Abstract
Amycolatopsis methanolica contains a 13.3-kb plasmid (pMEA300) that is present either as an integrated element or as an autonomously replicating plasmid. Conjugational transfer of pMEA300 results in pock formation, zones of growth inhibition that become apparent when plasmid-carrying donor cells develop in a confluent lawn of plasmid-lacking recipient cells. A 6.2-kb pMEA300 DNA region specifying the functions of conjugation and pock formation was sequenced, revealing 10 open reading frames. This is the first sequence of the transfer region of a plasmid from a nonstreptomycete actinomycete. No clear similarities were found between the deduced sequences of the 10 putative Tra proteins of pMEA300 and those of Streptomyces plasmids. All Tra proteins of pMEA300 thus may represent unfamiliar types. A detailed mutational analysis showed that at least four individual proteins, TraG (9,488 Da), TraH (12,586 Da), TraI (40,468 Da), and TraJ (81,109 Da), are required for efficient transfer of pMEA300. Their disruption resulted in a clear reduction in the conjugational transfer frequencies, ranging from (5.2 x 10(1))-fold (TraG) to (2.3 x 10(6))-fold (TraJ), and in reduced pock sizes. At least two putative proteins, TraA (10,698 Da) and TraB (31,442 Da), were shown to be responsible for pock formation specifically. Specific binding of the pMEA300-encoded KorA protein to the traA-korA intragenic region was observed.
Full Text
The Full Text of this article is available as a PDF (375.1 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
- Bibb M. J., Ward J. M., Kieser T., Cohen S. N., Hopwood D. A. Excision of chromosomal DNA sequences from Streptomyces coelicolor forms a novel family of plasmids detectable in Streptomyces lividans. Mol Gen Genet. 1981;184(2):230–240. doi: 10.1007/BF00272910. [DOI] [PubMed] [Google Scholar]
- Boccard F., Smokvina T., Pernodet J. L., Friedmann A., Guérineau M. The integrated conjugative plasmid pSAM2 of Streptomyces ambofaciens is related to temperate bacteriophages. EMBO J. 1989 Mar;8(3):973–980. doi: 10.1002/j.1460-2075.1989.tb03460.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Brolle D. F., Pape H., Hopwood D. A., Kieser T. Analysis of the transfer region of the Streptomyces plasmid SCP2. Mol Microbiol. 1993 Oct;10(1):157–170. doi: 10.1111/j.1365-2958.1993.tb00912.x. [DOI] [PubMed] [Google Scholar]
- Brown D. P., Idler K. B., Katz L. Characterization of the genetic elements required for site-specific integration of plasmid pSE211 in Saccharopolyspora erythraea. J Bacteriol. 1990 Apr;172(4):1877–1888. doi: 10.1128/jb.172.4.1877-1888.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chung C. T., Niemela S. L., Miller R. H. One-step preparation of competent Escherichia coli: transformation and storage of bacterial cells in the same solution. Proc Natl Acad Sci U S A. 1989 Apr;86(7):2172–2175. doi: 10.1073/pnas.86.7.2172. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Cohen A., Bar-Nir D., Goedeke M. E., Parag Y. The integrated and free states of Streptomyces griseus plasmid pSG1. Plasmid. 1985 Jan;13(1):41–50. doi: 10.1016/0147-619x(85)90054-x. [DOI] [PubMed] [Google Scholar]
- Fellay R., Frey J., Krisch H. Interposon mutagenesis of soil and water bacteria: a family of DNA fragments designed for in vitro insertional mutagenesis of gram-negative bacteria. Gene. 1987;52(2-3):147–154. doi: 10.1016/0378-1119(87)90041-2. [DOI] [PubMed] [Google Scholar]
- Gorbalenya A. E., Koonin E. V., Donchenko A. P., Blinov V. M. Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Res. 1989 Jun 26;17(12):4713–4730. doi: 10.1093/nar/17.12.4713. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hagège J., Boccard F., Smokvina T., Pernodet J. L., Friedmann A., Guérineau M. Identification of a gene encoding the replication initiator protein of the Streptomyces integrating element, pSAM2. Plasmid. 1994 Mar;31(2):166–183. doi: 10.1006/plas.1994.1018. [DOI] [PubMed] [Google Scholar]
- Hagège J., Pernodet J. L., Sezonov G., Gerbaud C., Friedmann A., Guérineau M. Transfer functions of the conjugative integrating element pSAM2 from Streptomyces ambofaciens: characterization of a kil-kor system associated with transfer. J Bacteriol. 1993 Sep;175(17):5529–5538. doi: 10.1128/jb.175.17.5529-5538.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hopwood D. A., Hintermann G., Kieser T., Wright H. M. Integrated DNA sequences in three streptomycetes form related autonomous plasmids after transfer to Streptomyces lividans. Plasmid. 1984 Jan;11(1):1–16. doi: 10.1016/0147-619x(84)90002-7. [DOI] [PubMed] [Google Scholar]
- Kataoka M., Kiyose Y. M., Michisuji Y., Horiguchi T., Seki T., Yoshida T. Complete nucleotide sequence of the Streptomyces nigrifaciens plasmid, pSN22: genetic organization and correlation with genetic properties. Plasmid. 1994 Jul;32(1):55–69. doi: 10.1006/plas.1994.1044. [DOI] [PubMed] [Google Scholar]
- Kataoka M., Kosono S., Seki T., Yoshida T. Regulation of the transfer genes of Streptomyces plasmid pSN22: in vivo and in vitro study of the interaction of TraR with promoter regions. J Bacteriol. 1994 Dec;176(23):7291–7298. doi: 10.1128/jb.176.23.7291-7298.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kendall K. J., Cohen S. N. Complete nucleotide sequence of the Streptomyces lividans plasmid pIJ101 and correlation of the sequence with genetic properties. J Bacteriol. 1988 Oct;170(10):4634–4651. doi: 10.1128/jb.170.10.4634-4651.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kendall K. J., Cohen S. N. Plasmid transfer in Streptomyces lividans: identification of a kil-kor system associated with the transfer region of pIJ101. J Bacteriol. 1987 Sep;169(9):4177–4183. doi: 10.1128/jb.169.9.4177-4183.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Klein P., Kanehisa M., DeLisi C. The detection and classification of membrane-spanning proteins. Biochim Biophys Acta. 1985 May 28;815(3):468–476. doi: 10.1016/0005-2736(85)90375-x. [DOI] [PubMed] [Google Scholar]
- Moretti P., Hintermann G., Hütter R. Isolation and characterization of an extrachromosomal element from Nocardia mediterranei. Plasmid. 1985 Sep;14(2):126–133. doi: 10.1016/0147-619x(85)90072-1. [DOI] [PubMed] [Google Scholar]
- Pernodet J. L., Simonet J. M., Guérineau M. Plasmids in different strains of Streptomyces ambofaciens: free and integrated form of plasmid pSAM2. Mol Gen Genet. 1984;198(2):35–41. doi: 10.1007/BF00328697. [DOI] [PubMed] [Google Scholar]
- Seifert H. S., Chen E. Y., So M., Heffron F. Shuttle mutagenesis: a method of transposon mutagenesis for Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1986 Feb;83(3):735–739. doi: 10.1073/pnas.83.3.735. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Shields D. C., Higgins D. G., Sharp P. M. GCWIND: a microcomputer program for identifying open reading frames according to codon positional G+C content. Comput Appl Biosci. 1992 Oct;8(5):521–523. doi: 10.1093/bioinformatics/8.5.521. [DOI] [PubMed] [Google Scholar]
- Strohl W. R. Compilation and analysis of DNA sequences associated with apparent streptomycete promoters. Nucleic Acids Res. 1992 Mar 11;20(5):961–974. doi: 10.1093/nar/20.5.961. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Vrijbloed J. W., Madoń J., Dijkhuizen L. A plasmid from the methylotrophic actinomycete Amycolatopsis methanolica capable of site-specific integration. J Bacteriol. 1994 Nov;176(22):7087–7090. doi: 10.1128/jb.176.22.7087-7090.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Walker J. E., Saraste M., Runswick M. J., Gay N. J. Distantly related sequences in the alpha- and beta-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1982;1(8):945–951. doi: 10.1002/j.1460-2075.1982.tb01276.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wright F., Bibb M. J. Codon usage in the G+C-rich Streptomyces genome. Gene. 1992 Apr 1;113(1):55–65. doi: 10.1016/0378-1119(92)90669-g. [DOI] [PubMed] [Google Scholar]
- Zotchev S. B., Soldatova L. I., Orekhov A. V., Schrempf H. Characterization of a linear extrachromosomal DNA element (pBL1) isolated after interspecific mating between Streptomyces bambergiensis and S. lividans. Res Microbiol. 1992 Nov-Dec;143(9):839–845. doi: 10.1016/0923-2508(92)90071-u. [DOI] [PubMed] [Google Scholar]
- de Boer L., Dijkhuizen L., Grobben G., Goodfellow M., Stackebrandt E., Parlett J. H., Whitehead D., Witt D. Amycolatopsis methanolica sp. nov., a facultatively methylotrophic actinomycete. Int J Syst Bacteriol. 1990 Apr;40(2):194–204. doi: 10.1099/00207713-40-2-194. [DOI] [PubMed] [Google Scholar]