@article{MTMT:34782533,
	title = {A new family of bacterial ribosome hibernation factors},
	url = {https://m2.mtmt.hu/api/publication/34782533},
	author = {Helena-Bueno, Karla and Rybak, Mariia Yu. and Ekemezie, Chinenye L. and Sullivan, Rudi and Brown, Charlotte R. and Dingwall, Charlotte and Basle, Arnaud and Schneider, Claudia and Connolly, James P. R. and Blaza, James N. and Csörgő, Bálint and Moynihan, Patrick J. and Gagnon, Matthieu G. and Hill, Chris H. and Melnikov, Sergey V.},
	doi = {10.1038/s41586-024-07041-8},
	journal-iso = {NATURE},
	journal = {NATURE},
	volume = {626},
	unique-id = {34782533},
	issn = {0028-0836},
	abstract = {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.},
	keywords = {MECHANISM; PROTEIN; ESCHERICHIA-COLI; STRUCTURAL BASIS; CRYSTAL-STRUCTURE; ELONGATION; TERMINATION; EF1-alpha; PEPTIDE-BOND FORMATION},
	year = {2024},
	eissn = {1476-4687},
	pages = {1125-1132},
	orcid-numbers = {Rybak, Mariia Yu./0000-0002-0478-0222; Blaza, James N./0000-0001-5420-2116; Csörgő, Bálint/0000-0003-0397-6845; Moynihan, Patrick J./0000-0003-4182-6223}
}

@article{MTMT:32682996,
	title = {Genetic Manipulation of a CAST of Characters in a Microbial Community.},
	url = {https://m2.mtmt.hu/api/publication/32682996},
	author = {Mozumdar, Deepto and Csörgő, Bálint and Bondy-Denomy, Joseph},
	doi = {10.1089/crispr.2022.29142.dmo},
	journal-iso = {CRISPR J},
	journal = {CRISPR JOURNAL},
	volume = {5},
	unique-id = {32682996},
	issn = {2573-1599},
	year = {2022},
	eissn = {2573-1602},
	pages = {4-6},
	orcid-numbers = {Csörgő, Bálint/0000-0003-0397-6845}
}

@article{MTMT:32106320,
	title = {Limited evolutionary conservation of multidrug resistance and collateral sensitivity (vol 36, pg 1601, 2019)},
	url = {https://m2.mtmt.hu/api/publication/32106320},
	author = {Apjok, Gábor and Boross, Gábor and Nyerges, Ákos and Fekete, Gergely and Lázár, Viktória and Papp, Balázs and Pál, Csaba and Csörgő, Bálint},
	doi = {10.1093/molbev/msab116},
	journal-iso = {MOL BIOL EVOL},
	journal = {MOLECULAR BIOLOGY AND EVOLUTION},
	volume = {38},
	unique-id = {32106320},
	issn = {0737-4038},
	keywords = {evolutionary biology; Biochemistry & Molecular Biology},
	year = {2021},
	eissn = {1537-1719},
	pages = {3029-3029},
	orcid-numbers = {Boross, Gábor/0000-0002-7208-5678; Nyerges, Ákos/0000-0002-1581-490X; Csörgő, Bálint/0000-0003-0397-6845}
}

@article{MTMT:32682998,
	title = {Anti-CRISPR protein applications. natural brakes for CRISPR-Cas technologies.},
	url = {https://m2.mtmt.hu/api/publication/32682998},
	author = {Marino, Nicole D and Pinilla-Redondo, Rafael and Csörgő, Bálint and Bondy-Denomy, Joseph},
	doi = {10.1038/s41592-020-0771-6},
	journal-iso = {NAT METHODS},
	journal = {NATURE METHODS},
	volume = {17},
	unique-id = {32682998},
	issn = {1548-7091},
	abstract = {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.},
	year = {2020},
	eissn = {1548-7105},
	pages = {471-479},
	orcid-numbers = {Csörgő, Bálint/0000-0003-0397-6845}
}

@article{MTMT:31686455,
	title = {A compact Cascade-Cas3 system for targeted genome engineering},
	url = {https://m2.mtmt.hu/api/publication/31686455},
	author = {Csörgő, Bálint and Leon, Lina M. and Chau-Ly, Ilea J. and Vasquez-Rifo, Alejandro and Berry, Joel D. and Mahendra, Caroline and Crawford, Emily D. and Lewis, Jennifer D. and Bondy-Denomy, Joseph},
	doi = {10.1038/s41592-020-00980-w},
	journal-iso = {NAT METHODS},
	journal = {NATURE METHODS},
	volume = {17},
	unique-id = {31686455},
	issn = {1548-7091},
	abstract = {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.},
	year = {2020},
	eissn = {1548-7105},
	pages = {1183+},
	orcid-numbers = {Csörgő, Bálint/0000-0003-0397-6845; Mahendra, Caroline/0000-0002-5893-1305}
}

@article{MTMT:31598543,
	title = {Targeted mutagenesis of multiple chromosomal regions in microbes},
	url = {https://m2.mtmt.hu/api/publication/31598543},
	author = {Csörgő, Bálint and Nyerges, Ákos and Pál, Csaba},
	doi = {10.1016/j.mib.2020.05.010},
	journal-iso = {CURR OPIN MICROBIOL},
	journal = {CURRENT OPINION IN MICROBIOLOGY},
	volume = {57},
	unique-id = {31598543},
	issn = {1369-5274},
	year = {2020},
	eissn = {1879-0364},
	pages = {22-30},
	orcid-numbers = {Csörgő, Bálint/0000-0003-0397-6845; Nyerges, Ákos/0000-0002-1581-490X}
}

@article{MTMT:31038930,
	title = {Chemical-genetic profiling reveals limited cross-resistance between antimicrobial peptides with different modes of action},
	url = {https://m2.mtmt.hu/api/publication/31038930},
	author = {Kintses, Bálint and Jangir, Pramod Kumar and Fekete, Gergely and Számel, Mónika and Méhi, Orsolya Katinka and Spohn, Réka and Daruka, Lejla and Martins, Ana and Hosseinnia, A. and Gagarinova, A. and Kim, S. and Phanse, S. and Csörgő, Bálint and Györkei, Ádám and Ari, Eszter and Lázár, Viktória and Nagy, István and Babu, M. and Pál, Csaba and Papp, Balázs},
	doi = {10.1038/s41467-019-13618-z},
	journal-iso = {NAT COMMUN},
	journal = {NATURE COMMUNICATIONS},
	volume = {10},
	unique-id = {31038930},
	issn = {2041-1723},
	year = {2019},
	eissn = {2041-1723},
	orcid-numbers = {Jangir, Pramod Kumar/0000-0001-8330-0655; Méhi, Orsolya Katinka/0009-0004-7918-913X; Csörgő, Bálint/0000-0003-0397-6845; Ari, Eszter/0000-0001-7774-1067}
}

@article{MTMT:30865039,
	title = {Integrated evolutionary analysis reveals antimicrobial peptides with limited resistance},
	url = {https://m2.mtmt.hu/api/publication/30865039},
	author = {Spohn, Réka and Daruka, Lejla and Lázár, Viktória and Martins, Ana and Vidovics, Fanni and Grézal, Gábor and Méhi, Orsolya Katinka and Kintses, Bálint and Számel, Mónika and Jangir, Pramod Kumar and Csörgő, Bálint and Györkei, Ádám and Bódi, Zoltán and Faragó, Anikó and Bodai, László and Földesi, Imre and Kata, Diána and Maróti, Gergely and Pap, Bernadett and Wirth, Roland and Papp, Balázs and Pál, Csaba},
	doi = {10.1038/s41467-019-12364-6},
	journal-iso = {NAT COMMUN},
	journal = {NATURE COMMUNICATIONS},
	volume = {10},
	unique-id = {30865039},
	issn = {2041-1723},
	abstract = {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.},
	year = {2019},
	eissn = {2041-1723},
	orcid-numbers = {Grézal, Gábor/0000-0003-1685-4791; Méhi, Orsolya Katinka/0009-0004-7918-913X; Jangir, Pramod Kumar/0000-0001-8330-0655; Csörgő, Bálint/0000-0003-0397-6845; Bodai, László/0000-0001-8411-626X; Földesi, Imre/0000-0002-3329-8136; Kata, Diána/0000-0002-4432-9380; Maróti, Gergely/0000-0002-3705-0461; Wirth, Roland/0000-0002-2383-2323}
}

@article{MTMT:30703953,
	title = {Limited evolutionary conservation of the phenotypic effects of antibiotic resistance mutations},
	url = {https://m2.mtmt.hu/api/publication/30703953},
	author = {Apjok, Gábor and Boross, Gábor and Nyerges, Ákos and Fekete, Gergely and Lázár, Viktória and Papp, Balázs and Pál, Csaba and Csörgő, Bálint},
	doi = {10.1093/molbev/msz109},
	journal-iso = {MOL BIOL EVOL},
	journal = {MOLECULAR BIOLOGY AND EVOLUTION},
	volume = {36},
	unique-id = {30703953},
	issn = {0737-4038},
	year = {2019},
	eissn = {1537-1719},
	pages = {1601-1611},
	orcid-numbers = {Boross, Gábor/0000-0002-7208-5678; Nyerges, Ákos/0000-0002-1581-490X; Csörgő, Bálint/0000-0003-0397-6845}
}

@article{MTMT:30636943,
	title = {Evolthon: A community endeavor to evolve lab evolution. A community endeavor to evolve lab evolution.},
	url = {https://m2.mtmt.hu/api/publication/30636943},
	author = {Strauss, Sivan Kaminski and Schirman, Dvir and Jona, Ghil and Brooks, Aaron N. and Kunjapur, Aditya M. and Ba, Alex N. Nguyen and Flint, Alice and Solt, Andras and Mershin, Andreas and Dixit, Atray and Yona, Avihu H. and Csörgő, Bálint and Busby, Bede Phillip and Hennig, Bianca P. and Pál, Csaba and Schraivogel, Daniel and Schultz, Daniel and Wernick, David G. and Agashe, Deepa and Levi, Dikla and Zabezhinsky, Dmitry and Russ, Dor and Sass, Ehud and Tamar, Einat and Herz, Elad and Levy, Emmanuel D. and Church, George M. and Yelin, Idan and Nachman, Iftach and Gerst, Jeffrey E. and Georgeson, Joseph M. and Adamala, Katarzyna P. and Steinmetz, Lars M. and Ruebsam, Marc and Ralser, Markus and Klutstein, Michael and Desai, Michael M. and Walunjkar, Nilima and Yin, Ning and Hefetz, Noa Aharon and Jakimo, Noah and Snitser, Olga and Adini, Omri and Kumar, Prashant and Smith, Rachel Soo Hoo and Zeidan, Razi and Hazan, Ronen and Rak, Roni and Kishony, Roy and Johnson, Shannon and Nouriel, Shira and Vonesch, Sibylle C. and Foster, Simmie and Dagan, Tal and Wein, Tanita and Karydis, Thrasyvoulos and Wannier, Timothy M. and Stiles, Timothy and Olin-Sandoval, Viridiana and Mueller, William F. and Bar-On, Yinon M. and Dahan, Orna and Pilpel, Yitzhak},
	doi = {10.1371/journal.pbio.3000182},
	journal-iso = {PLOS BIOL},
	journal = {PLOS BIOLOGY},
	volume = {17},
	unique-id = {30636943},
	issn = {1544-9173},
	abstract = {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.},
	keywords = {DIRECTED EVOLUTION; Biochemistry & Molecular Biology},
	year = {2019},
	eissn = {1545-7885},
	orcid-numbers = {Brooks, Aaron N./0000-0002-5309-7307; Csörgő, Bálint/0000-0003-0397-6845; Hazan, Ronen/0000-0001-9967-730X; Vonesch, Sibylle C./0000-0003-2485-1048}
}