Stem-loop structures in prokaryotic genomes

BMC Genomics

Volumn 7, Issue , 2006, Pages

  Petrillo, Mauro ^a   Silvestro, Giustina ^b   Di Nocera, Pier Paolo ^b   Boccia, Angelo ^a   Paolella, Giovanni ^a,b,c  

^a CEINGE BIOTECNOLOGIE AVANZATE   (Italy)

^b UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^c UNIVERSITY OF MOLISE   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; RNA; SPACER DNA; URIDINE;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENOME; BORDETELLA; CHROMOSOME ANALYSIS; CONTROLLED STUDY; ENTEROCOCCUS; FIRMICUTES; GENE FREQUENCY; GENE STRUCTURE; GENETIC TRANSCRIPTION; GENOME ANALYSIS; NONHUMAN; PROKARYOTE; PROMOTER REGION; RANDOM SAMPLE; STRAIN DIFFERENCE; STRUCTURE ANALYSIS; YERSINIA;

BASE COMPOSITION; DNA SHUFFLING; DNA, BACTERIAL; GENOME, BACTERIAL; NUCLEIC ACID CONFORMATION; REPETITIVE SEQUENCES, NUCLEIC ACID; SPECIES SPECIFICITY;

BACTERIA (MICROORGANISMS); FIRMICUTES; PROKARYOTA;

EID: 33749565015     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-170     Document Type: Article

References (51)

1. Borodina I, Krabben P, Nielsen J: Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism. Genome Res 2005, 15:820-829.
2. Hayashi T, Makino, K, Ohnishi M, Kurokawa K, Ishii K, Yokoyama K, Han CG, Ohtsubo E, Nakayama K, Murata T, Tanaka M, Tobe T, lida T, Takami H, Honda T, Sasakawa C, Ogasawara N, Yasunaga T, Kuhara S, Shiba T, Hattori M, Shinagawa H: Complete genome sequence of enterohemorrhagic Escherichia coll O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res 2001, 8:11-22.
3. Dobrindt U, Agerer F, Michaelis K, Janka A, Buchrieser C, Samuelson M, Svanborg C, Gottschalk G, Karch H, Hacker J: Analysis of genome plasticity in pathogenic and commensal Escherichia coli isolates by use of DNA arrays. J Bacterial 2003, 185:1831-1840.
4. Grifantini R, Bartolini E, Muzzi A, Draghi M, Frigimelica E, Berger J, Ratti G, Petracca R, Galli G, Agnusdei M, Giuliani MM, Santini L, Brunelli B, Tettelin H, Rappuoli R, Randazzo F, Grandi G: Previously unrecognized vaccine candidates against group B meningococcus identified by DNA microarrays. Nat Biotechnol 2002, 20:914-921.
5. Frank AC, Amiri H, Andersson SG: Genome deterioration, loss of repeated sequences and accumulation of junk DNA. Genetica 2002,115:1-12.
6. Achaz G, Coissac E, Netter P, Rocha EP: Associations between inverted repeats and the structural evolution of bacterial genomes. Genetics 2003, 164:1279-1289.
7. Audit B, Ouzounis CA: From genes to genomes, universal scale-invariant properties of microbial chromosome organisation. J Mol Biol 2003, 332:617-633.
8. Rocha EP, Danchin A: Gene essentiality determines chromosome organisation in bacteria. Nucleic Acids Res 2003, 31:6570-6577.
9. Chain PS, Carniel E, Larimer FW, Lamerdin J, Stoutland PO, Regala WM, Georgescu AM, Vergez LM, Land ML, Motin VL, Brubaker RR, Fowler J, Hinnebusch J, Marceau M, Medigue C, Simonet M, Chenal-Francisque V, Souza B, Dacheux D, Elliott JM, Derbise A, Hauser LJ, Garcia E: Insights into the evolution of Yersinia. pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc Natl Acad Sci U S A 2004, 101:13826-13831.
10. Hallin PF, Ussery DW. CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data. Bioinformatics 2004, 20:3682-3686.
11. van Belkum A, van Leeuwen W, Scherer S, Verbrugh H: Occurrence and structure-function relationship of pentameric short sequence repeats in microbial genomes. Res Microbiol 1999, 150:617-626.
12. Salaun L, Linz B, Suerbaum S, Saunders NJ: The diversity within an expanded and redefined repertoire of phase-variable genes in Helicobacter pylori. Microbiology 2004, 150:817-830.
13. Seffens W, Digby D: RNAs have greater negative folding free energies than shuffled or codon choice randomized sequences. Nucleic Acids Res 1999, 27:1578-1584.
14. Workman C, Krogh A: No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. Nucleic Acids Res 1999, 27:4816-4822.
15. Katz L, Burge CB: Widespread selection for local RNA secondary structure in coding regions of bacterial genes. Genome Res 2003, 13:2042-2051.
16. Henkin TM, Yanofsky C: Regulation by transcription attenuation in bacteria, how RNA provides instructions for transcription termination/ antitermination decisions. Bioessays 2002, 8:700-707.
17. Berg BL, Baron C, Stewart V: Nitrate-inducible formate, dehydrogenase in E. coll K12. II. Evidence that a mRNA stemloop structure is essential for decoding opal (UGA) as selenocysteine. J Biol Chem 1991, 33:22386-22391.
18. Martínez-Abarca F, Toro N: Group II introns in the bacterial world. Mol Microbiol 2000, 38:917-926.
19. Nudler E, Mironov AS: The riboswitch control of bacterial metabolism. Trends Biochem Sci 2004, 29:11-17.
20. Coburn GA, Mackie GA: Degradation of mRNA in Escherichia coli: an old problem with some new twists. Prog Nucleic Acid Res Mol Biol 1999, 62:55-108.
21. Gilson E, Saurin W, Perrin D, Bachellier S, Hofnung M: The BIME family of bacterial highly repetitive sequences. Res Microbiol 1991, 142:217-222.
22. De Gregorio E, Abrescia C, Carlomagno MS, Di Nocera PP: Ribonuclease III-mediated processing of specific Neisseria meningitidis mRNAs. Biochem J 2003, 374:799-805.
23. De Gregorio E, Silvestro G, Petrillo M, Carlomagno MS, Di Nocera PP: Genomic organization and functional properties of ERIC DNA repeats in Yersiniae. J Bact 2005, 187:7945-7954.
24. Krasilnikov AS, Podtelezhnikov A, Vologodskii A, Mirkin SM: Largescale effects of transcriptional DNA supercoiling in vivo. J Mol Biol 1999, 292:1149-1160.
25. Jin R, Novick RP: Role of the double-strand origin cruciform in pT181 replication. Plasmid 2001, 46:95-105.
26. Yamada K, Ariyoshi M, Morikawa K: Three-dimensional structural views of branch migration and resolution in DNA homologous recombination. Curr Opin Struct Biol 2004, 14:130-137.
27. Smith HO, Gwinn ML, Salzberg SL: DNA uptake signal sequences in naturally transformable bacteria. Res Microbial 1999, 150:603-616.
28. Davidsen T, Rodland EA, Lagesen K, Seeberg E, Rognes T, Tonjum T: Biased distribution of DNA uptake sequences towards genome maintenance genes. Nucleic Acids Res 2004, 32:1050-1058.
29. Parkhill J, Achtman M, James KD, Bentley SD, Churcher C, Klee SR, Morelli G,.Basham D, Brown D, Chillingworth T, Davies RM, Davis P, Devlin K, Feltwell T, Hamlin N, Holroyd S, Jagels K. Leather S, Moule S, Mungall K, Quail MA, Rajandream MA, Rutherford KM, Simmonds M, Skelton J, Whitehead S, Spratt BG, Barrell BG: Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491. Nature 2000, 404:502-506.
30. Claverie JM, Ogata H: The insertion of palindromic repeats in the evolution of proteins. Trends Biochem Sci 2003, 28:75-80.
31. Ermolaeva MD, Khalak HG, White O, Smith HO, Salzberg SL: Prediction of transcription terminators in bacterial genomes. J Mol Biol 2000, 301:27-33.
32. Lesnik EA, Sampath R, Levene HB, Henderson TJ, McNeil JA, Ecker DJ: Prediction of rho-independent transcriptional terminators in Escherichia coli. Nucleic Acids Res 2001, 29:3583-3594.
33. Unniraman S, Prakash R, Nagaraja V: Conserved economics of transcription termination in eubacteria. Nucleic Acids Res 2002, 30:675-684.
34. Bachellier S, Clement JM, Hofnung M: Short palindromic repetitive DNA elements in enterobacteria: a survey. Res Microbiol 1999, 150:627-639.
35. Aranda-Olmedo I, Tobes R, Manzanera M, Ramos JL, Marques S: Species-specific repetitive extragenic palindromic (REP) sequences in Pseudomonas putida. Nucleic Acids Res 2002, 30:1826-1833.
36. Qi D, Cuticchia AJ: Compositional symmetries in complete genomes. Bioinformatics 2001, 17:557-559.
37. Baisnee PF, Hampson S, Baldi P: Why are complementary DNA strands symmetric? Bioinformatics 2002, 18:1021-1033.
38. Robin S, Daudin JJ, Richard H, Sagot MF, Schbath S: Occurrence probability of structured motifs in random sequences. J Comput Biol 2002, 9:761-773.
39. Ingham CJ, Tennis J, Furneaux PA: Autogenous regulation of transcription termination factor Rho and the requirement for Nus factors in Bacillus subtilis. Mol Microbial 1999, 31:651-663.
40. Washburn RS, Marra A, Bryant AP, Rosenberg M, Gentry DR. Rho is not essential for viability or virulence in Staphylococcus aureus. Antimicrob Agents Chemother 2001, 45: 1099-1103.
41. Yang MT, Scott HB 2nd, Gardner JF: Transcription termination at the thr attenuator Evidence that the adenine residues upstream of the stem and loop structure are not required for termination. J Biol Chem 1995, 270:23330-23336.
42. Carlomagno MS, Riccio A, Bruni CB: Convergently functional, Rho-independent terminator in Salmonella typhimurium. J Bacteriol 1985, 163:362-368.
43. Abe H, Aiba H: Differential contributions of two elements of rho-independent terminator to transcription termination and mRNA stabilization. Biochimie 1996, 78:1035-1042.
44. Cisneros B, Court D, Sanchez A. Montanez C: Point mutations in a transcription terminator, lambda tl, that affect both transcription termination and RNA stability. Gene 1996, 181:127-133.
45. Storz G, Altuvia S, Wassarman KM: An abundance of RNA regulator. Annu Rev Biochem 2005, 74:199-217.
46. PostgreSQL Project 2005 [http://www.postgresql.com/index.html].
47. Boccia A, Petrillo M, di Bernardo D, Guffanti A, Mignone F, Confalonieri S, Luzi L, Pesole G, Paolella G, Ballabio A, Banfi S: DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes. Nucleic Acids Res 2005:D505-10.
48. Milanesi L, Petrillo M, Sepe L, Boccia A, D'Agostino N, Passamano M, Di Nardo S, Tasco G, Casadio R, Paolella G: Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity. BMC Bioinformatics 2005, 6(Suppl 4):S20.
49. Macke TJ, Ecker DJ, Gutell RR, Gautheret D, Case DA, Sampath R. RNAMotif, an RNA secondary structure definition and search algorithm. Nucleic Acids Res 2001, 29:4724-47350
50. Mathews DH, Sabina J, Zuker M, Turner DH: Expanded sequence dependence of thermodynamic parameters provides robust prediction of ma secondary structure. J Mol Biol 1999, 288:910-940.
51. Coward E: Shufflet, shuffling sequences while conserving the k-let counts Bioinformatics 1999, 12:1058-1059.