Coregulation of gene expression by White collar 1 and phytochrome in Ustilago maydis

Brych, Annika; Haas, Fabian B.; Parzefall, Katharina; Panzer, Sabine; Schermuly, Jeanette; Altmüller, Janine; Engelsdorf, Timo; Terpitz, Ulrich; Rensing, Stefan A.; Kiontke, Stephan; Batschauer, Alfred

doi:10.1016/j.fgb.2021.103570

Cited by 5 publications

(5 citation statements)

References 96 publications

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“…guizhouense. Similarly, as abovementioned, more DEGs were identified in far-red light than in red light in U. maydis [32]. However, in A. nidulans, red light governs the expression of more genes, where 1005 genes were differentially expressed after 15 min illumination of red light in comparison to 450 upon far-red light illumination [13].…”

Section: Plos Geneticssupporting

confidence: 55%

“…Nevertheless, light induction of a small proportion of genes is not governed by FphA, suggesting alternative mechanisms for red and far-red light sensing. By contrast, in the smut fungus Ustilago maydis, after 60 min illumination, 77 and 114 DEGs identified in red and far-red light, respectively, were all strictly regulated by phytochrome, as no DEGs were identified in the phytochrome deletion strain [32]. The results here demonstrated in T. guizhouense both red and far-red plug into HOG pathway via FPH1, whereas deletion of fph1 reduced the phosphorylation level of HOG1 but not disrupted it completely.…”

Section: Plos Geneticsmentioning

confidence: 52%

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Red and far-red light improve the antagonistic ability of Trichoderma guizhouense against phytopathogenic fungi by promoting phytochrome-dependent aerial hyphal growth

Sun,

Li,

et al. 2024

PLoS Genet

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Light as a source of information regulates morphological and physiological processes of fungi, including development, primary and secondary metabolism, or the circadian rhythm. Light signaling in fungi depends on photoreceptors and downstream components that amplify the signal to govern the expression of an array of genes. Here, we investigated the effects of red and far-red light in the mycoparasite Trichoderma guizhouense on its mycoparasitic potential. We show that the invasion strategy of T. guizhouense depends on the attacked species and that red and far-red light increased aerial hyphal growth and led to faster overgrowth or invasion of the colonies. Molecular experiments and transcriptome analyses revealed that red and far-red light are sensed by phytochrome FPH1 and further transmitted by the downstream MAPK HOG pathway and the bZIP transcription factor ATF1. Overexpression of the red- and far-red light-induced fluffy gene fluG in the dark resulted in abundant aerial hyphae formation and thereby improvement of its antagonistic ability against phytopathogenic fungi. Hence, light-induced fluG expression is important for the mycoparasitic interaction. The increased aggressiveness of fluG-overexpressing strains was phenocopied by four random mutants obtained after UV mutagenesis. Therefore, aerial hyphae formation appears to be a trait for the antagonistic potential of T. guizhouense.

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Section: Plos Geneticssupporting

confidence: 55%

Section: Plos Geneticsmentioning

confidence: 52%

Red and far-red light improve the antagonistic ability of Trichoderma guizhouense against phytopathogenic fungi by promoting phytochrome-dependent aerial hyphal growth

Sun,

Li,

et al. 2024

PLoS Genet

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“…A large number of light-regulated genes were also found in N. crassa, where 300 genes were under light control (5-240 min white light, microarrays) and in T. harzianum with 460 (blue light 34 sec followed by 30 min in the dark, RNAseq) genes [19,22]. In Ustilago maydis about 300 genes were blue-light regulated and additionally some responded to red or to far-red light [48]. Although the conditions in the different organisms were not identical, the number of regulated genes is comparable.…”

Section: Discussionmentioning

confidence: 98%

Genome-wide analyses of light-regulated genes in Aspergillus nidulans reveal a complex interplay between different photoreceptors and novel photoreceptor functions

Streng

Seibeld

et al. 2021

PLoS Genet

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Fungi sense light of different wavelengths using blue-, green-, and red-light photoreceptors. Blue light sensing requires the “white-collar” proteins with flavin as chromophore, and red light is sensed through phytochrome. Here we analyzed genome-wide gene expression changes caused by short-term, low-light intensity illumination with blue-, red- or far-red light in Aspergillus nidulans and found that more than 1100 genes were differentially regulated. The largest number of up- and downregulated genes depended on the phytochrome FphA and the attached HOG pathway. FphA and the white-collar orthologue LreA fulfill activating but also repressing functions under all light conditions and both appear to have roles in the dark. Additionally, we found about 100 genes, which are red-light induced in the absence of phytochrome, suggesting alternative red-light sensing systems. We also found blue-light induced genes in the absence of the blue-light receptor LreA. We present evidence that cryptochrome may be part of this regulatory cue, but that phytochrome is essential for the response. In addition to in vivo data showing that FphA is involved in blue-light sensing, we performed spectroscopy of purified phytochrome and show that it responds indeed to blue light.

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“…The light response systems in X. dendrorhous are relatively unknown, save white collar (Huang et al 2022). However, systems such as cryptochrome, BLUF-domain, rhodopsin, and photolyase are known in other fungi, including a distantly related basidiomycete Ustilago maydis (Yu & Fischer 2019;Brych et al 2016;Brych et al 2021). Therefore, we searched the X. dendrorhous CBS 6938 genome with BLAST for putative fungal photoreceptor proteins within the BLUF, rhodopsin, white collar, and cryptochrome families (Figure 3c).…”

Section: Transcriptomics Elucidates X Dendrorhous Photobiologymentioning

confidence: 99%

Omics driven onboarding of the carotenoid producing red yeastXanthophyllomyces dendrorhousCBS 6938

Tobin

Collins

Marsan

et al. 2023

Preprint

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Genomics has become the primary way to explore microbial diversity, because genetic tools are currently difficult to develop in non-model organisms. Here, we demonstrate that -omics can be leveraged to accelerate genetic tool development for the basidiomycete yeastXanthophyllomyces dendrorhousCBS 6938, the sole biotechnologically relevant organism in the Tremellomycete family. First, we sequence the genome. Then, we perform transcriptomics under a variety of conditions, focusing on light and oxidative stress. This data not only reveals novel photobiology and metabolic regulation, it also allows derivation of constitutive and regulated gene expression parts. Our analysis ofX. dendrorhousphotobiology shows for the first time that a complex system of white-collar and cryptochrome homologs mediate response to ultraviolet light (UV). Our analysis of metabolic regulation shows that UV activates DNA repair, aromatic amino acid and carotenoid biosynthesis and represses central carbon metabolism and the fungal-like apoptotic pathway. Thus,X. dendrorhousshows a dynamic response toward biosynthetic pathways for light-absorbing compounds and survival and away from energy production. We then define a modular cloning system, including antibiotic selections, integration sites, and reporter genes, and use the transcriptomics to derive strong constitutive and regulated promoters. Notably, we discover a novel promoter from a hypothetical gene that has 9-fold activation upon UV exposure. Thus, -omics-to-parts workflows can simultaneously provide useful genomic data and advance genetic tools for non-model microbes, particularly those without a closely related model organism. This approach will be broadly useful in current efforts to engineer diverse microbes.

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Coregulation of gene expression by White collar 1 and phytochrome in Ustilago maydis

Cited by 5 publications

References 96 publications

Red and far-red light improve the antagonistic ability of Trichoderma guizhouense against phytopathogenic fungi by promoting phytochrome-dependent aerial hyphal growth

Red and far-red light improve the antagonistic ability of Trichoderma guizhouense against phytopathogenic fungi by promoting phytochrome-dependent aerial hyphal growth

Genome-wide analyses of light-regulated genes in Aspergillus nidulans reveal a complex interplay between different photoreceptors and novel photoreceptor functions

Omics driven onboarding of the carotenoid producing red yeastXanthophyllomyces dendrorhousCBS 6938

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