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Revista Latinoamericana de Microbiología

2008, Number 1-2

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Microbiología 2008; 50 (1-2)

Physical and genetic map of the Gluconacetobacter diazotrophicus PAL5 chromosome

Martins LM, Bertalan M, Silva TA, Mega FL, Muniz PVL, Baldani JI, Bonifácio MO, Gomes FPC

Language: English
References: 40
Page: 19-28
PDF size: 191.07 Kb.


ABSTRACT

A macrorestriction map of the Gluconacetobacter diazotrophicus PAL5, an important nitrogen-fixing endophyte of several plants such as sugarcane, coffee, sweet potato and pineapple, was constructed using pulsed-field gel electrophoresis (PFGE) and DNA hybridization. For PFGE analysis, single and double digestions of the chromosome were carried out with I-CeuI, SwaIand PacI restriction enzymes. The resulting DNA fragments were positioned into physical map, using combinatory analysis of hybridization results, restriction enzymes sites position and DNA fragments length. G. diazotrophicus has 4 rrn operons into a circular chromosome, with estimated length of 4,240 Kb ± 41.6 Kb. The hybridization results allowed the positioning of 42 genetic markers on chromosome (39 single copy and 3 repeated elements), as well as the detection of 1 rrn operon with inverted orientation. The results contained in this paper were important to finish the genome assembly of the G. diazotrophicus PAL5, which was deposited and is available in the EMBL database.


REFERENCES

  1. Baldani JI, Baldani VLD. 2005. History on the biological nitrogen fixation research in graminaceous plants: special emphasis on the Brazilian experience. An. Acad. Bras. Ciênc. 77(3): 549-579.

  2. Baldani JI, Caruso L, Baldani VLD, Goi SR, Döbereiner J. 1997. Recent advances in BNF with non-legume plants. Soil Biol. Biochem. 29: 911-922.

  3. Blanco Y, Arroyo M, Legaz ME, Vicente C. 2005. Isolation from Gluconacetobacter diazotrophicus cell walls of specific receptors for sugarcane glycoproteins, which act as recognition factors. J. Chromatogr. 1093: 204-211.

  4. Blank WA, Stemke GW. 2000. A physical and genetic map of the Mycoplasma hyopneumoniae strain J genome. Can. J. Microbiol. 46: 832-840.

  5. Capela D, Barloy-Hubler F, Gouzy J, Bothe G, Ampe F, Batut J, Boistard P, Becker A, Boutry M, Cadieu E, Dréano S, Gloux S, Godrie T, Goffeau A, Kahn D, Kiss E, Lelaure V, Masuy D, Pohl T, Portetelle D, Pühler A, Purnelle B, Ramsperger U, Renard C, Thébault P, Vandenbol M, Weidner S, Galibert F. 2001. Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021. Proc. Natl. Acad. Sci. USA. 98: 9877-9882.

  6. Chan JWYF, Goodwin PH. 1999. A physical map of the chromosome of Xanthomonas campestris pv. Phaseoli var. fuscans BXPF65. FEMS Microbiol. Lett. 180: 85-90.

  7. Döbereiner J, Reis V, Lazarini AC. 1988. New N2 fixing bacteria in association with cereals and sugarcane, pp. 717–722. In H Bothe, FJ Briyn, WE Newton (Eds). Nitrogen Fixation. Gustav Fisher, Stuttgart, Cologne.

  8. Dudez AM, Chaillou S, Hissler L, Stentz R, Champomier-Vergès MC, Alpert CA, Zagorec M. 2002. Physical and genetic map of the Lactobacillus sakei 23K chromosome. Microbiology. 148: 421-431.

  9. El-Osta YGA, Hillier AJ, Davidson BE, Dobos M. 2002. Pulsed field gel electrophoretic analysis of the genome of Lactobacillus gasseri ATCC33323, and construction of a physical map. Electrophoresis. 23: 3321-3331.

  10. Estrada-de los Santos P, Bustillos-Cristales R, Caballero-Mellado J. 2001. Burkholderia, a genus rich in plant-associated nitrogen fixers with wide environmental and geographic distribution. Appl. Environ. Microbiol. 67: 2790-2798.

  11. Fischer K, Newton WE. 2005. Nitrogenase proteins from Gluconacetobacter diazotrophicus, a sugarcane-colonizing bacterium. Biochim. Biophys. ACTA. 1750: 154-165.

  12. Fuentes-Ramírez LE, Caballero-Mellado J, Sepúlveda J, Martínez-Romero E. 1999. Colonization of sugarcane by Acetobacter diazotrophicus is inhibited by high N-fertilization. FEMS Microbiol. Ecol. 29: 117-128.

  13. Gillis M, Kersters K, Hoste B, Janssens D, Kropprenstedt RM, Stephan MP, Teixeira KRS, Döbereiner J, Deley J. 1989. Acetobacter diazotrophicus sp. Nov., a nitrogen-fixing acetic acid bacterium associated with sugarcane. Int. J. Syst. Bacteriol. 39: 361-364.

  14. 14, Heber S, Hoheisel J, Vingron M. 2000. Application of bootstrap techniques to physical mapping. Genomics. 69: 235-241.

  15. 15, Kaneko T, Nakamura Y, Sato S, Minamisawa K, Uchiumi T, Sasamoto S, Watanabe A, Idesawa K, Irigushi M, Kawashima K, Kohara M, Matsumoto M, Shimpo S, Tsuruoka H, Wada T, Yamada M, Tabata S. 2002. Complete genomic sequence of Nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res. 9: 189-197.

  16. Lai Z, Jing J, Aston C, Clarke V, Apodaca J, Dimalanta ET, Carucci DJ, Gardner MJ, Mishra B, Anantharaman TS, Paxia S, Hoffman SL, Venter C, Huff EJ, Schwartz DC. 1999. A shotgun optical map of the entire Plasmodium falciparum genome. Nature. 23(3): 309-13.

  17. Lee S, Flores-Encarnación M, Contreras-Zentella M, Garcia-Flores L, Escamilla JE, Kennedy C. 2004. Indole-3-acetic acid biosynthesis is deficient in Gluconacetobacter diazotrophicus strains with mutations in cytochrome c biogenesis genes. J. Bacteriol. 186(16): 5384-5391.

  18. Llamas I, Sánchez MJ, Argandoña M, Béjar V, Quesada E, Moral AD. 2002. Analysis of the genome of the moderate halophile Halomonas eurihalina. Curr. Microbiol. 45: 233-239.

  19. Majumder R, Sengupta S, Khetawat G, Bhadra RK, Roychoudhury S, Das J. 1996. Physical map of the genome of Vibrio cholerae 569B and localization of genetic markers. J. Bacteriol. 178: 1105-1112.

  20. Marcone C, Seemüller E. 2001. A chromosome map of the European stone fruit yellows phytoplasma. Microbiology. 147: 1213-1221.

  21. Melkerson-Watson LJ, Rode CK, Zhang L, Foxman B, Bloch CA. 2000. Integrated genomic map from Uropathogenic Escherichia coli J96. Infect. Immun. 68: 5933-5942.

  22. Munõz-Rojas J, Caballero-Mellado J. 2003. Population dynamics of Gluconacetobacter diazotrophicus in sugarcane cultivars and its effect on plant growth. Microb. Ecol. 46: 454-464.

  23. Munõz-Rojas J, Fuentes-Ramírez LE, Caballero-Mellado J. 2005. Antagonism among Gluconacetobacter diazotrophicus strains in culture media and in endophytic association. FEMS Microbiol. Ecol. 54: 57-66.

  24. Muthukumarasamy R, Govindarajan M, Vadivelu M, Revathi G. 2006. N-fertilizer saving by the inoculation of Gluconacetobacter diazotrophicus and Herbaspirillum sp. in micropropagated sugarcane plants. Microbiol. Res. 161: 238-245.

  25. Muthukumarasamy R, Rebatí G, Seshadri S, Lakshminarasimhan C. 2002. Gluconacetobacter diazotrophicus (syn. Acetobacter diazotrophicus), a promising diazotrophic endophyte in tropics. Curr. Sci. 83(2): 137-145.

  26. Muthukumarasamy R, Revathi G, Vadivelu M. 2000. Antagonistic potential of N2-fixing Acetobacter diazotrophicus against Colletotrichum falcatum Went.: a causal organism of red-rot of sugarcane. Curr. Sci. 78: 1063-1065.

  27. Oana K, Okimura Y, Kawakami Y, Hayashida N, Shimosaka M, Okazaki M, Hayashi T, Ohnishi M. 2002. Physical and genetic map of Enterococcus faecium ATCC19434 and demonstration of intra and interspecific genomic diversity in enterococci. FEMS Microbiol. Lett. 207: 133-139.

  28. Padovan AC, Firrao G, Schneider B, Gibb KS. 2000. Chromosome mapping of the sweet potato little leaf phytoplasma reveals genome heterogeneity within the phytoplasmas. Microbiology. 146: 893-902.

  29. Piñon D, Casas M, Blanch M, Fontaniella B, Blanco Y, Vicente C, Solas MT, Legaz ME. 2002. Gluconacetobacter diazotrophicus, a sugar cane endosymbiont, produces a bacteriocin against Xanthomonas albilineans, a sugar cane pathogen. Microbiol. Res. 53: 345-351.

  30. Ramos-Díaz MA, Ramos JL. 1998. Combined Physical and genetic map of the Pseudomonas putida KT2440 chromosome. J. Bacteriol. 180: 6352-6363.

  31. Reis VM, Döbereiner J. 1998. Effect of high sugar concentration on nitrogenase activity of Acetobacter diazotrophicus. Arch. Microbiol. 171: 13-18.

  32. Reis VM, Olivares FL, Döbereiner J. 1994. Improved methodology for isolation and identification of Acetobacter diazotrophicus and confirmation of its endophytic habitat. World J. Microb. Biot. 10: 401-405.

  33. Römling U, Grothues D, Bautsch W, Tümmler B. 1989. A physical genome map of Pseudomonas aeruginosa PAO. EMBO J. 8: 4081-4089.

  34. Sambrook J, Russell DW. 2001. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.

  35. Shimizu T, Ohshima S, Ohtani K, Shimizu T, Hayashi H. 2001. Genomic map of Clostridium perfringens Strain 13. Microbiol. Immunol. 45: 179-189.

  36. Urquiaga S, Cruz HS, Boddey RM. 1992. Contribution of nitrogen fixation to sugarcane: nitrogen-15 and nitrogen-balance estimates. Soil Sci. Soc. Am. J. 56: 105-114.

  37. Villiers EP, Brayton KA, Zweygarth E, Allsopp BA. 2000. Genome size and genetic map of Cowdria ruminantium. Microbiology. 146: 2627-2634.

  38. Weinel C, Tümmler B, Hilbert H, Nelson KE, Kiewitz C. 2001. General method of rapid Smith/Birnstiel mapping adds for gap closure in shotgun microbial genome sequencing projects: application to Pseudomonas putida KT2440. Nucleic Acids Res. 29: e110.

  39. Widjaja R, Suwanto A, Tjahjono B. 1999. Genome size and macrorestriction map of Xanthomonas campestris pv. Glycines YR32 chromosome. FEMS Microbiol. Lett. 175: 59-68.

  40. Zé-Zé L, Tenreiro R, Paveia H. 2000. The Oenococcus oeni genome: physical and genetic mapping of strain GM and comparison with the genome of a divergent strain, PSU-1. Microbiology. 146: 3195-3204.




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