Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Genetic organization of a plasmid from an industrial wastewater bioreactor

  • 122 Accesses

  • 8 Citations


Pseudomonas strain CT14 was isolated from activated sludge. Strain CT14 contained a 55, 216 bp plasmid that was characterized by sequence analysis. The plasmid had a modular structure with 51 open reading frames (ORFs) that were distributed between two clearly demarcated domains. Domain I primarily contained genes for plasmid-related functions and a novel origin of replication. Domain II bore evidence of extensive transposition and recombination. Domain II contained several genes from a meta-cleavage pathway for aromatic rings. These genes appeared to have been recruited from different hosts. This observation suggests that sequencing pCT14 may have revealed an intermediate stage in the evolution of a new assemblage of meta-cleavage pathway genes.

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

Fig. 1
Fig. 2


  1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

  2. Bitton G (1994) Wastewater microbiology. Wiley-Liss, New York

  3. Bramucci MG, Nagarajan V (2000) Industrial wastewater bioreactors: sources of novel microorganisms for biotechnology. Trends Biotechnol 18:501–505

  4. Bramucci MG, McCutchen CM, Singh M, Thomas SM, Larsen BS, Buckholz J, Nagarajan V (2002a) Pure bacterial isolates that convert p-xylene to terephthalic acid. Appl Microbiol Biotechnol 58:255–259

  5. Bramucci MG, Singh M, Nagarajan V (2002b) Biotransformation of p-xylene and 2,6-dimethylnaphthalene by xylene monooxygenase cloned from a Sphingomonas isolate. Appl Microbiol Biotechnol 59:679–684

  6. Chattoraj DK (2000) Control of plasmid DNA replication by iterons: no longer paradoxical. Mol Microbiol 37:467–476

  7. Cheng Q, Thomas SM, Kostichka K, Valentine JR, Nagarajan V (2000) Genetic analysis of a gene cluster for cyclohexanol oxidation in Acinetobacter sp. strain SE19 by in vitro transposition. J Bacteriol 182:4744–4751

  8. Dogra C, Raina V, Pal R, Suar M, Lal S, Gartemann K, Holliger C, van der Meer JR, Lal R (2004) Organization of lin genes and IS6100 among different strains of hexachlorocyclohexane-degrading Sphingomonas paucimobilis: evidence for horizontal gene transfer. J Bacteriol 186:2225–2235

  9. Eckhardt T (1978) A rapid method for the identification of plasmid desoxyribonucleic acid in bacteria. Plasmid 1:584–588

  10. Gardner MN, Deane SM, Rawlings DE (2001) Isolation of a new broad-host-range IncQ-like plasmid, pTC-F14, from the acidophilic bacterium Acidithiobacillus caldus and analysis of the plasmid replicon. J Bacteriol 183:3303–3309

  11. Goebel M, Kranz OH, Kaschabek SR, Schmidt E, Pieper DE, Reineke W (2004) Microorganisms degrading chlorobenzene via a meta-cleavage pathway harbor highly similar chlorocatechol 2,3-dioxygenase-encoding gene clusters. Arch Microbiol 182:147–156

  12. Greated A, Lambertsen L, Williams PA, Thomas CM (2002) Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida. Environ Microbiol 4:856–871

  13. Hofer B, Backhaus S, Timmis KN (1994) The biphenyl/polychlorinated biphenyl-degradation locus (bph) of Pseudomonas sp. LB400 encodes four additional metabolic enzymes. Gene 144:9–16

  14. Igloi GL, Brandsch R (2003) Sequence of the 165-kilobase catabolic plasmid pAO1 from Arthrobacter nicotinovorans and identification of a pAO1-dependent nicotine uptake system. J Bacteriol 185:1976–1986

  15. Kholodii GY, Yurieva OV, Lomovskaya OL, Gorlenko Z, Mindlin SZ, Nikiforov VG (1993) Tn5053, a mercury resistance transposon with integron's ends. J Mol Biol 230:1103–1107

  16. Kholodii GY, Mindlin SZ, Bass IA, Yurieva OV, Minakhina SV, Nikiforov VG (1995) Four genes, two ends, and a res region are involved in transposition of Tn5053: a paradigm for a novel family of transposons carrying either a mer operon or an integron. Mol Microbiol 17:1189–1200

  17. Kostichka K, Thomas SM, Gibson KJ, Nagarajan V, Cheng Q (2001) Cloning and characterization of a gene cluster for cyclododecanone oxidation in Rhodococcus ruber SC1. J Bacteriol 183:6478–6486

  18. Lauf U, Muller C, Herrmann H (1998) The transposable elements resident on the plasmids of Pseudomonas putida strain H, Tn5501 and Tn5502, are cryptic transposons of the Tn3 family. Mol Gen Genet 259:674–678

  19. Lawrence JG, Roth JR (1996) Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143:1843–1860

  20. Leschziner AE, Boocock MR, Grindley ND (1995) The tyrosine-6 hydroxyl of gamma delta resolvase is not required for the DNA cleavage and rejoining reactions. Mol Microbiol 15:865–870

  21. Li W, Shi J, Wang X, Han Y, Tong W, Ma L, Liu B, Cai B (2004) Complete nucleotide sequence and organization of the naphthalene catabolic plasmid pND6-1 from Pseudomonas sp. strain ND6. Gene 336:231–240

  22. Maeda K, Nojiri H, Shintani M, Yoshida T, Habe H, Omori T (2003) Complete nucleotide sequence of carbazole/dioxin-degrading plasmid pCAR1 in Pseudomonas resinovorans strain CA10 indicates its mosaicity and the presence of large catabolic transposon Tn4676. J Mol Biol 326:21–33

  23. Mars AE, Kingma J, Kaschabek SR, Reineke W, Janssen DB (1999) Conversion of 3-chlorocatechol by various catechol 2,3-dioxygenases and sequence analysis of the chlorocatechol dioxygenase region of Pseudomonas putida GJ31. J Bacteriol 181:1309–1318

  24. Martinez B, Tomkins J, Wackett LP, Wing R, Sadowsky MJ (2001) Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP. J Bacteriol 183:5684–5697

  25. Minakhina S, Kholodii G, Mindlin S, Yurieva O, Nikiforov V (1999) Tn5053 family transposons are res site hunters sensing plasmidal res sites occupied by cognate resolvases. Mol Microbiol 33:1059–1068

  26. Nojiri H, Shintani M, Omori T (2004) Divergence of mobile genetic elements involved in the distribution of xenobiotic–catabolic capacity. Appl Microbiol Biotechnol 64:154–174

  27. Ochman H, Lawrence JG (1996) Phylogenetics and the amelioration of bacterial genomes. In: Neidhardt FC (ed) Escherichia coli and Salmonella: cellular and molecular biology, 2nd edn. ASM Press, Washington, DC, pp 2627–2637

  28. Page DT, Whelan KF, Colleran E (2001) Characterization of two autoreplicative regions of the IncHI2 plasmid R478: RepHI2A and RepHI1A(R478). Microbiology 147:1591–1598

  29. Paterson ES, Iyer VN (1997) Localization of the nic site of IncN conjugative plasmid pCU1 through formation of a hybrid oriT. J Bacteriol 179:5768–5776

  30. Paterson ES, More MI, Pillay G, Cellini C, Woodgate R, Walker GC, Iyer VN, Winans SC (1999) Genetic analysis of the mobilization and leading regions of the IncN plasmids pKM101 and pCU1. J Bacteriol 181:2572–2583

  31. Pullinger GD, Lax AJ (1992) Salmonella dublin virulence plasmid locus that affects bacterial growth under nutrient-limited conditions. Mol Microbiol 6:1631–1643

  32. Radnedge L, Davis MA, Youngren B, Austin SJ (1997) Plasmid maintenance functions of the large virulence plasmid of Shigella flexneri. J Bacteriol 179:3670–3675

  33. Romine MF, Stillwell LC, Wong KK, Thurston SJ, Sisk EC, Sensen C, Gaasterland T, Fredrickson JK, Saffer JD (1999) Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199. J Bacteriol 181:1585–1602

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

  35. Sentchilo VS, Perebituk AN, Zehnder AJB, van der Meer JR, (2000) Molecular diversity of plasmids bearing genes that encode toluene and xylene metabolism in Pseudomonas strains isolated from different contaminated sites in Belarus. Appl Environ Microbiol 66:2842–2852

  36. Thomas CM (2000) Paradigms of plasmid organization. Mol Microbiol 37:485–491

  37. Top EM, Springael D (2003) The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds. Curr Opin Biotechnol 14:262–269

  38. Vedler E, Vahter M, Heinaru A (2004) The Completely sequenced plasmid pEST4011 contains a novel IncP1 backbone and a catabolic transposon harboring tfd genes for 2,4-dichlorophenoxyacetic acid degradation. J Bacteriol 186:7161–7174

  39. Venkova-Canova T, Soberon NE, Ramirez-Romero MA, Cevallos MA (2004) Two discrete elements are required for the replication of a repABC plasmid: an antisense RNA and a stem-loop structure. Mol Microbiol 54:1431–1444

  40. Williams PA, Worsey MJ (1976) Ubiquity of plasmids in coding for toluene and xylene metabolism in soil bacteria: evidence for the existence of new TOL plasmids. J Bacteriol 125:818–828

Download references

Author information

Correspondence to Michael Bramucci.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Bramucci, M., Chen, M. & Nagarajan, V. Genetic organization of a plasmid from an industrial wastewater bioreactor. Appl Microbiol Biotechnol 71, 67–74 (2006). https://doi.org/10.1007/s00253-005-0119-2

Download citation


  • Activate Sludge
  • Inverted Repeat
  • Direct Repeat
  • Transposase Gene
  • Chlorocatechol