@article{MTMT:3241263, title = {Phenotypic heterogeneity promotes adaptive evolution}, url = {https://m2.mtmt.hu/api/publication/3241263}, author = {Bódi, Zoltán and Farkas, Zoltán and Nevozhay, D and Kalapis, Dorottya and Lázár, Viktória and Csörgő, Bálint and Nyerges, Ákos and Szamecz, Béla and Fekete, Gergely and Papp, Balázs and Araujo, H and Oliveira, JL and Moura, G and Santos, MAS and Szekely, T and Balazsi, G and Pál, Csaba}, doi = {10.1371/journal.pbio.2000644}, journal-iso = {PLOS BIOL}, journal = {PLOS BIOLOGY}, volume = {15}, unique-id = {3241263}, issn = {1544-9173}, abstract = {Genetically identical cells frequently display substantial heterogeneity in gene expression, cellular morphology and physiology. It has been suggested that by rapidly generating a subpopulation with novel phenotypic traits, phenotypic heterogeneity (or plasticity) accelerates the rate of adaptive evolution in populations facing extreme environmental challenges. This issue is important as cell-to-cell phenotypic heterogeneity may initiate key steps in microbial evolution of drug resistance and cancer progression. Here, we study how stochastic transitions between cellular states influence evolutionary adaptation to a stressful environment in yeast Saccharomyces cerevisiae. We developed inducible synthetic gene circuits that generate varying degrees of expression stochasticity of an antifungal resistance gene. We initiated laboratory evolutionary experiments with genotypes carrying different versions of the genetic circuit by exposing the corresponding populations to gradually increasing antifungal stress. Phenotypic heterogeneity altered the evolutionary dynamics by transforming the adaptive landscape that relates genotype to fitness. Specifically, it enhanced the adaptive value of beneficial mutations through synergism between cell-to-cell variability and genetic variation. Our work demonstrates that phenotypic heterogeneity is an evolving trait when populations face a chronic selection pressure. It shapes evolutionary trajectories at the genomic level and facilitates evolutionary rescue from a deteriorating environmental stress.}, keywords = {RESISTANCE; MUTATIONS; SELECTION; YEAST; GENERATION; GENOME; PLASTICITY; SACCHAROMYCES-CEREVISIAE; FLUCTUATION; GENE-EXPRESSION NOISE}, year = {2017}, eissn = {1545-7885}, orcid-numbers = {Csörgő, Bálint/0000-0003-0397-6845; Nyerges, Ákos/0000-0002-1581-490X} } @article{MTMT:3066805, title = {Indispensability of Horizontally Transferred Genes and Its Impact on Bacterial Genome Streamlining}, url = {https://m2.mtmt.hu/api/publication/3066805}, author = {Karcagi, Ildikó and Draskovits, Gábor and Umenhoffer, Kinga and Fekete, Gergely and Kovács, Károly and Méhi, Orsolya Katinka and Balikó, Gabriella and Szappanos, Balázs and Győrfy, Zsuzsanna and Fehér, Tamás and Bogos, Balázs and Blattner, FR and Pál, Csaba and Pósfai, György and Papp, Balázs}, doi = {10.1093/molbev/msw009}, journal-iso = {MOL BIOL EVOL}, journal = {MOLECULAR BIOLOGY AND EVOLUTION}, volume = {33}, unique-id = {3066805}, issn = {0737-4038}, abstract = {Why are certain bacterial genomes so small and compact? The adaptive genome streamlining hypothesis posits that selection acts to reduce genome size because of themetabolic burden of replicating DNA. To reveal the impact of genome streamlining on cellular traits, we reduced the Escherichia coli genome by up to 20% by deleting regions which have been repeatedly subjects of horizontal transfer in nature. Unexpectedly, horizontally transferred genes not only confer utilization of specific nutrients and elevate tolerance to stresses, but also allow efficient usage of resources to build new cells, and hence influence fitness in routine and stressful environments alike. Genome reduction affected fitness not only by gene loss, but also by induction of a general stress response. Finally, we failed to find evidence that the advantage of smaller genomes would be due to a reduced metabolic burden of replicating DNA or a link with smaller cell size. We conclude that as the potential energetic benefit gained by deletion of short genomic segments is vanishingly small compared with the deleterious side effects of these deletions, selection for reduced DNA synthesis costs is unlikely to shape the evolution of small genomes.}, keywords = {RESISTANCE; ESCHERICHIA-COLI; EVOLUTION; CELL-SIZE; REDUCTION; SMALL RNAS; DNA content; horizontal gene transfer; DIFFERENTIAL EXPRESSION ANALYSIS; genome engineering; REDUCED-GENOME; GROWING CULTURES; genome complexity; adaptive genome streamlining; genome reduction}, year = {2016}, eissn = {1537-1719}, pages = {1257-1269}, orcid-numbers = {Méhi, Orsolya Katinka/0009-0004-7918-913X; Szappanos, Balázs/0000-0002-5075-1799; Fehér, Tamás/0000-0001-9318-3640} } @article{MTMT:3038670, title = {A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species}, url = {https://m2.mtmt.hu/api/publication/3038670}, author = {Nyerges, Ákos and Csörgő, Bálint and Nagy, István and Bálint, Balázs and Bihari, Péter and Lázár, Viktória and Apjok, Gábor and Umenhoffer, Kinga and Bogos, Balázs and Pósfai, György and Pál, Csaba}, doi = {10.1073/pnas.1520040113}, journal-iso = {P NATL ACAD SCI USA}, journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, volume = {113}, unique-id = {3038670}, issn = {0027-8424}, abstract = {Currently available tools for multiplex bacterial genome engineering are optimized for a few laboratory model strains, demand extensive prior modification of the host strain, and lead to the accumulation of numerous off-target modifications. Building on prior development of multiplex automated genome engineering (MAGE), our work addresses these problems in a single framework. Using a dominant-negative mutant protein of the methyl-directed mismatch repair (MMR) system, we achieved a transient suppression of DNA repair in Escherichia coli, which is necessary for efficient oligonucleotide integration. By integrating all necessary components into a broad-host vector, we developed a new workflow we term pORTMAGE. It allows efficient modification of multiple loci, without any observable off-target mutagenesis and prior modification of the host genome. Because of the conserved nature of the bacterial MMR system, pORTMAGE simultaneously allows genome editing and mutant library generation in other biotechnologically and clinically relevant bacterial species. Finally, we applied pORTMAGE to study a set of antibiotic resistance-conferring mutations in Salmonella enterica and E. coli. Despite over 100 million y of divergence between the two species, mutational effects remained generally conserved. In sum, a single transformation of a pORTMAGE plasmid allows bacterial species of interest to become an efficient host for genome engineering. These advances pave the way toward biotechnological and therapeutic applications. Finally, pORTMAGE allows systematic comparison of mutational effects and epistasis across a wide range of bacterial species.}, keywords = {EXPRESSION; IN-VIVO; RESISTANCE; GENES; ESCHERICHIA-COLI; EVOLUTION; DNA-REPAIR; Synthetic biology; MUTL; REPAIR MUTANTS; methyl-directed mismatch repair; off-target effects; recombineering; genome engineering}, year = {2016}, eissn = {1091-6490}, pages = {2502-2507}, orcid-numbers = {Nyerges, Ákos/0000-0002-1581-490X; Csörgő, Bálint/0000-0003-0397-6845} } @article{MTMT:2924952, title = {Collateral sensitivity of antibiotic-resistant microbes}, url = {https://m2.mtmt.hu/api/publication/2924952}, author = {Pál, Csaba and Papp, Balázs and Lázár, Viktória}, doi = {10.1016/j.tim.2015.02.009}, journal-iso = {TRENDS MICROBIOL}, journal = {TRENDS IN MICROBIOLOGY}, volume = {23}, unique-id = {2924952}, issn = {0966-842X}, abstract = {Understanding how evolution of microbial resistance towards a given antibiotic influences susceptibility to other drugs is a challenge of profound importance. By combining laboratory evolution, genome sequencing, and functional analyses, recent works have charted the map of evolutionary trade-offs between antibiotics and have explored the underlying molecular mechanisms. Strikingly, mutations that caused multidrug resistance in bacteria simultaneously enhanced sensitivity to many other unrelated drugs (collateral sensitivity). Here, we explore how this emerging research sheds new light on resistance mechanisms and the way it could be exploited for the development of alternative antimicrobial strategies.}, year = {2015}, eissn = {1878-4380}, pages = {401-407} } @article{MTMT:2722014, title = {Genome-wide analysis captures the determinants of the antibiotic cross-resistance interaction network.}, url = {https://m2.mtmt.hu/api/publication/2722014}, author = {Lázár, Viktória and Nagy, István and Spohn, Réka and Csörgő, Bálint and Györkei, Ádám and Nyerges, Ákos and Horváth, Balázs and Vörös, Andrea and Busa-Fekete, Róbert and Hrtyan, Mónika and Bogos, Balázs and Méhi, Orsolya Katinka and Fekete, Gergely and Szappanos, Balázs and Kegl, B and Papp, Balázs and Pál, Csaba}, doi = {10.1038/ncomms5352}, journal-iso = {NAT COMMUN}, journal = {NATURE COMMUNICATIONS}, volume = {5}, unique-id = {2722014}, issn = {2041-1723}, abstract = {Understanding how evolution of antimicrobial resistance increases resistance to other drugs is a challenge of profound importance. By combining experimental evolution and genome sequencing of 63 laboratory-evolved lines, we charted a map of cross-resistance interactions between antibiotics in Escherichia coli, and explored the driving evolutionary principles. Here, we show that (1) convergent molecular evolution is prevalent across antibiotic treatments, (2) resistance conferring mutations simultaneously enhance sensitivity to many other drugs and (3) 27% of the accumulated mutations generate proteins with compromised activities, suggesting that antibiotic adaptation can partly be achieved without gain of novel function. By using knowledge on antibiotic properties, we examined the determinants of cross-resistance and identified chemogenomic profile similarity between antibiotics as the strongest predictor. In contrast, cross-resistance between two antibiotics is independent of whether they show synergistic effects in combination. These results have important implications on the development of novel antimicrobial strategies.}, year = {2014}, eissn = {2041-1723}, orcid-numbers = {Csörgő, Bálint/0000-0003-0397-6845; Nyerges, Ákos/0000-0002-1581-490X; Méhi, Orsolya Katinka/0009-0004-7918-913X; Szappanos, Balázs/0000-0002-5075-1799} } @article{MTMT:2749057, title = {Perturbation of iron homeostasis promotes the evolution of antibiotic resistance.}, url = {https://m2.mtmt.hu/api/publication/2749057}, author = {Méhi, Orsolya Katinka and Bogos, Balázs and Csörgő, Bálint and Pál, Ferenc and Nyerges, Ákos and Papp, Balázs and Pál, Csaba}, doi = {10.1093/molbev/msu223}, journal-iso = {MOL BIOL EVOL}, journal = {MOLECULAR BIOLOGY AND EVOLUTION}, volume = {31}, unique-id = {2749057}, issn = {0737-4038}, abstract = {Evolution of antibiotic resistance in microbes is frequently achieved by acquisition of spontaneous mutations during antimicrobial therapy. Here, we demonstrate that inactivation of a central transcriptional regulator of iron homeostasis (Fur) facilitates laboratory evolution of ciprofloxacin resistance in Escherichia coli. To decipher the underlying molecular mechanisms, we first performed a global transcriptome analysis and demonstrated that the set of genes regulated by Fur changes substantially in response to antibiotic treatment. We hypothesized that the impact of Fur on evolvability under antibiotic pressure is due to the elevated intracellular concentration of free iron and the consequent enhancement of oxidative damage-induced mutagenesis. In agreement with expectations, overexpression of iron storage proteins, inhibition of iron transport, or anaerobic conditions drastically suppressed the evolution of resistance, whereas inhibition of the SOS response-mediated mutagenesis had only a minor effect. Finally, we provide evidence that a cell permeable iron chelator inhibits the evolution of resistance. In sum, our work revealed the central role of iron metabolism in the de novo evolution of antibiotic resistance, a pattern that could influence the development of novel antimicrobial strategies.}, year = {2014}, eissn = {1537-1719}, pages = {2793-2804}, orcid-numbers = {Méhi, Orsolya Katinka/0009-0004-7918-913X; Csörgő, Bálint/0000-0003-0397-6845; Pál, Ferenc/0000-0002-0985-8578; Nyerges, Ákos/0000-0002-1581-490X} } @article{MTMT:2724012, title = {Network-level architecture and the evolutionary potential of underground metabolism}, url = {https://m2.mtmt.hu/api/publication/2724012}, author = {Notebaart, RA and Szappanos, Balázs and Kintses, Bálint and Pál, Ferenc and Györkei, Ádám and Bogos, Balázs and Lázár, Viktória and Spohn, Réka and Csörgő, Bálint and Wagner, A and Ruppin, E and Pál, Csaba and Papp, Balázs}, doi = {10.1073/pnas.1406102111}, journal-iso = {P NATL ACAD SCI USA}, journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, volume = {111}, unique-id = {2724012}, issn = {0027-8424}, abstract = {A central unresolved issue in evolutionary biology is how metabolic innovations emerge. Low-level enzymatic side activities are frequent and can potentially be recruited for new biochemical functions. However, the role of such underground reactions in adaptation toward novel environments has remained largely unknown and out of reach of computational predictions, not least because these issues demand analyses at the level of the entire metabolic network. Here, we provide a comprehensive computational model of the underground metabolism in Escherichia coli. Most underground reactions are not isolated and 45% of them can be fully wired into the existing network and form novel pathways that produce key precursors for cell growth. This observation allowed us to conduct an integrated genome-wide in silico and experimental survey to characterize the evolutionary potential of E. coli to adapt to hundreds of nutrient conditions. We revealed that underground reactions allow growth in new environments when their activity is increased. We estimate that at least similar to 20% of the underground reactions that can be connected to the existing network confer a fitness advantage under specific environments. Moreover, our results demonstrate that the genetic basis of evolutionary adaptations via underground metabolism is computationally predictable. The approach used here has potential for various application areas from bioengineering to medical genetics.}, year = {2014}, eissn = {1091-6490}, pages = {11762-11767}, orcid-numbers = {Szappanos, Balázs/0000-0002-5075-1799; Pál, Ferenc/0000-0002-0985-8578; Csörgő, Bálint/0000-0003-0397-6845} } @article{MTMT:2462917, title = {In vivo Activity of Optimized Apidaecin and Oncocin Peptides Against a Multiresistant, KPC-Producing Klebsiella Pneumoniae Strain}, url = {https://m2.mtmt.hu/api/publication/2462917}, author = {Ostorházi, Eszter and Nemes-Nikodém, Éva and Knappe, D and Hoffmann, R}, doi = {10.2174/09298665113206660107}, journal-iso = {PROTEIN PEPTIDE LETT}, journal = {PROTEIN AND PEPTIDE LETTERS}, volume = {21}, unique-id = {2462917}, issn = {0929-8665}, abstract = {The peptides Api88 and Onc72 are highly efficient to treat Escherichia coli bacteremia in mice. Here we extended the animal studies to a systemic murine infection model using a multidrug-resistant carbapenemase-producing Klebsiella pneumoniae clinical isolate. When administered intraperitoneally three times at 2.5, 5 and 10 mg/kg bodyweight to CD-1 mice infected with a KPC-producing K. pneumoniae strain, both Api88 and Onc72 reduced the bacterial counts by at least 5 log10 units, indicating that both peptides are active in vivo. Both peptide treatments increased significantly the survival rates and average survival times compared to untreated animals for all doses except for the highest dose of Onc72. This dose reduced the bacterial counts so fast that it most likely induced a sudden release of large amounts of toxic materials from the killed bacteria reducing the survival time even below that of untreated mice. In conclusion, both peptides were efficient in the lethal murine K. pneumoniae infection model, but the treatment protocol (i.e. dose and time points) has to be further optimized based on future pharmacokinetic studies.}, year = {2014}, eissn = {1875-5305}, pages = {368-373}, orcid-numbers = {Ostorházi, Eszter/0000-0002-9459-7316} } @article{MTMT:2458928, title = {Bacterial evolution of antibiotic hypersensitivity.}, url = {https://m2.mtmt.hu/api/publication/2458928}, author = {Lázár, Viktória and Singh, Gajinder Pal and Spohn, Réka and Nagy, István and Horváth, Balázs and Hrtyan, Mónika and Busa-Fekete, Róbert and Bogos, Balázs and Méhi, Orsolya Katinka and Csörgő, Bálint and Pósfai, György and Fekete, Gergely and Szappanos, Balázs and Kegl, B and Papp, Balázs and Pál, Csaba}, doi = {10.1038/msb.2013.57}, journal-iso = {MOL SYST BIOL}, journal = {MOLECULAR SYSTEMS BIOLOGY}, volume = {9}, unique-id = {2458928}, issn = {1744-4292}, abstract = {The evolution of resistance to a single antibiotic is frequently accompanied by increased resistance to multiple other antimicrobial agents. In sharp contrast, very little is known about the frequency and mechanisms underlying collateral sensitivity. In this case, genetic adaptation under antibiotic stress yields enhanced sensitivity to other antibiotics. Using large-scale laboratory evolutionary experiments with Escherichia coli, we demonstrate that collateral sensitivity occurs frequently during the evolution of antibiotic resistance. Specifically, populations adapted to aminoglycosides have an especially low fitness in the presence of several other antibiotics. Whole-genome sequencing of laboratory-evolved strains revealed multiple mechanisms underlying aminoglycoside resistance, including a reduction in the proton-motive force (PMF) across the inner membrane. We propose that as a side effect, these mutations diminish the activity of PMF-dependent major efflux pumps (including the AcrAB transporter), leading to hypersensitivity to several other antibiotics. More generally, our work offers an insight into the mechanisms that drive the evolution of negative trade-offs under antibiotic selection.}, year = {2013}, eissn = {1744-4292}, orcid-numbers = {Méhi, Orsolya Katinka/0009-0004-7918-913X; Csörgő, Bálint/0000-0003-0397-6845; Szappanos, Balázs/0000-0002-5075-1799} }