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Papers quoted in Current Contents on project 1-08-021


Quoted papers: 7
Other papers: 28
Total: 35


Title: Genetic instability and strain degeneration in Streptomyces rimosus

Authors:
Gravius, Birgit
Bezmalinović, Tajana (78374)
Hranueli, Daslav (16520)
Cullum, John
Journal: Appl. Environ. Microbiol.
Number: 7
ISSN: 0099-2240
Volume: 59
Year: 1993
Pages: from 2220 to 2228
Number of references: 35
Language: engleski
Summary: During the strain selection programme to improve oxytetracycline (OTC) production in Streptomyces rimosus R6 isolates appeared that showed extreme morphological instability. Propagation via spores gave much higher instability than for mycelial fragments. Five phenotypic traits were affected: sporulation, pigmentation, colony morphology, OTC-production and OTC-resistance. The variants were classified on the basis of OTC-resistance into three classes: Class I (99 % of variants) showed parental levels of resistance, but was very heterogeneous regarding the other phenotypes. No DNA rearrangements were detected in primary Class I variants. Class II (the OTC-sensitive variants) was phenotypically uniform and most variants carry the same large deletion of ca. 455 kb including the OTC-resistance gene otrB. Class III (increased OTC-resistance) is phenotypically uniform and the variants overproduce a brown pigment and OTC. Most of these variants also show a reproducible large scale DNA rearrangement, which probably includes deletion and a low level reiteration (3 to 4 copies) of a DNA fragment. "Revertants" of some Class I variants show a similar DNA rearrangement to the Class III variants, but there is extensive reiteration of sequences of about 200 kb including the otrB gene. The significance of these results for the problem of strain degeneration and overproduction of antibiotics is discussed.
Keywords: DNA amplification, Genome plasticity, Streptomyces lividans 66, Resistance, Oxytetracycline, Streptomyces glaucescens, Deletions, Biosynthesis, Streptomyces ambofaciens, Sequence

Title: Analysis of secondary integration sites for IS117 in Streptomyces lividans and their role in the generation of chromosomal deletions

Authors:
Smokvina, Tamara (111104)
Hopwood, David A.
Journal: Mol. Gen. Genet.
Number: 1-2
ISSN: 0940-9653
Volume: 239
Year: 1993
Pages: from 90 to 96
Number of references: 32
Language: engleski
Summary: IS117, the 2.6 kb mini-circle of S. coelicolor A3(2), is a transposable element previously shown to be integrated into two distant sites in the chromosome. When introduced into S. lividans, IS117 integrates into one preferred chromosomal site, but when this site was artificially deleted, IS117 integrated into many secondary sites. Nucleotide sequence analysis of several secondary integration sites revealed varying degrees of similarity with the preferred site, but no consensus sequence. Nevertheless, sites more similar to the preferred site tended to be occupied more often than those that are less similar. Insertion of IS117 into secondary sites in the chromosome of S. lividans sometimes mediated chromosomal rearrangements. It was shown that some strains containing IS117 integrated into secondary sites had suffered deletions of chromosomal DNA. Deletions were adjacent to the inserted element and were at least several kilobases long. The proposed model implicates homologous recombination between IS117 copies integrated into two different secondary sites in the same chromosome as a cause of the deletions.
Keywords: Mini-circle, transposable element, genetic instability, Streptomyces coelicolor A3(2), Target site, Sequence, Rearrangement, Tn10, DNA

Title: The temperate phages RP2 and RP3 of Streptomyces rimosus

Authors:
Rausch, Helmut
Vešligaj, Margareta (51960)
Počta, Darko
Biuković, Goran (172863)
Pigac, Jasenka (37185)
Cullum, John
Schmieger, Horst
Hranueli, Daslav (16520)
Journal: J. Gen. Microbiol.
Number: 10
ISSN: 0022-1287
Volume: 139
Year: 1993
Pages: from 2517 to 2524
Number of references: 37
Language: engleski
Summary: The oxytetracycline producing Streptomyces rimosus strains R6-65 and R7 (ATCC10970) are lysogenic for the two narrow host-range phages RP2 and RP3. Both phages are released at low frequency from the lysogenic strains and form plaques on "cured" S. rimosus strains. RP2 and RP3 are of similar shape with flexible tails and contain double-stranded DNA of about 70 % G+C with cohesive ends (group B1 of bacteriophage classification). The two phages also have identical, very slow, growth kinetics in S. rimosus, with a latent phase of about 6 h and a rise period of about 4 h. RP2 and RP3 are heteroimmune and they differ slightly in their size of phage particles and length of DNA (64.7 and 62.4 kb for RP2 and RP3, respectively). The restriction maps of the two phages are completely different, and hybridization experiments showed only one short region of sequence similarity (less than 430 bp); the two phages are thus essentially unrelated. Both phages lysogenize their hosts by recombination via defined attachment (att) sites. The positions of the attP sites have been localized on the restriction maps of RP2 and RP3 to restriction fragments of 800 and 300 bp, respectively. The prophages did not affect the level of oxytetracycline production or the genetic instability of this trait.
Keywords: Oxytetracycline biosynthesis, Cloning vectors, Streptomyces lividans, Plasnid, Genes, Site, Construction, DNA

Title: High G+C-content DNA markers for pulsed-field electrophoresis

Authors:
Gravius, Birgit
Cullum, John
Hranueli, Daslav (16520)
Journal: BioTechniques
Number: 1
ISSN: 0736-6205
Volume: 16
Year: 1994
Pages: from 52 to 52
Number of references: 9
Language: engleski
Summary: It has been suggested that G + C-content has an influence on the migration of DNA molecules in pulsed-field electrophoresis. Streptomyces species have a G + C-content of 70 - 74 %, probably the highest among prokaryotes. During work to establish a restriction map of a giant linear plasmid in S. rimosus, we encountered discrepancies when lambda ladder markers were used. We, therefore, examined the possibility of alternative high G + C-content markers. For this purpose, the temperate phages RP2 and RP3 of S. rimosus were considered. Their G + C-content is similar to chromosomal DNA and they have cohesive ends. In initial experiments, RP2 and RP3 DNA was embedded in agarose blocks and ladder formation was achieved by ligation. Later, phage particles were embedded in agarose and, after in situ DNA preparation, ladders were formed by spontaneous association. The ladders were examined by pulsed-field electrophoresis and compared to lambda ladder and Saccharomyces cerevisiae chromosome markers. The spontaneous association gave better results with less DNA degradation than the ligation procedure. An example of such a gel is shown in Fig. 1. RP2 and RP3 have sizes of 64.7 kb and 62.4 kb respectively. It can be seen in Fig. 1 that, particularly for lower molecular weight fragments, the high G + C-content molecules migrate faster than the lambda molecules (50 % G + C). Data was obtained for RP2 ladders from seven gels and for RP3 ladders from six gels run under the conditions in Fig. 1. In some cases, up to 10-mers of the phages ladders could be obtained. The apparent sizes of the RP2 and RP3 ladders (Y) were estimated from lambda ladder markers and these sizes were compared to the true sizes (X). These data gave a good fit with linear regression and there was no significant difference between RP2 and RP3, suggesting that G + C-content rather than specific sequence is important (RP2 and RP3 show little homology). The best fit linear regression line was: Y = 0.96 X - 18. Thus, the sizes of the G + C-rich fragments are all underestimated, but the relative error falls from over 30 % (for a 60 kb fragment) to 7.5 % (for a 500 kb fragment). These will lead to underestimates of genome sizes. A computer program was written to simulate this effect with an 8 Mb genome containing random restriction sites. When 15 sites were present an underestimate of about 7 % occurred, whereas this underestimate rose to 11 % with 30 sites. It appears that the pulse program used can affect the relative migration of G + C-rich fragments relative to lambda ladders. It is thus important to use appropriate marker molecules, when using pulsed-field electrophoresis to map G + C-rich DNA. Lower molecular weight ranges can be estimated using restriction digests of RP2 DNA: e.g., EcoRV gives four fragments of 30.0, 21.1, 12.1 and 1.5 kb. Other Streptomyces phages may also prove useful as markers (e.g. ŘC31 has cohesive ends and a G + C-content of 60 %).
Keywords: Pulsed-field gel electrophoresis, High G+C-content DNA markers, Bacteriophages, Lambda ladder, Actinophages, RP2 and RP3 ladders

Title: The 387 kb linear plasmid pPZG101 of Streptomyces rimosus and its interactions with the chromosome

Authors:
Gravius, Birgit
Glocker, Digna
Pigac, Jasenka (37185)
Pandža, Kenan
Hranueli, Daslav (16520)
Cullum, John
Journal: Microbiol.
Number: 9
ISSN: 1350-0872
Volume: 140
Year: 1994
Pages: from 2271 to 2277
Number of references: 34
Language: engleski
Summary: The linear plasmid of Streptomyces rimosus R6 was restriction mapped with the enzymes AseI, BfrI, DraI and XbaI. It is 387 kb in size and the ends are inverted repeats of at least 95 kb in length. Twenty spontaneous morphological variants and seventeen auxotrophic mutants were screened for changes in the plasmid. Two strains were found that had lost all plasmid sequences. Four strains had integrated parts of the plasmid into the chromosome. Restriction analysis suggested that at least three of the integrated strains had retained free plasmid ends. If it is assumed that the chromosome of S. rimosus R6 is linear, this might be explained by replacement of one or both chromsome ends by a plasmid end. One strain, which overproduced oxytetracycline, carried an enlarged linear plasmid of 1 Mb in size that had acquired chromosomal sequences from the oxytetracycline biosynthesis cluster.
Keywords: Nucleotide-sequence, Molecular-cloning, Streptomyces coelicolor A3(2), DNA plasmid, SCP1, Oxytetracycline, Genes, Biosynthesis, Expression, Streptomyces lividans

Title: Sequence analysis of cohesive ends of the actinophage RP3 genome and construction of a transducible shuttle vector

Authors:
Kinner, E
Počta, Darko
Stroer, S
Schmieger, H
Journal: FEMS Microbiol. Lett.
ISSN: 0378-1097
Volume: 118
Year: 1994
Pages: from 283 to 290
Number of references: 20
Language: engleski
Summary: The sequence of the cohesive ends of actinophage RP3 DNA has been determined. As with all other phages of Gram-positive bacteria that have been studied so far, RP3 DNA has 3'-protruding ends. A shutle cosmid has been constructed containing this cos area which can be efficiently transduced by phage RP3 to host cells of Streptomyces rimosus.
Keywords: Actinophage, cos site, Cohesive end, Transduction

Title: The actinophage RP3 DNA integrates site-specifically into the putative tRNA ARG (AGG) gene of Streptomyces rimosus

Authors:
Gabriel, K
Schmid, H
Rausch, Helmut
Journal: Nucleic. Acids Res.
Number: 1
ISSN: 0305-1048
Volume: 23
Year: 1995
Pages: from 58 to 63
Number of references: 34
Language: engleski
Summary: The temperate actinophage RP3 integrates site-specifically into the chromosome of Streptomyces rimosus R6-554. The phage attachment site attP and the hybrid attachment sites of the integrated prophage - attL and attR - were cloned and sequenced. The 54nt core sequence, common to all RP3 related attachment sites, comprises the 3' terminal end of a putative tRNA(Arg)(AGG) gene. AttB bears the complete tRNA gene which is restored in attL after integration, A 7.5kb HindIII fragment, bearing attP was used to construct an integrative plasmid to simulate the integration process in vivo and to localize the phage genes necessary for site specific integration. The int and xis genes were sequenced and compared to other recombination genes.
Keywords: Staphylococcal bacteriophage L54A, Nucleotide sequences, Escherichia coli, Plasmid, Recombination, Vectors, Cloning, Phage, Compilation, Streptomyces lividans


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