Analysis of DNA transcription termination sequences of gene coding for phaC1 polymerase in Pseudomonas species

• Autorzy: Możejko J. , Królicka M. , Ciesielski S.
• Języki publikacji: EN

Abstrakty

EN

Polyhydroxyalkanoates (PHAs) are natural polyesters that are synthesized by many bacteria as an intracellular carbon and energy compound. Medium-chain-length polyhydroxyalkanoates (mcl-PHAs) have gained much interest in research on microbial biopolymers because of their ease of chemical modification. Mcl-PHAs are naturally synthesized by Pseudomonas species by transformation of wide range of substrates. The physiological background of mcl-PHAs synthesis is known, and key genes engaged in this process are discovered already, but the knowledge about their molecular regulation is still limited. Especially, there is lack of information concerning the transcription termination of gene coding for PHA polymerase (phaC1). It is assumed that the main role could play Rho-independent termination, which is related to presence of palindromic sequences, which leads to formation of the hairpin structure and to dissociation of the ternary elongation complex (TEC). In this work, DNA sequences located after phaC1 gene belonging to nineteen Pseudomonas strains were investigated. Among all analyzed strains, five had palindromic sequences, typical for Rhoindependent terminators. Our results proved, that gene phaC1, coding for PHA polymerase, can be independently regulated only in some species.

Słowa kluczowe

EN

polyhydroxyalkanoates; Pseudomonas; sequence analysis; transcription terminator

PL

polihydroksykwasy; Pseudomonas; analiza sekwencji; terminator transkrypcji

• Wydawca: University of Warmia and Mazury in Olsztyn, Poland
• Czasopismo: Environmental Biotechnology
• Rocznik: 2011
• Tom: Vol. 7, No. 1
• Strony: 12--16
• Opis fizyczny: Bibliogr. 23 poz., rys., tab.

Twórcy

autor

Możejko J.

autor

Królicka M.

autor

Ciesielski S.

• Department of Environmental Biotechnology, University of Warmia and Mazury in Olsztyn, Słoneczna 45G, 10-718 Olsztyn, Poland, phone: (+48) (89) 5234144, FAX: (+48) (89) 5234131,

Bibliografia

• Artsimovitch, I., R. Landick. 1998. Interaction of a nascent RNA structure with RNA polymerase is required for hairpin-dependent transcriptional pausing but not for transcript release. Genes & Development 12: 3110-3122.
• Brodsky, L.I., A.V. Vasilyev, Y.L. Kalaydzidis, Y.S. Osipov, A.R.L. Tatuzov, S.I. Feranchuk. 1992. GeneBee: the Program Package for Biopolymer Structure Analysis. Dimacs 8: 127-139.
• Ciesielski, S., A. Cydzik-Kwiatkowska, T. Pokoj, E. Klimiuk. 2006. Molecular detection and diversity of medium-chain-length polyhydroxyalkanoates-producing bacteria enriched from activated sludge. Journal of Applied Microbiology 101: 190-199.
• Conte, E., V. Catara, S. Greco, M. Russo, R. Alicata, L. Strano, A. Lombardo, S.D. Silvestro, A. Catara. 2006. Regulation of polyhydroxyalkanoate synthases (phaC1 and phaC2) gene expression in Pseudomonas corrugata. Applied Microbiology and Biotechnology 72: 1054-1062.
• Epshtein, V., C.J. Cardinale, A.E. Ruckenstein, S. Borukhov, E. Nudler. 2007. An allosteric path to transcription termination. Molecular Cell 28: 991-1001.
• Ermolaeva, M.D., H.G. Khalak, O. White, H.O. Smith, S.L. Salzberg. 2000. Prediction of transcription terminators in bacterial genomes. Journal of Molecular Biology 301: 27-33.
• Gusarov, I., E. Nudler. 1999. The mechanism of intrinsic transcription termination. Molecular Cell 3: 495-504.
• Hoffman, N., B.H. Rehm. 2004. Regulation of polyhydroxyalkanoate biosynthesis in Pseudomonas putida and Pseudomonas aeruginosa. FEMS Microbiology Letters 237: 1-7.
• Kingsford, C.L., K. Ayanbule, S.L. Salzberg. 2007. Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA. Genome Biology 8: R22.
• Lesnik, E.A., R. Sampath, H.B. Levene, T.J. Henderson, J.A. McNeil, D. Ecker. 2001. Prediction of rho-independent transcriptional terminators in Escherichia coli. Nucleic Acids Research 29: 3583-3594.
• Madison, L.L., G.W. Huisman. 1999. Metabolic engineering of poly (3-hydroxyalkanoates): from DNA to plastic. Microbiology and Molecular Biology Reviews 63: 21-53.
• Mitra, A., K. Angamuthu, V. Nagaraja. 2008. Genome-wide analysis of the intrinsic terminators of transcription across the genus Mycobacterium. Tuberculosis 88: 566-575.
• Poirier, Y., C. Nawrath, C. Somerville. 1995. Production of polyhydroxyalkanoates, a family of biodegradable plastics and elastomers, in bacteria and plants. Biotechnology 13: 142-150.
• Schlegel, H.G., G. Gottschalk, R. von Bartha. 1961. Formation and utilization of poly-β-hydroxybutyric acid by Knallgas bacteria (Hydrogenomonas). Nature 191: 463-465.
• Schwartz, A., A.R. Rahmouni, M. Boudvillain. 2003. The functional anatomy of an intrinsic transcription terminator. The EMBO Journal 22: 3385-3394.
• Solaiman, D.K.Y., R.D. Ashby, G. Licciardello, V. Catara. 2008. Genetic organization of pha gene locus affects phaC expression, poly(hydroxyalkanoate) composition and granule morphology in Pseudomonas corrugata. Journal of Industrial Microbiology and Biotechnology 35: 111-120.
• Thompson, J.D., D.G. Higgins, T.J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680.
• Unniraman, S., P. Ranjana, V. Nagaraja. 2001. Alternate paradigm for intrinsic transcription termination in Eubacteria. The Journal of Biological Chemistry 276: 41850-41855.
• von Hippel, P.H. 1998. An integrated model of the transcription complex in elongation, termination and editing. Science 281: 660-665.
• Washio, T., J. Sasayama, M. Tomita. 1998. Analysis of complete genomes suggests that many procaryotes do not rely on hairpin formation in transcription termination. Nucleic Acids Research 26: 5456–5463.
• Wilson, K.S., P.H. von Hippel. 1995. Transcription termination at intrinsic terminators: The role of the RNA hairpin. Proceedings of the National Academy of Sciences of the United States of America 92: 8793-8797.
• Yachie, N., K. Arakawa, M. Tomita. 2006. On the interplay of gene positioning and the role of Rho-independent terminators in Escherichia coli. FEMS Microbiology Letters 580: 6909-6914.
• Yarnell, W.S., J.W. Roberts. 1999. Mechanism of intrinsic transcription termination and antitermination. Science 284: 611-615.