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PubMed1991

Molecular cloning and sequence analysis of the genome of chicken anaemia agent.

The replicative form (RF) DNA of chicken anaemia agent (CAA) was isolated and cloned into bacterial plasmids. After religation of the cloned CAA DNA and transfection into MDCC-MSB1 cells, the DNA could induce c.p.e. characteristic of that caused by CAA, and an antigen was produced which gave positive immunofluorescence when detected with an anti-CAA serum. Sanger sequencing of the 2298 bp genome revealed several open reading frames (ORFs); the major ORF encoded a polypeptide of 51.8K. In SDS-PAGE of CAA viral particles a 50K protein has been reported as the only detectable viral protein. The genomic region downstream of the major ORF had several predicted GC-rich inverted repeats, a poly(A) signal and four copies of an 18 bp repeat element. Database searches did not reveal any sequence with homology to the viral genomic DNA, nor to the amino acid sequence of any of the ORFs, apart from the N-terminal 40 amino acids of the major ORF which showed a limited similarity to the structure of protamines.

Amino Acid Sequence↗
PubMed2005

NovG, a DNA-binding protein acting as a positive regulator of novobiocin biosynthesis.

The biosynthetic gene cluster of the aminocoumarin antibiotic novobiocin contains two putative regulatory genes, i.e. novE and novG. The predicted gene product of novG shows a putative helix-turn-helix DNA-binding motif and shares sequence similarity with StrR, a well-studied pathway-specific transcriptional activator of streptomycin biosynthesis. Here functional proof is provided, by genetic and biochemical approaches, for the role of NovG as a positive regulator of novobiocin biosynthesis. The entire novobiocin cluster of the producer organism Streptomyces spheroides was expressed in the heterologous host Streptomyces coelicolor M512, and additional strains were produced which lacked the novG gene within the heterologously expressed cluster. These Delta novG strains produced only 2% of the novobiocin formed by the S. coelicolor M512 strains carrying the intact novobiocin cluster. The production could be restored by introducing an intact copy of novG into the mutant. The presence of novG on a multicopy plasmid in the strain containing the intact cluster led to almost threefold overproduction of the antibiotic, suggesting that novobiocin biosynthesis is limited by the availability of NovG protein. Furthermore, purified N-terminal His(6)-tagged NovG showed specific DNA-binding activity for the novG-novH and the cloG-cloY intergenic regions of the novobiocin and clorobiocin biosynthetic gene clusters, respectively. By comparing the DNA sequences of the fragments binding NovG, conserved inverted repeats were identified in both fragments, similar to those identified as the binding sites for StrR. The consensus sequence for the StrR and the putative NovG binding sites was GTTCRACTG(N)(11)CRGTYGAAC. Therefore, NovG and StrR apparently belong to the same family of DNA-binding regulatory proteins.

Bacterial Proteins↗
PubMed1988

Primary structure of barley genes encoding quinone and chlorophyll a binding proteins of photosystem II.

The psbA, psbD and psbC genes encoding the quinone binding D-1 and D-2 apoproteins and the 44 kD chlorophyll a-apoprotein 3 have been located in the chloroplast genome of barley. They are found on a 23 kbp SalI restriction endonuclease fragment in the large single copy region of the chloroplast DNA adjacent to the inverted repeat. As in other species the psbD and psbC genes have reading frames which overlap by 53 bp. They are transcribed in the same direction but translated with a frameshift of one nucleotide. Ten amino acid substitutions are found among the 18 N-terminal residues of the D-2 polypeptide if barley, spinach, tobacco, pea and the liverwort Marchantia are compared. Only 8 substitutions are present among the 335 other residues of the D-2 polypeptide. The amino acid residues located in the putative binding site for the special pair reaction center chlorophyll and the residues probably serving as ligands to non-heme iron in the D-1 and D-2 proteins of barley are strictly conserved when compared to those of purple bacteria and of other higher plants. Identity is also observed for the residues of importance in the binding of quinones.

Amino Acid Sequence↗
PubMed1984

Structure of circular copies of the 412 transposable element present in Drosophila melanogaster tissue culture cells, and isolation of a free 412 long terminal repeat.

We have isolated, from Drosophila melanogaster tissue culture cells, extrachromosomal circular forms of the transposable element 412, and have cloned some of them in bacteriophage lambda. A total of 24 clones have been analysed in detail by restriction and heteroduplex mapping. Seventeen clones are virtually identical, and contain complete 412 elements with one copy of the long terminal direct repeat (LTR). The remaining seven clones are all different and contain various rearrangements. Four have deletions, two have some 412 sequence substituted by other DNA and one has both an inversion and a deletion. The clone containing the inversion has two LTRs in inverted orientation and separated by a few thousand bases of 412 DNA. The base sequences of the two LTRs in this clone, and of the LTR in one of the 17 clones containing complete elements are very similar to that of the 481 base-pair LTR of a genomic 412 element. We have found no evidence, in either cloned or uncloned material, for 412 elements with two LTRs as a tandem direct repeat. We have found that there are several "free" 412 LTRs in genomic DNA from D. melanogaster strains Canton S and Oregon R, and from D. melanogaster tissue culture cells. We have cloned and sequenced one of these free LTRs. It is 475 base-pairs long and is flanked by a direct repeat four base-pairs long. This sequence differs from that of the 481 base-pair repeat at 16 places including a ten base deletion.

Animals↗
PubMed1998

Inhibition of human telomerase by 2'-O-methyl-RNA.

Telomerase, a ribonucleoprotein up-regulated in many types of cancers, possesses an RNA template necessary to bind and extend telomere ends. The intrinsic accessibility of telomerase to incoming nucleic acids makes the RNA template an ideal target for inhibition by oligonucleotides. We report here that 2'-O-methyl-RNA (2'-O-meRNA), an oligonucleotide chemistry known to exert sequence-specific effects in cell culture and animals, inhibits telomerase with potencies superior to those possessed by analogous peptide nucleic acids (PNAs). Potent inhibition relative to PNAs is surprising, because the binding affinity of 2'-O-meRNAs for complementary RNA is low relative to analogous PNAs. A 2'-O-meRNA oligomer with terminal phosphorothioate substitutions inhibits telomerase sequence-selectively within human-tumor-derived DU145 cells when delivered with cationic lipids. In contrast to the ability of 2'-O-meRNA oligomers to inhibit telomerase, the binding of a 2'-O-meRNA to an inverted repeat within plasmid DNA was not detectable, whereas binding of PNA was efficient, suggesting that the relative accessibility of the telomerase RNA template is essential for inhibition by 2'-O-meRNA. Inhibition of telomerase by 2'-O-meRNA will facilitate probing the link between telomerase activity and sustained cell proliferation and may provide a basis for the development of chemopreventive and chemotherapeutic agents.

Amino Acid Sequence↗
PubMed1999

Signal-dependent DNA binding and functional domains of the quorum-sensing activator TraR as identified by repressor activity.

TraR, a member of the LuxR family of quorum-sensing transcription factors, is responsible for the population density-dependent regulation of Ti plasmid conjugal transfer. The protein requires as coinducer an acyl-homoserine lactone signal molecule called AAI (Agrobacterium autoinducer) that is produced by the bacteria themselves. TraR only activates its target genes, making it difficult to determine whether interaction with AAI is required for binding DNA or for initiating transcription. To assess this, we converted TraR into a repressor by placing a copy of the tra box, an 18-bp inverted repeat believed to be the recognition site for this protein, over the -10 region of a promoter driving expression of lacZ. Repression of this promoter by TraR depended on AAI or, at higher concentrations, VAI, the closely related signal of Vibrio fischeri. C-terminal deletions as short as 2 aa and N-terminal deletions as short as 4 aa in TraR abolished both repressor and activator functions. The C-terminal mutants were strongly dominant over TraR, suggesting that they can form heteromultimers with the wild-type activator. Mutants of TraR with substitutions at Asp-10 and Gly-123 failed to activate a positively controlled reporter but continued to repress the chimeric promoter in an AAI-dependent manner. We conclude that TraR recognizes the tra box as its binding site, that binding of TraR to this site depends on AAI, and that the N-terminal half of the protein contains one or more domains that are required for activation but not for multimerization, for interaction with the acyl-homoserine lactone, or for DNA binding.

Agrobacterium tumefaciens↗
PubMed1998

The role of the T-box for the function of the vitamin D receptor on different types of response elements.

The nuclear hormone 1alpha,25-dihydroxyvitamin D3(VD) mainly functions through a heterodimer formed between the VD receptor (VDR) and the retinoid X receptor (RXR). This transcription factor complex specifically recognizes DNA sequences, referred to as VD response elements (VDREs), that are formed by two hexameric core binding motifs arranged either as direct repeats spaced by 3 nt (DR3) or inverted palindromes with nine intervening nucleotides (IP9). Gel shift clipping assays provided the first evidence that VDR-RXR heterodimers form different conformations on these two types of VDREs. Since the T-box within the C-terminal extension of the receptor DNA binding domain (DBD) was previously shown to form a dimerization interface with the partner receptor DBD when bound to DR-type response elements, all six amino acid residues of the VDR T-box were investigated for their role in VDR-RXR heterodimer complex formation on DR3- and IP9-type VDREs. Interestingly, the residue Phe93 (F93) was found to be critical on both types of VDREs, whereas the role of the residue Ile94 (I94) was found to depend on ionic strength of the binding reaction and the nature of the VDRE. However, under physiological conditions I94 was also shown to be critical on both VDRE types. The monitored differences between the two VDR-containing protein-DNA complexes helps in an understanding of the differential action of the nuclear hormone VD and its therapeutically important analogues.

Amino Acid Sequence↗
PubMed1985

Gene expression from both intronless and intron-containing Rous sarcoma virus clones is specifically inhibited by anti-sense RNA.

To distinguish the inhibitory effect of anti-sense RNA on translation from the effect on splicing, a plasmid (pLC32) was constructed from a cDNA clone of the Rous sarcoma virus (RSV) envelope gene (env) mRNA. Transcription of this plasmid results in the synthesis of RNA identical to the RSV env gene mRNA which does not require splicing to be expressed. Plasmids derived from pLC32 were also constructed in which the env gene coding sequence and 5' noncoding leader sequences were inserted in the opposite orientation relative to the RSV long terminal repeats (LTRs). pLC32 DNA transfected by the calcium phosphate coprecipitation technique efficiently rescued infectious virus from quail cells infected with an RSV mutant deleted in the env gene [R(-)Q cells], indicating that the intron sequences are dispensable in env gene expression. When the inverted constructs were cotransfected with pLC32, significantly less infectious virus was produced. The extent of the inhibition depended upon the concentration ratio of the two plasmids. The maximum inhibition (80%) occurred when the ratio of inverted constructs to pLC32 was 12:1. The inhibition is specific for the inverted orientation since cotransfection of pLC32 with several other plasmids containing viral LTRs and defective src and env genes at similar concentrations did not inhibit the production of infectious virus. In addition, the inverted constructs did not interfere with the expression of an LTR-driven chloramphenicol acetyltransferase gene. When cotransfected with a wild-type Prague A RSV DNA plasmid (pJD100), the inverted constructs also greatly inhibited expression and replication of virus in R(-)Q quail cells. These data suggest that the specific inhibition is caused by hybridization of complementary RNA transcribed from the inverted constructs to the env mRNA, thereby blocking its expression. The fact that expression of both intron-containing and intronless clones are inhibited to the same extent suggest that inhibition by anti-sense RNA from the env exon regions does not act at the level of RNA splicing.

Animals↗
PubMed1992

Cleavage of concatemeric DNA at the internal junction of "translocation" mutants of pseudorabies virus and inversion of their L component appear to be linked.

When pseudorabies virus (PrV) strains are grown in chicken embryo fibroblasts (CEF), variants ("translocation" mutants) arise in which there is a duplication of the leftmost sequences of the genome and their translocation in inverted orientation next to the internal inverted repeat bracketing the S component. In these variants, the UL becomes bracketed by inverted repeats and is found in two orientations relative to the Us. To study the cis-functions involved in cleavage of concatemeric DNA as well as those involved in inversion of the L component and to ascertain whether the two events are linked in the "translocation" mutants, a viral mutant (vLD68) was constructed in which the terminal 64 bp of the L component (that include sequences with homology to the pac 2 site of HSV) and the 4 terminal bp of the S component were deleted from the internal junction. Although revertants that have acquired the 68 bp at the internal junction emerge rapidly in populations of vLD68, analysis of the characteristics of this mutant revealed that: (1) the termini derived from both orientations of the L component include the 64 bp that have been deleted from the internal junction of vLD68; (2) in contrast to other "translocation" mutants, the internal junction of the vLD68 genome is not a good substrate for cleavage; (3) inversion of the L component of true vLD68 DNA does not occur or is rare; a good correlation exists in the populations of vLD68 between the proportion of revertants that have acquired an intact internal junction and the proportion of genomes with an L component that inverts. These results show that an intact internal junction in "translocation" mutants is necessary for both inversion of their L components and cleavage at their alternative internal junction. Since cleavage at the alternative junction will result in inversion of the L component, we conclude that inversion of the L component of "translocation" mutants of PrV can be attributed to cleavage of concatemeric DNA at the internal alternative junction.

Animals↗
PubMed1986

Cloning and fine mapping the DNA of equine herpesvirus type one defective interfering particles.

Equine herpesvirus type one (EHV-1) defective interfering (DI) particle DNA fragments were inserted into the XbaI site of the plasmid vector pACYC184. Five DI XbaI fragments, which ranged in molecular weight from 4.5 to 6.7 MDa, were selected for detailed analysis. Each DI DNA clone was labeled with 32P-deoxynucleotides by nick translation and hybridized to genomic digests of EHV-1 standard (STD) DNA bound to nitrocellulose. All five clones were shown to hybridize to DNA sequences derived from the left terminus (0.0-0.04 map units) of the long (L) region and from the short (S) region inverted repeats (IRs, 0.79-0.86 and 0.93-1.00 map units) of the STD EHV-1 genome. Restriction enzyme mapping studies and Southern blot hybridizations employing cloned STD virus DNA fragments as probes revealed that these EHV-1 DI clones contain two major domains: (1) an L terminal region which maps to 0.01-0.04 map units and is highly conserved among all five clones, and (2) a region homologous to the IRs which appears to vary between individual clones.

Cell Transformation, Neoplastic↗
PubMed2004

Supercoiling-induced DNA bending.

Local DNA bending is a critical factor for numerous DNA functions including recognition of DNA by sequence-specific regulatory binding proteins. Negative DNA supercoiling increases both local and global DNA dynamics, and this dynamic flexibility can facilitate the formation of DNA-protein complexes. We have recently shown that apexes of supercoiled DNA molecules are sites that can promote the formation of an alternative DNA structure, a cruciform, suggesting that these positions in supercoiled DNA are under additional stress and perhaps have a distorted DNA geometry. To test this hypothesis, we used atomic force microscopy to directly measure the curvature of apical positions in supercoiled DNA. The measurements were performed for an inherently curved sequence formed by phased A tracts and a region of mixed sequence DNA. For this, we used plasmids in which an inverted repeat and A tract were placed at precise locations relative to each other. Under specific conditions, the inverted repeat formed a cruciform that was used as a marker for the unambiguous identification of the A tract location. When the A tract and cruciform were placed diametrically opposite, this yielded predominantly nonbranched plectonemic molecules with an extruded cruciform and A tract localized in the terminal loops. For both the curved A tract and mixed sequence nonbent DNA, their localization to an apex increased the angle of bending compared to that expected for DNA unconstrained in solution. This is consistent with increased helical distortion at an apical bend.

Base Sequence↗
PubMed1981

Mobile dispersed genetic element MDG1 of Drosophila melanogaster: nucleotide sequence of long terminal repeats.

Long terminal repeats (LTRs) of two members of mdg1 family were sequenced. In the both cases, they are represented by perfect direct repeats 442 and 444 bp in length. Sixteen nucleotides in the LTRs of two different mdg1 elements are different. Each LTR contains slightly mismatched 16-nucleotide inverted repeats located at the ends of the LTR. Six base pairs closest to the termini of LTR form perfect inverted repeats. On the gene-distal sides of LTRs, short 4-nucleotide direct repeats are located, probably representing the duplication of a target DNA sequence arising from insertion of mdg. They are different in the two cases analyzed. Just as the other analyzed eukaryotic transposable elements, mdg1 starts with TGT and ends with ACA. Within the both strands of LTR, the sequences similar to Hogness box (a putative signal for RNA initiation, or a selector) and AATAAA blocks (putative polyadenylation signals) are present. The LTR of mdg1 contains many short direct and inverted repetitive sequences. These include a 10-nucleotide sequence forming a perfect direct repeat with the first ten nucleotides of the LTR. A region of LTR about 70 bp long is represented by simple repetitive sequences (TAT).

Animals↗
PubMed1986

Identification by antibody to a synthetic peptide of a protein specified by a diploid gene located in the terminal repeats of the L component of herpes simplex virus genome.

In the course of studies on the a sequences located at the termini of and at the junction between the L and S components of herpes simplex virus 1 DNA, J. Chou and B. Roizman (J. Virol. 57:629-637, 1986) noted that the a sequence acted as a gamma 1 promoter when fused to the structural sequence of the thymidine kinase gene, the b inverted repeat sequences located in the L component next to the a sequences contained an open reading frame predicted to encode the protein of 358 amino acids with a molecular weight of 37,054, and the transcription of an RNA homologous to the open reading frame initiated within the a sequence. The nucleotide sequence of the open reading frame predicted the presence of the triplet Ala-Thr-Pro repeated 10 times. To verify the existence of the predicted gene, designated gamma 134.5, a synthetic peptide consisting of the triplet Ala-Thr-Pro repeated 10 times was synthesized and used to raise antibodies in rabbits. The results were as follows. The antiserum to the peptide reacted with a 43,500-apparent-molecular-weight protein present in lysates of cells infected with herpes simplex virus 1 but not present in mock-infected or herpes simplex virus 2-infected cells. We genetically engineered a recombinant virus containing a single copy of a truncated gene. Concordant with predictions, the antibody reacted with a faster-migrating protein in cells infected with this recombinant. The gamma 134.5 gene product was soluble, and it accumulated primarily in the cytoplasm late in infection. The overlap of the domain of the gamma 134.5 gene with the a sequence raises the possibility that it acts in trans on the a sequence and is associated with one of the functions currently ascribed to the a sequences.

Amino Acid Sequence↗
PubMed1983

The terminal RNA stem-loop structure and 80 bp of spacer DNA are required for the formation of 3' termini of sea urchin H2A mRNA.

We have studied the exact sequence requirement for the formation of 3' termini of the sea urchin H2A mRNA in frog oocyte injection experiments. Point mutations destroying the symmetry of the inverted DNA repeat in the mRNA trailer coding sequences prevent the generation of genuine 3' termini. Mutants containing complementary base changes are pseudorevertants and allow the production of H2A mRNA with faithful 3' termini at wild-type levels. Our transcription analyses show that it is primarily the sequence of the transcribed strand that decides whether or not true 3' mRNA termini are produced. This is evidence that an RNA stem-loop structure, rather than a DNA cruciform, is essential for this process. Spacer sequences are absolutely required, because in their absence only H2A mRNA with spacer transcript extensions are found. Once the canonical CAAGAAAGA and flanking sequences are linked to the H2A gene, H2A messenger is synthesized at a suboptimal rate, which can be increased to wild-type levels by the addition of 80 bp of the spacer immediately adjacent to the H2A gene.

Animals↗
PubMed1994

The organization of the Pm promoter of the TOL plasmid reflects the structure of its cognate activator protein XylS.

The toluate catabolic operon carried by the TOL plasmid pWW0 of Pseudomonas putida is positively regulated by the benzoate-responsive XylS protein which, when activated, stimulates transcription from the operon promoter Pm. In this study, the mode in which XylS effects the activity of the Pm promoter was examined in vivo by genetic analysis of both protein and promoter variants. Substitution of His31Asp/Ser32Pro,Leu113Pro,Phe214Leu/Glu215A sp/Arg216Pro or Thr312Pro, all predicted to disrupt the secondary structure, renders XylS inactive and unable to compete with the native protein for activation of Pm. In contrast, Pro substitutions at Ser64 or Gly160 had no or only minor effects on XylS activity, and a protein with residual capacity to activate Pm resulted when Glu11 was altered to Pro. None of a collection of truncated variants, of XylS protein deleted for more than 10 terminal amino acids retained activity or were able to negatively interact the wild-type XylS protein. These data indicate that amino- and carboxy-terminal portions of the protein sequence depend on each other for the maintenance of their functional structure, rather than being arranged as independent domains. Pm promoter derivatives, in which the two half-sites of the direct repeat sequence that confers responsiveness to XylS were separated and/or inverted by one-half or one complete DNA helix turn, lost responsiveness in vivo. These results favour a model for XylS-mediated activation of Pm in which a tandem dimer is the protein form that binds the Pm promoter.

Amino Acid Sequence↗
PubMed1980

Inverted terminal repetition in vaccinia virus DNA encodes early mRNAs.

Vaccinia virus DNA contains a long inverted terminal repetition of MW approximately 6.8 x 10(6). A fragment of MW 6.3 X 10(6) from this repetition has been cloned in coliphage lambda and used to isolate RNA from virus-infected cells. Electron microscopy indicates that early RNAs are transcribed from the repeated sequence and cell-free translation shows that the RNAs code for polypeptides.

Bacteriophage lambda↗
PubMed1987

Efficient resolution of replicated poxvirus telomeres to native hairpin structures requires two inverted symmetrical copies of a core target DNA sequence.

The terminal hairpin sequences of the linear double-stranded DNA genome of the leporipoxvirus Shope fibroma virus (SFV) has been cloned in Saccharomyces cerevisiae and in recombination-deficient Escherichia coli as a palindromic insert within circular plasmid vectors. This sequence configuration is equivalent to the inverted repeat structure detected as a telomeric replicative intermediate during poxvirus replication in vivo. Previously, it has been shown that when circular plasmids containing this palindromic insert were transfected into SFV-infected cells, efficient replication and resolution generated linear minichromosomes with bona fide viral hairpin termini (A. M. DeLange, M. Reddy, D. Scraba, C. Upton, and G. McFadden, J. Virol. 59:249-259, 1986). To localize the minimal target DNA sequence required for efficient resolution, a series of staggered unidirectional deletions were constructed at both ends of the inverted repeat. Analyses of the resolution efficiencies of the various clones indicate that up to 240 base pairs (bp) centered at the symmetry axis were required for maximal resolution to minichromosomes. To investigate the role of the AT-rich central axis sequences, which in SFV include 8 nonpalindromic bp, a unique AflII site at the symmetry axis was exploited. Bidirectional deletions extending from this AflII site and insertions of synthetic oligonucleotides into one of the deletion derivatives were constructed and tested in vivo. The efficiency with which these plasmids resolved to linear minichromosomes with hairpin termini has enabled us to define the minimal target DNA sequence as two inverted copies of an identical DNA sequence between 58 and 76 bp in length. The nonpalindromic nucleotides, which, after resolution, constitute the extrahelical residues characteristic of native poxviral telomeres, were not required for resolution. The close resemblance of the SFV core target sequence to the analogous region from the orthopoxvirus vaccinia virus is consistent with a conserved mechanism for poxviral telomere resolution.

DNA↗
PubMed1985

Characterization and sequencing of the region containing gene N, the nutL site and tL1 terminator of bacteriophage phi 80.

We have cloned the early region of the major leftward operon of bacteriophage phi 80 DNA and determined the nucleotide sequence of the PL-nutL-tL1 segment. The genes and sites equivalent to lambda gene N, antiterminator nutL, and terminator tL1 were found in this region by functional tests using the recombinant plasmids carrying the transcriptional units Ptrp-tL1-galK, Ptrp-nutL-tL1-galK and PlacUV5-N. Sequence homologies were observed between the boxA of the phage 21 nutR site and the inverted repeat of the nut core in the nutL-equivalent site of phi 80. The N-equivalent gene of phi 80 codes for a protein with 98 amino acids. It is highly basic as is the lambda N protein. Recombinant plasmids carrying the phi 80-PL promoter and nut-equivalent site of phi 80 are lethal to the Escherichia coli host cell, but can be stably maintained in the presence of the phi 80-cI repressor.

Amino Acid Sequence↗