Genetic and Comparative Analyses Reveal an Alternative Secondary Structure in the Region of Nt 912 of Escherichia Coli 16S RRNA

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1995 Nov 7

PMID 7479839

Citations 8

Authors

J S Lodmell

R R Gutell

A E Dahlberg

Affiliations

Soon will be listed here.

Abstract

Mutations at position 912 of Escherichia coli 16S rRNA result in two notable phenotypes. The C-->U transition confers resistance to streptomycin, a translational-error-inducing antibiotic, while a C-->G transversion causes marked retardation of cell growth rate. Starting with the slow-growing G912 mutant, random mutagenesis was used to isolate a second site mutation that restored growth nearly to the wild-type rate. The second site mutation was identified as a G-->C transversion at position 885 in 16S rRNA. Cells containing the G912 mutation had an increased doubling time, abnormal sucrose gradient ribosome/subunit profile, increased sensitivity to spectinomycin, dependence upon streptomycin for growth in the presence of spectinomycin, and slower translation rate, whereas cells with the G912/C885 double mutation were similar to wild type in these assays. Comparative analysis showed there was significant covariation between positions 912 and 885. Thus the second-site suppressor analysis, the functional assays, and the comparative data suggest that the interaction between nt 912 and nt 885 is conserved and necessary for normal ribosome function. Furthermore, the comparative data suggest that the interaction extends to include G885-G886-G887 pairing with C912-U911-C910. An alternative secondary structure element for the central domain of 16S rRNA is proposed.

Citing Articles

Antibiotic drugs targeting bacterial RNAs.

Hong W, Zeng J, Xie J Acta Pharm Sin B. 2015; 4(4):258-65.

PMID: 26579393 PMC: 4629089. DOI: 10.1016/j.apsb.2014.06.012.

Linezolid-dependent function and structure adaptation of ribosomes in a Staphylococcus epidermidis strain exhibiting linezolid dependence.

Kokkori S, Apostolidi M, Tsakris A, Pournaras S, Stathopoulos C, Dinos G Antimicrob Agents Chemother. 2014; 58(8):4651-6.

PMID: 24890589 PMC: 4135981. DOI: 10.1128/AAC.02835-14.

Mutations conferring aminoglycoside and spectinomycin resistance in Borrelia burgdorferi.

Criswell D, Tobiason V, Lodmell J, Samuels D Antimicrob Agents Chemother. 2006; 50(2):445-52.

PMID: 16436695 PMC: 1366916. DOI: 10.1128/AAC.50.2.445-452.2006.

Solution probing of metal ion binding by helix 27 from Escherichia coli 16S rRNA.

Newby Lambert M, Hoerter J, Pereira M, Walter N RNA. 2005; 11(11):1688-700.

PMID: 16244134 PMC: 1370855. DOI: 10.1261/rna.2940705.

Isolation of antibiotic resistance mutations in the rRNA by using an in vitro selection system.

Cochella L, Green R Proc Natl Acad Sci U S A. 2004; 101(11):3786-91.

PMID: 15001709 PMC: 374322. DOI: 10.1073/pnas.0307596101.

References

Kunkel T . Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A. 1985; 82(2):488-92. PMC: 397064. DOI: 10.1073/pnas.82.2.488. View

Gautheret D, Damberger S, Gutell R . Identification of base-triples in RNA using comparative sequence analysis. J Mol Biol. 1995; 248(1):27-43. DOI: 10.1006/jmbi.1995.0200. View

Freier S, Kierzek R, Caruthers M, Neilson T, Turner D . Free energy contributions of G.U and other terminal mismatches to helix stability. Biochemistry. 1986; 25(11):3209-13. DOI: 10.1021/bi00359a019. View

Moazed D, Noller H . Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes. Cell. 1986; 47(6):985-94. DOI: 10.1016/0092-8674(86)90813-5. View

Montandon P, Wagner R, Stutz E . E. coli ribosomes with a C912 to U base change in the 16S rRNA are streptomycin resistant. EMBO J. 1986; 5(13):3705-8. PMC: 1167414. DOI: 10.1002/j.1460-2075.1986.tb04703.x. View

Osswald M, GREUER B, Brimacombe R, Stoffler G, Baumert H, FASOLD H . RNA-protein cross-linking in Escherichia coli 30S ribosomal subunits; determination of sites on 16S RNA that are cross-linked to proteins S3, S4, S5, S7, S8, S9, S11, S13, S19 and S21 by treatment with methyl p-azidophenyl acetimidate. Nucleic Acids Res. 1987; 15(8):3221-40. PMC: 340726. DOI: 10.1093/nar/15.8.3221. View

Moazed D, Noller H . Interaction of antibiotics with functional sites in 16S ribosomal RNA. Nature. 1987; 327(6121):389-94. DOI: 10.1038/327389a0. View

Gravel M, Melancon P . Cross-linking of streptomycin to the 16S ribosomal RNA of Escherichia coli. Biochemistry. 1987; 26(19):6227-32. DOI: 10.1021/bi00393a041. View

Sigmund C, Ettayebi M, Borden A, Morgan E . Antibiotic resistance mutations in ribosomal RNA genes of Escherichia coli. Methods Enzymol. 1988; 164:673-90. DOI: 10.1016/s0076-6879(88)64077-8. View

10.

Stern S, Powers T, Changchien L, Noller H . RNA-protein interactions in 30S ribosomal subunits: folding and function of 16S rRNA. Science. 1989; 244(4906):783-90. DOI: 10.1126/science.2658053. View

11.

Allen P, Noller H . Mutations in ribosomal proteins S4 and S12 influence the higher order structure of 16 S ribosomal RNA. J Mol Biol. 1989; 208(3):457-68. DOI: 10.1016/0022-2836(89)90509-3. View

12.

Harris E, Burkhart B, Gillham N, Boynton J . Antibiotic resistance mutations in the chloroplast 16S and 23S rRNA genes of Chlamydomonas reinhardtii: correlation of genetic and physical maps of the chloroplast genome. Genetics. 1989; 123(2):281-92. PMC: 1203800. DOI: 10.1093/genetics/123.2.281. View

13.

Triman K, Becker E, Dammel C, Katz J, Mori H, Douthwaite S . Isolation of temperature-sensitive mutants of 16 S rRNA in Escherichia coli. J Mol Biol. 1989; 209(4):645-53. DOI: 10.1016/0022-2836(89)92000-7. View

14.

Tapprich W, Dahlberg A . A single base mutation at position 2661 in E. coli 23S ribosomal RNA affects the binding of ternary complex to the ribosome. EMBO J. 1990; 9(8):2649-55. PMC: 552298. DOI: 10.1002/j.1460-2075.1990.tb07447.x. View

15.

Frattali A, Flynn M, De Stasio E, Dahlberg A . Effects of mutagenesis of C912 in the streptomycin binding region of Escherichia coli 16S ribosomal RNA. Biochim Biophys Acta. 1990; 1050(1-3):27-33. DOI: 10.1016/0167-4781(90)90136-p. View

16.

Bonny C, Montandon P, Stutz E . Analysis of streptomycin-resistance of Escherichia coli mutants. Biochim Biophys Acta. 1991; 1089(2):213-9. DOI: 10.1016/0167-4781(91)90010-j. View

17.

Powers T, Noller H . A functional pseudoknot in 16S ribosomal RNA. EMBO J. 1991; 10(8):2203-14. PMC: 452909. DOI: 10.1002/j.1460-2075.1991.tb07756.x. View

18.

Brimacombe R . RNA-protein interactions in the Escherichia coli ribosome. Biochimie. 1991; 73(7-8):927-36. DOI: 10.1016/0300-9084(91)90134-m. View

19.

Leclerc D, Melancon P . The interaction between streptomycin and ribosomal RNA. Biochimie. 1991; 73(12):1431-8. DOI: 10.1016/0300-9084(91)90175-z. View

20.

OConnor M, Goringer H, Dahlberg A . A ribosomal ambiguity mutation in the 530 loop of E. coli 16S rRNA. Nucleic Acids Res. 1992; 20(16):4221-7. PMC: 334129. DOI: 10.1093/nar/20.16.4221. View