Characterization of a 30S ribosomal subunit assembly intermediate found in Escherichia coli cells growing with neomycin or paromomycin

Archives of Microbiology

Volumn 189, Issue 5, 2008, Pages 441-449

  Foster, Cerrone ^a   Champney, W Scott ^a  

^a East Tennessee State University   (United States)

Author keywords

30S subunit; Aminoglycosides; Escherichia coli; Ribosome assembly

Indexed keywords

AMINOGLYCOSIDE ANTIBIOTIC AGENT; NEOMYCIN; PAROMOMYCIN; RIBOSOME RNA; RNA 16S;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; BACTERIAL CELL; BACTERIAL GROWTH; CONTROLLED STUDY; DRUG BINDING; ESCHERICHIA COLI; HYBRIDIZATION; ISOTOPE LABELING; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; RIBOSOME SUBUNIT; SEDIMENTATION; UPREGULATION;

ANTI-BACTERIAL AGENTS; BLOTTING, NORTHERN; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; NEOMYCIN; PAROMOMYCIN; RIBOSOMAL PROTEINS; RIBOSOME SUBUNITS, SMALL, BACTERIAL; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S;

ESCHERICHIA COLI; STAPHYLOCOCCUS AUREUS;

EID: 42449098958     PISSN: 03028933     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00203-007-0334-6     Document Type: Article

References (54)

1. Alix J-H (1993) Extrinsic factors in ribosome assembly. In: Nierhaus KH, Franceschi F, Subramanian AR, Erdmann VA, Wittmann-Liebold B (eds) The translational apparatus. Plenum, New York, pp 173-184
2. Anderson RM (1999) The pandemic of antibiotic resistance. Nat Med 5:147-149
3. Borovinskaya MA, Pai RD, Zhang W, Schuwirth BS, Holton JM, Hirokawa G, Kaji H, Kaji A, Cate JH (2007) Structural basis for aminoglycoside inhibition of bacterial ribosome recycling. Nat Struct Biol 14:727-732
4. Broderson DE, Clemons WM, Carter AP, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V (2000) The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit. Cell 103:1143-1154
5. Brosius J, Dull TJ, Noller HF (1980) Complete nucleotide sequence of a 23S ribosomal RNA gene from Escherichia coli. Proc Natl Acad Sci US 77:201-204
6. Bryskier A (2005) Antimicrobial agents. Antibacterials and antifungals. American Society for Microbiology, Washington
7. Carter AP, Clemons WM, Broderson DE, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V (2000) Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 407:340-348
8. Champney WS (1989) Reductive methods for isotopic labeling of antibiotics. Anal Biochem 181:90-95
9. Champney WS (2003) Bacterial ribosomal subunit assembly is an antibiotic target. Curr Top Med Chem 3:929-947
10. Champney WS (2006) The other target for ribosomal antibiotics. Inhibition of bacterial ribosomal subunit formation. Infect Disord Drug Targets 6:377-390
11. Chu DT, Plattner JJ, Katz L (1996) New directions in antibacterial research. J Med Chem 39:3853-3874
12. Culver GM (2003) Assembly of the 30S ribosomal subunit. Biopolymers 68:234-249
13. Dahlberg AE, Horodyski F, Keller P (1978) Interaction of neomycin with ribosomes and ribosomal ribonucleic acid. Antimicrob Agents Chemother 13:331-339
14. Farrell RE (1993) RNA Methodologies. Academic, San Diego
15. Fourmy D, Recht MI, Blanchard SC, Puglisi JD (1996) Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science 274:1367-1371
16. Fourmy D, Yoshizawa S, Puglisi JD (1998) Paromomycin binding induces a local conformational change in the A-site of 16 S rRNA. J Mol Biol 277:333-345
17. Garrett RA, Douthwaite SR, Liljas A, Matheson AT, Moore PB, Noller HF (eds) (2000) The ribosome. Structure, function, antibiotics, and cellular interactions. ASM, Washington
18. Gesteland R (1966) Isolation and characterization of ribonuclease I mutants of Escherichia coli. J Mol Biol 16:67-84
19. Geyl D, Bock A, Isono K (1981) An improved method for two-dimensional gel-electrophoresis: analysis of mutationally altered ribosomal proteins of Escherichia coli. Mol gen Genet 181:309-312
20. Giri L, Hill WE, Wittmann HG (1984) Ribosomal proteins. In: Anfinsen CB, Edsall JT, Richards FM (eds) Advances in protein chemistry. Academic, New York, pp 1-78
21. Hansen JL, Ippolito JA, Ban N, Nissen P, Moore PB, Steitz TA (2002) The structures of four macrolide antibiotics bound to the large ribosomal subunit. Mol Cell 10:117-128
22. Hansen JL, Moore PB, Steitz TA (2003) Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit. J Mol Biol 330:1061-1075
23. Himeno H, Hanawa-Suetsugu K, Kimura T, Takagi K, Sugiyama W, Shirata S, Mikami T, Odagiri F, Osanai Y, Wantanabe D, Goto S, Kalachnyuk L, Ushida C, Muto A (2004) A novel GTPase activated by the small subunit of ribosome. Nucleic Acids Res 32:5303-5309
24. Inoue K, Alsina J, Chen J, Inouye M (2003) Suppression of defective ribosome assembly in a rbfA deletion mutant by overexpression of Era, an essential GTPase in Escherichia coli. Mol Microbiol 48:1005-1016
25. Kaczanowska M, Ryden-Aulin M (2005) The YrdC protein - a putative ribosome maturation factor. Biochem Biophys Acta 1727:87-96
26. Kirsebom LA, Vittanen A, Mikkelsen NE (2006) Aminoglycoside interactions with RNAs and nucleases. Hoppe Seiler Physiol Chem 173:75-96
27. Kotra LP, Haddad J, Mobashery S (2000) Aminoglycosides: perspectives on mechanisms of action and resistance and strategies to counter resistance. Antimicrob Agents Chemother 44:3249-3256
28. Lando D, Cousin A-M, Raynaud J-P (1976) Paromomycin and dihydrostreptomycin binding to Escherichia coli ribosomes. Eur J Biochem 66:597-606
29. McGaha SM, Champney WS (2006) Hygromycin B inhibition of protein synthesis and ribosome biogenesis in Escherichia coli. Antimicrob Agents Chemother 51:591-596
30. Mehta R, Champney WS (2002) 30S ribosomal subunit assembly is a target for inhibition by aminoglycosides in Escherichia coli. Antimicrob Agents Chemother 46:1546-1549
31. Mehta R, Champney WS (2003) Neomycin and paromomycin inhibit 30S ribosomal subunit assembly in Staphylococcus aureus. Curr Microbiol 43:237-243
32. Miller JH (1972) Experiments in molecular genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor
33. Mingeot-LeClercq MP, Glupczynski Y, Tulkens PM (1999) Aminoglycosides: activity and resistance. Antimicrob Agents Chemother 43:727-737
34. Misumi M, Nishimura T, Komai T, Tanaka N (1978) Interaction of kanamycin and related antibiotics with the large subunit of ribosomes and the inhibition of translocation. Biochem Biophys Res Commun 84:358-365
35. Moore PB (2001) The ribosome at atomic resolution. Biochemistry 40:3243-3250
36. Nierhaus KH (1990) Reconstitution of ribosomes. In: Spedding G (eds) Ribosomes and protein synthesis. A practical approach. Oxford University Press, Oxford, pp 169-179
37. Nierhaus K, Bordash K, Homann HE (1973) Ribosomal proteins. In vivo assembly of Escherichia coli ribosomal proteins. J Mol Biol 74:587-597
38. Nomura M (1973) Assembly of bacterial ribosomes. Science 179:863-873
39. Ogle JM, Broderson DE, Clemons WM, Terry MJ, Carter AP, Ramakrishnan V (2001) Recognition of cognate transfer RNA by the 30S ribosomal subunit. Nature 292:897-902
40. Ogle JM, Murphy FV, Tarry MJ, Ramakrishnan V (2002) Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell 111:721-732
41. Ogle JM, Carter AP, Ramakrishnan V (2003) Insights into the decoding mechanism from recent ribosome structures. TIBS 28:259-266
42. Pfister P, Hobbie S, Brull C, Corti N, Vasella A, Westhof E, Bottger EC (2005) Mutagenesis of 16S rRNA C1409-G1491 base-pair differentiates between 6'OH and 6'NH3 aminoglycosides. J Mol Biol 346:467-475
43. Purohit P, Stern S (1994) Interactions of a small RNA with antibiotic and RNA ligands of the 30S subunit. Nature 370:659-662
44. Recht MI, Douthwaite S, Dahlquist KD, Puglisi JD (1999a) Effect of mutations in the A site of 16S RNA on aminoglycoside antibiotic-ribosome interactions. J Mol Biol 286:33-43
45. Recht MI, Douthwaite S, Puglisi JD (1999b) Basis for prokaryotic specificity of action of aminoglycoside antibiotics. EMBO J 18:3133-3138
46. Roets E, Adams E, Murithi I, Hoogmartens J (1995) Determination of the relative amounts of the B and C components of neomycin by thin-layer chromatography using fluorescence detection. J Chromatogr 696:131-138
47. Schlunzen F, Zarivach R, Harms J, Bashan A, Tocilj A, Albrecht R, Yonath A, Franceschi F (2001) Structural basis for the interaction of antibiotics with the peptidyltransferase centre in eubacteria. Nature 413:814-821
48. Silvers JA, Champney WS (2005) Accumulation and turnover of 23S ribosomal RNA in azithromycin-inhibited ribonuclease mutants of Escherichia coli. Arch Mikrobiol 184:66-77
49. Tor Y (2006) The ribosomal A-site as an inspiration for the design of RNA binders. Biochimie 88:1045-1051
50. Toutchstone J, Dobbins M (1983) Practice of thin layer chromatography, 2nd edn. Wiley-Interscience, New York
51. Usary J, Champney WS (2001) Erythromycin inhibition of 50S ribosomal subunit formation in Escherichia coli cells. Mol Microbiol 40:951-962
52. Vazquez D (1979) Inhibitors of protein biosynthesis. Springer, Berlin
53. Vourloumis D, Takahashi M, Winters GC, Simonsen KB, Ayida BK, Barluenga S, Qamar S, Shandrick S, Zhao Q, Hermann T (2002) Novel 2,5-dideoxystreptamine derivatives targeting the ribosomal decoding site RNA. Bioorg Med Chem Lett 12:3367-3372
54. Zhou Y, Vlad E, Sun Z, Ayida B, Winters G, Murphy D, Simonsen K, Vourloumis D, Fish S, Froelich J, Wall D, Hermann T (2005) Structure-guided discovery of novel aminoglycoside mimetics as antibacterial translation inhibitors. Antimicrob Agents Chemother 49:4942-4949