Publications

Synthetic genomes unveil the effects of synonymous recoding

Nyerges A^#, Chiappino-Pepe A, Budnik B, Baas-Thomas M, Flynn R, Yan S, Ostrov N, Liu M, Wang M, Zheng Q, Hu F, Chen K, Rudolph A, Chen D, Ahn J, Spencer O, Ayalavarapu V, Tarver A, Harmon-Smith M, Hamilton M, Blaby I, Yoshikuni Y, Hajian B, Jin A, Kintses B, Szamel M, Seregi V, Shen Y, Li Z, Church GM^#

bioRxiv, 2024 · PMCID: PMC11195188 · in revision

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A swapped genetic code prevents viral infections and gene transfer

Nyerges A^#, Vinke S, Flynn R, Owen SV, Rand E, Keen E, Budnik B, Narasimhan K, Marchand JA, Baas-Thomas M, Liu M, Chen K, Chiappino-Pepe A, Hu F, Baym M, Church GM^#

Nature, 2023 · Preprint: bioRxiv, July 2022

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Strategies to identify and edit improvements in synthetic genome segments episomally

Rudolph A, Nyerges A, Chiappino-Pepe A, Landon M, Baas-Thomas M, Church G

Nucleic Acids Research, 2023

DOI

Characterization of antibiotic resistomes by reprogrammed bacteriophage-enabled functional metagenomics in clinical strains

Apjok G, Szamel M, Christodoulou C, Seregi V, Vasarhelyi B, Stirling T, Eszenyi B, Sari T, Vidovics F, Nagrand E, Kovacs D, Szili P, Lantos I, Mehi O, Jangir P, Herczeg R, Galik B, Urban P, Gyenesei A, Draskovits G, Nyerges A, Fekete G, Bodai L, Zsindely N, Denes B, Yosef I, Qimron U, Papp B, Pal C, Kintses B

Nature Microbiology, 2023

DOI

Towards next-generation cell factories by rational genome-scale engineering

Yilmaz S, Nyerges A, van der Oost J, Church GM, Claassens NJ

Nature Catalysis, 2022

DOI

Recombineering and MAGE

Wannier TM, Ciaccia PN, Ellington AD, Filsinger GT, Isaacs FJ, Javanmardi K, Jones MA, Kunjapur AM, Nyerges A, Pal C, Schubert MG, Church GM

Nature Reviews Methods Primers, 2021

DOI

inPOSE: a flexible toolbox for chromosomal cloning and amplification of bacterial transgenes

Shukla RD, Zvara A, Avramucz A, Biketova AY, Nyerges A, Puskas LG, Feher T

Microorganisms, 2021

DOI

Hybrid Inhibitors of DNA Gyrase A and B: Design, Synthesis and Evaluation

Durcik M, Skok Z, Ilas J, Zidar N, Zega A, Szili PE, Draskovits G, Revesz T, Kikelj D, Nyerges A, Pal C, Masic LP, Tomasic T

Pharmaceutics, 2021

DOI

New dual ATP-competitive inhibitors of bacterial DNA gyrase and topoisomerase IV active against ESKAPE pathogens

Durcik M, Nyerges A, Skok Z, Skledar DG, Trontelj J, Zidar N, Ilas J, Zega A, Cruz CD, Tammela P, Welin M, Kimbung YR, Focht D, Benek O, Revesz T, Draskovits G, Szili PE, Daruka L, Pal C, Kikelj D, Masic LP, Tomasic T

European Journal of Medicinal Chemistry, 2021

DOI

ssDNA recombineering boosts in vivo evolution of nanobodies displayed on bacterial surfaces

Al-ramahi Y, Nyerges A, Margolles Y, Cerdan L, Ferenc G, Pal C, Fernandez LA, de Lorenzo V

Communications Biology, 2021

DOI

Rational design of balanced dual-targeting antibiotics with limited resistance

Nyerges A, Tomasic T, Durcik M, Revesz T, Szili P, Draskovits G, Bogar F, Skok Z, Zidar N, Ilas J, Zega A, Kikelj D, Daruka L, Kintses B, Vasarhelyi B, Foldesi I, Kata D, Welin M, Kimbung R, Focht D, Masic LP^#, Pal C^#

PLOS Biology 18, e3000819, 2020

Full text → DOI PDB 6TCK PDB 6TTG

Improved bacterial recombineering by parallelized protein discovery

Wannier TM, Nyerges A, Kuchwara HM, Czikkely M, Balogh D, Filsinger GT, Borders NC, Gregg CJ, Lajoie MJ, Rios X, Pal C, Church GM

Proceedings of the National Academy of Sciences, 2020

DOI

Synthetic genomes with altered genetic codes

Ostrov N, Nyerges A, Chiappino-Pepe A, Rudolph A, Baas-Thomas M, Church GM

Current Opinion in Systems Biology, 2020

DOI

Second-generation 4,5,6,7-tetrahydrobenzo[d]thiazoles as novel DNA gyrase inhibitors

Lamut A, Skok Z, Barancokova M, Gutierrez LJ, Cruz CD, Tammela P, Draskovits G, Szili PE, Nyerges A, Pal C, Molek P, Bratkovic T, Ilas J, Zidar N, Zega A, Enriz RD, Kikelj D, Tomasic T

Future Medicinal Chemistry, 2020

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Multiple-Site Diversification of Regulatory Sequences Enables Interspecies Operability of Genetic Devices

Hueso-Gil A, Nyerges A, Pal C, Calles B, de Lorenzo V

ACS Synthetic Biology, 2020

DOI

Dual Escherichia coli DNA Gyrase A and B Inhibitors with Antibacterial Activity

Fois B, Skok Z, Tomasic T, Ilas J, Zidar N, Zega A, Peterlin Masic L, Szili P, Draskovits G, Nyerges A, Pal C, Kikelj D

ChemMedChem, 2020

DOI

Targeted mutagenesis of multiple chromosomal regions in microbes

Csorgo B, Nyerges A, Pal C

Current Opinion in Microbiology, 2020

DOI

High-efficiency multi-site genomic editing (HEMSE) of Pseudomonas putida through thermoinducible ssDNA recombineering

Aparicio T, Nyerges A, Martinez-Garcia E, de Lorenzo V

iScience, 2020

DOI

CRISPR-interference-based modulation of mobile genetic elements in bacteria

Nyerges A, Balint B, Cseklye J, Nagy I, Pal C, Feher T^#

Synthetic Biology, 2019

DOI

Rapid evolution of reduced susceptibility against a balanced dual-targeting antibiotic through stepping-stone mutations

Szili P, Draskovits G, Revesz T, Bogar F, Balogh D, Martinek T, Daruka L, Spohn R, Vasarhelyi BM, Czikkely M, Kintses B, Grezal G, Ferenc G, Pal C^#, Nyerges A^#

Antimicrobial Agents and Chemotherapy, 2019

DOI

An optimised series of substituted N-phenylpyrrolamides as DNA gyrase B inhibitors

Tiz DB, Skok Z, Durcik M, Tomasic T, Masic LP, Ilas J, Zega A, Draskovits G, Revesz T, Nyerges A, Pal C, Cruz CD, Tammela P, Zigon D, Kikelj D, Zidar N

European Journal of Medicinal Chemistry, 2019

DOI

Enzyme promiscuity shapes adaptation to novel growth substrates

Guzman GI, Sandberg TE, LaCroix RA, Nyerges A, Papp H, de Raad M, King ZA, Hefner Y, Northen TR, Notebaart RA, Pal C, Palsson BO, Papp B, Feist AM

Molecular Systems Biology, 2019

DOI

Mismatch repair hierarchy of Pseudomonas putida revealed by mutagenic ssDNA recombineering of the pyrF gene

Aparicio T, Nyerges A, Nagy I, Pal C, Martinez-Garcia E, de Lorenzo V

Environmental Microbiology, 2019

DOI

Limited Evolutionary Conservation of the Phenotypic Effects of Antibiotic Resistance Mutations

Apjok G, Boross G, Nyerges A, Fekete G, Lazar V, Papp B, Pal C, Csorgo B

Molecular Biology and Evolution, 2019

DOI

Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance

Nyerges A^#, Csorgo B, Draskovits G, Kintses B, Szili P, Ferenc G, Revesz T, Ari E, Nagy I, Balint B, Vasarhelyi BM, Bihari P, Szamel M, Balogh D, Papp H, Kalapis D, Papp B, Pal C^#

Proceedings of the National Academy of Sciences 115, E5726-E5735, 2018

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Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota

Kintses B, Mehi O, Ari E, Szamel M, Gyorkei A, Jangir PK, Nagy I, Pal F, Fekete G, Tengolics R, Nyerges A, Liko I, Balint A, Molnar T, Balint B, Vasarhelyi BM, Bustamante M, Papp B, Pal C

Nature Microbiology, 2018

DOI

A standardized workflow for surveying recombinases expands bacterial genome-editing capabilities

Ricaurte DE, Martinez-Garcia E, Nyerges A, Pal C, de Lorenzo V, Aparicio T

Microbial Biotechnology, 2018

DOI

Antibiotic-resistant bacteria show widespread collateral sensitivity to antimicrobial peptides

Lazar V, Martins A, Spohn R, Daruka L, Grezal G, Fekete G, Szamel M, Jangir PK, Kintses B, Csorgo B, Nyerges A, Gyorkei A, Kincses A, Der A, Walter FR, Deli MA, Urban E, Hegedus Z, Olajos G, Mehi O, Balint B, Nagy I, Martinek TA, Papp B, Pal C

Nature Microbiology, 2018

DOI

New N-phenylpyrrolamide DNA gyrase B inhibitors: Optimization of efficacy and antibacterial activity

Durcik M, Lovison D, Skok Z, Durante Cruz C, Tammela P, Tomasic T, Benedetto Tiz D, Draskovits G, Nyerges A, Pal C, Ilas J, Peterlin Masic L, Kikelj D, Zidar N

European Journal of Medicinal Chemistry, 2018

DOI

Genome-Wide Abolishment of Mobile Genetic Elements Using Genome Shuffling and CRISPR/Cas-Assisted MAGE Allows the Efficient Stabilization of a Bacterial Chassis

Umenhoffer K, Draskovits G, Nyerges A, Karcagi I, Bogos B, Timar E, Csorgo B, Herczeg R, Nagy I, Feher T, Pal C, Posfai G

ACS Synthetic Biology, 2017

DOI

Phenotypic heterogeneity promotes adaptive evolution

Bodi Z, Farkas Z, Nevozhay D, Kalapis D, Lazar V, Csorgo B, Nyerges A, Szamecz B, Fekete G, Papp B, Araujo H, Oliveira JL, Moura G, Santos MAS, Jr TS, Balazsi G, Pal C

PLOS Biology, 2017

DOI

A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species

Nyerges A, Csorgo B^*, Nagy I, Balint B, Bihari P, Lazar V, Apjok G, Umenhoffer K, Bogos B, Posfai G, Pal C^#

Proceedings of the National Academy of Sciences, 2016

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System-level genome editing in microbes

Csorgo B, Nyerges A, Posfai G, Feher T

Current Opinion in Microbiology, 2016

DOI

Conditional DNA repair mutants enable highly precise genome engineering

Nyerges A, Csorgo B, Nagy I, Latinovics D, Szamecz B, Posfai G, Pal C^#

Nucleic Acids Research 42, e62, 2014

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Perturbation of Iron Homeostasis Promotes the Evolution of Antibiotic Resistance

Mehi O, Bogos B, Csorgo B, Pal F, Nyerges A, Papp B, Pal C

Molecular Biology and Evolution, 2014

DOI

Genome-wide analysis captures the determinants of the antibiotic cross-resistance interaction network

Lazar V, Nagy I, Spohn R, Csorgo B, Gyorkei A, Nyerges A, Horvath B, Voros A, Busa-Fekete R, Hrtyan M, Bogos B, Mehi O, Fekete G, Szappanos B, Kegl B, Papp B, Pal C

Nature Communications, 2014

DOI

Synthetic 57-Codon Genome and Methods for Multi-Omics-Based Genome Synthesis

Nyerges AJ, Church GM

US Provisional Application 63/560,144, 2024

Genetic firewall based on an amino-acid-swapped genetic code

Nyerges AJ, Church GM

International Patent Application PCT/US2023/069468, 2022

Methods for making and using genomically recoded cells

Nyerges AJ, Church GM

International Patent Application PCT/US2021/062177, 2021

Mutagenizing Intracellular Nucleic Acids

Nyerges AJ, Pal C, Csorgo B, Kintses B

PCT/EP2017/082574 · US10669537B2 — granted in the US & 25 EU countries · outlicensed (2x)

New Class of DNA Gyrase and/or Topoisomerase IV Inhibitors with Activity Against Gram-Positive and Gram-Negative Bacteria

Tomasic T, Zidar N, Durcik M, Ilas J, Zega A, Durante Cruz C, Tammela P, Pal C, Nyerges AJ, Kikelj D, Masic LP

PCT/EP2019/073412 · US12258342B2 — granted in the US