Fungi are nature’s recyclers,allowing for ecological nutrient cycling and,in turn,the continuation of life on Earth.Some fungi inhabit the human microbiome where they can provide health benefits,while others are oppo...Fungi are nature’s recyclers,allowing for ecological nutrient cycling and,in turn,the continuation of life on Earth.Some fungi inhabit the human microbiome where they can provide health benefits,while others are opportunistic pathogens that can cause disease.Yeasts,members of the fungal kingdom,have been domesticated by humans for the production of beer,bread,and,recently,medicine and chemicals.Still,the great untapped potential exists within the diverse fungal kingdom.However,many yeasts are intractable,preventing their use in biotechnology or in the development of novel treatments for pathogenic fungi.Therefore,as a first step for the domestication of new fungi,an efficient DNA delivery method needs to be developed.Here,we report the creation of superior conjugative plasmids and demonstrate their transfer via conjugation from bacteria to 7 diverse yeast species including the emerging pathogen Candida auris.To create our superior plasmids,derivatives of the 57 kb conjugative plasmid pTA-Mob 2.0 were built using designed gene deletions and insertions,as well as some unintentional mutations.Specifically,a cluster mutation in the promoter of the conjugative gene traJ had the most significant effect on improving conjugation to yeasts.In addition,we created Golden Gate assembly-compatible plasmid derivatives that allow for the generation of custom plasmids to enable the rapid insertion of designer genetic cassettes.Finally,we demonstrated that designer conjugative plasmids harboring engineered restriction endonucleases can be used as a novel antifungal agent,with important applications for the development of next-generation antifungal therapeutics.展开更多
Here we review how evolving species concepts have been applied to understand yeast diversity.Initially,a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells,an...Here we review how evolving species concepts have been applied to understand yeast diversity.Initially,a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells,and growth profiles.Later the biological species concept was added,which applied data from mating experiments.Biophysical measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology,leading to a sequence-based species concept using comparisons of parts of the ribosomal DNA.At present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy,including yeasts,because various studies revealed a relatively good correlation between the biological species concept and sequence divergence.The application of genome information is becoming increasingly common,and we strongly recommend the use of complete,rather than draft genomes to improve our understanding of species and their genome and genetic dynamics.Complete genomes allow in-depth comparisons on the evolvability of genomes and,consequently,of the species to which they belong.Hybridization seems a relatively common phenomenon and has been observed in all major fungal lineages that contain yeasts.Note that hybrids may greatly differ in their post-hybridization development.Future in-depth studies,initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes,such as hybridization.展开更多
The name of the second author was incorrectly captured in the initial online publication,and due to an error at the proofs stage,several proof corrections had been left undone.The original online article has been corr...The name of the second author was incorrectly captured in the initial online publication,and due to an error at the proofs stage,several proof corrections had been left undone.The original online article has been corrected.展开更多
基金Defense Advanced Research Projects Agency(DARPA),Agreement Number:D18AC00035 to B.J.KNatural Sciences and Engineering Research Council of Canada(NSERC)grant number:RGPIN-2018-06172 to B.J.K.)+5 种基金CIHR Project Grant(PJT 162195)to R.S.SNatural Sciences and Engineering Research Council of Canada(NSERC)grants to M.A.LCIFAR Azrieli Global Scholar Award(Fungal Kingdom:Threats and Opportunities)to R.S.SCIHR Project Grant(PJT 159708)to D.R.E.,G.B.G,and B.J.KIn addition,the following trainees were sponsored by NSERC Scholarships:R.R.C,S.H.,J.M.,D.P.N.,M.P.M.S,E.J.L.W.EvoFunPath Fellowship(NSERC CREATE)-M.A-T.
文摘Fungi are nature’s recyclers,allowing for ecological nutrient cycling and,in turn,the continuation of life on Earth.Some fungi inhabit the human microbiome where they can provide health benefits,while others are opportunistic pathogens that can cause disease.Yeasts,members of the fungal kingdom,have been domesticated by humans for the production of beer,bread,and,recently,medicine and chemicals.Still,the great untapped potential exists within the diverse fungal kingdom.However,many yeasts are intractable,preventing their use in biotechnology or in the development of novel treatments for pathogenic fungi.Therefore,as a first step for the domestication of new fungi,an efficient DNA delivery method needs to be developed.Here,we report the creation of superior conjugative plasmids and demonstrate their transfer via conjugation from bacteria to 7 diverse yeast species including the emerging pathogen Candida auris.To create our superior plasmids,derivatives of the 57 kb conjugative plasmid pTA-Mob 2.0 were built using designed gene deletions and insertions,as well as some unintentional mutations.Specifically,a cluster mutation in the promoter of the conjugative gene traJ had the most significant effect on improving conjugation to yeasts.In addition,we created Golden Gate assembly-compatible plasmid derivatives that allow for the generation of custom plasmids to enable the rapid insertion of designer genetic cassettes.Finally,we demonstrated that designer conjugative plasmids harboring engineered restriction endonucleases can be used as a novel antifungal agent,with important applications for the development of next-generation antifungal therapeutics.
基金SS and JH were supported by NIH/NIAID R37 MERIT Award AI39115-23NIH/NIAID R01 Award AI50113-16+1 种基金and NIH/NIAID R01 Award AI133654-03EJL was supported by BBSRC Award BB/L022508/1.DB was supported by DFG Award BE 2201/23-1 and BE 2201/28-1.JH is also co-director and fellow of the CIFAR program Fungal Kingdom:Threats&Opportunities.MCA acknowledges USDA Hatch project 1010662.
文摘Here we review how evolving species concepts have been applied to understand yeast diversity.Initially,a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells,and growth profiles.Later the biological species concept was added,which applied data from mating experiments.Biophysical measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology,leading to a sequence-based species concept using comparisons of parts of the ribosomal DNA.At present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy,including yeasts,because various studies revealed a relatively good correlation between the biological species concept and sequence divergence.The application of genome information is becoming increasingly common,and we strongly recommend the use of complete,rather than draft genomes to improve our understanding of species and their genome and genetic dynamics.Complete genomes allow in-depth comparisons on the evolvability of genomes and,consequently,of the species to which they belong.Hybridization seems a relatively common phenomenon and has been observed in all major fungal lineages that contain yeasts.Note that hybrids may greatly differ in their post-hybridization development.Future in-depth studies,initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes,such as hybridization.
文摘The name of the second author was incorrectly captured in the initial online publication,and due to an error at the proofs stage,several proof corrections had been left undone.The original online article has been corrected.
