Allen Buskirk 
Department of Molecular Biology and Genetics 
Johns Hopkins University School of Medicine 
702 Pre‐Clinical Teaching Building (PCTB) 
725 N. Wolfe St 
Baltimore, MD 21205 
410 955‐2382 

The Buskirk group studies protein synthesis with a focus on ribosome stalling and the mechanisms that cells use to restart or recycle stalled ribosomes. In 2014 the group moved to Hopkins to the lab of our long‐term collaborator Rachel Green, where we continue to pursue these projects with independent NIH funding.


Research Overview

Pauses in translation occur when the ribosome encounters strong secondary structures or clusters of rare codons in mRNA transcripts. Pauses can also be induced by interactions of the nascent polypeptide with the exit tunnel and active site. Through genetic screens, we identified nascent peptide sequences that block peptidyl transfer and peptide release (Woolstenhulme 2013). The fact that many of these motifs pause ribosomes at consecutive Pro codons helped to establish that Pro acts as both a poor peptidyl donor and a poor peptidyl acceptor. We are interested in the mechanism of how consecutive Pro residues alter the active site geometry within the ribosome to inhibit peptidyl transfer as well as how elongation factor P (EFP) counteracts this effect, alleviating pausing at polyproline motifs.

When ribosomes stall for prolonged periods of time, for example at the 3’‐end of mRNAs lacking a stop codon, they are rescued and recycled by the conserved tmRNA‐SmpB complex or by ArfA/B in certain species. These factors must distinguish stalled ribosomes from actively translating ones to avoid aborting productive protein synthesis. We continue to study how this selectivity is achieved using genetic methods and pre‐steady state kinetics (Miller 2014).

Variations in elongation rates have been implicated in gene regulation, mRNA decay, and protein folding. We are working with Patricia Clark and the Protein Translation Research Network to further characterize the effect of elongation rate on protein folding. The ribosome profiling method developed by Ingolia and Weissman may provide a means to further flesh out promising links between translational pauses and important biological outcomes. We have improved the resolution of bacterial ribosome profiling data and analyzed the effects of pausing in cells lacking EFP (Woolstenhulme 2015), and we continue to develop and employ this technique to identify and characterize translational pauses.



  1. Weaver J, Mohammad F, Buskirk AR, Storz G. (2019) Identifying Small Proteins by Ribosome Profiling with Stalled Initiation Complexes. MBio
    PubMed Link | Link to Article
  2. Mohammad F, Green R, Buskirk AR. (2019) A systematically-revised ribosome profiling method for bacteria reveals pauses at single-codon resolution. Elife
    PubMed Link | Link to Article
  3. Buskirk AR. (2018) Toxins that Trash Translation. Mol Cell 70: 759-760
    PubMed Link | Link to Article
  4. Schuller AP, Wu CC, Dever TE, Buskirk AR, Green R. (2017) eIF5A Functions Globally in Translation Elongation and Termination. Mol Cell 66: 194-205.e5
    PubMed Link | Link to Article
  5. Buskirk AR, Green R. (2017) Ribosome pausing, arrest and rescue in bacteria and eukaryotes. Philos Trans R Soc Lond B Biol Sci
    PubMed Link | Link to Article
  6. Hwang JY, Buskirk AR. (2017) A ribosome profiling study of mRNA cleavage by the endonuclease RelE. Nucleic Acids Res 45: 327-336
    PubMed Link | Link to Article
  7. Mohammad F, Woolstenhulme CJ, Green R, Buskirk AR. (2016) Clarifying the Translational Pausing Landscape in Bacteria by Ribosome Profiling. Cell Rep 14: 686-694
    PubMed Link | Link to Article
  8. Woolstenhulme CJ, Guydosh NR, Green R, Buskirk AR. (2015) High-precision analysis of translational pausing by ribosome profiling in bacteria lacking EFP. Cell Rep 11: 13-21
    PubMed Link | Link to Article
  9. Starosta AL, Lassak J, Peil L, Atkinson GC, Woolstenhulme CJ, Virumae K, Buskirk AR, Tenson T, Remme J, Jung K, Wilson DN. (2014) A conserved proline triplet in Val‐tRNA synthetase and the origin of elongation factor P. Cell Rep 9: 1‐8.
  10. Kurita D, Miller MR, Muto A, Buskirk AR, Himeno H (2014). Rejection of tmRNA‐SmpB after GTP hydrolysis by EF‐Tu on ribosomes stalled on intact mRNA. RNA 20: 1‐9
  11. Woolstenhulme CJ and Buskirk AR (2014). “Isolation of ribosome stalling motifs from random libraries” in Regulatory Nascent Peptides, Ed. Koreaki Ito, Springer, Japan
  12. Miller MR and Buskirk AR (2014). The SmpB C‐terminal tail helps tmRNA to recognize and enter stalled ribosomes. Front Microbiol 5: 462
  13. Miller MR and Buskirk AR (2014). An unusual mechanism for EF‐Tu activation during tmRNA‐mediated ribosome rescue. RNA 20: 228‐35
  14. Gutierrez E, Shin BS, Woolstenhulme CJ, Kim JR, Saini P, Buskirk AR, Dever TE (2013). eIF5A promotes translation of polyproline motifs. Mol Cell 51: 35‐45
  15. Woolstenhulme CJ, Parajuli S, Healey DW, Valverde DP, Petersen EN, Starosta AL, Guydosh NR, Johnson WE, Wilson DN, Buskirk AR (2013). Nascent peptides that block protein synthesis in bacteria. Proc Natl Acad Sci 110: E878‐87
  16. Buskirk AR and Green R (2013). Getting past polyproline pauses. Science 339: 38‐9