Photosynthetic and plastid performance effects of photoreceptors

ABSTRACT

Photoreceptors facilitate plants in adjusting their growth and development according to their ever-changing surroundings. Modifications in plant architecture, chloroplast positioning, and structure, alongside changes in chloroplast protein and pigment composition, mainly in the photosynthetic apparatus, aid in optimising photosynthesis, allowing for effective conversion of solar energy into chemical energy while avoiding damage from excess light. Photoreceptors, such as phytochromes, cryptochromes, phototropins, and UVR8, play a crucial role in decoding environmental cues and transforming them into multifaceted signals leading to changes in gene expression and post-translational processes both in the nucleus and the plastids. Not only the initial development of etioplasts or proplastids into chloroplasts in seedlings or young tissues, but also the diurnal cycles from darkness to light or the transitional stages prevailing in shaded environments challenge the adaptation processes of photosynthesis in the daily life of a plant and are tightly controlled by photoreceptors.

KEYWORDS:

• Plastid
• photosynthesis
• photoreceptor
• PhANG

Introduction

Sunlight is the basis of all plant life on Earth, providing the solar energy that is converted into chemical energy by photosynthetic organisms such a plants, algae and photosynthetic bacteria through a process called photosynthesis, storing the energy in chemical bonds, primarily in carbohydrates. Incident light can vary in intensity, direction, quality and timing, providing essential information for plants to survive in their respective environment. This information is decoded by a number of different photoreceptors that are specifically designed to detect the UV, blue (B) and red (R) parts of the light spectrum. The main photoreceptors in plants are the red/far-red (R/FR) light sensitive phytochromes (phy), the B light sensitive cryptochromes (cry) and phototropins (phot), and the UV-B light sensitive UVR8 (Kami et al. 2010) (Figure 1). With these photoreceptors, plants can sense their ever-changing environment and adapt by regulating growth and development thus optimising their ability to harvest the solar energy. Throughout a plant’s life, it faces various challenges, including establishing photosynthesis in germinating seeds and developing chloroplasts in newly formed tissues. Additionally, the plant must constantly adjust to changes in light conditions, such as the day-night cycle or shade versus sun. The photoreceptors are responsible for monitoring these conditions and relay the information to the nucleus and the chloroplast. The absorption spectra of the photoreceptors overlap largely with the absorption spectra of the chlorophylls and carotenoids, those pigments that absorb light for photosynthesis, underscoring the importance of sensing light that is relevant for this process (Figure 1).

Figure 1. Photoreceptors in higher plants. The graph illustrates the absorption spectra of a plant extract due to the presence of chlorophyll a, b, and carotenoids. The photoreceptors responsible for perceiving different light qualities and their subsequent physiological effects on photosynthesis are also highlighted.

Function and role of photoreceptors in plants

The phytochrome photoreceptors are highly conserved in land plants and are encoded by a small gene family (Cheng et al. 2021). Three distinct clades can be distinguished in seed plants: PHYA, PHYB/D/E and PHYC (Mathews 2010). Five genes exist in A. thaliana (PHYA-E), whereas rice and many other Gramineae contain only three phytochrome genes (PHYA, PHYB and PHYC), demonstrating variation and evolutionary adaptation among plant species. A light labile and a light stable phytochrome pool were described before sequence information was available, corresponding to A. thaliana phyA and phyB-E, respectively (Sharrock and Quail 1989). Phytochromes play a crucial role in the regulation of processes such as seed germination, de-etiolation, photoperiodism, flowering and growth.

Phytochromes are soluble chromoproteins attached to a phytochromobiline (PΦB) chromophore and form dimers. They exist in two major interconvertible conformations, one that absorbs primarily in the R (P_r; 650–670 nm) and one that absorbs in the FR (P_fr; 705–740 nm) regions of the spectrum (Rockwell et al. 2006). The P_r state is the inactive form, whereas the P_fr state, which is generated upon R light excitation, is biologically active and translocates from the cytoplasm to the nucleus. Activated phytochromes can revert to their P_r conformation either by FR light (fast reaction) or by darkness and higher temperature (dark reversion, slower reaction) (Rockwell et al. 2006; Klose et al. 2020). The P_r and P_fr forms have slightly overlapping absorption spectra, so both conformations are in a dynamic photoequilibrium in ambient light with the balance depending on the proportion of R and FR light present in the environment.

PhyB is the main R light sensor, and phyB-dependent responses require high levels of P_fr relative to total phytochrome, which is achieved by a high R:FR ratio in the light. PhyB is inactivated under monochromatic FR light or when more FR light is present compared to R light, for example in a canopy shade. PhyA is considered to be the FR light receptor, as due to the equilibrium between the two conformations and a complex system of photocycling the accumulation of its P_fr form in the nucleus and the induction of signal transduction under FR-light conditions becomes possible (Rausenberger et al. 2011). In contrast to phyB, phyA can be induced by most wavelengths of light (including FR), and is activated at much lower light intensities compared to phyB (Shinomura et al. 1996). As a result, phyA responses are not reversible by FR light as compared to those of phyB (Mathews 2006).

The cryptochromes (cry1 and cry2 in A. thaliana) play vital roles at all stages of plant growth and development, including during de-etiolation, cotyledon expansion and opening, hypocotyl elongation and flowering time (Wang and Lin 2020; Ponnu and Hoecker 2022). Furthermore, they are significant contributors to entraining the circadian clock and early dawn gene expression (Balcerowicz et al. 2011; Lopez et al. 2021). Similar to the phytochromes also cryptochromes vary in protein stability, cry2 is very photolabile and is degraded within a few hours of exposure to B light, whereas cry1 is light stable (Lin et al. 1998). Cryptochromes contain a photolyase-homologous region at their N-terminus, which binds non-covalently to the chromophore, a flavin adenine dinucleotide (FAD) (Losi and Gartner 2012). The N-terminal domain also coordinates the homodimerization of cryptochromes upon photoactivation (Wang and Lin 2020). The activated state can be reverted to inactive monomers by darkness in a temperature-dependent manner – this reversion also being reminiscent of the phytochromes (Herbel et al. 2013).

Phototropins (phot1 and phot2 in A. thaliana), also act as B light photoreceptors, and are known for their central role in plant phototropism, but are also important for stomatal opening and leaf or chloroplast movement (Briggs et al. 2001; Christie et al. 2015). They possess highly conserved domains consisting of two light, oxygen, or voltage (LOV) domains in the N-terminus, along with a serine/threonine kinase domain in the C-terminus. The LOV domains serve as light sensing units because they bind flavin mononucleotides (FMN) as chromophores. When the FMNs absorb B light, they form a covalent bond with a cysteine residue in the LOV domain inducing a conformational change of the protein, which is relayed to the C-terminal kinase domain. As a result, the enzymatic activity of the kinase is enhanced, which leads to autophosphorylation (Okajima 2016). Subsequently, the kinase domain transmits this signal to downstream components within the signalling pathway.

The UV-B photoreceptor UV RESISTANCE LOCUS 8 (UVR8) is the only receptor without an attached chromophore, but instead contains tryptophans that absorbs UV-B (Podolec et al. 2021). Upon UV-B irradiation, UVR8 disintegrates from its dimeric form into monomers and subsequently accumulates in the nucleus. Here, it interacts with other signalling proteins, ultimately regulating gene expression and activating various protective mechanisms such as flavonoid synthesis and enzymes that repair UV-B-induced DNA damage (Morales et al. 2013; Podolec et al. 2021).

In most cases, the signal transduction downstream of the different photoreceptors involves several intermediates, some of which are shared, leading to the fine-tuning of gene expression. In addition to this general role in all aspects of growth regulation during the life of a plant, photoreceptors also have a more direct impact on regulating plastids and the photosynthetic capacity. Target genes of photoreceptors include the so-called PhANGs (photosynthesis-associated nuclear genes), and additional genes involved in chloroplast development, maintenance or metabolism. Therefore, changes in environmental light conditions lead to differential activation of photoreceptors, affecting chloroplast development and function, protection, and photosynthetic performance.

Plants have evolved several ways to maximise photosynthetic light capture while minimising light damage to the chloroplasts. Morphological and growth characteristics include changes in plant architecture, leaf angle or thickness. Chloroplasts themselves can vary in their number per cell and their positioning within the cell. Within the chloroplasts, modifications of the photosynthetic apparatus affect photosynthesis more directly. Many metabolic and catabolic processes in chloroplasts are also photoreceptor-dependently light-regulated and affect photosynthesis such as the biosynthesis of the pigments and co-factors.

It is important to distinguish between the light sensed by these photoreceptors or by biochemical and metabolic signals within the chloroplast. Light signalling downstream of photoreceptors mainly alters gene expression leading to changes in developmental processes (photomorphogenesis). On the other hand, light perceived without the involvement of photoreceptors is usually a warning system against excess or imbalanced light conditions.

Photosynthetic performance and adaptation through the effects of different light spectra

Light with a wavelength of 400 - 700 nm is commonly referred to as photosynthetically active radiation (PAR), which is mainly the B to the R part of the spectrum. In higher plants, the antenna proteins in the thylakoid membrane (LIGHT HARVESTING COMPLEX; LHC) contain carotenoids, chlorophyll (chl) a and chl b molecules (Figure 1). The absorbed energy is transferred to the photosystems to drive photosynthesis. Excess energy that has been absorbed must be disposed of, so as not to damage the chloroplasts due to reactive intermediates (Bassi and Dall’osto 2021).

There is a slight bias between photosystem I (PSI) and photosystem II (PSII) as the PSI can also utilise wavelengths above 700 nm (FR light). This is due to the association of several Chl a molecules, which bind differently to the PSI-LHC complex and thereby undergo a red shift (so-called “red chlorophylls”) (Jensen et al. 2007; Croce and van Amerongen 2013; Akhtar and Lambrev 2020; Hu et al. 2021; Wang et al. 2021).

The light-driven electron transport reaction from PSII to PSI leads to the formation of ATP and NADPH, providing energy for carbohydrate assimilation. Monitoring light quality within chloroplasts without photoreceptors can occur by detecting unequal excitation of the two photosystems. This can lead to changes in the redox state of the electron carrier plastoquinone (Shimizu et al. 2010).

Although R light (600 - 680 nm) is reported to have the highest quantum yield of CO₂ fixation per absorbed photon compared to other monochromatic light, supplementation with R light alone impairs plant growth partially due to inefficient activation of PSI (Hogewoning et al. 2012). Monochromatic R light changes plant architecture and leads to elongation processes, reduced plant biomass and leaf area, and often to a decreased chlorophyll content especially by overactivation of phyB (Landi et al. 2020). In apple seedlings (Malus domestica) R light resulted in disorganised palisade tissues, reduced chlorophyll content, and chloroplasts that had short, thick, and swollen structures with tightly stacked basal grana and abundant starch grains (Li et al. 2021).

FR photons have low photosynthetic activity and primarily only excite PSI (Jensen et al. 2007; Croce and van Amerongen 2013; Zhen and van Iersel 2017). However, when added to a background of 400 - 700 nm photons, FR increases photosynthesis (Zhen and Bugbee 2020). Under monochromatic FR light angiosperms will not turn green because one of the later steps of the chlorophyll biosynthesis is not activated (see below). Green plants can survive for some time under FR light, but the amount of chlorophyll decreases, thylakoids develop thicker grana stacks, the amount of antenna proteins increases compared to the photosystems and a gradual loss of PSI can be observed in Arabidopsis (Hu et al. 2021). FR light can trigger phytochrome-dependently a kind of senescence and induce chlorophyll breakdown (Lim et al. 2018; Hu et al. 2021).

Plants exposed to monochromatic B light show a reduction in the photosynthetic efficiency compared to white light, which was enhanced in cry mutants suggesting the involvement of this photoreceptor (Liu and van Iersel 2021). However, by increasing the amount of B light in the total light spectrum, the photosynthetic capacity can be improved (Terfa et al. 2013; Izzo et al. 2021). Studies on apple seedlings demonstrated that B light, in contrast to R light, promoted the development of leaf tissue structures and chloroplasts, as leaves had tightly arranged palisade tissue with dense chloroplasts, which increased light absorption (Li et al. 2021). In lettuce (Lactuca sativa), an increase in the amount of B light, combined with monochromatic R light, appears to enhance photosynthetic efficiency per leaf area due to a greater abundance of chloroplasts. Monochromatic B or R light increased leaf area but reduced chlorophyll content and leaf thickness compared to dichromatic light (Izzo et al. 2021).

In response to B light, phot2 was reported to promote the development of cylindrical palisade cells (Kozuka et al. 2011), but also the cell elongation in the palisade tissue that leads to thicker leaves under high-light is induced by B light, and both classes of blue light receptors are involved (Hoshino et al. 2019).

Although UV light is not directly photosynthetically active, it affects photosynthesis in a dose-dependent manner. Low-intensity UV-B, which peaks around 295 to 300 nm, initiates a cascade of physiological responses including flavonoid synthesis, increased production of photosynthetic pigments, inhibition of hypocotyl growth, and improved photosynthetic efficiency of both PSI and PSII (Lidon and Ramalho 2011). On the other hand, plants experience varying degrees of damage when exposed to high-intensity UV-B radiation. As a result, they undergo a decline in their photosynthetic pigments and overall efficiency, primarily caused by damage to the PSII reaction centre proteins (Takahashi et al. 2010). The phyB mutant seem to be more affected by UV light perhaps due to the already lower content of carotenoids and UV-absorbing pigments in this mutant (Kreslavski et al. 2021).

These monochromatic approaches are important to study the effects of light perceived by one or a group of photoreceptors and to identify those light qualities that are important for the observed changes (Landi et al. 2020). There is a good understanding of how photoreceptors influence plant growth and architecture. And although we are beginning to grasp how specific light qualities, alone or in combination, affect photosynthetic capacity and efficiency, more research is needed to link the effect of light quality with photosynthetic plasticity and to define the role of the specific photoreceptors in this process. Further studies, particularly with photoreceptor mutants in various species, are necessary to disentangle the pathways.

Not only the light quality but also light intensity plays an important role as too much or too little can diminish photosynthesis. Excess light (more light than what can be used for photosynthesis) triggers metabolic alterations and redox imbalances as surplus electrons and excitation energy are transmitted to molecular oxygen. This process generates harmful molecules, including reactive oxygen species (ROS), peroxides, and radicals, which can act as signalling molecules and lead to photooxidative stress (Leister and Kleine 2016). Ultimately, this stress can result in cell death (D’Alessandro et al. 2020). Excess light, mostly detected by metabolic imbalances, can also be directly sensed by photoreceptors, which then relay signals by modulating gene expression. Cryptochromes, for example, induce the production of protective substances that safeguard the photosynthetic machinery from oxidative harm and enhance the synthesis of UV-absorbing anthocyanin pigments (Ponnu and Hoecker 2022).

The inherent immobility of plants necessitates mechanisms to optimise photosynthesis under conditions of excessive or limited light availability. Plant architecture affecting photosynthetic performance is controlled by photoreceptors, such as leaf angle, leaf thickness and stomatal density. Increased stomata density mediated by phyB results in increased transpiration rate which could be advantageous to promote photosynthesis under high irradiances but leads to a highwater loss. In turn, this can be compensated by a smaller leaf area (Boccalandro et al. 2009). Potato (Solanum tuberosum) plants overexpressing PHYB achieve higher photosynthetic rates per plant with thicker palisade tissue leading to a higher chlorophyll content (Thiele et al. 1999). Phytochrome signalling also affects cell division and expansion, cell cycle regulation and translation processes, and thus regulates the rate of leaf development in Arabidopsis by controlling leaf initiation and meristematic activity (Halliday et al. 2003; Li et al. 2011; Romanowski et al. 2021).

Leaf positioning and the upward growth of the petioles in Arabidopsis requires phot1 and phot2 (Inoue et al. 2008). With an increase of B light, rapeseed (Brassica napus) leaves change from wrinkled blades with down-rolled margins to flat blades and slightly up-rolled margins and have more layers of palisade tissue, whereas there was only one under R light (Shengxin et al. 2016). This phototropin-dependent leaf positioning and flattening enhances light capture under low-light conditions and avoids photodamage under high-light conditions.

In addition to changes at the organ level, a mechanism used by plants at the cellular level is the light-dependent chloroplast movement with accumulation and avoidance responses (Wada et al. 2018). The accumulation response involves the aggregation of chloroplasts in response to low-light levels, with the chloroplasts positioned primarily in the peripheral cytoplasmic layer perpendicular to the direction of incident light. This allows for increased light absorption and subsequent increase in photosynthetic efficiency. Conversely, the avoidance response causes chloroplasts to move away from regions characterised by high light intensity, aligning parallel to the light direction thus safeguarding against damage caused by excessive light absorption (Wada 2013). B light has been identified as the effective wavelength governing chloroplast movement and although cryptochromes serve as regulators of early B light-induced genes, phototropins control the chloroplast-actin (cp-actin) filament formation, which is crucial for effective chloroplast movement (Goh 2009). It has been observed that cp-actin filaments surround the chloroplast and a few minutes after photoinduction they disappeared at the irradiated site, and a newly polymerised structure that consists of dense short actin filaments emerges at the leading edge of the chloroplast just before and during movement (Wada et al. 2018).

Phot1 predominantly induces the accumulation response, while phot2 contributes to the accumulation response under low fluences of B light, but is critical for the avoidance response under higher light intensities (Kagawa et al. 2001; Sakai et al. 2001). The avoidance response is only initiated when photosynthetic inhibition is close to its maximum, suggesting that chloroplast movement is a result of reaching the maximum photosynthetic yield. Phototropins are localised in the plasma membrane, but especially phot2 can associate with the chloroplast outer envelope under strong B light and this is required for the avoidance response (Kong et al. 2013; Ishishita et al. 2020).

Chloroplast movement is exclusive to land plants and aquatic plants that maintain a consistent orientation relative to the sky and is not found in organisms that exhibit continuous movement or are planktonic. Plants with impaired chloroplast avoidance movement such as phot1 or phot2 are also impaired in recovering from short-term high light stress, especially if they were low-light adapted beforehand, emphasising the importance of chloroplast movement (Howard et al. 2019).

Integration of light signals in the plastids and their impact on gene expression to optimise photosynthetic performance

While chloroplast movement and number, leaf anatomy, or leaf movement indirectly affect photosynthetic performance, either by protecting the photosynthetic machinery or by optimising orientation to sunlight to enhance light harvesting, changes in gene expression can affect photosynthesis and the chloroplast status in a more direct way.

Due to the fact that plastids are derived from a photosynthetic cyanobacterial ancestor that was taken up by an eukaryote in an endosymbiotic event (Zimorski et al. 2014) and the loss of genetic material to the nucleus in the course of evolution (Ku et al. 2015), theses organelles had to be integrated into a network of signals that relate their respective states to each other. Chloroplasts, as semi-autonomous organelles, still possess their own genome and gene expression systems. The chloroplast genome, referred to as the plastome, contains about 50 - 150 genes, including genes related to photosynthesis and essential components of the transcription and translation processes within the plastids (Daniell et al. 2016).

To achieve synchronised responses within plant cells, anterograde (nucleus-to-plastid) and retrograde (plastid-to-nucleus) signals are employed to fine-tune the expression of genetic information within those organelles (Leister et al. 2011; Kleine and Leister 2016; Jan et al. 2022). This process ensures the proper assembly and balanced composition of the multiple protein complexes in the chloroplasts, which consist of proteins encoded in the chloroplast and the nucleus (Singh et al. 2015).

A low percentage of the 3500 - 4000 proteins needed in the chloroplast are encoded in the chloroplast itself (Leister 2003; Timmis et al. 2004; Richly and Leister 2004), yet the expression of these genes is crucial for a functional chloroplast. Many nuclear genes are involved in the expression of these plastid genes, which is one way in which the nucleus controls the development of the chloroplast. This is reflected by the fact the expression of about 30% of the nuclear encoded genes alters when the plant is exposed to light and in particular genes that express plastid-targeted proteins are affected (Ma et al. 2001).

Plastid genes in higher plants are transcribed by two different RNA polymerases, the plastid-encoded RNA polymerase (PEP) and the nuclear-encoded plastid RNA polymerase (NEP) (Borner et al. 2015; Tadini et al. 2020). When plastids are in the heterotrophic state, the NEP, which is a monomeric RNA polymerase of the T3-T7 bacteriophage type, is the major RNA polymerase, although the core subunits of PEP also seem to be present (Ji et al. 2021). Thus, PEP already plays a role in the etioplast during seed germination and provides basal transcription of photosynthesis-related genes already in the dark (Demarsy et al. 2006). Nevertheless, the role of NEP is to mainly express housekeeping genes in proplastids and etioplasts.

When a plant is exposed to light for the first time its developmental programme changes drastically (Figure 2). These changes are collectively known as the de-etiolation process (Hernandez-Verdeja et al. 2020). The most obvious change is the greening of the cotyledons due to the accumulation of chlorophyll. Etioplasts or proplastids undergo differentiation into chloroplasts (photoautotrophic state) and develop thylakoid membranes, within which the pigments and proteins necessary to capture light energy during photosynthesis and transfer this energy are localised. These phenotypic adjustments represent a cascade of light-induced molecular and physiological changes that are regulated on multiple levels.

Figure 2. Schematic view of the regulation of the expression of the plastid encoded genes by photoreceptors in the dark and the light. The transition from the heterotrophic (dark) to the photoautotrophic (in the light) state is depicted left to right. Nuclear-encoded NEP induces the expression of housekeeping genes and PEP. In the light, nuclear-encoded factors assist in assembling the PEP complex leading to the formation of functional photosynthetic complexes. The colour code specifies the photoreceptors involved in regulating the nuclear-encoded factors. N, nucleus; CP, chloroplast; PS, Photosynthesis. Please refer to the text for further details.

Upon light exposure the PEP starts to play the central role during photomorphogenesis (Liebers et al. 2017; Hernandez-Verdeja et al. 2020; Palomar et al. 2022). Experiments in tomato suggest that cry2 stimulates the PEP activity and reduces NEB activity, leading to an upregulation of photosynthesis-related genes and downregulation of the plastid housekeeping genes upon light exposure (Facella et al. 2017). In Arabidopsis, it could be shown that during dark-to-R-light transition phytochromes, particularly phyA and phyB, are required for PEP-dependent gene expression (Yoo et al. 2019). The PEP is composed of four core subunits (encoded by the genes rpoA, rpoB, rpoC1 and rpoC2), which are expressed by the NEP in the plastids (Steiner et al. 2011). As a bacteria-like RNA polymerase, a relic of the endosymbiotic origin of the plastid, PEP has to interact with sigma factors (SIG) that help the polymerase to bind the appropriate promoter and initiate the transcription process (Hu and Bogorad 1990; Tiller and Link 1995).

Six sigma factors have been found in the A. thaliana nuclear genome. SIG2 and SIG6 are essential for successful photomorphogenesis and mutants lacking these proteins have pale green cotyledons in contrast to sig1, 3, 4 and 5 which look like wild type (Woodson et al. 2013). The expression of the sigma factors in the nucleus are under the control of the different photoreceptors, this being the most direct way of how photoreceptors can influence the expression of plastid genes: phytochromes induce SIG1 (phyB), SIG2 (phyA, phyB), SIG5 (phyB), and SIG6 (phyA, phyB), while cryptochrome affects the transcription of SIG5 and SIG1 (Chi et al. 2015; Dubreuil et al. 2017). SIG3 and 4 seem to play minor or more specific roles.

SIG1 initiates in the plastid the transcription of a specific subset of chloroplast genes encoding for the core subunits of the photosystems, such as psaA (PSI) and psbD (PSII), the large subunit of the RUBISCO, and rpoB (subunit of PEP), especially in older plants, and is therefore crucial for maintaining a balanced expression of the PSI and PSII components in the plastids to maintain photosynthetic efficiency (Onda et al. 2008; Shimizu et al. 2010; Macadlo et al. 2020).

SIG2 expression is activated by phyA and phyB in the nucleus and its presence in the plastid induces the expression of several plastid-encoded genes for subunits of the photosystems such as psaJ, psbA, psbD, psbB, psbN and several tRNAs (Kanamaru et al. 2001; Hanaoka et al. 2003; Nagashima et al. 2004; Oh and Montgomery 2013; Woodson et al. 2013). One of the tRNAs reduced in sig2 is the PEP-dependently expressed glutamyl-tRNA (tRNA^Glu), which is important as a precursor for chlorophyll and haem biosynthesis. Furthermore, it has been demonstrated that tRNA^Glu inhibits NEP´s transcriptional activity. As a result, in sig2 NEP activity is not reduced, which interferes with PEP activity and hinders chloroplast development (Hanaoka et al. 2005). Additionally, SIG2 plays a crucial role in phytochrome-mediated photomorphogenesis, especially under R and FR light conditions by influencing the regulation of PhANGs in response to the functional state of the plastids (retrograde signalling). Therefore, it coordinates the balance in the expression of genes encoded in both the plastid and the nucleus to form the protein complexes in the chloroplast in accordance to the environmental light requirements. The severity of the phenotype of mutants that lacks SIG2 suggests that SIG2 is one of the more important sigma factors affecting several aspects of development and photosynthetic performance (Oh and Montgomery 2013; Oh et al. 2018).

The sig6 mutants also display the chlorophyll deficiency phenotype similar to sig2, but specifically in cotyledons, as most of the PEP-dependent transcripts encoding photosynthesis-related proteins, but also tRNAs and rRNAs, are reduced in sig6 seedlings at an early stage of development, but are restored to wild-type levels at a later stage of development (Ishizaki et al. 2005; Palomar et al. 2022).

SIG5 is especially important for the B light-mediated expression of psbD, encoding for one subunit of the PSII reaction centre (Nagashima et al. 2004; Onda et al. 2008). The abundance of SIG5 transcripts depends on the intensity of B light, perceived by cry1 and cry2, with cry1 being more important at higher light intensities (Onda et al. 2008). Interestingly, this B light regulated expression of psbD is not observed in gymnosperms or basal angiosperms and seems to have been acquired later in evolution (Shimmura et al. 2017). In addition, SIG5 is also regulated in part by redox- and phytochrome-mediated light signalling (Mellenthin et al. 2014) and is involved in gating the nuclear circadian oscillator to control the rhythms of chloroplast gene expression which is primarily mediated by cryptochrome (Noordally et al. 2013; Belbin et al. 2017).

At least 12 proteins are associated with the PEP core and are referred to as PAPs (PEP-associated proteins) (Steiner et al. 2011; Pfalz and Pfannschmidt 2013). Loss-of-function mutants of these subunits often have albino or pale-green phenotypes with arrested plastid development not solely in Arabidopsis but also in maize or rice, similar to sig2 and 6 (Steiner et al. 2011). Some PAPs can play important roles as transcription factors by binding DNA and thus supporting the initiation, elongation, or termination of transcription, others have RNA binding domains, e.g. some are pentatricopeptide repeat (PPR) proteins (such as PAP2), playing important roles during transcription elongation, or some have more regulatory or protective functions (for reviews see Pfannschmidt et al. 2015; Kindgren and Strand 2015; Tadini et al. 2020). PAP10, for example, is a thioredoxin z with a role in chloroplast gene expression and its redox regulation perhaps fine-tuning PEP function, as a loss-of-function mutant is not able to grow autotrophically (Wimmelbacher and Bornke 2014). The Fe-Superoxide-Dismutases FSD2 and PAP4/FSD3, as well as PEP-RELATED DEVELOPMENT ARRESTED1 (PRDA1) protect PEP from oxidative stress by converting superoxides to hydrogen peroxide (H₂O₂) (Myouga et al. 2008; Qiao et al. 2013; Gallie et al. 2019).

In dark-grown lines where phyB is constitutively activated by a mutation or in a PHYTOCHROME-INTERACTING FACTOR (PIF) quadruple mutant (pif1pif3pif4pif5; pifq), PEP assembly could be detected, suggesting that phyB activates the assembly and the PIFs, which are negative regulators of photomorphogenesis downstream of phytochromes (see below), repress this process (Dubreuil et al. 2017; Yoo et al. 2019). Regulation can be achieved by activating PAP and SIG expression in the nucleus through phytochrome-dependent degradation of PIFs, which releases the repression of these genes. PIF3 binding motives, such as a G-box motif, have been found in the promoters of most PAP genes, all SIG genes, and PLASTID REDOX INSENSITIVE (PRIN)2, encoding a protein needed for PEP activity (Leivar and Quail 2011; Zhang et al. 2013; Dubreuil et al. 2017). Surprisingly, the expression levels of many PAPs were relatively high during dark conditions, but decreased upon transition from dark to light, although three PAPs (PAP2, PAP10, and PAP11) and PRDA1 were phytochrome-dependently up-regulated in the light (Qiao et al. 2013; Oh and Montgomery 2013; Hwang et al. 2022).

Several of the PEP-associated proteins play roles in both the chloroplast and the nucleus, such as REGULATOR OF CHLOROPLAST BIOGENESIS (RCB), NUCLEAR CONTROL OF PEP ACTIVITY (NCP), HEMERA (pTAC12/HMR/PAP5) and PAP8/pTAC6 (Hernandez-Verdeja et al. 2020). RCB and its paralog NCP, both non-catalytic thioredoxin-like proteins, are up-regulated in the light and are involved in phytochrome-signalling leading to the degradation of PIFs, which consequently initiates the PEP assembly in the chloroplasts and thus the expression of PEP-dependent genes (Yoo et al. 2019; Yang et al. 2019). In the chloroplast, RCB and NCP are only weakly associated with PEP, but NCP has been shown to promote the assembly of the PEP complex (Yang et al. 2019).

Similar to rcb and ncp, the hmr mutant shows a long hypocotyl and albino phenotype (Chen et al. 2010). In the nucleus, HMR interacts with photoactivated phytochromes and is also involved in the degradation of PIFs, thereby activating the expression of PIF-repressed genes (Galvao et al. 2012; Qiu et al. 2015; Nevarez et al. 2017). HMR has the ability to bind single-stranded DNA and RNA (Pfalz et al. 2015) and is suggested to act as a transcriptional co-activator (Qiu et al. 2015). In the chloroplast, as a PAP, it is essential for the functional transcription of photosynthesis-associated plastid-encoded genes (Galvao et al. 2012; Qiu et al. 2015). HMR also interacts with another dually localised protein, PAP8/pTAC6, in the nucleus (Gao et al. 2011; Yu et al. 2013). PAP8/pTAC6 is involved in the regulation and DNA/RNA metabolism of chloroplast gene transcription and involved in the light-signalling downstream of phyB (Leivar and Monte 2014; Liebers et al. 2020). PAP8 in the plastid is crucial for the transcription of the photosynthesis-associated plastid-encoded genes by PEP, which, similar to HMR, is the cause of the albino phenotype of the knock-out mutant (Liebers et al. 2020).

Not only the presence of all PAP proteins in the chloroplast, but also their assembly into a complex appears to be tightly regulated by light-activated phytochromes and PIFs as their counterparts (Figure 2). In Arabidopsis, PEP forms a 1000-kDa complex in R light, which can be detected already after 1 h of illumination, but not in darkness, and the assembly is inhibited in mutants lacking phyA and phyB during the dark-to-R-light transition (Yoo et al. 2019). FR light perceived by phyA, and B light perceived by cry1 and cry2, appear to be sufficient to trigger PEP assembly (Hwang et al. 2022). PEP activity is dependent on the presence of PAPs, SIGs and several other proteins such as PRIN2, NCP and RCB supporting that photoreceptors, especially phytochromes, control transcription of genes encoding for the PEP complex, its assembly and activity (Kindgren et al. 2012; Yoo et al. 2019).

By proteomic and genetic analysis, it is estimated that more than 50 proteins influencing PEP activity or downstream processes are expressed in the nucleus (Yu et al. 2014). Plastid-encoded genes, due to their bacterial ancestry, are generally organised into polycistronic operons and require extensive processing, stabilisation, editing and intron splicing prior to translation for which many nuclear factors are necessary (Leister et al. 2017; Manavski et al. 2018; Small et al. 2023). For only a few of these factors the impact of photoreceptors has been analysed. BPG2 (BRZ-INSENSITIVE PALE GREEN 2), which is required for the greening process in Arabidopsis, binds to chloroplast 16S and 23S ribosomal RNAs, which affects the translation in the plastid and the accumulation of the photosynthetic apparatus. Its own expression in the nucleus is controlled by phytochrome (Kim et al. 2012). Inactivation of another RNA-binding protein, ATAB2, affects the biogenesis of Arabidopsis thylakoid membranes, the synthesis of the photosystem reaction centre subunits, and its loss leads to an albino phenotype. Its role in activating chloroplast mRNA translation has been proposed. Cry1 and cry2 and to a lesser extent phyA are important for ATAB2 expression in the nucleus (Barneche et al. 2006). Cryptochromes and phytochromes also regulate the expression of HIGH CHLOROPHYLL FLUORESCENCE173 (HCF173), which encodes a protein important for PSII biogenesis due to its role in the translation initiation of the D1 synthesis (Fukazawa et al. 2020).

The import of all these nuclear-encoded factors into the plastids is mediated mainly by the TOC/TIC complex localised in the outer and inner envelope membranes of the chloroplast. Cry1 appears to play a key role in optimizing the establishment of the TOC/TIC apparatus, as many of the genes encoding for subunits are rapidly induced by B light in a cry1-dependent manner (Fukazawa et al. 2020). Therefore, on several levels, regulators emerge as key components that link the information from photoreceptors to the coordinated transcription and translation of the plastome and thus to the establishment and functional regulation of the chloroplast and photosynthesis. The dual-localised proteins are hypothesised to play an integral role in controlling the nuclear-chloroplast coordination by being present in both organelles and, as part of the phytochrome signalling network, making phytochrome one of the most important regulators of PEP-dependent genes in the plastid (Nevarez et al. 2017). It is striking that many of the genes encoding for proteins responsible for transcriptional and post-transcriptional modifications of plastids, especially many chloroplastic RNA binding proteins, PAPs and sigma factors are expressed in a phytochrome-dependent manner (Griffin et al. 2020). On the other hand, cryptochromes are also strong regulators of plastome gene expression (Facella et al. 2017). In particular, cryptochrome-dependent ATAB2 strongly affects the core proteins of PSI, whereas SIG5 is important for the B light-mediated expression of a PSII core protein. Whether cryptochrome is more important for the photosystem-related proteins and phytochromes for the factors that regulate the expression remains to be determined.

Integration of light signals in the nucleus and their impact on gene expression to optimize photosynthetic performance

Skotomorphogenesis refers to the developmental processes that occur in the absence of light. It includes growth patterns such as hypocotyl elongation and the formation of an apical hook, folded cotyledons to protect the apical meristem. The goal of skotomorphogenesis is for the seedling to reach light to be able to establish photosynthesis (Liebers et al. 2017). During skotomorphogenesis, phytochromes and cryptochromes remain inactive in the cytosol (phyA-E, cry1) or the nucleus (cry1, cry2). One of the key players in the integration of the presence or absence of light signals is the COP1/SPA complex (Ponnu and Hoecker 2021). Within this complex, COP1 (CONSTITUTIVE PHOTOMORPHOGENIC 1) functions as the enzymatic unit as it possesses a E3 ligase activity and a WD40 repeat domain to bind to targets to be ubiquitinated, while SPA (SUPPRESSOR OF PHYA-105) serves as the regulatory unit responsible for the substrate affinity of COP1. SPA proteins are a small protein family of four proteins (SPA1 - 4) that heterodimerization with COP1. The complex is a tetramer consisting of a COP1 dimer with a combination of two SPA proteins (SPA homo-/heterodimers) (Zhu et al. 2008).

The presence of the COP1/SPA complex in the dark leads to the ubiquitination of transcription factors involved in photomorphogenesis, such as HY5 (LONG HYPOCOTYL 5; (Oyama et al. 1997)), its homolog HYH (HY5-HOMOLOG; (Holm et al. 2002)), the bHLH (basic helix-loop-helix) factor HFR1 (LONG HYPOCOTYL IN FAR-RED 1; (Fairchild et al. 2000; Fankhauser and Chory 2000; Soh et al. 2000)) and the Myb factor LAF1 (LONG AFTER FAR-RED LIGHT1; (Ballesteros et al. 2001)). These ubiquitinated proteins are then targeted for proteasomal degradation by the ubiquitin-26S-proteasome system (Ponnu and Hoecker 2021). Loss of this complex in either cop1 or a spa quadruple mutant results in constitutive photomorphogenesis, i.e. some developmental programs that normally occur in the light are carried out in the dark, including the activation of PhANGs, nevertheless the mutants are still pale, as light is required for one of the final steps of chlorophyll biosynthesis (Wei and Deng 1996; Laubinger et al. 2004).

Phytochrome-interacting factors (PIFs) are another group of negative regulators of photomorphogenesis and chloroplast development (Leivar and Monte 2014). In Arabidopsis, eight members of the PIF family are known, each possessing a basic helix-loop-helix structure that facilitates DNA binding and dimerisation. In the dark, PIF1, PIF3, PIF4 and PIF5 are primarily responsible for skotomorphogenesis and inhibit chloroplast development by repressing PhANGs, but also PAP- and SIG-encoding genes in the nucleus (Stephenson et al. 2009; Leivar and Monte 2014; Balcerowicz 2020). Thus, SIG1, SIG3, SIG5 and SIG6 are induced in a dark-grown pifq seedling (Hwang et al. 2022). PIF1 additionally enhances the E3 ligase activity of COP1, enforcing the skotomorphogenic programme (Xu et al. 2014). Similar to cop1 mutants, a dark-grown pifq mutant de-etiolates and chloroplast biogenesis initiates with the formation of rudimentary prothylakoid membranes in parallel with the activation of PhANGs (Leivar et al. 2008).

In addition, ethylene-binding F-box proteins (EBFs) are degraded by the COP1/SPA complex, which in turn stabilises EIN3 (ETHYLENE-INSENSITIVE 3), a transcription factor in the ethylene pathway that mediates seedling emergence from soil by integrating light signal or the lack thereof with soil pressure. EIN3 can interact with PIFs and together they bind to the promoter regions of LHC genes thereby arresting the differentiation of etioplasts into chloroplasts in buried seeds. Dark-grown ein3 mutants show constitutive PhANG activation despite lacking obvious photomorphogenic phenotypes in comparison to cop1 (Liu et al. 2017).

Photomorphogenesis represents the developmental processes that occurs in the presence of light, initiating photosynthesis and expression of PhANGs and additional factors needed for chloroplast development (Figure 3). As COP1 is also present in light, the COP1/SPA complex must be inactivated on the posttranslational level to start the photomorphogenic programme (Zhu et al. 2008; Balcerowicz et al. 2011). Once light activates the photoreceptors, this gradual inactivation of the COP1/SPA complex begins to allow the expression of genes important for photomorphogenesis, but some E3 ligase activity is still present during this dark-to-light transition.

Figure 3. Schematic model of the dynamics of the core factors needed to regulate PhANG expression in the nucleus during darkness, transitional periods and in the light. The triangles depict varying levels of active protein found within the cell. Proteins coded in blue stabilise while those coded in red lead to activation or inactivation or degradation. Expression regulators are shown in a square, and interacting regulators are shown in a circle. The asterisk (*) denotes activated photoreceptors. Please refer to the text for further details.

Light-activated phytochromes (P_fr) are transported to the nucleus where they can interact (among other proteins) with SPA and COP1 leading to the destabilisation of the COP1/SPA complex. SPA1 and 2 are degraded in a phyA-dependent manner, limiting COP1 activity as no complex can be formed due to lack of SPA (Balcerowicz et al. 2011; Chen et al. 2015). Light-activated cryptochromes undergo a conformational change leading to polyoligomerization (Wang and Lin 2020; Ponnu and Hoecker 2021). These nuclear localised cry1 and cry2 interact with COP1 and B light enhances the cry2–COP1 interaction, which leads to an increased inactivation and dissociation of the COP1/SPA complex (Holtkotte et al. 2017; Ponnu et al. 2019). Furthermore, activated cryptochromes interact with SPA, causing its destabilisation.

Another mechanism to inactivate COP1 is the phytochrome- and cryptochrome-mediated nuclear exclusion of COP1 (von Arnim and Deng 1994; Pacin et al. 2014). Furthermore, post-translational modifications and ubiquitination by other E3 ligases also regulate COP1 activity and nuclear abundance.

Inactivating PIFs is another critical step, as they are a central mechanism for turning off the expression of PhANGs (Favero 2020). All PIFs can interact with phyB, PIF1 and 3 can interact additionally with phyA (Pham et al. 2018). Activated phytochromes promote PIF degradation in response to light by phosphorylation and further non-COP1-dependent ubiquitination and degradation in the proteasome (Xu et al. 2015). SPA1 can induce rapid phosphorylation of PIF1 by forming a phyB-PIF1-SPA1 complex (Paik et al. 2019). The dual-localised proteins RCB, NCP, HMR and PAP8 have been shown to be involved in targeting PIFs phytochrome-dependently to nuclear photobodies (subnuclear microenvironments formed around activated phytochromes and their interacting components), leading to their degradation (Chen et al. 2010; Galvao et al. 2012; Leivar and Monte 2014; Qiu et al. 2015; Nevarez et al. 2017; Yoo et al. 2019; Yang et al. 2019; Liebers et al. 2020).

RCB directly interacts with phyA and phyB, albeit in a light-independent manner, and is required for photobody formation (Yang et al. 2019). HMR interacts with photoactivated phytochromes and PIF proteins and is involved in the degradation of PIF1 and PIF3 in the light (Galvao et al. 2012; Qiu et al. 2015; Nevarez et al. 2017). PAP8 is also required for photobody formation and thus involved in the light-signalling downstream of phyB, as also in pap8 PIF degradation is impaired (Leivar and Monte 2014; Liebers et al. 2020). Phytochromes seem to be the main factor controlling the degradation and re-accumulation of PIF proteins in plants growing in light/dark cycles generating a daily alternation in the abundance of these transcription factors (Soy et al. 2012).

Most of the primary targets of the COP1/SPA complex in the dark are factors that positively regulate photomorphogenesis and the PhANG expression and upon inactivation of the COP1/SPA complex and the PIFs these get activated and stabilised (Seluzicki et al. 2017). Many of them have been identified in screens looking for phytochrome signalling mutants for elongated hypocotyls under R or FR light such as HY5, HFR1 and LAF1 (Oyama et al. 1997; Fairchild et al. 2000; Fankhauser and Chory 2000; Soh et al. 2000; Ballesteros et al. 2001). HFR1 and LAF1 are transcription factors that specifically regulate the expression of phyA-responsive genes (Jang et al. 2007). Additionally, HFR1, an bHLH protein that cannot bind to DNA, can heterodimerize with PIFs, which prevents them from binding to their target genes and destabilises them (Fairchild et al. 2000; Xu et al. 2017).

Due to its versatility HY5 is a central regulator of photomorphogenesis, since it directly or indirectly controls about one-third of gene expression in the entire Arabidopsis genome (Chattopadhyay et al. 1998; Gangappa and Botto 2016). The hy5 mutant is characterised by a long hypocotyl under R and FR light, supporting the fact that it acts under the control of phyA and phyB. In addition, HY5 has been shown to act downstream of cryptochromes and its own expression is increased after UV-B treatment (Gangappa and Botto 2016). Carotenoid and chlorophyll levels are severely reduced in the hy5 mutant as HY5 binds to the G-box in the promoter region of the genes that encode factors important for the biosynthesis of the pigments for the photosynthetic apparatus (Toledo-Ortiz et al. 2014). However, HY5 and PIFs compete for the binding to the G-box element and regulate it antagonistically (Toledo-Ortiz et al. 2014) (Figure 3). This results in a dynamic regulation of the expression of common target genes and thus chloroplast development in response to light, but also temperature, implementing diurnal expression patterns and buffering against sudden changes in environmental conditions. HY5, for example, seems to be especially important to regulate photosynthetic capacity at cooler temperatures (Toledo-Ortiz et al. 2014). HY5 appears to contribute to the light-dependent up-regulation of several nuclear-encoded, but chloroplast-localised RNA-binding proteins, thereby modulating plastid gene expression downstream of phytochromes and cryptochromes (Griffin et al. 2020). HY5 itself is also regulated at the transcriptional level, as HY5/HYH, B-BOX DOMAIN PROTEINs (BBXs), and CALMODULIN 7 (CAM7) contribute to the induction of HY5 by binding directly to its promoter (Lee et al. 2007; Abbas et al. 2014; Xu et al. 2016, 2018; Xu 2020). The close homolog of HY5, HYH, has partially overlapping functions, however HYH predominantly acts as a positive regulator of photomorphogenesis in B light (Holm et al. 2002).

The BBX family of transcription factors is a class of zinc finger transcription factors, and 32 BBX members have been identified in A. thaliana that have distinct functions in the light signalling pathway (Gangappa and Botto 2014). Some of them (BBX4, BBX21–23) promote photomorphogenesis, whereas others (BBX24, 25, 28, 30–32) inhibit it (Yadav et al. 2020). Transcript levels of BBX16, BBX24, BBX25, BBX30, BBX31 and BBX32, but not of BBX20 and BBX21, peak phytochrome- and cryptochrome-dependently within an hour after dawn (Balcerowicz et al. 2021). Many BBX proteins depend on HY5 for their function; one mechanism is on the protein level by directly binding to HY5 and enhancing (BBX20–23) or repressing (BBX24, BBX25, BBX28, BBX30 and BBX31) HY5’s transcriptional activity towards target genes (Gangappa et al. 2013, 2013; Xu et al. 2018; Heng et al. 2019; Xu 2020; Bursch et al. 2020; Song et al. 2020). Furthermore, several BBX proteins can bind to the HY5 promoter to modulate the expression of HY5, and HY5 can bind to several BBX promoters to modulate them, thereby creating a feedback loop (Gangappa et al. 2013; Xu et al. 2016). A direct impact on photosynthesis has been shown in AtBBX21-overexpressing potato (Solanum tuberosum) plants that have more chlorophyll, a higher photosynthesis rate and stomatal conductance with a significant increase in photosynthetic gene expression leading to a higher tuber yield (Crocco et al. 2018; Gomez-Ocampo et al. 2021). BBX32, HY5, COP1, SPA and cry1 were identified in a transcriptomic analysis to be key regulators for acclimation to high light at the chloroplast level, and also Arabidopsis plants overexpressing BBX32 were severely impaired in acclimation to high light and displayed perturbed expression of PhANGs under low light and after exposure to high light (Alvarez-Fernandez et al. 2021). BBX16, on the other hand, promotes photomorphogenesis in moderate light and is repressed after chloroplast damage (Veciana et al. 2022), whereas overexpression of BBX14 or BBX16 de-represses PhANGs (Atanasov et al. 2023).

Another group of transcription factors identified as central to the expression of PhANGs, especially genes encoding for enzymes important for chlorophyll biosynthesis and chloroplast development, are the GOLDEN2-LIKE (GLK) transcription factors belonging to the Myb group (Waters et al. 2009; Martin et al. 2016). Arabidopsis GLK1 and GLK2 are homologous and act redundantly, as double mutants are pale green and their chloroplasts have reduced grana-thylakoids (Fitter et al. 2002). Transcription of GLK1 is repressed by PIFs in darkness but in the light phytochromes, HY5 and PAP8 induce GLK expression (Oh and Montgomery 2013; Martin et al. 2016; Liebers et al. 2020). Besides the role of GLKs in antograde signalling they also play a role in the retrograde signalling pathway (Leister and Kleine 2016). GLKs can bind directly to promoters, especially to the G-box of PhANGs, such as LHCB, which leads to expression (Waters et al. 2009). Furthermore, HY5 interacts directly with GLK to promote gene expression (Hernandez-Verdeja et al. 2020). Overexpression of maize (Zea mays) GLK proteins in rice (Oryza sativa) led to higher chlorophyll contents and photosynthetic performance (Yeh et al. 2022). BBX14, a target of GLK1, is important for the acclimation to high-light integrating photomorphogenetic and retrograde signals (Leister and Kleine 2016; Atanasov et al. 2023).

Via GLK1 the brassinosteroid pathway modulates photomorphogenesis and chloroplast development as GLK1 can interact with the BRASSINOSTEROID INSENSITIVE2 (BIN2), a negative regulator in the brassinosteroid pathway (Zhang et al. 2021; Zhao et al. 2022). In the dark, BR signalling is activated resulting in the inhibition of BIN2 kinase activity and thus leads to the dephosphorylation of GLK1 and its degradation. In the light, BIN2 is activated by HY5 and stabilised by light-activated phyA and phyB (Zhao et al. 2022), which leads to GLK1 phosphorylation and stabilisation, and allows the expression of chloroplast-development-related genes (Zhang et al. 2021). A bin2 mutant with a constitutive brassinosteroid response (gain-of-function) exhibits a reduced numbers of thylakoids per grana stack, suggesting that BIN2 also positively regulates chloroplast development. In darkness or in low light PIFs can activate REPRESSOR OF PHOTOSYNTHETIC GENES 1 (RPGE1) and RPGE2 by binding to their promoter. The encoded proteins inhibit the DNA binding activity and dimerisation of GLK proteins, therefore they can no longer activate the PhANGs (Kim et al. 2023).

Furthermore, the heterogenous group of Z-box binding factors (ZBFs) can bind to the G-box in LHC and RBCS promoters (Mallappa et al. 2006; Gangappa et al. 2013; Yadav et al. 2020). Both MYC2/ZBF1 and GBF1/ZBF2 act downstream of cry1 and cry2 photoreceptors, in contrast CAM7/ZBF3, operates downstream of multiple photoreceptors under B, R and FR light (Gangappa et al. 2013). In light, MYC2/ZBF1 inhibits LHC and RBCS expression, whereas GBF1/ZBF1 and CAM7/ZBF3 regulates them positively (Gangappa et al. 2013).

It becomes increasingly clear that transcription factors located downstream of photoreceptors regulate PhANGs in a complex but partially antagonistic way, enabling them to acclimate to prevailing light conditions and react to abrupt changes in the light environment (Figure 3).

Turning green

Greening of plants is important at the seedling stage (de-etiolation), where etioplasts of dark-grown seedlings develop into chloroplasts upon light induction (Solymosi and Schoefs 2010). In adult tissues a transition from proplastid to chloroplast occurs as meristematic cells develop into green tissues. Both processes appear to share regulatory pathways and a change in the transcriptome coincides not only with changes in the protein and pigment composition, but also with changes in plastid morphology leading to chloroplast maturation (Dubreuil et al. 2018; Armarego-Marriott et al. 2019, 2020). Chlorophyll accumulation is the first visible indicator of the transition to photomorphogenesis and autophototrophic growth. The structure of chlorophylls is a tetrapyrrole ring, similar to that of haem, but with a central magnesium instead of an iron. Chlorophylls absorb light energy and are involved in the transfer of energy. Excited chlorophylls are able to interact with oxygen, leading to the production of reactive singlet oxygen, which is detrimental for plant growth and can lead to cell death. Already the over-accumulation of its precursor protochlorophyllide (Pchlide) can lead to cellular photooxidative damage. Therefore, due to its highly reactive nature chlorophylls need to be bound to proteins. Hence, not only the biosynthesis of the chlorophyll itself, but also the expression of the genes encoding for the chlorophyll-binding proteins need to be tightly controlled and are critical to establish a functional photosynthesis (Tanaka et al. 2011). The major proteins, besides the photosystems, that bind chlorophyll are the antenna proteins, LHCs.

Chlorophyll biosynthesis takes place in the plastid, but all the necessary enzymes are encoded in the nucleus. The biosynthetic pathway can be divided into two phases: the dark phase and the light-dependent phase. Dark-grown angiosperm plant seedlings are yellowish (due to the presence of carotenoids) and accumulate only the chlorophyll precursor Pchlide in the cotyledons; only upon light induction chlorophyll can be synthetised. The first step of chlorophyll biosynthesis in higher plants is the conversion of glutamate to 5-aminolevulinic acid (ALA). The abundance of the tRNA^Glu needed as precursor is regulated by SIG2. HEMA is the main glutamyl-tRNA reductase that catalyzes this rate-limiting step. The expression of HEMA1, but not HEMA2, is mainly induced by phytochrome, especially phyA, and HY5 and its antagonists, the PIFs, are essential for light signal integration (McCormac et al. 2001; McCormac and Terry 2002a; Stephenson et al. 2009). Regulation of this step is important not only to prevent the accumulation of photoreactive metabolic intermediates in the dark during the initial phase of de-etiolation, but also to ensure a balanced diurnal supply of the precursor.

Two ALA molecules are combined to a porphobilinogen and the enzyme responsible is the ALA Dehydratase (HEMB1). HEMB1 is regulated by the two transposase-derived transcription factors FHY3 (FAR-RED ELONGATED HYPOCOTYLS 3) and FAR1 (FAR-RED-IMPAIRED RESPONSE), which act downstream of phyA and are positive regulators of chlorophyll biosynthesis. Interaction of FHY3 with PIF1 represses HEMB1 expression (Tang et al. 2012). Porphobilinogen is converted by several steps into protoporphyrin IX (Proto IX) and this is the branching point between chlorophyll and haem biosynthesis. The committing step mediated by the magnesium chelatase inserts the Mg into ProtoIX, resulting in Pchlide (Tanaka et al. 2011). The Mg chelatase consists of several subunits, CHLH, CHLI and CHLHD, with CHLH being the one that binds the tetrapyrrole. The CHLH gene is induced already after few hours of light but not CHLI and CHLD. ZEITLUPE (ZTL), an F-box protein containing a LOV domain, which has been described as a B light photoreceptor, interacts with CHLH in the presence of light, leading to its ubiquitination and degradation via the 26S-proteasome pathway (Yu et al. 2022). GENOME UNCOUPLER (GUN)4 protects CHLH from this degradation and enhances the enzymes activity. Both their transcription is mediated by phyA and phyB with some influence from the cryptochromes (Larkin et al. 2003; Stephenson and Terry 2008; Tanaka et al. 2011). The importance of the negative regulation of the tetrapyrrole biosynthesis by the PIFs can be observed as pif1 and pif3 mutants accumulate high levels of Pchlide in the dark which causes severe photooxidative damage upon light exposure due to the generation of ROS (Op den Camp et al. 2003; Huq et al. 2004; Moon et al. 2008; Stephenson et al. 2009). The repression of CHLH by PIFs in darkness is removed in light where HY5 activates transcription (Moon et al. 2008; Stephenson and Terry 2008; Stephenson et al. 2009). PIF3 and HY5 reciprocally regulate also the expression of BBX11 by binding to its promoter, allowing BBX11 to modulate the expression of genes such as HEMA1 and CHLH (Job and Datta 2021).

The Pchlide forms a complex with the enzyme protochlorophyllide oxidoreductase (POR) and NADPH in etioplasts, resulting in the formation of the so-called prolamellar body. This semi-crystalline structure is composed of lipids and proteins, with the POR being the most abundant protein and stoichiometrically matching the amount of Pchlide. When dark-grown plant seedlings are exposed to light, the POR-Pchlide-NADPH complex absorbs light of shorter wavelength than FR light and catalyse the rapid conversion of Pchlide to Chlide, which is then esterified to the mature chlorophyll (Fujita 1996; Heyes and Hunter 2005; Masuda and Fujita 2008). This dependence on photoactivation can only be found in angiosperms as all other plants and cyanobacteria contain an additional, light-independent enzyme, that allows greening even in the dark.

In A. thaliana three POR enzymes were identified: PORA, PORB and PORC (Armstrong et al. 1995; Su et al. 2001; Masuda et al. 2003) (Figure 4). PORA and PORB are expressed in the dark and during etiolation. PhyA is crucial to significantly decreased PORA expression in A. thaliana seedlings after illumination. PORA was also reported to be downregulated in sig2 mutant seedlings under extended R light exposure (Oh et al. 2018) and in sig2 and sig6 under white light (Martin et al. 2016). EIN3 interacts with PIF1 to inhibit Pchlide over-accumulation in the dark but also upregulates PORA and PORB expression directly (Zhong et al. 2009). The Myb-like transcription factor REVEILLE1 (RVE1) was found to act downstream of phyB to activate PORA expression (Xu et al. 2015; Jiang et al. 2016). RPGE2 overexpression lines and the glk1glk2 double mutant have paler leaves and in these lines many genes encoding for enzymes involved in chlorophyll biosynthesis are repressed such as HEMA1, CHLH and PORA (Waters et al. 2009). Additionally, if photoactivated phytochrome interacts with cytosolic PENTA1 (PNT1) the translation of PORA mRNA is inhibited (Paik et al. 2012).

Figure 4. Schematic view of the regulation of the three POR genes present in Arabidopsis thaliana. PORA, B, and C catalyse the synthesis of Chlide from Pchlide, which is the light-dependent step in chlorophyll biosynthesis. Factors that activate or repress in the dark (bottom) and light (top) are indicated. Arrows and bars represent positive and negative regulation, respectively. The position of the + represents the light condition in which the respective POR genes are highly expressed. Please refer to the text for further details.

PORC expression is maintained at low levels in darkness by PIF1, which binds to the PORC promoter (Moon et al. 2008). BRAHMA (BRM), a SWI2/SNF2 chromatin-remodelling ATPase, interacts with PIF1 leading to changed levels of histone H3 lysine 4 tri-methylation (H3K4me3) at the PORC locus suggesting that additional mechanisms such as epigenetic markers play a role in fine tuning chlorophyll biosynthesis (Zhang et al. 2017). As a result, a brm mutant greens faster but accumulates less Pchlide. The strong upregulation of PORC by light is mediated at least in part by HY5. After photoactivation of POR and the formation of chlorophyll, the prolamellar body disperses and thylakoid membranes are formed. Within few hours photosynthetic activity can be detected and the chloroplast are fully matured in 6 - 24 h (Pipitone et al. 2021).

A further highly regulated step in this biosynthetic pathway is the chlorophyll(ide) a oxygenase (CAO). This enzyme is responsible for the synthesis of chl b from chl a and thus for the ratio of chl a/b present in plants (Tanaka and Tanaka 2007; Tanaka et al. 2011). In higher plants the photosystems and core antenna preferentially bind chl a, while peripheral antenna complexes (LHC) bind both chl a and chl b. The use of chl b in the antenna could provide an advantage because of its slightly different absorption spectrum from chl a thereby enabling to harvest more photons. Additionally, chl b binds more tightly to LHC which could stabilise LHC (Tanaka and Tanaka 2011). In RPGE2 overexpression lines and the glk1glk2 double mutants CAO is repressed leading to a higher chl a/b ratio, substantiating that the RPGE and GLK proteins regulate CAO antagonistically (Kim et al. 2023).

In conclusion, it seems that all steps to generate chlorophyll, especially the rate-limiting steps, seem to be under the control of photoreceptors. The single phytochrome mutants in A. thaliana surprisingly do not show a strong impact on chloroplasts development and greening under laboratory conditions. A phyB mutant has reduced chlorophyll levels but no drastic deficiency in photosynthetic capacity or efficiency could be observed (Yoshida et al. 2018), and greening was attenuated in a phyAphyB double mutant during the dark-to-light transition under R light (Yoo et al. 2019). Nevertheless, a quintuple phytochrome mutant can still produce chlorophyll and develop chloroplasts under R light, although R light is no longer able to alter transcription patterns rendering it more or less blind to the R light signal in this respect (Strasser et al. 2010; Hu et al. 2013). A quadruple mutant cry1cry2phot1phot2 of A. thaliana could also still accumulate chlorophyll suggesting that all photoreceptors play a role in chlorophyll biosynthesis (Ohgishi et al. 2004). In contrast, a triple phyAphyBphyC mutant in rice lacks detectable synthesis of chlorophyll (Takano et al. 2009). In rice, phyB plays a positive role in the regulation of chlorophyll biosynthesis as already a phyB mutant has a lower chlorophyll content than the wild type under white or R light but a higher expression of PORA.

FR light is not energetic enough to activate POR enzymes for chlorophyll biosynthesis in Angiosperms. Furthermore, it has been observed that seedings kept under FR light are also no longer able to green when they are transferred to white light (van Tuinen et al. 1995; Barnes et al. 1996). This FR block of greening phenotype coincides with losing the prolamellar body in the FR light and damage to the plastid. Additionally, the accumulation of large amounts of ROS was associated with a reduction in POR levels and accumulation of reactive Pchlide. When FR-grown plants were exposed to white light, this led to photooxidative damage and the loss of expression of the nuclear genes such as HEMA1 and LHCB (McCormac and Terry 2002b; Schoefs and Franck 2003; Buhr et al. 2008). This process is mediated by phyA as in phyA and in a subset of phyA-signalling mutants such as fhy1, fhy3, fin2-1, fin5-1and pat1-1 (Barnes et al. 1996; Soh et al. 1998; Bolle et al. 2000; Cho et al. 2003) this phenotype is abolished. This has been attributed to the repression of PORA by phyA under FR light whereas in a phyA mutant PORA protein can accumulate (Runge et al. 1996). Another mutant that is able to green after FR light is the sig6 mutant, which also shows increased levels of HEMA1, PENTA and PORA (Alameldin et al. 2020). None of the other sig mutants have this phenotype, neither has hy5.

If at the branching point after ProtoIX an iron ion instead of a Mg²⁺ is inserted by the ferrochelatase (FC1 and FC2) this leads to the biosynthesis of haem, an important electron carrier, but also to the biosynthesis of phytochromobilin, the cofactor of phytochromes (Papenbrock et al. 2000). In contrast to the chlorophyll pathway FC1 and FC2 are not light-regulated as phytochromobilin is already needed in dark-grown plants to associate with the phytochrome apoprotein.

The first and rate-determining step after haem synthesis is the synthesis of Biliverdin IXa by haem oxidases (HO), which are often encoded by small gene families (Emborg et al. 2006; Mahawar and Shekhawat 2018). Loss of the major HO in the hy1 mutant and thereby the synthesis of the chromophore for all phytochromes leads to a more chlorotic phenotype than a phyABDE quadruple mutant, implying that accumulation of biliverdin could have additional effects such as a feedback inhibition on ALA synthesis that than also reduces chlorophyll biosynthesis. The second step of the chromophore synthesis is mediated by the PΦB synthase, with SIG2 phytochrome-dependently coordinating its expression and thereby the accumulation of phytochromobilin (Kohchi et al. 2001; Oh and Montgomery 2013). The synthesised phytochromobilin is transported by unknown transporters into the cytoplasm where it assembles with the phytochrome apoprotein.

Isoprenoid biosynthesis in the plastids

The other pathway in the plastids that is important for photosynthesis-related pigments is the isoprenoid pathway leading to carotenoid biosynthesis. Carotenoids are integral accessory pigments in the light absorbing antenna, contributing to light harvesting and expanding the range of light quality that can be used for photosynthesis but also protect the photosynthetic apparatus from excess light (Simkin et al. 2022). Especially in the de-etiolation process, carotenoids play an essential photoprotective role minimising the potentially damaging effects of light on the photosynthetic machinery. Additionally, chlorophyllide needs to fuse with phytyl-PP, which is derived from the isoprenoid pathway, to form chlorophyll. Therefore, the production of carotenoids and chlorophylls has to be controlled in an interdependent manner, which in part is regulates by circadian gating of isoprenoid pathway genes thereby controlling the biosynthesis of chlorophyll and carotenoids (Toledo-Ortiz et al. 2010). Phytochrome-mediated light signals are major cues regulating carotenoid biosynthesis in plants, PIFs are involved in downregulating the accumulation of carotenoids in the dark, especially by repressing the PHYTOENE SYNTHASE, which is encoding for the rate-determining enzyme of carotenoid biosynthesis (Toledo-Ortiz et al. 2010). When PIFs are degraded by light and HY5 becomes available, carotenoids are rapidly synthesised to coordinate with chlorophyll biosynthesis, thus facilitating the assembly of functional photosynthetic machinery.

Adaptation to ambient light changes

Chloroplast establishment and development during de-etiolation or in newly developing leaves is imperative for initiating photosynthesis. Nevertheless, throughout their lifespan, plants must monitor changes in light conditions, including day-to-day circadian rhythm and adaptation to shade caused by their own upper leaves or neighbouring plants. The same key players will determine the growth, expression pattern, and photosynthetic performance through their equilibrium. One environmental condition in which light quality plays a major role is canopy shade (Martinez-Garcia and Rodriguez-Concepcion 2023). In leaves exposed to full sunlight, B and R light is absorbed by the chlorophylls and carotenoids for photosynthesis while most of the FR light is reflected (Ballare and Pierik 2017; Franklin 2008; Pierik and de Wit 2014; Ruberti et al. 2012; Vandenbussche et al. 2005). Reflected FR light allows plants to detect the density of a population (neighbour detection) via the phytochrome system (Pierik and de Wit 2014). Leaves or plants under a canopy perceive a reduced light intensity, depleted in UV-B, B and R wavelengths but still containing FR light causing a decrease in the R:FR ratio. The lower this R:FR ratio is the denser the canopy. Phytochromes sense this ratio and induce growth changes, with a distinction between plant species with Shade Avoidance Responses (SAR) from those with Shade Tolerance Responses. While shade-avoiding species use the SAR to escape and outgrow their competition, shade-tolerant species respond by measures to increase their survival rates under the dense canopy. The SARs result in elongation of stems and petioles, narrow leaf blades (by limiting cell division and expansion), thinner leaves, upward leaf movement (hyponasty), which promotes growth so that leaves could reach areas with more direct sunlight at the expense of reduced leaf area and a lower chl a/b ratio (Huber et al. 2021; Franklin 2008; Mullen et al. 2006; Pierik and de Wit 2014; Morelli et al. 2021). Adjustment of photosynthetic capacity can be observed in shade-avoiders as changes in photosynthesis-related gene expression, pigment accumulation, and chloroplast ultrastructure such as grana stacks that are thicker and have more layers (Morelli et al. 2021). This allows shaded leaves to fine-tune their photosynthetic machinery to function optimally under extremely low light conditions maintaining a positive carbon (Brouwer et al. 2014).

PhyB is the major player in SARs, while phyA mediates the negative feedback regulation of the SARs to prevent exaggerated responses to shade, especially under dense canopy and to discriminate shade events from night (Casal 2013). In the shade all photoreceptors are less activated, but due to the higher proportion of FR light in the shade phyA gets activated whereas phyB is ratio-dependently inactivated. This stabilises PIFs, which can then suppress the factors required for photomorphogenesis, such as GLK, impacting PhANG expression.

Not only is GLK expression reduced in shade, but also the now upregulated RPGE proteins inhibit the DNA-binding activity of GLK1 (Kim et al. 2023). For shadow-responses, the balance between HFR1 and PIFs, especially PIF7, seems to be important as HFR1 modifies SAS responses by forming heterodimers with PIFs and thereby disabling them (Hornitschek et al. 2009; Galstyan et al. 2011). In the shade‐tolerant Cardamine hirsuta HFR1 inhibits hypocotyl elongation in shade and represses shade‐induced genes. In contrast to the shade-avoiding Arabidopsis thaliana the HFR1 protein is more stable as it binds less efficiently to COP1 thereby attenuating PIF to a higher degree (Paulisic et al. 2021). PIF7 itself mediates epigenetic reprogramming by increased H3.3 incorporation into chromatin to promote the transcriptional response to shade in Arabidopsis (Yang et al. 2023). BBX21 and BBX22 were found to have a negative effect on SAR regulation, while BBX24 and BBX25 were found to promote it (Crocco et al. 2010; Gangappa et al. 2013; Saura-Sanchez et al. 2023).

Shade-tolerant species employ diverse strategies, but often increase their chances of survival by decreasing growth rates through reduced stem and petiole elongation in low light conditions, as well as by developing thinner leaves and a lower chl a/b ratio (due to increased activity of CAO), an increasing PSII/PSI ratio, thus elevating the maximum potential carbon gain (Lichtenthaler et al. 1981; Melis 1984; Niinemets et al. 1998; Biswal et al. 2012; An et al. 2022). In Camellina sinensis (tea) it was observed that chloroplasts in shaded leaves were more abundant, rounder and had bigger stacks of grana thylakoids (Liu et al. 2020). Furthermore, it could be shown that under shade PHYA, CRY1, GLK1 and LHCB expression was increased, whereas HY5 was decreased, and no changes for PIFs and COP1 could be seen. Genes encoding for proteins involved in chlorophyll biosynthesis were increased, including HEMA1, suggesting that tea is more a shade tolerant plant compared to Arabidopsis and shows the opposite behaviour (Liu et al. 2020).

Leaves below the canopy can be exposed to brief periods of high photon flux density (PFD) when light, due to gaps in the canopy or wind movement, penetrates. These so-called sunflecks lead to a significant increase in carbon uptake in the shaded understories of forests and in the lower sections of canopies or cereal crops (Way and Pearcy 2012; Kaiser et al. 2018, 2020; Long et al. 2022). Phytochromes and UVR8 sense these fluctuating light conditions, with the UV-B signal serving as a distinct indicator of sunlight that counters the consequences of shade avoidance responses (Ballare and Pierik 2017; Ballare and Austin 2019; Tavridou et al. 2020; Sharma et al. 2023). The UVR8 dimer/monomer ratio responds quantitatively and reversibly to the intensity of sunflecks (Moriconi et al. 2018). UV-light induced signal transduction helps then to avoid UV-B damage by increasing the expression of genes involved in photoprotection (Sellaro et al. 2011). The induction of HY5 expression by UVR8 suppresses then shade avoidance responses.

Light and temperature act synergistically as high light intensity usually leads to higher temperature but high light and cold temperatures or low light (as in shade) and high temperatures can be a challenge to maintain photosynthesis and can cause a problem with the carbon balance (Vasseur et al. 2011; Romero-Montepaone et al. 2020; Schwenkert et al. 2022). Both these environmental factors are interacting also on the level of photoreceptors. PhyB has been shown to be inactivated by higher temperatures, which leads to the stabilisation of PIF4. HMR and RCB are part of the stabilisation complex in the nucleus, which in turn activates thermo-responsive genes (Qiu et al. 2021). Additionally, the distribution of COP1 between cytosol and nucleus is light and temperature-dependent as light promotes nuclear export of COP1, whereas warm temperature and shade promote nuclear accumulation of COP1, leading to the degradation of the positive photomorphogenic factors such as HY5 (Pacin et al. 2014; Park et al. 2017).

Cold signalling is integrated by phyB through the positive regulation of freezing tolerance as cold-stabilised phyB modulates the expression, among others, of PIF genes (Kerbler and Wigge 2023). B light improves photosynthetic efficiency during prolonged exposure to cold and freezing temperatures by maintaining the expression of SIG5 through HY5 and HYH, ensuring the expression of psbD and psaC in the plastome. Additionally, gating by the circadian clock also plays a role in this process, suggesting that this mechanism protects plants on cold, bright mornings (Cano-Ramirez et al. 2023).

Regulation by photoreceptors is a multilayered process

Most of our knowledge how photoreceptors regulate gene expression is based on protein–protein interaction and the identification of transcription factors for specific cis-elements. Furthermore, there is growing evidence how a functional interplay between chromatin regulators and transcription factors regulate responses to the changing light environments (Wang et al. 2022). Several examples of links between photoreceptors and chromatin-status of genes important for chloroplast development or PhANGS have been identified (Patitaki et al. 2022). Nonetheless, this research is still at the beginning with more interdependencies to be discovered.

One level of regulation are the histone modifications. Histone H2A.Z is an evolutionarily conserved H2A variant, which plays essential roles in transcriptional regulation. The replacement of H2A with H2A.Z is catalysed by the SWR1 (SWI2/SNF2-RELATED 1 CHROMATIN REMODELING) complex. Photoactivated phyB and cry1 interact with the SWR1 complex subunits SWC6 and ARP6 (ACTIN-RELATED PROTEIN 6), promoting H2A.Z substitution at some loci and thereby regulating gene expression especially targeted by HY5 (Mao et al. 2021). PIFs remove H2A.Z by interaction with EIN6 ENHANCER (EEN), the Arabidopsis thaliana homolog of the chromatin remodelling complex subunit INO80 Subunit 6 (Willige et al. 2021). The R:FR ratio of shade de-phosphorylates PIF7 which then binds to its target genes and INO80 and induces H2A.Z removal leading to the transcription of the target genes. Activation of gene expression in the shade is accompanied by H3.3 enrichment, which is mediated by PIF7 recruiting the histone chaperone anti-silencing factor 1 (ASF1) and HIRA, a histone regulator, to the chromatin (Yang et al. 2023).

During dark-to-light transitions, the activation of photosynthetic genes correlates with histone acetylation changes (Charron et al. 2009; Bourbousse et al. 2012, 2019). A histone deacetylase, HDA15, interacts with PIF3, and decrease the acetylation levels of the target genes, thereby repressing chlorophyll biosynthesis and photosynthesis genes the dark. PIF3 and HDA15 are dissociated from the target genes upon exposure to R light (Liu et al. 2013). The HDA19 deacetylase is a negative regulator of the light signalling pathway and is involved in regulating PHYA expression by reducing H3K9 acetylation levels but also impacts other light-regulated genes such as RBCS and LHC (Jang et al. 2011). HDA19 is recruited by HY5 to the chromatin regions of HY5 and BBX22, thereby reducing the accessibility and repressing them (Jing et al. 2021). Furthermore, HDA19 forms a complex with the Mediator subunit MED25 and PIF1/PIF3 which target HDA19 to loci where histone acetylation is then reduced, therefore chromatin accessibility, one way how PIF1/PIF3 can repress transcription phytochrome-dependently (Guo et al. 2023).

The histone demethylase JUMONJI (JMJ)17 is important for the dark-to-light transition in etiolated seedlings as dark-grown seedlings of jmj17 accumulated a high concentration of Pchlide and are pale in light. JMJ17 and BRM, interacting with PIF1, bind promoters to demethylate H3K4me3 and in this way suppresses PORC expression in the dark which is released upon light exposure demonstrating how epigenetic markers play a role in fine-tuning chlorophyll biosynthesis (Zhang et al. 2017; Islam et al. 2021).

Phytochromes can further control protein localisation by alternative promoter selection or influence proteins, especially factors important for RNA splicing, phytochrome signalling (such as SPA3), the circadian clock, and photosynthesis by alternative splicing (Shikata et al. 2014; Ushijima et al. 2017; Careno et al. 2023).

Taken together, photoreceptors control gene expression of PhANGs and other chloroplast-related genes on multiple layers, which are still not entirely comprehended. These adjustments can integrate short- or long-term changes in the environment or daily cycles. Their importance can be illustrated by the coordinated regulation of chlorophyll biosynthesis and the production of chlorophyll-binding proteins, which guards against damage to the chloroplast. Additionally, these changes facilitate the assembling of essential multi-protein complexes required for photosynthesis (McCormac and Terry 2002a).

Concluding remarks and outlook

Photoreceptors have mostly undergone characterisation through the study of loss-of-function mutants, particularly in Arabidopsis thaliana, over the last few decades. These studies have primarily focused on their physiological roles, but there is increasing data on how they affect photosynthesis and a clearer picture of the regulatory network between light perception and the effect on photosynthesis is forming. As chloroplasts are becoming recognised as key players in many adaptive processes (Garcia-Molina et al. 2020; Schwenkert et al. 2022), this knowledge adds another layer of information, helping to understand how chloroplasts are linked to nuclear processes – a regulation that evolved due to the endosymbiotic event. Understanding the function of photoreceptors under various light qualities is vital for comprehending natural processes and studying different adaptation strategies found in a diverse range of plants. Factors important for optimising photosynthesis include not only direct changes in gene expression, but also additional regulation levels through mechanisms such as chromatin modifications, protein stability, controlled degradation to inactivate signal transduction, and protein-protein interactions that can activate or inactivate signalling events. Complexity arises because this regulation affects at least two cell compartments: the nucleus and the chloroplast. Changes in gene expression not only affect genes directly involved in the photosynthetic apparatus or pigment biosynthesis, but also impact chloroplast development, positioning processes, and growth adaptations at the organ level. On all levels, photoreceptors have been shown to impact these developmental processes, emphasising the role of light quality and intensity in coordinating this complex process. However, much more research is needed to fully understand how the signalling pathways are intertwined.

Additionally, knowledge of this interplay holds significance for horticulture as the application of LED combinations for crop cultivation continues to increase. The spectral composition of LED lighting can be optimised to enhance photosynthetic performance, producing high yields. Nevertheless, the impact of light on signalling molecules is frequently disregarded. However, light signals perceived by photoreceptors can potentially direct plant development towards desired phenotypes by influencing the development of chloroplasts and allocation of photosynthetic products. This necessitates comprehensive knowledge of how light quality impacts different developmental processes in different species.

Acknowledgment

The authors would like to thank Dario Leister for his support.

Disclosure statement

No potential conflict of interest was reported by the author(s).