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

Abstract

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.

Light regulates the degradation of the regulatory protein VE-1 in the fungus Neurospora crassa

“…WC proteins have been described in most fungi together with other photoreceptors like phytochromes, cryptochromes, and rhodopsins [ 12 , 13 ]. In Aspergillus nidulans , WC proteins interact with the phytochrome in a light sensing complex capable of sensing red light (phytochrome) and blue light (WC proteins) [ 16 , 17 ].…”

Use of red, far-red, and near-infrared light in imaging of yeasts and filamentous fungi

“…intensity of UV radiation, temperature, or consequences of elevated temperature such as decreased humidity. Genome-wide transcription studies demonstrated that large groups of genes are controlled by this important environmental factor (Rosales-Saavedra et al 2006 ; Chen et al 2009 ; Fuller et al 2013 ; Bayram et al 2016 ; Tagua et al 2020 ; Yu et al 2020 , 2021 ). Light of different wavelengths can regulate germination, vegetative growth, asexual and sexual development, stress responses, pathogenic or symbiotic relationships, metabolism including mycotoxin production and circadian rhythm in fungi (Ruger-Herreros et al 2011 ; Yu and Fischer 2019 ; Díaz and Larrondo 2020 ; Schumacher and Gorbushina 2020 ), and these observations should always be taken into consideration in any illuminated fungal cultures.…”

“…It is important to note that fungi can differentiate between less and more red shifted (e.g. λ ≅ 700 nm and λ ≅ 760 nm) illumination with marked alterations in conidiogenesis, germination of conidia, and even in illumination-responsive changes in global gene expression patterns (Yu et al 2021 ). In order to facilitate the shift towards the near-infrared spectrum in microscopic techniques used in Mycology, the scope of on-going and future fungal physiological, developmental, and omics-based studies should be expanded to cover the near-infrared spectrum of light as well.…”

“…It is an outstanding feature of the creatures belonging to the Kingdom of Fungi that they can sense light (Idnurm et al 2010 ; Molin et al 2020 ) and filamentous fungi can even distinguish between colours owing to their versatile photoreceptors (Yu and Fischer 2019 ; Yu et al 2020 , 2021 ). Not surprisingly, these organisms respond to incident light adequately and this response will affect nearly all aspects of fungal life (Yu and Fisher 2019).…”

“…Not surprisingly, these organisms respond to incident light adequately and this response will affect nearly all aspects of fungal life (Yu and Fisher 2019). Excessive light elicits stress response as well, and vivid communication with various stress sensing, signalling, and stress response pathways have been elucidated (Fuller et al 2013 ; Yu et al 2016 , 2019 , 2021 ; Bodvard et al 2017 ; Igbalajobi et al 2019 ; Molin et al 2020 ). Well-documented overlaps with oxidative stress responses (Chen et al 2009 ; Fuller et al 2013 , 2015 ; Molin et al 2020 ; Tagua et al 2020 ) clearly indicate the generation of harmful reactive oxygen species (ROS) alarming oxidative stress defence especially at short wavelengths (Fuller et al 2015 ; Igbalajobi et al 2019 ).…”