THE TRNA DIHYDROURIDINE SYNTHASE DUSA HAS A DISTINCT MECHANISM IN OPTIMIZING TRNAS FOR TRANSLATION
2025
Schultz SK, Hossain N, Barnes L, Koutmou KS, Kothe U*
submitted, bioRxiv DOI: DOI: 10.1101/2025.08.28.672980
A TRANSFER RNA MODIFICATION DRIVES GENOME-WIDE SYNONYMOUS RECODING ACROSS HUMAN COMMENSAL BACTERIAL FAMILIES
2025
Katanski CD, Pathirage C, Chang J, Veseli I, Smith TJ, Foo M, Wu Y, Hou Y, Tran A, Rudzka D, Bayat Tork MA, Lolans K, Willis A, Tang W, Eren AM, Federle M, Koutmou KS, Pan T*
submitted
TYLA IS A 23S AND 16S 2'-O-METHYLCYTIDINE METHYLTRANSFERASE IMPORTANT FOR RIBOSOME ASSEMBLY IN BACILLUS SUBTILIS
2025
Hibma JL, Munson LM, Jones JD, Nye TM, Koutmou KS*, Simmons LA*
under revision, bioRxiv DOI: 10.1101/2025.04.21.649808
NASCENT CHAIN MISFOLDING SLOWS TRANSLATION AND STIMULATES CO-TRANSLATIONAL MRNA DECAY
2025
Chang S, Kawalerski R, Tardu M, Martin S, Koutmou KS, Coller J*
submitted
PUS7 CYTOPLASMIC LOCALIZATION DIRECTS A PSEUDOURIDINE-MEDIATED CELLULAR STRESS RESPONSE
2025
Ruan M, Engels SM, Burroughs MR, Bloch D, Fanari O, Akeson S, Weidmann CA, Rouhanifard S, Jain M, Contreras LM, Koutmou KS*
under revision
DE NOVO NANOPORE SEQUENCING OVERREPRESENTS RNA MODIFICATION LANDSCPE
2024
Jones JD, Goemann CLC, Wiegand T, Nemudryi A, Ruan M, Li X, Tardu M, Kennedy RT, Wiedenheft B, Koutmou, KS*
under revision
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, (DOI: 10.1093/nar/gkae796)
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, (DOI: 10.1038/s41467-024-51301-0)
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
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
