of p21 protein (26.6%, p = 0.096). However, no significant correlation between expression of p21 protein and Ki-67 LI was observed. The p53 LI was not an independent prognostic factor in 93 surviving patients by multivariate survival analysis (p = 0.069). However, the 5-year survival rate of 50 patients with a low level of p53 LI (p53 LI (< or = 10%, 78.3%) was significantly better than that of 43 patients with a high level of p53 LI (p53 LI > 10%, 62.1%, p = 0.045). CONCLUSIONS: Accumulation of mutated p53 protein might suppress the expression of p21 protein in gastric adenocarcinoma, and cancer cells with overexpression of mutated p53 protein might have a high proliferative activity.

Adenocarcinoma↗

Mex67p of Schizosaccharomyces pombe interacts with Rae1p in mediating mRNA export.

We identified the Schizosaccharomyces pombe mex67 gene (spmex67) as a multicopy suppressor of rae1-167 nup184-1 synthetic lethality and the rae1-167 ts mutation. spMex67p, a 596-amino-acid-long protein, has considerable sequence similarity to the Saccharomyces cerevisiae Mex67p (scMex67p) and human Tap. In contrast to scMEX67, spmex67 is essential for neither growth nor nuclear export of mRNA. However, an spmex67 null mutation (Deltamex67) is synthetically lethal with the rae1-167 mutation and accumulates poly(A)(+) RNA in the nucleus. We identified a central region (149 to 505 amino acids) within spMex67p that associates with a complex containing Rae1p that complements growth and mRNA export defects of the rae1-167 Deltamex67 synthetic lethality. This region is devoid of RNA-binding, N-terminal nuclear localization, and the C-terminal nuclear pore complex-targeting regions. The (149-505)-green fluorescent protein (GFP) fusion is found diffused throughout the cell. Overexpression of spMex67p inhibits growth and mRNA export and results in the redistribution of the diffused localization of the (149-505)-GFP fusion to the nucleus and the nuclear periphery. These results suggest that spMex67p competes for essential mRNA export factor(s). Finally, we propose that the 149-505 region of spMex67p could act as an accessory factor in Rae1p-dependent transport and that spMex67p participates at various common steps with Rae1p export complexes in promoting the export of mRNA.

Active Transport, Cell Nucleus↗

Targeted screening for induced mutations.

With the accumulation of large-scale sequence data, emphasis in genomics has shifted from determining gene structure to testing gene function, and this relies on reverse genetic methodology. Here we explore the feasibility of screening for chemically induced mutations in target sequences in Arabidopsis thaliana. Our TILLING (Targeting Induced Local Lesions IN Genomes) method combines the efficiency of ethyl methanesulfonate (EMS)-induced mutagenesis with the ability of denaturing high-performance liquid chromatography (DHPLC) to detect base pair changes by heteroduplex analysis. Importantly, this method generates a wide range of mutant alleles, is fast and automatable, and is applicable to any organism that can be chemically mutagenized.

Alleles↗

The clinical importance and prognostic implications of microsatellite instability in sporadic cancer.

AIMS: The genetic abnormality known as microsatellite instability (MSI), first identified in colorectal cancer in 1993, has subsequently been recognised in other malignancies. These cancers are caused by a defect in the nuclear mismatch repair system, allowing mutations to accumulate with every cellular division. Hereditary Non Polyposis Colon Cancers (HNPCC) and associated malignancies demonstrating MSI have a unique histological appearance, improved prognosis and altered response to chemotherapy and radiotherapy. This review examines the incidence of MSI and its clinical significance in commonly occurring solid malignancies. METHOD: A medline based literature search was performed using the key words 'Microsatellite Instability' and the name of the specific malignancy being investigated. Additional original papers were obtained from citations in those articles identified in the original medline search. RESULTS: MSI has been detected in many solid malignancies although the definition of instability applied has been variable. It is most commonly found in sporadic malignancies that also occur in the HNPCC syndrome such as colorectal, stomach, endometrial and ovarian cancer. MSI may impart a favorable prognosis in colorectal, gastric, pancreatic and probably oesophageal cancers but a poor prognosis in non small cell lung cancer. In clinical studies colorectal cancers demonstrating MSI respond better to chemotherapy while in vitro studies using MSI positive cell lines show resistance to radiotherapy and chemotherapy. CONCLUSION: MSI may be a useful genetic marker in prognosis and could be an influential factor in deciding treatment options. However, in many cancers its significance remains unclear and more evaluation is required.

Colorectal Neoplasms↗

Roles of evolution, quantum mechanics and point mutations in origins of cancer.

The fact point genetic lesions--which provide the species with an ability to respond favorably to changing environmental conditions--are also specifically compatible with "activating" point mutation sensitive, evolutionarily conserved proto-oncogenes and gene p53 implies an additional function for evolutionary processes. In particular, this suggests that evolutionary point lesions may also be designed to remove from the gene pool those genomes which have accumulated advanced levels of evolutionary-induced mutations, thereby protecting the species from the adverse consequences of accumulating mutations beyond an unsafe upper limit. This hypothesis is used to construct a mutation model polynomial for incidence of human cancer as a function of age. The model assumes that point lesion sensitive proto-oncogenes and "p53-type" genes are evolutionarily conserved and must exhibit wild-type genetic information at fertilization for proper growth. Subsequently, evolutionary lesions populate these conserved domains, eventually causing point lesion sensitive genes to yield amino acid substituted proteins capable of participation in transforming normal cells to cancer. The mechanism for evolutionary base substitutions is a time-dependent Topal-Fresco process in which the required unusual tautomers are provided by proton exchange tunneling (see, W.G. Cooper, 1992a). The very good agreement between incidence of cancer data and the model is consistent with the hypothesis that duplex DNA has been evolutionarily designed to supplying an optimum rate of point mutation variation for purposes of (a) providing the species with the ability to respond favorably to changing environmental conditions and (b) to protect the species from adverse consequences of accumulating excessive mutations. (e.g., W.G. Cooper, 1992b). As a result of identifying "tunneling sensitive" DNA codes, consequences of evolutionary lesions in diploid and haploid human genomes are evaluated. The "faster evolving" oocyte genome may be responsible for most evolutionary traits, whereas evolutionarily conserved domains may be supplied by the "slower evolving" male haploid genome. Evidence from fragile X genetic systems support this conclusion. The model further illustrates how fragile X genetic properties could be a result of evolutionary lesions altering genetic specificities of "tunneling sensitive" CGG codes to specify DNA synthesis initiation codons, CUG or UUG. This could cause reinitiation of DNA synthesis and the addition of more CGG codes to the "tunneling sensitive" segment of consecutive (CGG)n repeats which would explain how (CGG)n segments are "expanded" during oogenesis.

Age Factors↗