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PubMed2003

Regulatory network of acid resistance genes in Escherichia coli.

Overexpression of the response regulator EvgA confers an acid-resistant phenotype to exponentially growing Escherichia coli. This acid resistance is partially abolished by deletion of ydeP, yhiE or ydeO, genes induced by EvgA overexpression. Microarray analysis identified two classes of operons (genes). The first class contains seven operons induced by EvgA overexpression in the absence of ydeO, an AraC/XylS regulator gene. The second class contains 12 operons induced by YdeO overexpression. Operons in the second class were induced by EvgA overexpression only in the presence of ydeO. EvgA is likely to directly upregulate operons in the first class, and indirectly upregulate operons in the second class via YdeO. Analysis using the motif-finding program alignace identified an 18 bp inverted repeat motif in six upstream regions of all seven operons directly regulated by EvgA. Gel mobility shift assays showed the specific binding of EvgA to the six sequences. Introduction of mutations into the inverted repeats upstream of ydeP and b1500-ydeO resulted in reduction in EvgA-induced ydeP and ydeO expression and acid resistance. These results suggest that EvgA binds to the inverted repeats and upregulates the downstream genes. Overexpression of YdeP, YdeO and YhiE conferred acid resistance to exponentially growing cells, whereas GadX overexpression did not. Microarray analysis also identified several GadX-activated genes. Several genes induced by overexpression of YdeO and GadX overlapped; however, yhiE was induced only by YdeO. The acid resistance induced by YdeO overexpression was abolished by deletion of yhiE, gadC, slp-yhiF, hdeA or hdeD, genes induced by YdeO overexpression, suggesting that several genes orchestrate YdeO-induced acid resistance. We propose a model of the regulatory network of the acid resistance genes.

Acids↗
PubMed1994

Cloning and DNA sequence analysis of the region containing attP of the temperate phage phi AR29 of Prevotella ruminicola AR29.

Phage phi AR29 was shown to exist as a prophage integrated into the chromosome of Prevotella ruminicola AR29. By DNA hybridization studies, the point of integrative recombination on the phage genome (attP) was located on a 4.5 kb EcoRV fragment. After preliminary mapping with restriction endonucleases, a 2.8 kb EcoRV/HindIII fragment was isolated, cloned in Escherichia coli and sequenced. DNA hybridization localized the attP site to the vicinity of an internal DraI site. Sequence analysis showed the presence of several direct and inverted repeats around the attP site, with consensus core sequences similar to the integrase binding sites of phage lambda. Two open reading frames are present adjacent to attP (ORF1 and ORF2). The predicted polypeptide product of ORF1 has a region of structural similarity to known integrases. Although the predicted product of ORF2 shows at best weak homology with known excisionases, no other ORFs occur in the sequence upstream from ORF1, leaving ORF2 as the most likely candidate for this role. However, if ORF2 does represent an xis gene, then this putative integration module would possess a notable difference from that of other temperate phages in the inversion of the positions of int and xis relative to attP. The proposed phi AR29 integration module is being used to develop phage-based integrative vector systems for the genetic manipulation of rumen bacteria.

Amino Acid Sequence↗
PubMed1988

Location of the relaxation complex nick site within the minimal origin of transfer region of RK2.

Transfer of plasmid DNA during bacterial conjugation begins at a specific site: the origin of transfer (oriT). The oriT region of the broad host range plasmid RK2 is located on a 250 bp fragment. Deletions involving either end of this region reduce transfer function, indicating that an extended sequence is required for optimal oriT activity. The single-strand nick induced by the RK2 DNA-protein relaxation complex is located adjacent to the 19 bp inverted repeat within the minimal oriT sequence. These results provide strong evidence that the plasmid relaxation event induced in vitro represents the nicking reaction that initiates DNA transfer at oriT during conjugation.

DNA, Bacterial↗
PubMed2003

The IS1111 family members IS4321 and IS5075 have subterminal inverted repeats and target the terminal inverted repeats of Tn21 family transposons.

IS5075 and IS4321 are closely related (93.1% identical) members of the IS1111 family that target a specific position in the 38-bp terminal inverted repeats of Tn21 family transposons and that are inserted in only one orientation. They are 1,327 bp long and have identical ends consisting of short inverted repeats of 12 bp with an additional 7 bp (TAATGAG) or 6 bp (AATGAG) to the left of the left inverted repeats and 3 bp (AGA) or 4 bp (AGAT) to the right of the right inverted repeat. Circular forms of IS5075 and IS4321 in which the inverted repeats are separated by abutting terminal sequences (AGATAATGAG) were detected. A similar circular product was found for the related ISPa11. Transposition of IS4321 into the 38-bp target site was detected, but a flanking duplication was not generated. The precisely reconstituted target site was also identified. Over 50 members of the IS1111 family were identified. They encode related transposases, have related inverted repeats, and include related bases that lie outside these inverted repeats. In some, the flanking bases number 5 or 6 on the left and 4 or 3 on the right. Specific target sites were found for several of these insertion sequence (IS) elements. IS1111 family members therefore differ from the majority of IS elements, which are characterized by terminal inverted repeats and a target site duplication, and from members of the related IS110 family, which do not have obvious inverted repeats near their termini.

Amino Acid Sequence↗
PubMed1992

Organization of repeated sequences in the region downstream to rRNA genes in the rDNA episome of Entamoeba histolytica.

The E. histolytica rDNA episome consists of a 3.7 kb HindIII fragment located downstream of the rDNA inverted repeats. We have determined the complete nucleotide sequence of this fragment and have shown that it is comprised of two families of short tandem repeats, the 170 bp DraI repeat and the 144 bp ScaI repeat. Each DraI repeat unit consists of 12-mer sequences with near complete homology to yeast consensus autonomously replicating sequence. In addition, a 21-mer subrepeat structure is also present in each unit. The sequence of the ScaI repeat is about 90% homologous with the sequence of another family of 145 bp tandem repeats, the PvuI repeats reported to be present upstream of the rRNA genes (3). Compared with most other parts of the rDNA episome, the downstream region showed frequent restriction fragment length polymorphism. This was due to changes in the number of tandem DraI repeat units. The loss of these repeats might explain how rDNA length heterogeneity observed in the clones of HM1:IMSS could have arisen. On the other hand, the number of ScaI repeat units in these clones remained unchanged. The repeat units found in the 3.7 kb HindIII fragment show superficial resemblance to equivalent regions of the intergenic spacers of higher eukaryotes. Moreover, these repeated sequences seem to be specific for the pathogenic strain of E. histolytica.

Animals↗
PubMed1997

A Prevotella ruminicola B(1)4 operon encoding extracellular polysaccharide hydrolases.

When Escherichia coli XL1-Blue MRA (P2) was infected with lambda DNA containing Prevotella ruminicola B(1)4 chromosomal DNA, only a few plaques produced beta-1,4-endoglucanase activity, and all of these had mannanase activity. Positive phage contained a 17-kb SacI DNA fragment that gave six bands after EcoRI digestion. The EcoRI fragments were ligated into pBluescript and sequenced. The order of the fragments was verified by PCR and by restriction mapping. The DNA sequence contained 6 open reading frames (ORFs). The 4th and 5th ORFs encoded two related beta-1,4-endoglucanases. E. coli clones carrying ORF5 and ORF6 had beta-1,4-endoglucanase and mannanase activities, while a clone carrying only ORF6 hydrolyzed mannan but not carboxymethylcellulose. The 6th ORF had three regions of homology to mannanase A from Pseudomonas fluorescens. Based on these results, ORF6 encoded the mannanase gene. The 3rd ORF had 10 regions of homology with cellulose-binding protein A from Clostridium cellulovorans. The 1st and 2nd ORFs had no significant homology to genes or amino acid sequences in GeneBank or SwissProt. All of the ORFs except 1 encoded a potential signal peptide sequence. The upstream region of ORF1 contained four direct repeats and four inverted repeat elements, but no apparent sigma70 sequence-like promoter was present. The segment of DNA containing the 6 ORFs was preceded and followed by potential transcription termination signals suggesting a single transcriptional unit.

Amino Acid Sequence↗
PubMed1988

Helix stability and the mechanism of cruciform extrusion in supercoiled DNA molecules.

The kinetic properties of cruciform extrusion in supercoiled DNA molecules fall into two main classes. C-type cruciforms extrude in the absence of added salt, at relatively low temperatures, with large activation energies, while S-type cruciforms exhibit no extrusion in the absence of salt, and maximal rates at 50 mM NaCl, with activation energies about one quarter those of the C-type. These diverse properties are believed to reflect two distinct pathways for the extrusion process, and are determined by the nature of the sequences which form the context of the inverted repeat. C-type kinetics are conferred by A + T rich sequences, implying a role of helix stability in the selection. In this study we have shown that: 1. Helix-destabilising solvents (dimethyl formamide and formamide) facilitate extrusion by normally S-type molecules at low temperatures in the absence of salt. 2. C-type extrusion is strongly suppressed by low concentrations (2-4 microM) distamycin, at which concentrations S-type extrusion is enhanced. 3. Some extrusion occurs in a C-type construct in the presence of 50 mM NaCl. This is increased by addition of 3 microM distamycin, under which conditions extrusion becomes effectively S-type. Thus S-type constructs can behave in a quasi-C-type manner in the presence of helix-destabilising solvents, and C-type extrusion is suppressed by binding a compound which stabilises A + T rich regions of DNA. Helix destabilisation leads to C-type behaviour, while helix stabilisation results in S-type properties. These studies demonstrate the influence of contextual helix stability on the selection of kinetic mechanism of cruciform extrusion.

Bacteriocin Plasmids↗
PubMed2005

Binding and transcriptional activation of non-flagellar genes by the Escherichia coli flagellar master regulator FlhD2C2.

The gene hierarchy directing biogenesis of peritrichous flagella on the surface of Escherichia coli and other enterobacteria is controlled by the heterotetrameric master transcriptional regulator FlhD(2)C(2). To assess the extent to which FlhD(2)C(2) directly activates promoters of a wider regulon, a computational screen of the E. coli genome was used to search for gene-proximal DNA sequences similar to the 42-44 bp inverted repeat FlhD(2)C(2) binding consensus. This identified the binding sequences upstream of all eight flagella class II operons, and also putative novel FlhD(2)C(2) binding sites in the promoter regions of 39 non-flagellar genes. Nine representative non-flagellar promoter regions were all bound in vitro by active reconstituted FlhD(2)C(2) over the K(D) range 38-356 nM, and of the nine corresponding chromosomal promoter-lacZ fusions, those of the four genes b1904, b2446, wzz(fepE) and gltI showed up to 50-fold dependence on FlhD(2)C(2) in vivo. In comparison, four representative flagella class II promoters bound FlhD(2)C(2) in the K(D) range 12-43 nM and were upregulated in vivo 30- to 990-fold. The FlhD(2)C(2)-binding sites of the four regulated non-flagellar genes overlap by 1 or 2 bp the predicted -35 motif of the FlhD(2)C(2)-activated sigma(70) promoters, as is the case with FlhD(2)C(2)-dependent class II flagellar promoters. The data indicate a wider FlhD(2)C(2) regulon, in which non-flagellar genes are bound and activated directly, albeit less strongly, by the same mechanism as that regulating the flagella gene hierarchy.

Artificial Gene Fusion↗
PubMed1993

DNA sequence analysis of the major breakpoint cluster region of the BCR gene rearranged in Philadelphia-positive human leukemias.

We sought sequence characteristics that might explain the apparent high recombination frequency of the 5-kb BglII segment containing M-bcr exons 1, 2 and 3, and the intron to exon 4. An Alu sequence (subfamily Sx), in 5'-->3' orientation, lay in the middle of a 3-kb region that contains the great majority of Philadelphia chromosome breakpoint sites. The breakpoint of only one out of five chronic myeloid leukemia patients, for whom the BCR breakpoint site had been sequenced, was located within this Alu. Other features of interest for recombination were a 51-bp AT-rich region close to the 3' end, six hypervariable minisatellite consensus octamers, GC[A/T]GG[A/T]GG, six lymphoid recombinase heptamer signal sequences, one nonamer and a 16-bp inverted repeat. Dot matrix comparisons of the 5-kb M-bcr sequence with a 3-kb m-bcr2 segment showed significant homology only in corresponding Alu sequences.

Base Sequence↗
PubMed2005

Complete chloroplast genome sequence of Gycine max and comparative analyses with other legume genomes.

Lack of complete chloroplast genome sequences is still one of the major limitations to extending chloroplast genetic engineering technology to useful crops. Therefore, we sequenced the soybean chloroplast genome and compared it to the other completely sequenced legumes, Lotus and Medicago. The chloroplast genome of Glycine is 152,218 basepairs (bp) in length, including a pair of inverted repeats of 25,574 bp of identical sequence separated by a small single copy region of 17,895 bp and a large single copy region of 83,175 bp. The genome contains 111 unique genes, and 19 of these are duplicated in the inverted repeat (IR). Comparisons of Glycine, Lotus and Medicago confirm the organization of legume chloroplast genomes based on previous studies. Gene content of the three legumes is nearly identical. The rpl22 gene is missing from all three legumes, and Medicago is missing rps16 and one copy of the IR. Gene order in Glycine, Lotus, and Medicago differs from the usual gene order for angiosperm chloroplast genomes by the presence of a single, large inversion of 51 kilobases (kb). Detailed analyses of repeated sequences indicate that many of the Glycine repeats that are located in the intergenic spacer regions and introns occur in the same location in the other legumes and in Arabidopsis, suggesting that they may play some functional role. The presence of small repeats of psbA and rbcL in legumes that have lost one copy of the IR indicate that this loss has only occurred once during the evolutionary history of legumes.

Base Sequence↗
PubMed2006

Complete plastid genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms.

BACKGROUND: Carrot (Daucus carota) is a major food crop in the US and worldwide. Its capacity for storage and its lifecycle as a biennial make it an attractive species for the introduction of foreign genes, especially for oral delivery of vaccines and other therapeutic proteins. Until recently efforts to express recombinant proteins in carrot have had limited success in terms of protein accumulation in the edible tap roots. Plastid genetic engineering offers the potential to overcome this limitation, as demonstrated by the accumulation of BADH in chromoplasts of carrot taproots to confer exceedingly high levels of salt resistance. The complete plastid genome of carrot provides essential information required for genetic engineering. Additionally, the sequence data add to the rapidly growing database of plastid genomes for assessing phylogenetic relationships among angiosperms. RESULTS: The complete carrot plastid genome is 155,911 bp in length, with 115 unique genes and 21 duplicated genes within the IR. There are four ribosomal RNAs, 30 distinct tRNA genes and 18 intron-containing genes. Repeat analysis reveals 12 direct and 2 inverted repeats > or = 30 bp with a sequence identity > or = 90%. Phylogenetic analysis of nucleotide sequences for 61 protein-coding genes using both maximum parsimony (MP) and maximum likelihood (ML) were performed for 29 angiosperms. Phylogenies from both methods provide strong support for the monophyly of several major angiosperm clades, including monocots, eudicots, rosids, asterids, eurosids II, euasterids I, and euasterids II. CONCLUSION: The carrot plastid genome contains a number of dispersed direct and inverted repeats scattered throughout coding and non-coding regions. This is the first sequenced plastid genome of the family Apiaceae and only the second published genome sequence of the species-rich euasterid II clade. Both MP and ML trees provide very strong support (100% bootstrap) for the sister relationship of Daucus with Panax in the euasterid II clade. These results provide the best taxon sampling of complete chloroplast genomes and the strongest support yet for the sister relationship of Caryophyllales to the asterids. The availability of the complete plastid genome sequence should facilitate improved transformation efficiency and foreign gene expression in carrot through utilization of endogenous flanking sequences and regulatory elements.

Amino Acid Sequence↗
PubMed2001

Transposition of IS10 from the host Escherichia coli genome to a plasmid may lead to cloning artefacts.

During recloning of Nicotiana tabacum L. repetitive sequence R8.3 in Escherichia coli, a modified clone that differed from the original by the insertion of an IS10 sequence was unintentionally produced. The insert was flanked by a 9-bp direct repeat derived from the R8.3 sequence, the 9-bp duplication of acceptor DNA in the site of insertion being a characteristic of IS10 transposition events. A database search using the FASTA program showed IS10 and other prokaryotic IS elements inserted into numerous eukaryotic clones. Unexpectedly, the IS10, which is not a natural component of the E. coli genome, appeared to be by far the most frequent contaminant of DNA databases among several IS sequences tested. In the GenEMBL database, the IS10 query sequence yielded positive scores with more than 500 eukaryotic clones. Insertions of shortened IS10 sequences having only one intact terminal inverted repeat were commonly found. Most full-length IS10 insertions (32 out of 40 analyzed) were flanked by 9-bp direct repeats having the consensus 5'-NPuCNN-NGPyN-3' with a strong preference for 5'-TGCTNA-GNN-3'. One insertion was flanked by an inverted repeat of more than 400 bp in length. PCR amplification and Southern analysis revealed the presence of IS10 sequences in E. coli strains commonly used for DNA cloning, including some reported to be Tn10-free. No IS10-specific PCR product was obtained with N. tabacum or human DNA. Our data suggest that transposition of IS10 elements may accompany cloning steps, particularly into large BAC vectors. This might lead to the relatively frequent contamination of DNA databases by this bacterial sequence. It is estimated that one in approximately every thousand eukaryotic clone in the databases is contaminated by IS-derived sequences. We recommend checking submitted sequences for the presence of IS10 and other IS elements. In addition, DNA databases should be corrected by removing contaminating IS sequences.

Animals↗
PubMed1996

Novel role for Sp1 in phorbol ester enhancement of human platelet thromboxane receptor gene expression.

Expression of platelet thromboxane receptors is transcriptionally increased during megakaryocytic differentiation stimulated by phorbol 12-myristate 13-acetate (PMA). We previously cloned and characterized the promoter region of the human thromboxane receptor gene and localized PMA-responsive elements to a region between 1.84 and 1.95 kilobase pairs (kb) 5' of the transcription initiation site (D'Angelo, D. D., Davis, M. G., Houser, W. A., Eubank, J. J., Ritchie, M. E., and Dorn, G. W., II (1995) Circ. Res. 77, 466-474). Herein we report the localization of the PMA response element to a 14-nucleotide C-rich sequence, flanked by an octanucleotide inverted repeat, located -1.938 to -1.925 kb 5' of the transcription start site of this gene. We further identify the PMA-responsive enhancer factor that binds to this C-rich sequence as Sp1. Heterologous thromboxane receptor gene promoter/thymidilate kinase reporter constructs transfected into K562 cells exhibited PMA responsiveness when the C-rich element was included with additional 3' sequence from -1.924 to -1.84 kb. However, mutations of the C-rich element that disrupted a GC box located on the inverse strand eliminated PMA responsiveness and, in gel mobility shift assays, eliminated binding of Sp1. PMA treatment of K562 cells significantly increased, by 5-fold, Sp1 binding to the C-rich element and increased both phosphorylated and nonphosphorylated Sp1 protein levels by 2-fold. Furthermore, PMA treatment transiently increased Sp1 mRNA levels prior to increasing thromboxane receptor mRNA, suggesting that up-regulation of Sp1 contributes to up-regulation of thromboxane receptors. Finally, we have detected an unidentified K562 nuclear protein that binds specifically to the sense strand of the C-rich sequence overlapping the Sp1 binding site and that, by stabilizing a double stem-loop conformation of this DNA segment, may also play a role in Sp1 regulation of this gene. These studies are the first to describe regulatory and regulated roles for Sp1 in PMA-responsive gene expression and suggest that modulation of Sp1 levels controls thromboxane receptor expression during megakaryocytic differentiation.

Base Composition↗
PubMed1994

Transpogenes: the transposition-like integration of short sequence DNA into the yeast 2 micron plasmid creates the STB locus and plasmid-size polymorphism.

The type-2 2 mu plasmid of industrial yeast strains exhibits extensive size polymorphism in the STB (plasmid stability) locus and IR (inverted repeat)-right region. Comparative DNA sequence analyses of STB alleles identified a 38-bp sequence flanked by a 25-bp direct repeat as the underlying structural motif. Variable unequal recombination within the direct repeat accounted for the observed polymorphism of STB alleles. IR-right polymorphism was observed to result from tandem duplication of a 22-bp sequence flanked by a 9-bp direct repeat. The flanking direct repeats marked both loci as originating from the transposition-like integration of short DNA fragments. We call these structures transpogenes and note that these are hybrid structures of host and foreign DNA which can evolve into functional loci.

Base Sequence↗
PubMed2002

Genome analysis and strain comparison of correia repeats and correia repeat-enclosed elements in pathogenic Neisseria.

Whole genome sequences of Neisseria meningitidis strains Z2491 and MC58 and Neisseria gonorrhoeae FA1090 were analyzed for Correia repeats (CR) and CR-enclosed elements (CREE). A total of 533, 516, and 256 copies of CR and 270, 261, and 102 copies of CREE were found in these three genomes, respectively. The lengths of CREE range from 28 to 348 bp, and the lengths of multicopy CREE appear mainly in the ranges of 154 to 156 bp and 105 to 107 bp. The distribution of CREE lengths is similar between the two N. meningitidis genomes, with a greater number of 154- to 156-bp CREE (163 and 152 copies in N. meningitidis strain Z2491 and N. meningitidis strain MC58, respectively) than 105- to 107-bp CREE (72 and 77 copies). In the N. gonorrhoeae strain FA1090 genome there are relatively more 105- to 107-bp CREE (51 copies) than 154- to 156-bp CREE (36 copies). The genomic distribution of 107-bp CREE also shows similarity between the two N. meningitidis strains (15 copies share the same loci) and differences between N. meningitidis strains and N. gonorrhoeae FA1090 (only one copy is located in the same locus). Detailed sequence analysis showed that both the terminal inverted repeats and the core regions of CREE are composed of distinct basic sequence blocks. Direct TA dinucleotide repeats exist at the termini of all CREE. A survey of DNA sequence upstream of the sialyltransferase gene, lst, in several Neisseria isolates showed that 5 N. meningitidis strains contain a 107-bp CREE in this region but 25 N. gonorrhoeae strains show an exact absence of a 105-bp sequence block (i.e., the 107-bp CREE without a 5' TA dinucleotide) in the same region. Whole-genome sequence analysis confirmed that this 105-bp indel exists in many homologous 107-bp CREE loci. Thus, we postulate that all CREE are made of target TA with indels of various lengths. Analysis of 107-bp CREE revealed that they exist predominantly in intergenic regions and are often near virulence, metabolic, and transporter genes. The abundance of CREE in Neisseria genomes suggests that they may have played a role in genome organization, function, and evolution. Their differential distribution in different pathogenic Neisseria strains may contribute to the distinct behaviors of each Neisseria species.

Base Sequence↗
PubMed1991

Tc4, a Caenorhabditis elegans transposable element with an unusual fold-back structure.

We have identified and characterized a family of transposable elements in the nematode Caenorhabditis elegans. The Tc4 transposable element family is present at about 20 copies per haploid genome in the C. elegans Bristol and Bergerac strains. Although Tc4 transposition events have not been observed in these wild-type strains, we have identified Tc4 transposition events in the mut-2 mutant strain TR679, in which the elements Tc1 and Tc3 also transpose at a higher frequency than in the wild type. We determined the sequence of one Tc4 element. This 1.6-kilobase element contains almost perfect inverted terminal repeats of 774 base pairs (bp) with a 57-bp unique internal sequence. Tc4 is a fold-back element, but its long inverted terminal repeats, unlike those of the fold-back elements of other organisms, do not consist of multiple short repeats. In the two cases studied, Tc4 insertion resulted in duplication of a TNA trinucleotide target site. The family of Tc4 elements differs from other C. elegans transposable element families in structure, degree of structural heterogeneity, and target-site specificity.

Animals↗
PubMed1991

Codon usage and G + C content in Bradyrhizobium japonicum genes are not uniform.

To date, the sequences of 45 Bradyrhizobium japonicum genes are known. This provides sufficient information to determine their codon usage and G + C content. Surprisingly, B. japonicum nodulation and NifA-regulated genes were found to have a less biased codon usage and a lower G + C content than genes not belonging to these two groups. Thus, the coding regions of nodulation genes and NifA-regulated genes could hardly be identified in codon preference plots whereas this was not difficult with other genes. The codon frequency table of the highly biased genes was used in a codon preference plot to analyze the RSRj alpha 9 sequence which is an insertion sequence (IS)-like element. The plot helped identify a new open reading frame (ORF355) that escaped previous detection because of two sequencing errors. These were now corrected. The deduced gene product of ORF355 in RSRj alpha 9 showed extensive similarity to a putative protein encoded by an ORF in the T-DNA of Agrobacterium rhizogenes. The DNA sequences bordering both ORFs showed inverted repeats and potential target site duplications which supported the assumption that they were IS-like elements.

Amino Acid Sequence↗
PubMed2003

Spontaneous chromosome circularization and amplification of a new amplifiable unit of DNA belonging to the terminal inverted repeats in Streptomyces ambofaciens ATCC 23877.

In Streptomyces, the linear chromosomal DNA is highly unstable and undergoes large rearrangements usually at the extremities. These rearrangements consist of the deletion of several hundred kilobases, often associated with the amplification of an adjacent sequence, AUD ( amplifiable unit of DNA). In Streptomyces ambofaciens, two amplifiable regions (AUD6 and AUD90), located approximately 600 kb and 1,200 kb from the right chromosomal end respectively, have been characterized. Here, the isolation and molecular characterization of a new S. ambofaciens mutant strain exhibiting a green-pigmented phenotype is described; the wild-type produces a gray pigment. In this mutant, both chromosome ends were deleted, which probably led to circularization of the chromosome. These deletions were associated with amplification of a sequence belonging to the chromosomal terminal inverted repeats (TIRs), which might constitute the new fragment generated by the chromosomal circularization.

Bacterial Proteins↗