Anatomy of Escherichia coli ribosome binding sites

Journal of Molecular Biology

Volumn 313, Issue 1, 2001, Pages 215-228

  Shultzaberger, Ryan K ^a,b   Bucheimer, R Elaine ^c   Rudd, Kenneth E ^d   Schneider, Thomas D ^b  

^a UNIVERSITY OF MARYLAND   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c UNIVERSITY OF VIRGINIA   (United States)

^d UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

Author keywords

Information theory; Ribosome; Sequence logo; Sequence walker; Shine Dalgarno

Indexed keywords

BACTERIAL PROTEIN; RIBOSOME RNA;

ARTICLE; BINDING SITE; CODON; ESCHERICHIA COLI; GENOME; MATHEMATICAL ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE; PROMOTER REGION; RIBOSOME; RNA BINDING; SEQUENCE ANALYSIS; TRANSLATION INITIATION;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; PROKARYOTA;

EID: 0035850734     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.5040     Document Type: Article

References (59)

1. Ribosomes and translation
2. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution
3. Structure of the 30S ribosomal subunit
4. Translational initiation in prokaryotes
5. Characterization of translational initiation sites in E. coli
6. Information content of binding sites on nucleotide sequences
7. Compilation of E. coli ribosome binding sites
8. Initiation of translation in prokaryotes and eukaryotes
9. The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: Complementarity to nonsense triplets and ribosome binding sites
10. Selection of the mRNA translation initiation region by Escherichia coli ribosomes
11. Influence of mRNA on determinants on translational initiation in Escherichia coli
12. Posttranscriptional regulatory mechanisms in Escherichia coli
13. Quantitative analysis of ribosome binding sites in E. coli
14. Determination of the optimal aligned spacing between the Shine-Dalgarno sequence and the translation initiation codon of Escherichia coli mRNAs
15. Contacts between 16S ribosomal RNA and mRNA, within the spacer region separating the AUG initiator codon and the Shine-Dalgarno sequence; a site-directed cross-linking study
16. Translation initiation in Escherichia coli: Sequences within the ribosome binding site
17. Detection of Escherichia coli ribosome binding at translational initiation sites in the absence of tRNA
18. A mathematical theory of communication
19. Sequence logos, machine/channel capacity. Maxwell's demon, and molecular computers: A review of the theory of molecular machines
20. Information analysis of Fis binding sites
21. Using sequence logos and information analysis of Lrp DNA binding sites to investigate discrepancies between natural selection and SELEX
22. OxyR and SoxRS regulation of fur
23. Sequence logos: A new way to display consensus sequences
24. Information content of individual genetic sequences
25. Sequence walkers: A graphical method to display how binding proteins interact with DNA or RNA sequences
26. Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli
27. Theory of molecular machines. II. Energy dissipation from molecular machines
28. Fast multiple alignment of ungapped DNA sequences using information theory and a relaxation method
29. Combining diverse evidence for gene recognition in completely sequenced bacterial genomes
30. Starts of bacterial genes: Estimating the reliability of computer predictions
31. The complete genome sequence of Escherichia coli K-12
32. EcoGene: A genome sequence database for Escherichia coli K-12
33. Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites
34. Molecular biology of pyridine nucleotide biosynthesis in Escherichia coli. Cloning and characterization of quinolinate synthesis genes nadA and nadB
35. GeneMarkS: A self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
36. Hidden Markov models in computational biology, applications to protein modeling
37. Identification of an intragenic ribosome binding site that affects expression of the B gene of the Escherichia coli proton-translocating ATPase (unc) operon
38. Transcription attenuation
39. Harmonic motion; harmonic oscillator
40. Theory of molecular machines. I. Channel capacity of molecular machines
41. Information analysis of sequences that bind the replication initiator RepA
42. Reading of DNA sequence logos: Prediction of major groove binding by information theory
43. Interdependence of the position and orientation of SoxS binding sites in the transcriptional activation of the class I subset of Escherichia coli superoxide-inducible promoters
44. Structure of a bacterial 30S ribosomal subunit at 5.5 Å resolution
45. Ribosome-messenger recognition: mRNA target sites for ribosomal protein S1
46. Ribosomal protein S1 is required for translation of most, if not all, natural mRNAs in Escherichia coli in vivo
47. The location of mRNA in the ribosomal 30S initiation complex; site-directed cross-linking of mRNA analogues carrying several photo- reactive labels simultaneously on either side of the AUG start codon
48. The cross-link from the upstream region of mRNA to ribosomal protein S7 is located in the C-terminal peptide: Experimental verification of a prediction from modeling studies
49. Arrangement of messenger RNA on Escherichia coli ribosomes with respect to 10 16S rRNA cross-linking sites
50. The database of ribosomal cross-links: An update
51. Optimised parameters for RNA double-helices
52. The structural basis of ribosome activity in peptide bond synthesis
53. Discrimination by Escherichia coli initiation factor IF3 against initiation on non-canonical codons relies on complementarity rules
54. Secondary structure of the ribosome binding site determines translational efficiency: A quantitative analysis
55. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
56. Information analysis of human splice site mutations
57. Naturally occurring nucleosome positioning signals in human exons and introns