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COMBINING NANOPORE DIRECT RNA SEQUENCING WITH MOLECULAR GENETICS AND MASS SPECTROMETRY FOR ANALYSIS OF T-LOOP BASE MODIFICATIONS ACROSS 42 YEAST ISOACCEPTORS

2024

Shaw EA, Thomas NK, Jones JD, Abu-Shumays RL, Vaaler AL, Akeson M, Koutmou KS, Jain M, Garcia DM

Nucleic Acids Research, in press 

 

N1-METHYLPSEUDOURIDINE AND PSEUDOURIDINE MODIFICATIONS IMPACT AMNO ACID MISINCORPORATION DURING TRANSLATION 

2024

Monroe JG, Eyler DE, Mitchell L, Deb I, Bojankowski A, Srinivas P, Dunham C, Roy B, Frank AZ, Koutmou KS*

Nature Communications, in press

 

CONSERVED 5-METHYLURIDINE TRNA MODIFICATION MODULATES RIBOSOME TRANSLOCATION

2024

JD Jones, MK Franco, RN Giles, DE Eyler, M Tardu, TJ Smith, LR Snyder, YS Polikanov, RT Kennedy, RO Niederer, KS Koutmou

PNAS (DOI: 10.1073/pnas.2401743121)

 

ADENOSINE MODIFICATIONS IMPEDE SARS-CoV-2 RNA-DEPENDENT RNA TRANSCRIPTION

2024

LR Snyder, I Kilde, A Nemudryi, B Wiedenheft, M Koutmos, KS Koutmou

RNA (DOI: 10.1261/rna.079991.124)

 

ANTICODON STEM-LOOP tRNA MODIFICATIONS INFLUENCE CODON DECODING AND FRAME MAINTENANCE DURING TRANSLATION

2023

TJ Smith, R Giles, KS Koutmou

Seminars in Cell and Developmental Biology (DOI: 10.1016/j.semcdb.2023.06.003)

 

DIRECT SEQUENCING OF TOTAL S. CEREVISIAE TRNAS BY LC-MS/MS

2023

JD Jones, KM Simcox, RT Kennedy, KS Koutmou

RNA (DOI: 10.1261/rna.079656.123)

 

A HUMANIZED YEAST MODEL REVEALS DOMINANT-NEGATIVE PROPERTIES OF NEUROPATHY-ASSOCIATED ALANYL-TRNA SYNTHETASE MUTATIONS

2023

R Meyer-Schuman, S Marte, TJ Smith, S Feely, M Kennerson, G Nicholson, M Shy, KS Koutmou, A Antonellis

Human Molecular Genetics (DOI: 10.1093/hmg/ddad054)

 

METHYLATED GUANOSINE AND URIDINE MODIFICATIONS IN S. CEREVISIAE MRNAS MODULATE TRANSLATION

2023

JD Jones, MK Franco, TJ Smith, LR Snyder, A Anders, BT Ruotolo, RT Kennedy, KS Koutmou

RSC ChemBio (DOI: 10.1039/D2CB00229A)

NUCLEASE P1 DIGESTION FOR BOTTOM-UP RNA SEQUENCING OF MODIFIED SIRNA THERAPEUTICS

2023

JD Jones, K Grassmyer, RT Kennedy, KS Koutmou, T Maloney

Analytical Chemistry (DOI: 10.1021/acs.analchem.2c04902)

SEQUENCE-SPECIFIC PROGRAMMABLE CAPTURE AND CONCENTRATION OF VIRAL RNA BY TYPE III CRISPR SYSTEM ENHANCES DIAGNOSTIC

2022

A Nemudraia, A Nemudryi, M Buyukyoruk, AM Scherffius, T Zahl, T Wiegand, S Pandey, J Nichols, L Hall, A McVey, HH Lee, R Wilkinson, LR Snyder, JD Jones, KS Koutmou, A Santiago-Frangos, B Wiedenheft

Nature Communications (DOI: 10.1038/s41467-022-35445-5)

MAPPING MRNA MODIFICATIONS FOR FUNCTIONAL STUDIES

2022

JD Jones, DE Eyler, KS Koutmou

Nature Biotechnology  (DOI: 10.1038/s41587-022-01537-2)

SUPPORTING STUDENT LEARNING IN BIOCHEMISTRY USING A SCIENCE COMMUNICATION FOCUSED WRITING ASSIGNMENT

2022

SA Finkenstaedt-Quinn, NF Garza, CA Wilhelm, KS Koutmou, GV Shultz

Journal of Chemical Education (DOI: 10.1021/acs.jchemed.2c00171)

CGG REPEATS TRIGGER TRANSLATIONAL FRAMESHIFTING TO GENERATE AGGREGATION-PRONE CHIMERIC PROTEINS IN NEURONS

2022

SE Wright, CM Rodriguez, J Monroe, J Xing, A Krans, BN Flores, V Barsur, MI Ivanova, KS Koutmou, SJ Barmada, PK Todd

Nucleic Acids Research (DOI: 10.1093/nar/gkac626)

MRNA AND TRNA MODIFICATION STATES INFLUENCE RIBOSOME SPEED AND FRAME MAINTENANCE DURING POLY(LYSINE) PEPTIDE SYNTHESIS

2022

TJ Smith, M Tardu, HJ Khatri, KS Koutmou

Journal of Biological Chemistry (DOI: 10.1016/j.jbc.2022.102039)

***Selected as an Editor's Choice article

CHEMICAL MODIFICATIONS TO MRNA NUCLEOBASES IMPACT TRANSLATION ELONGATION AND TERMINATION

2022

MK Franco and KS Koutmou

Biophysical Chemistry (DOI: 10.1016/j.bpc.2022.106780)

***Article featured on the journal cover

THE CAMP SIGNALING PATHWAY REGULATES EPE1 PROTEIN LEVELS AND HETEROCHROMATIN ASSEMBLY

2022

S Jia, K Bao, CM Shan, X Chen, G Raiymbek, JG Monroe, KS Koutmou, K Ragunathan, C Lu, L Berchowitz

PLoS Genetics (DOI: 10.1371/journal.pgen.1010049​)

PSEUDOURIDINE SYNTHASE 7 IS AN OPPORTUNISTIC ENZYME THAT BINDS AND MODIFIES SUBSTRATES WITH DIVERSE SEQUENCES AND STRUCTURES

2022

MK Purchal, DE Eyler, M Tardu, MK Franco, MM Korn, T Khan, R McNassor, R Giles, K Lev, H Sharma,  J Monroe, L Mallik, M Koutmos, KS Koutmou

PNAS (DOI: 10.1073/pnas.2109708119)

IN VITRO INVESTIGATION OF TRANSLATIONAL FIDELITY ON MODIFIED CODONS

2021

JG Monroe, TJ Smith, KS Koutmou

Methods Enzymology (DOI: 10.1016/bs.mie.2021.06.011)

COMMUNICATING SCIENCE TO THE GENERAL PUBLIC THROUGH A BIOCHEMISTRY WRITING ASSIGNMENT

2021

Garza N, Finkenstaedt-Quinn S, Wilhelm, C, Koutmou K, Shultz G

Journal of Chemical Education (DOI: 10.1021/acs.jchemed.0c01176)

A MOLECULAR LEVEL PERSPECTIVE ON THE FREQUENCY, DISTRIBUTION AND POSSIBLE CELLULAR ROLES OF MRNA MODIFICATIONS

2020

JD Jones, J Monroe and KS Koutmou

WIREs RNA (DOI: 10.1002/wrna.1586)

***Recognized as a “top cited article 2020-2021” in WIREs RNA

PSEUDOURIDINYLATION OF MRNA CODING SEQUENCES ALTERS TRANSLATION

2019

DE Eyler, MK Franco, Z Batool, MZ Wu, ML Debuke, M Dobosz-Bartoszek, JD Jones, Y Polikanov, B Roy, KS Koutmou

PNAS (DOI: 10.1073/pnas.1821754116)

IDENTIFICATION AND QUANTIFICATION OF MODIFIED NUCLEOSIDES IN SACCHAROMYCES CEREVISIAE MRNAS

2019

M Tardu, JD Jones, RT Kennedy, Q Lin, KS Koutmou

ACS Chemical Biology (DOI: 10.1021/acschembio.9b00369)

SYNTHESIS AT THE SPEED OF CODONS

2015

KS Koutmou, A Radhakrishnan, R Green

Trends in Biomedical Sciences

TRANSLATIONAL CONTROL BY LYSINE-ENCODING A-RICH SEQUENCES

2015

L Arthur, S Pavlovic-Djuranovic, KS Koutmou, R Green, P Szczesny, S Djuranovic

Science Advances

SID-1 EXTRACELLULAR DOMAIN SELECTIVELY BINDS LONG DSRNA AND IS REQUIRED FOR RNA TRANSPORT BY SID-1

2015

W Li, KS Koutmou, DJ Leahy, M Li

Journal of Biological Chemistry

RIBOSOMES SLIDE ON LYSINE-ENCODING HOMOPOLYMERIC A STRETCHES

2015

KS Koutmou, AP Schuller, JL Brunelle, A Radhakrishnan, S Djuranovic, R Green

eLife

RF3:GTP PROMOTES RAPID DISSOCIATION OF THE CLASS 1 TERMINATION FACTOR

2014

KS Koutmou, ME McDonald, JL Brunelle, R Green

RNA

THE RNR MOTIF OF B. SUBTILIS RNASE P PROTEIN INTERACTS WITH BOTH PRNA AND PRE-TRNA TO STABILIZE AN ACTIVE CONFORMER

2011

KS Koutmou, JJ Day-Storms, CA Fierke

RNA

A DIVALENT CATION STABILIZES THE ACTIVE CONFORMATION OF THE B. SUBTILIS RNASE P•PRE-TRNA COMPLEX: A ROLE FOR AN INNER-SPHERE METAL ION IN RNASE P

2010

J Hsieh, KS Koutmou, D Rueda, M Koutmos, NG Walter, CA Fierke

Journal of Molecular Biology

NMR AND XAS REVEAL AN INNER-SPHERE METAL BINDING SITE IN THE P4 HELIX OF THE METALLO-RIBOZYME RIBONUCLEASE P

2010

KS Koutmou, A Casiano-Negroni, M Getz, S Paczini, AJ Andrews, JE Penner-Hahn, HM Al-Hashimi, CA Fierke

Proceedings of the National Academy of Sciences

PROTEIN–PRECURSOR TRNA CONTACT LEADS TO SEQUENCE-SPECIFIC RECOGNITION OF 5′ LEADERS BY BACTERIAL RIBONUCLEASE P

2010

KS Koutmou, NH Zahler, JC Kurz, FE Campbell, ME Harris, CA Fierke

Journal of Molecular Biology

KINETIC MECHANISM OF BACTERIAL RNASE P

2009

KS Koutmou, J Hsieh, CA Fierke

Protein Reviews, Volume 10: Ribonuclease P (book chapter)

IMPORTANCE OF RNA-PROTEIN INTERACTIONS IN BACTERIAL RIBONUCLEASE P STRUCTURE AND CATALYSIS

2007

JK Smith, J Hsieh, CA Fierke

Biopolymers

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