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JOHNSON, ARLEN W

Arlen W Johnson

Professor
Molecular Biosciences


Ribosome assembly in eukaryotic cells

arlen@austin.utexas.edu

Phone: 512-475-6350

Office Location
NMS 1.126

Postal Address
2506 SPEEDWAY
AUSTIN, TX 78712

Research in Arlen Johnson's Lab

My lab is interested in how cells manufacture ribosomes and ensure that they function correctly for decoding your genome during translation. Since working out the pathway for cytoplasmic maturation of the large ribosomal subunit more than 10 years ago (Lo et al Mol Cell, 2010), we have become interested in the general question of how the newly made ribosome is checked for function before it is licensed for translation. We found that the proper assembly of the P-site, close to the catalytic center of the ribosome, is assessed by several proteins that appear to be mimics of translation factors, leading us to propose that the 60S subunit undergoes a "test drive" before it is released into the pool of active ribosomes. In collaboration with Dr. David Taylor's lab, we used cryo-electron microscopy to determine the structures of multiple intermediates of the maturing large subunit to understand how the catalytic center of the ribosome is completed (Zhou et al, Nat Comm 2019). We are continuing to establish a mechanistic understanding of ribosome maturation.

In contrast to the large subunit of the ribosome, which catalyzes polypeptide synthesis, the small subunit is responsible for decoding. A critical intermediate in assembly of the small subunit is the SSU Processome, which is scaffolded by the non-coding U3 snoRNA. In order for the SSU Processome to be rearranged into a mature small subunit, U3 must be removed. In particular, U3 blocks the folding of the central pseudoknot, an RNA element that coordinates all the RNA domains of the small subunit. We identified the RNA helicase Dhr1 as the enzyme that unwinds U3 snoRNA from the pre-ribosomal RNA. We are interested in understanding how the timing of Dhr1 unwinding activity is controlled to ensure that unwinding occurs only after completing the major assembly events of the small subunit. To this end, we have identified a network of factors involved in Dhr1 function and we are using a suite of approaches, including molecular genetics, biochemistry and structural biology, to understand their role in the timing of Dhr1 function.

Publications:

2014 Sulima SO, Gülay SP, Anjos M, Patchett S, Meskauskas A, Johnson AW, Dinman J, Ekaryotic rpL10 Drives Intrinsic Ribosomal Rotation. Nucleic Acids Res. 42: 2049-63

2014 Sulima SO, Patchett S, Advani VM, de Keersmaecker K, Johnson AW, Dinman J, Bypass of the pre-60S ribosomal quality control as a pathway to oncogenesis. PNAS(USA). 111: 5640-5.

2014 Sardana R, Zhu J, Johnson AW, Physical and functional interactions between the methyltransferase Bud23 and the essential DEAH-box RNA helicase Ecm16. Mol Cell Biol. 34 :2208-2220.

2013 Sardana R, White JP, Johnson AW, The rRNA methyltransferase Bud23 shows functional interaction with components of the SSU processome and RNase MRP, RNA 19: 828-840 view

2013 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 Gen 48: 186-190 view

2012 Sardana R, Johnson AW, The methyltransferase adaptor protein Trm112 is involved in biogenesis of both ribosomal subunits, MBC 23: 4313-4322 view

2012 Integrity of the P-site is probed during maturation of the 60S ribosomal subunit, Bussiere C, Hashem Y, Arora S, Frank J, Johnson AW., J Cell Bio 197: 747-759 view

2010 J. Sengupta, C. Bussiere, J. Pallesen, M. West, AW. Johnson, and J. Frank, Characterization of the nuclear export adaptor protein Nmd3 in association with the 60S ribosomal subunit, J Cell Biol 189: 1079-1086 view

2010 K.Y. Lo, Z. Li, CBussiere, S. Bresson, EM Marcotte, and AW Johnson, Defining the pathway of cytoplasmic maturation of the 60S ribosomal subunit, Mol Cell 39: 196-208 view

2010 Panse VG, Johnson AW., Maturation of eukaryotic ribosomes: acquisition of functionality, Trends Biochem Sci 35: 260-266 view

2009 Lo KY, Li Z, Wang F, Marcotte EM, Johnson AW, Ribosome stalk assembly requires the dual-specificity phosphatase Yvh1 for the exchange of Mrt4 with P0, J Cell Biol 186: 849-862 view

2009 Li Z, Lee I, Moradi E, Hung NJ, Johnson AW, Marcotte EM, Rational extension of the ribosome biogenesis pathway using network-guided genetics, PLoS Biol 7: 1000213 view

2009 Lo KY, Johnson AW., Reengineering Ribosome Export, Mol Biol Cell 20: 1545-1554 view

2008 Hung NJ, Lo KY, Patel SS, Helmke K, Johnson AW, Arx1 is a nuclear export receptor for the 60S ribosomal subunit in yeast, Mol Biol Cell 19: 734-744

2008 White J, Li Z, Sardana R, Bujnicki JM, Marcotte EM, Johnson AW., Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits., Mol Cell Biol 28: 3151-3161 view

2007 Meyer AE, Hung NJ, Yang P, Johnson AW, The specialized cytosolic J-protein, Jjj l, functions in 60S ribosomal subunit biogenesis, PNAS U.S.A. 104: 1558-63

2007 Hedges J, Chen YI, West M, Bussiere C, Johnson AW, Mapping the functional domains of yeast NMD3, the nuclear export adapter for the 60 S ribosomal subunit, J Biol Chem 281: 36579-36587

2007 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 282: 14028-14037

2007 Hofer A, Bussiere C, Johnson AW, Mutational analysis of the ribosomal protein Rpl10 from yeast, J Biol Chem 282: 32630-32639

2006 Hung NJ, Johnson AW, Nuclear recycling of the pre-60S ribosomal subunit-associated factor Arx1 depends on Rei1 in Saccharomyces cerevisiae, Mol Cell Biol 26: 3718-3727

2005 Wang L, Lewis, M, Johnson AW, Domain interactions within the Ski2/3/8 complex and between the Ski complex and Ski7p, RNA 11: 1291-1302

2005 West M, West M, Johnson AW, Defining the order in which Nmd3p and Rpl10p load onto nascent 60S ribosomal subunits, MCB 25: 3802-3813

2005 Hedges J, West M, Johnson AW, Release of the export adapter, Nmd3p, from the 60S ribosomal subunit requires Rpl10p and the cytoplasmic GTPase Lsg1p, EMBO 24: 567-579

2001 Ho H-N, Kallstrom G, Johnson AW, Nmd3p is a Crm1p-dependent adapter protein for nuclear export of the large ribosomal subunit, J Cell Bio 151: 1057-1066