1887

Abstract

Rü61a, which utilizes quinaldine as sole source of carbon and energy, was shown to contain a conjugative linear plasmid of approximately 110 kb, named pAL1. It exhibits similarities with other linear plasmids from in that it has proteins covalently attached to its 5′ ends. Southern hybridization with probes for the genes encoding quinaldine 4-oxidase and -acetylanthranilate amidase indicated that pAL1 contains the gene cluster encoding the degradation of quinaldine to anthranilate. A mutant of strain Rü61a that had lost pAL1 indeed could not convert quinaldine, but was still able to grow on anthranilate. Conjugative transfer of pAL1 to the plasmid-less mutant of strain Rü61a and to DSM 420 (pAO1) occurred at frequencies of 5·4×10 and 2·0×10 per recipient, respectively, and conferred the ability to utilize quinaldine. Five other quinaldine-degrading Gram-positive strains were isolated from soil samples; 16S rDNA sequence analysis suggested the closest relationship to different species. Except for strain K2-29, all isolates contained a pAL1-like linear plasmid carrying genes encoding quinaldine conversion. A 478 bp fragment that on pAL1 represents an intergenic region showed 100 % sequence identity in all isolates harbouring a pAL1-like plasmid, suggesting horizontal dissemination of the linear plasmid among the genus .

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2005-02-01
2024-03-28
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References

  1. Agapova S. R., Andreeva A. L., Starovoitov I. I., Vorob'eva L. I., Ternet'ev P. B. 1992; Plasmids for biodegradation of 2,6-dimethylpyridine, 2,4-dimethylpyridine, and pyridine in strains of Arthrobacter. Mol Gen Mikrobiol Virusol 5:610–13 in Russian
    [Google Scholar]
  2. Bao K., Cohen S. N. 2001; Terminal proteins essential for the replication of linear plasmids and chromosomes in Streptomyces. Genes Dev 15:1518–1527 [CrossRef]
    [Google Scholar]
  3. Bao K., Cohen S. N. 2003; Recruitment of terminal protein to the ends of Streptomyces linear plasmids and chromosomes by a novel telomere-binding protein essential for linear DNA replication. Genes Dev 17:774–785 [CrossRef]
    [Google Scholar]
  4. Barton B. M., Harding G. P., Zuccarelli A. J. 1995; A general method for detecting and sizing large plasmids. Anal Biochem 226:235–240 [CrossRef]
    [Google Scholar]
  5. Bertani G. 2004; Lysogeny at mid-twentieth century: P1, P2, and other experimental systems. J Bacteriol 186:595–600 [CrossRef]
    [Google Scholar]
  6. Brandsch R., Decker K. 1984; Isolation and partial characterization of plasmid DNA from Arthrobacter oxidans . Arch Microbiol 138:15–17 [CrossRef]
    [Google Scholar]
  7. Brown S. E., Knudson D. L., Ishimaru C. A. 2002; Linear plasmid in the genome of Clavibacter michiganensis subsp.sepedonicus . J Bacteriol 184:2841–2844 [CrossRef]
    [Google Scholar]
  8. Cacciari I., Lippi D. 1987; Arthrobacters: successful arid soil bacteria: a review. Arid Soil Res Rehabil 1:1–30
    [Google Scholar]
  9. Chang P.-C., Cohen S. N. 1994; Bidirectional replication from an internal origin in a linear Streptomyces plasmid. Science 265:952–954 [CrossRef]
    [Google Scholar]
  10. Chang P.-C., Kim E.-S., Cohen S. N. 1996; Streptomyces linear plasmids that contain a phage-like, centrally located, replication origin. Mol Microbiol 22:789–800 [CrossRef]
    [Google Scholar]
  11. Chauhan A., Jain R. K. 2000; Degradation of o-nitrobenzoate via anthranilic acid (o-aminobenzoate) by Arthrobacter protophormiae: a plasmid-encoded new pathway. Biochem Biophys Res Commun 267:236–244 [CrossRef]
    [Google Scholar]
  12. Chauhan A., Chakraborti A. K., Jain R. K. 2000; Plasmid-encoded degradation of p-nitrophenol and 4-nitrocatechol by Arthrobacter protophormiae. Biochem Biophys Res Commun 270:733–740 [CrossRef]
    [Google Scholar]
  13. Chen C. W., Yu T.-W., Lin Y.-S., Kieser H. M., Hopwood D. A. 1993; The conjugative plasmid SLP2 of Streptomyces lividans is a 50 kb linear molecule. Mol Microbiol 7:925–932 [CrossRef]
    [Google Scholar]
  14. Coleman N. V., Spain J. C. 2003; Distribution of the coenzyme M pathway of epoxide metabolism among ethene- and vinyl chloride-degrading Mycobacterium strains. Appl Environ Microbiol 69:6041–6046 [CrossRef]
    [Google Scholar]
  15. Crespi M., Messens E., Caplan A. B., van Montagu M., Desomer J. 1992; Fasciation induction by the phytopathogen Rhodococcus fascians depends upon a linear plasmid encoding a cytokinin synthase gene. EMBO J 11:795–804
    [Google Scholar]
  16. Crocker F. H., Fredrickson J. K., White D. C., Ringelberg D. B., Balkwill D. L. 2000; Phylogenetic and physiological diversity of Arthrobacter strains isolated from unconsolidated subsurface sediments. Microbiology 146:1295–1310
    [Google Scholar]
  17. Dabrock B., Keßeler M., Averhoff B., Gottschalk G. 1994; Identification and characterization of a transmissible linear plasmid from Rhodococcus erythropolis BD2 that encodes isopropylbenzene and trichloroethene catabolism. Appl Environ Microbiol 60:853–860
    [Google Scholar]
  18. Dembek G., Rommel T., Lingens F., Höke H. 1989; Degradation of quinaldine by Alcaligenes sp. and by Arthrobacter sp. FEBS Lett 246:113–116 [CrossRef]
    [Google Scholar]
  19. Eaton R. W. 2001; Plasmid-encoded phthalate catabolic pathway in Arthrobacter keyseri 12B. J Bacteriol 183:3689–3703 [CrossRef]
    [Google Scholar]
  20. Fetzner S. 1998; Bacterial degradation of pyridine, indole, quinoline, and their derivatives under different redox conditions. Appl Microbiol Biotechnol 49:237–250 [CrossRef]
    [Google Scholar]
  21. Fetzner S. 2002; Oxygenases without requirement for cofactors or metal ions. Appl Microbiol Biotechnol 60:243–257 [CrossRef]
    [Google Scholar]
  22. Flagan S., Ching W. K., Leadbetter J. R. 2003; Arthrobacter strain VAI-A utilizes acyl-homoserine lactone inactivation products and stimulates quorum signal biodegradation byVariovorax paradoxus . Appl Environ Microbiol 69:909–916 [CrossRef]
    [Google Scholar]
  23. Furukawa K., Chakrabarty A. M. 1982; Involvement of plasmids in total degradation of chlorinated biphenyls. Appl Environ Microbiol 44:619–629
    [Google Scholar]
  24. Gartemann K.-H., Eichenlaub R. 2001; Isolation and characterization of IS1409, an insertion element of 4-chlorobenzoate-degrading Arthrobacter sp. strain TM1, and development of a system for transposon mutagenesis. J Bacteriol 183:3729–3736 [CrossRef]
    [Google Scholar]
  25. Hayakawa T., Tanaka T., Sakaguchi K., Otake N., Yonehara H. 1979; A linear plasmid-like DNA in Streptomyces sp. producing lankacidin group antibiotics. J Gen Appl Microbiol 25:255–260 [CrossRef]
    [Google Scholar]
  26. Hayatsu M., Hirano M., Nagata T. 1999; Involvement of two plasmids in the degradation of carbaryl by Arthrobacter sp. strain RC100. Appl Environ Microbiol 65:1015–1019
    [Google Scholar]
  27. Hund H.-K., de Beyer A., Lingens F. 1990; Microbial metabolism of quinoline and related compounds. VI. Degradation of quinaldine by Arthrobacter sp. Biol Chem Hoppe-Seyler 371:1005–1008 [CrossRef]
    [Google Scholar]
  28. Igloi G. L., 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 [CrossRef]
    [Google Scholar]
  29. Kalkus J., Reh M., Schlegel H. G. 1990; Hydrogen autotrophy of Nocardia opaca strains is encoded by linear megaplasmids. J Gen Microbiol 136:1145–1151 [CrossRef]
    [Google Scholar]
  30. Kalkus J., Dorrie C., Fischer D., Reh M., Schlegel H. G. 1993; The giant linear plasmid pHG207 from Rhodococcus sp. encoding hydrogen autotrophy: characterization of the plasmid and its termini. J Gen Microbiol 139:2055–2065 [CrossRef]
    [Google Scholar]
  31. Kinashi H., Shimaji M., Sakai A. 1987; Giant linear plasmids in Streptomyces which code for antibiotic biosynthesis genes. Nature 328:454–456 [CrossRef]
    [Google Scholar]
  32. Kinoshita-Iramina C., Kitahara M., Doi K., Ogata S. 1997; A conjugative linear plasmid in Streptomyces laurentii ATCC31255. Biosci Biotechnol Biochem 61:1469–1473 [CrossRef]
    [Google Scholar]
  33. König C., Eulberg D., Lakner S., Seibert V., Kaschabek S. R, Gröning J., Schlömann M. 2004; A linear megaplasmid, p1CP, carrying the genes for chlorocatechol catabolism of Rhodococcus opacus 1CP. Microbiology 150:3075–3087 [CrossRef]
    [Google Scholar]
  34. Kosono S., Maeda M., Fuji F., Arai H., Kudo T. 1997; Three of the seven bphC genes of Rhodococcus erythropolis TA421, isolated from a termite ecosystem, are located on an indigenous plasmid associated with biphenyl degradation. Appl Environ Microbiol 63:3282–3285
    [Google Scholar]
  35. Le Dantec C., Winter N., Gicquel B., Vincent V., Picardeau M. 2001; Genomic sequence and transcriptional analysis of a 23-kilobase mycobacterial linear plasmid: evidence for horizontal transfer and identification of plasmid maintenance systems. J Bacteriol 183:2157–2164 [CrossRef]
    [Google Scholar]
  36. MacNeil D. J., Gewain K. M., Ruby C. L., Dezeny G., Gibbons P. H., MacNeil T. 1992; Analysis of Streptomyces avermitilis genes required for avermectin biosynthesis utilizing a novel integration vector. Gene 111:61–68 [CrossRef]
    [Google Scholar]
  37. Meinhardt F., Schaffrath R., Larsen M. 1997; Microbial linear plasmids. Appl Microbiol Biotechnol 47:329–336 [CrossRef]
    [Google Scholar]
  38. Musialowski M. S., Flett F., Scott G. B., Hobbs G., Smith C. P., Oliver S. G. 1994; Functional evidence that the principal DNA replication origin of the Streptomyces coelicolor chromosome is close to thednaA-gyrB region. J Bacteriol 176:5123–5125
    [Google Scholar]
  39. Muyzer G., Teske A., Wirsen C. O., Jannasch H. W. 1995; Phylogenetic relationships of Thiomicrospira species and their identification in deep-sea hydrothermal vent samples by denaturing gradient gel electrophoresis of 16S rDNA fragments. Arch Microbiol 164:165–172 [CrossRef]
    [Google Scholar]
  40. Olsen G. J., Matsuda H., Hagstrom R., Overbeek R. 1994; fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput Appl Biosci 10:41–48
    [Google Scholar]
  41. Parschat K., Hauer B., Kappl R., Kraft R., Hüttermann J., Fetzner S. 2003; Gene cluster of Arthrobacter ilicis Rü61a involved in the degradation of quinaldine to anthranilate. Characterization and functional expression of the quinaldine 4-oxidase qoxLMS genes. J Biol Chem 278:27483–27494 [CrossRef]
    [Google Scholar]
  42. Picardeau M., Vincent V. 1997; Characterization of large linear plasmids in mycobacteria. J Bacteriol 197:2753–2756
    [Google Scholar]
  43. Picardeau M., Vincent V. 1998; Mycobacterial linear plasmids have an invertron-like structure related to other linear replicons in actinomycetes. Microbiology 144:1981–1988 [CrossRef]
    [Google Scholar]
  44. Polo S., Guerini O., Sosio M., Deho G. 1998; Identification of two linear plasmids in the actinomycete Planobispora rosea. Microbiology 144:2819–2825 [CrossRef]
    [Google Scholar]
  45. Qin Z., Shen M., Cohen S. N. 2003; Identification and characterization of a pSLA2 plasmid locus required for linear DNA replication and circular plasmid stable inheritance in Streptomyces lividans . J Bacteriol 185:6575–6582 [CrossRef]
    [Google Scholar]
  46. Rainey F. A., Ward-Rainey N., Kroppenstedt R. M., Stackebrandt E. 1996; The genus Nocardiopsis represents a phylogenetically coherent taxon and a distinct actinomycete lineage: proposal ofNocardiopsaceae fam. nov. Int J Syst Bacteriol 46:1088–1092 [CrossRef]
    [Google Scholar]
  47. Ravel J., Schrempf H., Hill R. T. 1998; Mercury resistance is encoded by transferable giant linear plasmids in two Chesapeake Bay Streptomyces strains. Appl Environ Microbiol 64:3383–3388
    [Google Scholar]
  48. Ravel J., Wellington E. M., Hill R. T. 2000; Interspecific transfer of Streptomyces giant linear plasmids in sterile amended soil microcosms. Appl Environ Microbiol 66:529–534 [CrossRef]
    [Google Scholar]
  49. Redenbach M., Bibb M., Gust B., Seitz B., Spychaj A. 1999; The linear plasmid SCP1 of Streptomyces coelicolor A3(2) possesses a centrally located replication origin and shows significant homology to the transposon Tn4811. Plasmid 42:174–185 [CrossRef]
    [Google Scholar]
  50. Röger P., Erben A., Lingens F. 1990; Degradation of isoquinoline by Alcaligenes faecalis Pa and Pseudomonas diminuta 7. Biol Chem Hoppe-Seyler 371:511–513 [CrossRef]
    [Google Scholar]
  51. Sajjaphan K., Shapir N., Wackett L. P., Palmer M., Blackmon B., Tomkins J., Sadowsky M. J. 2004; Arthrobacter aurescens TC1 atrazine catabolism genes trzN, atzB, and atzC are linked on a 160-kilobase region and are functional inEscherichia coli. Appl Environ Microbiol 70:4402–4407 [CrossRef]
    [Google Scholar]
  52. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  53. Sanger F., Nicklen S., Coulson A. R. 1977; DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463–5467 [CrossRef]
    [Google Scholar]
  54. Schenk S., Hoelz A., Krauss B., Decker K. 1998; Gene structures and properties of enzymes of the plasmid-encoded nicotine catabolism of Arthrobacter nicotinovorans . J Mol Biol 284:1323–1339 [CrossRef]
    [Google Scholar]
  55. Schmitz A., Gartemann K. H., Fiedler J., Grund E., Eichenlaub R. 1992; Cloning and sequence analysis of genes for dehalogenation of 4-chlorobenzoate from Arthrobacter sp. strain SU. Appl Environ Microbiol 58:4068–4071
    [Google Scholar]
  56. Shimizu S., Kobayashi H., Masai E., Fukuda M. 2001; Characterization of the 450-kb linear plasmid in a polychlorinated biphenyl degrader, Rhodococcus sp. strain RHA1. Appl Environ Microbiol 67:2021–2028 [CrossRef]
    [Google Scholar]
  57. Smith T. F., Waterman M. S. 1981; Comparison of Bio-Sequences. Adv Appl Math 2:482–489 [CrossRef]
    [Google Scholar]
  58. Spatz K., Redenbach M, Köhn H. 2002; Characterization of the Streptomyces violaceoruber SANK95570 plasmids pSV1 and pSV2. FEMS Microbiol Lett 213:87–92 [CrossRef]
    [Google Scholar]
  59. Stecker C., Johann A., Herzberg C., Averhoff B., Gottschalk G. 2003; Complete nucleotide sequence and genetic organization of the 210-kilobase linear plasmid of Rhodococcus erythropolis BD2. J Bacteriol 185:5269–5274 [CrossRef]
    [Google Scholar]
  60. Stephan I., Tshisuaka B., Fetzner S., Lingens F. 1996; Quinaldine 4-oxidase from Arthrobacter sp. Rü61a. A versatile procaryotic molybdenum-containing hydroxylase active towards N-heterocycles and aromatic aldehydes. Eur J Biochem 236:155–162 [CrossRef]
    [Google Scholar]
  61. Suwa M., Sugino H., Sasaoka A., Mori E., Fujii S., Shinkawa H., Nimi O., Kinashi H. 2000; Identification of two polyketide synthase gene clusters on the linear plasmid pSLA2-L in Streptomyces rochei . Gene 246:123–131 [CrossRef]
    [Google Scholar]
  62. Swofford D. L. 2002 paup* – Phylogenetic Analysis Using Parsimony and Other Methods, 4.0 Sunderland, MA: Sinauer Associates;
    [Google Scholar]
  63. Turnbull G. A., Ousley M., Walker A., Shaw E., Morgan J. A. W. 2001; Degradation of substituted phenylurea herbicides by Arthrobacter globiformis strain D47 and characterization of a plasmid-associated hydrolase gene,puhA . Appl Environ Microbiol 67:2270–2275 [CrossRef]
    [Google Scholar]
  64. Vieira J., Messing J. 1982; The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene 19:259–268 [CrossRef]
    [Google Scholar]
  65. Weinberger M., Kolenbander P. E. 1979; Plasmid-determined 2-hydroxypyridine utilization by Arthrobacter crystallopoietes. Can J Microbiol 25:329–334 [CrossRef]
    [Google Scholar]
  66. Woodcock D. M., Crowther P. J., Doherty J., Jefferson S., DeCruz E., Noyer-Weidner M., Smith S. S., Michael M. Z., Graham M. W. 1989; Quantitative evaluation of Escherichia coli host strains for tolerance to cytosine methylation in plasmid and phage recombinants. Nucleic Acids Res 17:3469–3478 [CrossRef]
    [Google Scholar]
  67. Yang C.-C., Huang C.-H., Li C.-Y., Tsay Y.-G., Lee S.-C., Chen C. W. 2002; The terminal proteins of linear Streptomyces chromosomes and plasmids: a novel class of replication priming proteins. Mol Microbiol 43:297–305 [CrossRef]
    [Google Scholar]
  68. Zaitsev G. M., Tsoi T. V., Grishenkov V. G., Plotnikova E. G., Boronin A. M. 1991; Genetic control of degradation of chlorinated benzoic acids in Arthrobacter globiformis, Corynebacterium sepedonicum and Pseudomonas cepacia strains. FEMS Microbiol Lett 65:171–176
    [Google Scholar]
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