Biopolym. Cell. 2010; 26(4):279-285.
http://dx.doi.org/10.7124/bc.000160
Molecular and Cell Biotechnologies
A mobile genetic element in Serratia marcescens, a causative agent of onion disease
1Ovcharenko L. P., 1Voznyuk T. M., 1Zaetz I. E., 1Potopalsky A. I., 2, 3Reva O. N., 1Kozyrovska N. O.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680
  2. D. K. Zabolotny Institute of Microbiology and Virology, NAS of Ukraine
    154, Academika Zabolotnogo Str., Kyiv, Ukraine, 03680
  3. University of Pretoria
    Pretoria, South Africa

Abstract

Aim. To screen mobile genetic elements (MGE) in the bacterium which caused decay of field-grown onion bulb and to study an integron and gene cassettes associated. Methods. Polymerase chain reaction (PCR) and PCR products sequencing were used for both the bacterium and MGE identification. Terminally-labeled Restriction Fragment Length Polymorphism (TRFLP) analysis was performed for detection of any bacterium in the onion bulb tissue. Results. The bacterium, which caused field-grown onion decay, was identified by nucleotide sequence analysis of the 16S rRNA genes to be S. marcescens known as phytopathogen. However, this isolate did not respond to specific primers designed for pathogenic strains. Inoculation of onion (Allium cepa L.), Arabidopsis thaliana (L.) Heyhn, and lettuce (Lactuca sativa) seeds resulted in biomass promotion of symptomless plants. PCR revealed the presence of a class 1 integron in S. marcescens IMBG291 which represents the first isolation of this integron in phytopathogenic Serratia species. The gene cassettes harbored by the integron have been represented with the promoterless genes encoded formimino-glutamate deiminase and ascorbate-specific phosphotransferase system enzyme IIC, and with additional three senseless sequences flanked by a 59-bp element. Conclusion. S. marcescens IMBG291 exhibited plant growth promotion or pathogenicity, depending on the environmental situation, due to horizontally acquired new gene cassettes located in the integron.
Keywords: Serratia marcescens, onion disease, integron, gene cassettes
Full text: (PDF, in English)

References

[1] Cother E. J., Dowling V. Bacteria associated with internal breakdown of onion bulbs and their possible role in disease expression Plant Pathol 1986 35, N 3:329–336.
[2] Yum J. H., Yong D., Lee K., Kim H. S., Chong Y. A new integron carrying VIM-2 metallo-beta-lactamase gene cassette in a Serratia marcescens isolate. Diagn. Microbiol. Infect. Dis 2002 42, N 3:217–219.
[3] Edwards U., Rogal T., Bloecker M., Boettger E. C. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA Nucl. Acids Res 1989 17, N 19:7843–7853.
[4] Kurz C. L., Chauvet S., Andres E., Aurouze M., Vallet I., Michel G. P., Uh M., Celli J., Filloux A., De Bentzmann S., Steinmetz I., Hoffmann J. A., Finlay B. B., Gorvel J. P., Ferrandon D., Ewbank J. J. Virulence factors of the human opportunistic pathogen Serratia marcescens identified by in vivo screening EMBO J 2003 22, N 7:1451–1460.
[5] Ryu C. M., Murphy J. F., Mysore K. S., Kloepper J. W. Plant growth-promoting rhizobacteria systemically protect Arabidopsis thaliana against Cucumber mosaic virus by a salicylic acid and NPR1-independent and jasmonic acid-dependent signaling pathway Plant J 2004 39, N 3:381–392.
[6] Selvakumar G., Mohan M., Kundu S., Gupta A. D., Joshi P., Nazim S., Gupta H. S. Cold tolerance and plant growth promotion potential of Serratia marcescens strain SRM (MTCC 8708) isolated from flowers of summer squash (Cucurbita pepo) Lett. Appl. Microbiol 2008 46, N 2:171–175.
[7] Pair S. D., Bruton B. D., Mitchell F., Fletcher J., Wayadande A., Melcher U. Overwintering squash bugs harbor and transmit the causal agent of cucurbit yellow vine disease J. Econ. Entomol 2004 97, N 1:74–78.
[8] Bruton B. D., Mitchell F., Fletcher J., Pair S. D., Wayadande A., Melcher U., Brady J., Bextine B., Popham T. W. Serratia marcescens, a phloem-colonizing, squash bug-transmitted bacterium: causal agent of cucurbit yellow vine disease Plant Dis 2003 87:937–944.
[9] Acar J. F. Serratia marcescens infections. Infect. Control. 1986; 7, N 5:273–278.
[10] Crowley D., Cryan B., Lucey B. First detection of a class 2 integron among clinical isolates of Serratia marcescens. Br. J. Biomed. Sci. 2008; 65, N 2:86–89.
[11] Miller J. H. Experiments in molecular genetics New York: Cold Spring Harbor Lab. Publ., 1972 436 p.
[12] LeBlanc D. J., Lee L. N. Rapid screening procedure for detection of plasmids in streptococci. J. Bacteriol. 1979; 140, N 3:1112–1115.
[13] Zhang Q., Melcher U., Zhou L., Najar F. Z., Roe B. A., Fletcher J. Genomic comparison of plant pathogenic and nonpathogenic Serratia marcescens strains by suppressive subtractive hybridization Appl. Environ. Microbiol 2005 71, N 12:7716–7723.
[14] Melcher U., Mitchell F., Fletcher J., Bruton B. New primer sets distinguish the cucurbit yellow vine bacterium from an insect endosymbiont. Phytopathology. 1999; 89, suppl P. 95–99.
[15] Podolich O., Laschevskyy V., Ovcharenko L., Kozyrovska N., Pirttila A. M. Methylobacterium sp. resides in unculturable state in potato tissues in vitro and becomes culturable after induction by Pseudomonas fluorescens IMGB163 J. Appl. Microbiol 2009–106, N 3:728–737.
[16] Liu W. T., Marsh T. L., Cheng H., Forney L. J. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Appl. Environ. Microbiol. 1997; 63, N 11 P. 4516–4522.
[17] Nield B. S., Holmes A. J., Gillings M. R., Recchia G. D., Mabbutt B. C., Nevalainen K. M. H., Stokes H. W. Recovery of new integron classes from environmental DNA FEMS Microbiol. Lett 2001 195, N 1:59–65.
[18] Stokes H. W., Holmes A. J., Nield B. S., Holley M. P., Nevalainen K. M. H., Mabbutt B. C., Gillings M. R. Gene cassette PCR: sequence-independent recovery of entire genes from environmental DNA Appl. Environ. Microbiol 2001 67, N 11:5240–5246.
[19] Levesque C., Piche L., Larose C., Roy P. H. PCR mapping of integrons reveals several novel combinations of resistance genes Antimicrob. Agents Chemother 1995 39, N 1 P. 185–191.
[20] Hu Z., Zhao W. H. Identification of plasmidand integronborne blaIMP-1 and blaIMP-10 in clinical isolates of Serratia marcescens J. Med. Microbiol 2009 58, pt 2:217– 221.
[21] Marty-Arbona R., Xu C., Steele S., Weeks A., Kuty G. F., Seibert C. M., Raushel F. M. Annotating enzymes of unknown function: N-formimino-L-glutamate deiminase is a member of the amidohydrolase superfamily Biochemistry 2006 45, N 7:1997–2005.
[22] Yew W., Gerlt J. Utilization of L-ascorbate by Escherichia coli K-12: assignments of functions to products of the yjf-sga and yia-sgb operons J. Bacteriol 2002 184, N 1:302–306.
[23] Gyaneshwar P., James E. K., Mathan N., Reddy P. M., Reinhold-Hurek B., Ladha E. K. Endophytic colonization of rice by a diazotrophic strain of Serratia marcescens J. Bacteriol 2001 183, N 8:2634–2645.
[24] Joss M., Koenig J., Labbate M., Polz M., Gillings M., Stokes H., Doolittle W., Boucher Y. ACID: annotation of cassette and integron data BMC Bioinformatics 2009 10:118–124.
[25] Kozyrovska N. O. Integrons as a key tool in bacteria evolution Biopolym. Cell. 2004 20, N 5:388–397.
[26] Peng C.-F., Lee M.-F., Fu H.-T., Chen Y.-J., Hsu H.-J. Characterization of class 1 integrons and antimicrobial resistance in CTX-M-3-producing Serrratia marcescens isolates from Southern Taiwan. Jpn. J. Infect. Dis. 2007; 60, N 5 P. 250–256.
[27] Recchia G. D., Hall R. M. Origins of the mobile gene cassettes found in integrons Trends Microbiol 1997 5, N 10 P. 389–394.
[28] Hu L., Phillips A. T. Organization and multiple regulation of histidine utilization genes in Pseudomonas putida. J. Bacteriol. 1988; 170, N 9:4272–4279.
[29] Taghavi S., Garafola C., Monchy S., Newman L., Hoffman A., Weyens N., Barac T., Vangronsveld J., van der Lelie D. Genome survey and characterization of endophytic bacteria exhibiting a beneficial effect on growth and development of poplar trees Appl. Environ. Microbiol 2009 75, N 3 P. 748–757.
[30] Kleerebezem M., Boekhorst J., van Kranenburg R., Molenaar D., Kuipers O. P., Leer R., Tarchini R., Peters S. A., Sandbrink H. M., Fiers M. W., Stiekema W., Lankhorst R. M., Bron P. A., Hoffer S. M., Groot M. N., Kerkhoven R., de Vries M., Ursing B., de Vos W. M., Siezen R. J. Complete genome sequence of Lactobacillus plantarum WCFS1 Proc Nat. Acad. Sci. USA 2003 100, N 4:1990–1995.
[31] Boucher Y., Nesbo C. L., Joss M. J., Robinson A., Mabbutt B. C., Gillings M. R., Doolittle W. F., Stokes H. W. Recovery and evolutionary analysis of complete integron gene cassette arrays from Vibrio BMC Evol. Biol 2006 6:3–8.
[32] Li X., Shi L., Yang W., Li L., Yamasaki Sh. New array of aacA4-catB3-dfrA1 gene cassettes and a noncoding cassette from a class-1-integron-positive clinical strain of Pseudomonas aeruginosa Antimicrob. Agents Chemother 2006 50, N 6:2278–2279.