Genome size in bacteria

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 69, Issue 4, 1996, Pages 293-303

  Trevors, J T ^a  

^a UNIVERSITY OF GUELPH   (Canada)

Author keywords

Bacteria; Electrophoresis; Evolution; Genome; Microbiology; Restriction modification

Indexed keywords

RESTRICTION ENDONUCLEASE;

BACTERIAL GENETICS; DNA CLEAVAGE; DNA RECOMBINATION; EVOLUTION; GENE MAPPING; GENOME; MOLECULAR WEIGHT; NONHUMAN; PRIORITY JOURNAL; REVIEW;

BACTERIA (MICROORGANISMS);

EID: 0030055201     PISSN: 00036072     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF00399618     Document Type: Review

References (73)

1. Anagnostopoulos C, Piggot PJ & Hoch JA (1993) The genetic map of Bacillus subtilis. In: Sonenshein AL, Hoch JA & Losick R (Eds) Bacillus subtilis and Other Gram-Positive Bacteria. (pp 425-461) Am. Soc. Microbiol., Washington, DC
2. Bachman BJ (1987) Linkage map of Escherichia coli K12, edition 7. In: Ingraham JL, Low KB, Magasanik B, Schaechter M & Umbarger HE (Eds) Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, Vol. 2. (pp 807-876) Am. Soc. Microbiol., Washington, DC
3. Bakken LR & Olsen RA (1989) DNA-content of soil bacteria of different cell size. Soil Biol. Biochem. 21: 789-793
4. Bautsch W, Grothnes E & Tummler B (1988) Genome fingerprinting of Pseudomonas aeruginosa by two-dimensional field inversion gel electrophoresis. FEMS Microbiol. Lett. 52: 255-258
5. Bennett PM & Grinsted J (Eds) (1984) Methods in Microbiology: Plasmid technology Vol. 17. Academic Press, New York
6. Blackburn GM & Gait MJ (1990) Nucleic Acids in Chemistry and Biology. IRL Press, Oxford, UK
7. Boehringer Mannheim GmbH, Biochemica (1993) Guide to Genome Analysis and Mapping, Mannheim 31, Germany
8. Boronin AM (1992a) Diversity of Pseudomonas plasmids: to what extent? FEMS Microbiol. Lett. 100: 461-468
9. _ (1992b) Diversity and relationship of Pseudomonas plasmids. In: Galli E, Silver S, Witholt B (Eds) Pseudomonas: Molecular Biology and Biotechnology (pp 329-340) Am. Soc. Microbiol., Washington, DC
10. Bourgeois Le P, Mata M & Ritzenthaler P (1989) Genome comparison of Lactococcus strains by pulsed-field gel electrophoresis. FEMS Microbiol. Lett. 59: 65-70
11. Brock TD & Madigan M (1991) Biology of Microorganisms. Prentice Hall, Englewood Cliffs, New Jersey
12. Broda P (1979) Plasmids. Freeman, San Francisco, CA
13. Carle GF & Olsen MV (1987) Orthogonal-field-alternation gel electrophoresis. In: Wu R (Ed) Methods in Enzymology: Recombinant DNA Vol. 155 (pp 468-482) Academic Press, New York
14. Carle GF, Frank M & Olsen MV (1986) Electrophoretic separations of large DNA molecules by periodic inversion of the electric field. Science 232: 65-68
15. Chater KF & Hopwood DA (1989a) Diversity of bacterial genetics. In: Hopwood DA & Chater KF (Eds) Genetics of Bacterial Diversity (pp 23-52) Academic Press, New York
16. Charlebois RL, Hofman JD, Schalkwyk LC, Lam WL & Doolittle WF (1989) Genome mapping in halobacteria. Can. J. Microbiol. 35: 21-29
17. Chu G, Vollrath D & Davis RW (1986) Separation of large DNA molecules by contour-clamped homogeneous electric fields. Science 234: 1582-1585
18. Claus H, Rotlich H & Filip Z (1992) DNA fingerprints of Pseudomonas spp. using rotating field electrophoresis. Microb. Releases 1: 11-16
19. Coetzee DJ, Kock JLF & Pretorias GHJ (1987) The value of orthognonal-field-alternation gel electrophoresis as a rapid identification process for some species representing the genus Saccharomyces. J. Microbiol. Meths. 7: 219-223
20. Cooper S (1991) Bacterial. Growth and Division, Academic Press, New York
21. Dawson C, Owen RJ & Beck A (1987) A method for rapid extraction of Providencia chromosomal DNA and restriction enzyme digestion in agarose pellets. Lett. Appl. Microbiol. 5: 41-45
22. Dobritsa SV (1985) Restriction analysis of the Frankia spp. genome. FEMS Microbiol. Lett. 29: 123-128
23. Douglas SE & Carr N (1988) Examination of genetic relatedness of marine Synechococcus spp. by using restriction fragment length polymorphisms. Appl. Environ. Microbiol. 54: 3071-3078
24. Finnen RL, Dhanvantari BN & Trevors JT (1990) Restriction endonuclease digestion and field inversion agarose gel electrophoresis of genome DNA and conventional agarose gel electrophoresis of plasmids of Clavibacter michiganensis pv. michiganensis. J. Microbiol. Meths. 12: 57-64
25. Flanagan JL, Ventra L & Weiss AS (1989) Rapid methods for preparation and cleavage of bacterial DNA for pulsed-field electrophoresis. Nucleic Acids Res. 17: 814
26. FMC Bioproducts (1988) Dissolving InCert agarose for preparation of gel plugs. FMC Bioproducts, Rockland ME, USA
27. Genthner FJ, Hook LA, Strohl WR (1985) Determination of the molecular mass of bacterial genomic DNA and plasmid copy number by high-pressure liquid chromatography. Appl. Environ. Microbiol. 50: 1007-1013
28. Giovannnetti L, Ventura S, Bazzicalupo M, Fani M, Materassi R (1990) DNA restriction fingerprint analysis of the soil bacterium Azospirillium. J. Gen. Microbiol. 136: 1161-1166
29. Grimont F & Grimont PAD (1991) DNA fingerprinting. In: Stackebrandt & Goodfellow M (Eds) Nucleic Acid Techniques in Bacterial Systematics (pp 249-279) John Wiley, New York
30. Grothues D & Tummler D (1987) Genome analysis of Pseudomonas aeruginosa by field inversion gel electrophoresis. FEMS Microbiol. Lett. 48: 419-422
31. Holloway BW & Morgan AF (1986) Genome organization in Pseudomonas. Ann. Rev. Microbiol. 40: 79-105
32. Holloway BW, Escuadra MD, Morgan AF, Saffery R & Krishnapillai (1992) The new approaches to whole genome analysis of bacteria. FEMS Microbiol. Lett. 100: 101-106
33. Itaya M (1993) Physical map of the Bacillus subtilis 168 chromosome. In: Sonenshein AL, Hoch JA & Losick R (Eds) Bacillus subtilis and Other Gram-Positive Bacteria (pp 463-471) Am. Soc. Microbiol., Washington, DC
34. Jordens JZ & Hall LMC (1988) Characterisation of methicillin-resistant Staphylococcus aureus isolates by restriction endonuclease digestion of chromosomal DNA. J. Med. Microbiol. 27: 117-123
35. Kessler C, Neumaier PS & Wolf W (1985) Recognition sequences of restriction endonucleases and methylases - a review. Gene 33: 1-102
36. Krawiec S & Riley M (1990) Organization of the bacterial chromosome. Microbiol. Rev. 54: 502-539
37. Kreig NR & Holt JG (1984) Bergey's Manual of Systematic Bacteriology Vol. 1-4. Williams and Wilkins, Baltimore
38. Kucherlapati R & Smith GR (Eds) (1988) Genetic Recombination. Am. Soc. Microbiol., Washington, DC
39. Kuijper EJ, Oudbier JH, Stuifbergen WNHM, Jansz A & Zanen HC (1987) Application of whole-cell DNA restriction endonuclease profiles to the epidemology of Clostridium difficile-induced diarrhea. J. Clin. Microbiol. 25: 751-753
40. Lee JJ, Smith HO & Redfield RJ (1989) Organization of the Haemophilus influenzae Rd genome. J. Bacteriol. 171: 3016-3024
41. Leung K, Trevors JT, Elsas JD van (1995a) Extraction and amplification of DNA from the rhizosphere and rhizoplane of plants. In: Trevors JT & Elsas JD van (Eds) Nucleic Acids in the Environment: Methods and Applications. Springer-Verlag, Germany
42. Leung K, Cassidy MB, Holmes SB, Lee H & Trevors JT (1995b) Survival of k-carrageenan-encapsulated and unencapsulated Pseudomonas aeruginosa UG2Lr cells in forest soil monitored by polymerase chain reaction and spread plating. FEMS Microbiol. Ecol. 16: 71-82
43. Levine JD (1991) Low frequency restriction enzymes in pulsed field electrophoresis. Bio/Technology 9: 1033-1036
44. McClelland M, Jones R, Patel Y & Nelson M (1987) Restriction endonucleases for pulsed field mapping of bacterial genomes. Nucleic Acids Res. 15: 5985
45. Mielenz JR, Jackson LE, O'Hara F & Shanmugam KT (1979) Fingerprinting bacterial chromosomal DNA with restriction endonuclease EcoRI: comparison of Rhizobium spp. and identification of mutants. Can. J. Microbiol. 25: 803-807
46. Mortlock RP (Ed) (1992) The Evolution of Metabolic Function. CRC Press, Boca Raton, USA
47. Nagy A, Vagvolgyi C & Ferenczy L (1995) Simple method for obtaining chromosomal DNA for orthogonal filed alternation gel electrophoresis analysis of Phaffia rhodozyma. BioTechniques 18: 63-65
48. Owen RJ (1989) Chromosomal DNA fingerprinting - a new method of species and strain identification applicable to microbial pathogens. J. Med. Microbiol. 30: 89-99
49. Price C & Bickle TA (1986) A possible role for DNA restriction in bacterial evolution. Microbiol. Sci. 3: 296-299
50. Riley M (1989) Constancy and change in bacterial genomes. In: Poindexter JS & Leadbetter ER (Eds) Bacteria in Nature (pp 359-388) Plenum Press, New York
51. Riley M & Krawiec S (1987) Genome organization. In: Ingraham JL, Low KB, Magasanik B, Schaechter M & Umbarger HE (Eds) Escherichia coli and Salmonella typhimurium: Cellular and MolecularBiology, Vol. 2 (pp 967-981) Am. Soc. Microbiol., Washington, DC
52. Riley M & Drlica K (Eds) The Bacterial Chromosome. Am. Soc. Microbiol., Washington, DC
53. Romling U, Grouthes D, Bautsch W & Tummler B (1992) A physical map of Pseudomonas aeruginosa. EMBO J. 8: 4081-4089
54. Sambrook J, Fritsch EF & Maniatis T (1989) Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor
55. Sanderson KE & Jurley JA (1987) Linkage map of Salmonella typhimurium. In: Ingraham JL, Low KB, Magasanik B, Schaechter M & Umbarger HE (Eds) Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, Vol. 2 (pp 877-918) Am. Soc. Microbiol., Washington, DC
56. Schwartz DC & Cantor CR (1984) Separation of yeast chromosome-sized DNAs by pulsed filed gradient gel electrophoresis. Cell 37: 67-75
57. Smith CL & Cantor CR (1987) Purification, specific fragmentation and separation of large DNA molecules. In: Wu R (Ed) Methods in Enzymology: Recombinant DNA, Vol. 155 (pp 449-467) Academic Press, New York
58. Smith CL & Condemine G (1990) New approaches for physical mapping of small genomes. J. Bacteriol. 172: 1167-1172
59. Sonenshein AL, Hoch JA & Losick R (Eds) (1993) Bacillus subtilis and Other Gram-Positive Bacteria. Am. Soc. Microbiol., Washington, DC
60. Sorbal BWS, Sadowsky MJ & Atherly AG (1990) Genome analysis of Bradyrhizobium japonicum serocluster 123 field isolates by using field inversion gel electrophoresis. Appl. Environ. Microbiol. 56: 1949-1953
61. Stouthamer AH & Kooijman SALM (1989) Why it pays for bacteria to delete disused DNA and to maintain megaplasmids. Antonie van Leeuwenhoek 63: 39-43
62. Thomas CM (1987) Plasmid replication. In: Hardy KG (Ed) Plasmids: A practical Approach (pp 7-36) IRL Press, Oxford, UK
63. Trevors JT (1985) Bacterial plasmid isolation and purification. J. Microbiol. Meths. 3: 259-271
64. _ (1992) Extraction of DNA from soil: a review. Microbial Releases 1: 3-9
65. Trevors JT & Finnen RL (1992) Bacterial genome analysis by field inversion agarose gel electrophoresis. Am. Biol. Teacher 54: 226-229
66. Vary PS (1993) The genetic map of Bacillus megaterium. In: Sonenshein AL, Hoch JA & Losick R (Eds) Bacillus subtilis and Other Gram-Positive Bacteria (pp 425-461) Am. Soc. Microbiol., Washington, DC
67. Viljoen BC, Kock JLF & Coetzee DJ (1988) Orthogonal-field-alternation gel electrophoresis banding patterns of some asporogenous yeast and their respective ascosporogenous states. System. Appl. Microbiol. 10: 228-230
68. Wallace DC & Morowitz HJ (1973) Genome size and evolution. Chromosoma 40: 121-126
69. Wren BW & Tabaqchali S (1987) Restriction endonuclease DNA analysis of Clostridium difficile. J. Clin. Microbiol. 25: 2402-2404
70. Young JPW (1989) The population genetics of bacteria. In: Hopwood DA & Chater KF (Eds) Genetics of Bacterial Diversity (pp 417-438) Academic Press, New York
71. Young M & Cole ST (1993) Clostridium. In: Sonenshein AL, Hoch JA & Losick R (Eds) Bacillus subtilis and Other Gram-Positive Bacteria (pp 35-52) Am. Soc. Microbiol., Washington, DC
72. Ziegler A, Geiger KH, Ragoussis J & Szalay G (1987) A new electrophoresis apparatus for separating very large DNA molecules. J. Clin. Chem. Clin. Biochem. 25: 578
73. Zar JH (1974) Biostatistical Analysis. Prentice-Hall, Inc., Englewood Cliffs, New Jersey