TY - JOUR AU - Apjok, Gábor AU - Boross, Gábor AU - Nyerges, Ákos AU - Fekete, Gergely AU - Lázár, Viktória AU - Papp, Balázs AU - Pál, Csaba AU - Csörgő, Bálint TI - Limited evolutionary conservation of the phenotypic effects of antibiotic resistance mutations JF - MOLECULAR BIOLOGY AND EVOLUTION J2 - MOL BIOL EVOL VL - 36 PY - 2019 IS - 8 SP - 1601 EP - 1611 PG - 11 SN - 0737-4038 DO - 10.1093/molbev/msz109 UR - https://m2.mtmt.hu/api/publication/30703953 ID - 30703953 LA - English DB - MTMT ER - TY - JOUR AU - Nyerges, Ákos AU - Csörgő, Bálint AU - Draskovits, Gábor AU - Kintses, Bálint AU - Szili, Petra AU - Ferenc, Györgyi AU - Révész, Tamás AU - Ari, Eszter AU - Nagy, István AU - Bálint, Balázs AU - Vásárhelyi, Bálint Márk AU - Bihari, Péter AU - Számel, Mónika AU - Balogh, Dávid AU - Papp, Henrietta AU - Kalapis, Dorottya AU - Papp, Balázs AU - Pál, Csaba TI - Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance. JF - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA J2 - P NATL ACAD SCI USA VL - 115 PY - 2018 IS - 25 SP - E5726 EP - E5735 PG - 10 SN - 0027-8424 DO - 10.1073/pnas.1801646115 UR - https://m2.mtmt.hu/api/publication/3390047 ID - 3390047 N1 - COIS Conflict of interest statement: A.N., B.C., B.K., and C.P. have filed a patent : application toward the European Patent Office. I.N., B.B., B.M.V., and P.B. had : consulting positions at SeqOmics Biotechnology Ltd. at the time the study was : conceived. SeqOmics Biotechnology Ltd. was not directly involved in the design : and execution of the experiments or in the writing of the manuscript. Hiányzó szerző: 'http' Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, 6726, Hungary Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, 6720, Hungary Nucleic Acid Synthesis Laboratory, Institute of Plant Biology, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, 6726, Hungary Department of Genetics, Eötvös Loránd University, Budapest, 1053, Hungary Sequencing Laboratory, SeqOmics Biotechnology Ltd., Mórahalom, 6782, Hungary Sequencing Platform, Institute of Biochemistry, Biological Research Centre of the Hungarian, Academy of Sciences, Szeged, 6726, Hungary Department of Microbiology and Immunology, University of California, San Francisco, CA 94143 Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian, Academy of Sciences, Szeged, 6726, Hungary Cited By :20 Export Date: 8 December 2020 CODEN: PNASA Correspondence Address: Nyerges, Á.; Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of SciencesHungary; email: nyerges.akos@brc.mta.hu AB - Antibiotic development is frequently plagued by the rapid emergence of drug resistance. However, assessing the risk of resistance development in the preclinical stage is difficult. Standard laboratory evolution approaches explore only a small fraction of the sequence space and fail to identify exceedingly rare resistance mutations and combinations thereof. Therefore, new rapid and exhaustive methods are needed to accurately assess the potential of resistance evolution and uncover the underlying mutational mechanisms. Here, we introduce directed evolution with random genomic mutations (DIvERGE), a method that allows an up to million-fold increase in mutation rate along the full lengths of multiple predefined loci in a range of bacterial species. In a single day, DIvERGE generated specific mutation combinations, yielding clinically significant resistance against trimethoprim and ciprofloxacin. Many of these mutations have remained previously undetected or provide resistance in a species-specific manner. These results indicate pathogen-specific resistance mechanisms and the necessity of future narrow-spectrum antibacterial treatments. In contrast to prior claims, we detected the rapid emergence of resistance against gepotidacin, a novel antibiotic currently in clinical trials. Based on these properties, DIvERGE could be applicable to identify less resistance-prone antibiotics at an early stage of drug development. Finally, we discuss potential future applications of DIvERGE in synthetic and evolutionary biology. LA - English DB - MTMT ER - TY - JOUR AU - Colin, P-Y AU - Kintses, Bálint AU - Gielen, F AU - Miton, CM AU - Fischer, G AU - Mohamed, MF AU - Hyvönen, M AU - Morgavi, DP AU - Janssen, DB AU - Hollfelder, F TI - Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics JF - NATURE COMMUNICATIONS J2 - NAT COMMUN VL - 6 PY - 2015 PG - 12 SN - 2041-1723 DO - 10.1038/ncomms10008 UR - https://m2.mtmt.hu/api/publication/2998416 ID - 2998416 N1 - Megjegyzés-25258911 Hiányzó Jelleg: 'JOUR\n\nArticle' Admin megjegyzés-25258911 tblcategory: (Category) ('JOUR\n\nArticle') #Jelleg AB - Unculturable bacterial communities provide a rich source of biocatalysts, but their experimental discovery by functional metagenomics is difficult, because the odds are stacked against the experimentor. Here we demonstrate functional screening of a million-membered metagenomic library in microfluidic picolitre droplet compartments. Using bait substrates, new hydrolases for sulfate monoesters and phosphotriesters were identified, mostly based on promiscuous activities presumed not to be under selection pressure. Spanning three protein superfamilies, these break new ground in sequence space: promiscuity now connects enzymes with only distantly related sequences. Most hits could not have been predicted by sequence analysis, because the desired activities have never been ascribed to similar sequences, showing how this approach complements bioinformatic harvesting of metagenomic sequencing data. Functional screening of a library of unprecedented size with excellent assay sensitivity has been instrumental in identifying rare genes constituting catalytically versatile hubs in sequence space as potential starting points for the acquisition of new functions. LA - English DB - MTMT ER -