Abstract
Multicopy single-stranded DNA is found as a small single-stranded RNA-DNA complex in certain wild-type strains of Escherichia coli as well as in other gram-negative bacteria. Using the promoter region of the previously characterized retron-Ec107 from E. coli ECOR70, I constructed a chromosomally located lacZ operon fusion. Examination of expression from the PEc107 promoter showed that activity increased sharply when cells entered stationary phase in rich medium or when they were starved for phosphate. The nucleotide guanosine-3',5'-bispyrophosphate was found to be a positive regulator of retron-Ec107 expression. Its presence is required for starvation-induced transcription of retron-Ec107 and multicopy single-stranded DNA production. It was also found that expression from the retron promoter is independent of the sigma factor sigmaS.
Full Text
The Full Text of this article is available as a PDF (390.9 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Bohannon D. E., Connell N., Keener J., Tormo A., Espinosa-Urgel M., Zambrano M. M., Kolter R. Stationary-phase-inducible "gearbox" promoters: differential effects of katF mutations and role of sigma 70. J Bacteriol. 1991 Jul;173(14):4482–4492. doi: 10.1128/jb.173.14.4482-4492.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chomczynski P., Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987 Apr;162(1):156–159. doi: 10.1006/abio.1987.9999. [DOI] [PubMed] [Google Scholar]
- Dhundale A., Lampson B., Furuichi T., Inouye M., Inouye S. Structure of msDNA from Myxococcus xanthus: evidence for a long, self-annealing RNA precursor for the covalently linked, branched RNA. Cell. 1987 Dec 24;51(6):1105–1112. doi: 10.1016/0092-8674(87)90596-4. [DOI] [PubMed] [Google Scholar]
- Donnenberg M. S., Kaper J. B. Construction of an eae deletion mutant of enteropathogenic Escherichia coli by using a positive-selection suicide vector. Infect Immun. 1991 Dec;59(12):4310–4317. doi: 10.1128/iai.59.12.4310-4317.1991. [DOI] [PMC free article] [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]
- Gentry D. R., Cashel M. Cellular localization of the Escherichia coli SpoT protein. J Bacteriol. 1995 Jul;177(13):3890–3893. doi: 10.1128/jb.177.13.3890-3893.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gentry D. R., Hernandez V. J., Nguyen L. H., Jensen D. B., Cashel M. Synthesis of the stationary-phase sigma factor sigma s is positively regulated by ppGpp. J Bacteriol. 1993 Dec;175(24):7982–7989. doi: 10.1128/jb.175.24.7982-7989.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hernandez V. J., Bremer H. Escherichia coli ppGpp synthetase II activity requires spoT. J Biol Chem. 1991 Mar 25;266(9):5991–5999. [PubMed] [Google Scholar]
- Herzer P. J., Inouye S., Inouye M. Retron-Ec107 is inserted into the Escherichia coli genome by replacing a palindromic 34bp intergenic sequence. Mol Microbiol. 1992 Feb;6(3):345–354. doi: 10.1111/j.1365-2958.1992.tb01477.x. [DOI] [PubMed] [Google Scholar]
- Herzer P. J., Inouye S., Inouye M., Whittam T. S. Phylogenetic distribution of branched RNA-linked multicopy single-stranded DNA among natural isolates of Escherichia coli. J Bacteriol. 1990 Nov;172(11):6175–6181. doi: 10.1128/jb.172.11.6175-6181.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Inouye M., Inouye S. Retrons and multicopy single-stranded DNA. J Bacteriol. 1992 Apr;174(8):2419–2424. doi: 10.1128/jb.174.8.2419-2424.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Inouye S., Herzer P. J., Inouye M. Two independent retrons with highly diverse reverse transcriptases in Myxococcus xanthus. Proc Natl Acad Sci U S A. 1990 Feb;87(3):942–945. doi: 10.1073/pnas.87.3.942. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Inouye S., Inouye M. The retron: a bacterial retroelement required for the synthesis of msDNA. Curr Opin Genet Dev. 1993 Oct;3(5):713–718. doi: 10.1016/s0959-437x(05)80088-7. [DOI] [PubMed] [Google Scholar]
- Kawaguchi T., Herzer P. J., Inouye M., Inouye S. Sequence diversity of the 1.3 kb retron (retron-Ec107) among three distinct phylogenetic groups of Escherichia coli. Mol Microbiol. 1992 Feb;6(3):355–361. doi: 10.1111/j.1365-2958.1992.tb01478.x. [DOI] [PubMed] [Google Scholar]
- Lampson B. C., Inouye M., Inouye S. Survey of multicopy single-stranded DNAs and reverse transcriptase genes among natural isolates of Myxococcus xanthus. J Bacteriol. 1991 Sep;173(17):5363–5370. doi: 10.1128/jb.173.17.5363-5370.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lampson B. C., Inouye S., Inouye M. msDNA of bacteria. Prog Nucleic Acid Res Mol Biol. 1991;40:1–24. doi: 10.1016/s0079-6603(08)60838-7. [DOI] [PubMed] [Google Scholar]
- Lampson B. C., Sun J., Hsu M. Y., Vallejo-Ramirez J., Inouye S., Inouye M. Reverse transcriptase in a clinical strain of Escherichia coli: production of branched RNA-linked msDNA. Science. 1989 Feb 24;243(4894 Pt 1):1033–1038. doi: 10.1126/science.2466332. [DOI] [PubMed] [Google Scholar]
- Lampson B. C., Viswanathan M., Inouye M., Inouye S. Reverse transcriptase from Escherichia coli exists as a complex with msDNA and is able to synthesize double-stranded DNA. J Biol Chem. 1990 May 25;265(15):8490–8496. [PubMed] [Google Scholar]
- Lange R., Fischer D., Hengge-Aronis R. Identification of transcriptional start sites and the role of ppGpp in the expression of rpoS, the structural gene for the sigma S subunit of RNA polymerase in Escherichia coli. J Bacteriol. 1995 Aug;177(16):4676–4680. doi: 10.1128/jb.177.16.4676-4680.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lange R., Hengge-Aronis R. Growth phase-regulated expression of bolA and morphology of stationary-phase Escherichia coli cells are controlled by the novel sigma factor sigma S. J Bacteriol. 1991 Jul;173(14):4474–4481. doi: 10.1128/jb.173.14.4474-4481.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lange R., Hengge-Aronis R. The cellular concentration of the sigma S subunit of RNA polymerase in Escherichia coli is controlled at the levels of transcription, translation, and protein stability. Genes Dev. 1994 Jul 1;8(13):1600–1612. doi: 10.1101/gad.8.13.1600. [DOI] [PubMed] [Google Scholar]
- Lerner C. G., Inouye M. Low copy number plasmids for regulated low-level expression of cloned genes in Escherichia coli with blue/white insert screening capability. Nucleic Acids Res. 1990 Aug 11;18(15):4631–4631. doi: 10.1093/nar/18.15.4631. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lim D., Maas W. K. Reverse transcriptase-dependent synthesis of a covalently linked, branched DNA-RNA compound in E. coli B. Cell. 1989 Mar 10;56(5):891–904. doi: 10.1016/0092-8674(89)90693-4. [DOI] [PubMed] [Google Scholar]
- McCann M. P., Kidwell J. P., Matin A. The putative sigma factor KatF has a central role in development of starvation-mediated general resistance in Escherichia coli. J Bacteriol. 1991 Jul;173(13):4188–4194. doi: 10.1128/jb.173.13.4188-4194.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Metzger S., Sarubbi E., Glaser G., Cashel M. Protein sequences encoded by the relA and the spoT genes of Escherichia coli are interrelated. J Biol Chem. 1989 Jun 5;264(16):9122–9125. [PubMed] [Google Scholar]
- Neidhardt F. C., Bloch P. L., Smith D. F. Culture medium for enterobacteria. J Bacteriol. 1974 Sep;119(3):736–747. doi: 10.1128/jb.119.3.736-747.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ochman H., Selander R. K. Standard reference strains of Escherichia coli from natural populations. J Bacteriol. 1984 Feb;157(2):690–693. doi: 10.1128/jb.157.2.690-693.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Prentki P., Krisch H. M. In vitro insertional mutagenesis with a selectable DNA fragment. Gene. 1984 Sep;29(3):303–313. doi: 10.1016/0378-1119(84)90059-3. [DOI] [PubMed] [Google Scholar]
- Rice S. A., Bieber J., Chun J. Y., Stacey G., Lampson B. C. Diversity of retron elements in a population of rhizobia and other gram-negative bacteria. J Bacteriol. 1993 Jul;175(13):4250–4254. doi: 10.1128/jb.175.13.4250-4254.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Rice S. A., Lampson B. C. Phylogenetic comparison of retron elements among the myxobacteria: evidence for vertical inheritance. J Bacteriol. 1995 Jan;177(1):37–45. doi: 10.1128/jb.177.1.37-45.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schreiber G., Metzger S., Aizenman E., Roza S., Cashel M., Glaser G. Overexpression of the relA gene in Escherichia coli. J Biol Chem. 1991 Feb 25;266(6):3760–3767. [PubMed] [Google Scholar]
- Shimamoto T., Inouye M., Inouye S. The formation of the 2',5'-phosphodiester linkage in the cDNA priming reaction by bacterial reverse transcriptase in a cell-free system. J Biol Chem. 1995 Jan 13;270(2):581–588. doi: 10.1074/jbc.270.2.581. [DOI] [PubMed] [Google Scholar]
- Simons R. W., Houman F., Kleckner N. Improved single and multicopy lac-based cloning vectors for protein and operon fusions. Gene. 1987;53(1):85–96. doi: 10.1016/0378-1119(87)90095-3. [DOI] [PubMed] [Google Scholar]
- Singer M., Kaiser D. Ectopic production of guanosine penta- and tetraphosphate can initiate early developmental gene expression in Myxococcus xanthus. Genes Dev. 1995 Jul 1;9(13):1633–1644. doi: 10.1101/gad.9.13.1633. [DOI] [PubMed] [Google Scholar]
- Svitil A. L., Cashel M., Zyskind J. W. Guanosine tetraphosphate inhibits protein synthesis in vivo. A possible protective mechanism for starvation stress in Escherichia coli. J Biol Chem. 1993 Feb 5;268(4):2307–2311. [PubMed] [Google Scholar]
- Tanaka K., Takayanagi Y., Fujita N., Ishihama A., Takahashi H. Heterogeneity of the principal sigma factor in Escherichia coli: the rpoS gene product, sigma 38, is a second principal sigma factor of RNA polymerase in stationary-phase Escherichia coli. Proc Natl Acad Sci U S A. 1993 Apr 15;90(8):3511–3515. doi: 10.1073/pnas.90.8.3511. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Temin H. M. Reverse transcriptases. Retrons in bacteria. Nature. 1989 May 25;339(6222):254–255. doi: 10.1038/339254a0. [DOI] [PubMed] [Google Scholar]
- Vieira J., Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 1982 Oct;19(3):259–268. doi: 10.1016/0378-1119(82)90015-4. [DOI] [PubMed] [Google Scholar]
- Viswanathan M., Inouye M., Inouye S. Myxococcus xanthus msDNA.Mx162 exists as a complex with proteins. J Biol Chem. 1989 Aug 15;264(23):13665–13671. [PubMed] [Google Scholar]
- Xiao H., Kalman M., Ikehara K., Zemel S., Glaser G., Cashel M. Residual guanosine 3',5'-bispyrophosphate synthetic activity of relA null mutants can be eliminated by spoT null mutations. J Biol Chem. 1991 Mar 25;266(9):5980–5990. [PubMed] [Google Scholar]