Chemically related 4,5-linked aminoglycoside antibiotics drive subunit rotation in opposite directions

Michael R Wasserman; Arto Pulk; Zhou Zhou; Roger B Altman; John C Zinder; Keith D Green; Sylvie Garneau-Tsodikova; Jamie H Doudna Cate; Scott C Blanchard

doi:10.1038/ncomms8896

Chemically related 4,5-linked aminoglycoside antibiotics drive subunit rotation in opposite directions

Nat Commun. 2015 Jul 30:6:7896. doi: 10.1038/ncomms8896.

Authors

Michael R Wasserman¹, Arto Pulk², Zhou Zhou¹, Roger B Altman¹, John C Zinder³, Keith D Green⁴, Sylvie Garneau-Tsodikova⁴, Jamie H Doudna Cate², Scott C Blanchard⁵

Affiliations

¹ Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA.
² 1] Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA [2] Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, USA.
³ Tri-Institutional Training Program in Chemical Biology, Weill Cornell Medical College, Rockefeller University, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.
⁴ Department of Pharmaceutical Sciences, University of Kentucky College of Pharmacy, Lexington, Kentucky 40536, USA.
⁵ 1] Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA [2] Tri-Institutional Training Program in Chemical Biology, Weill Cornell Medical College, Rockefeller University, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.

Abstract

Dynamic remodelling of intersubunit bridge B2, a conserved RNA domain of the bacterial ribosome connecting helices 44 (h44) and 69 (H69) of the small and large subunit, respectively, impacts translation by controlling intersubunit rotation. Here we show that aminoglycosides chemically related to neomycin-paromomycin, ribostamycin and neamine-each bind to sites within h44 and H69 to perturb bridge B2 and affect subunit rotation. Neomycin and paromomycin, which only differ by their ring-I 6'-polar group, drive subunit rotation in opposite directions. This suggests that their distinct actions hinge on the 6'-substituent and the drug's net positive charge. By solving the crystal structure of the paromomycin-ribosome complex, we observe specific contacts between the apical tip of H69 and the 6'-hydroxyl on paromomycin from within the drug's canonical h44-binding site. These results indicate that aminoglycoside actions must be framed in the context of bridge B2 and their regulation of subunit rotation.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Aminoglycosides / metabolism
Aminoglycosides / pharmacology*
Anti-Bacterial Agents / metabolism
Anti-Bacterial Agents / pharmacology*
Binding Sites
Escherichia coli
Escherichia coli Proteins / drug effects
Escherichia coli Proteins / metabolism
Framycetin / metabolism
Framycetin / pharmacology
Neomycin / metabolism
Neomycin / pharmacology
Paromomycin / metabolism
Paromomycin / pharmacology
RNA, Bacterial / drug effects*
RNA, Bacterial / metabolism
Ribosome Subunits, Large, Bacterial / drug effects*
Ribosome Subunits, Large, Bacterial / metabolism
Ribosome Subunits, Small, Bacterial / drug effects*
Ribosome Subunits, Small, Bacterial / metabolism
Ribosomes / drug effects
Ribosomes / metabolism
Ribostamycin / metabolism
Ribostamycin / pharmacology
Rotation

Substances

Aminoglycosides
Anti-Bacterial Agents
Escherichia coli Proteins
RNA, Bacterial
Ribostamycin
Framycetin
neamine
Paromomycin
Neomycin

Abstract

Publication types

MeSH terms

Substances

Grants and funding