Skip to main content
SpringerLink
Log in

Nucleotide sequence analysis of small cryptic plasmid pGP2 from Acetobacter estunensis

  • Section Cellular and Molecular Biology
  • Published:
Biologia Aims and scope Submit manuscript

Abstract

Complete nucleotide sequence of plasmid pGP2 from Acetobacter estunensis GP2 was identified after initial cloning of EcoRI fragment followed by preparation of deletion derivatives. Its size was defined to 2,797 bp and several sites for several restriction enzymes were revealed by DNA sequencing. Sequence analysis predicts three putative open reading frames (ORFs). ORF1 shows significant identity with the bacterial excinuclease α-subunit, ORF2 is a putative replication protein with low similarity with other Acetobacter plasmid’s replication proteins, and ORF3 encodes a class B acid phosphatase/phosphotransferase. The replication module comprises a DnaA box like sequence, direct repeats, a potential prokaryotic promoter and a rep gene. The rep module is similar with several θ-replicating, iteron-containing modules from plasmids, suggesting pGP2 replication may follow the same course. Any phenotypic character determinant gene is absent in pGP2, suggesting this plasmid to be cryptic. However, a pGP2 derivative plasmid, containing the putative pGP2 rep region, can replicate and is stably maintained in Acetobacter and Escherichia coli strains; it can also carry foreign DNA fragments. Thus, pGP2-X could serve as a cloning shuttle vector between these bacteria. Prepared deletion derivatives of plasmid pGP2 suggested that Rep protein is essential for plasmid replication in host bacteria. In its natural host, A. estunensis GP2, pGP2 maintains a four-times lower copy number than in E. coli.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

Abbreviations

AAB:

acetic acid bacteria

CCM:

Czech Collection of Microorganisms

HTH:

helix-turn-helix

ori :

origin of replication

KnR :

kanamycin resistance

ORF:

open reading frame

RBS:

ribosome-binding site

rep :

replication

References

  • Abeles A.L., Reaves L.D. & Austin S.J. 1990. A single DnaA box is sufficient for initiation from the P1 plasmid origin. J. Bacteriol. 172: 4386–4391.

    CAS  PubMed  Google Scholar 

  • Adachi O., Moonmangmee D., Toyama H., Yamada M., Shinagawa E. & Matsushita K. 2003. New developments in oxidative fermentation. Appl. Microbiol. Biotechnol. 60: 643–653.

    CAS  PubMed  Google Scholar 

  • Altschul S.F., Madden T.L., Schaffer A., Zhang J., Zhang W., Miller W. & Lipman D.J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389–3402.

    Article  CAS  PubMed  Google Scholar 

  • Barany F. 1985. Single-stranded hexameric linkers: a system for inphase insertion mutagenesis and protein engineering. Gene 37: 111–123.

    Article  CAS  PubMed  Google Scholar 

  • Beppu T. 1993. Genetic organization of Acetobacter for acetic acid fermentation. Antonie Van Leeuwenhoek 64: 121–135.

    Article  PubMed  Google Scholar 

  • Bilská V. & Grones J. 2003. Optimalisation of transformation and electroporation of plasmid DNA with AC1 replicon into Acetobacter pasteurianus. Biologia 58: 1029–1035.

    Google Scholar 

  • Birmboim H.C. & Doly J. 1979. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acid Res. 7: 1513–1523.

    Article  Google Scholar 

  • Burian J., Stuchlík S. & Kay W.W. 1999. Replication control of a small cryptic plasmid of Escherichia coli. J. Mol. Biol. 294: 49–65.

    Article  CAS  PubMed  Google Scholar 

  • Cleenwerck I., Vandemeulebroecke K., Janssens D. & Swings J. 2002. Re-examination of the genus Acetobacter, with descriptions of Acetobacter cerevisiae sp. nov. and Acetobacter malorum sp. nov. Int. J. Sys. Evol. Microbiol. 52: 1551–1558.

    Article  CAS  Google Scholar 

  • Cohen S. N. 1993. Bacterial plasmids: their extraordinary contribution to molecular genetics. Gene 135: 67–76.

    Article  CAS  PubMed  Google Scholar 

  • Coucheron D.H. 1991. An Acetobacter xylinum insertion sequence element associated with inactivation of cellulose production. J. Bacteriol. 173: 5723–5731.

    CAS  PubMed  Google Scholar 

  • del Solar G., Giraldo R., Ruiz-Echevarria M.J., Espinosa M. & Diaz-Orejas R. 1998. Replication and control of circular bacterial plasmids. Microbiol. Mol. Biol. Rev. 62: 434–464.

    PubMed  Google Scholar 

  • Dodd I.B. & Egan J.B. 1990. Improved detection of helix-turn-helix DNA-binding motifs in protein sequences. Nucleic Acids Res. 18: 5019–5026.

    Article  CAS  PubMed  Google Scholar 

  • Fomenkov A., Xiao J. & Xu S. 1995. Nucleotide sequence of a small plasmid isolated from Acetobacter pasteurianus. Gene 158: 143–144.

    Article  CAS  PubMed  Google Scholar 

  • Francia M.V., Varsaki A., Garcillan-Barcia M.P., Latorre C., Drainas C. & de la Cruz F. 2004. A classification scheme for mobilization regions of bacterial plasmids. FEMS Microbiol. Rev. 28: 79–100.

    Article  CAS  PubMed  Google Scholar 

  • Fujiwara M., Fukushi K., Takai M., Hayashi J., Fukaya M., Okumura H. & Kawamura Y. 1992. Construction of shuttle vectors derivated from Acetobacter xylinum for cellulose producing bacterium Acetobacter xylinum. Biotechnol. Lett. 14: 593–542.

    Article  Google Scholar 

  • Fukaya M., Takemura H., Okumura H., Kawamura Y., Horinouchi S. & Beppu T. 1990. Cloning of gene responsible for acetic acid resistance in Acetobacter aceti. J. Bacteriol. 172: 2096–2104.

    CAS  PubMed  Google Scholar 

  • Garcia de Viedma D., Giraldo R., Rivas G., Fernandez-Tresguerres E. & Diaz-Orejas R. 1996. A leucine zipper motif determines different functions in a DNA replication protein. EMBO J. 15: 925–934.

    CAS  PubMed  Google Scholar 

  • Giraldo R., Nieto C., Fernandez-Tresguerres M.E. & Diaz-Orejas R. 1989. Bacterial zipper. Nature 342: 866.

    Article  CAS  PubMed  Google Scholar 

  • Gouby A., Teyssier C., Vecina F., Marchandin H., Granolleras C., Zorgniotti I. & Jumas-Bilak E. 2007. Acetobacter cibinongensis bacteremia in human. Emerg. Infect. Dis. 13: 784–785.

    CAS  PubMed  Google Scholar 

  • Grones P. & Grones J. 2010. Cloning, expression, purification and characterization of replication protein from plasmid pGP2 from Acetobacter estunensis. Advan. Biosci. Biotechnol. 1: 417–425.

    Article  Google Scholar 

  • Grones J., Králová A. & Turňa J. 1993. Characterisation of replicon from pAC1 plasmid from Acetobacter pasteurianus. Biochem. Biophys. Res. Commun. 191: 26–31.

    Article  CAS  PubMed  Google Scholar 

  • Grones J., Škereňová M., Bederková K. & Turňa J. 1989. Isolation and characterisation of plasmid pAC1 from Acetobacter pasteurianus. Biologia 44: 1181–1186.

    Google Scholar 

  • Grones J. & Turňa J. 1992. Construction of shuttle vectors for the cloning to Escherichia coli and Acetobacter pasteurianus cells. Folia Microbiol. 37: 395–400.

    Article  CAS  Google Scholar 

  • Grones J. & Turňa J. 1995. Transformation of microorganism with the plasmid replicon from pAC1 from Acetobacter pasteurianus. Biochem. Biophys. Res Commun. 206: 942–947.

    Article  CAS  PubMed  Google Scholar 

  • Hall T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/ NT. Nucleic Acids Symposium Series 41: 95–98.

    CAS  Google Scholar 

  • Helinski D.R., Toukdarian A.E. & Novick R.P. 1996. Replication control and other stable maintenance mechanisms of plasmids, pp. 2295–2324. In: Neidhardt F.C., Curtiss III R., Ingraham J., Lin E.C.C., Low K.B., Magasanik B., Reznikoff W.S., Riley M., Schaechter M. & Umbarger H. (eds), Escherichia coli and Salmonella: Cellular and Molecular Biology (2nd Ed.), ASM Press, Washington DC.

    Google Scholar 

  • Higgins C.F., Hyde S.C., Mimmack M.M., Gileadi U., Gill D.R. & Gallagher M.P. 1990. Binding protein-dependent transport systems. J. Bioenerg. Biomembr. 22: 571–592.

    Article  CAS  PubMed  Google Scholar 

  • Hisano T., Hata Y., Fujii T., Liu J.Q., Kurihara T., Esaki N. & Soda K. 1996. Crystal structure of L-2-haloacid dehalogenase from Pseudomonas sp. YL. An α/β hydrolase structure that is different from the α/β hydrolase fold. J. Biol. Chem. 271: 20322–20330.

    Article  CAS  PubMed  Google Scholar 

  • Huang Y. & Kowalski D. 2003. WEB-THERMODYNE: sequence analysis software for profiling DNA helical stability. Nucleic Acids Res. 31: 3819–3821.

    Article  CAS  PubMed  Google Scholar 

  • Kanhere A. & Bansal M. 2005. A novel method for prokaryotic promoter prediction based on DNA stability. BMC Bioinformatics 6: 1.

    Article  PubMed  Google Scholar 

  • Kersters K., Lisdiyanti P., Komagata K. & Swings J. 2006. The family Acetobacteraceae: the genera Acetobacter, Acidomonas, Asaia, Gluconacetobacter, Gluconobacter, and Kozakia, pp. 163–200. In: Dworkin M., Falkow S., Rosenberg E., Schleifer K.H. & Stackebrandt E. (eds), The Prokaryotes, 3rd Ed, Vol. 5, Springer-Verlag, New York.

    Chapter  Google Scholar 

  • Khan S.A. & Chattoraj D.K. 1998. Initiation of DNA replication in phages and plasmids — a workshop summary. Plasmid 40: 1–11.

    Article  CAS  PubMed  Google Scholar 

  • Kobe B. & Kajava A.V. 2001. The leucine-rich repeat as a protein recognition motif. Curr. Opin. Struct. Biol. 11: 725–732.

    Article  CAS  PubMed  Google Scholar 

  • Krahulec J., Kretová M. & Grones J. 2003. Characterisation of plasmids purified from Acetobacter pasteurianus 2374. Biochem. Biophys. Res. Commun. 310: 95–98.

    Article  Google Scholar 

  • Kretová M., Szemes T., Laco J., Gronesová P. & Grones J. 2005. Analysis of replication region of the cryptic plasmid pAG20 from Acetobacter aceti 3620. Biochem. Biophys. Res. Commun. 328: 27–31.

    Article  PubMed  Google Scholar 

  • Kues U. & Stahl U. 1989. Replication of plasmids in gram-negative bacteria. Microbiol. Rev. 53: 332–343.

    Google Scholar 

  • Lambert B., Kersters K., Gossele F., Swings J. & De Ley J. 1981. Gluconobacters from honey bees. Antonie Van Leeuwenhoek 47: 147–157.

    Article  CAS  PubMed  Google Scholar 

  • Lisdiyanti P., Kawasaki H., Seki T., Yamada Y., Uchimura T. & Komagata K. 2001. Identification of Acetobacter strains isolated from Indonesian sources, and proposals of Acetobacter syzygii sp. nov., Acetobacter cibinongensis sp. nov., and Acetobacter orientalis sp. nov. J. Gen. Appl. Microbiol. 47: 119–131.

    Article  CAS  PubMed  Google Scholar 

  • Martinez-Bueno M., Valdivia E., Galvez A. & Maqueda M. 2000. pS86, a new θ-replicating plasmid from Enterococcus faecalis. Curr. Microbiol. 41: 257–261.

    Article  CAS  PubMed  Google Scholar 

  • Monleón D., Martinez-Vicente M., Esteve V., Yim L., Prado S., Armengod M.E. & Celta B. 2007. Structural insights into the GTPase domain of Escherichia coli MnmE protein. Proteins 66: 726–739.

    Article  PubMed  Google Scholar 

  • Narasimhan G., Bu C., Gao Y., Wang X., Xu N. & Mathee K. 2002. Mining for motifs in protein sequences. J. Comput. Biol. 9: 707–720.

    Article  CAS  PubMed  Google Scholar 

  • Nath N. & Deb J.K. 1995. Partial characterization of small plasmids from Corynebacterium renale. Plasmid 34: 229–233.

    Article  CAS  PubMed  Google Scholar 

  • Nieto C., Giraldo D.R., Fernandez-Tresguerres E. & Diaz-Orejas R. 1992. Genetic and functional analysis of the basic replicon of pPS10, a plasmid specific for Pseudomonas isolated from Pseudomonas syringae pathovar savastanoi. J. Mol. Biol. 223: 415–426.

    Article  CAS  PubMed  Google Scholar 

  • Nobusato A., Uchiyama I., Ohashi S. & Kobayashi I. 2000. Insertion with long target duplication: a mechanism for gene mobility suggested from comparison of two related bacterial genomes. Gene 259: 99–108.

    Article  CAS  PubMed  Google Scholar 

  • Notredame C., Higgins D. & Heringa J. 2000. “T-Coffee“: a novel method for multiple sequence alignments. J. Mol. Biol. 302: 205–217.

    Article  CAS  PubMed  Google Scholar 

  • Okumura H., Uozumi T. & Beppu T. 1985. Construction of plasmid vectors and genetic transformation system for Acetobacter aceti. Agric. Biol. Chem. 49: 1011–1017.

    CAS  Google Scholar 

  • Park K. & Chattoraj D.K. 2001. DnaA boxes in the P1 plasmid origin: the effect of their position on the directionality of replication and plasmid copy number. J. Mol. Biol. 310: 69–81.

    Article  CAS  PubMed  Google Scholar 

  • Prust C., Hoffmeister M., Liesegang H., Wiezer A., Fricke W.F., Ehrenreich A., Gottschalk G. & Deppenmeier U. 2005. Complete genome sequence of the acetic acid bacterium Gluconobacter oxydans. Nat. Biotechnol. 23: 195–200.

    Article  CAS  PubMed  Google Scholar 

  • Pushnova E.A., Michael G. & Yu Sheng Z. 2000. An easy and accurate agarose gel assay for quantitation of bacterial plasmid copy numbers. Anal. Biochem. 284: 70–76.

    Article  CAS  PubMed  Google Scholar 

  • Ryu J.H., Kim S.H., Lee H.Y., Bai J.Y., Nam Y.D., Bae J.W., Lee D.G., Shin S.C., Ha E.M. & Lee W.J. 2008. Innate immune homeostasis by the homeobox gene caudal and commensalgut mutualism in Drosophila. Science 319: 777–782.

    Article  CAS  PubMed  Google Scholar 

  • Sällström B. & Andersson S.G. 2005. Genome reduction in the alpha-Proteobacteria. Curr. Opin. Microbiol. 8: 579–585

    Article  PubMed  Google Scholar 

  • Sambrook J., Fritsch E.F. & Maniatis T. 1989. Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

    Google Scholar 

  • Schaper S. & Messer W. 1995. Interaction of the initiator protein DnaA of Escherichia coli with its DNA target. J. Biol. Chem. 270: 17622–17626.

    Article  CAS  PubMed  Google Scholar 

  • Silva L.R., Cleenwerck I., Rivas R., Swings J., Trujillo M.E., Willems A. & Velázquez E. 2006. Acetobacter oeni sp. nov., isolated from spoiled red wine. Int. J. Sys. Evol. Microbiol. 56: 21–24.

    Article  CAS  Google Scholar 

  • Singh S.K. & Banerjee P.C. 2006. High-yielding plasmid extraction method from acidophilic heterotrophic bacteria of the genus Acidiphilium. Anal. Biochem. 356: 229–234.

    Article  CAS  PubMed  Google Scholar 

  • Su X.C., Schaeffer P.M., Loscha K.V., Gan P.H., Dixon N.E. & Otting G. 2006. Monomeric solution structure of the helicasebinding domain of Escherichia coli DanG primase. FEBS J. 273: 4997–5009.

    Article  CAS  PubMed  Google Scholar 

  • Takemura H., Horinouchi S. & Beppu T. 1991. Novel insertion sequence IS1380 from Acetobacter pasteurianus is involved in loss of ethanol-oxidizing ability. J. Bacteriol. 173: 7070–7076.

    CAS  PubMed  Google Scholar 

  • Tamaki T., Fukaya M., Takemura H., Tayama K., Okumura H., Kawamura Y., Nishiyama M., Horinouchi S. & Beppu T. 1991. Cloning and sequencing of the gene cluster encoding two subunits of membrane-bound alcohol dehydrogenase from Acetobacter polyoxogenes. Biochim. Biophys. Acta 1088: 292–300.

    CAS  PubMed  Google Scholar 

  • Trček J., Raspor P. & Teuber M. 2000. Molecular identification of Acetobacter isolates from submerged vinegar production, sequence analysis of plasmid pJK2-1 and application in the development of a cloning vector. Appl. Microbiol. Biotechnol. 53: 289–295.

    Article  PubMed  Google Scholar 

  • Tyrell R., Verschueren K.H., Dodson E.J., Murshudov G.N., Addy C. & Wilkinson A.J. 1997. The structure of the cofactor-binding fragment of the LysR family member, CysB: a familiar fold with surprising subunit arrangement. Structure 5: 1017–1032.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Molecular Biology, Comenius University, Mlynska dolina B2-122, SK-84215, Bratislava 4, Slovakia

    Peter Grones & Jozef Grones

Authors
  1. Peter Grones
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jozef Grones
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jozef Grones.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Grones, P., Grones, J. Nucleotide sequence analysis of small cryptic plasmid pGP2 from Acetobacter estunensis . Biologia 66, 221–228 (2011). https://doi.org/10.2478/s11756-011-0017-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.2478/s11756-011-0017-2

Key words

Search

Navigation