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PubMed1998

A novel unusual DNA structure formed in an inverted repeat sequence.

A potential to form a non-cruciform unusual DNA structure was shown at the inverted repeat DNA sequence of a fish satellite DNA. The recombinant plasmid harboring a member of the EcoRI satellite family of Sillago japonica (Percoidei, Sillaginidae) was subjected to S1 nuclease treatment, and the cutting sites were mapped by primer extension assay. The S1 nuclease attacked the 3'-half of the inverted repeat but not the middle part of symmetry under various salt conditions, suggesting that this unusual DNA structure is different from the DNA cruciform and a conventional intramolecular triplex structure. In the presence of 200 mM potassium chloride, the typical DNA cruciform has extruded, suggesting that certain purine-purine-pyrimidine base triads are involved in the formation of this unusual DNA structure. These results support the occurrence of a novel unusual DNA structure formed in the inverted repeat sequence.

Animals↗
PubMed1988

A Bacillus thuringiensis subsp. israelensis gene encoding a 125-kilodalton larvicidal polypeptide is associated with inverted repeat sequences.

A gene encoding a 125-kilodalton (kDa) mosquitocidal delta-endotoxin was cloned from the 72-MDa resident plasmid of Bacillus thuringiensis subsp. israelensis. This gene is similar in its 3' region to the gene encoding the 135-kDa protein previously cloned (C. Bourgouin, A. Klier, and G. Rapoport, Mol. Gen. Genet. 205:390-397, 1986). Escherichia coli recombinant clones harboring the 125-kDa gene were toxic to larvae of the three mosquito species Aedes aegypti, Anopheles stephensi, and Culex pipiens. In addition, the B. thuringiensis subsp. israelensis DNA fragment carrying the 125-kDa protein gene contains two sets of inverted repeat sequences, identified either by the S1 nuclease method or by electron microscopic observation. The structural organization of inverted repeat sequences and of the 125-kDa gene was analyzed and suggests that this B. thuringiensis subsp. israelensis delta-endotoxin gene is located within a transposable element.

Aedes↗
PubMed1994

Identification of the region that determines the specificity of binding of the transposases encoded by Tn3 and gamma delta to the terminal inverted repeat sequences.

To analyze the region that determines the specificity of binding of the Tn3 transposase to the terminal inverted repeat sequences (IR), we first determined the nucleotide sequence of a Tn3-family transposon, gamma delta, which is supposed to encode a transposase similar to that of Tn3. gamma delta was 5981 bp in length and contained three coding frames: Two were the genes, tnpA and tnpR, encoding transposase (1002 amino acids) and resolvase/repressor (183 amino acids), respectively, and the third, named tnpX, encoding a protein (698 amino acids) of unknown function but containing two NTP-binding motifs. Utilizing the tnpA sequence, we then constructed a series of Tn3-gamma delta hybrid genes encoding chimeric proteins in the N-terminal segments of the transposases (amino acid position 1 to 242 of Tn3 or 1' to 243' of gamma delta), which has been previously shown to be responsible for specific binding of transposase to IR sequences in Tn3. Examination of their DNA-binding activities revealed that the subsegment of the N-terminus from amino acid position 1 to 109 determines the specificity of binding to the IR sequences. The third coding frame found in gamma delta, tnpX, is located downstream of tnpR and is expressed from the tnpR promoter in the absence of the tnpR gene product, resolvase/repressor, to produce a protein that inhibits the growth of the host cells. Possible roles of this protein are discussed.

Amino Acid Sequence↗
PubMed2000

Characterization of the replication origin (Ori(S)) and adjoining parts of the inverted repeat sequences of the pseudorabies virus genome.

The DNA sequence of a 2.4 kbp fragment located in the internal and terminal inverted repeat sequences of the pseudorabies virus genome determined in this study closes a gap between the previously described genes for the ICP4 and ICP22 homologues. The novel sequence contains no conserved herpesvirus open reading frames. Northern blot and cDNA analyses revealed a viral immediate-early transcript of 1.8 kb, which is spliced by the removal of two small introns close to its 5' end and which presumably represents the mRNA of the downstream open reading frame encoding the ICP22 homologue. Upstream of the transcribed region, an imperfect set of three directly repeated sequences was identified. Each of them contains a complementary pair of the alphaherpesvirus origin-binding protein recognition motif GTTCGCAC, spaced by AT-rich sequences. In vitro studies confirmed that the DNA fragment analysed includes a functional origin of viral DNA replication.

Animals↗
PubMed1986

An inverted repeat sequence of the IncFI plasmid ColV2-K94 increases multimerization-mediated plasmid instability.

A detailed physical map of the region of the IncFI plasmid ColV2-K94 containing the Rep1 replicon, a Tn903 transposon, and an inverted repeat structure (X1) with unknown properties was prepared by cloning restriction fragments into pBR325. Inserts carrying the 1.2 kb repeated sequence of X1, but not the IS903 sequence of Tn903, had a destabilizing effect on pBR325 and pBR322 plasmid maintenance. One of these derivatives, pWS139, was studied further and was shown to have elevated levels of multimeric DNA forms; this resulted in decreased copy number and plasmid instability, as multimerization reduces the effective number of randomly segregating plasmids per cell. A ColV2-K94 miniplasmid, which has a copy number much lower than that of ColE1-derived vectors, was also less stably inherited if it contained the X1 structure. This destabilizing effect of the X1 repeat sequence was dependent on the RecA function, but not the RecB or the RecC functions of the host. These results suggest that the inverted repeat sequence of the X1 structure serves as a 'hot-spot' for generalized recombination. Thus, when present in cis, this sequence can generate plasmid instability because plasmid molecules are readily converted into multimeric forms through enhanced recombination at this site.

Chromosome Mapping↗
PubMed1984

Inverted repeat sequences flank a Bacillus thuringiensis crystal protein gene.

Two sets of inverted repeat DNA sequences, IR2150 and IR1750, were discovered flanking the crystal protein gene on the 75-kilobase plasmid of Bacillus thuringiensis subsp. kurstaki HD73. A restriction map of ca. 40 kilobases around the crystal protein gene was constructed, and the positions of the copies of IR2150 and IR1750 were determined. Three copies of IR2150 were found flanking the crystal protein gene in an inverted orientation, and one partial and three intact copies of IR1750 were found in both inverted and direct orientations around the gene. Hybridization experiments with fragments from within IR2150 and IR1750 demonstrated the presence of multiple copies of these sequences on the chromosome of B. thuringiensis subsp. kurstaki HD73 and also revealed a strong correlation between the presence of these sequences and the presence of the crystal protein gene on plasmids from 14 strains of B. thuringiensis.

Bacillus thuringiensis↗
PubMed1990

Tn3 transposition immunity is conferred by the transposase-binding domain in the terminal inverted-repeat sequence of Tn3.

A series of mutant terminal inverted repeats (IRs), having 2 bp substitutions at various sites within the 38-bp IR sequence of the ampicillin-resistance transposon Tn3, were tested for transposition immunity to Tn3. Mutations within region 1-10 in the IR did not affect transposition immunity, while mutations within region 13-38 inactivated the immunity function. These two regions corresponded to domain A which was not bound specifically by Tn3 transposase and to domain B which was bound by the transposase, respectively. This indicates that specific binding of transposase to domain B within the IR sequence is responsible for transposition immunity.

Ampicillin Resistance↗
PubMed1982

Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence is lost.

We examined the arrangement of sequences common to seven angiosperm chloroplast genomes. The chloroplast DNAs of spinach, petunia and cucumber are essentially colinear. They share with the corn chloroplast genome a large inversion of approximately 50 kb relative to the genomes of three legumes--mung bean, pea and broad bean. There is one additional rearrangement, a second, smaller inversion within the 50 kb inversion, which is specific to the corn genome. These two changes are the only detectable rearrangements that have occurred during the evolution of the species examined (corn, spinach, petunia, cucumber and mung bean) whose chloroplast genomes contain a large inverted repeat sequence of 22-25 kb. In contrast, we find extensive sequence rearrangements in comparing the pea and broad bean genomes, both of which have deleted one entire segment of the inverted repeat, and also in comparing each of these to the mung bean genome. Thus there is a relatively stable arrangement of sequences in those genomes with the inverted repeat and a much more dynamic arrangement in those that have lost it. We discuss several explanations for this correlation, including the possibility that the inverted repeat may play a direct role in maintaining a conserved arrangement of chloroplast DNA sequences.

Base Sequence↗
PubMed1989

Effects of variation of inverted-repeat sequences on reactions mediated by the transposase of Tn21.

The frequencies of one-ended transposition and normal transposition of derivatives of Tn21 that contain mutant inverted-repeat sequences (IRs) have been measured. In general, there was a linear relationship between the log of the frequency of one-ended transposition of a mutant IR and the log of the frequency of normal transposition of an element flanked by a wild-type IR at one end and by the mutant IR at the other. This implied that one-ended and normal transposition share the rate-limiting step that determines the frequency of transposition and that both IRs are involved in the rate-limiting step in normal transposition. Surprisingly, it was found that only the outer 18 base pairs of the IR of Tn21 engaged accurately in both one-ended and normal transposition, at about 1% of the frequency of the wild-type IR.

Base Sequence↗
PubMed1997

Deletion of the S component inverted repeat sequence c' and the nonessential genes U(S)1 through U(S)5 from the herpes simplex virus type 1 genome substantially impairs productive viral infection in cell culture and pathogenesis in the rat central nervous system.

A distinctive feature of the genetic make-up of herpes simplex virus type 1 (HSV-1), a human neurotropic virus, is that approximately half of the 81 known viral genes are not absolutely required for productive infection in Vero cells, and most can be individually deleted without substantially impairing viral replication in cell culture. If large blocks of contiguous viral genes could be replaced with foreign DNA sequences, it would be possible to engineer highly attenuated recombinant HSV-1 gene transfer vectors capable of carrying large cellular genes or multiple genes having related functions. We report the isolation and characterization of an HSV-1 mutant, designated d311, containing a 12 kb deletion of viral DNA located between the L-S Junction a sequence and the U(S)6 gene, spanning the S component inverted repeat sequence c' and the nonessential genes U(S)1 through U(S)5. Replication of d311 was totally inhibited in rat B103 and mouse Neuro-2A neuroblastoma cell lines, and was reduced by over three orders of magnitude in human SK-N-SH neuroblastoma cells compared to wild-type (wt) HSV-1 KOS. This suggested that the deleted genes, while nonessential for replication in Vero cells, play an important role in HSV replication in neuronal cells, particularly those of rodent origin. Unlike wt KOS which replicated locally and spread to other regions of brain following stereotactic inoculation into rat hippocampus, d311 was unable to replicate and spread within the brain, and did not cause any apparent local neuronal cell damage. These results demonstrate that d311 is highly attenuated for the rat central nervous system. d311 and other mutants of HSV containing major deletions of the nonessential genes within U(S) have the potential to serve as useful tools for gene transfer applications to brain.

Animals↗
PubMed1984

Equalization of the inverted repeat sequences of the pseudorabies virus genome by intermolecular recombination.

During a study designed to identify changes in the genomes that are observed in mutant populations of pseudorabies virions, a thymidine kinase-defective population of virions which contains genomes that possess inverted repeated sequences of unequal sizes has been identified. This population of virions has been used to ascertain the mechanism and rates of equalization of the repeats. Results showed that when the virions were passed in cell cultures at high multiplicities of infection (either once or several times), one-half of the molecules had repeats of equal size and one-half had repeats of unequal size. This result is to be expected if conditions allowing a high degree of intermolecular recombination involving exchange of repeats exist. The process of intermolecular exchange of inverted repeats is rapid and the DNA molecules were at equilibrium by the time a virion had produced a small plaque. If the virions were passed in cell culture at low multiplicities of infection, they acquired genomes with equal-size repeats. This is probably due to segregation of the virions which had acquired genomes with equal repeats by recombination; in the absence of coinfection of the cells with virions containing genomes with different repeat sizes, heterogeneity of the repeats could not be generated. The fact that virions containing genomes with equal repeats are usually isolated from nature can thus be attributed to equalization of the repeats which results from intermolecular recombination, followed by segregation. A special mechanism ensuring equalization of repeats, such as one repeat acting as a template for the synthesis (or repair) of the other, need therefore not be invoked.

Animals↗
PubMed1991

Functional analysis of the two domains in the terminal inverted repeat sequence required for transposition of Tn3.

Bacterial transposon Tn3 has a 38-bp terminal inverted repeat (IR) sequence. The IR sequence has been divided into two domains, A and B, of which domain B is bound by transposase, and domain A is not Here, we defined the two domains more precisely by constructing three IR mutants with a 2-bp substitution at relevant sites within the IR sequence, followed by examination of the binding of transposase to the fragments containing these IR mutants: domain A was located at bp 1-11, whereas domain B was at bp 12-38. To see if the two domains in the IR are functionally distinct, we constructed mini-Tn3 derivatives flanked by two IRs with various 2-bp substitutions within domain A or B, and analyzed their ability to mediate cointegration. The mini-Tn3 derivatives flanked by IR(A+ B+) and IR(A- B+) [or IR(A+ B-)] and those flanked by IR(A-B+) and IR(A+ B-) mediate cointegration more efficiently than the mini-Tn3 derivatives flanked by two IR(A- B+)s or by two IR(A+ B-)s. These results and others presented here indicate that the two domains of IR are functionally distinct in promoting cointegration.

Base Sequence↗
PubMed1990

Single gene encodes glycophospholipid-anchored and asymmetric acetylcholinesterase forms: alternative coding exons contain inverted repeat sequences.

Polymorphic forms of acetylcholinesterase are tethered extracellularly either as dimers membrane-anchored by a glycophospholipid or as catalytic subunits disulfidelinked to a collagen tail that associates with the basal lamina. Genomic clones of acetylcholinesterase from T. californica revealed that individual enzyme forms are encoded within a single gene that yields multiple mRNAs. Each enzyme form is encoded in three exons: the first two exons, bases -22 to 1502 and 1503 to 1669, encode sequence common to both forms, while alternative third exons encode a hydrophobic C-terminal region, to which a glycophospholipid is added upon processing, and a nonprocessed C-terminus, yielding a catalytic subunit that disulfide-links with a collagen-like structural unit. The 3' untranslated region of each alternative exon contains tandem repeat sequences that are inverted with respect to the other exon. This may either dictate alternative exon usage by formation of cis stem-loops or affect the abundance of translatable mRNA by trans-hybridization between the alternative spliced mRNA species.

Acetylcholinesterase↗
PubMed1984

Both inverted repeat sequences located at the ends of IS1 provide promoter functions.

Escherichia coli RNA polymerase was found to bind specifically to restriction fragments containing either end of IS1. DNase I footprint analyses indicate that RNA polymerase protects approximately 70 base-pairs at each end of IS1, including the left or right terminal inverted repeat sequences in IS1 (termed insL or insR, respectively) as well as some non-IS1 sequence directly adjacent to each end of IS1. Analysis of transcripts from the left terminal region of IS1 shows that the insL sequence contains a promoter (named insPL), and that RNA synthesis initiates apparently at one in a stretch of five adenylate residues within insL and continues toward the interior region of IS1. Interestingly, most of the resulting transcripts contain polyuridylate residues (more than 5 U residues) at their 5'-ends. Analysis of transcripts from the right terminal region of IS1 indicates that the insR sequence also contains a promoter (named insPR). RNA synthesis initiates specifically at an adenylate residue within insR and continues toward the interior region of IS1, i.e. in the opposite direction to RNA synthesis initiating at insPL, which is present at the other end of IS1. We propose that insPL is used to make the messenger RNA for the IS1-encoded genes insA and insB, while insPR might be used to synthesize an anti-mRNA and thereby negatively regulate insPL.

Base Sequence↗
PubMed1992

Involvement of a large inverted repeated sequence in a recombinational rearrangement of the mitochondrial genome of the higher fungus Agrocybe aegerita.

Southern hybridization of the total DNA of Agrocybe aegerita with cloned mitochondrial (mt) probes revealed a sequence homology between two distant mitochondrial restriction fragments. From the mtDNA restriction map and the distribution of restriction sites on the cross-hybridizing mitochondrial fragments, two copies of a large inverted repeated sequence (IR) of 3 kbp were located on the mitochondrial genome. These IR sequences divided the 80 kbp mtDNA into two single-copy regions of 24 kbp (SSC) and 50 kbp (LSC). For the first time in higher fungi, this IR sequence has been shown to be involved in an intramolecular homologous recombinational event. Such a rearrangement led to an inversion of the orientation of the two unique-copy regions, without any change in mtDNA complexity. The location of the recombinational event was compared with previously reported plant and fungal mitochondrial rearrangements and the potential role of the IR sequence was discussed.

Basidiomycota↗
PubMed1990

Two domains in the terminal inverted-repeat sequence of transposon Tn3.

Tn3 and related transposons have terminal inverted repeats (IR) of about 38 bp that are needed as sites for transposition. We made mini-Tn3 derivatives which had a wild-type IR of Tn3 at one end and either the divergent IR of the Tn3-related transposon, gamma delta or IS101, or a mutant IR of Tn3 at the other end. We then examined both in vivo transposition (cointegration between transposition donor and target molecules) of these mini-Tn3 elements and in vitro binding of Tn3-encoded transposase to their IRs. None of the elements with an IR of gamma delta or IS101 mediated cointegration efficiently. This was due to inefficient binding of transposase to these IR. Most mutant IR also interfered with cointegration, even though transposase bound to some mutant IR as efficiently as it did to wild type. This permitted the Tn3 IR sequence to be divided into two domains, named A and B, with respect to transposase binding. Domain B, at positions 13-38, was involved in transposase binding, whereas domain A, at positions 1-10, was not. The A domain may contain the sequence recognized by some other (e.g., host) factor(s) to precede the actual cointegration event.

Base Sequence↗
PubMed1994

Marek's disease virus type 1-specific phosphorylated proteins pp38 and pp24 with common amino acid termini are encoded from the opposite junction regions between the long unique and inverted repeat sequences of viral genome.

The nucleotide sequence of the junction region between the long unique (UL) and terminal inverted repeat (TRL) sequences of Marek's disease (MD) virus type 1 (MDV1) DNA revealed the presence of a rightward open reading frame of 155 amino acids. The ORF inserted into an eukaryotic expression vector transiently expressed an antigen in the cytoplasm of COS7 cells which reacted with the monoclonal antibody M21 against an MDV1-specific phosphorylated protein complex consisting of at least the proteins pp38 and pp24. In addition, RNA synthesized in vitro from the ORF under the control of the T7 promoter was translated in vitro using rabbit reticulocyte lysates. A polypeptide of about 24 kDa was immunoprecipitated with M21 antibody. Thus, the MDV1-specific phosphorylated proteins pp38 and pp24 with common amino termini are encoded in the opposite junction regions between the UL and IRL and between the UL and TRL, respectively, of the MDV1 genome. The pp38 gene is transcribed leftward from the viral genome, while the pp24 gene was shown here to be transcribed rightward in a MD tumor cell line as well as in cells productively infected with MDV1.

Amino Acid Sequence↗
PubMed1995

Specific binding of the NikA protein to one arm of 17-base-pair inverted repeat sequences within the oriT region of plasmid R64.

Products of the nikA and nikB genes of plasmid R64 have been shown to form a relaxation complex with R64 oriT DNA and to function together as an oriT-specific nickase. We purified the protein product of the nikA gene. The purified NikA protein bound specifically to the oriT region of R64 DNA. Gel retardation assays and DNase I footprinting analyses indicated that the NikA protein bound only to the right arm of 17-bp inverted repeat sequences; the right arm differed from the left arm by a single nucleotide. The binding site is proximal to the nick site and within the 44-bp oriT core sequence. Binding of the NikA protein induced DNA bending within the R64 oriT sequence.

Bacterial Proteins↗