DOI: 10.1073/pnas.071527498. A novel site of antibiotic action in the ribosome: Interaction of evernimicin with the large ribosomal subunit

A novel site of antibiotic action in the ribosome: Interaction of evernimicin with the large ribosomal subunit

10.1073/pnas.071527498

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

Evernimicin (Evn), an oligosaccharide antibiotic, interacts with the large ribosomal subunit and inhibits bacterial protein synthesis. RNA probing demonstrated that the drug protects a specific set of nucleotides in the loops of hairpins 89 and 91 of 23S rRNA in bacterial and archaeal ribosomes. Spontaneous Evn-resistant mutants ofHalobacterium halobiumcontained mutations in hairpins 89 and 91 of 23S rRNA. In the ribosome tertiary structure, rRNA residues involved in interaction with the drug form a tight cluster that delineates the drug-binding site. Resistance mutations in the bacterial ribosomal protein L16, which is shown to be homologous to archaeal protein L10e, cluster to the same region as the rRNA mutations. The Evn-binding site overlaps with the binding site of initiation factor 2. Evn inhibits activity of initiation factor 2in vitro, suggesting that the drug interferes with formation of the 70S initiation complex. The site of Evn binding and its mode of action are distinct from other ribosome-targeted antibiotics. This antibiotic target site can potentially be used for the development of new antibacterial drugs.

Bibliography

Belova, L., Tenson, T., Xiong, L., McNicholas, P. M., & Mankin, A. S. (2001). A novel site of antibiotic action in the ribosome: Interaction of evernimicin with the large ribosomal subunit. Proceedings of the National Academy of Sciences, 98(7), 3726â3731.

Authors 5

Larissa Belova (first)
Tanel Tenson (additional)
Liqun Xiong (additional)
Paul M. McNicholas (additional)
Alexander S. Mankin (additional)

References 50 Referenced 85

E Cundliffe The Molecular Basis of Antibiotic Action, eds E F Gale, E Cundliffe, P E Reynolds, M H Richmond, M J Waring (Wiley, New York), pp. 402–545 (1981). / The Molecular Basis of Antibiotic Action by Cundliffe E (1981)
10.1126/science.285.5434.1722
10.1038/370659a0
10.1126/science.289.5481.920
R A Garrett, C Rodriguez-Fonseca Ribosomal RNA: Structure, Evolution, Processing, and Function in Protein Biosynthesis, eds R A Zimmermann, A E Dahlberg (CRC, Boca Raton, FL), pp. 327–355 (1996). / Ribosomal RNA: Structure, Evolution, Processing, and Function in Protein Biosynthesis by Garrett R A (1996)
10.1016/S0021-9258(17)44232-3
10.1128/AAC.44.5.1121-1126.2000
10.1128/AAC.44.3.732-738.2000
10.1128/AAC.44.11.3101-3106.2000
10.1128/AAC.44.6.1413-1417.2000
10.1016/0092-8674(89)90128-1
10.1016/S0076-6879(88)64076-6
10.1083/jcb.38.2.337
10.1006/jmbi.1996.0454
10.1016/S0076-6879(88)64064-X
C Merryman, H F Noller RNA:Protein Interactions, A Practical Approach, ed C W J Smith (Oxford Univ. Press, Oxford), pp. 237–253 (1998). (10.1093/oso/9780199636518.003.0010) / RNA:Protein Interactions, A Practical Approach by Merryman C (1998)
10.1006/jmbi.1997.1387
10.1139/m89-022
A S Mankin Archaea: A Laboratoy Manual, eds F T Robb, A R Place, K R Sowers, H J Schreier, S DasSarma, E M Fleischmann (Cold Spring Harbor Lab. Press, Plainview, NY), pp. 209–216 (1995). / Archaea: A Laboratoy Manual by Mankin A S (1995)
10.1016/S0732-8893(98)00093-5
10.1093/nar/15.6.2431
10.1038/342142a0
10.1016/0022-2836(67)90271-9
10.1006/prep.1994.1018
10.1074/jbc.272.28.17425
10.1006/abbi.1996.0136
10.1006/jmbi.1996.0116
10.1126/science.289.5481.905
10.1101/gr.6.5.454
10.1016/S0968-0004(00)89080-5
10.1006/jmbi.1996.0737
10.1093/nar/7.5.1321
10.1007/BF00330532
10.1006/jmbi.1999.3247
10.1111/j.1432-1033.1987.tb11453.x
10.1073/pnas.72.3.844
10.1093/nar/28.1.33
10.1126/science.278.5338.631
10.1021/bi991866o
10.1021/bi00001a014
10.1073/pnas.89.14.6535
10.1016/0022-2836(75)90215-6
10.1006/bbrc.1998.9664
10.1016/S0300-9084(80)80071-X
10.1016/0300-9084(91)90140-V
10.1016/S0021-9258(19)57002-8
10.1128/jb.174.4.1333-1338.1992
10.1128/AAC.44.12.3425-3427.2000
10.3201/eid0605.000521
R R Gutell Ribosomal RNA: Structure, Evolution, Processing, and Function in Protein Biosynthesis, eds R A Zimmermann, A E Dahlberg (CRC, Boca Raton, FL), pp. 111–128 (1996). / Ribosomal RNA: Structure, Evolution, Processing, and Function in Protein Biosynthesis by Gutell R R (1996)

Dates

Type	When
Created	23 years, 1 month ago (July 26, 2002, 10:44 a.m.)
Deposited	1 year, 7 months ago (Jan. 4, 2024, 12:11 a.m.)
Indexed	6 days, 11 hours ago (Aug. 28, 2025, 8:30 a.m.)
Issued	24 years, 5 months ago (March 20, 2001)
Published	24 years, 5 months ago (March 20, 2001)
Published Online	24 years, 5 months ago (March 20, 2001)
Published Print	24 years, 5 months ago (March 27, 2001)

Funders 0

None

BibTeX

@article{Belova_2001, title={A novel site of antibiotic action in the ribosome: Interaction of evernimicin with the large ribosomal subunit}, volume={98}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.071527498}, DOI={10.1073/pnas.071527498}, number={7}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Belova, Larissa and Tenson, Tanel and Xiong, Liqun and McNicholas, Paul M. and Mankin, Alexander S.}, year={2001}, month=mar, pages={3726–3731} }

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