TY - JOUR AU - Földi, Csenge Anna AU - Merényi, Zsolt AU - Bálint, Balázs AU - Csernetics, Árpád AU - Miklovics, Nikolett AU - WU, HONGLI AU - Hegedüs, Botond AU - Virágh, Máté AU - HOU, Zhihao AU - Liu, Xiao-Bin AU - Galgóczi, László Norbert AU - Nagy, László TI - Snowball: a novel gene family required for developmental patterning of fruiting bodies of mushroom-forming fungi (Agaricomycetes) JF - MSYSTEMS J2 - MSYSTEMS VL - 9 PY - 2024 IS - 3 PG - 25 SN - 2379-5077 DO - 10.1128/msystems.01208-23 UR - https://m2.mtmt.hu/api/publication/34579740 ID - 34579740 N1 - Funding Agency and Grant Number: Hungarian Academy of Sciences [LP2019-13/2019]; Momentum Program of the Hungarian Academy of Sciences; National Research Development and Innovation Office [142188]; OTKA [KDP-17-4/PALY-2021]; Doctoral Student Scholarship Program of the Co-operative Doctoral Program; Ministry of Innovation and Technology; National Research, Development and Innovation Fund Funding text: This research was funded by the Momentum Program of the Hungarian Academy of Sciences (LP2019-13/2019) and the National Research Development and Innovation Office (Grant No. OTKA 142188). Prepared with the support of the Doctoral Student Scholarship Program of the Co-operative Doctoral Program (KDP-17-4/PALY-2021) of the Ministry of Innovation and Technology financed from the National Research, Development and Innovation Fund. AB - Fruiting bodies of mushroom-forming fungi (Agaricomycetes) are complex multicellular structures, with a spatially and temporally integrated developmental program that is, however, currently poorly known. In this study, we present a novel, conserved gene family, Snowball (snb), termed after the unique, differentiation-less fruiting body morphology of snb1 knockout strains in the model mushroom Coprinopsis cinerea. snb is a gene of unknown function that is highly conserved among agaricomycetes and encodes a protein of unknown function. A comparative transcriptomic analysis of the early developmental stages of differentiated wild-type and non-differentiated mutant fruiting bodies revealed conserved differentially expressed genes which may be related to tissue differentiation and developmental patterning fruiting body development. LA - English DB - MTMT ER - TY - JOUR AU - Bálint, Balázs AU - Merényi, Zsolt AU - Hegedüs, Botond AU - Grigoriev, Igor V AU - HOU, Zhihao AU - Földi, Csenge Anna AU - Nagy, László TI - ContScout: sensitive detection and removal of contamination from annotated genomes JF - NATURE COMMUNICATIONS J2 - NAT COMMUN VL - 15 PY - 2024 IS - 1 PG - 12 SN - 2041-1723 DO - 10.1038/s41467-024-45024-5 UR - https://m2.mtmt.hu/api/publication/34556725 ID - 34556725 AB - Contamination of genomes is an increasingly recognized problem affecting several downstream applications, from comparative evolutionary genomics to metagenomics. Here we introduce ContScout, a precise tool for eliminating foreign sequences from annotated genomes. It achieves high specificity and sensitivity on synthetic benchmark data even when the contaminant is a closely related species, outperforms competing tools, and can distinguish horizontal gene transfer from contamination. A screen of 844 eukaryotic genomes for contamination identified bacteria as the most common source, followed by fungi and plants. Furthermore, we show that contaminants in ancestral genome reconstructions lead to erroneous early origins of genes and inflate gene loss rates, leading to a false notion of complex ancestral genomes. Taken together, we offer here a tool for sensitive removal of foreign proteins, identify and remove contaminants from diverse eukaryotic genomes and evaluate their impact on phylogenomic analyses. LA - English DB - MTMT ER - TY - JOUR AU - Tengölics, Roland AU - Szappanos, Balázs AU - Mülleder, M AU - Kalapis, Dorottya AU - Grézal, Gábor AU - Sajben, Cs AU - Agostini, F AU - Mokochinski, Joao Benhur AU - Bálint, Balázs AU - Nagy, LG AU - Ralser, M AU - Papp, Balázs TI - The metabolic domestication syndrome of budding yeast JF - PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA J2 - P NATL ACAD SCI USA VL - 121 PY - 2024 IS - 11 PG - 11 SN - 0027-8424 DO - 10.1073/pnas.2313354121 UR - https://m2.mtmt.hu/api/publication/34479463 ID - 34479463 LA - English DB - MTMT ER - TY - JOUR AU - Sahu, Neha AU - Indic, Boris AU - Wong-Bajracharya, Johanna AU - Merényi, Zsolt AU - Ke, Huei-Mien AU - Ahrendt, Steven AU - Monk, Tori-Lee AU - Kocsubé, Sándor AU - Drula, Elodie AU - Lipzen, Anna AU - Bálint, Balázs AU - Henrissat, Bernard AU - Andreopoulos, Bill AU - Martin, Francis M. AU - Bugge Harder, Christoffer AU - Rigling, Daniel AU - Ford, Kathryn L. AU - Foster, Gary D. AU - Pangilinan, Jasmyn AU - Papanicolaou, Alexie AU - Barry, Kerrie AU - LaButti, Kurt AU - Virágh, Máté AU - Koriabine, Maxim AU - Yan, Mi AU - Riley, Robert AU - Champramary, Simang AU - Plett, Krista L. AU - Grigoriev, Igor V. AU - Tsai, Isheng Jason AU - Slot, Jason AU - Sipos, György AU - Plett, Jonathan AU - Nagy, László TI - Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria JF - NATURE MICROBIOLOGY J2 - NAT MICROBIOL VL - 8 PY - 2023 IS - 9 SP - 1668 EP - 1681 PG - 27 SN - 2058-5276 DO - 10.1038/s41564-023-01448-1 UR - https://m2.mtmt.hu/api/publication/34105677 ID - 34105677 N1 - Biological Research Center, Synthetic and Systems Biology Unit, Szeged, Hungary Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary Functional Genomics and Bioinformatics Group, Faculty of Forestry, Institute of Forest and Natural Resource Management, University of Sopron, Sopron, Hungary Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW, Australia Biodiversity Research Center, Academia Sinica, Taipei, Taiwan US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary ELKH-SZTE Fungal Pathogenicity Mechanisms Research Group, University of Szeged, Szeged, Hungary Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Université, Marseille, France INRAE, UMR 1163, Biodiversité et Biotechnologie Fongiques, Marseille, France DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia Université de Lorraine, INRAE, UMR 1136 ‘Interactions Arbres/Microorganismes’, Centre INRAE Grand Est – Nancy, Champenoux, France Department of Biology, Section of Terrestrial Ecology, University of Copenhagen, København Ø, Denmark Department of Biosciences, University of Oslo, Blindern, Oslo, Norway Swiss Federal Research Institute WSL, Birmensdorf, Switzerland School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, United Kingdom Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, United States Department of Plant Pathology, The Ohio State University, Columbus, OH, United States Department of Microbiology, Soochow University, Taipei, Taiwan Cited By :2 Export Date: 31 January 2024 Correspondence Address: Nagy, L.G.; Biological Research Center, Hungary; email: lnagy@fungenomelab.com LA - English DB - MTMT ER - TY - JOUR AU - Nagy, László AU - Vonk, P. J. AU - Kunzler, M. AU - Földi, Csenge Anna AU - Virágh, Máté AU - Ohm, R. A. AU - Hennicke, F. AU - Bálint, Balázs AU - Csernetics, Árpád AU - Hegedüs, Botond AU - HOU, Zhihao AU - Liu, Xiao-Bin AU - Nan, S. AU - PAREEK, MANISH AU - Sahu, Neha AU - Szathmari, B. AU - Varga, Torda AU - Wu, H. AU - Yang, X. AU - Merényi, Zsolt TI - Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes JF - STUDIES IN MYCOLOGY J2 - STUD MYCOL VL - 104 PY - 2023 IS - 1 SP - 1 EP - 85 PG - 85 SN - 0166-0616 DO - 10.3114/sim.2022.104.01 UR - https://m2.mtmt.hu/api/publication/34084250 ID - 34084250 N1 - Funding Agency and Grant Number: European Research Council [758161]; "Momentum" program of the Hungarian Academy of Sciences [LP2019-13/2019]; Hungarian National Research, Development, and Innovation Office [GINOP-2.3.2-15-2016-00052]; Szeged Scientists Academy; Szeged Scientists Academy under Hungarian Ministry of Innovation and Technology [FEIF/646-4/2021-ITM_SZERZ]; Doctoral Student Scholarship Program of the Co-operative Doctoral Program of the Ministry of Innovation and Technology; National Research, Development and Innovation Fund [KDP-17-4/PALY-2021]; National Talent Programme of Hungarian Government [NTP-NFTO-21-B-0074]; Hungarian Government; German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) [HE 7849/3-1] Funding text: We are grateful to all friends and colleagues who, over the years, inspired our work on fruiting body development through collaborations or discussions. We appreciate the help of Levente Karaffa in making sense of Acetyl-CoA production and basic metabolism. We appreciate the permission of Francis Martin and Jason Tsai to use photographs of L. bicolor and M. kentingensis in Fig. 1, respectively. We are grateful to Annegret Kohler for providing pre-publication access to the transcriptome of L. bicolor.This work was supported by the European Research Council (grant no. 758161 to L.G.N.) , the "Momentum" program of the Hungarian Academy of Sciences (contract No. LP2019-13/2019 to L.G.N.) , the Hungarian National Research, Development, and Innovation Office (contract No. GINOP-2.3.2-15-2016-00052) , the Szeged Scientists Academy under the sponsorship of the Hungarian Ministry of Innovation and Technology (FEIF/646-4/2021-ITM_SZERZ, to B.Sz., A. Cs. And L.G.N.) and with the professional support of the Doctoral Student Scholarship Program of the Co-operative Doctoral Program of the Ministry of Innovation and Technology financed from the National Research, Development and Innovation Fund (KDP-17-4/PALY-2021, to Cs.F.) . T.V. was supported by the National Talent Programme (NTP-NFTOE-21-B-0074) of the Hungarian Government. FH gratefully acknowledges funding from the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) under grant HE 7849/3-1. AB - Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi (Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for similar to 10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. LA - English DB - MTMT ER - TY - JOUR AU - Merényi, Zsolt AU - Krizsán, Krisztina AU - Sahu, Neha AU - Liu, Xiao-Bin AU - Bálint, Balázs AU - Stajich, Jason E. AU - Spatafora, Joseph W. AU - Nagy, László TI - Genomes of fungi and relatives reveal delayed loss of ancestral gene families and evolution of key fungal traits JF - NATURE ECOLOGY & EVOLUTION J2 - NAT ECOL EVOL VL - 7 PY - 2023 SP - 1221 EP - 1231 PG - 11 SN - 2397-334X DO - 10.1038/s41559-023-02095-9 UR - https://m2.mtmt.hu/api/publication/34065895 ID - 34065895 N1 - Funding Agency and Grant Number: Momentum Program of the Hungarian Academy of Sciences [LP2019-13/2019]; European Research Council [758161] Funding text: AcknowledgementsWe appreciate the critical comments of B. Papp and E. Ocana-Pallares on the earlier version of the manuscript. A. Csikasz-Nagy and A. Hubai are thanked for the useful discussions on PCL cyclins and multivariate methods, respectively. We thank M. C. Aime for permission to utilize unpublished genomic data of Tritirachium sp. This work was funded by the Momentum Program of the Hungarian Academy of Sciences (LP2019-13/2019) and by the European Research Council (Grant No. 758161) (both to L.G.N.). AB - Fungi are ecologically important heterotrophs that have radiated into most niches on Earth and fulfil key ecological services. Despite intense interest in their origins, major genomic trends of their evolutionary route from a unicellular opisthokont ancestor to derived multicellular fungi remain poorly known. Here we provide a highly resolved genome-wide catalogue of gene family changes across fungal evolution inferred from the genomes of 123 fungi and relatives. We show that a dominant trend in early fungal evolution has been the gradual shedding of protist genes and the punctuated emergence of innovation by two main gene duplication events. We find that the gene content of non-Dikarya fungi resembles that of unicellular opisthokonts in many respects, owing to the conservation of protist genes in their genomes. The most rapidly duplicating gene groups included extracellular proteins and transcription factors, as well as ones linked to the coordination of nutrient uptake with growth, highlighting the transition to a sessile osmotrophic feeding strategy and subsequent lifestyle evolution as important elements of early fungal history. These results suggest that the genomes of pre-fungal ancestors evolved into the typical filamentous fungal genome by a combination of gradual gene loss, turnover and several large duplication events rather than by abrupt changes. Consequently, the taxonomically defined Fungi represents a genomically non-uniform assemblage of species. Fungi exhibit remarkable morphological and ecological diversity. An analysis of the genomes of 123 fungi and relatives shows gradual loss of protist genes, major gene turnover and duplication leading to the evolution of modern traits of filamentous fungi. LA - English DB - MTMT ER - TY - JOUR AU - Imre, Gergely AU - Takács, Bertalan Vilmos AU - Czipa, Erik AU - Drubi, Andrea AU - Jaksa, Gábor AU - Latinovics, Dóra AU - Nagy, Andrea AU - Karkas, Réka AU - Hudoba, Liza AU - Vásárhelyi, Bálint Márk AU - Pankotai-Bodó, Gabriella AU - Blastyák, András AU - Hegedűs, Zoltán AU - Germán, Péter AU - Bálint, Balázs AU - Ahmed Abdullah, Khaldoon Sadiq AU - Kopasz, Anna Georgina AU - Kovács, Anita Kármen AU - Nagy, László AU - Sükösd, Farkas AU - Pintér, Lajos AU - Rülicke, Thomas AU - Barta, Endre AU - Nagy, István AU - Haracska, Lajos AU - Mátés, Lajos TI - Prolonged activity of the transposase helper may raise safety concerns during DNA transposon-based gene therapy JF - MOLECULAR THERAPY-METHODS AND CLINICAL DEVELOPMENT J2 - MOL THER-METH CLIN D VL - 29 PY - 2023 SP - 145 EP - 159 PG - 15 SN - 2329-0501 DO - 10.1016/j.omtm.2023.03.003 UR - https://m2.mtmt.hu/api/publication/33708483 ID - 33708483 LA - English DB - MTMT ER - TY - JOUR AU - Grézal, Gábor AU - Spohn, Réka AU - Méhi, Orsolya Katinka AU - Dunai, Anett AU - Lázár, Viktória AU - Bálint, Balázs AU - Nagy, István AU - Pál, Csaba AU - Papp, Balázs TI - Plasticity and stereotypic rewiring of the transcriptome upon bacterial evolution of antibiotic resistance JF - MOLECULAR BIOLOGY AND EVOLUTION J2 - MOL BIOL EVOL VL - 40 PY - 2023 IS - 2 SN - 0737-4038 DO - 10.1093/molbev/msad020 UR - https://m2.mtmt.hu/api/publication/33632100 ID - 33632100 N1 - Funding Agency and Grant Number: Lendulet program of the Hungarian Academy of Sciences [LP-2009-013/2012, LP-2012-32/2018]; ELKH Lenduelet program [LP-2017-2010/2020]; Wellcome Trust WT [098016/Z/11/Z]; European Research Council [648364, 862077]; National Research, Development and Innovation Office; Ministry for Innovation and Technology [KKP KH125616, 126506, RRF-2.3.1-21-2022-00006, GINOP-2.3.2-15-2016-00026, GINOP-2.3.2-15-2 016-00014, GINOP-2.3.2-15-2 016-00020]; National Laboratory of Biotechnology Grant [2022-2.1.1-NL-2022-00008]; European Union [739593]; NKFIH [FK124254]; Janos Bolyai Research Fellowship from the Hungarian Academy of Sciences [BO/608/21] Funding text: This work was supported by the "Lendulet" program of the Hungarian Academy of Sciences LP-2009-013/2012 (B.P.), LP-2012-32/2018 (C.P.), the ELKH Lenduelet program LP-2017-2010/2020 (C.P.), the Wellcome Trust WT 098016/Z/11/Z (B.P.), The European Research Council H2020-ERC-2014-CoG 648364-Resistance Evolution (C.P.), and H2020-ERC-2019-PoC 862077-Aware (C.P.), the National Research, Development and Innovation Office and the Ministry for Innovation and Technology under the "Frontline" program KKP KH125616 and 126506 (B.P. and C.P.), RRF-2.3.1-21-2022-00006 (B.P.), GINOP-2.3.2-15-2016-00026 (iChamber, B.P.), GINOP-2.3.2-15-2 016-00014 (EVOMER, C.P. and B.P.), GINOP-2.3.2-15-2 016-00020 (MolMedEx TUMORDNS, C.P.), National Laboratory of Biotechnology Grant 2022-2.1.1-NL-2022-00008 (C.P. and B.P.), The European Union's Horizon 202 0 research and innovation program under grant agreement No 739593 (B.P.). NKFIH grant FK124254 (O.M.), the Janos Bolyai Research Fellowship from the Hungarian Academy of Sciences BO/608/21 (R.S.). AB - Bacterial evolution of antibiotic resistance frequently has deleterious side effects on microbial growth, virulence, and susceptibility to other antimicrobial agents. However, it is unclear how these trade-offs could be utilized for manipulating antibiotic resistance in the clinic, not least because the underlying molecular mechanisms are poorly understood. Using laboratory evolution, we demonstrate that clinically relevant resistance mutations in Escherichia coli constitutively rewire a large fraction of the transcriptome in a repeatable and stereotypic manner. Strikingly, lineages adapted to functionally distinct antibiotics and having no resistance mutations in common show a wide range of parallel gene expression changes that alter oxidative stress response, iron homeostasis, and the composition of the bacterial outer membrane and cell surface. These common physiological alterations are associated with changes in cell morphology and enhanced sensitivity to antimicrobial peptides. Finally, the constitutive transcriptomic changes induced by resistance mutations are largely distinct from those induced by antibiotic stresses in the wild-type. This indicates a limited role for genetic assimilation of the induced antibiotic stress response during resistance evolution. Our work suggests that diverse resistance mutations converge on similar global transcriptomic states that shape genetic susceptibility to antimicrobial compounds. LA - English DB - MTMT ER - TY - JOUR AU - Merényi, Zsolt AU - Virágh, Máté AU - Gluck-Thaler, Emile AU - Slot, Jason C AU - Kiss, Brigitta AU - Varga, Torda AU - Geösel, András AU - Hegedüs, Botond AU - Bálint, Balázs AU - Nagy, László TI - Gene age shapes the transcriptional landscape of sexual morphogenesis in mushroom forming fungi (Agaricomycetes) JF - ELIFE J2 - ELIFE VL - 11 PY - 2022 SN - 2050-084X DO - 10.7554/eLife.71348 UR - https://m2.mtmt.hu/api/publication/32673548 ID - 32673548 N1 - Funding Agency and Grant Number: Hungarian National Research, Development, and Innovation OfficeNational Research, Development & Innovation Office (NRDIO) - Hungary [GINOP-2.3.2-15-2016-00052]; 'Momentum' program of the Hungarian Academy of Sciences [LP2019-13/2019]; European Research CouncilEuropean Research Council (ERC)European Commission [758161] Funding text: We are thankful to Otto Miettinen for permission to utilize unpublished genomic data of Aphanobasidium pseudotsugae. We acknowledge support by the Hungarian National Research, Development, and Innovation Office (contract no. GINOP-2.3.2-15-2016-00052), the 'Momentum' program of the Hungarian Academy of Sciences (contract no. LP2019-13/2019 to LGN) and the European Research Council (grant no. 758161 to LGN). AB - Multicellularity has been one of the most important innovations in the history of life. The role of regulatory evolution in driving transitions to multicellularity is being increasingly recognized; however, patterns and drivers of transcriptome evolution are poorly known in many clades. We here reveal that allele-specific expression, natural antisense transcripts and developmental gene expression, but not RNA editing or a developmental hourglass act in concert to shape the transcriptome of complex multicellular fruiting bodies of fungi. We find that transcriptional patterns of genes are strongly predicted by their evolutionary age. Young genes showed more expression variation both in time and space, possibly because of weaker evolutionary constraint, calling for partially non-adaptive interpretations of evolutionary changes in the transcriptome of multicellular fungi. Gene age also correlated with function, allowing us to separate fruiting body gene expression related to simple sexual development from that potentially underlying complex morphogenesis. Our study highlighted a transcriptional complexity that provides multiple speeds for transcriptome evolution, but also that constraints associated with gene age shape transcriptomic patterns during transitions to complex multicellularity in fungi.Competing Interest StatementThe authors have declared no competing interest. LA - English DB - MTMT ER - TY - JOUR AU - Gallegos-Monterrosa, Ramses AU - Christensen, Mathilde Nordgaard AU - Barchewitz, Tino AU - Koppenhofer, Sonja AU - Priyadarshini, B. AU - Bálint, Balázs AU - Maróti, Gergely AU - Kempen, Paul J. AU - Dragos, Anna AU - Kovacs, Akos T. TI - Impact of Rap-Phr system abundance on adaptation of Bacillus subtilis JF - COMMUNICATIONS BIOLOGY J2 - COMMUN BIOL VL - 4 PY - 2021 IS - 1 SN - 2399-3642 DO - 10.1038/s42003-021-01983-9 UR - https://m2.mtmt.hu/api/publication/32020399 ID - 32020399 AB - Microbes commonly display great genetic plasticity, which has allowed them to colonize all ecological niches on Earth. Bacillus subtilis is a soil-dwelling organism that can be isolated from a wide variety of environments. An interesting characteristic of this bacterium is its ability to form biofilms that display complex heterogeneity: individual, clonal cells develop diverse phenotypes in response to different environmental conditions within the biofilm. Here, we scrutinized the impact that the number and variety of the Rap-Phr family of regulators and cell-cell communication modules of B. subtilis has on genetic adaptation and evolution. We examine how the Rap family of phosphatase regulators impacts sporulation in diverse niches using a library of single and double rap-phr mutants in competition under 4 distinct growth conditions. Using specific DNA barcodes and whole-genome sequencing, population dynamics were followed, revealing the impact of individual Rap phosphatases and arising mutations on the adaptability of B. subtilis. Ramses Gallegos-Monterrosa, Mathilde Nordgaard Christensen, and colleagues investigate how a single or double deletion of the rap-phr genes, parts of peptide-based quorum sensing systems, impacts the sporulation and biofilm formation of B. subtilis under four different conditions and a multitude of strains. Using strain-specific barcoding and complete genome sequencing, the authors show that competitive selection is driven by acquired mutations, and that selected strains demonstrate increased spore fitness relative to their ancestors and wild types. LA - English DB - MTMT ER -