@article{MTMT:34579740, title = {Snowball: a novel gene family required for developmental patterning of fruiting bodies of mushroom-forming fungi (Agaricomycetes)}, url = {https://m2.mtmt.hu/api/publication/34579740}, author = {Földi, Csenge Anna and Merényi, Zsolt and Bálint, Balázs and Csernetics, Árpád and Miklovics, Nikolett and WU, HONGLI and Hegedüs, Botond and Virágh, Máté and HOU, Zhihao and Liu, Xiao-Bin and Galgóczi, László Norbert and Nagy, László}, doi = {10.1128/msystems.01208-23}, journal-iso = {MSYSTEMS}, journal = {MSYSTEMS}, volume = {9}, unique-id = {34579740}, issn = {2379-5077}, abstract = {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.}, year = {2024}, eissn = {2379-5077}, orcid-numbers = {Merényi, Zsolt/0000-0003-1114-3739; Virágh, Máté/0000-0002-2278-1288; HOU, Zhihao/0000-0002-7510-458X; Galgóczi, László Norbert/0000-0002-6976-8910} } @article{MTMT:34556725, title = {ContScout: sensitive detection and removal of contamination from annotated genomes}, url = {https://m2.mtmt.hu/api/publication/34556725}, author = {Bálint, Balázs and Merényi, Zsolt and Hegedüs, Botond and Grigoriev, Igor V and HOU, Zhihao and Földi, Csenge Anna and Nagy, László}, doi = {10.1038/s41467-024-45024-5}, journal-iso = {NAT COMMUN}, journal = {NATURE COMMUNICATIONS}, volume = {15}, unique-id = {34556725}, issn = {2041-1723}, abstract = {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.}, year = {2024}, eissn = {2041-1723}, orcid-numbers = {Merényi, Zsolt/0000-0003-1114-3739; HOU, Zhihao/0000-0002-7510-458X} } @article{MTMT:34479463, title = {The metabolic domestication syndrome of budding yeast}, url = {https://m2.mtmt.hu/api/publication/34479463}, author = {Tengölics, Roland and Szappanos, Balázs and Mülleder, M and Kalapis, Dorottya and Grézal, Gábor and Sajben, Cs and Agostini, F and Mokochinski, Joao Benhur and Bálint, Balázs and Nagy, LG and Ralser, M and Papp, Balázs}, doi = {10.1073/pnas.2313354121}, journal-iso = {P NATL ACAD SCI USA}, journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, volume = {121}, unique-id = {34479463}, issn = {0027-8424}, year = {2024}, eissn = {1091-6490}, orcid-numbers = {Szappanos, Balázs/0000-0002-5075-1799; Grézal, Gábor/0000-0003-1685-4791} } @article{MTMT:34105677, title = {Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria}, url = {https://m2.mtmt.hu/api/publication/34105677}, author = {Sahu, Neha and Indic, Boris and Wong-Bajracharya, Johanna and Merényi, Zsolt and Ke, Huei-Mien and Ahrendt, Steven and Monk, Tori-Lee and Kocsubé, Sándor and Drula, Elodie and Lipzen, Anna and Bálint, Balázs and Henrissat, Bernard and Andreopoulos, Bill and Martin, Francis M. and Bugge Harder, Christoffer and Rigling, Daniel and Ford, Kathryn L. and Foster, Gary D. and Pangilinan, Jasmyn and Papanicolaou, Alexie and Barry, Kerrie and LaButti, Kurt and Virágh, Máté and Koriabine, Maxim and Yan, Mi and Riley, Robert and Champramary, Simang and Plett, Krista L. and Grigoriev, Igor V. and Tsai, Isheng Jason and Slot, Jason and Sipos, György and Plett, Jonathan and Nagy, László}, doi = {10.1038/s41564-023-01448-1}, journal-iso = {NAT MICROBIOL}, journal = {NATURE MICROBIOLOGY}, volume = {8}, unique-id = {34105677}, issn = {2058-5276}, year = {2023}, eissn = {2058-5276}, pages = {1668-1681}, orcid-numbers = {Merényi, Zsolt/0000-0003-1114-3739; Ke, Huei-Mien/0000-0001-5527-0815; Ahrendt, Steven/0000-0001-8492-4830; Kocsubé, Sándor/0000-0001-7839-0510; Drula, Elodie/0000-0002-9168-5214; Henrissat, Bernard/0000-0002-3434-8588; Martin, Francis M./0000-0002-4737-3715; Bugge Harder, Christoffer/0000-0002-6973-5633; Rigling, Daniel/0000-0002-4338-5364; Papanicolaou, Alexie/0000-0002-3635-6848; Barry, Kerrie/0000-0002-8999-6785; LaButti, Kurt/0000-0002-5838-1972; Virágh, Máté/0000-0002-2278-1288; Grigoriev, Igor V./0000-0002-3136-8903; Tsai, Isheng Jason/0000-0002-2123-5058; Sipos, György/0000-0002-6666-1384; Plett, Jonathan/0000-0003-0514-8146} } @article{MTMT:34084250, title = {Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes}, url = {https://m2.mtmt.hu/api/publication/34084250}, author = {Nagy, László and Vonk, P. J. and Kunzler, M. and Földi, Csenge Anna and Virágh, Máté and Ohm, R. A. and Hennicke, F. and Bálint, Balázs and Csernetics, Árpád and Hegedüs, Botond and HOU, Zhihao and Liu, Xiao-Bin and Nan, S. and PAREEK, MANISH and Sahu, Neha and Szathmari, B. and Varga, Torda and Wu, H. and Yang, X. and Merényi, Zsolt}, doi = {10.3114/sim.2022.104.01}, journal-iso = {STUD MYCOL}, journal = {STUDIES IN MYCOLOGY}, volume = {104}, unique-id = {34084250}, issn = {0166-0616}, abstract = {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.}, keywords = {Development; UBIQUITIN-PROTEASOME SYSTEM; mushroom; Comparative genomics; DIFFERENTIAL EXPRESSION ANALYSIS; FASCICLIN-LIKE PROTEIN; MATING-TYPE GENES; functional annotation; Cell wall remodelling; CELL-WALL INTEGRITY; BIOTIN-BINDING PROTEINS; MUSHROOM COPRINOPSIS-CINEREA; fruiting body morphogenesis; FATTY-ACID DESATURASE; BASIDIOMYCETE FLAMMULINA-VELUTIPES}, year = {2023}, eissn = {1872-9797}, pages = {1-85}, orcid-numbers = {Virágh, Máté/0000-0002-2278-1288; HOU, Zhihao/0000-0002-7510-458X; Varga, Torda/0000-0002-2597-9126; Merényi, Zsolt/0000-0003-1114-3739} } @article{MTMT:34065895, title = {Genomes of fungi and relatives reveal delayed loss of ancestral gene families and evolution of key fungal traits}, url = {https://m2.mtmt.hu/api/publication/34065895}, author = {Merényi, Zsolt and Krizsán, Krisztina and Sahu, Neha and Liu, Xiao-Bin and Bálint, Balázs and Stajich, Jason E. and Spatafora, Joseph W. and Nagy, László}, doi = {10.1038/s41559-023-02095-9}, journal-iso = {NAT ECOL EVOL}, journal = {NATURE ECOLOGY & EVOLUTION}, volume = {7}, unique-id = {34065895}, issn = {2397-334X}, abstract = {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.}, keywords = {MECHANISMS; ORIGIN; ECOLOGY; ALIGNMENT; PHYLOGENETIC ANALYSIS; Tree}, year = {2023}, eissn = {2397-334X}, pages = {1221-1231}, orcid-numbers = {Merényi, Zsolt/0000-0003-1114-3739} } @article{MTMT:33708483, title = {Prolonged activity of the transposase helper may raise safety concerns during DNA transposon-based gene therapy}, url = {https://m2.mtmt.hu/api/publication/33708483}, author = {Imre, Gergely and Takács, Bertalan Vilmos and Czipa, Erik and Drubi, Andrea and Jaksa, Gábor and Latinovics, Dóra and Nagy, Andrea and Karkas, Réka and Hudoba, Liza and Vásárhelyi, Bálint Márk and Pankotai-Bodó, Gabriella and Blastyák, András and Hegedűs, Zoltán and Germán, Péter and Bálint, Balázs and Ahmed Abdullah, Khaldoon Sadiq and Kopasz, Anna Georgina and Kovács, Anita Kármen and Nagy, László and Sükösd, Farkas and Pintér, Lajos and Rülicke, Thomas and Barta, Endre and Nagy, István and Haracska, Lajos and Mátés, Lajos}, doi = {10.1016/j.omtm.2023.03.003}, journal-iso = {MOL THER-METH CLIN D}, journal = {MOLECULAR THERAPY-METHODS AND CLINICAL DEVELOPMENT}, volume = {29}, unique-id = {33708483}, year = {2023}, eissn = {2329-0501}, pages = {145-159}, orcid-numbers = {Vásárhelyi, Bálint Márk/0000-0003-1782-8691; Kovács, Anita Kármen/0000-0001-9805-1647} } @article{MTMT:33632100, title = {Plasticity and stereotypic rewiring of the transcriptome upon bacterial evolution of antibiotic resistance}, url = {https://m2.mtmt.hu/api/publication/33632100}, author = {Grézal, Gábor and Spohn, Réka and Méhi, Orsolya Katinka and Dunai, Anett and Lázár, Viktória and Bálint, Balázs and Nagy, István and Pál, Csaba and Papp, Balázs}, doi = {10.1093/molbev/msad020}, journal-iso = {MOL BIOL EVOL}, journal = {MOLECULAR BIOLOGY AND EVOLUTION}, volume = {40}, unique-id = {33632100}, issn = {0737-4038}, abstract = {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.}, year = {2023}, eissn = {1537-1719}, orcid-numbers = {Grézal, Gábor/0000-0003-1685-4791; Méhi, Orsolya Katinka/0009-0004-7918-913X} } @article{MTMT:32673548, title = {Gene age shapes the transcriptional landscape of sexual morphogenesis in mushroom forming fungi (Agaricomycetes)}, url = {https://m2.mtmt.hu/api/publication/32673548}, author = {Merényi, Zsolt and Virágh, Máté and Gluck-Thaler, Emile and Slot, Jason C and Kiss, Brigitta and Varga, Torda and Geösel, András and Hegedüs, Botond and Bálint, Balázs and Nagy, László}, doi = {10.7554/eLife.71348}, journal-iso = {ELIFE}, journal = {ELIFE}, volume = {11}, unique-id = {32673548}, issn = {2050-084X}, abstract = {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.}, year = {2022}, eissn = {2050-084X}, orcid-numbers = {Merényi, Zsolt/0000-0003-1114-3739; Virágh, Máté/0000-0002-2278-1288; Slot, Jason C/0000-0001-6731-3405; Varga, Torda/0000-0002-2597-9126; Geösel, András/0009-0001-5044-8220} } @article{MTMT:32020399, title = {Impact of Rap-Phr system abundance on adaptation of Bacillus subtilis}, url = {https://m2.mtmt.hu/api/publication/32020399}, author = {Gallegos-Monterrosa, Ramses and Christensen, Mathilde Nordgaard and Barchewitz, Tino and Koppenhofer, Sonja and Priyadarshini, B. and Bálint, Balázs and Maróti, Gergely and Kempen, Paul J. and Dragos, Anna and Kovacs, Akos T.}, doi = {10.1038/s42003-021-01983-9}, journal-iso = {COMMUN BIOL}, journal = {COMMUNICATIONS BIOLOGY}, volume = {4}, unique-id = {32020399}, abstract = {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.}, year = {2021}, eissn = {2399-3642}, orcid-numbers = {Maróti, Gergely/0000-0002-3705-0461; Dragos, Anna/0000-0003-4136-986X} }