Light-sensing toolkit of cyanobacteria: photoreceptors, signaling and photomorphogenesis

Introduction

Light is a fundamental environmental factor governing the physiology, development, and ecological distribution of cyanobacteria and other phototrophs. It serves a dual role: acting as the primary energy source for carbon fixation and as a critical environmental stimulus (Wu et al., 2025). In photoautotrophic cyanobacteria, these signals allow precise regulation of growth, development, morphology, and stress responses in alignment with the prevailing light environment (Gupta et al., 2026; Tiwari et al., 2025).

Cyanobacteria perform oxygenic photosynthesis, utilizing photons to excite chlorophyll molecules within photosystems I and II (Gisriel, 2024). This photochemistry drives the electron transfer to produce ATP and NADPH, which subsequently power carbon dioxide fixation via the Calvin–Benson–Bassham cycle (Liu, 2016). Because energy capture efficiency is governed by light intensity, spectral quality, and photoperiod, light availability directly regulates growth and global primary productivity. For example, the unicellular genera Prochlorococcus and Synechococcus contribute to 20–40% of contemporary marine primary production, highlighting their essential role in global biogeochemical cycles (Sánchez-Baracaldo, 2015; Moore et al., 2019). Beyond carbon fixation, many cyanobacteria utilize nitrogenase to convert atmospheric nitrogen into bioavailable ammonia (Nawaz et al., 2024). This dual metabolic capacity integrates the carbon and nitrogen cycles, establishing cyanobacteria as ecological keystones in both ancient and modern environments (Lucius and Hagemann, 2024).

Beyond energy transduction, light serves as a vital signaling cue, prompting cyanobacteria to sense and acclimatize to the fluctuating environmental conditions. These microbes possess a variety of specialized photoreceptors that monitor quality and quantity of light (Rockwell and Lagarias, 2024; Mullineaux, 2001). For instance, to optimize light-harvesting efficiency under shifting spectral conditions, the green/red-sensing photoreceptor RcaE in Fremyella diplosiphon regulates chromatic acclimation (CA). CA drives the dynamic remodeling of the phycobilisomes (PBSs), the primary light-harvesting antenna complex, in response to light quality (Kehoe and Grossman, 1996; Wiltbank and Kehoe, 2019). Thus, activation of photoreceptors trigger signaling cascades that modulate gene expression, metabolic flux, and broader physiological responses in cyanobacteria.

Additionally, cyanobacterial light responses are highly relevant to biotechnology, as the ability to modulate photosynthetic efficiency directly impacts the synthesis of high-value metabolites, biomass accumulation, and biofuel production (Pandey et al., 2025; Montgomery, 2014; Majhi, 2025). Given their ecological significance and evolutionary adaptations, further investigation into light-dependent responses is essential to unlock their full potential for sustainable biotechnology. This review integrates molecular, physiological, and ecological insights to provide a comprehensive framework for future research in photobiology and applied cyanobacterial systems. By synthesizing well-established mechanisms and identifying critical knowledge gap, we aim to provide a roadmap for advancing both our fundamental understanding and the practical applications of these organisms.

Photoreceptors: coordinating light perception and cellular responses

The light-sensing network comprises specialized photoreceptors utilized by plants, algae, and various microorganisms to monitor specific wavelengths (Elahi and Baker, 2024). Cyanobacteria possess a sophisticated sensory repertoire that facilitates rapid physiological adjustment to fluctuating light regimes, enabling them to thrive across diverse ecological niches. Phytochromes, for instance, are chromophore-binding proteins specialized for sensing shifts in light quality (Oliinyk et al., 2017; Li et al., 2023; Montgomery and Lagarias, 2002). These receptors modulate critical processes such as pigment composition, cellular morphology, and motility utilizing signal transduction pathways involving two-component kinase systems (Gupta et al., 2023; Gutu and Kehoe, 2012). Once light is detected, sensory domains transmit signal to response regulators or secondary messengers, which subsequently trigger targeted physiological responses (Gupta et al., 2023). This intricate molecular architecture not only ensures survival in nature but also offers significant potential for optogenetic and biotechnological applications. The following sections provides a comprehensive examination of the specific photoreceptors found in cyanobacteria.

Cyanobacterial phytochromes

Cyanobacterial phytochromes (Cphs), like their plant counterparts, represent a broad class of photochromic bilin-binding photoreceptors. Their photosensory core module is composed of Per/ARNT/Sim (PAS), cGphosphodiesterase/adenylate cyclase/FhlA (GAF), and Phytochrome (PHY) domains; specifically, the GAF domain binds a bilin chromophore, while the PAS and PHY domains provide billin lyase activity and stabilize the photostate (Rockwell and Lagarias, 2010, 2017; Montgomery and Lagarias, 2002). The bilin chromophore attaches through thioether linkage to a conserved cysteine residue of GAF domain (Rockwell and Lagarias, 2017). Based on domain arrangement, the phytochrome superfamily is divided into three distinct groups. The Group I, classical phytochromes, has peculiar ‘knotted’ PAS-GAF-PHY tri-domain structure, and is widely distributed among plants, cyanobacteria and other bacteria. Group II lacks a PAS domain, consisting only of the GAF-PHY domains. Group III (cyanobacteriochromes, CBCRs) are unique to cyanobacteria and will be discussed in detail in subsequent sections (Rockwell and Lagarias, 2024; Oliinyk et al., 2017).

The model cyanobacterium Synechocystis sp. PCC 6803 encodes several phytochrome homologs, including the classical Cph1, Cph2 and PlpA (Montgomery and Lagarias, 2002). Cph1 exhibits reversible red/far-red photoresponse and functions as a light-regulated kinase that transfers phosphate groups to its cognate response regulator Rcp1 (response regulator for cyanobacterial phytochrome) (Psakis et al., 2011). In contrast, Cph2 perceives blue-green light and lacks canonical histidine kinase activity. Instead, it utilizes GGDEF and EAL domains to modulate cyclic-di-GMP levels in a light-dependent manner (Moon et al., 2011). Furthermore, the phytochrome-like protein PlpA is essential for blue light-dependent growth regulation (Lamparter et al., 1997; Wilde et al., 1997).

In Anabaena, the red/far-red photoreceptor AphC contains three GAF domains, two of which possess conserved cysteine residues required for covalent bilin chromophore attachment. AphC possess a histidine kinase domain that couples far-red light perception to a signaling relay involving the CyaC cyclase, ultimately modulating intracellular cAMP levels (Rockwell et al., 2011; Okamoto et al., 2004). Structural investigations have further demonstrated that a conserved tyrosine residue within the GAF domain of AphC is critical for photoisomerization, facilitating the chromophore’s configurational change in response to light (Ulijasz et al., 2010). Consequently, these photoreceptors function as molecular switches, regulating downstream outputs based on the relative proportions of red and far-red light as detected by their chromophores.

Cyanobacteriochromes: spectral tuning and photocycle dynamics

CBCRs are unique and widespread light-sensing proteins found exclusively in cyanobacteria. These chromoproteins facilitate the perception of an expansive spectral range, spanning from near-ultraviolet to near-infrared wavelengths (Rockwell and Lagarias, 2024; Ikeuchi and Ishizuka, 2008). This remarkable spectral diversity is achieved through the covalent attachment of phycocyanobilin (PCB), a linear tetrapyrrole chromophore. The biosynthesis of PCB from biliverdin IXα is catalyzed by the pcyA-encoded enzyme phycocyanobilin:ferredoxin oxidoreductase (Frankenberg and Lagarias, 2003). Unlike classical phytochromes, which typically require a PAS-GAF-PHY tri-domain architecture, CBCRs often utilize a single GAF domain for light absorption by chromophore attached to cysteine residue through thioether linkage (Villafani et al., 2020; Nagae et al., 2021, 2024; Ikeuchi and Ishizuka, 2008). Upon light absorption, the covalently bound bilin undergoes reversible photoisomerization 15Z to 15E through configurational change around C15 and C16 double bond (Figure 1). This configurational change alters absorption characteristics and triggers downstream signaling (Hirose et al., 2013; Nagae et al., 2021, 2024). CBCRs are coupled to various C-terminal output domains, including histidine kinases, methyl-accepting chemotaxis proteins, and cyclic nucleotide-modulating enzymes (e.g., GGDEF and EAL domains). Through these diverse signaling modules (Figure 1), CBCRs regulate critical cellular processes such as phototaxis, cell aggregation, CA, and the modulation of intracellular c-di-GMP levels (Enomoto et al., 2015; Kirpich et al., 2018; He et al., 2018; Fukushima et al., 2011).

The CBCRs are categorized into different subfamilies based on chromophore, primary sequence elements and mechanism of photochromic shift in the chromophore (Fushimi et al., 2016; Ikeuchi and Ishizuka, 2008). Several CBCRs are known till date, containing dual cysteine residues, one canonical cysteine and second cysteine residue residing in conserved Aspartate-Xaa-Cysteine-phenyalanine (DXCF) motif of the CBCRs (Hoshino and Narikawa, 2023). The second Cys covalently binds through thioether linkage to the C10 carbon of the chromophore. The 15Z configuration of chromophore binds to first cysteine through C3 of A ring and second cysteine binds to the C10 carbon of the chromophore (Hoshino and Narikawa, 2023). The photoisomerization of 15Z to 15E enable releasing of the thioether linkage between C10 and DXCF Cys. This results in a larger difference in the light absorption of the two states of the CBCRs (Hoshino and Narikawa, 2023; Nagae et al., 2021, 2024). The other class of CBCRs contain DXCIP motif lacking canonical cysteine (Hoshino and Narikawa, 2023). There are several CBCRs exhibiting wide spectral shift for sensing blue/green, red/green, blue/orange, ultraviolet/blue light (Rockwell and Lagarias, 2024). Table 1 summarizes different photoreceptors found in cyanobacteria with their categorization, chromophores, and response/catalytic domain.

Table 1. Cyanobacterial photoreceptors to sense and acclimatize different light conditions.

Cph, Cyanobacterial phytochromes; Rfp, Red/Far-Red phytochrome; Plp, Phytochrome-like protein; Aph, Anabaena Phytochrome-like photoreceptor; Rca, Regulator of chromatic acclimation; Cca, Complementary chromatic acclimation; Cik, Circadian input kinase; Ses, Sessility; Ptx, Phototaxis; Pix, Phototaxis; CyHR, Cyanobacterial halorhodopsins; CyR, Cyanorhodopsin; DGC, Diguanylate Cyclase; PDE, Phosphodiesterase; MCP, Methyl accepting Chemotaxis Protein; HAMP, Histidine kinases Adenylate cyclases Methyl accepting Proteins; LOV, Light Oxygen Voltage domain; PHR, Photolyase related domain; MTHF, Methyltetrahydrofolate; NA, Categorization not available.

Cyanobacteria utilize species-specific CBCR-mediated mechanisms to facilitate phototaxis in response to quantity and quality of light (Figure 2). For instance, Synechocystis sp. PCC 6803 relies on PixJ and UirS, to coordinate both positive and negative phototaxis, while Nostoc punctiforme employs PtxD to regulate hormogonium motility. Similarly, Synechococcus elongatus utilizes PixJ (also known as TaxD1) for phototaxis (Yoshihara et al., 2000; Song et al., 2011; Campbell et al., 2015). Beyond motility, CBCRs and related phytochrome-like proteins regulate structural and metabolic adjustments (Table 1). The CBCR RcaE, first identified in Fremyella diplosiphon, is a master regulator of CA (Conley et al., 1988). RcaE possesses a covalently attached phycocyanobilin (PCB) chromophore to a conserved cysteine residue which sense red (Pr form) and green (Pg form) light ratio (Figure 2). The photoisomerization of chromophore together with protonation and deprotonation events are critical signal for sensing light color and driving CA in F. diplosiphon (Kehoe and Grossman, 1996; Kamo et al., 2025; Nagae et al., 2021, 2024). In Synechococcus elongatus PCC 7942, the circadian clock controls global gene expression in response to diurnal cycles. The KaiABC oscillator is synchronized by CikA, a GAF-containing protein that acts alongside KaiA as a redox sensor for the quinone pool (Ivleva et al., 2006; Mutsuda et al., 2003; Swan et al., 2018). This sensory integration allows the circadian clock to reset during light-to-dark transitions. Collectively, these sophisticated signaling proteins enable cyanobacteria to remain highly adaptable, rapidly converting environmental light cues into diverse photobiological responses.

In addition to above mentioned CBCRs, the novel red/green CBCR, Slr1393, has been discovered recently in Synechocystis sp. PCC 6803 that contain three GAF domain and one histidine kinase domain at its C-terminal. Similar to other CBCRs, Slr1393 has PCB chromophore attached to third GAF domain and attain conformational change under red-green light around C15=C16 of chromophore. The dark (Pr, absorb red light) and photoactive (Pg, absorb green light) states of chromophore has a chromic shift of 116 nm to succeed the response to prevailing light environment (Xu et al., 2020; Köhler et al., 2023).

Rhodopsin-mediated photoresponse in cyanobacteria

Rhodopsins are a family of seven helical membrane-bound photoreceptors that utilize a retinal chromophore for light absorption and energy transduction (Hasegawa-Takano et al., 2024). The retinal chromophore undergoes a cis-trans conformational change in response to light signal to catalyze functional output of rhodopsin. Though the information on cyanobacterial rhodopsin is quite limited, these photosensors are divided into two clades, i.e., cyanobacterial halorhodopsins (CyHR) and cyanorhodopsin (CyR). Recently, a new clade has been identified namely, cyanorhodopsin-II, which function as a light-driven outward proton (H⁺) pump (Hasegawa-Takano et al., 2024). In Anabaena (Nostoc) sp. PCC 7120, an operon was identified containing several open reading frames, including genes encoding a green-light-activated sensory rhodopsin and a small 14 kDa soluble protein hypothesized to function as a signal transducer (Hasegawa et al., 2020). Under illumination at 549 nm and 537 nm, the rhodopsin exists in two photointerconvertible stable isoforms characterized by distinct retinal configurations (all-trans and 13-cis). This light-driven interconversion suggests a regulatory role in light-sensing (Hasegawa-Takano et al., 2024). Functional studies in heterologous systems have shown that while cyanobacterial rhodopsin forms a functional retinal-binding photoreceptor in Escherichia coli, co-expression with the 14 kDa protein significantly enhances the light-induced response (Hasegawa et al., 2020). This synergy suggests that the small soluble protein is a direct mediator of rhodopsin-dependent signaling. Consequently, cyanobacterial rhodopsin may function analogously to phytochromes, acting as light-sensitive regulators that modulate gene expression in response to environmental cues.

Spectral tuning in cyanobacteria

Blue-green-teal light responses

Blue-light perception is primarily mediated by cryptochromes, phototropins, and Blue-Light-Using FAD domain-containing proteins (BLUF) (Table 1; Gupta et al., 2023). A putative cryptochrome identified in Synechocystis is flavin-containing photoreceptor that lacks typical light-activated photolyase activity known as cryptochrome Drosophila, Arabidopsis, Synechocystis, Homo (DASH). Despite this, it exhibits high structural homology to DNA-binding photolyases, suggesting a role in DNA interaction and transcriptional regulation (Hitomi et al., 2000; Brudler et al., 2003). Another major class of blue-light sensors utilizes the conserved BLUF domain, which is widespread across bacteria and cyanobacteria. A prominent example is PixD (slr1694) in Synechocystis sp. PCC 6803, which regulates phototactic behavior (Hahn et al., 2006). Although PixD lacks a canonical output domain, yeast two-hybrid assays have demonstrated its direct interaction with the response regulator PixE (Okajima et al., 2005).

The first crystal structure of a cyanobacterial BLUF domain, resolved for Tll0078 (TePixD) from Thermosynechococcus elongatus BP-1, showed an intramolecular hydrogen-bonded FAD chromophore. In this architecture, the conserved residues Gln50 and Tyr8 are essential for mediating blue light-driven photochemistry (Okajima et al., 2006). The Synechocystis PixD structure exhibit high homology to TePixD, further confirming the functional roles of these conserved Gln and Tyr residues. Additionally, structural analysis identified Trp91 as a light-responsive residue that interacts with the flavin and undergoes a significant conformational rearrangement upon illumination (Yuan et al., 2006). Through these precise molecular shifts, BLUF proteins regulate diverse physiological processes in cyanobacteria, including photosystem stoichiometry, phototaxis, biofilm formation, and light avoidance. Furthermore, BLUF proteins modulate the levels of cyclic di-GMP, a key regulator of cellular motility and biofilm development (Enomoto et al., 2023; Jenal et al., 2017).

Cyanobacteria also utilize phototropin-like receptors containing LOV (light/oxygen/voltage) domains (Table 1), which are specialized subset of the PAS domain superfamily (Crosson et al., 2003). The first prokaryotic phototropin-related protein identified was YtvA from Bacillus subtilis, which binds flavin mononucleotide (FMN) and exhibits photochemical properties analogous to those of plant phototropins (Losi et al., 2002). In cyanobacteria, LOV domains are often integrated into complex multi-domain signaling proteins. For example, Slr0359 in Synechocystis sp. PCC 6803 features a modular architecture comprising LOV, GAF, GGDEF, and EAL domains, suggesting a sophisticated integration of multiple environmental signals (Fiedler et al., 2005). Similarly, Anabaena sp. PCC 7120 encodes several LOV-containing proteins coded by alr1229, all2875, and alr3170 genes (Ohmori et al., 2001). The LOV domains of All2875 and Alr3170 bind FMN and undergo blue light-dependent photocycles facilitated by a conserved cysteine residue essential for photoactivity (Narikawa et al., 2006).

In Thermosynechococcus vulcanus (Figure 2), the CBCRs SesA, SesB, and SesC constitute a light-responsive network that controls cell aggregation via c-di-GMP signaling (Enomoto et al., 2015, 2018). Under blue light, SesA functions as a diguanylate cyclase, increasing intracellular c-di-GMP concentrations to promotes cell aggregation (Enomoto et al., 2014). Conversely, SesB is responsive to teal light and primarily exhibit phosphodiesterase activity; it reduces c-di-GMP levels to inhibit aggregation (Enomoto et al., 2015). The network’s sensitivity is further refined by SesC, which modulates c-di-GMP levels in a wavelength-dependent manner, increasing the messenger under blue light and decreasing it under green light (Enomoto et al., 2015). This coordinated regulatory circuit facilitates the precise control of aggregation and photosynthetic activity, allowing the organism to adapt rapidly fluctuating light regimes.

Ultraviolet radiation sensing in cyanobacteria

Cyanobacteria exhibit several UV-B-dependent behavioral responses, including photosystem stoichiometry rearrangement in Synechococcus elongatus PCC 7942 (Campbell et al., 1998) and various photoavoidance strategies (Montgomery, 2007). In Synechocystis sp. PCC 6803, UV-A-induced phototaxis is regulated by the CBCRs PixJ1 (TaxD1) and Cph2, alongside the ETR1-related UV intensity sensor, UirS (Fiedler et al., 2005; Song et al., 2011; Moon et al., 2011; Moon et al., 2012). UirS is a membrane-bound photoreceptor (Figure 2) that mediates light-avoidance by detecting UV-A signals and initiating a phosphorylation cascade to activate the response regulator LsiR (Song et al., 2011). Cph2 inhibits positive phototaxis under low-intensity UV-A, whereas PixJ1 stimulates positive phototactic movement in response to both UV-A and blue light (Moon et al., 2011; Yoshihara et al., 2000; Moon et al., 2012). Beyond behavioral adjustments, cyanobacteria synthesize photoprotective compounds such as mycosporine-like amino acids (MAAs) and scytonemins to mitigate UV-induced damage. While the biosynthetic pathways for these industrially relevant compounds are well characterized, the specific sensory proteins responsible for UV-B perception (280–320 nm) remain unidentified, though the existence of a specialized UV-B photoreceptor has been proposed (Portwich and Garcia-Pichel, 2000).

Photosynthetic electron transport chain as a redox signaling hub

While photoreceptors physically perceive light through structural conformational changes that trigger transcriptional regulation (Rockwell and Lagarias, 2024), the photosynthetic electron transport chain (PETC) functions as a chemical sensor of light quality and quantity. Fluctuations in the redox state of PETC components serve as primary stimuli for the retrograde signaling that controls gene expression (Ritter et al., 2020). The redox poise of PSII and PSI is governed by the flux of electrons through the thylakoid-bound carriers (Gu, 2023). Linear electron transport involves the coordinated action of PSII, the Cytb₆f complex, mobile electron carriers (PQ and PC), PSI, Fd, and FMN. This pathway facilitates electron transfer along a redox potential gradient to generate the strong reductant NADPH and a proton motive force across the thylakoid membrane to drive ATP synthesis (Rochaix, 2011; Tiwari et al., 2025). Within the PETC, the photo-excited reaction center of PSII and PSI generate highly negative reduction potentials, facilitating the spontaneous downhill movement of electrons through successive redox pairs (Gu et al., 2023). Consequently, any imbalance in the efficiency of these complexes, often caused by light stress, acts as a sensory signal. This redox poise activates a variety of responses including, activation of repair mechanisms, photoprotective quenching, or the structural remodeling of the photosynthetic apparatus (Gollan and Aro, 2020).

The thylakoid membrane serves as a dynamic hub for light-driven redox reactions. Deviations from the optimal redox state of the thylakoid components trigger distinct signaling cascades designed to restore optimal reduction potential (Gu et al., 2023). This redox status is highly sensitive to fluctuations in light intensity, particular under high-light stress. Key components within the PETC, specifically the primary electron acceptor of PSII (Q_A⁻), PQ pool, and Fd, function as putative sensors that monitor these shifts in thylakoid redox potential (Ritter et al., 2020; Wilde and Hihara, 2016). The change in thylakoid redox potential and the generation of reactive oxygen species (ROS) by PETC serve as primary sensory inputs that activate redox-signaling pathways in cyanobacteria (Ritter et al., 2020). Specifically, the redox poise of the PQ pool regulates a diverse array of photosynthesis-related genes. In Synechococcus elongatus PCC 7942, the oxidation state of the PQ pool is a critical regulator of the circadian clock (Cohen and Golden, 2015; Kim et al., 2012). Consequently, the transcription of numerous genes involved in photosynthesis and cell division genes is strictly dependent on the redox status of PQ pool (Ivleva et al., 2006; Wood et al., 2010; Miyagishima et al., 2005; Li and Sherman, 2000). The KaiA component of the KaiABC circadian oscillator senses the oxidized state of the PQ pool, subsequently driving the temporal expression of photosynthesis and cell division genes (Fang et al., 2025). This regulation is mediated via the SasA-RpaA two component system, where the sensory protein SasA interacts with its cognate response regulator RpaA, to regulate global transcription rhythms (Takai et al., 2006).

The accumulation of reduced PQ (PQH₂) serves as a proxy for oxidative stress, reflecting accelerated electron trafficking within the PETC under high light conditions. This state leads to the formation of superoxide and hydrogen peroxide radicals which can compromise the structural integrity of the thylakoid membrane (Ritter et al., 2020). These shifts in thylakoid redox potential are perceived by global stress-responsive sensor kinase Hik33 in Synechocystis sp. PCC 6803 and NblS in Synechococcus elongatus PCC 7942 (Kanesaki et al., 2007; van Waasbergen et al., 2002). Hik33 is a sensor histidine kinase that monitors redox status likely through its PAS domain to regulate the expression of high-light-inducible genes such as hliA, hliB, rpoD3 and nblA (Figure 3). This regulation is coordinated with the response regulator RpaB (Kadowaki et al., 2016). It acts as a transcriptional repressor by binding to High Light Response 1(HLR1) sequences located upstream numerous photosynthesis-related genes (Kappell and van Waasbergen, 2007; Seki et al., 2007; Seino et al., 2009; Hanaoka and Tanaka, 2008; Kato et al., 2011). The signaling state of this system is governed by light intensity: under low light, Hik33 remains unphosphorylated, and RpaB exist in unphosphorylated state, binding to the upstream regulatory regions of high-light-responsive genes to inhibit their expression (Rachedi et al., 2020). However, activation of Hik33 under high light phosphorylates RpaB (Figure 3); resulting its release from the promoter regions and subsequent induction of high-light-responsive genes (Kato et al., 2022).

Signal transduction: two-component systems and second messengers

Signal transduction in cyanobacteria relies on a framework of two-component systems and chemotaxis-like cascades mediated through second messengers, including c-di-GMP, cAMP, and Ca²⁺. This integrated architecture enables these organisms to rapidly detect and respond to fluctuating environmental conditions (Montgomery, 2007; Gupta et al., 2023). A canonical two-component system consists of sensor histidine kinase (HK) and a cognate response regulator (RR). Upon perceiving environmental stimulus, the HK undergoes autophosphorylation at a conserved histidine residue. Subsequently, the HK transfers this phosphate group to an aspartate residue on the receiver domain of the RR (Römling et al., 2005). These RRs often possess modular C-terminal output domain such as KEGG, SENTRA, COG, GGDEF, and EAL that control gene expression, motility and stress response (Römling et al., 2005). In some cyanobacterial models, including Nostoc punctiforme, S. elongatus PCC 7942, systems such as Hik2-Rre1 and NblS-RpaB serve as master regulator (Wilde and Hihara, 2016). These systems integrate light and redox signals to modulate the photosynthetic machinery and coordinate response to salt and osmotic stress (Ibrahim et al., 2016; Tsurumaki and Tanaka, 2025).

In several cyanobacteria, GGDEF and EAL domains function as light-regulated enzymatic modules that modulate intracellular c-di-GMP levels. The prevalence of these domains suggests that c-di-GMP serve as a critical second messenger in diverse light-signaling pathways, including those controlling cell size, aggregation, phototaxis, and complex developmental processes such as heterocyst differentiation (Enomoto et al., 2023; Zeng et al., 2023; Enomoto et al., 2014). In addition to c-di-GMP, cyclic AMP (cAMP) acts as a pivotal signaling molecule, particularly filamentous cyanobacterium in Anabaena cylindrica. Its intracellular concentration is highly sensitive to light quality; cAMP levels increase rapidly under far-red light and decrease significantly in response to red light (Ohmori et al., 2002). This wavelength-dependent flux suggests a direct link between the light signaling and the metabolic tuning of the cell.

Furthermore, cyanobacteria utilize calcium ions (Ca²⁺) as a vital second messenger. In Synechocystis sp. PCC 6803, the ability of cells to orient and migrate towards light is strictly dependent on Ca²⁺ flux (Moon et al., 2004). Notably, Ca²⁺ in particular has the ability to directly modulate adenylate cyclase activity, thereby influencing the synthesis of cAMP in response to environmental stimuli. Through the sophisticated coordination of c-di-GMP, cAMP, and Ca²⁺ signaling cascades, cyanobacteria can precisely fine-tune their motility, photosynthetic capacity, stress tolerance, and complex developmental transitions (Ohmori et al., 2002; Ohmori and Okamoto, 2004; Terauchi and Ohmori, 2004).

Light spectrum-driven photobiological responses

Cyanobacteria employ variety of strategies to optimize photosynthetic efficiency and ecological fitness under varying light regimes. Acclimation to these regimes represents one of the most essential and intricate physiological responses, allowing organisms to navigate shifts in both spectral quality and irradiance intensity (Gupta et al., 2023; Mondal et al., 2024). A primary acclimation strategy involves the dynamic control of photosystem stoichiometry, adjusting PSII/PSI ratio, to ensure efficient electron flux and maintain thylakoid redox equilibrium (Mullineaux, 2014). Furthermore, many cyanobacteria utilize CA, a phenomenon of antenna remodeling. CA involves altering the pigment composition of the PBS light-harvesting complexes to optimize photosynthetic efficiency based on the prevailing light wavelengths (Mondal et al., 2024; Gupta et al., 2023). Consequently, spectrum exerts a profound influence on both pigment composition and photosystem ratios. These interconnected adjustments ensure effective distribution of excitation energy, allowing cyanobacteria to sustain robust photosynthetic performance while mitigating the risk of photodamage across diverse aquatic and terrestrial light environments.

Light-dependent adjustment of photosystem stoichiometry

Cyanobacteria possess remarkable plasticity in regulating the stoichiometry of PSII relative to PSI. This regulation is essential for maintaining the redox equilibrium between the PQ pool and downstream electron acceptors (Calzadilla and Kirilovsky, 2020; Van Stokkum et al., 2025). The relative abundance and operating efficiency of these complexes are modulated by light quality, irradiance intensity, and nutrient availability (Tiwari et al., 2025). Cyanobacteria balance their excitation energy by physically shifting (state transitions) PBSs between PSII and PSI (Van Stokkum et al., 2025). The absorbed light energy is transferred by PBSs to the reaction center of the photosystem; in state 1, light energy is channeled to PSII, whereas in state 2, the energy is diverted to PSI (Kirilovsky, 2015; Zhang et al., 2024). Beyond these rapid shifts, long-term acclimation involves a fundamental reorganization of PSI: PSII ratio, which typically ranges from 5:1 to 2:1 in cyanobacteria. For examples, Synechocystis sp. PCC 6803 maintains a two- to fivefold excess PSI relative to PSII. This is higher than the 1:1 to 1:2 ratios observed in plants or the approximately 1:1 ratio typical of most eukaryotic phototrophs (Shen et al., 1993; Murakami, 1997; Kirilovsky, 2015).

Luimstra et al. (2018) demonstrates that spectral quality is a primary determinant of photosystem stoichiometry. Cyanobacteria exhibit significantly higher growth rates under orange or red light compared to blue light. This physiological advantage arises from the absorption spectra of phycobiliproteins (PBPs); the component of PBSs, which efficiently capture orange and red wavelengths and channel the excitation energy toward PSII. Under these conditions, the subsequent reduction of PQ pool triggers state 2 transition. To maintain redox equilibrium and compensate for the high PSII excitation, cyanobacteria typically increase their PSI: PSII ratio (Luimstra et al., 2018). In contrast, blue light preferentially excites PSI in cyanobacteria. Because PBPs lack significant absorption in the blue region of the spectrum, blue light exposure creates an excitation imbalance: an energy surplus at PSI and a concomitant deficit at the PSII side of the PETC (Luimstra et al., 2018; Mullineaux, 2014). To counteract this imbalance, the cells initiate a state 1 transition, where the PBSs associate with PSII to maximize light-harvesting capacity for the under-excited reaction center. Consequently, the PSI: PSII ratio is notably lower in blue-light-acclimated cells compared to those grown under longer wavelengths (Luimstra et al., 2018).

The PSII/PSI ratio is highly sensitive to fluctuating environmental parameters beyond spectral quality. Under low-intensity or far-red light, cyanobacteria promote the accumulation of PSI to maximize light-harvesting capacity and electron transport. However, high-light exposure often leads to a reduction in the PSI: PSII ratio. By limiting PSI abundance, the cell effectively restricts the potential for excessive ROS generation and subsequently photodamage (Dobson et al., 2021; Kopečná et al., 2012). Nutrient availability, particularly iron, impose a constraint on these stoichiometric adjustments. PSI is an iron-intensive complex, and therefore, iron limitation results in a marked decrease in PSI abundance, disrupting photosynthetic stoichiometry. To mitigate this loss, cyanobacteria induce the expression of the iron-stress-induced protein, IsiA. This protein forms a light-harvesting ring around remaining PSI cores, effectively increasing the functional antenna size. This structural adaptation partially compensates for the reduction in total PSI content (Nagao et al., 2023). Thus, the regulation of photosystem stoichiometry is a multi-modal process influenced by the interplay of light intensity and nutrient status. These integrated responses allow the photosynthetic apparatus to remain robust and adaptive under dynamic environmental conditions.

Photosystem stoichiometry in cyanobacteria is primarily governed by the redox state of the PQ pool. This metabolic signal integrates multiple environmental inputs, including irradiance intensity, spectral quality, and nutrition availability (Schuurmans et al., 2014). The signal transduction pathway is mediated by a two-component regulatory system. The change in PQ redox state is detected by the histidine kinase Hik2, a homolog of the chloroplast sensor kinase (CSK). It autophosphorylate and transfer the phosphate group to the cognate response regulators, Rre1 and RppA (Ibrahim et al., 2016; Bairagi et al., 2022). Phosphorylated RppA regulate the expression of photosystem core genes, thereby balancing excitation energy distribution and optimizing electron flux between PSII and PSI through stoichiometric adjustments (Ritter et al., 2020). Concurrently, Phosphorylated Rre1 activates the transcription of genes encoding PBSs components, facilitating antenna remodeling (Ibrahim et al., 2016; Li and Sherman, 2000). In addition to its role in stoichiometry, RppA serve as a global regulator of pigment biosynthesis. Under high-light stress, RppA modulates the synthesis of chlorophyll, carotenoids, PBPs, and PSI subunits (Yu et al., 2025). This coordinated regulation of photosynthetic apparatus minimizes the production of singlet oxygen and other ROS, thereby protecting the cell from photo-oxidative damage.

Chromatic acclimation: tailoring light-harvesting systems to spectral shift

Photomorphogenesis is a dynamic process through which organisms respond to a changing photoenvironment by adjusting cellular metabolism, growth, and development (Mondal et al., 2024; Gupta et al., 2023). Cyanobacteria exhibit significant physiological plasticity, adjusting their photosynthetic efficiency to optimize productivity and fitness across diverse light regimes (Tiwari et al., 2025). In aquatic environments, both the intensity and spectral quality of light vary dramatically with depth. Surface waters are typically characterized by a prevalence of red light, whereas shorter wavelength, such as green light, penetrates deeper into the water column (Sanfilippo et al., 2019). To navigate these light gradients, several cyanobacteria have evolved sophisticated adaptation and/or acclimatization strategies to maximize the capture of available photons (Kehoe and Gutu, 2006; Singh et al., 2010; Singh and Montgomery, 2011). The most prominent form of photomorphogenesis in cyanobacteria is CA. This phenomenon allows cyanobacteria to dynamically remodel their photosynthetic pigment composition in response to light cues, ensuring optimal light-harvesting efficiency and competitive fitness under varying spectral conditions (Mondal et al., 2024; Montgomery, 2016).

CA is reversible and ecologically important phenomenon first documented in the filamentous cyanobacterium Oscillatoria sancta (Gaidukov, 1902). This landmark study demonstrated that cyanobacteria can undergo dramatic color change in response to the spectral quality of ambient light by modulating the composition of their primary light harvesting complexes, the PBSs (Bennett and Bogorad, 1973).

Phycobilisomes remodeling in response to spectral changes

The PBS is the primary light harvesting antenna for PSII in cyanobacteria. These macromolecular complexes are anchored on the cytoplasmic surface of the thylakoid membrane, where they efficiently funnel excitation energy to the reaction centers (Mondal et al., 2024). Structurally, the PBS is a mega-complex composed of PBPs having covalently attached linear tetrapyrrole chromophores, the phycobilins (Sui, 2021). The diverse absorption spectra of these chromophores allow cyanobacteria to exploit various regions of visible spectrum. There are four varieties of PBPs: allophycocyanin (APC; λ_max ~650 nm), phycocyanin (PC; λ_max ~620 nm), phycoerythrin (PE; λ_max ~565 nm), and phycoerythrocyanin (PEC; λ_max, 568 nm). The association between chromophore and apoprotein is very specific, APC and PC covalently bind phycocyanobilin (PCB), while PE binds phycoerythrobilin (PEB) and/or phycourobilin (PUB), while PEC associate with phycoviobilin (PVB) chromophore (Fu et al., 1979; Bryant, 1982; O'carra et al., 1980; Killilea and O'Carra, 1985).

PBSs exhibit significant morphological diversity across cyanobacteria species (Sui, 2021). However, despite variation, all PBSs share a fundamental structural blueprint consisting of a central core and radiating peripheral rods. The precise spatial orientation and orderly arrangement of PBPs within these subassemblies are mediated by specialized linker polypeptides (Tiwari et al., 2025). The αL_CM linker polypeptides help to adhere complete PBS structure to the thylakoid membrane, and hence, ensure the tight association of PBS with PSII (Capuano et al., 1991). To maximize energy transfer efficiently, PBPs are arranged along an excitation energy gradient. In this downhill energy funnel, pigments with shorter absorption wavelength (such as PE or PC) are located at the distal ends of the peripheral rods. They transfer energy to APC core, which absorb longer wavelengths and is positioned at the base of the PBS, nearest to the thylakoid membrane (Mondal et al., 2024). Cyanobacterial CA is categorized into distinct types based on the specific pigments and structural components involved in this remodeling process under varying light conditions.

Diversity of chromatic acclimation in cyanobacteria

Based on the specific wavelengths perceived and the resulting shifts in pigment composition, CA in cyanobacteria is categorized into seven types: CA1 to CA7 (Figure 4). Each CA type is characterized by a specific set of sensory kinases that perceive spectral quality and initiate signal transduction through cognate response regulators to modulate the response. The diversity of these signaling pathways reflects the evolution of various species specific to ecological niches and fluctuating light environment. In the following sections, we describe the unique spectral combinations and regulatory mechanisms that define each type of CA in cyanobacteria.

Red and green light responses: type I, II, and III CA

Red (RL) and green light (GL) are predominantly harvested by PC and PE, respectively. The structural remodeling of the peripheral rods within the PBS is a critical to ensure efficient photosynthesis (Tounsi et al., 2023). However, in cyanobacterial species lacking PE, such as Synechocystis sp. PCC 6803, CA is restricted to the modulation of linker polypeptides that fine-tune excitation energy transfer between the photosystems (Hirose et al., 2008). Synechocystis sp. PCC 6803 exhibit type I CA, which is regulated by the CcaS sensor histidine kinase and its cognate response regulator, CcaR (Figure 4). A CpcG linker connects rods to core in PBSs under RL, which helps in transfer of energy from the peripheral rods through the APC core to PSII. CcaS induces the expression of the CpcL linker under GL. CpcL directly connects the rods to the photosystems without core and results in a core-independent transfer of excitation energy (Hirose et al., 2008).

Another type of CA is found in PC and PE-containing cyanobacteria. Type II CA is present in the filamentous cyanobacterium Nostoc punctiforme PCC 73102. The CcaS/R two component system only induces the expression of PE and increase the length of rods under GL (Figure 4). Conversely, the inactivation of CcaS/R signaling system under RL inhibits PE accumulation, causing decreased size of PBS rods (Hirose et al., 2010). Thus, in Type II CA, the synthesis of PE is specifically regulated without any significant change in PC levels.

Type III CA exhibits the most robust remodeling of PBS architecture, characterized by the reciprocal substitution of PC and PE in the peripheral portions of the rods (Gaidukov, 1902; Grossman, 2003). The freshwater cyanobacterium Fremyella diplosiphon serves as the primary model for studying this process (Figure 4). In Fremyella diplosiphon, PC is divided into constitutive PC (PCc) and inducible PC (PCi). The PCc is always present in the inner part of rods while PCi is only synthesized and incorporated in the periphery of rods under specific light conditions (Oelmüller et al., 1988; Bryant, 1981). Type III CA is defined by a swap at the distal ends of the rods. The distal portions of the rods are composed of PCi under RL whereas it is replaced by the PE under GL. This intricate molecular switching is governed by the phytochromes-like photoreceptor RcaE and its mechanistic details are discussed in subsequent section.

Blue and green light responses: type IV CA

Marine Synechococcus sp. RS9916 execute type IV CA where remodeling occurs at the level of the chromophore rather than the protein moiety (Palenik, 2001). In this type of CA, the size of the rods of the PBS remains a constant, but their spectral absorbance is tuned by shifting the ratio of two chromophores bound to PE. PUB absorbs blue light (BL) while PEB absorbs GL (Six et al., 2007). Recent study proposed that transcription factors FciA and FciB function as the primary sensors to activate BL/GL signaling axis (Kehoe et al., 2025). The activation of FciA under BL induces accumulation of MpeZ, a specialized phycobilin lyase-isomearse, which isomerizes PEB into PUB. This increases the PUB: PEB ratio in PE, optimizing the antenna for blue light harvesting. Conversely, the activation of FciB under GL inhibits accumulation of MpeZ due to repression of its transcription, and hence, prevents isomerization of PEB into PUB (Kehoe et al., 2025). This results in low PUB: PEB ratio in PE, shifting the absorption peak toward green wavelengths (Figure 4). Type IV CA is of significant biotechnological interest (Tounsi et al., 2023), particularly for open pond cultivation and high-density photobioreactors. In these systems, increasing cell turbidity often creates a self-shading environment enriched in green and blue light. Therefore, the spectral plasticity of Synechococcus sp. could significantly enhance biomass productivity in such light-limited conditions.

Red and far-red light responses: type V and VI CA

This category of CA is observed in both terrestrial and aquatic cyanobacteria. Type V CA is exclusively found in the marine cyanobacterium Acaryochloris marina (Gan and Bryant, 2015), which is unique among cyanobacteria for its reliance on chlorophyll d as its primary photosynthetic pigment to absorb far-red light (FRL), in addition to the traces of chlorophyll a (Figure 4). Unlike most cyanobacteria, A. marina lacks the canonical hemidiscoidal PBS architecture, instead it possesses simple rod-shaped PBSs (Swingley et al., 2008). The sensory mechanism for RL perception in this cyanobacterium is still not well characterized. However, the remodeling of the PBS is unique: under RL, the PC-containing rod-shaped PBSs are synthesized to harvest light and transfer excitation energy to PSII. Conversely, in a predominantly FRL environment, these PBSs are degraded or detached as the cell shifts its energy-harvesting burden entirely to the chlorophyll d-rich photosystems (Hamaguchi et al., 2021; Petrova et al., 2024; Oliver et al., 2025).

Type VI CA, also known as far-red light photoacclimation (FaRLip), is present in a terrestrial cyanobacterium Leptolyngbya JSC-1. This CA involves a massive, coordinated remodeling of PSII, PSI and the PBS core under FRL (Oliver et al., 2025). The FaRLip signaling cascade is consists of the RfpABC system (Figure 4), which plays an important role in regulating the expression of photosystems and PBS core genes (Gan et al., 2014; Soulier et al., 2020). RfpA is a photoreceptor for FRL which transduce signal through the response regulators RfpB and RfpC to induce the remodeling of photosystems and PBSs. Under FRL, the chlorophyll a-containing antennae of PSII and PSI are replaced by subunits that bind chlorophyll d and f. These pigments possess strong absorption maxima in the FR region of the electromagnetic spectrum, allowing organism to survive in environments where visible light is limiting. Furthermore, the PBS core subunit, ApcE1, is replaced by the FRL-inducible variant ApcE2, shifting the absorption maxima of PCB to FR region (Gan et al., 2014). This structural transition minimizes photochemical losses and ensures efficient energy harvesting and transfer to the remodeled photosystems.

Yellow and green light responses: type VII CA

Leptolyngbya sp. PCC 6406 is the primary model for Type VII CA, a specialized acclimation strategy characterized by the reciprocal regulation of PEC and PC under GL and RL, respectively, in the rods of PBS (Hirose et al., 2019). This spectral response is mediated by the CcaS/CcaR two-component system (Figure 4). Under GL, the sensory protein CcaS autophosphorylate and activate its cognate response regulator CcaR. This signaling event induces the transcription of genes encoding PEC and linkers (Hirose et al., 2019). PEC requires binding of PCB and its isomer PVB to the αβ hexamers that are assembled through linker polypeptides to form PEC rods (Hirose et al., 2019). While the role of the CcaS/CcaR system and the presence of lyase or isomerase activity have been confirmed, further genetic and biochemical investigations are required to fully understand the regulatory network of type VII CA.

Molecular signaling and genetic control of type III CA

Type III CA is the most extensively studied photomorphogenic response in cyanobacteria, particularly within the freshwater model organism F. diplosiphon. This organism displays dramatic phenotypic plasticity, appearing blue-green under RL and brick-red under GL due to the reciprocal regulation of inducible PC and PE (Oelmüller et al., 1988). The production of PCi is controlled by two operons—cpcB2A2 and cpcH2I2D2—which together referred as the cpc2 operon. The cpcB2A2 operon encodes α and β subunits of PCi, while the cpcH2I2D2 operon is involved in the synthesis of three linker proteins that assemble PCi into the PBS (Conley et al., 1985, 1988; Stowe-Evans et al., 2004; Casey and Grossman, 1994).

The core of the PBS is encoded by the apcA1B1 genes (Conley et al., 1986; Houmard et al., 1988), core-linker protein is encoded by the apcC gene, whereas core-membrane linker protein is encoded by the apcE gene (Houmard et al., 1990). The genes for the core subunits and their linkers remain constitutively expressed and equally abundant across spectral conditions, the rod composition is strictly light-dependent (Houmard et al., 1990). The CpeR and RcaE are key light-responsive proteins. CpeR is a small activator protein necessary for the expression of the cpeBA operon under GL, promoting the synthesis of PE (Cobley et al., 2002).

The Rca, DpxA, and Cgi signaling hub: the fine-tuning switches of type III CA

The Regulator of Chromatic Acclimation (Rca) system is a phytochrome-like, multi-component phosphorelay that acts as the primary fine-tuning switch for pigment reciprocity (Kehoe and Grossman, 1996; Terauchi et al., 2004). The second, less characterized pathway is the control of green light induction (Cgi) system, which is required for activating genes involved in PE biosynthesis under GL (Federspiel and Grossman, 1990). Together, two systems allow F. diplosiphon to fine tune light harvesting under changing light conditions.

The Rca system includes light-sensing protein RcaE and two response regulators, RcaF and RcaC. RcaE has a molecular weight of 74 kDa and exhibits histidine kinase activity. Structurally, RcaE is composed of 705 amino acids and features three distinct domains: an N-terminal PAS (PER-ARNT-SIM) domain, a GAF domain responsible for chromophore binding, and a C-terminal kinase domain (Kehoe and Grossman, 1996; Terauchi et al., 2004). The ΔrcaE color blind mutant strain of F. diplosiphon cannot differentiate between GL and RL, and exhibits a distinct black pigmentation due to the moderate accumulation of both PC and PE. This is linked to the intermediate expression levels of cpc2, cpeBA, and cpeCDE (Alvey et al., 2003; Seib and Kehoe, 2002). Mutations affecting the histidine residue in RcaE disrupt its ability to phosphorylate downstream response regulators (RRs), leading to excessive PE accumulation regardless of light conditions. These findings underscore the critical role of the histidine residue in RcaE for light-dependent signaling and RR activation (Kehoe and Grossman, 1997; Hirose et al., 2013).

RcaF is the second component and the first response regulator in the Rca signaling pathway. It is a 124-amino-acid protein containing a single receiver domain with conserved aspartate and lysine residues. Loss of RcaF leads to a constitutive red phenotype under both RL and GL (Kehoe and Grossman, 1997). The second response regulator, RcaC, operates downstream of RcaF and consists of 651 amino acids. It features two receiver domains, a histidine phosphotransfer domain, and a DNA-binding domain (Li and Kehoe, 2008). The conserved aspartate residues at positions 51 and 576 are phosphorylated in a light-dependent manner (Chiang et al., 1992). RcaC directly binds to promoter regions to execute transcriptional control of PC and PE genes.

In RL, the kinase activity of RcaE phosphorylates RcaF, which subsequently transfers the phosphate to RcaC. Phosphorylated RcaC activates transcription of cpcB2A2 operon and linkers while simultaneously repressing cpeCDE and cpeBA operons (Figure 5) (Alvey et al., 2003; Seib and Kehoe, 2002; Casey and Grossman, 1994). In GL (Figure 6), RcaE function as a phosphatase, dephosphorylating the system. Unphosphorylated RcaC cannot bind its target promoters, leading to the downregulation of PCi and the lifting of repression on the PE genes (Terauchi et al., 2004).

Another CBCR, DpxA (decreased phycoerythrin expression), acts as a fine-control knob. Unlike RcaE, which affects both PC and PE, DpxA specifically repress PE accumulation. It perceives teal (λ_max = 494 nm) and yellow (λ_max = 568 nm) lights (Figure 7), allowing the cells to distinguish between more subtle spectral shifts (Wiltbank and Kehoe, 2016). Fremyella diplosiphon also regulates PE by a unique GL responsive Cgi mechanism (Figure 6) which was originally identified in mutants lacking the RcaE photoreceptor where residual PE level changes were observed in GL (Alvey et al., 2003; Li and Kehoe, 2005, 2008). This pathway represents a non-traditional regulatory framework that operates post-transcriptionally. It involves the translation initiation factor IF3a, encoded by the infC gene. Under RL, IF3a represses the translation of the cpeC operon, providing an additional safeguard against leaky PE production (Gutu et al., 2013; Wiltbank and Kehoe, 2016). Thus, Cgi pathway highlights a novel framework of gene expression regulation in response to light.

Photoregulation of cell morphology and carboxysome plasticity

In F. diplosiphon, Type III CA involves coordinated reconfiguration of cellular morphology and filament length to maximize radiant energy capture (Figures 5, 6). This photomorphogenic shift is tightly coupled to the spectral environment (Montgomery, 2008). Cells adopt a rectangular/rod-shaped morphology and longer filaments under GL. This shape provides an increased surface area to volume ratio, which accommodate expanded thylakoid membranes for efficient light harvesting (Montgomery, 2008). Under RL, cells transition to a spherical shape with shorter filaments (Bordowitz and Montgomery, 2008). This morphological shortening is associated with higher oxidative stress; indeed, treatment with reducing agent can reverts these cells to longer, rod-shaped forms by decreasing ROS levels (Singh and Montgomery, 2012). The shift between spherical and rod-shaped cells is governed by the light-dependent regulation of MreBCD cytoskeletal complex. The mre genes encode cytoskeleton proteins essential for maintaining the rod-shaped structural integrity of the cell (Singh and Montgomery, 2014). This pathway is controlled by a BolA, a stress-inducible transcription factor (Aldea et al., 1988; Santos et al., 1999). Under RL, phosphorylated RcaE activates the transcription of bolA. The resulting BolA protein represses the mreB (Figure 5), leading to the characteristic spherical cell shape. Conversely, under GL, RcaE remains unphosphorylated and cannot activate bolA expression. The lack of BolA-mediated inhibition allows for higher MreB accumulation (Figure 6), promoting the rectangular cell morphology (Singh and Montgomery, 2014, 2015). The morphological changes are intrinsically linked to the cell’s redox state. Under RL, PBSs preferentially funnel energy to PSII, leading to over-excitation and increased ROS production compared to GL (Singh and Montgomery, 2012). Recent study highlight that RcaE is a central integrator of these oxidative stress responses. RL-activated RcaE improves cellular resilience by upregulating antioxidant defense mechanisms, whereas cells are more susceptible to H₂O₂-mediated stress under GL when RcaE is inactive (Gupta et al., 2026).

Beyond morphology, RcaE also affects carboxysome biogenesis: the proteinaceous organelles responsible for carbon fixation. RcaE modulates the transcription and stoichiometry of the carboxysome components in Fremyella diplosiphon (Rohnke et al., 2018). RcaE regulates the expression of shell protein CcmK2 and nucleation factor CcmM. In RcaE-deficient mutants, an imbalance occurs where shell and scaffolding proteins are overproduced while the primary enzyme, Rubisco, remains constant or decreases. Also, the ratio of full length and truncated version of CcmM protein is altered in the absence of functional RcaE (Rohnke et al., 2020). These molecular alterations result in the assembly of smaller, more numerous carboxysomes with compromised structural integrity. RcaE ensures the proper spatial distribution of carboxysomes within the cell. Disruption of this signaling impairs carbon fixation efficiency, demonstrating that RcaE directly integrates light cues with central metabolic adjustments, independent of the ROS or cell-shape pathways (Rohnke et al., 2018).

Ecological and biotechnological implications of light acclimation

Cyanobacteria are central to global biogeochemical cycles, and their success in diverse habitats is largely due to their capacity for light acclimation. This physiological plasticity shapes community structures and ensures ecosystem stability by optimizing photosynthetic efficiency under fluctuating light regimes (Montgomery, 2022). In aquatic systems, where spectral quality shifts with depth and turbidity, CA allows cyanobacteria to maintain stable primary productivity (Zavřel et al., 2024).

Cyanobacterial niche partitioning is facilitated by mechanisms like spectral tuning and photosystem remodeling (Ulrich et al., 2021). For example, species capable of FaRLiP dominate shaded microhabitats and benthic niches where longer wavelengths predominate, while chromatically flexible taxa thrive in dynamic light environments like shallow lakes or microbial mats (Gisriel et al., 2023). By extending oxygenic photosynthesis into the far-red region, cyanobacteria significantly expand the ecological footprint of the biosphere (Gan et al., 2014). The cyanobacterium Oscillatoria sp. Malviya-1 represents a mat-forming species capable of performing efficient photosynthesis under various light conditions (Maurya et al., 2023). However, the specific type of CA strategies it employs to survive under different light environments remains unclear. Furthermore, acclimation to fluctuating irradiance minimizes oxidative stress and photodamage, supporting resilience in extreme environments such as coastal zones, deserts, and Polar Regions. In terrestrial ecosystems, these acclimated cyanobacterial communities are vital for soil crust formation, nitrogen fixation, carbon sequestration.

The principles of light acclimation offer transformative opportunities for sustainable biotechnology. Since light is primary determinant of yield, industrial cultivators can use programmable LEDs to mimic natural acclimation responses, maximizing biomass or directing metabolic flux toward high-value compounds like PBPs, carotenoids, lipids, and carbohydrates, etc. Integrating FaRLiP or other CA genes into crop plants or heterologous cyanobacterial strains shall be the direction of future research which could allow for efficient growth under filtered or low-light conditions, reducing competition for visible light in high-density cultures. Cyanobacteria capable of far-red acclimation hold potential for life-support systems in space, where light spectra differ significantly from Earth’s surface (Gan et al., 2014). It is also possible to design CBCR-based optogenetic systems that respond to particular wavelength, enabling diversified control on metabolic processes and spatiotemporal control of gene expression using light colors. Additionally, many CBCRs are easier to integrate into heterologous hosts, such as bacteria, plants, and yeast, due to their small size and straightforward bilin-binding requirements. These characteristics make CBCRs useful building blocks to develop synthetic systems for metabolic engineering and photobiotechnology, programmable bioreactors, and light-responsive biosensors or gene expression switches. Therefore, ecological adaptability of cyanobacteria to diverse light regimes not only underpins their global distribution and ecological resilience but also offers powerful opportunities for biotechnological exploitation. Harnessing the principles of light acclimation through ecological insight, genetic modification, and photobioreactor optimization can substantially enhance the efficiency and sustainability of cyanobacterial biotechnology.

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Footnotes

Edited by: Siddhartha Dutta, Sister Nivedita University, India

Reviewed by: Robert Luciński, Adam Mickiewicz University in Poznań, Poland

Rajani Singh, Jawaharlal Nehru University, India