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PubMed1984

Properties of Streptomyces phage SLE111.

Phage SLE111 infecting Streptomyces levoris 1331 was morphological different from most actinophages described and yielded very high titres (10(11) p.f.u/ml) after lytic growth. Typical morphological changes of infected hyphae were observed by phase contrast and electron microscopy of ultrathin sections. The double-stranded, linear DNA (44.2 +/- 1.3 kb) was characterized, according to electron microscopic analysis, by absence of cohesive ends, of terminal redundance, and circular permutation. A stem-loop structure containing inverted repeats of about 200 bp was identified by electron microscopy in two alternative positions in the SLE111 genome.

Bacteriophages↗
PubMed2026

Dynamic balance of CRISPR-Cas immunity and resistance plasmid anti-immunity mediated by a bifunctional protein AcrIE10.

Despite targeting by CRISPR-Cas system, antimicrobial resistance plasmids are prevalent in clinical isolates of carbapenem-resistant Klebsiella pneumoniae which represent a major public health threat. A stable co-existence of plasmids and CRISPR-Cas systems is mediated by anti-CRISPR (Acr) proteins. Here, we report that previously identified AcrIE10 encoded by a resistance plasmid combines two functions: it inhibits CRISPR immunity by directly binding Cas7* subunit through its Acr domain, and acts as an Acr-associated (Aca) protein that self-represses the transcription of Acr locus. AcrIE10 is an example of an Aca protein that utilizes N-terminal ribbon-helix-helix (RHH) domain to specifically recognize the inverted repeat (IR) region in its own promoter. Crucially, a dimerization of AcrIE10 dimers is required for the effective binding to the IR and self-repression, while stoichiometry-dependent interaction with Cas7* facilitates transition to de-repressed state. These findings elucidate molecular mechanisms by which AcrIE10 operates as a dual functionAcr-Aca protein to achieve a delicate balance between host CRISPR-Cas immunity and plasmid anti-defense.

Klebsiella pneumoniae↗
PubMed1986

Isolation of point mutations in bacteriophage Mu attachment regions cloned in a lambda::mini-Mu phage.

Twenty-one derivatives of a lambda::mini-Mu phage containing point mutations in the Mu attachment regions were isolated after mutD mutagenesis and selection for relief from Mu-specific replicative interference of lambda growth. DNA sequence analysis revealed that the single left-end mutant had suffered a T----C transition at position 1 of the Mu sequence, while the remaining 20 right-end mutants contained single base-pair insertions or deletions within the terminal 19 base pairs. A genetic assay showed that the right-end mutations revealed by sequencing were necessary for relief of the replicative inhibition of lambda growth. The properties of these mutants suggest that the terminal 2-base-pair and subterminal 8-base-pair inverted repeats are important for Mu-specific replicative transposition.

Bacteriophage lambda↗
PubMed1988

Trans-splicing in chloroplasts: the rps 12 loci of Nicotiana tabacum.

The rps12 gene in tobacco chloroplasts consists of three exons that code for a polypeptide with homology to Escherichia coli ribosomal protein S12. C-terminal exons 2 and 3 of rps12 are located in the inverted repeat regions of the tobacco chloroplast genome. Exon 1 of rps12 is 29 kilobase pairs downstream of the nearest copy of exons 2 and 3 and 69 kilobase pairs away from the distal copy of exons 2 and 3. RNA gel blot hybridization analysis and primer extension sequencing of cDNA to rps12 encoding RNAs indicate that exon 1 and exons 2 and 3 are encoded on separate transcripts. Exon 1 and exons 2 and 3 are covalently ligated in the correct reading frame in rps12 mRNA. These results indicate that a bimolecular (trans-) splicing event occurs during the formation of mature rps12 mRNA.

Chloroplasts↗
PubMed2000

Dimerization interfaces of v-erbA homodimers and heterodimers with retinoid X receptor alpha.

The oncoprotein v-ErbA, a member of the zinc finger transcription factor superfamily, is a mutated version of thyroid hormone receptor alpha1 that is virtually incapable of binding T3. v-ErbA and other members of this family can bind as homodimers and heterodimers with retinoid X receptors to specific DNA sequences arranged as direct, inverted, or everted repeats. At least two regions in the C-terminal domain, the I box (10 and 11 helices in v-ErbA and thyroid hormone receptors) and the 20-amino acid region are involved in dimerization. However, it has not been entirely understood how these receptors dimerize on differently oriented core motifs and whether the domain(s) responsible for homodimerization and heterodimerization are identical. Therefore, deletions of the entire 20-amino acid region, the 10 helix, the 11 helix, and point mutations within these regions of v-ErbA were made by site-directed mutagenesis. The mutant proteins were tested for their ability to form v-ErbA homodimers and heterodimers with retinoid X receptor alpha on differently oriented core motifs by electrophoretic mobility shift assay. Transient transfections were performed to determine the dominant negative activity of the v-ErbA mutants. The data indicate that different dimerization interfaces are used for v-ErbA homodimerization and heterodimerization with retinoid X receptor alpha, and different dimerization interfaces are used on differently oriented core motifs. The data are of general interest because the information improves our understanding of the role of these dimerization interfaces in the mechanism of action not only of v-ErbA but also of other members of the superfamily.

Amino Acid Sequence↗
PubMed2003

Monosomy 1p36 breakpoint junctions suggest pre-meiotic breakage-fusion-bridge cycles are involved in generating terminal deletions.

Terminal deletions of 1p36 result in a mental retardation syndrome that is presumably caused by haploinsufficiency of a number of genes. Although monosomy 1p36 is the most commonly observed terminal deletion syndrome in humans, the molecular mechanism(s) that generates and stabilizes terminal deletions of 1p36 is not completely understood. Our previous molecular analysis of a large cohort of monosomy 1p36 subjects demonstrated that deletion sizes vary widely from approximately 1 Mb to >10.5 Mb in the most distal portion of 1p36 with no single common breakpoint. In this report, we have identified the precise breakpoint junctions in three subjects with apparently pure terminal deletions of 1p36 ranging from 2.5 to 4.25 Mb. These junctions revealed one deletion to be stabilized by telomeric repeat sequences and two to have terminal deletions associated with cryptic interrupted inverted duplications at the ends of the chromosomes. These interrupted inverted duplication/deletion breakpoints are reminiscent of those seen in tumor cell lines that have undergone breakage-fusion-bridge (BFB) cycles leading to gene amplification. We propose a pre-meiotic model for the formation of these deletions in which a terminally deleted chromosome is generated in the germ line and passes through at least one BFB cycle to produce gametes with terminal deletions associated with interrupted inverted duplications. These data suggest that, on a molecular level, seemingly pure terminal deletions visualized cytogenetically may be more complex, and BFB cycles may play an important role in generating terminal deletions associated with genetic disease in humans.

Animals↗
PubMed1989

Relationship between the pel genes of the pelADE cluster in Erwinia chrysanthemi strain B374.

In this paper, we have used filter hybridization and nucleotide sequencing to analyse the relationship between the three genes of the pelADE cluster in the Erwinia chrysanthemi (Ech) strain B374. This cluster encodes for three of the five pectate lyase proteins that are involved in the maceration and soft-rotting of plant tissue, an important trait in Ech pathogenicity. Southern hybridization revealed homology between each of the three pel genes. A 3560 bp DNA fragment containing the pelE and pelD genes was sequenced. These two genes show extensive homology in the coding regions but only low homology in the 5' and 3' non-coding regions. However both genes exhibit sequences homologous to the Escherichia coli CAP-binding site consensus sequence upstream of the start codon and an inverted repeat sequence which may act as a rho-independent transcriptional terminator after the translational stop. The pel genes of Ech B374 were also compared with the already sequenced pel genes of EC16, another Ech strain.

Amino Acid Sequence↗
PubMed1999

Autogenous regulation of the Bacillus anthracis pag operon.

Protective antigen (PA) is an important component of the edema and lethal toxins produced by Bacillus anthracis. PA is essential for binding the toxins to the target cell receptor and for facilitating translocation of the enzymatic toxin components, edema factor and lethal factor, across the target cell membrane. The structural gene for PA, pagA (previously known as pag), is located on the 182-kb virulence plasmid pXO1 at a locus distinct from the edema factor and lethal factor genes. Here we show that a 300-bp gene located downstream of pagA is cotranscribed with pagA and represses expression of the operon. We have designated this gene pagR (for protective antigen repressor). Two pagA mRNA transcripts were detected in cells producing PA: a short, 2.7-kb transcript corresponding to the pagA gene, and a longer, 4.2-kb transcript representing a bicistronic message derived from pagA and pagR. The 3' end of the short transcript mapped adjacent to an inverted repeat sequence, suggesting that the sequence can act as a transcription terminator. Attenuation of termination at this site results in transcription of pagR. A pagR mutant exhibited increased steady-state levels of pagA mRNA, indicating that pagR negatively controls expression of the operon. Autogenous control of the operon may involve atxA, a trans-acting positive regulator of pagA. The steady-state level of atxA mRNA was also increased in the pagR mutant. The mutant phenotype was complemented by addition of pagR in trans on a multicopy plasmid.

Amino Acid Sequence↗
PubMed2001

The DIRS1 group of retrotransposons.

Only three retrotransposons of the DIRS1 group have previously been described: DIRS1 from the slime mold Dictyostelium discoideum, PAT from the nematode Panagrellus redivivus, and Prt1 from the zygomycetous fungus Phycomyces blakesleeanus. Analyses of the reverse transcriptase sequences encoded by these elements suggest that they are related to the long terminal repeat (LTR) retroelements, such as the Ty3/gypsy retrotransposons and the vertebrate retroviruses. The DIRS1-group elements, however, have several unusual structural features which distinguish them from typical LTR elements: (1) they lack the capacity to encode DDE-type integrases or aspartic proteases; (2) they have open reading frames (ORFs) of unknown function; (3) they integrate without creating duplications of their target sites; and (4) although they are bordered by terminal repeats, these sequences differ from typical LTRs in that they are either inverted repeats or "split" direct repeats. Because of the small number of DIRS1-like elements described, and the unusual structures of these elements, little is known about their evolution, distribution, and replication mechanisms. Here, we report the identification of several new DIRS1-like retrotransposons, including elements from nematodes, sea urchins, fish, and amphibia. We also present evidence for the existence of DIRS1-like sequences in the human genome. In addition, we show that the lack of DDE-type integrase genes from elements of the DIRS1 group is explained by the finding that the previously uncharacterized ORFs of these elements encode proteins related to the site-specific recombinase of bacteriophage lambda. The presence of lambda-recombinase-like genes in DIRS1 elements also accounts for the lack of target-site duplications for these elements and may be related to the unusual structures of their terminal repeats.

Amino Acid Sequence↗
PubMed1987

Characterization of the terminal sequences flanking the transposon that carries the Escherichia coli enterotoxin STII gene.

The Escherichia coli enterotoxin STII gene is flanked by two repeat sequences, approx. 600 bp each and 8 kb apart. This 9-kb DNA fragment has been shown to transpose as a unit and is thus considered a transposon. It is presently designated as Tn4521. In this study, the two terminal sequences of Tn4521 cloned in pPS1 were localized, isolated, and characterized. The two terminal sequences were found to be composed of IS2 sequences and were in an inverted repeat orientation. However, neither repeat contained a complete IS2. The LTR contained bp 1-722, whereas the RTR contained bp 17-536 and 969-1327, all three of the IS2 sequence.

Bacterial Toxins↗
PubMed1984

Nucleotide sequence of the 5'-terminal coding region for pre-rRNA and mature 17S rRNA in Tetrahymena thermophila rDNA.

The 5'-terminus of 35S pre-rRNA and mature 17S rRNA of Tetrahymena thermophila was mapped on cloned rDNA fragments by S1 nuclease protection experiments. A single site for transcription initiation was observed when pre-rRNA prepared by three different methods was used as RNA probe. These mapping results were unambiguously confirmed by sequencing the 5'-terminal region of in vitro capped 35S pre-rRNA. DNA sequence analysis of about 520 nucleotides upstream of the transcription initiation site revealed several distinct sets of highly conserved repeat sequences. In addition, the 840 nucleotides downstream of the transcription initiation site (+ 1) was determined and shown to include the 5'-terminus of the 17S rRNA coding region at position + 647. A region surrounding the position + 195 contains an inverted repeat sequence which could be the structural basis for the recently described premature transcription termination event in this organism (Kister et al. (1983) Nucl. Acids Res. 11, 3487-3502).

Animals↗
PubMed1991

Cloning of the maize rough dwarf virus genome: molecular confirmation of the plant-reovirus classification scheme and identification of two large nonoverlapping coding domains within a single genomic segment.

The segmented double-stranded RNA genome of maize rough dwarf virus, a plant-infecting reovirus of the genus Fijivirus, was cloned and partially characterized. Nucleotide sequence analysis of full-length cDNA clones corresponding to genomic segments S6, S7, and S8 revealed each segment to contain the conserved terminal oligonucleotide sequences (+) 5' AAGUUUUUU------UGUC 3' and adjacent, segment-specific, regions of inverted complementarity (inverted repeats), a structural motif previously reported for members of the genus Phytoreovirus. Genomic segment S6 was completely sequenced and found to consist of 2193 base pairs. Computer analysis indicated that the coding strand contained two large nonoverlapping open reading frames consisting of 363 and 310 codons and located in the 5'- and 3'-terminal domains, respectively. This was confirmed by cell-free translation studies with synthetic transcripts and denatured genomic RNA. However, only the product of the 5'-proximal open reading frame, a 40-kDa polypeptide, was efficiently expressed in vitro from the full-length S6 coding strand. This represents the first case in which a reovirus genomic segment was found to contain two large open reading frames in a nonoverlapping configuration, suggesting possible alternative strategies for regulation of gene expression by members of this genus. The combined results provide a molecular confirmation of the current classification scheme for plant-infecting reoviruses. Furthermore, the fact that the same terminal structural motif is conserved across genera provides additional evidence that these elements serve an important functional role during genome transcription or replication.

Amino Acid Sequence↗
PubMed1980

Ubiquitous, interspersed repeated sequences in mammalian genomes.

DNA base sequence comparisons demonstrate that the principal family of 300-nucleotide interspersed human DNA sequences, the repetitive double-strand regions of HeLa cell heterogeneous nuclear RNA, and specific RNA polymerase III in vitro transcripts of cloned human DNA sequences are all representatives of a closely related family of sequences. A segment of approximately 30 residues of these sequences is highly conserved in mammalian evolution because it is also present in the interspersed repeated DNA sequences of Chinese hamsters. Further DNA sequence comparisons demonstrate that a portion of this highly conserved segment of repetitive mamalian DNA sequence is similar to a sequence found within a low molecular weight RNA that hydrogen-bonds to poly(A)-terminated RNA molecules of Chinese hamsters and a sequence that forms half of a perfect inverted repeat near the origin of DNA replication in papovaviruses.

Animals↗
PubMed1980

Expression of the vaccinia virus genome: analysis and mapping of mRNAs encoded within the inverted terminal repetition.

We have investigated the organization of transcriptional units within a 9000 bp segment of the terminally repeated region of the DNA genome of vaccinia virus, which uses its own enzyme system to synthesize mRNA within the cytoplasm of infected cells. RNA splicing, which has been demonstrated for DNA viruses that replicate within the nucleus of infected cells, does not appear to be involved in the formation of these first vaccinia virus mRNAs to be examined. Three immediate early mRNAs, approximately 1050, 600 and 1100 nucleotides long, were mapped between 3.21 and 4.24, 6.54 and 7.16, and 7.20 and 8.23 kb from the end of the genome, respectively. The direction of transcription was toward the end of the genome for the two larger mRNAs and in the opposite direction for the smallest one. Additional minor RNAs, which were larger in size, were mapped between and to the same DNA strand as the mRNAs of 1050 and 1100 nucleotides. No evidence for interrupted genes was obtained by nuclease S1 analysis after hybridization of RNA to labeled DNA. In addition, the 5' ends of the mRNAs, which were specifically labeled by in vitro capping, hybridized to DNA adjacent to the body of the message.

DNA, Recombinant↗
PubMed1993

Murine radiation myeloid leukaemogenesis: relationship between interstitial telomere-like sequences and chromosome 2 fragile sites.

While the specific nature of chromosomal fragile sites and their relationship to human leukaemogenesis remain obscure, there is evidence that chromosomal fragility may, in some circumstances, be associated with telomere-like repeat sequences and that chromosome 2 fragility in the mouse is involved in the initiation of myeloid leukaemia by ionising radiation. Here we describe the molecular cloning and characterisation of two murine telomere-like sequences, one having an inverted repeat structure and the other a simple tandem repeat organisation. The inverted telomere repeat clone generates an in situ chromosome 2 hybridisation pattern very similar to the distribution of the radiation-sensitive fragile sites previously found to be associated with leukaemogenic initiation. Furthermore, statistical comparison of the distributions of radiation induced breakpoints and sites of inverted telomere repeat hybridization indicates concordance at all chromosome 2 sites excluding the terminal regions. These data are discussed with respect to mechanisms of radiation-induced, site-specific chromosome 2 rearrangement and their implications for leukaemogenic initiation.

Acute Disease↗
PubMed1983

Mitochondrial DNA of an African trypanosome.

The maxicircles of African trypanosome kDNA are the genetic equivalent of other mitochondrial DNAs, but the function of minicircles is unknown. The maxicircle of Trypanosoma brucei 164 encodes conventional mitochondrial gene products and is largely but not completely transcribed. Nucleotide sequence analysis of a region not found to be transcribed revealed numerous translation termination codons in all three reading frames of both strands and numerous inverted repeats, suggesting that this segment does not have polypeptide-coding function. This segment may encode a t-RNA and has a sequence resembling a consensus sequence found in mitochondrial introns, thus implying that transcript processing occurs in trypanosome mitochondria. While several cloned minicircles had distinct restriction maps reflecting T brucei minicircle heterogeneity, one segment of the minicircle contained a sequence that was conserved by minicircles from other trypanosome strains and species. Of nine mutants unable to grow as the respiring procyclic forms, seven were devoid of kDNA. The other two mutants retained normal amounts of all maxicircle restriction fragments and normal amounts of those minicircle sequences tested. Minicircle alterations probably occur in these mutants, since the kDNA does not stain with Giemsa and bands at an altered density in cesium chloride/ethidium bromide density gradients.

Animals↗
PubMed1982

Molecular cloning and nucleotide sequencing of the gene for E. coli cAMP receptor protein.

The crp gene of E. coli, which codes for cAMP receptor protein (CRP), has been cloned in the plasmid pBR322 on the basis of a genetic complementation. One of the recombinant plasmids, pHA1, was shown to direct the synthesis of CRP in a cell-free system. The location of the crp gene was determined by constructing subclones carrying various portions of pHA1. The nucleotide sequence of the crp gene has been determined. The coding region consists of 627 base pairs (bp), which specify a protein of 209 amino acids. The predicted amino acid sequence from the DNA sequence is consistent with the amino acid sequence partially known and the amino acid composition of CRP. After the coding region, there is a G-C rich inverted repeat sequence followed by a run of Ts, which could be a terminator of the crp gene. A possible promoter sequence was found about 180 bp upstream from the initiation codon and was shown to act as a promoter in vitro and in vivo. There are two dyad symmetry regions in a 167 bp leader sequence.

Amino Acid Sequence↗
PubMed1999

Repression of IS200 transposase synthesis by RNA secondary structures.

The IS 200 transposase, a 16 kDa polypeptide encoded by the single open reading frame (ORF) of the insertion element, has been identified using an expression system based on T7 RNA polymerase. In wild-type IS 200, two sets of internal inverted repeats that generate RNA secondary structures provide two independent mechanisms for repression of transposase synthesis. The inverted repeat located near the left end of IS 200 is a transcriptional terminator that terminates read-through transcripts before they reach the IS 200 ORF. The terminator is functional in both directions and may terminate >80% of transcripts. Another control operates at the translational level: transposase synthesis is inhibited by occlusion of the ribosome-binding site (RBS) of the IS 200 ORF. The RBS (5'-AGGGG-3') is occluded by formation of a mRNA stem-loop structure whose 3' end is located only 3 nt upstream of the start codon. This mechanism reduces transposase synthesis approximately 10-fold. Primer extension experiments with AMV reverse transcriptase have provided evidence that this stem-loop RNA structure is actually formed. Tight repression of transposase synthesis, achieved through synergistic mechanisms of negative control, may explain the unusually low transposition frequency of IS 200.

Base Pairing↗