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PubMed1984

Structure of the genome of equine herpesvirus type 3.

Restriction endonuclease mapping studies were performed to determine the molecular structure of the genome of equine herpesvirus type 3 (EHV-3). Purified EHV-3 DNA, either unlabeled or 32P-labeled, was analyzed using the restriction enzymes BamHI, BclI, BglII, EcoRI, and HindIII. The findings that four 0.5 M (molar) fragments were present, that two of these were terminal fragments, and that all 0.5 M fragments contained homologous DNA sequences as judged by DNA hybridization analyses indicated that DNA sequences located at one terminus are repeated within the molecule and that two populations of molecules exist with regard to the arrangement of this pair of shared sequences. Mapping of BamHI, BclI, BglII, EcoRI, and HindIII fragments by double digestion of intact EHV-3 DNA, reciprocal digestion of isolated restriction enzyme fragments, and blot hybridization experiments revealed that the EHV-3 genome is a linear, double-stranded DNA molecule with a molecular size of 96.2 +/- 0.48 MDa and is comprised of two covalently linked segments, designated L (long) and S (short). The S region is approximately 22.9 MDa in size and consists of a unique segment (Us) of approximately 5.8 MDa bracketed by 8.5 MDa inverted repeat sequences that allow the S region to invert relative to the fixed L region which is approximately 73.3 MDa in size and consists only of unique sequences. Thus, these data confirm that EHV-3 DNA exists in two isomeric forms and has a molecular structure similar to that of the genomes of EHV-1 (B. E. Henry, S. A. Robinson, S. A. Dauenhauer, S. S. Atherton, G. S. Hayward, and D. J. O'Callaghan, Virology 115, 97-114, 1981; D. J. O'Callaghan, G. A. Gentry, and C. C. Randall, "The Herpesvirus," Vol. 2, pp. 215-318, Plenum, New York, 1983; D. J. O'Callaghan, B. E. Henry, J. H. Wharton, S. A. Dauenhauer, R. B. Vance, J. Staczek, and R. A. Robinson, "Developments in Molecular Virology," Vol. 1, pp. 387-418, Nijhoff, The Hague, 1981; W. T. Ruyechan, S. A. Dauenhauer, and D. J. O'Callaghan, J. Virol., 42, 297-300, 1982), pseudorabies virus (W. Stevely, J. Virol., 22, 232-234, 1977; T. Ben-Porat, F. J. Rixon, and M. L. Blankenship, Virology, 95, 285-294, 1979), varicella-zoster virus (A. M. Dumas, J. L. Geelen, M. W. Weststrate, P. Wertheim, and J. Van Der Noordaa, J. Virol., 39, 390-400, 1981; S. E. Straus, H. S. Aulakh, W. T. Ruyechan, J. Hay, T. A. Casey, G. F. Vande Woude, J. Owens, and H. A. Smith, J. Virol., 40, 516-525, 1981.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2002

Transposon-like Correia elements: structure, distribution and genetic exchange between pathogenic Neisseria sp.

Correia elements are a prominent feature of all four Neisseria genome sequences. We report an in silico analysis of the structure and genomic distribution of these elements and some preliminary biochemical data. Correia elements fall into four major families, distinguished by a 50 bp internal deletion and five point mutations. The elements resemble a transposon with 25 bp inverted repeats and a TA duplication at the target site. Within the element there is a functional integration host factor binding site. The genomic distribution of Correia elements is essentially random except for some small Correia-less regions apparently acquired by horizontal transfer. Phylogenetic analysis suggests that their presence predates the divergence of Neisseria meningitidis and Neisseria gonorrhoeae.

Bacterial Proteins↗
PubMed1985

Structure of the promoter of the rat type II procollagen gene.

We have isolated several overlapping genomic clones which contain the 5' terminal portion of the rat pro-alpha 1 (II) chain gene. These clones span about 20 kilobases (kb) of contiguous DNA containing 15 kb of the gene and 5 kb of the 5' flanking sequence. Electron microscopic analysis of mRNA-DNA hybrids by R-looping shows that collectively these clones contain 16 exons which code for approximately one-third of the pro-alpha 1 (II) chain. The sizes of the exons are small, except for the first exon which is relatively large. The nucleotide sequence of the first exon and the 1000 base pairs (bp) preceding it was determined. The first exon contains a 150-bp untranslated segment and an 85-bp sequence coding for the signal peptide and a part of the NH2-terminal propeptide of type II collagen. The segment preceding the transcription initiation site contains the "TATA" box and several G + C-rich stretches, whereas the "CAT" box is not evident between -70 and -120. The hexanucleotide sequence 5'-GGGCGG-3' is found in three different places between -200 and the TATA box. The inverted complement sequence of this hexanucleotide, 5'-CCGCCC-3', is located around both -220 and -450. The hexanucleotide and its inverted sequence have been found previously in the promoter region of the tk gene of herpes virus. These sequences are known to function in a mutually dependent manner as transcription signals for the tk gene; thus, they may play a role in determining the level of transcription of this cartilage gene. The hexanucleotide, 5'-CCGCCC-3', is also found in the 21-base pair repeats of the SV40 promoter and the promoter region of hydroxymethylglutaryl-CoA reductase gene. The sequence 5'-GTGGTTAGA-3' located around -280 is identical to the "core" sequence that has been reported as enhancer element in both viral and cellular genes. These unusual structures may be related to the tissue-specific expression of this gene.

Animals↗
PubMed1991

Transcriptional analysis of the UL1 gene of equine herpesvirus 1: a gene conserved in the genome of defective interfering particles.

Defective interfering particles (DIPs) of equine herpesvirus type 1 (EHV-1) are biologically active, in that they mediate the coestablishment of oncogenic transformation and persistent infection in permissive, primary hamster embryo fibroblasts. The DIP genome is composed of EHV-1 sequences originating from the L-terminus (mapping units (m.u.) 0.00-0.023), the junction of the unique long (UL) region and the internal inverted repeat (IR) (m.u. 0.78-0.79 and 0.99-1.00), and the central portion of the IR (m. u. 0.83-0.87 and 0.91-0.95). The nature of one of the genes (UL1) mapping at the L-terminus was analyzed at the RNA level by Northern blot hybridization and S1 nuclease analyses. These data, and DNA sequencing analyses reported previously revealed that the UL1 gene: (1) contains a major open reading frame (ORF) of 258 amino acids, (2) is a homologue of the ORF2 gene of varicella zoster virus (VZV), (3) is conserved in the genome of DIPs of EHV-1, (4) encodes a 1.2-kb early (E) mRNA that is transcribed toward the short region of the genome, (5) utilizes a transcription initiation site approximately 1,120 nucleotides from the L-terminus, and (6) utilizes a transcription termination site approximately 2211 nucleotides from the L-terminus. These initial studies serve as the basis of future work to determine the function of the UL1 gene in cytolytic infection, and its potential role in EHV-1 persistent infection.

Animals↗
PubMed2006

IS911 transpososome assembly as analysed by tethered particle motion.

Initiation of transposition requires formation of a synaptic complex between both transposon ends and the transposase (Tpase), the enzyme which catalyses DNA cleavage and strand transfer and which ensures transposon mobility. We have used a single-molecule approach, tethered particle motion (TPM), to observe binding of a Tpase derivative, OrfAB[149], amputated for its C-terminal catalytic domain, to DNA molecules carrying one or two IS911 ends. Binding of OrfAB[149] to a single IS911 end provoked a small shortening of the DNA. This is consistent with a DNA bend introduced by protein binding to a single end. This was confirmed using a classic gel retardation assay with circularly permuted DNA substrates. When two ends were present on the tethered DNA in their natural, inverted, configuration, Tpase not only provoked the short reduction in length but also generated species with greatly reduce effective length consistent with DNA looping between the ends. Once formed, this 'looped' species was very stable. Kinetic analysis in real-time suggested that passage from the bound unlooped to the looped state could involve another species of intermediate length in which both transposon ends are bound. DNA carrying directly repeated ends also gave rise to the looped species but the level of the intermediate species was significantly enhanced. Its accumulation could reflect a less favourable synapse formation from this configuration than for the inverted ends. This is compatible with a model in which Tpase binds separately to and bends each end (the intermediate species) and protein-protein interactions then lead to synapsis (the looped species).

Binding Sites↗
PubMed1986

Archaebacteria: transcription and processing of ribosomal RNA sequences in Halobacterium cutirubrum.

The chromosome of Halobacterium cutirubrum contains a single ribosomal RNA gene cluster. The 5' to 3' organization of genes within this 6-kpb region is: 16S, alanine tRNA, 23S, 5S, cysteine tRNA. The entire gene cluster is transcribed as a single long primary transcript; processing of mature RNA sequences from the 5' region of the transcript begins prior to the completion of synthesis at the 3' end. There are five conserved octanucleotide direct repeats (TGCGAACG) in the 900-bp 5'-flanking sequence in front of the 16S gene. The positions of these repeat sequences correspond to the different 5' ends of the primary transcript and probably represent the RNA polymerase start sites. The 16S and 23S rRNA genes are surrounded by long nearly perfect inverted repeat sequences. These sequences probably form duplex structures in the primary transcript and are recognized by an RNaseIII-like endonuclease activity that carries out the initial excision of the precursor 16S and 23S rRNA sequences. These precursors are rapidly trimmed tot he mature 16S and 23S molecules and assembled into ribosomal particles. The processing sites for 5S rRNA appear to be at or very near to the mature ends of the 5S molecule. The tRNA sequences are processed with reduced efficiency from the primary transcript. Nuclease cuts have been detected at the ends as well as in the middle of the cysteine tRNA sequence suggesting that there may be alternative processing pathways, one resulting in proper excision of the mature tRNA sequence and the other resulting in improper excision and degradation of the tRNA sequence. The transcription termination sequence is believed to be at or beyond an AT-rich sequence preceded by a GC-rich sequence located distal to the cysteine tRNA gene.

Base Sequence↗
PubMed2001

Molecular cloning and characterization of groESL operon in Streptococcus pneumoniae.

GroEL is a major target of the immune defense in infection and seems to be negatively regulated by HrcA in gram-positive organisms. However, HrcA's mechanism has not been elucidated. To elucidate the role of groEL in Streptococcus pneumoniae, the groESL operon was cloned in Escherichia coli. The promoter region of the pneumococcal groESL operon contained a sigmaA type promoter and an inverted repeat (CIRCE). A Northern blot analysis of the groESL operon demonstrated that the groESL operon is transcribed as a bicistronic mRNA, and reached maximum expression 7.5 to 10 min after heat shock. A primer extension analysis showed a potential transcription start point at 155 bp upstream of the translation start site, preceding the groES gene. The putative negative regulator of the groEL gene, hrcA, of S. pneumoniae was recovered by PCR-based chromosomal walking from grpE locus. A sequence analysis showed a sigmaA type promoter flanked by 2 CIRCE elements. His-tagged HrcA was overexpressed as a soluble form in E. coli and bound to the CIRCE regions in the promoter of both groESL and dnaK operons in vitro. Additionally, a helix-loop helix motif, a putative DNA binding domain, was found at the C-terminal of HrcA. These results will help to determine the nature of HrcA in the groESL repression.

Amino Acid Sequence↗
PubMed1987

Insertion of adenovirus type 12 DNA in the vicinity of an intracisternal A particle genome in Syrian hamster tumor cells.

In the adenovirus type 12 (Ad12)-induced hamster tumor T1111(2) about 10 Ad12 genome equivalents were integrated at different sites. One of the integrated copies proved unstable and was lost from the cellular genome or rearranged upon passage of the cell line, H1111(2), established from this tumor. This unstable site of junction between the left terminus of Ad12 DNA and hamster DNA and the preinsertion site from BHK21 hamster cells was cloned, sequenced, and analyzed. The junction site showed several peculiarities. At the left terminus of Ad12 DNA, the first 64 nucleotides were deleted. At a distance of 127 nucleotides to the left from this junction site, an internal dispersed fragment of Ad12 DNA comprising nucleotides 1290 to 1361 of the authentic Ad12 DNA sequence was inserted into cellular DNA in an inverted orientation relative to the complete Ad12 genome that was located in its vicinity. The 127-nucleotide sequence between the intact Ad12 genome and the separate 72-base-pair (bp) Ad12 DNA fragment was cellular, but it was not identical to the preinsertion sequence at this location. The sequences flanking the termini of the dispersed 72-bp Ad12 DNA fragment were characterized by direct repeats of 9 or 10 nucleotides. To the left of Ad12 nucleotide 1361 in the separate 72-bp fragment, about 620 cellular nucleotides followed which were identical at the occupied and at the preinsertion sites. It was conceivable that the separate 72-bp Ad12 DNA fragment and the cellular sequence of 127 bp to its right had been transposed en bloc from another unknown location. Abutting the 620 nucleotides of cellular DNA to the left of this block, the 3'-terminal sequence of an endogenous, intracisternal A particle (IAP) genome of hamster cells was detected. The possible significance of the proximity of an IAP sequence to an inserted Ad12 genome with respect to the transformation event, to the instability at this site, or to the transcriptional activity of this region is not known. The 620 bp of cellular DNA between the 72-bp Ad12 DNA fragment and the end of the long terminal repeat of the hamster IAP sequence was apparently of a unique type. Transcriptional activity was not found in the approximate region between nucleotides -620 (to the left) and +350 (to the right) relative to the site of Ad12 DNA insertion, but was found outside these boundaries.

Adenoviridae↗
PubMed2001

Mutational analysis of the repeated open reading frames, ORFs 63 and 70 and ORFs 64 and 69, of varicella-zoster virus.

Varicella-zoster virus (VZV) open reading frame 63 (ORF63), located between nucleotides 110581 and 111417 in the internal repeat region, encodes a nuclear phosphoprotein which is homologous to herpes simplex virus type 1 (HSV-1) ICP22 and is duplicated in the terminal repeat region as ORF70 (nucleotides 118480 to 119316). We evaluated the role of ORFs 63 and 70 in VZV replication, using recombinant VZV cosmids and PCR-based mutagenesis to make single and dual deletions of these ORFs. VZV was recovered within 8 to 10 days when cosmids with single deletions were transfected into melanoma cells along with the three intact VZV cosmids. In contrast, VZV was not detected in transfections carried out with a dual deletion cosmid. Infectious virus was recovered when ORF63 was cloned into a nonnative AvrII site in this cosmid, confirming that failure to generate virus was due to the dual ORF63/70 deletion and that replication required at least one gene copy. This requirement may be related to our observation that ORF63 interacts directly with ORF62, the major immediate-early transactivating protein of VZV. ORF64 is located within the inverted repeat region between nucleotides 111565 and 112107; it has some homology to the HSV-1 Us10 gene and is duplicated as ORF69 (nucleotides 117790 to 118332). ORF64 and ORF69 were deleted individually or simultaneously using the VZV cosmid system. Single deletions of ORF64 or ORF69 yielded viral plaques with the same kinetics and morphology as viruses generated with the parental cosmids. The dual deletion of ORF64 and ORF69 was associated with an abnormal plaque phenotype characterized by very large, multinucleated syncytia. Finally, all of the deletion mutants that yielded recombinants retained infectivity for human T cells in vitro and replicated efficiently in human skin in the SCIDhu mouse model of VZV pathogenesis.

Animals↗
PubMed1994

Isolation and characterization of the gene encoding histone H2A from Trypanosoma cruzi.

In the present paper we report the isolation and characterization of the sequence of two genomic DNA fragments coding for the histone H2A of Trypanosoma cruzi. An analysis of the predicted amino acid sequence shows the presence of the amino-terminal motif characteristic of the H2A histones proteins and the Lys-Lys motif reported to be the site for the ubiquitin attachment. Southern blots of total parasite DNA probed with the H2A sequence suggested that the T. cruzi histone H2A gene is encoded in two independent gene clusters. The molecular karyotyping of the parasite indicated that these two clusters locate in a single chromosome of about 700 kb in length. The T. cruzi H2A mRNA is polyadenylated as are the basal histone mRNAs of higher eukaryotes and the histone mRNAs of yeast. By polymerase chain reaction amplification and sequencing and by S1 mapping we determined respectively the 5' and 3' end of the gene showing that the miniexon is added to the mRNA 71 nucleotides upstream of the ATG initiation codon and that the polyadenylation site locates in nucleotide position 773-775 close to invert repeats.

Amino Acid Sequence↗
PubMed1990

Stem-loop structures at the 3' end of tobacco Rubisco large subunit mRNA.

There are two inverted repeat nucleotide (nt) sequences, each capable of forming a stem-loop structure (sls) at the 3' end of the tobacco Rubisco large subunit mRNA (rbcL). The smaller sls is followed by a larger sls. The in vivo functions of the 3' sls of the rbcL mRNA were characterized using the Escherichia coli system. S 1 mapping of the rbcL transcripts synthesized in E. coli revealed that the 3' end of a major transcript in the bacterial cell is almost identical to the 3' end of authentic chloroplast (cp) rbcL mRNA. This native 3' end is located 4 nt downstream from the larger sls for the cp mRNA and 6 nt for the bacterial transcript, respectively. Deletion experiments show that the larger sls is essential for producing the native 3' end of rbcL mRNA in E. coli. The sls do not function as an efficient transcription terminator but can stabilize upstream mRNA segments in vivo.

Base Sequence↗
PubMed2003

The vanG glycopeptide resistance operon from Enterococcus faecalis revisited.

Acquired VanG-type resistance to vancomycin (MIC = 16 micro g ml(-1)) but susceptibility to teicoplanin in Enterococcus faecalis BM4518 and WCH9 is due to the inducible synthesis of peptidoglycan precursors ending in d-alanine-d-serine. The vanG cluster, assigned to a chromosomal location, was composed of genes recruited from various van operons. The 3' end encoded VanG, a d-Ala:d-Ser ligase, VanXY(G), a putative bifunctional d,d-peptidase and VanT(G), a serine racemase: VanG and VanT(G) were implicated in the synthesis of d-Ala:d-Ser as in VanC- and VanE-type strains. Upstream from the structural genes for these proteins were vanW(G) with unknown function and vanY(G) containing a frameshift mutation which resulted in premature termination of the encoded protein and accounted for the lack of UDP-MurNAc-tetrapeptide in the cytoplasm. Without the frameshift mutation, VanY(G) had homology with Zn2+ dependent d,d-carboxypeptidases. The 5' end of the gene cluster contained three genes vanU(G), vanR(G) and vanS(G) encoding a putative regulatory system, which were co-transcribed constitutively from the PY(G) promoter, whereas transcription of vanY(G),W(G),G,XY(G),T(G) was inducible and initiated from the P(YG) promoter. Transfer of VanG-type glycopeptide resistance to E. faecalis JH2-2 was associated with the movement, from chromosome to chromosome, of genetic elements of c. 240 kb carrying also ermB-encoded erythromycin resistance. Sequence determination of the flanking regions of the vanG cluster in donor and transconjugants revealed the same 4 bp direct repeats and 22 bp imperfect inverted repeats that delineated the large element.

3' Flanking Region↗
PubMed1998

DNA-binding activity of wild-type p53 protein is mediated by the central part of the molecule and controlled by its C terminus.

The DNA binding activity of wild type p53 is central to its activity. The "central" part of the molecule, where most mutations appear in primary human tumors, is the actual DNA binding domain. The C-terminal part was shown to exert a negative effect on the DNA binding activity. In the present study we show that while anti-p53 antibodies recognizing the C terminus of the wild type p53 facilitate DNA binding activity, blocking of the wild type specific epitope by specific anti-p53 antibodies, inhibited the DNA binding activity of the wild type p53 protein. An alternatively spliced p53 protein exhibits an augmented DNA binding activity. The fact that most p53 mutants have lost the wild type p53 conformation specific epitope, coupled with the observation that blocking of this site by binding specific antibodies, prevents the interaction of wild type p53 with DNA, suggests that maintaining the correct structural conformation of this site is central for DNA binding activity. Still, the internal structure of the p53 target and particularly the length of the sequence between the two tandem inverted repeats, is critical for protein-DNA interaction behavior.

Antibodies, Monoclonal↗
PubMed1992

RNA processing modulates the expression of the arcDABC operon in Pseudomonas aeruginosa.

Anaerobic growth of Pseudomonas aeruginosa on arginine depends on the arcDABC operon encoding the enzymes of the arginine deiminase pathway. The co-ordinate, anaerobic induction of these enzymes requires the FNR-like regulatory protein ANR, which activates the arc promoter lying upstream from arcD. By Northern hybridization experiments, three abundant arcA, arcAB and arcABC transcripts and three minor arcDA, arcDAB and arcDABC transcripts could be detected. The 5' ends of the arcA, arcAB and arcABC mRNAs were determined by S1 and primer extension mapping. These 5' ends appear to be generated by endonucleolytic cleavage (processing) in arcD mRNA rather than by a second promoter; this was concluded from the effects of insertion and deletion mutations in arcD. Intergenic inverted repeats between arcA and arcB as well as between arcB and arcC were shown to be involved in the formation of 3' ends of arc transcripts. Deletion of either intergenic region in the P. aeruginosa chromosome led to the loss of the arcA or arcAB transcript, respectively. Dot blot experiments revealed that arc mRNAs extracted from the wild-type strain had similar chemical half-lives in the arcA, arcB and arcC regions, ranging from 16 to 13 minutes. The half-life of arcD mRNA, by contrast, was significantly shorter, suggesting that this mRNA segment may be destabilized by the processing cuts within arcD. Deletion of the putative intergenic stem-loop structures did not result in a dramatic loss of arc mRNA stability. Thus, the intergenic hairpin structures do not contribute importantly to the overall mRNA stability; they might act primarily as partial transcription terminators and locally protect the 3' ends from exonuclease action. The expression levels of the four Arc proteins correlated approximately with the relative abundance of the corresponding mRNA segments. In conclusion, mRNA processing and, presumably, partial termination of transcription contribute to differential gene expression within the arc operon.

Amino Acid Transport Systems↗
PubMed1999

Target and specificity of a nuclear gene product that participates in mRNA 3'-end formation in Chlamydomonas chloroplasts.

Chloroplast mRNA maturation is catalyzed by nucleus-encoded processing enzymes. We previously described a recessive nuclear mutation (crp3) that affects 3'-end formation of several chloroplast mRNAs in Chlamydomonas reinhardtii (Levy, H., Kindle, K. L., and Stern, D. B. (1997) Plant Cell 9, 825-836). In the crp3 background, atpB mRNA lacking a 3'-inverted repeat normally required for stability accumulates as a discrete transcript. The mutation also affects the atpA gene cluster; polycistronic mRNAs with psbI or cemA 3'-ends accumulate to a lower level in the crp3 background. Here, we demonstrate that the crp3 mutation also alters 3'-end formation of psbI mRNA and cemA-containing mRNAs. A novel 3'-end is formed in monocistronic psbI transcripts, and this is the only terminus observed when the psbI 3'-untranslated region is fused to an aadA reporter gene. Accumulation of mRNAs with 3'-ends between cemA and atpH, which is immediately downstream, was reduced. However, this sequence was not recognized as a 3'-end formation element in chimeric genes. The crp3 mutation was able to confer stability to three different atpB 3'-stem-loop-disrupting mutations that lack sequence similarity, but are located at a similar distance from the translation termination codon. We propose that the wild-type CRP3 gene product is part of the general 3' --> 5' processing machinery.

3' Untranslated Regions↗
PubMed2004

Differential effect of small ubiquitin-like modifier (SUMO)-ylation of the androgen receptor in the control of cooperativity on selective versus canonical response elements.

The androgen receptor (AR) can be small ubiquitin-like modifier (SUMO)-ylated in its amino-terminal domain at lysines 385 and 511. This SUMO-ylation is responsive to several agonists, but is not induced by the pure antagonist hydroxyflutamide. We show that the main site of interaction of Ubc9, the SUMO-1 conjugating enzyme, resides in transcription activation unit 5. Overexpression of SUMO-1 represses the AR-mediated transcription, and this effect is abolished after mutating both SUMO-1 acceptor sites. On the other hand, the mutation of lysine 385 clearly affects the cooperativity of the receptor on multiple hormone response elements. Lysine 511 is not implicated in this function. Surprisingly, these effects on cooperativity clearly depend on the nature of the response elements. When selective androgen response elements, which are organized as direct repeats of 5'-TGTTCT-3'-like sequences, were tested, the lysine 385 mutation did not increase the androgen response. Point mutations changing the direct-repeat elements into inverted-repeat elements restored the effects of the lysine 385 mutation on cooperativity. In conclusion, SUMO-ylation of the AR might have a differential function in the control of cooperativity, depending on the conformation of the AR dimer bound to DNA.

Amino Acid Motifs↗
PubMed1991

Structure of the gas vesicle plasmid in Halobacterium halobium: inversion isomers, inverted repeats, and insertion sequences.

Halobacterium-halobium NRC-1 harbors a 200-kb plasmid, pNRC100, which contains a cluster of genes for synthesis of buoyant gas-filled vesicles. Physical mapping of pNRC100 by using pulsed-field gel electrophoresis showed the presence of a large (35 to 38-kb) inverted repeat (IR) sequence. Inversion isomers of pNRC100 were demonstrated by Southern hybridization analysis using two restriction enzymes, AflII and SfiI, that cut asymmetrically within the intervening small single-copy region and the large single-copy region, respectively, but not within the large IRs. No inversion isomers were observed for a deletion derivative of pNRC100 lacking one IR, which suggests that both copies are required for inversion to occur. Additionally, the identities and approximate positions of 17 insertion sequences (IS) in pNRC100 were determined by Southern hybridization and limited nucleotide sequence analysis across the IS element-target site junctions: ISH2, a 0.5-kb element, was found in four copies; ISH3, a 1.4-kb heterogeneous family of elements, was present in seven copies; ISH8, a 1.4-kb element, was found in five copies; and ISH50, a 1.0-kb element, was present in a single copy. The large IRs terminated at an ISH2 element at one end and an ISH3 element at the other end. pNRC100 is similar in structure to chloroplast and mitochondrial genomes, which contain large IRs and other large halobacterial and prokaryotic plasmids that are reservoirs of IS elements but lack the large IRs.

Base Sequence↗
PubMed2002

The Enterococcus faecalis gene encoding the novel general stress protein Gsp62.

The Enterococcus faecalis general stress protein Gsp62 was purified using two-dimensional gel electrophoresis and its 25 N-terminal amino acid sequence determined. Analysis of the corresponding gene revealed that the gsp62 product is a 172 aa protein. Transcriptional analysis of gsp62 gave evidence for a monocistronic mRNA, the synthesis of which was induced at the onset of stationary phase and in response to heat shock, acid pH, detergents (i.e. SDS or bile salts), ethanol, tert-butyl hydroperoxide, sodium chloride and, to a lesser extent, hydrogen peroxide. 5' rapid amplification of cDNA ends by PCR experiments showed that gsp62 transcription initiates 30 nt upstream of the ATG start codon. Although gsp62 expression was induced in response to various stresses, its disruption had no significant effect on the cell survival after each individual stress. Two-dimensional protein gels from wild-type and mutant cells revealed no pleiotropic effect of the mutation on protein synthesis. Transcriptional fusions with the lacL lacM beta-galactosidase genes showed that an inverted repeat located upstream of the promoter is required for transcriptional induction by environmental stresses but not by entrance into stationary phase. Two distinct mechanisms responding to different signals are thus involved in gsp62 induction.

Amino Acid Sequence↗

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