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Promoters from a cold-adapted bacterium: definition of a consensus motif and molecular characterization of UP regulative elements

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Although low-temperature tolerant micro-organisms were discovered long ago, limited information is still available on the transcription machinery in cold-adapted bacteria. This knowledge represents a necessary background for the investigation of the adaptation of gene-expression mechanisms at low temperatures. The recent development of a shuttle genetic system for the transformation of the cold-adapted Gram-negative bacterium Pseudoalteromonas haloplanktis strain TAC125 has made possible the isolation of the psychrophilic promoters described in this paper. TAC125 genomic DNA fragments were cloned in the shuttle vector and the promoter-containing recombinant clones were selected for their ability to express a promoter-less lacZ gene. The nucleotide sequence of several selected inserts and the transcription start points of the transcribed m-RNAs were determined. A promoter consensus sequence for Pseudoalteromonas haloplanktis TAC125 was proposed on the basis of a sequence comparison between the various active promoters. Furthermore, the identification and the functional characterization of two UP elements from this cold-adapted bacterium are also reported.

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  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Biol Chem 215:403–410

    Article  CAS  Google Scholar 

  • Birolo L, Tutino ML, Fontanella B, Gerday C, Mainolfi K, Pascarella S, Sannia G, Vinci F, Marino G (2000) Aspartate aminotransferase from the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125: cloning, expression, properties, and molecular modelling. Eur J Biochem 267:2790–2802

    CAS  PubMed  Google Scholar 

  • Blatny JM, Brautaset T, Winther-Larsen HC, Haugan K, Valla S (1997) Construction and use of a versatile set of broad-host-range cloning and expression vectors based on the RK2 replicon. Appl Environ Microbiol 63:370–379

    PubMed  Google Scholar 

  • Cao GJ, Sarkar N (1992) Identification of the gene for an Escherichia coli poly(A) polymerase. Proc Natl Acad Sci USA 89:10380–10384

    CAS  PubMed  Google Scholar 

  • Chattopadhyay MA, Jagannadham MV (2001) Maintenance of membrane fluidity in Antarctic bacteria. Mol Biol 24:386–388

    Article  Google Scholar 

  • Corpet F (1988) Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 16:10881–10890

    CAS  PubMed  Google Scholar 

  • D’Amico S, Claverie P, Collins T, Georlette D, Gratia E, Hoyoux A, Meuwis MA, Feller G, Gerday C (2002) Molecular basis of cold adaptation. Philos Trans R Soc Lond B 357:917–925

    Article  CAS  Google Scholar 

  • Doree SM, Mulks MH (2001) Identification of an Actinobacillus pleuropneumoniae consensus promoter structure. J Bacteriol 183:1983–1989

    Article  CAS  PubMed  Google Scholar 

  • Estrem ST, Ross W, Gaal T, Chen ZW, Niu W, Ebright RH, Gourse RL (1999) Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit. Genes Dev 13:2134–2147

    CAS  PubMed  Google Scholar 

  • Gourse RL, Ross W, Gaal T (2000) UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition. Mol Microbiol 37:687–695

    Article  CAS  PubMed  Google Scholar 

  • Hanahan D (1983) Studies on transformation of Escherichia coli with plasmids. J Mol Biol 166:557–580

    CAS  PubMed  Google Scholar 

  • Hirvonen CA, Ross W, Wozniak CE, Marasco E, Anthony JR, Aiyar SE, Newburn VH, Gourse RL (2001) Contributions of UP elements and the transcription factor FIS to expression from the seven rrn P1 promoters in Escherichia coli. J Bacteriol 183:6305–6314

    Article  CAS  PubMed  Google Scholar 

  • Hoyoux A, Jennes I, Dubois P, Genicot S, Dubail F, Francois JM, Baise E, Feller G, Gerday C (2001) Cold-adapted beta-galactosidase from the Antarctic psychrophile Pseudoalteromonas haloplanktis. Appl Environ Microbiol 67:1529–1535

    Article  CAS  PubMed  Google Scholar 

  • Lisser S, Margalit H (1993) Compilation of E. coli mRNA promoter sequences. Nucleic Acids Res 21:1507–1516

    CAS  PubMed  Google Scholar 

  • Merkel WK, Nichols BP (1996) Characterization and sequence of the Escherichia coli panBCD gene cluster. FEMS Microbiol Lett 143:247–252

    Article  CAS  PubMed  Google Scholar 

  • Rao L, Ross W, Appleman JA, Gaal T, Leirmo S, Schlax PJ, Record MT Jr, Gourse RL (1994) Factor independent activation of rrnB P1: an “extended” promoter with an upstream element that dramatically increases promoter strength. J Mol Biol 235:1421–1435

    CAS  PubMed  Google Scholar 

  • Ross W, Gosink KK, Salomon J, Igarashi K, Zou C, Ishihama A, Severinov K, Gourse RL (1993) A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. Science 262:1407–1413

    CAS  PubMed  Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.

    Google Scholar 

  • Tascon RI, Rodriguez-Ferri EF, Gutierrez-Martin CB, Rodriguez-Barbosa I, Berche P, Vazquez-Boland JA (1993). Transposon mutagenesis in Actinobacillus pleuropneumoniae with a Tn10 derivative. J Bacteriol 175:5717–5722

    CAS  PubMed  Google Scholar 

  • Thomas T, Kumar N, Cavicchioli R (2001) Effects of ribosomes and intracellular solutes on activities and stabilities of elongation factor 2 proteins from psychrotolerant and thermophilic methanogens. J Bacteriol 183:1974–1982

    CAS  PubMed  Google Scholar 

  • Tosco A, Birolo L, Madonna S, Lolli G, Sannia G, Marino G (2003) GroEL from the psychrophilic bacterium Pseudoalteromonas haloplanktis TAC 125: molecular characterization and gene cloning. Extremophiles 7:17–28

    CAS  PubMed  Google Scholar 

  • Tutino ML, Duilio A, Parrilli R, Remaut E, Sannia G, Marino G (2001) A novel replication element from an Antarctic plasmid as a tool for the expression of proteins at temperature. Extremophiles 5:257–264

    Article  CAS  PubMed  Google Scholar 

  • Ulsen P van, Hillebrand M, Kainz M, Collard R, Zulianello L,Putte P van de , Gourse RL, Goosen N (1997) Function of the C-terminal domain of the alpha subunit of Escherichia coli RNA polymerase in basal expression and integration host factor-mediated activation of the early promoter of bacteriophage Mu. J Bacteriol 179:530–537

    PubMed  Google Scholar 

  • Uma S, Jadhav RS, Kumar GS, Shivaji S, Ray MK (1999) A RNA polymerase with transcriptional activity at 0 degrees C from the Antarctic bacterium Pseudomonas syringae. FEBS Lett 453:313–317

    Article  CAS  PubMed  Google Scholar 

  • Vossen JM van der, Lelie D van der, Venema (1987) Isolation and characterization of Streptococcus cremoris Wg2-specific promoters. Appl Environ Microbiol 53:2452–2357

    PubMed  Google Scholar 

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This work was supported by grants from the Ministero dell’Università e della Ricerca Scientifica (Progetti di Rilevante Interesse Nazionale 2002, U.O. Gennaro Marino) and from Regione Campania L.R. 41/94. Support from the National Center of Excellence in Molecular Medicine (MIUR, Rome) and from the Regional Center of Competence (CRdC ATIBB, Regione Campania, Naples) is gratefully acknowledged.

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Correspondence to Angela Duilio.

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Communicated by G. Antranikian

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Duilio, A., Madonna, S., Tutino, M.L. et al. Promoters from a cold-adapted bacterium: definition of a consensus motif and molecular characterization of UP regulative elements. Extremophiles 8, 125–132 (2004).

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