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PubMed2001

Quorum sensing in Vibrio fischeri: analysis of the LuxR DNA binding region by alanine-scanning mutagenesis.

LuxR is the transcriptional activator for quorum-sensing control of luminescence in Vibrio fischeri. A series of alanine-scanning mutants spanning a predicted helix-turn-helix region in the DNA binding domain of LuxR was constructed, and the activity of each of the LuxR mutant proteins in recombinant Escherichia coli was investigated. The region covered by the mutagenesis spanned residues 190 to 224. About half of the alanine-scanning mutants showed activities similar to that of the wild-type LuxR: at least two were positive-control mutants, four appeared to be defective in DNA binding, and several others were characterized as DNA binding affinity mutants. This analysis, taken together with information about other bacterial transcription factors, provides insights into amino acid residues in LuxR that are involved in DNA binding and transcriptional activation.

Alanine↗

PubMed1998

A DNA self-assembled monolayer for the specific attachment of unmodified double- or single-stranded DNA.

A novel method for DNA surface immobilization and a paradigm for the attachment of unmodified DNA of any length or sequence are described herein. The development of a DNA self-assembled monolayer (DNA-SAM) that incorporates a DNA-thiol into a monolayer of inert alkane thiolates is reported. This DNA-SAM specifically hybridized complementary oligonucleotides while resisting the nonspecific adsorption of noncomplementary DNA and irrelevant proteins. Duplex DNA, having a single-stranded "capture tail," specifically bound to the DNA-SAM if the sequence of the "tail" was complementary to DNA presented in the SAM. The sense strand of the hybridized duplex DNA could be covalently attached to the surface by an enzymatic ligation reaction (leaving the anti-sense strand dissociable). DNA-binding proteins specifically bound to these surfaces only if their cognate sites were present in the duplex DNA.

Adsorption↗

PubMed2006

Ros-induced histone modifications and their role in cell survival and cell death.

Much is known about the distal DNA damage repair response. In particular, many of the enzymes and auxiliary proteins that participate in DNA repair have been characterized. In addition, knowledge of signaling pathways activated in response to DNA damage is increasing. In contrast, comparatively less is known of DNA damage-sensing molecules or of the specific alterations to chromatin structure recognized by such DNA damage sensors. Thus, precisely how chromatin structure is altered in response to DNA damage and how such alterations regulate DNA repair processes remain important unanswered questions. In vertebrates, phosphorylation of the histone variant H2A.X occurs rapidly after double-strand break formation, extends over megabase chromatin domains, and is required for stable accumulation of repair proteins at damage foci. We have shown that reactive oxygen species (ROS)-induced DNA single-strand breaks induce the incorporation of 32P specifically into histone H3. ADP-Ribosylation of histones may stimulate local chromatin relaxation to facilitate the repair process, and, indeed, histone ribosylation preceded DNA damage-induced histone H3 phosphorylation. However, H3 phosphorylation occurred concomitant with overall chromatin condensation, as revealed by decreased sensitivity of chromatin to digestion by micrococcal nuclease and by DAPI staining of nuclei. Inhibitors of the ERK and p38MAPK pathways and inhibition of poly(ADP-ribose) polymerase all reduced ROS-induced H3 phosphorylation, chromatin condensation, and cell death. Precisely how changes in the post-translational modification of histone H3 regulate the survival response remains unclear. Attempts to determine the precise site of histone H3 phosphorylation, putative histone H3 kinases, and histone H3 interacting proteins are underway.

Animals↗

PubMed2005

ATM and p21 cooperate to suppress aneuploidy and subsequent tumor development.

The DNA damage checkpoint protein kinase mutated in ataxia telangiectasia (ATM) is involved in sensing and transducing DNA damage signals by phosphorylating and activating downstream target proteins that are implicated in the regulation of cell cycle progression and DNA repair. Atm-/- cells are defective in cellular proliferation mediated by the Arf/p53/p21 pathway. In this report, we show that increased expression of p21 (also known as Waf1 or CDKN1a) in Atm-/- cells serves as a cellular defense mechanism to suppress further chromosomal instability (CIN) and tumor development because Atm-/- p21-/- mice are predisposed to carcinomas and sarcomas with intratumoral heterogeneity. It was found that Atm-deficient cells are defective in metaphase-anaphase transition leading to abnormal karyokinesis. Moreover, Atm-/- p21-/- primary embryonic fibroblasts exhibit increased CIN compared with either Atm-/- or p21-/- cells. The increased CIN is manifested at the cellular level by increased chromatid breaks and elevated aneuploid genome in Atm-/- p21-/- cells. Finally, we showed that the role of p21 in a CIN background induced by loss of Atm is to suppress numerical CIN but not structural CIN. Our data suggest that the development of aneuploidy precedes tumor formation and implicates p21 as a major tumor suppressor in a genome instability background.

Aneuploidy↗

PubMed2004

The Mre11 complex and ATM: a two-way functional interaction in recognising and signaling DNA double strand breaks.

Mutations in components of the Mre11/Rad50/Nbs1 complex give rise to genetic disorders characterized by neurological abnormalities, radiosensitivity, cell cycle checkpoint defects, genomic instability and cancer predisposition. Evidence exists that this complex associates with chromatin during DNA replication and acts as a sensor of double strand breaks (dsbs) in DNA after exposure to radiation. A series of recent reports provides additional support that the complex senses breaks in DNA and relays this information to ATM, mutated in ataxia-telangiectasia (A-T), which in turn activates pathways for cell cycle checkpoint activation. Paradoxically members of the Mre11 complex are also downstream of ATM in these pathways. Here, Lavin attempts to make sense of this sensing mechanism with reference to a series of recent reports on the topic.

Ataxia Telangiectasia Mutated Proteins↗

PubMed1999

Evolution of the genetic code: the nonsense, antisense, and antinonsense codes make no sense.

According to the molecular recognition theory, the complementarity of the sense and nonsense DNA strands is reflected in a complementarity of polypeptides and the corresponding nonsense polypeptides. A comparison of the sense and nonsense code matrices, and of the antisense and antinonsense code matrices, either by visual inspection or by comparing the corresponding hydrophobicity matrices (e.g. by simply adding them together), revealed no complementarity of these pairs of matrices in terms of possible attractive physical forces. Instead, it was evident that the codes divide the amino acids into two major groups: hydrophilic and hydrophobic, a division which is directly correlated with the folding property of proteins. A simple primordial genetic code distinguishing between these two types of amino acids would have been capable of generating three-dimensionally folded peptides, which could stabilize coding RNAs by forming ribonucleoprotein complexes. This evolutionary scheme is reflected in the present organisation of information processing and storage in essentially all organisms. RNAs are processed and translated into proteins by ribonucleoproteins, while other steps in information retrieval and processing, such as DNA replication, transcription, protein folding and posttranslational processing, are catalyzed by proteins. This shows that the evolution of DNA as an information storage medium was a secondary event, unrelated to the evolution of the genetic code. From the primordial hydrophilic/hydrophobic (f.ex. Leu/Arg) code, evolution proceeded by introduction of a catalytic amino acid (Ser). The further evolution of the code has mainly served to increase the number of functional hydrophilic amino acids, since there has not been a great advantage in increasing the number of structural, hydrophobic amino acids. At some stage during the evolution of the genetic code, double-stranded DNA was introduced as a maximally safe genetic copy of RNA. This required the action of highly specific enzymes, and was therefore preceded by the refinement of the genetic code. As a conclusion of this evolutionary scheme, it can be inferred that, in general only the sense strand encodes proteins.

Codon, Nonsense↗

PubMed1998

Applied pressure enhances cell proliferation through mitogen-activated protein kinase activation in mesangial cells.

Progressive renal diseases lead to prolonged glomerular hypertension, which induces the proliferation of mesangial cells. This proliferation is thought to be involved in the development of renal injury. Here we investigate mitogen-activated protein kinase (MAPK) activation and cell proliferation in mesangial cells under conditions of high pressure. After pressure-load, the phosphorylation level of MAPK (at Tyr-204) increases rapidly with a peak at 1 min, although the amount of MAPK remains almost constant during pressure-load. To confirm the activation of MAPK, we carried out an immunoprecipitation-kinase assay. MAPK activity during pressure-load shows kinetics similar to that of the tyrosine phosphorylation. In contrast, c-Jun N-terminal kinase 1 (JNK1) phosphorylation falls below basal levels in response to high pressure. Immunocytochemical observations show phosphorylated MAPK in the nucleus at 10 min. The expression of c-Fos, a nuclear transcription factor, is induced by high pressure, and the induction is significantly inhibited by PD98059 (50 microM), an upstream MAPK/extracellular signal-regulated kinase kinase (MEK) inhibitor of MAPK. The expression of the c-Jun that is induced by JNK1 activation remains unchanged during pressure-load. MAPK phosphorylation and cell proliferation by applied pressure are significantly inhibited by genistein, a tyrosine kinase inhibitor in a dose-dependent manner, but not by protein kinase C inhibitors, chelerythrine and GF109203X. Genistein also blocks pressure-induced tyrosine phosphorylation of proteins with molecular masses of 35, 53, and 180 kDa. To clarify the physiological role in MAPK activation under high pressure conditions, we transfected antisense MAPK DNA into mesangial cells. The antisense DNA (2 microM) inhibited MAPK expression by 80% compared with expression in the presence of sense or scrambled DNA, and significantly blocked pressure-induced cell proliferation. Treatment of cells with MEK inhibitor also produced a similar result. MEK inhibitor strongly suppresses DNA synthesis induced by pressure-load. Cyclin D1 expression is significantly increased under high pressure conditions, and the increase is blocked by treatment with MEK inhibitor. These findings show that pressure-load, a novel activator of MAPK, induces the activation of tyrosine kinases, and enhances the proliferation of mesangial cells, probably through cyclin D1 expression.

Animals↗

PubMed2003

XRad17 is required for the activation of XChk1 but not XCds1 during checkpoint signaling in Xenopus.

The DNA damage/replication checkpoints act by sensing the presence of damaged DNA or stalled replication forks and initiate signaling pathways that arrest cell cycle progression. Here we report the cloning and characterization of Xenopus orthologues of the RFCand PCNA-related checkpoint proteins. XRad17 shares regions of homology with the five subunits of Replication factor C. XRad9, XRad1, and XHus1 (components of the 9-1-1 complex) all show homology to the DNA polymerase processivity factor PCNA. We demonstrate that these proteins associate with chromatin and are phosphorylated when replication is inhibited by aphidicolin. Phosphorylation of X9-1-1 is caffeine sensitive, but the chromatin association of XRad17 and the X9-1-1 complex after replication block is unaffected by caffeine. This suggests that the X9-1-1 complex can associate with chromatin independently of XAtm/XAtr activity. We further demonstrate that XRad17 is essential for the chromatin binding and checkpoint-dependent phosphorylation of X9-1-1 and for the activation of XChk1 when the replication checkpoint is induced by aphidicolin. XRad17 is not, however, required for the activation of XCds1 in response to dsDNA ends.

Amino Acid Sequence↗

PubMed1992

Coordinate regulation of replication and virion sense gene expression in wheat dwarf virus.

We have investigated the relationship between viral DNA replication and virion sense gene expression in wheat dwarf virus (WDV), a member of the geminivirus group, by testing a series of deletion mutants in transfected Triticum monococcum (einkorn) protoplasts. Mutants contained a transcription fusion of the chloramphenicol acetyltransferase coding sequence to the virion sense promoter that replaced the viral coat protein coding sequence. The deletion analysis revealed that WDV replication and virion sense transcription can proceed independently and are controlled in part by nonoverlapping elements in the large intergenic region. These data and those from a C2 open reading frame (ORF) frameshift mutant also showed that the product of the C2 ORF (C1-C2 protein) is independently involved in both DNA replication and activation of the virion sense promoter. The amino acid sequences encoded by C2, which are highly conserved in the geminivirus group, show some homology to the DNA binding domain of the myb-related class of plant transcription factors. The possible involvement of the host in controlling the function of the C1-C2 protein and the implication of these data for the development of WDV-based gene vectors are discussed.

Amino Acid Sequence↗

PubMed1989

Analysis of parvovirus infections using strand-specific hybridization probes.

The autonomous parvoviruses cause a broad spectrum of acute and chronic infections of animals and man. The discrimination of sites of viral replication from sites of viral sequestration is an important goal in elucidating the pathogenesis of these diseases. It is possible to employ strand-specific RNA hybridization probes in such analyses because a 'plus' sense probe will react with single stranded virion DNA and duplex replicative form DNA, but a 'minus' sense probe will react preferentially with obligate replicative intermediates (duplex replicative form DNA and mRNA). Strand-specific RNA hybridization probes were developed for the Aleutian mink disease parvovirus (ADV) and were used to study acute and chronic infections of mink. Such probes were capable of differentiating replicative intermediates (duplex replicative form DNA and mRNA) from single-stranded virion DNA in Southern blot analysis and in strand-specific in situ hybridization. ADV infection of seronegative newborn mink kits causes an acute, cytopathic infection of type II alveolar cells. Replication in these cells is highly permissive and is characterized by high levels of replicative intermediates and virion DNA. A fatal respiratory distress syndrome and hyaline membrane formation result from impaired surfactant production by the infected type II cells. On the other hand, ADV infection of adult mink is associated with a persistent infection and a disorder of the immune regulation. The target cells for viral replication in adult mink are confined to the lymphoid system and the bone marrow. Replication in these cells, which are probably lymphocytes, is restricted, and characterized by greatly reduced levels of replicative intermediates and virion DNA. It, therefore, seems that disease in the infected adult mink results from a restricted infection by ADV. Large amounts of virion DNA can also be demonstrated in locations where replication cannot be detected and apparently represents sequestration of virion particles by elements of the reticuloendothelial system. Thus, replication and sequestration can, in fact, be distinguished by the strand-specific in situ hybridization. These studies indicate that strand-specific in situ hybridization is a potentially valuable method for studying the pathogenesis of parvovirus infections.

Aleutian Mink Disease↗

PubMedDate not supplied

Overexpression of the human aldehyde dehydrogenase class I results in increased resistance to 4-hydroperoxycyclophosphamide.

A correlation between overexpression of aldehyde dehydrogenase and resistance to oxazaphosphorines, widely used anticancer agents, has been shown. To investigate the direct role of the human aldehyde dehydrogenase class 1 (ALDH-1) in the resistance to one of these agents, 4-hydroperoxycyclophosphamide (4-HC), an active metabolite of cyclophosphamide, neomycin-selectable plasmid or retroviral constructs harboring the wild-type ALDH-1 complementary DNA in the sense orientation were transfected into K562 leukemic cell lines. Polymerase chain reaction (PCR) analysis confirmed the presence of vector DNA in the stably transfected K562 cells. Reverse transcriptase PCR and Northern and Western blot analysis showed expression of ALDH-1 mRNA and protein in the cells transfected with ALDH-1 in the sense orientation but not in cells transfected with vector alone. The activity of the expressed ALDH-1 was demonstrated using spectrophotometric assay. Stably transfected K562 cells were subjected to various doses of 4-HC, and cell viability was assayed using clonogenic cell culture in semisolid medium. Results demonstrate that K562 cells transfected with ALDH-1 in the sense orientation display increased resistance to 4-HC compared with wild-type or vector-transfected K562 cells. Furthermore, the addition of diethylaminobenzaldehyde, a specific inhibitor for ALDH-1, restored the sensitivity of the ALDH-1-expressing K562 cells to 4-HC. Thus, the data pinpoint the direct role of ALDH-1 in the protection against 4-HC cytotoxicity.

Aldehyde Dehydrogenase↗

PubMed1987

Total nucleotide sequences of the infectious cloned DNAs of bean golden mosaic virus.

Complete nucleotide sequences of the infectious cloned DNA components (DNA A and B) of bean bolden mosaic virus were determined. The DNA A (2585 nucleotides) and DNA B (2647 nucleotides) have little sequence homology with each other, but both A and B contain a common region of 205 nucleotides. A possible large hairpin structure is detected in the common region. Nucleotide sequences of DNAs A and B revealed the presence of 8 potential coding regions for proteins (m.w. greater than 10,000). Among them, four open reading frames (ORFs 1-4) encode proteins of m.w. 30,000 or greater, and are individually coded in virion DNA A and B senses (+) and their complementary senses (-), respectively. The other four ORFs 5-8 are in virion DNA B(+) and its complementary sense (-). All of the ORFs 1-4 have regulatory signals for RNA synthesis (TATAA/T) in the region 5' upstream from a potential start codon ATG.

Base Sequence↗

PubMed2006

Nucleic acid-functionalized Pt nanoparticles: Catalytic labels for the amplified electrochemical detection of biomolecules.

Nucleic acid-functionalized Pt nanoparticles (Pt-NPs) act as catalytic labels for the amplified electrochemical detection of DNA hybridization and aptamer/protein recognition. Hybridization of the nucleic acid-modified Pt-NPs with a sensing nucleic acid/analyte DNA complex associated with an electrode enables the amperometric, amplified, detection of the DNA by the Pt NP electrocatalyzed reduction of H2O2 (sensitivity limit, 1 x 10(-11) M). Similarly, the association of aptamer-functionalized Pt- NPs to a thrombin aptamer/thrombin complex associated with an electrode allowed the amplified, electrocatalytic detection of thrombin with a sensitivity limit corresponding to 1 x 10(-9) M.

Aptamers, Nucleotide↗

PubMed1996

Chalcone synthase cosuppression phenotypes in petunia flowers: comparison of sense vs. antisense constructs and single-copy vs. complex T-DNA sequences.

Flower pigmentation patterns were scored in 185 sense Chalcone synthase (Chs) transgenotes and 85 antisense Chs transgenotes; upon first flowering, 139 (75%) of sense transgenotes were found to be phenotypically altered, as were 70 (82%) of the antisense transgenotes. The observed patterns document the range of phenotypic variations that occur, as well as confirm and extend the finding that sense Chs constructs produce several types of morphology-based flower pigmentation patterns that antisense Chs constructs do not. Long-term monitoring for epigenetic variations in one population of 44 sense Chs transgenotes showed that 43 (98%) were capable of producing a cosuppression phenotype. The primary determinant of sense-specific patterns of cosuppression of Chs was found to be the repetitiveness and organization pattern of the transgene, not 'position effects' by, or 'readthrough' from, flanking plant DNA sequences. The degree of cosuppression observed in progeny of transgenotes carrying multiple, dispersed copies as compared to that observed with a single copy of the transgene suggests that sense cosuppression of Chs is subject to a transgene dosage effect.

Acyltransferases↗

PubMed2005

Nonrandom clusters of palindromes in herpesvirus genomes.

Palindromes are symmetrical words of DNA in the sense that they read exactly the same as their reverse complementary sequences. Representing the occurrences of palindromes in a DNA molecule as points on the unit interval, the scan statistics can be used to identify regions of unusually high concentration of palindromes. These regions have been associated with the replication origins on a few herpesviruses in previous studies. However, the use of scan statistics requires the assumption that the points representing the palindromes are independently and uniformly distributed on the unit interval. In this paper, we provide a mathematical basis for this assumption by showing that in randomly generated DNA sequences, the occurrences of palindromes can be approximated by a Poisson process. An easily computable upper bound on the Wasserstein distance between the palindrome process and the Poisson process is obtained. This bound is then used as a guide to choose an optimal palindrome length in the analysis of a collection of 16 herpesvirus genomes. Regions harboring significant palindrome clusters are identified and compared to known locations of replication origins. This analysis brings out a few interesting extensions of the scan statistics that can help formulate an algorithm for more accurate prediction of replication origins.

Data Interpretation, Statistical↗

PubMed2005

[Molecular characteristics of DNA-A of tomato leaf curl Guangdong virus isolate G2].

Virus isolate G2 was isolated from tomato plants showing leaf curl symptoms in Guangdong. The complete nucleotide sequence of G2 DNA-A was determined to be 2744 nucleotides encoding six potential ORFs, with two (AV1 and AV2) in virus sense and four (AC1, AC2, AC3 and AC4) in complementary sense. G2 DNA-A has a typical characteristics of Begomovirus genome organization. BLAST results showed that G2 DNA-A belonged to the Begomovirus of Geminiviridae. Pairwise comparisons of G2 DNA-A with those of other 41 begomoviruses indicated that G2 DNA-A was most closely related to that of Papaya leaf curl China virus isolate G10 (PaLCuCNV-[G10]) (82.8% sequence identity). The intergenic region (IR) of G2 differed to great extent with other begomoviruses (30.9%-81.8% nucleotide sequence identity); when individual encoded proteins were compared, the CP of G2 had relatively high amino acid sequence identity (77.6%-99.2%) with other begomoviruses whereas the AC4 of G2 had less amino acid sequence identity (43.5%-78.8%). Phylogenetic analysis based on the DNA-A sequences also showed that G2 was less related to the reported begomoviruses. These results revealed that G2 infecting Guangdong tomato might be a previously unreported species of Begomovirus, for which the name Tomato leaf curl Guangdong Virus (ToLCGDV) is proposed.

Amino Acid Sequence↗

PubMed1997

Synthesis and anti-influenza virus-A activity of circular dumbbell RNA DNA chimeric oligonucleotides.

We have designed a new type of antisense oligonucleotide, containing two hairpin loop structures with RNA/DNA base pairs (sense (RNA) and antisense (DNA)) in the double helical stem (nicked and circular dumbbell DNA/RNA chimeric oligonucleotides). The reaction of the nicked and circular dumbbell DNA/RNA chimeric oligonucleotides with RNase H gave the corresponding anti-DNA together with the sense RNA cleavage products. These oligonucleotides were more resistant to exonuclease attack. We also describe the anti-Fluv activities of circular dumbbell DNA/RNA chimeric oligonucleotides.

Antiviral Agents↗

PubMed1994

Stable expression in rat glioma cells of sense and antisense nucleic acids to a human multifunctional DNA repair enzyme, APEX nuclease.

We have cloned mouse and human cDNAs for a multifunctional DNA repair enzyme (APEX nuclease) having apurinic/apyrimidinic (AP) endonuclease, 3',5' exonuclease, DNA 3' repair diesterase and DNA 3'-phosphatase activities. To investigate the biological role of APEX nuclease, sense or antisense APEX RNA was stably expressed at a high level in cultured rat glioma cells by introducing plasmids (pABWN-HAPX1F for expression of sense RNA or pABWN-HAPX2R for expression of antisense RNA) constructed from the human APEX cDNA and an expression vector pABWN. Multiple copies of the construct were integrated into the glioma cells transfected with pABWN-HAPX1F or pABWN-HAPX2R. These transfectants showed markedly high expression of RNA hybridizable to human APEX cDNA, indicating the expression of the sense or antisense RNA. Activity blotting analyses of salt extracts of these transfectants showed that the sense RNA-expressed cells had higher AP endonuclease activity and that the antisense RNA-expressed cells had extremely lower AP endonuclease activity than the control cells. The APEX nuclease-depressed glioma cells became more sensitive to methyl methanesulfonate and hydrogen peroxide than the control cells or the APEX nuclease-overexpressed cells. The results indicate that APEX nuclease plays an important role in repair of DNA damage caused by these genotoxic agents. The present stable expression systems for the sense and antisense APEX RNAs should be useful for analyzing the biological functions such as an antimutagenic function of the enzyme.

Animals↗