Publications
2023
​
A single 2'-O-methylation of ribosomal RNA gates assembly of a functional ribosome. Yelland JN, Bravo JPK, Black JJ, Taylor DW, Johnson AW. Nat Struct Mol Biol. 2023 Jan;30(1):91-98. doi: 10.1038/s41594-022-00891-8.
​
2022
​
Release of the ribosome biogenesis factor Bud23 from small subunit precursors in yeast. Black JJ, Johnson AW. RNA. 2022 Mar;28(3):371-389. doi: 10.1261/rna.079025.121.
​
2021
​
Genetics animates structure: leveraging genetic interactions to study the dynamics of ribosome biogenesis. Black JJ & Johnson AW. Current Genetics. 2021 Apr 12. doi: 10.1007/s00294-021-01187-y.
​
2020
​
Bud23 promotes the final disassembly of the small subunit Processome in Saccharomyces cerevisiae. Black JJ, Sardana R, Elmir EW, Johnson AW. PLoS Genetics. 2020 Dec 11;16(12):e1009215. doi: 10.1371/journal.pgen.1009215.
​
2019
​
The L1 stalk is required for efficient export of nascent large ribosomal subunits in yeast. Musalgaonkar S, Black JJ, Johnson AW. RNA. 2019 Nov;25(11):1549-1560. doi: 10.1261/rna.071811.119.
​
Tsr4 is a cytoplasmic chaperone for the ribosomal protein Rps2 in Saccharomyces cerevisiae. Black JJ, Musalgaonkar S, Johnson AW. Mol. Cell. Biol. 2019 June 10. doi: 10.1128/MCB.00094-19.
​
Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome. Zhou, Y, Musalgaonkar, S, Johnson, AW and Taylor, DW. Nature Communications. 2019 Feb 27;10(1):958. doi: 10.1038/s41467-019-08880-0.
​
2018
​
Utp14 interaction with the small subunit processome. Black JJ, Wang Z, Goering LM, Johnson AW. RNA. 2018 24:1214-1228. doi: 10.1261/rna.066373.118.
2017
​
The T-cell leukemia related rpl10-R98S mutant traps the 60S export adapter Nmd3 in the ribosomal P site in yeast. Patchett S, Musalgaonkar S, Malyutin AG, Johnson AW. PLoS Genet. 2017 Jul 17;13(7):e1006894.
​
Low frequency mutations in ribosomal proteins RPL10 and RPL5 in multiple myeloma. Hofman IJ, Patchett S, van Duin M, Geerdens E, Verbeeck J, Michaux L, Delforge M, Sonneveld P, Johnson AW, De Keersmaecker K. Haematologica. 2017 Apr 20. pii: haematol.2016.162198.
​
Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis. Malyutin AG, Musalgaonkar S, Patchett S, Frank J, Johnson AW. EMBO J. 2017 Feb 8. pii: e201696012.
​
Bcp1 Is the Nuclear Chaperone of Rpl23 in Saccharomyces cerevisiae. Ting YH, Lu TJ, Johnson AW, Shie JT, Chen BR, Kumar S S, Lo KY. J Biol Chem. 2017 Jan 13;292(2):585-596.
2016
​
Utp14 Recruits and Activates the RNA Helicase Dhr1 To Undock U3 snoRNA from the Preribosome. Zhu J, Liu X, Anjos M, Correll CC, Johnson AW. Mol Cell Biol. 2016 Jan 4;36(6):965-78.
2015
​
The DEAH-box helicase Dhr1 Dissociates U3 from the pre-rRNA to promote formation of the Central Pseudoknot. Sardana R., Liu, X., Granneman, S., Zhu, J., Gill, M., Papoulas, O., Marcotte, E.M., Tollervey, D., Correll, C.C. and Johnson, A.W. PLOS Biology, PLoS Biol. 2015 Feb 24;13(2):e1002083.
​
Understanding Biases in Ribosome Profiling Experiments Reveals Signatures of Translation Dynamics in Yeast. Hussmann JA, Patchett S, Johnson A, Sawyer S, Press WH. PLoS Genet. 2015 Dec 11;11(12):e1005732. doi: 10.1371/journal.pgen.1005732. eCollection 2015 Dec.
2014
​
Genetic analysis of the ribosome biogenesis factor Ltv1 of Saccharomyces cerevisiae. Merwin JR, Bogar LB, Poggi SB, Fitch RM, Johnson AW, Lycan DE. Genetics. 2014 Nov;198(3):1071-85. doi: 10.1534/genetics.114.168294. Epub 2014 Sep 10.
​
Physical and functional interactions between the methyltransferase Bud23 and the essential DEAH-box RNA helicase Ecm16. Sardana, R., J, Zhu and A.W. Johnson. Mol Cell Biol. 2014 Jun 15;34(12):2208-2220.
​
Sergey O., Sulima S.O., S. Patchett, V.M. Advani, K. de Keersmaecker, A.W. Johnson and J.D. Dinman. Bypass of the pre-60S ribosomal quality control as a pathway to oncogenesis. PNAS(USA). 2014 111:5640-5.
​
2013
​
​
Hartl TA, Ni J, Cao J, Suyama KL, Patchett S, Bussiere C, Gui DY, Tang S, Kaplan DD, Fish M, Johnson AW, Scott MP. 2013. Regulation of ribosome biogenesis by nucleostemin 3 promotes local and systemic growth in Drosophila. Genetics. 2013 194:101-15. Epub 2013 Feb 22. PMCID:PMC3632458
2012
​
CD Castle, R Sardana, V Dandekar, A.W. Johnson V Borgianini and C Denicourt. Las1 interacts with Grc3 polynucleotide kinase and regulates ribosome synthesis in Saccharomyces cerevisiae. Nucleic Acids Res.2012 Nov 21. [Epub ahead of print]
​
De Keersmaecker, K, Atak ZK, Li N, Vicente C, Patchett S, Girardi T, Gianfelici V, Geerdens E, Clappier E, Porcu M, Lahortiga I, Lucà R, Yan J, Hulselmans G, Vranckx H, Vandepoel R, Sweron B, Jacobs K, Mentens N, Wlodarska I, Cauwelier B, Cloos J, Soulier J, Uyttebroeck A, Bagni C, Hassan BA, Vandenberghe P, Johnson AW, Aerts S, Cools J. Exome sequencing identifies mutation in CNOT3 and ribosomal genes RPL5 and RPL10 in T-cell acute lymphoblastic leukemia. Nat Genet. 2012 Dec 23. doi: 10.1038/ng.2508. [Epub ahead of print]
​
Sardana, R. and A.W.Johnson. The methyltransferase adaptor protein Trm112 is involved in biogenesis of both ribosomal subunits. Mol Bio Cell. (2012) 23:4313-22.
​
Bussiere, C., Y. Hashem, S. Arora, J. Frank and A.W. Johnson. Integrity of the P-site is probed during maturation of the 60S ribosomal subunit. J Cell Biol. (2012) 197:747-59. (Received an editorial highlight “The ribosome runs a systems test”)
2011
​
Johnson AW, Ellis SR. Of blood, bones, and ribosomes: is Shwachman-Diamond syndrome a ribosomopathy? Genes Dev. 2011 May 1;25(9):898-900.
2010
​
Lo, K.-Y., S. Bresson, Z. Li, E.M. Marcotte and A.W. Johnson. Defining the Pathway of cytoplasmic maturation of the 60S ribosomal subunit. Mol Cell (2010) 39:196-208.
​
Sengupta, J., C. Bussiere, M. West, A.W. Johnson, and J. Frank. Characterization of the nuclear export adaptor protein Nmd3 in association with the 60S ribosomal subunit. J Cell Biol (2010) 189:179-86.
​
Fassio, C., B. Schofield, R. M. Seiser, A.W. Johnson and D. Lycan. Dominant mutations in the late 40S biogenesis factor Ltv1 affect export and cytoplasmic maturation of the small ribosomal subunit in S. cerevisiae. Genetics (2010) 185:199-209.
​
Panse VG, Johnson AW. Maturation of eukaryotic ribosomes: acquisition of functionality. Trends Biochem Sci. 2010 May;35(5):260-6. Review.
Prior to 2010
​
Lo, K.-Y., Z. Li, F. Wang, E.M. Marcotte and A.W. Johnson. Ribosome stalk assembly requires the dual specificity phosphatase Yvh1 for the exchange of Mrt4 with P0. J Cell Biol. (2009) 186: 849-862.
​
Li, Z, I. Lee, E. Moradi, N.-J. Hung, A.W. Johnson*, and E.M. Marcotte. Rational Extension of the Ribosome Biogenesis Pathway Using Network-Guided Genetics. PLoS Biology. (2009) 7(10):e1000213. (*: co-corresponding author)
​
Lo, K.-Y. and A.W. Johnson. Re-engineering Ribosome Export. Mol Biol Cell (2009) 19:734-44. Jan 14. [Epub ahead of print]
​
White, J., Z. Li, R. Sardana, J.M. Bujnicki, E.M. Marcotte and A.W. Johnson. Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits. Mol Cell Biol (2008) 28:3151-61. Epub 2008 Mar 10.
​
Hung, N.-J., K.-Y. Lo, S.S. Patel, K. Helmke and A.W. Johnson. Arx1 is a Nuclear Export Receptor for the 60S Ribosomal Subunit in Yeast. Mol Biol Cell (2008) 19:734-44. Epub 2007 Dec 12.
​
Hofer, A., C. Bussiere and A.W. Johnson. Mutational analysis of the ribosomal protein RPL10 from yeast. J Biol Chem. (2007) 282:32630-9.
​
West M, Hedges JB, Lo KY, Johnson, AW, Novel Interaction of the 60S Ribosomal Subunit Export Adapter Nmd3 at the Nuclear Pore Complex. J Biol Chem. (2007) 282:14028-37. Epub 2007 Mar 8.
​
Meyer AE, Hung NJ, Yang P, Johnson, AW, Craig EA. The Specialized cytosolic J-protein, Jjj1, functions in 60S ribosomal subunit biogenesis. Proc Natl Acad Sci USA. (2007) 104:1558-63. Epub 2007 Jan 22.
​
John Hedges, Yen-I Chen, Matthew West, Cyril Bussiere and Johnson, AW, Mapping the functional domains of yeast NMD3, the Nuclear Export Adapter for the 60S Ribosomal Subunit. (2006) 281:36579-87. Epub 2006 Oct 2.
​
Hung, N-J and Johnson, AW. Nuclear recycling of the pre-60S ribosomal subunit associated factor Arx1 depends on Rei1 in S. cerevisiae. (2006) Mol Cell Biol. 26(10):3718-3727.
​
Luo, W, Johnson, AW and Bentley, DL. The role of Rat1 in coupling mRNA 3’ end processing to transcription termination: implications for a unified allosteric-torpedo model. (2006) 20(8): 954-965.
​
Wang L, Lewis MS, Johnson AW. Domain interactions within the Ski2/3/8 complex and between the Ski complex and Ski7p. (2005) RNA.11(8):1291-302.
​
West M, Hedges JB, Chen A, Johnson AW. Defining the order in which Nmd3p and Rpl10p load onto nascent 60S ribosomal subunits. (2005) Mol Cell Biol.25(9):3802-13.
​
Hedges J, West M, Johnson AW. Release of the export adapter, Nmd3p, from the 60S ribosomal subunit requires Rpl10p and the cytoplasmic GTPase Lsg1p. (2005) EMBO J. 24(3):567-79. Epub 2005 Jan 20.
​
Kallstrom, G., Hedges, J. and Johnson AW. The Putative GTPases Nog1p and Lsg1p Are Required for 60S Ribosomal Subunit Biogenesis and Are Localized to the Nucleus and Cytoplasm, Respectively. (2003) Mol Cell Biol. 23(12):4344-55.
​
Trotta CR, Lund E, Kahan L, Johnson AW, Dahlberg JE. Coordinated nuclear export of 60S ribosomal subunits and NMD3 in vertebrates. (2003) EMBO J. 22(11):2841-51.
​
Johnson, A. W., J. H-N. Ho, G. Kallstrom, C.Trotta, E. Lund, L.Kahan, J. Hedges, J. Dahlberg. Nuclear Export of the Large Ribosomal Subunit. Cold Spring Harb. Symp. Quant. Biol. (2001) 66:599-605. Cold Spring Harbor Press.
​
Brown, J. T. and A. W. Johnson. A cis-acting element known to block 3’ mRNA degradation enhances expression of polyA-minus mRNA in wild-type yeast cells and phenocopies a ski mutant. (2001) RNA. 7:1566-1577
​
Ho, J. H.-N., G. Kallstrom and A. W. Johnson. Nmd3p is a Crm1-dependent adapter protein for nuclear export of the large ribosomal subunit. (2000) J Cell Biol. 151:1057-1066.
​
Ho, J. H.-N., G. Kallstrom and A. W. Johnson. Nascent 60S ribosomal subunits enter the free 60S pool bound by Nmd3p. (2000) RNA 6:1625-1634.
​
Xue, Y., X. Bai, I. Lee, G. Kallstrom, J. H.-N. Ho, J. T. Brown, A. Stevens and A. W. Johnson. Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p. Mol. Cell. Biol. 20 (2000) 4006-4015.
​
Brown, J. T., X. Bai and A. W. Johnson. The yeast antiviral proteins Ski2p, Ski3p and Ski8p exist as a complex in vivo. RNA 6 (2000) 449-457.
​
Brown, Justin T, X. Yang and A. W. Johnson. Inhibition of mRNA turnover in yeast by an xrn1 mutation enhances the requirement for eIF4E binding to eIF4G and for proper capping of transcripts by Ceg1p. Genetics 155 (2000) 31-42.
​
Ho, J. and A. W. Johnson. NMD3 encodes an essential cytoplasmic protein required for stable 60S ribosomal subunits in Saccharomyces cerevisiae. Mol. Cell. Biol. 19 (1999) 2389-2399.
​
Page, A. M., K. K. Davis, C. Molineux, R. D. Kolodner and A. W. Johnson. Mutational analysis of Exoribonuclease1 from Saccharomyces cerevisiae. Nucleic Acids Res. 26 (1998) 3707-3716.
​
Johnson, A. W. Rat1p and Xrn1p are functionally interchangeable exoribonucleases that are restricted to and required in the nucleus and cytoplasm respectively. Mol. Cell. Biol. 17 (1997) 6122-6130.