TY - JOUR AU - Helena-Bueno, Karla AU - Rybak, Mariia Yu. AU - Ekemezie, Chinenye L. AU - Sullivan, Rudi AU - Brown, Charlotte R. AU - Dingwall, Charlotte AU - Basle, Arnaud AU - Schneider, Claudia AU - Connolly, James P. R. AU - Blaza, James N. AU - Csörgő, Bálint AU - Moynihan, Patrick J. AU - Gagnon, Matthieu G. AU - Hill, Chris H. AU - Melnikov, Sergey V. TI - A new family of bacterial ribosome hibernation factors JF - NATURE J2 - NATURE VL - 626 PY - 2024 IS - 8001 SP - 1125 EP - 1132 PG - 26 SN - 0028-0836 DO - 10.1038/s41586-024-07041-8 UR - https://m2.mtmt.hu/api/publication/34782533 ID - 34782533 N1 - Funding Agency and Grant Number: Newcastle University NUORS 2021 Award; James W. McLaughlin Fellowship Fund; Medical Research Council [MR/N013840/1]; Biotechnology and Biological Sciences Research Council UK [BB/T008695/1]; UKRI Future Leader Fellowship [MR/T040742/1]; Lenduelet (Momentum) Program of the Hungarian Academy of Sciences [LP2022-4/2022a]; National Institutes of Health [R01GM136936]; Welch Foundation [H-2032-20230405]; Wellcome Trust & Royal Society Sir Henry Dale Fellowship [221818/Z/20/Z]; Royal Society [RGS/R2/202003]; Medical Research Council; Newcastle University Structural Biology Laboratory; Biotechnology and Biological Sciences Research Council; Wellcome Trust [206161/Z/17/Z]; Sealy and Smith Foundation; York Centre of Excellence in Mass Spectrometry; Engineering and Physical Sciences Research Council [EP/K039660/1, EP/M028127/1]; Yorkshire Forward; Northern Way Initiative; Wellcome Trust [BI28576]; Wellcome Trust [221818/Z/20/Z] Funding Source: Wellcome Trust Funding text: We thank B. Javid, Z. Lightowlers, B. van der Berg and H. Murray for comments on the manuscript; J. Turkenburg and S. Hart for work supporting the York cryo-EM facility; and A. Kereszt for providing the conjugative strain E. coli BW29427. This work was financed by the Newcastle University NUORS 2021 Award (to K.H.-B.), the James W. McLaughlin Fellowship Fund (to M.Yu.R.), the Medical Research Council (MR/N013840/1 to C.L.E.), the Biotechnology and Biological Sciences Research Council UK (BB/T008695/1 to C.R.B.), a UKRI Future Leader Fellowship (MR/T040742/1 to J.N.B.), the Lenduelet (Momentum) Program of the Hungarian Academy of Sciences (LP2022-4/2022a to B.C.), a National Institutes of Health grant (R01GM136936 to M.G.G.), a Welch Foundation grant (H-2032-20230405 to M.G.G.), a Wellcome Trust & Royal Society Sir Henry Dale Fellowship (221818/Z/20/Z to C.H.H.) and the Royal Society (RGS/R2/202003 to S.V.M.). This project was undertaken on the NSBL Cluster and the Viking Cluster, which are high-performance compute facilities provided by Newcastle University and the University of York, respectively. We are grateful for computational support from the University of York High Performance Computing service, Viking and the Research Computing team, and support from the Newcastle University Structural Biology Laboratory. We also acknowledge the York cryo-EM facility supported by the Wellcome Trust (206161/Z/17/Z) and the York Centre of Excellence in Mass Spectrometry that was created with a capital investment through Science City York and supported by the Engineering and Physical Sciences Research Council (EP/K039660/1; EP/M028127/1) and Yorkshire Forward with funds from the Northern Way Initiative. We also acknowledge Diamond UK for access to and support of the cryo-EM facilities at the UK national electron Bio-Imaging Centre, proposal BI28576, financed by the Wellcome Trust, the Medical Research Council and the Biotechnology and Biological Sciences Research Council. We are grateful to M. Sherman for advice and support; K.-Y. Wong and J. Perkyns for computational support; and to the Sealy and Smith Foundation for supporting the Sealy Center for Structural Biology at the University of Texas Medical Branch. For the purpose of open access, the authors have applied a CC BY public copyright license to any author accepted manuscript version arising from this submission. AB - To conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage1,2. In bacteria, two families of hibernation factors have been described, but the low conservation of these proteins and the huge diversity of species, habitats and environmental stressors have confounded their discovery3-6. Here, by combining cryogenic electron microscopy, genetics and biochemistry, we identify Balon, a new hibernation factor in the cold-adapted bacterium Psychrobacter urativorans. We show that Balon is a distant homologue of the archaeo-eukaryotic translation factor aeRF1 and is found in 20% of representative bacteria. During cold shock or stationary phase, Balon occupies the ribosomal A site in both vacant and actively translating ribosomes in complex with EF-Tu, highlighting an unexpected role for EF-Tu in the cellular stress response. Unlike typical A-site substrates, Balon binds to ribosomes in an mRNA-independent manner, initiating a new mode of ribosome hibernation that can commence while ribosomes are still engaged in protein synthesis. Our work suggests that Balon-EF-Tu-regulated ribosome hibernation is a ubiquitous bacterial stress-response mechanism, and we demonstrate that putative Balon homologues in Mycobacteria bind to ribosomes in a similar fashion. This finding calls for a revision of the current model of ribosome hibernation inferred from common model organisms and holds numerous implications for how we understand and study ribosome hibernation. A study identifies a new bacterial ribosome hibernation factor, Balon, and describes its association with EF-Tu and its initiation of mRNA-independent hibernation during protein synthesis. LA - English DB - MTMT ER - TY - JOUR AU - Mozumdar, Deepto AU - Csörgő, Bálint AU - Bondy-Denomy, Joseph TI - Genetic Manipulation of a CAST of Characters in a Microbial Community. JF - CRISPR JOURNAL J2 - CRISPR J VL - 5 PY - 2022 IS - 1 SP - 4 EP - 6 PG - 3 SN - 2573-1599 DO - 10.1089/crispr.2022.29142.dmo UR - https://m2.mtmt.hu/api/publication/32682996 ID - 32682996 N1 - Journal Article; Review LA - English DB - MTMT ER - 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 multidrug resistance and collateral sensitivity (vol 36, pg 1601, 2019) JF - MOLECULAR BIOLOGY AND EVOLUTION J2 - MOL BIOL EVOL VL - 38 PY - 2021 IS - 7 SP - 3029 EP - 3029 PG - 1 SN - 0737-4038 DO - 10.1093/molbev/msab116 UR - https://m2.mtmt.hu/api/publication/32106320 ID - 32106320 LA - English DB - MTMT ER - TY - JOUR AU - Marino, Nicole D AU - Pinilla-Redondo, Rafael AU - Csörgő, Bálint AU - Bondy-Denomy, Joseph TI - Anti-CRISPR protein applications. natural brakes for CRISPR-Cas technologies. TS - natural brakes for CRISPR-Cas technologies. JF - NATURE METHODS J2 - NAT METHODS VL - 17 PY - 2020 IS - 5 SP - 471 EP - 479 PG - 9 SN - 1548-7091 DO - 10.1038/s41592-020-0771-6 UR - https://m2.mtmt.hu/api/publication/32682998 ID - 32682998 N1 - Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.; Review AB - Clustered, regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes, a diverse family of prokaryotic adaptive immune systems, have emerged as a biotechnological tool and therapeutic. The discovery of protein inhibitors of CRISPR-Cas systems, called anti-CRISPR (Acr) proteins, enables the development of more controllable and precise CRISPR-Cas tools. Here we discuss applications of Acr proteins for post-translational control of CRISPR-Cas systems in prokaryotic and mammalian cells, organisms and ecosystems. LA - English DB - MTMT ER - TY - JOUR AU - Csörgő, Bálint AU - Leon, Lina M. AU - Chau-Ly, Ilea J. AU - Vasquez-Rifo, Alejandro AU - Berry, Joel D. AU - Mahendra, Caroline AU - Crawford, Emily D. AU - Lewis, Jennifer D. AU - Bondy-Denomy, Joseph TI - A compact Cascade-Cas3 system for targeted genome engineering JF - NATURE METHODS J2 - NAT METHODS VL - 17 PY - 2020 IS - 12 SP - 1183+ PG - 24 SN - 1548-7091 DO - 10.1038/s41592-020-00980-w UR - https://m2.mtmt.hu/api/publication/31686455 ID - 31686455 N1 - Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, United States Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States Chan-Zuckerberg Biohub, San Francisco, CA, United States Plant Gene Expression Center, United States Department of Agriculture, Albany, CA, United States Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, United States Cited By :9 Export Date: 27 May 2021 Correspondence Address: Bondy-Denomy, J.; Department of Microbiology and Immunology, United States; email: Joseph.Bondy-Denomy@ucsf.edu Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, United States Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States Chan-Zuckerberg Biohub, San Francisco, CA, United States Plant Gene Expression Center, United States Department of Agriculture, Albany, CA, United States Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, United States Cited By :10 Export Date: 25 August 2021 Correspondence Address: Bondy-Denomy, J.; Department of Microbiology and Immunology, United States; email: Joseph.Bondy-Denomy@ucsf.edu AB - This work repurposes the Type I-C Cascade-Cas3 system fromPseudomonas aeruginosato achieve large deletions in bacterial genomes.CRISPR-Cas technologies have enabled programmable gene editing in eukaryotes and prokaryotes. However, the leading Cas9 and Cas12a enzymes are limited in their ability to make large deletions. Here, we used the processive nuclease Cas3, together with a minimal Type I-C Cascade-based system for targeted genome engineering in bacteria. DNA cleavage guided by a single CRISPR RNA generated large deletions (7-424 kilobases) inPseudomonas aeruginosawith near-100% efficiency, while Cas9 yielded small deletions and point mutations. Cas3 generated bidirectional deletions originating from the programmed site, which was exploited to reduce theP. aeruginosagenome by 837 kb (13.5%). Large deletion boundaries were efficiently specified by a homology-directed repair template during editing with Cascade-Cas3, but not Cas9. A transferable 'all-in-one' vector was functional inEscherichia coli,PseudomonassyringaeandKlebsiella pneumoniae, and endogenous CRISPR-Cas use was enhanced with an 'anti-anti-CRISPR' strategy.P. aeruginosaType I-C Cascade-Cas3 (PaeCas3c) facilitates rapid strain manipulation with applications in synthetic biology, genome minimization and the removal of large genomic regions. LA - English DB - MTMT ER - TY - JOUR AU - Csörgő, Bálint AU - Nyerges, Ákos AU - Pál, Csaba TI - Targeted mutagenesis of multiple chromosomal regions in microbes JF - CURRENT OPINION IN MICROBIOLOGY J2 - CURR OPIN MICROBIOL VL - 57 PY - 2020 SP - 22 EP - 30 PG - 9 SN - 1369-5274 DO - 10.1016/j.mib.2020.05.010 UR - https://m2.mtmt.hu/api/publication/31598543 ID - 31598543 N1 - Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, United States Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, 69117, Germany Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, 6726, Hungary Department of Genetics, Harvard Medical School, Boston, MA 02115, United States Export Date: 8 December 2020 CODEN: COMIF Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, United States Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, 69117, Germany Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, 6726, Hungary Department of Genetics, Harvard Medical School, Boston, MA 02115, United States Export Date: 9 February 2021 CODEN: COMIF Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, United States Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, 69117, Germany Synthetic and Systems Biology Unit, Biological Research Centre, Szeged, 6726, Hungary Department of Genetics, Harvard Medical School, Boston, MA 02115, United States Export Date: 25 August 2021 CODEN: COMIF LA - English DB - MTMT ER - TY - JOUR AU - Kintses, Bálint AU - Jangir, Pramod Kumar AU - Fekete, Gergely AU - Számel, Mónika AU - Méhi, Orsolya Katinka AU - Spohn, Réka AU - Daruka, Lejla AU - Martins, Ana AU - Hosseinnia, A. AU - Gagarinova, A. AU - Kim, S. AU - Phanse, S. AU - Csörgő, Bálint AU - Györkei, Ádám AU - Ari, Eszter AU - Lázár, Viktória AU - Nagy, István AU - Babu, M. AU - Pál, Csaba AU - Papp, Balázs TI - Chemical-genetic profiling reveals limited cross-resistance between antimicrobial peptides with different modes of action JF - NATURE COMMUNICATIONS J2 - NAT COMMUN VL - 10 PY - 2019 IS - 1 SN - 2041-1723 DO - 10.1038/s41467-019-13618-z UR - https://m2.mtmt.hu/api/publication/31038930 ID - 31038930 N1 - Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary HCEMM-BRC Translational Microbiology Lab, Szeged, Hungary Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary Department of Biochemistry, University of Regina, Regina, SK, Canada Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada Department of Genetics, Eötvös Loránd University, Budapest, Hungary Sequencing Platform, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary Department of Microbiology and Immunology, University of California, San Francisco, United States Faculty of Biology, Technion – Israel Institute of Technology, Haifa, Israel Export Date: 6 January 2020 Correspondence Address: Kintses, B.; Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research CentreHungary; email: kintses.balint@brc.hu Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary HCEMM-BRC Translational Microbiology Lab, Szeged, Hungary Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary Department of Biochemistry, University of Regina, Regina, SK, Canada Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada Department of Genetics, Eötvös Loránd University, Budapest, Hungary Sequencing Platform, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary Department of Microbiology and Immunology, University of California, San Francisco, United States Faculty of Biology, Technion – Israel Institute of Technology, Haifa, Israel Export Date: 23 January 2020 Correspondence Address: Kintses, B.; Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research CentreHungary; email: kintses.balint@brc.hu Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary HCEMM-BRC Translational Microbiology Lab, Szeged, Hungary Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary Department of Biochemistry, University of Regina, Regina, SK, Canada Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada Department of Genetics, Eötvös Loránd University, Budapest, Hungary Sequencing Platform, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary Department of Microbiology and Immunology, University of California, San Francisco, United States Faculty of Biology, Technion – Israel Institute of Technology, Haifa, Israel Cited By :1 Export Date: 24 August 2020 Correspondence Address: Kintses, B.; Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research CentreHungary; email: kintses.balint@brc.hu Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary HCEMM-BRC Translational Microbiology Lab, Szeged, Hungary Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary Department of Biochemistry, University of Regina, Regina, SK, Canada Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, Canada Department of Genetics, Eötvös Loránd University, Budapest, Hungary Sequencing Platform, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary Department of Microbiology and Immunology, University of California, San Francisco, United States Faculty of Biology, Technion – Israel Institute of Technology, Haifa, Israel Cited By :3 Export Date: 8 December 2020 Correspondence Address: Kintses, B.; Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research CentreHungary; email: kintses.balint@brc.hu LA - English DB - MTMT ER - TY - JOUR AU - Spohn, Réka AU - Daruka, Lejla AU - Lázár, Viktória AU - Martins, Ana AU - Vidovics, Fanni AU - Grézal, Gábor AU - Méhi, Orsolya Katinka AU - Kintses, Bálint AU - Számel, Mónika AU - Jangir, Pramod Kumar AU - Csörgő, Bálint AU - Györkei, Ádám AU - Bódi, Zoltán AU - Faragó, Anikó AU - Bodai, László AU - Földesi, Imre AU - Kata, Diána AU - Maróti, Gergely AU - Pap, Bernadett AU - Wirth, Roland AU - Papp, Balázs AU - Pál, Csaba TI - Integrated evolutionary analysis reveals antimicrobial peptides with limited resistance JF - NATURE COMMUNICATIONS J2 - NAT COMMUN VL - 10 PY - 2019 PG - 13 SN - 2041-1723 DO - 10.1038/s41467-019-12364-6 UR - https://m2.mtmt.hu/api/publication/30865039 ID - 30865039 N1 - Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary Department of Laboratory Medicine, University of Szeged, Szeged, Hungary Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary Department of Biotechnology, University of Szeged, Szeged, Hungary Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel University of California, San Francisco, Department of Microbiology and Immunology, San Francisco, CA, United States Cited By :19 Export Date: 24 August 2020 Correspondence Address: Pál, C.; Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research CentreHungary; email: cpal@brc.hu Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary Department of Laboratory Medicine, University of Szeged, Szeged, Hungary Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary Department of Biotechnology, University of Szeged, Szeged, Hungary Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel University of California, San Francisco, Department of Microbiology and Immunology, San Francisco, CA, United States Cited By :32 Export Date: 14 January 2021 Correspondence Address: Pál, C.; Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research CentreHungary; email: cpal@brc.hu Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary Department of Laboratory Medicine, University of Szeged, Szeged, Hungary Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary Department of Biotechnology, University of Szeged, Szeged, Hungary Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel University of California, San Francisco, Department of Microbiology and Immunology, San Francisco, CA, United States Cited By :54 Export Date: 30 July 2021 Correspondence Address: Pál, C.; Synthetic and Systems Biology Unit, Hungary; email: cpal@brc.hu Chemicals/CAS: chloramphenicol, 134-90-7, 2787-09-9, 56-75-7; indolicidin, 140896-21-5; pexiganan, 172820-23-4, 147664-63-9; polymyxin B, 1404-26-8, 1405-20-5; pr 39, 139637-11-9; protamine, 11061-43-1, 9007-31-2, 9012-00-4; tachyplesin, 118231-04-2; Anti-Infective Agents; Antimicrobial Cationic Peptides Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary HCEMM-BRC Metabolic Systems Biology Lab, Szeged, Hungary Department of Biochemistry and Molecular Biology, University of Szeged, Szeged, Hungary Department of Laboratory Medicine, University of Szeged, Szeged, Hungary Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary Department of Biotechnology, University of Szeged, Szeged, Hungary Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel University of California, San Francisco, Department of Microbiology and Immunology, San Francisco, CA, United States Cited By :58 Export Date: 25 August 2021 Correspondence Address: Pál, C.; Synthetic and Systems Biology Unit, Hungary; email: cpal@brc.hu AB - Antimicrobial peptides (AMPs) are promising antimicrobials, however, the potential of bacterial resistance is a major concern. Here we systematically study the evolution of resistance to 14 chemically diverse AMPs and 12 antibiotics in Escherichia coli. Our work indicates that evolution of resistance against certain AMPs, such as tachyplesin II and cecropin P1, is limited. Resistance level provided by point mutations and gene amplification is very low and antibiotic-resistant bacteria display no cross-resistance to these AMPs. Moreover, genomic fragments derived from a wide range of soil bacteria confer no detectable resistance against these AMPs when introduced into native host bacteria on plasmids. We have found that simple physicochemical features dictate bacterial propensity to evolve resistance against AMPs. Our work could serve as a promising source for the development of new AMP-based therapeutics less prone to resistance, a feature necessary to avoid any possible interference with our innate immune system. LA - English DB - MTMT ER - 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 - Strauss, Sivan Kaminski AU - Schirman, Dvir AU - Jona, Ghil AU - Brooks, Aaron N. AU - Kunjapur, Aditya M. AU - Ba, Alex N. Nguyen AU - Flint, Alice AU - Solt, Andras AU - Mershin, Andreas AU - Dixit, Atray AU - Yona, Avihu H. AU - Csörgő, Bálint AU - Busby, Bede Phillip AU - Hennig, Bianca P. AU - Pál, Csaba AU - Schraivogel, Daniel AU - Schultz, Daniel AU - Wernick, David G. AU - Agashe, Deepa AU - Levi, Dikla AU - Zabezhinsky, Dmitry AU - Russ, Dor AU - Sass, Ehud AU - Tamar, Einat AU - Herz, Elad AU - Levy, Emmanuel D. AU - Church, George M. AU - Yelin, Idan AU - Nachman, Iftach AU - Gerst, Jeffrey E. AU - Georgeson, Joseph M. AU - Adamala, Katarzyna P. AU - Steinmetz, Lars M. AU - Ruebsam, Marc AU - Ralser, Markus AU - Klutstein, Michael AU - Desai, Michael M. AU - Walunjkar, Nilima AU - Yin, Ning AU - Hefetz, Noa Aharon AU - Jakimo, Noah AU - Snitser, Olga AU - Adini, Omri AU - Kumar, Prashant AU - Smith, Rachel Soo Hoo AU - Zeidan, Razi AU - Hazan, Ronen AU - Rak, Roni AU - Kishony, Roy AU - Johnson, Shannon AU - Nouriel, Shira AU - Vonesch, Sibylle C. AU - Foster, Simmie AU - Dagan, Tal AU - Wein, Tanita AU - Karydis, Thrasyvoulos AU - Wannier, Timothy M. AU - Stiles, Timothy AU - Olin-Sandoval, Viridiana AU - Mueller, William F. AU - Bar-On, Yinon M. AU - Dahan, Orna AU - Pilpel, Yitzhak TI - Evolthon: A community endeavor to evolve lab evolution. A community endeavor to evolve lab evolution. TS - A community endeavor to evolve lab evolution. JF - PLOS BIOLOGY J2 - PLOS BIOL VL - 17 PY - 2019 IS - 3 PG - 17 SN - 1544-9173 DO - 10.1371/journal.pbio.3000182 UR - https://m2.mtmt.hu/api/publication/30636943 ID - 30636943 N1 - Funding Agency and Grant Number: Minerva Center for Live Emulation of Genome Evolution [AZ 5746940763]; [SPP1819] Funding text: YP was supported by The Minerva Center for Live Emulation of Genome Evolution AZ 5746940763, TD was supported by SPP1819 Rapid adaptation The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript AB - In experimental evolution, scientists evolve organisms in the lab, typically by challenging them to new environmental conditions. How best to evolve a desired trait? Should the challenge be applied abruptly, gradually, periodically, sporadically? Should one apply chemical mutagenesis, and do strains with high innate mutation rate evolve faster? What are ideal population sizes of evolving populations? There are endless strategies, beyond those that can be exposed by individual labs. We therefore arranged a community challenge, Evolthon, in which students and scientists from different labs were asked to evolve Escherichia coli or Saccharomyces cerevisiae for an abiotic stresslow temperature. About 30 participants from around the world explored diverse environmental and genetic regimes of evolution. After a period of evolution in each lab, all strains of each species were competed with one another. In yeast, the most successful strategies were those that used mating, underscoring the importance of sex in evolution. In bacteria, the fittest strain used a strategy based on exploration of different mutation rates. Different strategies displayed variable levels of performance and stability across additional challenges and conditions. This study therefore uncovers principles of effective experimental evolutionary regimens and might prove useful also for biotechnological developments of new strains and for understanding natural strategies in evolutionary arms races between species. Evolthon constitutes a model for community-based scientific exploration that encourages creativity and cooperation. LA - English DB - MTMT ER -