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| Open AccessAspergillus fumigatus mitogen-activated protein kinase MpkA is involved in gliotoxin production and self-protection
Aspergillus fumigatus produces the mycotoxin gliotoxin which is important for virulence. Here, de Castro et al characterise how excess production and subsequent fungal toxicity is controlled by the mitogen-activated protein kinase MpkA.
- Patrícia Alves de Castro
- , Camila Figueiredo Pinzan
- & Gustavo H. Goldman
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Article
| Open AccessFungal antigenic variation using mosaicism and reassortment of subtelomeric genes’ repertoires
Here the authors find that surface antigenic variation of the human pathogenic fungus Pneumocystis jirovecii involves mosaicism and reassortment of the repertoire of 80 genes present in each strain, from which single genes are retrieved for mutually exclusive expression.
- Caroline S. Meier
- , Marco Pagni
- & Philippe M. Hauser
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| Open AccessRegulation of symbiotic interactions and primitive lichen differentiation by UMP1 MAP kinase in Umbilicaria muhlenbergii
The mechanisms regulating fungal-algal interactions during the formation of lichen symbioses are not clear. Here, Wang et al. establish conditions conducive to symbiotic interactions and lichen differentiation using a fungus amenable to genetic manipulation, showing the importance of a MAP kinase in lichen development.
- Yanyan Wang
- , Rong Li
- & Jin-Rong Xu
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Article
| Open AccessOrigin of fungal hybrids with pathogenic potential from warm seawater environments
Most clinical isolates of the pathogenic yeast Candida orthopsilosis are hybrids of two parental lineages, only one of which has been identified. Here, del Olmo et al. show that C. orthopsilosis strains isolated from warm seawater are hybrids closely related to clinical isolates, and identify the missing parental lineage, thus providing a more complete view of the genomic evolution of this species.
- Valentina del Olmo
- , Verónica Mixão
- & Toni Gabaldón
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Article
| Open AccessCryptococcus neoformans adapts to the host environment through TOR-mediated remodeling of phospholipid asymmetry
Here, Ristow et al show that the environmental fungus Cryptococcus adapts to the higher carbon dioxide levels present in human tissue through activation of the Target-of-Rapamycin stress response pathway leading to reorganization of its outer membrane lipids and host adaptation.
- Laura C. Ristow
- , Andrew J. Jezewski
- & Damian J. Krysan
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Article
| Open AccessMultifactor transcriptional control of alternative oxidase induction integrates diverse environmental inputs to enable fungal virulence
Metabolic flexibility allows fungi to invade hostile niches. Here, Liu et al. dissect the molecular mechanisms by which Candida albicans upregulates virulence-enabling alternative oxidase expression in response to host-relevant respiratory stresses.
- Zhongle Liu
- , Pauline Basso
- & Leah E. Cowen
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Article
| Open AccessA host defense peptide mimetic, brilacidin, potentiates caspofungin antifungal activity against human pathogenic fungi
Current treatment of fungal infections is threatened by emerging antifungal drug resistance. In this work, the authors explore the synergistic activity of a host defense peptide mimetic, brilacidin, with caspofungin against a panel of fungal strains.
- Thaila Fernanda dos Reis
- , Patrícia Alves de Castro
- & Gustavo H. Goldman
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Article
| Open AccessMajor proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi
Asian soybean rust caused by Phakopsora pachyrhizi is an important plant pathogen, but an accurate genome assembly for this fungus has been lacking. This study sequenced three independent P. pachyrhizi isolates and generated reference quality assemblies and genome annotations, representing a critical step for further in-depth studies of this pathogen and the development of new methods of control.
- Yogesh K. Gupta
- , Francismar C. Marcelino-Guimarães
- & H. Peter van Esse
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| Open AccessLarge-scale identification of genes involved in septal pore plugging in multicellular fungi
Multicellular fungi have septal pores that allow cytoplasmic exchange between adjacent cells; cell wounding and other stress conditions induce septal pore closure. Here, Mamun et al. determine the subcellular localization of hundreds of uncharacterized proteins in a multicellular fungus, identifying 62 proteins associated with the septum. Of these, 23 proteins are involved in septal pore plugging upon hyphal wounding.
- Md. Abdulla Al Mamun
- , Wei Cao
- & Jun-ichi Maruyama
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Article
| Open AccessRegulatory basis for reproductive flexibility in a meningitis-causing fungal pathogen
Pathogenic fungi of the genus Cryptococcus can undergo bisexual and unisexual reproduction. Here, the authors construct a gene-deletion library for over 100 transcription factor genes in Cryptococcus deneoformans and provide insights into regulatory cascades that are specific for each reproductive mode.
- Pengjie Hu
- , Hao Ding
- & Linqi Wang
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Article
| Open AccessVarying strength of selection contributes to the intragenomic diversity of rRNA genes
Ribosomal RNA genes are abundant in eukaryotic genomes and code for the universal and essential RNA components of the ribosome. This study uncovers high sequence diversity of the genes within a single species and discusses the contribution of selection in the evolution of ribosomal RNA.
- Daniel Sultanov
- & Andreas Hochwagen
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Article
| Open AccessCRISPR-Cas12a induced DNA double-strand breaks are repaired by multiple pathways with different mutation profiles in Magnaporthe oryzae
In this work, Huang and colleagues describe variation in DNA repair outcomes due to distinct repair mechanisms following CRISPR targeting of different loci in the plant pathogenic fungus Magnaporthe oryzae.
- Jun Huang
- , David Rowe
- & David E. Cook
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| Open AccessUbiquitin proteolysis of a CDK-related kinase regulates titan cell formation and virulence in the fungal pathogen Cryptococcus neoformans
The pathogenic yeast Cryptococcus neoformans forms large, so-called ‘titan cells’ during infection. Here, Cao et al. show that a ubiquitin ligase inhibits this process by targeting for degradation a CDK-related kinase that stimulates titan cell formation.
- Chengjun Cao
- , Keyi Wang
- & Chaoyang Xue
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| Open AccessUnlocking the functional potential of polyploid yeasts
Domesticated industrial yeast strains are sterile, which hampers to breed strains with novel properties. Here, the authors employ the genetics paradigm return-to-growth to induce genome wide recombination in two sterile polyploid industrial yeasts and identify clones with superior biotechnological traits.
- Simone Mozzachiodi
- , Kristoffer Krogerus
- & Gianni Liti
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| Open AccessForward and reverse genetic dissection of morphogenesis identifies filament-competent Candida auris strains
Some isolates of the emerging fungal pathogen Candida auris can form cellular aggregates or filaments. Here, Santana and O’Meara use Agrobacterium-mediated transformation and a CRISPR-Cas9 system to identify several genes that regulate C. auris morphogenesis.
- Darian J. Santana
- & Teresa R. O’Meara
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Article
| Open AccessAborting meiosis allows recombination in sterile diploid yeast hybrids
Hybrids are often considered evolutionary dead ends because they do not generate viable offspring. Here, the authors show that sterile yeast hybrids generate genetic diversity through meiotic-like recombination by aborting meiosis and return to asexual growth.
- Simone Mozzachiodi
- , Lorenzo Tattini
- & Gianni Liti
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Article
| Open AccessA small molecule produced by Lactobacillus species blocks Candida albicans filamentation by inhibiting a DYRK1-family kinase
Alterations of the mucosal microbiota, including Lactobacillus bacteria, are associated with infections caused by the fungus Candida albicans. Here, MacAlpine et al. show that some Lactobacillus strains produce a small molecule that blocks C. albicans filamentation and biofilm formation, and thus virulence, through inhibition of a fungal kinase.
- Jessie MacAlpine
- , Martin Daniel-Ivad
- & Leah E. Cowen
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| Open AccessChanges in the distribution of fitness effects and adaptive mutational spectra following a single first step towards adaptation
Analyses of both natural and experimental evolution suggest that adaptation depends on the evolutionary past and adaptive potential decreases over time. Here, by tracking yeast adaptation with DNA barcoding, the authors show that such evolutionary phenomena can be observed even after a single adaptive step.
- Dimitra Aggeli
- , Yuping Li
- & Gavin Sherlock
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Article
| Open AccessModerate levels of 5-fluorocytosine cause the emergence of high frequency resistance in cryptococci
Pathogenic fungi rapidly develop resistance to the antifungal agent 5-fluorocytosine (5-FC). Here, Chang et al. explore the mechanisms by which Cryptococcus develops 5-FC resistance at a high frequency, including mutations in several genes and altered levels of key metabolites.
- Yun C. Chang
- , Ami Khanal Lamichhane
- & Kyung J. Kwon-Chung
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| Open AccessUncovering de novo gene birth in yeast using deep transcriptomics
Genome-wide studies of de novo genes have tended to focus on genomic open reading frames (ORFs). Here, Blevins et al. use deep transcriptomics and synteny information to identify de novo transcripts in the yeast Saccharomyces cerevisiae, many of which are expressed from the alternative DNA strand.
- William R. Blevins
- , Jorge Ruiz-Orera
- & M. Mar Albà
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Article
| Open AccessA conserved regulator controls asexual sporulation in the fungal pathogen Candida albicans
Transcription factor Rme1 regulates meiosis and pseudohyphal growth in baker’s yeast, but its role in the meiosis-defective pathogen Candida albicans is unclear. Here, Hernández-Cervantes et al. show that Rme1 activates the expression of genes required for formation of asexual spores in Candida species.
- Arturo Hernández-Cervantes
- , Sadri Znaidi
- & Christophe d’Enfert
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| Open AccessGenome-wide functional analysis of phosphatases in the pathogenic fungus Cryptococcus neoformans
Phosphatases are key components in cellular signalling networks. Here, the authors present a systematic functional analysis of phosphatases of the fungal pathogen Cryptococcus neoformans, revealing roles in virulence, stress responses, O-mannosylation, retromer function and other processes.
- Jae-Hyung Jin
- , Kyung-Tae Lee
- & Yong-Sun Bahn
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Article
| Open AccessStability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP
Pop1 and 6 are subunits of RNase P and RNase MRP, which process ribosomal and tRNAs. The authors show that when Pop1 and 6 are impaired, the telomerase subunit Est1 binds telomerase RNA at normal levels, but the binding is unstable. As a result, nuclear import of the telomerase holoenzyme is inhibited.
- P. Daniela Garcia
- , Robert W. Leach
- & Virginia A. Zakian
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Article
| Open AccessDe novo emergence of adaptive membrane proteins from thymine-rich genomic sequences
There is increasing evidence that protein-coding genes can emerge de novo from noncoding genomic regions. Vakirlis et al. propose that sequences encoding transmembrane polypeptides can emerge de novo in thymine-rich genomic regions and provide organisms with fitness benefits.
- Nikolaos Vakirlis
- , Omer Acar
- & Anne-Ruxandra Carvunis
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Article
| Open AccessDNA repair by Rad52 liquid droplets
Genome dynamics allow cells to repair DNA double-strand breaks (DSBs), which are highly toxic DNA lesions. Here the authors reveal that in S. cerevisiae, Rad52 DNA repair proteins assemble in liquid droplets that work with dynamic nuclear microtubules to relocalize lesions to the nuclear periphery for repair.
- Roxanne Oshidari
- , Richard Huang
- & Karim Mekhail
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Article
| Open AccessEmergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation
Strain Ug99 of the wheat stem rust pathogen, Puccinia graminis f. sp. tritici, is a major threat to global food security. Here, the authors present genomic analyses supporting that Ug99 arose as a result of non-sexual genetic exchange between dikaryotic ancestors.
- Feng Li
- , Narayana M. Upadhyaya
- & Melania Figueroa
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Article
| Open AccessA ‘parameiosis’ drives depolyploidization and homologous recombination in Candida albicans
Mating of Candida albicans produces tetraploid products that return to the diploid state via a non-meiotic process known as concerted chromosome loss (CCL). Here, Anderson et al. show high recombination rates during CCL and identify factors that are essential for chromosome stability and recombination during CCL.
- Matthew Z. Anderson
- , Gregory J. Thomson
- & Richard J. Bennett
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Article
| Open AccessPervasive function and evidence for selection across standing genetic variation in S. cerevisiae
Genetic architecture underlies the complexity of heritable traits. Here, the authors perform high-resolution genetic mapping of metabolic traits in S. cerevisiae and show evidence for selection across standing genetic variation.
- Christopher M. Jakobson
- , Richard She
- & Daniel F. Jarosz
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| Open AccessSystematic analysis reveals the prevalence and principles of bypassable gene essentiality
An essential gene may become non-essential when another gene is mutated. Here, the authors investigate this type of digenic interaction, termed ‘bypass of essentiality’, in the fission yeast Schizosaccharomyces pombe, and show that bypassable essential genes are common and share certain features.
- Jun Li
- , Hai-Tao Wang
- & Li-Lin Du
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Article
| Open AccessWheat microbiome bacteria can reduce virulence of a plant pathogenic fungus by altering histone acetylation
The molecular mechanisms behind the interactions between bacteria and fungi are largely unclear. Here, Chen et al. show that a compound secreted by bacteria from the wheat head microbiome inhibits growth and virulence of a plant pathogenic fungus by manipulating fungal histone modification.
- Yun Chen
- , Jing Wang
- & Zhonghua Ma
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| Open AccessThe Candida albicans transcription factor Cas5 couples stress responses, drug resistance and cell cycle regulation
Cas5 is a transcriptional regulator of responses to cell wall stress in the fungal pathogen Candida albicans. Here, Xie et al. show that Cas5 also modulates cell cycle dynamics and responses to antifungal drugs.
- Jinglin L. Xie
- , Longguang Qin
- & Leah E. Cowen
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| Open AccessAn integrated genomic and transcriptomic survey of mucormycosis-causing fungi
Fungi of the order Mucorales can cause life-threatening infections. Here, Chibucos et al. present genomic and transcriptomic analyses of a diverse set of Mucorales fungi, shedding light on their evolution and identifying potential therapeutic targets in the pathogens and the host.
- Marcus C. Chibucos
- , Sameh Soliman
- & Vincent M. Bruno
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Article
| Open AccessExperimental evolution reveals that high relatedness protects multicellular cooperation from cheaters
Maintenance of cooperation in multicellular organisms is hypothesized to depend on high relatedness among cells. Here, Bastiaans et al. provide empirical support for this hypothesis by directly comparing the evolutionary stability of multicellular cooperation in experimental lines of a fungus kept at either high or low relatedness.
- Eric Bastiaans
- , Alfons J. M. Debets
- & Duur K. Aanen
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Article
| Open AccessPrevalent mutator genotype identified in fungal pathogen Candida glabrata promotes multi-drug resistance
The fungal pathogen Candida glabrata readily acquires resistance to multiple types of antifungal drugs. Here, Healey et al. show that C. glabrataclinical isolates often carry mutations in a gene involved in DNA mismatch repair, and this is associated with increased propensity to develop antifungal resistance.
- Kelley R. Healey
- , Yanan Zhao
- & David S. Perlin
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Article
| Open AccessGenome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts
Pneumocystis jirovecii is a fungus that can cause life-threatening pneumonia in immunocompromised patients. Here, the authors sequence the genomes of P. jirovecii and two other Pneumocystisspecies, and show the unexpected absence of chitin (a near universal fungal cell wall component).
- Liang Ma
- , Zehua Chen
- & Joseph A. Kovacs
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| Open AccessGenetic interactions contribute less than additive effects to quantitative trait variation in yeast
This study uses a large number of crosses between a common lab strain and vineyard-isolated strain of yeast, and estimates the phenotypic variance for various quantitative traits. Using this data set, the authors show additive quantitative trait loci (QTL) and QTL–QTL interactions to be on average 43% and 9%, respectively.
- Joshua S. Bloom
- , Iulia Kotenko
- & Leonid Kruglyak
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Article
| Open AccessGlobal analysis of fungal morphology exposes mechanisms of host cell escape
Several pathogenic fungi such as Candida albicans undergo transitions between single-celled forms and multicellular filaments. Here the authors perform a genome-scale analysis of C. albicansand show that, contrary to common belief, filamentation is not required for escape from host immune cells.
- Teresa R. O’Meara
- , Amanda O. Veri
- & Leah E. Cowen
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Article
| Open AccessOrigins of multicellular evolvability in snowflake yeast
The first steps in the transition to multicellularity remain poorly understood. Here, the authors demonstrate that disrupting a single gene in yeast results in multicellular clusters that develop clonally and possess a high degree of multicellular heritability, predisposing them to multicellular adaptation.
- William C. Ratcliff
- , Johnathon D. Fankhauser
- & Michael Travisano
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Article
| Open AccessMultiple recent horizontal transfers of a large genomic region in cheese making fungi
Horizontal gene transfers are known to play an important role in prokaryote evolution but their impact and prevalence in eukaryotes is less clear. Here, the authors sequence the genomes of cheese making fungi P. roqueforti and P. camemberti, and provide evidence for recent horizontal transfers of a large genomic region.
- Kevin Cheeseman
- , Jeanne Ropars
- & Yves Brygoo
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| Open AccessReconstructing genome evolution in historic samples of the Irish potato famine pathogen
Phytophthora infestanscaused the potato famine in the nineteenth century. Martinet al. sequence the nuclear genomes of five archival samples of the pathogen and compare these to extant specimens allowing the reconstruction of the evolutionary history of P. infestans.
- Michael D. Martin
- , Enrico Cappellini
- & M. Thomas P. Gilbert
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Article
| Open AccessA network of genes connects polyglutamine toxicity to ploidy control in yeast
Expansion of polyglutamines correlates with neuronal death in Huntington’s disease. Here the authors show that, in haploid yeast cells, the toxic effect of polyglutamine expression is associated with the disruption of the septin ring and cells may escape from toxicity by hyperploidization.
- Christoph J.O. Kaiser
- , Stefan W. Grötzinger
- & Klaus Richter
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Article
| Open AccessEffector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations
Leptosphaeria maculans is a plant pathogen that causes stem canker of oilseed rape. Rouxel et al. sequence and describe the key features of the L. maculansgenome, including partitioning into AT-rich blocks that are enriched in effector genes and transposable elements affected by repeat-induced point mutation.
- Thierry Rouxel
- , Jonathan Grandaubert
- & Barbara J. Howlett