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    Hemizygosity Enables a Mutational Transition Governing Fungal Virulence and Commensalism. Liang Shen-Huan,Anderson Matthew Z,Hirakawa Matthew P,Wang Joshua M,Frazer Corey,Alaalm Leenah M,Thomson Gregory J,Ene Iuliana V,Bennett Richard J Cell host & microbe Candida albicans is a commensal fungus of human gastrointestinal and reproductive tracts, but also causes life-threatening systemic infections. The balance between colonization and pathogenesis is associated with phenotypic plasticity, with alternative cell states producing different outcomes in a mammalian host. Here, we reveal that gene dosage of a master transcription factor regulates cell differentiation in diploid C. albicans cells, as EFG1 hemizygous cells undergo a phenotypic transition inaccessible to "wild-type" cells with two functional EFG1 alleles. Notably, clinical isolates are often EFG1 hemizygous and thus licensed to undergo this transition. Phenotypic change corresponds to high-frequency loss of the functional EFG1 allele via de novo mutation or gene conversion events. This phenomenon also occurs during passaging in the gastrointestinal tract with the resulting cell type being hypercompetitive for commensal and systemic infections. A "two-hit" genetic model therefore underlies a key phenotypic transition in C. albicans that enables adaptation to host niches. 10.1016/j.chom.2019.01.005
    Phenotypic diversification by enhanced genome restructuring after induction of multiple DNA double-strand breaks. Muramoto Nobuhiko,Oda Arisa,Tanaka Hidenori,Nakamura Takahiro,Kugou Kazuto,Suda Kazuki,Kobayashi Aki,Yoneda Shiori,Ikeuchi Akinori,Sugimoto Hiroki,Kondo Satoshi,Ohto Chikara,Shibata Takehiko,Mitsukawa Norihiro,Ohta Kunihiro Nature communications DNA double-strand break (DSB)-mediated genome rearrangements are assumed to provide diverse raw genetic materials enabling accelerated adaptive evolution; however, it remains unclear about the consequences of massive simultaneous DSB formation in cells and their resulting phenotypic impact. Here, we establish an artificial genome-restructuring technology by conditionally introducing multiple genomic DSBs in vivo using a temperature-dependent endonuclease TaqI. Application in yeast and Arabidopsis thaliana generates strains with phenotypes, including improved ethanol production from xylose at higher temperature and increased plant biomass, that are stably inherited to offspring after multiple passages. High-throughput genome resequencing revealed that these strains harbor diverse rearrangements, including copy number variations, translocations in retrotransposons, and direct end-joinings at TaqI-cleavage sites. Furthermore, large-scale rearrangements occur frequently in diploid yeasts (28.1%) and tetraploid plants (46.3%), whereas haploid yeasts and diploid plants undergo minimal rearrangement. This genome-restructuring system (TAQing system) will enable rapid genome breeding and aid genome-evolution studies. 10.1038/s41467-018-04256-y
    Reversion of a fungal genetic code alteration links proteome instability with genomic and phenotypic diversification. Bezerra Ana R,Simões João,Lee Wanseon,Rung Johan,Weil Tobias,Gut Ivo G,Gut Marta,Bayés Mónica,Rizzetto Lisa,Cavalieri Duccio,Giovannini Gloria,Bozza Silvia,Romani Luigina,Kapushesky Misha,Moura Gabriela R,Santos Manuel A S Proceedings of the National Academy of Sciences of the United States of America Many fungi restructured their proteomes through incorporation of serine (Ser) at thousands of protein sites coded by the leucine (Leu) CUG codon. How these fungi survived this potentially lethal genetic code alteration and its relevance for their biology are not understood. Interestingly, the human pathogen Candida albicans maintains variable Ser and Leu incorporation levels at CUG sites, suggesting that this atypical codon assignment flexibility provided an effective mechanism to alter the genetic code. To test this hypothesis, we have engineered C. albicans strains to misincorporate increasing levels of Leu at protein CUG sites. Tolerance to the misincorporations was very high, and one strain accommodated the complete reversion of CUG identity from Ser back to Leu. Increasing levels of Leu misincorporation decreased growth rate, but production of phenotypic diversity on a phenotypic array probing various metabolic networks, drug resistance, and host immune cell responses was impressive. Genome resequencing revealed an increasing number of genotype changes at polymorphic sites compared with the control strain, and 80% of Leu misincorporation resulted in complete loss of heterozygosity in a large region of chromosome V. The data unveil unanticipated links between gene translational fidelity, proteome instability and variability, genome diversification, and adaptive phenotypic diversity. They also explain the high heterozygosity of the C. albicans genome and open the door to produce microorganisms with genetic code alterations for basic and applied research. 10.1073/pnas.1302094110