Identification and localization of differences between Escherichia coli and Salmonella typhimurium genomes by suppressive subtractive hybridization

Molecular and General Genetics

Volumn 262, Issue 4-5, 1999, Pages 721-729

  Bogush, M L ^a   Velikodvorskaya, T V ^a   Lebedev, Yu B ^a   Nikolaev, L G ^a   Lukyanov, S A ^a   Fradkov, A F ^a   Pliyev, B K ^a   Boichenko, M N ^b   Usatova, G N ^b   Vorobiev, A A ^b   Andersen, G L ^c   Sverdlov, E D ^a  

^a SHEMYAKIN OVCHINNIKOV INSTITUTE OF BIOORGANIC CHEMISTRY   (Russian Federation)

^b I M SECHENOV FIRST MOSCOW STATE MEDICAL UNIVERSITY   (Russian Federation)

^c LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

Author keywords

Escherichia coli; Salmonella typhimurium; Subtractive hybridization

Indexed keywords

BACTERIAL DNA;

ARTICLE; DNA HYBRIDIZATION; ESCHERICHIA COLI; EVOLUTION; GENE MAPPING; GENE SEQUENCE; GENETIC ANALYSIS; NONHUMAN; PRIORITY JOURNAL; SALMONELLA TYPHIMURIUM; SPECIES DIFFERENCE;

BASE SEQUENCE; DNA PRIMERS; ESCHERICHIA COLI; GENOME, BACTERIAL; NUCLEIC ACID HYBRIDIZATION; SALMONELLA TYPHIMURIUM; SUBTRACTION TECHNIQUE;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA; PROKARYOTA; SALMONELLA TYPHIMURIUM; TYPHIMURIUM;

EID: 17444450836     PISSN: 00268925     EISSN: None     Source Type: Journal    
DOI: 10.1007/s004380051134     Document Type: Article

References (43)

1. Abouhamad WN, Manson MD (1994) The dipeptide permease of Escherichia coli closely resembles other bacterial transport systems and shows growth-phase-dependent expression. Mol Microbiol 14:1077-1092
2. Akopyants NS, Fradkov A, Diatchenko L, Hill JE, Siebert PD, Lukyanov SA, Sverdlov ED, Berg DE (1998) PCR-based subtractive hybridization and differences in gene content among strains of Helicobacter pylori. Proc Natl Acad Sci USA 95:13108-13113
3. 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
4. Blattner FR, et al (1997) The complete genome sequence of Escherichia coli K-12. Science 277:1453-1461
5. Brown PK, Curtis R III (1996) Unique chromosomal regions associated with virulence of an avian pathogenic Escherichia coli strain. Proc Natl Acad Sci USA 93:11149-11154
6. Diatchenko L, Lau YF, Campbell AP, Chenchik A, Moqadam F, Huang B, Lukyanov S, Lukyanov K, Gurskaya N, Sverdlov ED, Siebert PD (1996) Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci USA 93:6025-6030
7. Galakatos NG, Daub E, Botstein D, Walsh CT (1986) Biosynthetic alr alanine racemase from Salmonella typhimurium: DNA and protein sequence determination. Biochemistry 25:3255-3260
8. Giaever HM, Styrvold OB, Kaasen I, Strom AR (1988) Biochemical and genetic characterization of osmoregulatory trehalose synthesis in Escherichia coli. J Baceriol 170:2841-2849
9. Graumann PL, Marahiel MA (1998) A superfamily of proteins that contain the cold-shock domain. Trends Biochem Sci 23:286-290
10. Gurskaya NG, Diatchenko L, Chenchik A, Siebert PD, Khaspekov GL, Lukyanov KA, Vagner LL, Ermolaeva OD, Lukyanov SA, Sverdlov ED (1996) Equalizing cDNA subtraction based on selective suppression of polymerase chain reaction: cloning of Jurkat cell transcripts induced by phytohemaglutinin and phorbol 12-myristate 13-acetate. Anal Biochem 240:90-97
11. Heinrichs DE, Yethon JA, Whitfield C (1998) Molecular basis for structural diversity in the core region of the lipopolysaccarides of Escherichia coli and Salmonella enterica. Mol Microbiol 30:221-232
12. Heinzinger NK, Fujimoto SY, Clark MA, Moreno MS, Barrett EL (1995) Sequence analysis of the phs operon in Salmonella typhimurium and the contribution of thiosulfate reduction to anaerobic energy metabolism. J Bacteriol 177:2813-2820
13. Hill CW, Sandt CH, Vlazny DA (1994) Rhs elements of Escherichia coli: a family of genetic composites each encoding a large mosaic protein. Mol Microbiol 12:865-871
14. Kaniga K, Trollinger D, Galan JE (1995) Homologs of the Shigella IpaB and IpaC invasins are required for Salmonella typhimurium entry into cultured epithelial cells. J Bacteriol 177:7078-7085
15. Kimata K, Inada T, Tagami H, Aiba H (1998) A global represser (Mlc) is involved in glucose induction of the ptsG gene encoding major glucose transporter in Escherichia coli. Mol Microbiol 29:1509-1519
16. Kwon O, Bhattacharyya DK, Meganathan R (1996) Menaquinone (vitamin K2) biosynthesis: overexpression, purification, and properties of o-succinylbenzoyl-coenzyme A synthetase from Escherichia coli. J Bacteriol 178:6778-6781
17. Lawrence JG, Ochman H (1998) Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci USA 95:9413-9417
18. Lazar SW, Almiron M, Tormo A, Kolter R (1998) Role of the Escherichia coli SurA protein in stationary-phase survival. J Bacteriol 180:5704-5711
19. Lin RJ, Capage M, Hill CW (1984) A repetitive DNA sequence, rhs, responsible for duplications within the Escherichia coli K-12 chromosome. J Mol Biol 177:1-18
20. Lukyanov KA, Launer GA, Tarabykin VS, Zaraisky AG, Lukyanov SA (1995) Inverted terminal repeats permit the average length of amplified DNA fragments to be regulated during preparation of cDNA libraries by polymerase chain reaction. Anal Biochem 229:198-202
21. Mahairas GG, Sabo PJ, Hickey MJ, Singh DC, Stover CK (1996) Molecular analysis of genetic differences between Mycobacterium bovis BCG and virulent M. bovis. J Bacteriol 178:1274-1282
22. Maneewannakul S, Maneewannakul K, Ippen-Ihler K (1992) Characterization, localization, and sequence of F transfer region products: the pilus assembly gene product TraW and a new product, TrbI. J Bacteriol 174:5567-5574
23. Merkel WK, Nickols BP (1996) Characterization and sequence of the Escherichia coli panBCD gene cluster. FEMS Microbiol Lett 143:247-252
24. Murray MG, Thompson WF (1980) Rapid isolation of high-molecular-weight plant DNA. Nucleic Acids Res 8:4321-4325
25. Mushegian AR, Koonin EV (1996) A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc Natl Acad Sci USA 93:10268-10273
26. Park SJ, Chao G, Gunsalus RP (1997) Aerobic regulation of the suc ABCD genes of Escherichia coli, which encode alpha-keto-glutarate dehydrogenase and succinyl coenzyme A synthetase: roles of ArcA, Fnr, and the upstream sdhCDAB promoter. J Bacteriol 179:4138-4142
27. Parker CT, Pradel E, Schnaitman CA (1992) Identification and sequences of the lipopolysaccharide core biosynthetic genesrfaQ, rfaP, and rfaG of Escherichia coli K-12. J Bacteriol 174:930-934
28. Pradel E, Parker CT, Schnaitman CA (1992) Structures of the rfaB, rfaI, rfaJ, and rfaS genes of Escherichia coli K-12 and their roles in assembly of the lipopolysaccharide core. J Bacteriol 174:4736-4745
29. Rice SA, Bieber J, Chun JY, Stacey G, Lampson BC (1993) Diversity of retron elements in a population of Rhizobia and other gram-negative bacteria. J Bacteriol 175:4250-4254
30. Riley M, Krawiec S (1987) Genome organization. In: Neidhardt FC, Ingraham JL, Low KB, Magasanik B, Schaechter M, Umbarger HE (eds) Escherichia coli and Salmonella typhimurium: cellular and molecular biology. American Society for Microbiol, Washington DC, pp 967-981
31. Riley M, Sanderson KE (1990) Comparative genetics of Escherichia coli and Salmonella typhimurium. In: Drlica K, Riley M (eds) The Bacterial chromosome. American Society for Microbiology, Washington DC, pp 85-95
32. Roux B, Walsh CT (1993) p-Aminobenzoate synthesis in Escherichia coli: mutational analysis of three conserved amino acid residues of the amidotransferase PabA. Biochemistry 32:3763-3768
33. Sadosky AB, Davidson A, Lin RJ, Hill CW (1989) rhs gene family of Escherichia coli K-12. J Bacteriol 171:636-642
34. Silverstone AE, Goman M, Scaife JG (1972) Alt: a new factor involved in the synthesis of RNA by E. coli. Mol Gen Genet 118:223-234
35. Somers JM, Kay WW (1983) Genetic fine structure of the tricarboxylate transport (tct) locus of Salmonella typhimurium. Mol Gen Genet 190:20-26
36. Strathdee CA, Johnson WM (1995) Identification of epidemiologic markers for Neisseria meningitidis using difference analysis. Gene 166:105-110
37. Styrvold OB, Strom AR (1991) Synthesis, accumulation, and excretion of trehalose in osmotically stressed Escherichia coli K-12 strains: influence of amber suppressors and function of the periplasmic trehalase. J Bacteriol 173:1187-1192
38. Suh S, Escalante-Semerena JC (1995) Purification and initial characterization of the ATP: corrinoid adenosyltransferase encoded by the cob A gene of Salmonella typhimurium. J Bacteriol 177:921-925
39. Tas E, Kaijalainen S, Saano A, Lindstrom K (1994) Isolation of a Rhizobium galegae strain-specific DNA probe. Microb Releases 2:231-237
40. Tinsley CR, Nassif X (1996) Analysis of the genetic differences between Neisseria meningitidis and Neisseria gonorrhoeae: two closely related bacteria expressing two different pathogenicities. Proc Natl Acad Sci USA 93:11109-11114
41. Watarai M, Tobe T, Yoshikawa M, Sasakawa C (1995) Contact of Shigella with host cells triggers release of Ipa invasins and is an essential function of invasiveness. EMBO J 14:2461-2470
42. Wigley DB, Derrick JP, Shaw WV (1990) The serine acetyltransferase from Escherichia coli. Over-expression, purification and preliminary crystallographic analysis. FEBS Lett 277:267-271
43. Yamanaka K, Fang L, Inouye M (1998) The CspA family in Escherichia coli: multiple gene duplication for stress adaptation. Mol Microbiol 27:247-255