Mechanism of action of ABCF ATPases during translation

• Applicant: Professor Dr. Daniel Nicodemus Wilson
• Subject Area: Structural Biology ; Biochemistry
• Term: from 2018 to 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 398213262

• Final Report Year: 2022

Final Report Abstract

While ATP-binding cassette (ABC) proteins are well-known as membrane-bound transporters, the ABCF class lack the transmembrane domain and of those classified appear to have roles involved in fundamental intracellular pathways, such as protein synthesis. In this project, we have characterized three ABC ATPases from eukaryotes, namely, eEF3, New1p and Gcn1, revealing that all three bind to overlapping sites on the ribosome, yet have diverse functions. Our structures suggest that eEF3 plays a role in E-site tRNA release by directly interacting with the L1 stalk, whereas New1p appears to have a distinct role that is probably related to facilitating stalled ribosomes to translate again. Finally, we show that Gcn1 actually binds to a disome comprising a stalled leading ribosome and a following colliding ribosome, revealing how Gcn1 can act as a sensor to respond to diverse stress events within the cell. Unlike the eukaryotic ABC proteins, we show that the bacterial ARE-ABCF ATPases all bind within the E-site and have an antibiotic resistance determinant that reaches towards the PTC to facilitate drug release via distinct allosteric mechanisms. We hope that by understanding these resistance mechanisms, this will provide a basis for development of novel antimicrobial agents to overcome these resistance mechanisms.

Publications

• Structural basis for antibiotic resistance mediated by the Bacillus subtilis ABCF ATPase VmlR. Proc Natl Acad Sci USA. 2018 Sep 4;115(36):8978-8983
  Crowe-McAuliffe C, Graf M, Huter P, Takada H, Abdelshahid M, Nováček J, Murina V, Atkinson GC, Hauryliuk V, Wilson DN
  
• A role for the Saccharomyces cerevisiae ABCF protein New1 in translation termination/recycling. Nucleic Acids Res. 2019 Sep 19;47(16):8807-8820
  Kasari V, Pochopien AA, Margus T, Murina V, Turnbull K, Zhou Y, Nissan T, Graf M, Nováček J, Atkinson GC, Johansson MJO, Wilson DN, Hauryliuk V
  
• Target protection as a key antibiotic resistance mechanism. Nat Rev Microbiol. 2020 Nov;18(11):637-648
  Wilson DN, Hauryliuk V, Atkinson GC, O'Neill AJ
  
• RqcH and RqcP catalyze processive poly-alanine synthesis in a reconstituted ribosome-associated quality control system. Nucleic Acids Res. 2021 Aug 20;49(14):8355-8369
  Takada H, Crowe-McAuliffe C, Polte C, Sidorova ZY, Murina V, Atkinson GC, Konevega AL, Ignatova Z, Wilson DN, Hauryliuk V
  
• Structural Basis for Bacterial Ribosome- Associated Quality Control by RqcH and RqcP. Molecular Cell. 2021 Jan 7;81(1):115-126.e7
  Crowe-McAuliffe C, Takada H, Murina V, Polte C, Kasvandik S, Tenson T, Ignatova Z, Atkinson GC, Wilson DN, Hauryliuk V
  
• Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens. Nat Commun. 2021 Jun 11;12(1):3577
  Crowe-McAuliffe C, Murina V, Turnbull KJ, Kasari M, Mohamad M, Polte C, Takada H, Vaitkevicius K, Johansson J, Ignatova Z, Atkinson GC, O'Neill AJ, Hauryliuk V, Wilson DN
  
• Structure of Gcn1 bound to stalled and colliding 80S ribosomes. Proc Natl Acad Sci USA. 2021 Apr 6;118(14):e2022756118
  Pochopien AA, Beckert B, Kasvandik S, Berninghausen O, Beckmann R, Tenson T, Wilson DN
  
• Yeast translation elongation factor eEF3 promotes late stages of tRNA translocation. EMBO J. 2021 Mar 15;40(6):e106449
  Ranjan N, Pochopien AA, Chih-Chien Wu C, Beckert B, Blanchet S, Green R, V Rodnina M, Wilson DN
  
• Structural basis for PoxtA-mediated resistance to phenicol and oxazolidinone antibiotics. Nat Commun. 2022 Apr 6;13(1):1860
  Crowe-McAuliffe C, Murina V, Turnbull KJ, Huch S, Kasari M, Takada H, Nersisyan L, Sundsfjord A, Hegstad K, Atkinson GC, Pelechano V, Wilson DN, Hauryliuk V