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Light Sensing and Responses in Fungi

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Light Sensing and Responses in Fungi REVIEWS Light sensing and responses in fungi Zhenzhong Yu and Reinhard Fischer * Abstract | Light controls important physiological and morphological responses in fungi. Fungi can sense near-ultraviolet, blue, green, red and far-red light using up to 11 photoreceptors and signalling cascades to control a large proportion of the genome and thereby adapt to environmental conditions. The blue-light photoreceptor functions directly as a transcriptional regulator in the nucleus, whereas the red-light-sensing and far-red-light-sensing phytochrome induces a signalling pathway to transduce the signal from the cytoplasm to the nucleus. Green light can be sensed by retinal-binding proteins, known as opsins, but the signalling mechanisms are not well understood. In this Review , we discuss light signalling processes in fungi, their signalling cascades and recent insights into the integration of light signalling pathways with other regulatory circuits in fungal cells. Chromophore Most animals use light to obtain crucial information retinal-containing green-light sensors and proteins with An organic molecule that about their environment, including information about a linear tetrapyrrole as the chromophore that function as absorbs light in the visible their orientation as well as visual information obtained red-light sensors. Most fungi contain at least two types of spectrum. Photoreceptors are through highly sophisticated sensory organs. Plants use photoreceptors, and some even contain all three. Some proteins containing a chromophore, which upon light to optimize the exposure of their leaves for pho- blue-light photoreceptors reside in the nucleus and can light absorption cause tosynthesis and to control the flowering period or seed directly control gene expression, whereas the red-light structural changes of the formation. Many microorganisms, such as filamentous receptor phytochrome has nuclear and cytoplasmic attached protein. fungi, use light as a source of information. They are functions and is linked to the transcriptional machin- equipped with several photosensory systems and can ery through other signalling modules. Both blue-light Flavin An organic molecule with a respond to different light intensities and wavelengths and red-light receptors also control the DNA structure 1–5 characteristic tricyclic (colours) (Fig. 1). of certain target genes and thereby their transcription. heterocycle (isoalloxazine). Fungi have a crucial role in the remineralization The green-light photoreceptor is a transmembrane pro- of organic matter, are important plant and animal path- tein, and it is still unclear how signalling occurs. There Linear tetrapyrrole An organic molecule ogens and are frequently used in industry, for instance, is also evidence that a particular blue-light receptor (an composed of four five-atom in the production of secondary metabolites or cata- orthologue of white collar 1 (WC-1)) can sense green rings. They can be cyclic, as in lytic enzymes. Hence, advances in the study of fun- light16. In all cases, light causes primary changes of the haemoglobin, or linear, like gal biology should help to further our understanding attached chromophore, which in turn lead to confor- in biliverdin. of their pathogenicity and improve their application mational changes of the proteins and changes in their 6 Phytochrome to biotechnology . activities. Thereby, light controls the activity of many A protein that contains a linear Although fungal light responses have been studied for genes and metabolic and morphogenetic pathways. tetrapyrrole as a chromophore more than 50 years, the availability of hundreds of fungal One question that arises is why fungi use such complex and absorbs red and far-red genome sequences and the recent developments of novel photosensory systems. light. It is the main photosensor of plants and controls experimental approaches, such as genome-wide expres- Fungi live in many different habitats, ranging from morphogenesis. sion analyses or whole-genome sequencing to identify the desert to the tropics, and their environment changes mutations, have provided novel insights into fungal light frequently and often drastically. Even in moderate zones, sensing and signalling pathways. It was shown that in the soil conditions may change dramatically over the several fungi the expression of a large proportion of the course of a day. There are two strategies to cope with Karlsruhe Institute of genome is regulated by light and that, thus, light affects this challenge: adapt physiologically or escape and Technology (KIT) — South many aspects of fungal life. Furthermore, light signalling conquer new habitats. Many fungi produce spores for Campus, Institute for Applied may be tightly linked with other pathways such as sporu- dispersal, and light is a reliable informational source to Biosciences, Department of lation, primary metabolic pathways or the production of indicate air exposure, which in some fungi is required Microbiology, Karlsruhe, 7–15 Germany. secondary metabolites or hydrolytic enzymes . to induce sporulation and/or the formation of a fruit- 17,18 (Fig. 2) *e-mail: reinhard.fischer@ Only a few different photoreceptors developed during ing body . Spores have a thick, pigmented cell KIT.edu evolution. Such photoreceptor proteins always contain wall for protection and may be covered with very resist- 19 https://doi.org/10.1038/ an organic molecule as the chromophore, which absorbs ant hydrophobins . Once spores germinate, hyphae s41579-018-0109-x visual light. There are flavin-binding blue-light receptors, may be fully exposed to harmful ultraviolet light, and NATURE REVIEWS | MICROBIOLOGY REVIEWS connected to other signalling cascades, developmental pathways and metabolic networks. Fungi may also adapt their physiology in addition to developmental programmes. If their habitat dries out, fungi respond by producing compatible solutes to prevent water loss21. This occurs frequently if fungi approach the surface of organic substrates and are Phytochrome exposed to light. Therefore, light can be regarded as an alerting system to prepare fungi for stressful conditions before they arise. Such changes in the environment also WCC occur during the day–night cycle, and many fungi use HOG VVD pathway Processes controlled by light a circadian clock system to foresee regularly changing and photoreceptors: environments and be prepared for the upcoming day • Spore germination or night22,23. Among other factors, light is an important • Vegetative growth input into the clock system, and in Neurospora crassa • Asexual and sexual development and other fungi, the light-sensing and circadian clock AtfA • Circadian clock systems share the blue-light photoreceptor WC-1 (REF.24). • Phototropism Nevertheless, genes can be independently regulated by DNA • Stress response light, by the clock or by both25. • Secondary metabolism Finally, some fungi can not only detect differences in ? ? • Pathogenicity the colour (wavelength) and intensity of light but also Opsin Cryptochrome • Nutrient uptake sense the direction of illumination, as exemplified by the phototropism of the sporangiophore of Phycomyces blakesleeanus26,27 (Fig. 2). ? The numerous examples of light responses in fungi BLUF? Photolyase indicate the complexity of light sensing and signal transduction and a crucial role in regulating fungal life (Figs 1,2). Because fungi are amenable to most molecular, genetic, cell-biological, physiological and biochemical Fig. 1 | Photoreceptors in filamentous fungi and overview of light-controlled methods, they serve as model systems to understand processes. Fungi contain flavin-binding blue-light receptors, retinal-containing green-light regulatory networks in eukaryotic cells. sensors, known as opsins, and proteins with a linear tetrapyrrole as a chromophore that In this Review, we summarize the structural basis function as red-light sensors (phytochromes). Three major classes of blue-light receptors for light sensing in filamentous fungi and explore the are distinguished: the light, oxygen and voltage (LOV) domain-containing proteins such as light signalling mechanisms for blue-light, green-light white collar 1 (WC-1) or vivid (VVD), the blue-light sensor using FAD (BLUF) proteins and the cryptochrome and photolyase protein family. Those photoreceptors can be found in both and red-light photoreceptors. Finally, we review our cur- the cytoplasm and the nucleus, and the green-light photoreceptor is a transmembrane rent understanding of crosstalk of the light signalling protein. One of the main response outputs of light signalling is the control of gene pathways with other cellular pathways. expression, and hence the light signal has to be transmitted into the nuclei. In the case of blue-light signalling through the white collar complex (WCC) (comprising WC-1 and The structural basis for light sensing WC-2), the WCC resides in the nucleus and directly regulates gene expression. For clock Most cellular pathways are driven by proteins, and thus functioning, shuttling of the WCC between the cytoplasm and the nucleus is important147. physical signals need to be transmitted to the protein By contrast, cytoplasmic phytochromes use the high osmolarity glycerol (HOG) signalling level. In the case of light sensing, signal amplification module for signal transduction from the cytoplasm to the nucleus. At the end of the HOG and decoding of small conformational changes in the pathway is the AtfA transcription factor, which induces gene expression. However, a chromophore
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