Two Cyanobacterial Photoreceptors Regulate Photosynthetic Light Harvesting by Sensing Teal, Green, Yellow, and Red Light

Chromatic acclimation in cyanobacteria renders robust photosynthesis and fitness in dynamic light environment: Recent advances and future perspectives

Cyanobacteria are photoautotrophic organisms that use light and water as a source of energy and electrons, respectively, to fix atmospheric carbon dioxide and release oxygen as a by-product during photosynthesis. However, photosynthesis and fitness of organisms are challenged by seasonal and diurnal fluctuations in light environments. Also, the distribution of cyanobacteria in a water column is subject to changes in the light regime. The quality and quantity of light change significantly in low and bright light environments that either limit photochemistry or result in photoinhibition due to an excess amount of light reaching reaction centers. Therefore, cyanobacteria have to adjust their light-harvesting machinery and cell morphology for the optimal harvesting of light. This adjustment of light-harvesting involves remodeling of the light-harvesting complex called phycobilisome or incorporation of chlorophyll molecules such as chlorophyll d and f into their light-harvesting machinery. Thus, photoacclimation responses of cyanobacteria at the level of pigment composition and cell morphology maximize their photosynthetic ability and fitness under a dynamic light environment. Cyanobacteria exhibit different types of photoacclimation responses that are commonly known as chromatic acclimation (CA). In this work, we discuss different types of CA reported in cyanobacteria and present a molecular mechanism of well-known type 3 CA where phycoerythrin and phycocyanin of phycobilisome changes according to light signals. We also include other aspects of type 3 CA that have been recently studied at a molecular level and highlight the importance of morphogenes, cytoskeleton, and carboxysome proteins. In summary, CA gives a unique competitive benefit to cyanobacteria by increasing their resource utilization ability and fitness.

Red/green cyanobacteriochromes acquire isomerization from phycocyanobilin to phycoviolobilin

Cyanobacteriochromes (CBCRs) are unique cyanobacteria-specific photoreceptors that share a distant relation with phytochromes. Most CBCRs contain conserved cysteine residues known as canonical Cys, while some CBCRs have additional cysteine residues called second Cys within the DXCF motif, leading to their classification as DXCF CBCRs. They typically undergo a process where they incorporate phycocyanobilin (PCB) and subsequently isomerize it to phycoviolobilin (PVB). Conversely, CBCRs with conserved Trp residues and without the second Cys are called extended red/green (XRG) CBCRs. Typical XRG CBCRs bind PCB without undergoing PCB-to-PVB isomerization, displaying red/green reversible photoconversion, and there are also atypical CBCRs that exhibit diverse photoconversions. We discovered novel XRG CBCRs with Cys residue instead of the conserved Trp residue. These novel XRG CBCRs exhibited the ability to isomerize PCB to PVB, displaying green/teal reversible photoconversion. Through sequence- and structure-based comparisons coupled with mutagenesis experiments, we identified three amino acid residues, including the Cys residue, crucial for facilitating PCB-to-PVB isomerization. This research expands our understanding of the diversity of XRG CBCRs, highlighting the remarkable molecular plasticity of CBCRs.

Teal-light absorbing cyanobacterial phytochrome superfamily provides insights into the diverse mechanisms of spectral tuning and facilitates the engineering of photoreceptors for optogenetic tools

Cyanobacteriochromes (CBCRs) are distinctive tetrapyrrole (bilin)-binding photoreceptors exclusively found in cyanobacteria. Unlike canonical phytochromes, CBCRs require only a GAF (cGMP-phosphodiesterase/adenylate cyclase/FhlA) domain for autolyase activity to form a bilin adduct via a Cys residue and cis-trans photoisomerization. Apart from the canonical Cys, which attaches covalently to C31 in the A-ring of the bilin, some GAF domains of CBCRs contain a second-Cys in the Asp-Xaa-Cys-Phe (DXCF) motif, responsible for isomerization of phycocyanobilin (PCB) to phycoviolobilin (PVB) and/or for the formation of a reversible 2nd thioether linkage to the C10. Unlike green/teal-absorbing GAF proteins lacking ligation activity, the second-Cys in another teal-absorbing lineage (DXCF blue/teal group) exhibits both isomerization and ligation activity due to the presence of the Tyr instead of His next to the canonical Cys. Herein, we discovered an atypical CBCR GAF protein, Tpl7205g1, belonging to the DXCF blue/teal group, but having His instead of Tyr next to the first-Cys. Consistent with its subfamily, the second-Cys of Tpl7205g1 did not form a thioether linkage at C10 of PCB, showing only isomerization activity. Instead of forming 2nd thioether linkage, this novel GAF protein exhibits a pH-dependent photocycle between protonated 15Z and deprotonated 15E. Site-directed mutagenesis to the GAF scaffolds revealed its combined characteristics, including properties of teal-DXCF CBCRs and red/green-absorbing CBCRs (XRG CBCRs), suggesting itself as the evolutionary bridge between the two CBCR groups. Our study thus sheds light on the expanded spectral tuning characteristics of teal-light absorbing CBCRs and enhances feasibility of engineering these photoreceptors.

Responding to light signals: a comprehensive update on photomorphogenesis in cyanobacteria

Cyanobacteria are ancestors of chloroplast and perform oxygen-evolving photosynthesis similar to higher plants and algae. However, an obligatory requirement of photons for their growth results in the exposure of cyanobacteria to varying light conditions. Therefore, the light environment could act as a signal to drive the developmental processes, in addition to photosynthesis, in cyanobacteria. These Gram-negative prokaryotes exhibit characteristic light-dependent developmental processes that maximize their fitness and resource utilization. The development occurring in response to radiance (photomorphogenesis) involves fine-tuning cellular physiology, morphology and metabolism. The best-studied example of cyanobacterial photomorphogenesis is chromatic acclimation (CA), which allows a selected number of cyanobacteria to tailor their light-harvesting antenna called phycobilisome (PBS). The tailoring of PBS under existing wavelengths and abundance of light gives an advantage to cyanobacteria over another photoautotroph. In this work, we will provide a comprehensive update on light-sensing, molecular signaling and signal cascades found in cyanobacteria. We also include recent developments made in other aspects of CA, such as mechanistic insights into changes in the size and shape of cells, filaments and carboxysomes.

Novel cyanobacteriochrome photoreceptor with the second Cys residue showing atypical orange/blue reversible photoconversion

Cyanobacteriochromes (CBCRs) are cyanobacterial linear tetrapyrrole-binding photoreceptors distantly related to phytochromes. Only the GAF domain is needed for chromophore incorporation and proper photoconversion of the CBCRs. Most CBCR GAF domains possess the canonical Cys residue stably ligating to the chromophore. DXCF-type CBCR GAF domains also possess a second Cys residue within the DXCF motif. This second Cys residue reversibly ligates to the C10 of the chromophore. The Cys adduct formation is mostly observed for the dark-adapted state but not for the photoproduct state. In this study, we discovered novel CBCR GAF domains with a DXCI motif instead of the DXCF motif. Since these CBCR GAF domains are categorized into two subfamilies (DXCI-1 and DXCI-2), the GAF domains from each subfamily were analyzed. Although the CBCR GAF domain belonging to the DXCI-2 subfamily showed orange/green reversible photoconversion without transient Cys ligation, the CBCR GAF domain belonging to the DXCI-1 subfamily showed reversible photoconversion between an orange-absorbing dark-adapted state and a blue-absorbing photoproduct state. This indicates that the second Cys residue is covalently bound to the C10 of the chromophore in the photoproduct state but not in the dark-adapted state. Since the covalent bond formation in the photoproduct state is atypical, site-directed mutagenesis was conducted to understand the molecular mechanism of this GAF domain. The Ile residue within the DXCI motif may be key for covalent bond formation in the photoproduct state.

Whole-genome sequence of the filamentous diazotrophic cyanobacterium Tolypothrix sp. PCC 7712 and its comparison with non-diazotrophic Tolypothrix sp. PCC 7601

Cyanobacteria are highly promising microorganisms in forthcoming biotechnologies. Besides the systematic development of molecular tools for genetic engineering, the design of chassis strains and novel reactor concepts are in focus. The latter includes capillary biofilm reactors (CBR), which offer a high surface area-to-volume ratio and very high cell densities. In this context, Tolypothrix sp. PCC 7712 was found to be highly suited for this reactor system due to maximal surface coverage, extraordinarily strong biofilm attachment, and high biomass formation. Here, we provide the genome sequence of Tolypothrix sp. PCC 7712 to potentially allow targeted strain engineering. Surprisingly, it was almost identical to an available incomplete genome draft of Tolypothrix sp. PCC 7601. Thus, we completely sequenced this strain as well and compared it in detail to strain PCC 7712. Comparative genome analysis revealed 257 and 80 unique protein-coding sequences for strains PCC 7601 and PCC 7712, respectively. Clustering genomes based on average nucleotide identity (ANI) and 16S rRNA homology showed 99.98% similarity and only minor distance, respectively, between the two strains in contrast to 21 other cyanobacterial genomes. Despite these high similarities, both strains differ in the ability to fix atmospheric nitrogen and show specific sequence variations, which are discussed in the paper.

Multiple Light-Dark Signals Regulate Expression of the DEAD-Box RNA Helicase CrhR in Synechocystis PCC 6803

Since oxygenic photosynthesis evolved in the common ancestor of cyanobacteria during the Archean, a range of sensing and response strategies evolved to allow efficient acclimation to the fluctuating light conditions experienced in the diverse environments they inhabit. However, how these regulatory mechanisms are assimilated at the molecular level to coordinate individual gene expression is still being elucidated. Here, we demonstrate that integration of a series of three distinct light signals generate an unexpectedly complex network regulating expression of the sole DEAD-box RNA helicase, CrhR, encoded in Synechocystis sp. PCC 6803. The mechanisms function at the transcriptional, translational and post-translation levels, fine-tuning CrhR abundance to permit rapid acclimation to fluctuating light and temperature regimes. CrhR abundance is enhanced 15-fold by low temperature stress. We initially confirmed that the primary mechanism controlling crhR transcript accumulation at 20 °C requires a light quantity-driven reduction of the redox poise in the vicinity of the plastoquinone pool. Once transcribed, a specific light quality cue, a red light signal, was required for crhR translation, far-red reversal of which indicates a phytochrome-mediated mechanism. Examination of CrhR repression at 30 °C revealed that a redox- and light quality-independent light signal was required to initiate CrhR degradation. The crucial role of light was further revealed by the observation that dark conditions superseded the light signals required to initiate each of these regulatory processes. The findings reveal an unexpected complexity of light-dark sensing and signaling that regulate expression of an individual gene in cyanobacteria, an integrated mechanism of environmental perception not previously reported.

A hybrid type of chromatic acclimation regulated by the dual green/red photosensory systems in cyanobacteria

Cyanobacteria are phototrophic bacteria that perform oxygenic photosynthesis. They use a supermolecular light-harvesting antenna complex, the phycobilisome (PBS), to capture and transfer light energy to photosynthetic reaction centers. Certain cyanobacteria alter the absorption maxima and/or overall structure of their PBSs in response to the ambient light wavelength-a process called chromatic acclimation (CA). One of the most well-known CA types is the response to green and red light, which is controlled by either the RcaEFC or CcaSR photosensory system. Here, we characterized a hybrid type of CA in the cyanobacterium Pleurocapsa sp. Pasteur Culture Collection (PCC) 7319 that uses both RcaEFC and CcaSR systems. In vivo spectroscopy suggested that strain PCC 7319 alters the relative composition of green-absorbing phycoerythrin and red-absorbing phycocyanin in the PBS. RNA sequencing and promoter motif analyses suggested that the RcaEFC system induces a gene operon for phycocyanin under red light, whereas the CcaSR system induces a rod-membrane linker gene under green light. Induction of the phycoerythrin genes under green light may be regulated through a yet unidentified photosensory system called the Cgi system. Spectroscopy analyses of the isolated PBSs suggested that hemidiscoidal and rod-shaped PBSs enriched with phycoerythrin were produced under green light, whereas only hemidiscoidal PBSs enriched with phycocyanin were produced under red light. PCC 7319 uses the RcaEFC and CcaSR systems to regulate absorption of green or red light (CA3) and the amount of rod-shaped PBSs (CA1), respectively. Cyanobacteria can thus flexibly combine diverse CA types to acclimate to different light environments.

Chromatic Acclimation Processes and Their Relationships with Phycobiliprotein Complexes

Chromatic acclimation (CA) is a widespread mechanism for optimizing the composition of phycobiliprotein complexes to maximize the cyanobacterial light capture efficiency. There are seven CA types, CA1-CA7, classified according to various photoregulatory pathways. Here, we use sequence analyses and bioinformatics to predict the presence of CA types according to three GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA)-containing photoreceptors, CcaS (cyanobacterial chromatic acclimation sensor), RcaE (regulator of chromatic adaptation), and RfpA (regulator for far-red photoacclimation). These photoreceptors were classified into three different phylogenetic groups leading different CA types in a diverse range of cyanobacteria. Combining with genomic information of phycobilisome compositions, the CA capabilities of various cyanobacteria were conjectured. Screening 65 accessible cyanobacterial genomes, we defined 19 cyanobacteria that have the capability to perform far-red light photoacclimation (FaRLiP) under the control of RfpA. Forty out of sixty-five cyanobacteria have the capability to perform green/red light photoacclimation, although they use different photoreceptors (RcaE and/or CcaS) and photoregulatory pathways. The reversible response of photoreceptors in CA regulation pathways trigged by changed light conditions reflects the flexibility of photoregulatory mechanisms in cyanobacteria and the putative independent evolutionary origin of photoacclimation types.

Reflections on Cyanobacterial Chromatic Acclimation: Exploring the Molecular Bases of Organismal Acclimation and Motivation for Rethinking the Promotion of Equity in STEM

Cyanobacteria are photosynthetic organisms that exhibit characteristic acclimation and developmental responses to dynamic changes in the external light environment. Photomorphogenesis is the tuning of cellular physiology, development, morphology, and metabolism in response to external light cues. The tuning of photosynthetic pigmentation, carbon fixation capacity, and cellular and filament morphologies to changes in the prevalent wavelengths and abundance of light have been investigated to understand the regulation and fitness implications of different aspects of cyanobacterial photomorphogenesis. Chromatic acclimation (CA) is the most common form of photomorphogenesis that has been explored in cyanobacteria. Multiple types of CA in cyanobacteria have been reported, and insights gained into the regulatory pathways and networks controlling some of these CA types. I examine the recent expansion of CA types that occur in nature and provide an overview of known regulatory factors involved in distinct aspects of cyanobacterial photomorphogenesis. Additionally, I explore lessons for cultivating success in scientific communities that can be drawn from a reflection on existing knowledge of and approaches to studying CA.

Light quality, oxygenic photosynthesis and more

Oxygenic photosynthesis takes place in thylakoid membranes (TM) of cyanobacteria, algae, and higher plants. It begins with light absorption by pigments in large (modular) assemblies of pigment-binding proteins, which then transfer excitation energy to the photosynthetic reaction centers of photosystem (PS) I and PSII. In green algae and plants, these light-harvesting protein complexes contain chlorophylls (Chls) and carotenoids (Cars). However, cyanobacteria, red algae, and glaucophytes contain, in addition, phycobiliproteins in phycobilisomes that are attached to the stromal surface of TM, and transfer excitation energy to the reaction centers via the Chl a molecules in the inner antennas of PSI and PSII. The color and the intensity of the light to which these photosynthetic organisms are exposed in their environment have a great influence on the composition and the structure of the light-harvesting complexes (the antenna) as well as the rest of the photosynthetic apparatus, thus affecting the photosynthetic process and even the entire organism. We present here a perspective on 'Light Quality and Oxygenic Photosynthesis', in memory of George Christos Papageorgiou (9 May 1933-21 November 2020; see notes a and b). Our review includes (1) the influence of the solar spectrum on the antenna composition, and the special significance of Chl a; (2) the effects of light quality on photosynthesis, measured using Chl a fluorescence; and (3) the importance of light quality, intensity, and its duration for the optimal growth of photosynthetic organisms.

The Red Edge: Bilin-Binding Photoreceptors as Optogenetic Tools and Fluorescence Reporters

This review adds the bilin-binding phytochromes to the Chemical Reviews thematic issue "Optogenetics and Photopharmacology". The work is structured into two parts. We first outline the photochemistry of the covalently bound tetrapyrrole chromophore and summarize relevant spectroscopic, kinetic, biochemical, and physiological properties of the different families of phytochromes. Based on this knowledge, we then describe the engineering of phytochromes to further improve these chromoproteins as photoswitches and review their employment in an ever-growing number of different optogenetic applications. Most applications rely on the light-controlled complex formation between the plant photoreceptor PhyB and phytochrome-interacting factors (PIFs) or C-terminal light-regulated domains with enzymatic functions present in many bacterial and algal phytochromes. Phytochrome-based optogenetic tools are currently implemented in bacteria, yeast, plants, and animals to achieve light control of a wide range of biological activities. These cover the regulation of gene expression, protein transport into cell organelles, and the recruitment of phytochrome- or PIF-tagged proteins to membranes and other cellular compartments. This compilation illustrates the intrinsic advantages of phytochromes compared to other photoreceptor classes, e.g., their bidirectional dual-wavelength control enabling instant ON and OFF regulation. In particular, the long wavelength range of absorption and fluorescence within the "transparent window" makes phytochromes attractive for complex applications requiring deep tissue penetration or dual-wavelength control in combination with blue and UV light-sensing photoreceptors. In addition to the wide variability of applications employing natural and engineered phytochromes, we also discuss recent progress in the development of bilin-based fluorescent proteins.

Natural diversity provides a broad spectrum of cyanobacteriochrome-based diguanylate cyclases

Cyanobacteriochromes (CBCRs) are spectrally diverse photosensors from cyanobacteria distantly related to phytochromes that exploit photoisomerization of linear tetrapyrrole (bilin) chromophores to regulate associated signaling output domains. Unlike phytochromes, a single CBCR domain is sufficient for photoperception. CBCR domains that regulate the production or degradation of cyclic nucleotide second messengers are becoming increasingly well characterized. Cyclic di-guanosine monophosphate (c-di-GMP) is a widespread small-molecule regulator of bacterial motility, developmental transitions, and biofilm formation whose biosynthesis is regulated by CBCRs coupled to GGDEF (diguanylate cyclase) output domains. In this study, we compare the properties of diverse CBCR-GGDEF proteins with those of synthetic CBCR-GGDEF chimeras. Our investigation shows that natural diversity generates promising candidates for robust, broad spectrum optogenetic applications in live cells. Since light quality is constantly changing during plant development as upper leaves begin to shade lower leaves-affecting elongation growth, initiation of flowering, and responses to pathogens, these studies presage application of CBCR-GGDEF sensors to regulate orthogonal, c-di-GMP-regulated circuits in agronomically important plants for robust mitigation of such deleterious responses under natural growing conditions in the field.

Photomorphogenesis in the Picocyanobacterium Cyanobium gracile Includes Increased Phycobilisome Abundance Under Blue Light, Phycobilisome Decoupling Under Near Far-Red Light, and Wavelength-Specific Photoprotective Strategies

Photomorphogenesis is a process by which photosynthetic organisms perceive external light parameters, including light quality (color), and adjust cellular metabolism, growth rates and other parameters, in order to survive in a changing light environment. In this study we comprehensively explored the light color acclimation of Cyanobium gracile, a common cyanobacterium in turbid freshwater shallow lakes, using nine different monochromatic growth lights covering the whole visible spectrum from 435 to 687 nm. According to incident light wavelength, C. gracile cells performed great plasticity in terms of pigment composition, antenna size, and photosystem stoichiometry, to optimize their photosynthetic performance and to redox poise their intersystem electron transport chain. In spite of such compensatory strategies, C. gracile, like other cyanobacteria, uses blue and near far-red light less efficiently than orange or red light, which involves moderate growth rates, reduced cell volumes and lower electron transport rates. Unfavorable light conditions, where neither chlorophyll nor phycobilisomes absorb light sufficiently, are compensated by an enhanced antenna size. Increasing the wavelength of the growth light is accompanied by increasing photosystem II to photosystem I ratios, which involve better light utilization in the red spectral region. This is surprisingly accompanied by a partial excitonic antenna decoupling, which was the highest in the cells grown under 687 nm light. So far, a similar phenomenon is known to be induced only by strong light; here we demonstrate that under certain physiological conditions such decoupling is also possible to be induced by weak light. This suggests that suboptimal photosynthetic performance of the near far-red light grown C. gracile cells is due to a solid redox- and/or signal-imbalance, which leads to the activation of this short-term light acclimation process. Using a variety of photo-biophysical methods, we also demonstrate that under blue wavelengths, excessive light is quenched through orange carotenoid protein mediated non-photochemical quenching, whereas under orange/red wavelengths state transitions are involved in photoprotection.

PhotoModPlus: A web server for photosynthetic protein prediction from genome neighborhood features

A new web server called PhotoModPlus is presented as a platform for predicting photosynthetic proteins via genome neighborhood networks (GNN) and genome neighborhood-based machine learning. GNN enables users to visualize the overview of the conserved neighboring genes from multiple photosynthetic prokaryotic genomes and provides functional guidance on the query input. In the platform, we also present a new machine learning model utilizing genome neighborhood features for predicting photosynthesis-specific functions based on 24 prokaryotic photosynthesis-related GO terms, namely PhotoModGO. The new model performed better than the sequence-based approaches with an F1 measure of 0.872, based on nested five-fold cross-validation. Finally, we demonstrated the applications of the webserver and the new model in the identification of novel photosynthetic proteins. The server is user-friendly, compatible with all devices, and available at bicep.kmutt.ac.th/photomod.

Pump-Probe Circular Dichroism Spectroscopy of Cyanobacteriochrome TePixJ Yields: Insights into Its Photoconversion

The bilin-containing photoreceptor TePixJ, a member of the cyanobacteriochrome (CBCR) family of phytochromes, switches between blue-light-absorbing and green-light-absorbing states in order to drive phototaxis in Thermosynechococcus elongatus. Its photoswitching process involves the formation of a thioether linkage between the C10 carbon of phycoviolobilin and the sidechain of Cys494 during the change in state from green-absorbing to blue-absorbing forms. Complex changes in the binding pocket propagate the signal to other domains for downstream signaling. Here, we report time-resolved circular dichroism experiments in addition to pump-probe absorption measurements for interpretation of the biophysical mechanism of the green-to-blue photoconversion process of this receptor.

A photoproduct of DXCF cyanobacteriochromes without reversible Cys ligation is destabilized by rotating ring twist of the chromophore

Cyanobacteriochrome photoreceptors (CBCRs) ligate linear tetrapyrrole chromophores via their first (canonical) Cys residue and show reversible photoconversion triggered by light-dependent Z/E isomerization of the chromophore. Among the huge repertoire of CBCRs, DXCF CBCRs contain a second Cys residue within the highly conserved Asp-Xaa-Cys-Phe (DXCF) motif. In the typical receptors, the second Cys covalently attaches to the 15Z-chromophore in the dark state and detaches from the 15E-chromophore in the photoproduct state, whereas atypical ones that lack reversible ligation activity show red-shifted absorption in the dark state due to a more extended π-conjugated system. Moreover, some DXCF CBCRs show blue-shifted absorption in the photoproduct state due to the twisted geometry of the rotating ring. During the process of rational color tuning of a certain DXCF CBCR, we unexpectedly found that twisted photoproducts of some variant molecules showed dark reversion to the dark state, which prompted us to hypothesize that the photoproduct is destabilized by the twisted geometry of the rotating ring. In this study, we comprehensively examined the photoproduct stability of the twisted and relaxed molecules derived from the same CBCR scaffolds under dark conditions. In the DXCF CBCRs lacking reversible ligation activity, the twisted photoproducts showed faster dark reversion than the relaxed ones, supporting our hypothesis. By contrast, in the DXCF CBCRs exhibiting reversible ligation activity, the twisted photoproducts showed no detectable photoconversion. Reversible Cys adduct formation thus results in drastic rearrangement of the protein-chromophore interaction in the photoproduct state, which would contribute to the previously unknown photoproduct stability.

Evolution-inspired design of multicolored photoswitches from a single cyanobacteriochrome scaffold

Cyanobacteriochromes (CBCRs) are small, bistable linear tetrapyrrole (bilin)-binding light sensors which are typically found as modular components in multidomain cyanobacterial signaling proteins. The CBCR family has been categorized into many lineages that roughly correlate with their spectral diversity, but CBCRs possessing a conserved DXCF motif are found in multiple lineages. DXCF CBCRs typically possess two conserved Cys residues: a first Cys that remains ligated to the bilin chromophore and a second Cys found in the DXCF motif. The second Cys often forms a second thioether linkage, providing a mechanism to sense blue and violet light. DXCF CBCRs have been described with blue/green, blue/orange, blue/teal, and green/teal photocycles, and the molecular basis for some of this spectral diversity has been well established. We here characterize AM1_1499g1, an atypical DXCF CBCR that lacks the second cysteine residue and exhibits an orange/green photocycle. Based on prior studies of CBCR spectral tuning, we have successfully engineered seven AM1_1499g1 variants that exhibit robust yellow/teal, green/teal, blue/teal, orange/yellow, yellow/green, green/green, and blue/green photocycles. The remarkable spectral diversity generated by modification of a single CBCR provides a good template for multiplexing synthetic photobiology systems within the same cellular context, thereby bypassing the time-consuming empirical optimization process needed for multiple probes with different protein scaffolds.

Acclimation process of the chlorophyll d-bearing cyanobacterium Acaryochloris marina to an orange light environment revealed by transcriptomic analysis and electron microscopic observation

The cyanobacterium Acaryochloris marina MBIC 11017 (A. marina 11017) possesses chlorophyll d (Chl. d) peaking at 698 nm as photosystem reaction center pigments, instead of chlorophyll a (Chl. a) peaking at 665 nm. About 95% of the total chlorophylls is Chl. d in A. marina 11017. In addition, A. marina 11017 possesses phycobilisome (PBS) supercomplex to harvest orange light and to transfer the absorbing energy to the photosystems. In this context, A. marina 11017 utilizes both far-red and orange light as the photosynthetic energy source. In the present study, we incubated A. marina 11017 cells under monochromatic orange and far-red light conditions and performed transcriptional and morphological studies by RNA-seq analysis and electron microscopy. Cellular absorption spectra, transcriptomic profiles, and microscopic observations demonstrated that PBS was highly accumulated under an orange light condition relative to a far-red light condition. Notably, transcription of one cpcBA operon encoding the phycobiliprotein of the phycocyanin was up-regulated under the orange light condition, but another operon was constitutively expressed under both conditions, indicating functional diversification of these two operons for light harvesting. Taking the other observations into consideration, we could illustrate the photoacclimation processes of A. marina 11017 in response to orange and far-red light conditions in detail.

Chromatic Acclimation in Cyanobacteria: A Diverse and Widespread Process for Optimizing Photosynthesis

Chromatic acclimation (CA) encompasses a diverse set of molecular processes that involve the ability of cyanobacterial cells to sense ambient light colors and use this information to optimize photosynthetic light harvesting. The six known types of CA, which we propose naming CA1 through CA6, use a range of molecular mechanisms that likely evolved independently in distantly related lineages of the Cyanobacteria phylum. Together, these processes sense and respond to the majority of the photosynthetically relevant solar spectrum, suggesting that CA provides fitness advantages across a broad range of light color niches. The recent discoveries of several new CA types suggest that additional CA systems involving additional light colors and molecular mechanisms will be revealed in coming years. Here we provide a comprehensive overview of the currently known types of CA and summarize the molecular details that underpin CA regulation.

Photosynthetic protein classification using genome neighborhood-based machine learning feature

Identification of novel photosynthetic proteins is important for understanding and improving photosynthetic efficiency. Synergistically, genome neighborhood can provide additional useful information to identify photosynthetic proteins. We, therefore, expected that applying a computational approach, particularly machine learning (ML) with the genome neighborhood-based feature should facilitate the photosynthetic function assignment. Our results revealed a functional relationship between photosynthetic genes and their conserved neighboring genes observed by 'Phylo score', indicating their functions could be inferred from the genome neighborhood profile. Therefore, we created a new method for extracting patterns based on the genome neighborhood network (GNN) and applied them for the photosynthetic protein classification using ML algorithms. Random forest (RF) classifier using genome neighborhood-based features achieved the highest accuracy up to 87% in the classification of photosynthetic proteins and also showed better performance (Mathew's correlation coefficient = 0.718) than other available tools including the sequence similarity search (0.447) and ML-based method (0.361). Furthermore, we demonstrated the ability of our model to identify novel photosynthetic proteins compared to the other methods. Our classifier is available at http://bicep2.kmutt.ac.th/photomod_standalone, https://bit.ly/2S0I2Ox and DockerHub: https://hub.docker.com/r/asangphukieo/photomod.

Blue-/Green-Light-Responsive Cyanobacteriochromes Are Cell Shade Sensors in Red-Light Replete Niches

Cyanobacteriochrome (CBCRs) photoreceptors show various photochemical properties, but their ecophysiological functions remain elusive. Here, we report that the blue/green CBCRs SesA/B/C can serve as physiological sensors of cell density. Because cyanobacterial cells show lower transmittance of blue light than green light, higher cell density gives more green-light-enriched irradiance to cells. The cell-density-dependent suppression of cell aggregation under blue-/green-mixed light and white light conditions support this idea. Such a sensing mechanism may provide information about the cell position in cyanobacterial mats in hot springs, the natural habitat of Thermosynechococcus. This cell-position-dependent SesA/B/C-mediated regulation of cellular sessility (aggregation) might be ecophysiologically essential for the reorganization and growth of phototrophic mats. We also report that the green-light-induced dispersion of cell aggregates requires red-light-driven photosynthesis. Blue/green CBCRs might work as shade detectors in a different niche than red/far-red phytochromes, which may be why CBCRs have evolved in cyanobacteria.

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Blue- and green-light-sensing cyanobacteriochromes can be sensors of cell density

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They may provide information about the cell position in microbial mats

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Green-light-induced dispersion of aggregates needs red-light-driven photosynthesis

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Cyanobacteriochromes might work in a different niche than red/far-red phytochromes

Diverse light responses of cyanobacteria mediated by phytochrome superfamily photoreceptors

Cyanobacteria are an evolutionarily and ecologically important group of prokaryotes. They exist in diverse habitats, ranging from hot springs and deserts to glaciers and the open ocean. The range of environments that they inhabit can be attributed in part to their ability to sense and respond to changing environmental conditions. As photosynthetic organisms, one of the most crucial parameters for cyanobacteria to monitor is light. Cyanobacteria can sense various wavelengths of light and many possess a range of bilin-binding photoreceptors belonging to the phytochrome superfamily. Vital cellular processes including growth, phototaxis, cell aggregation and photosynthesis are tuned to environmental light conditions by these photoreceptors. In this Review, we examine the physiological responses that are controlled by members of this diverse family of photoreceptors and discuss the signal transduction pathways through which these photoreceptors operate. We highlight specific examples where the activities of multiple photoreceptors function together to fine-tune light responses. We also discuss the potential application of these photosensing systems in optogenetics and synthetic biology.

Protochromic absorption changes in the two-cysteine photocycle of a blue/orange cyanobacteriochrome

Cyanobacteriochromes (CBCRs) are phytochrome-related photosensors with diverse spectral sensitivities spanning the entire visible spectrum. They covalently bind bilin chromophores via conserved cysteine residues and undergo 15Z/15E bilin photoisomerization upon light illumination. CBCR subfamilies absorbing violet-blue light use an additional cysteine residue to form a second bilin-thiol adduct in a two-Cys photocycle. However, the process of second thiol adduct formation is incompletely understood, especially the involvement of the bilin protonation state. Here, we focused on the Oscil6304_2705 protein from the cyanobacterium Oscillatoria acuminata PCC 6304, which photoconverts between a blue-absorbing 15Z state ( ^15Z Pb) and orange-absorbing 15E state ( ^15E Po). pH titration analysis revealed that ^15Z Pb was stable over a wide pH range, suggesting that bilin protonation is stabilized by a second thiol adduct. As revealed by resonance Raman spectroscopy, ^15E Po harbored protonated bilin at both acidic and neutral pH, but readily converted to a deprotonated green-absorbing 15Z state ( ^15Z Pg) at alkaline pH. Site-directed mutagenesis revealed that the conserved Asp-71 and His-102 residues are required for second thiol adduct formation in ^15Z Pb and bilin protonation in ^15E Po, respectively. An Oscil6304_2705 variant lacking the second cysteine residue, Cys-73, photoconverted between deprotonated ^15Z Pg and protonated ^15E Pr, similarly to the protochromic photocycle of the green/red CBCR subfamily. Time-resolved spectroscopy revealed ^15Z Pg formation as an intermediate in the ^15E Pr-to- ^15Z Pg conversion with a significant solvent-isotope effect, suggesting the sequential occurrence of 15EP-to-15Z photoisomerization, deprotonation, and second thiol adduct formation. Our findings uncover the details of protochromic absorption changes underlying the two-Cys photocycle of violet-blue-absorbing CBCR subfamilies.

Light Intensity and Nitrogen Concentration Impact on the Biomass and Phycoerythrin Production by Porphyridium purpureum

Several factors have the potential to influence microalgae growth. In the present study, nitrogen concentration and light intensity were evaluated in order to obtain high biomass production and high phycoerythrin accumulation from Porphyridium purpureum. The range of nitrogen concentrations evaluated in the culture medium was 0.075-0.450 g L^-1 and light intensities ranged between 30 and 100 μmol m^-2 s^-1. Surprisingly, low nitrogen concentration and high light intensity resulted in high biomass yield and phycoerythrin accumulation. Thus, the best biomass productivity (0.386 g L^-1 d^-1) and biomass yield (5.403 g L^-1) were achieved with NaNO₃ at 0.075 g L^-1 and 100 μmol m^-2 s^-1. In addition, phycoerythrin production was improved to obtain a concentration of 14.66 mg L^-1 (2.71 mg g^-1 of phycoerythrin over dry weight). The results of the present study indicate that it is possible to significantly improve biomass and pigment production in Porphyridium purpureum by limiting nitrogen concentration and light intensity.

Protein Engineering of Dual-Cys Cyanobacteriochrome AM1_1186g2 for Biliverdin Incorporation and Far-Red/Blue Reversible Photoconversion

Cyanobacteria have cyanobacteriochromes (CBCRs), which are photoreceptors that bind to a linear tetrapyrrole chromophore and sense UV-to-visible light. A recent study revealed that the dual-Cys CBCR AM1_1186g2 covalently attaches to phycocyanobilin and exhibits unique photoconversion between a Pr form (red-absorbing dark state, λ_max = 641 nm) and Pb form (blue-absorbing photoproduct, λ_max = 416 nm). This wavelength separation is larger than those of the other CBCRs, which is advantageous for optical tools. Nowadays, bioimaging and optogenetics technologies are powerful tools for biological research. In particular, the utilization of far-red and near-infrared light sources is required for noninvasive applications to mammals because of their high potential to penetrate into deep tissues. Biliverdin (BV) is an intrinsic chromophore and absorbs the longest wavelength among natural linear tetrapyrrole chromophores. Although the BV-binding photoreceptors are promising platforms for developing optical tools, AM1_1186g2 cannot efficiently attach BV. Herein, by rationally introducing several replacements, we developed a BV-binding AM1_1186g2 variant, KCAP_QV, that exhibited reversible photoconversion between a Pfr form (far-red-absorbing dark state, λ_max = 691 nm) and Pb form (λ_max = 398 nm). This wavelength separation reached 293 nm, which is the largest among the known phytochrome and CBCR photoreceptors. In conclusion, the KCAP_QV molecule developed in this study can offer an alternative platform for the development of unique optical tools.

Surface colour: An overlooked aspect in the study of cyanobacterial biofilm formation

Cyanobacteria can grow as biofilms, communities that colonize surfaces and that play a fundamental role in the ecology of many diverse habitats and in the conversion of industrial production to green platforms. Although biofilm growth is known to be significantly affected by several characteristics, the effect of colour surface is an overlooked aspect that has not yet been investigated. In this study, we describe the effect of colour hues (white, red, blue and black) on the growth of cyanobacterial biofilms on air-exposed substrates. We measured growth, architecture, pigment production and levels of ATP and reactive oxygen species in cyanobacterial biofilms formed on different coloured substrates. The study findings demonstrate, for the first time, that the colour of a surface affects biofilm formation at the air-solid interface (with more biomass accumulating on white and red substrates than on blue and black substrates) and also alters the biofilm architecture. In addition, the roles of chromatic adaptation, phototrophic cells and reactive oxygen species as intermediates between colour sensing and biofilm response are discussed. Our results support the importance of colour as a new factor that favours surface colonization by cyanobacteria and its contribution to biofilm formation.

Distinctive Properties of Dark Reversion Kinetics between Two Red/Green-Type Cyanobacteriochromes and their Application in the Photoregulation of cAMP Synthesis

Cyanobacteriochromes (CBCRs) are photoreceptors that bind to a linear tetrapyrrole within a conserved cGMP-phosphodiesterase/adenylate cyclase/FhlA (GAF) domain and exhibit reversible photoconversion. Red/green-type CBCR GAF domains that photoconvert between red- (Pr) and green-absorbing (Pg) forms occur widely in various cyanobacteria. A putative phototaxis regulator, AnPixJ, contains multiple red/green-type CBCR GAF domains. We previously reported that AnPixJ's second domain (AnPixJg2) but not its fourth domain (AnPixJg4) shows red/green reversible photoconversion. Herein, we found that AnPixJg4 showed Pr-to-Pg photoconversion and rapid Pg-to-Pr dark reversion, whereas AnPixJg2 showed a barely detectable dark reversion. Site-directed mutagenesis revealed the involvement of six residues in Pg stability. Replacement at the Leu294/Ile660 positions of AnPixJg2/AnPixJg4 showed the highest influence on dark reversion kinetics. AnPixJg2_DR6, wherein the six residues of AnPixJg2 were entirely replaced with those of AnPixJg4, showed a 300-fold faster dark reversion than that of the wild type. We constructed chimeric proteins by fusing the GAF domains with adenylate cyclase catalytic regions, such as AnPixJg2-AC, AnPixJg4-AC and AnPixJg2_DR6-AC. We detected successful enzymatic activation under red light for both AnPixJg2-AC and AnPixJg2_DR6-AC, and repression under green light for AnPixJg2-AC and under dark incubation for AnPixJg2_DR6-AC. These results provide platforms to develop cAMP synthetic optogenetic tools.

Fluorescence Properties of a Novel Cyanobacteriochrome GAF Domain from Spirulina that Exhibits Moderate Dark Reversion

Cyanobacteriochromes (CBCRs) are biliproteins for photoreception that are present in cyanobacteria. These proteins possess one or more unique cGMP-specific phosphodiesterase/adenylate cyclase/FhlA (GAF) domains that can covalently bind the linear tetrapyrrole (bilin). Light absorption triggers the photoisomerization of bilin between the 15Z and 15E photostates. The 15E photoproduct of some CBCR GAF domains can revert to the stable 15Z state in the absence of light. In some cases, this property makes these domains function as sensors of light intensity or as red/dark optogenetic switches. However, there have been few reports regarding the applicability of these fluorescent properties. Here, we report a red/green cyanobacteriochrome GAF domain from Spirulina subsalsa, designated SPI1085g3, which exhibited photoconversion from the red-absorbing dark state (Pr, λmax = 642 nm) to the orange-absorbing photoproduct state (Po, λmax = 590 nm), and exhibited moderate dark reversion (t_1/2 = 3.3 min) from the Po state to the Pr state. The SPI1085g3 Pr state exhibited intense red fluorescence (λmax = 662 nm), with a quantum yield of 0.14. The fluorescence was switched off by red light irradiation and increased in the dark. Replacement of Cys448 of SPI1085g3 with Ser resulted in a slightly improved fluorescence quantum yield and nearly 13-fold faster dark reversion (t_1/2 = 15.2 s) than that of the wild type. This novel red/dark-switchable fluorescent biliprotein expands the present repertoire and diversity of photoswitchable fluorescent protein candidates.

Dawn illumination prepares desert cyanobacteria for dehydration

Desert biological soil crusts (BSC), among the harshest environments on Earth, are formed by the adhesion of soil particles to polysaccharides excreted mainly by filamentous cyanobacteria (see [1] and references therein). These species are the main primary producers in this habitat where they cope with various stressors including frequent hydration-dehydration cycles. Water is mainly provided as early-morning dew, followed by dehydration with rising temperatures and declining relative humidity. Earlier studies focused on community structure and cyanobacterial activities in various BSCs [1,2]. They identified genes present in dehydration-tolerant, but not -sensitive cyanobacteria [3], and suggested that abiotic conditions during natural dehydration (Figure 1A) are critical for the recovery upon rewetting. Inability of Leptolyngbya ohadii, which is abundant in the BSC examined here, to recover after rapid desiccation (Figure 1B) [4] suggested that the cells must prepare themselves toward forthcoming dehydration, but the nature of the signal involved was unknown. We show here that the rising dawn illumination, perceived by photo-sensors, serves as the signal inciting BSC-inhabiting cyanobacteria to prepare for forthcoming dehydration. L. ohadii filaments were exposed to simulated natural conditions from the morning of October 14^th 2009, using our environmental chamber that enables accurate reproduction of BSC environment [4] (Supplemental Figure S1A). Samples were withdrawn at specific time points (Figure 1A), followed by RNA extraction and global transcript profiling (accession PRJNA391854). Four hours of dehydration led to up-regulation of 567 genes and down-regulation of 1597 (by more than 2-fold). Since BSC-inhabiting organisms have not been used as genetic models, the functions of 3258 (43.5% of the 7487 L. ohadii genes [3]) are unknown. Nevertheless, a pronounced rise in transcript levels of genes involved in carbon metabolism, transport, osmolyte production, energy dissipation and other cellular activities was observed. On the other hand, a declining transcript abundance for genes involved in light harvesting, photosynthetic metabolism, protein biosynthesis, cell division and other pathways was detected. The analysis unraveled clear distinctions between early- and late-responding genes. Supplemental Table S1 lists the 40 strongest differentially expressed genes verified by RT-qPCR and used in further analyses.

Decomposition of cyanobacterial light harvesting complexes: NblA-dependent role of the bilin lyase homolog NblB

Phycobilisomes, the macromolecular light harvesting complexes of cyanobacteria are degraded under nutrient-limiting conditions. This crucial response is required to adjust light excitation to the metabolic status and avoid damage by excess excitation. Phycobilisomes are comprised of phycobiliproteins, apo-proteins that covalently bind bilin chromophores. In the cyanobacterium Synechococcus elongatus, the phycobiliproteins allophycocyanin and phycocyanin comprise the core and the rods of the phycobilisome, respectively. Previously, NblB was identified as an essential component required for phycocyanin degradation under nutrient starvation. This protein is homologous to bilin-lyases, enzymes that catalyze the covalent attachment of bilins to apo-proteins. However, the nblB-inactivated strain is not impaired in phycobiliprotein synthesis, but rather is characterized by aberrant phycocyanin degradation. Here, using a phycocyanin-deficient strain, we demonstrate that NblB is required for degradation of the core pigment, allophycocyanin. Furthermore, we show that the protein NblB is expressed under nutrient sufficient conditions, but during nitrogen starvation its level decreases about two-fold. This finding is in contrast to an additional component essential for degradation, NblA, the expression of which is highly induced under starvation. We further identified NblB residues required for phycocyanin degradation in vivo. Finally, we demonstrate phycocyanin degradation in a cell-free system, thereby providing support for the suggestion that NblB directly mediates pigment degradation by chromophore detachment. The dependence of NblB function on NblA revealed using this system, together with the results indicating presence of NblB under nutrient sufficient conditions, suggests a rapid mechanism for induction of pigment degradation, which requires only the expression of NblA.

Molecular characterization of DXCF cyanobacteriochromes from the cyanobacterium Acaryochloris marina identifies a blue-light power sensor

Cyanobacteriochromes (CBCRs) are linear tetrapyrrole-binding photoreceptors that sense a wide range of wavelengths from ultraviolet to far-red. The primary photoreaction in these reactions is a Z/E isomerization of the double bond between rings C and D. After this isomerization, various color-tuning events establish distinct spectral properties of the CBCRs. Among the various CBCRs, the DXCF CBCR lineage is widely distributed among cyanobacteria. Because the DXCF CBCRs from the cyanobacterium Acaryochloris marina vary widely in sequence, we focused on these CBCRs in this study. We identified seven DXCF CBCRs in A. marina and analyzed them after isolation from Escherichia coli that produces phycocyanobilin, a main chromophore for the CBCRs. We found that six of these CBCRs covalently bound a chromophore and exhibited variable properties, including blue/green, blue/teal, green/teal, and blue/orange reversible photoconversions. Notably, one CBCR, AM1_1870g4, displayed unidirectional photoconversion in response to blue-light illumination, with a rapid dark reversion that was temperature-dependent. Furthermore, the photoconversion took place without Z/E isomerization. This observation indicated that AM1_1870g4 likely functions as a blue-light power sensor, whereas typical CBCRs reversibly sense two light qualities. We also found that AM1_1870g4 possesses a GDCF motif in which the Asp residue is swapped with the next Gly residue within the DXCF motif. Site-directed mutagenesis revealed that this swap is essential for the light power-sensing function of AM1_1870g4. This is the first report of a blue-light power sensor from the CBCR superfamily and of photoperception without Z/E isomerization among the bilin-based photoreceptors.

Characterization of the genuine type 2 chromatic acclimation in the two Geminocystis cyanobacteria

Certain cyanobacteria can adjust the wavelengths of light they absorb by remodeling their photosynthetic antenna complex phycobilisome via a process called chromatic acclimation (CA). Although several types of CA have been reported, the diversity of the molecular mechanisms of CA among the cyanobacteria phylum is not fully understood. Here, we characterized the molecular process of CA of Geminocystis sp. strains National Institute of Environmental Studies (NIES)-3708 and NIES-3709. Absorption and fluorescence spectroscopy revealed that both strains dramatically alter their phycoerythrin content in response to green and red light. Whole-genome comparison revealed that the two strains share the typical phycobilisome structure consisting of a central core and peripheral rods, but they differ in the number of rod linkers of phycoerythrin and thus have differing capacity for phycoerythrin accumulation. RNA sequencing analysis suggested that the length of phycoerythrin rods in each phycobilisome is strictly regulated by the green light and red light-sensing CcaS/R system, whereas the total number of phycobilisomes is governed by the excitation-balancing system between phycobilisomes and photosystems. We reclassify the conventional CA types based on the genome information and designate CA of the two strains as genuine type 2, where components of phycoerythrin, but not rod-membrane linker of phycocyanin, are regulated by the CcaS/R system.

Bacterial Phytochromes, Cyanobacteriochromes and Allophycocyanins as a Source of Near-Infrared Fluorescent Probes

Bacterial photoreceptors absorb light energy and transform it into intracellular signals that regulate metabolism. Bacterial phytochrome photoreceptors (BphPs), some cyanobacteriochromes (CBCRs) and allophycocyanins (APCs) possess the near-infrared (NIR) absorbance spectra that make them promising molecular templates to design NIR fluorescent proteins (FPs) and biosensors for studies in mammalian cells and whole animals. Here, we review structures, photochemical properties and molecular functions of several families of bacterial photoreceptors. We next analyze molecular evolution approaches to develop NIR FPs and biosensors. We then discuss phenotypes of current BphP-based NIR FPs and compare them with FPs derived from CBCRs and APCs. Lastly, we overview imaging applications of NIR FPs in live cells and in vivo. Our review provides guidelines for selection of existing NIR FPs, as well as engineering approaches to develop NIR FPs from the novel natural templates such as CBCRs.

Seeing new light: recent insights into the occurrence and regulation of chromatic acclimation in cyanobacteria

Cyanobacteria exhibit a form of photomorphogenesis termed chromatic acclimation (CA), which involves tuning metabolism and physiology to external light cues, with the most readily recognized acclimation being the alteration of pigmentation. Historically, CA has been represented by three types that occur in organisms which synthesize green-light-absorbing phycoerythrin (PE) and red-light-absorbing phycocyanin (PC). The distinct CA types depend upon whether organisms adjust levels of PE (type II), both PE and PC (type III, also complementary chromatic acclimation), or neither (type I) in response to red or green wavelengths. Recently new forms of CA have been described which include responses to blue and green light (type IV) or far-red light (FaRLiP). Here, the molecular bases of distinct forms of CA are discussed.

Light regulation of pigment and photosystem biosynthesis in cyanobacteria

Most cyanobacteria are obligate oxygenic photoautotrophs, and thus their growth and survival is highly dependent on effective utilization of incident light. Cyanobacteria have evolved a diverse set of phytochromes and cyanobacteriochromes (CBCRs) that allow cells to respond to light in the range from ∼300nm to ∼750nm. Together with associated response regulators, these photosensory proteins control many aspects of cyanobacterial physiology and metabolism. These include far-red light photoacclimation (FaRLiP), complementary chromatic acclimation (CCA), low-light photoacclimation (LoLiP), photosystem content and stoichiometry (long-term adaptation), short-term acclimation (state transitions), circadian rhythm, phototaxis, photomorphogenesis/development, and cellular aggregation. This minireview highlights some discoveries concerning phytochromes and CBCRs as well as two acclimation processes that improve light harvesting and energy conversion under specific irradiance conditions: FaRLiP and CCA.

Hydrophobic Residues near the Bilin Chromophore-Binding Pocket Modulate Spectral Tuning of Insert-Cys Subfamily Cyanobacteriochromes

Cyanobacteriochromes (CBCRs) are a subfamily of phytochrome photoreceptors found exclusively in photosynthetic cyanobacteria. Four CBCRs containing a second Cys in the insert region (insert-Cys) have been identified from the nonheterocystous cyanobacterium Microcoleus B353 (Mbr3854g4 and Mbl3738g2) and the nitrogen fixing, heterocystous cyanobacterium Nostoc punctiforme (NpF2164g3 and NpR1597g2). These insert-Cys CBCRs can sense light in the near-UV to orange range, but key residues responsible for tuning their colour sensitivity have not been reported. In the present study, near-UV/Green (UG) photosensors Mbr3854g4 (UG1) and Mbl3738g2 (UG2) were chosen for further spectroscopic analysis of their spectral sensitivity and tuning. Consistent with most dual-Cys CBCRs, both UGs formed a second thioether linkage to the phycocyanobilin (PCB) chromophore via the insert-Cys. This bond is subject to breakage and relinkage during forward and reverse photoconversions. Variations in residues equivalent to Phe that are in close contact with the PCB chromophore D-ring in canonical red/green CBCRs are responsible for tuning the light absorption peaks of both dark and photoproducts. This is the first time these key residues that govern light absorption in insert-Cys family CBCRs have been identified and characterised.

Mechanisms and fitness implications of photomorphogenesis during chromatic acclimation in cyanobacteria

Photosynthetic organisms absorb photons and convert light energy to chemical energy through the process of photosynthesis. Photosynthetic efficiency is tuned in response to the availability of light, carbon dioxide and nutrients to promote maximal levels of carbon fixation, while simultaneously limiting the potential for light-associated damage or phototoxicity. Given the central dependence on light for energy production, photosynthetic organisms possess abilities to tune their growth, development and metabolism to external light cues in the process of photomorphogenesis. Photosynthetic organisms perceive light intensity and distinct wavelengths or colors of light to promote organismal acclimation. Cyanobacteria are oxygenic photosynthetic prokaryotes that exhibit abilities to alter specific aspects of growth, including photosynthetic pigment composition and morphology, in responses to changes in available wavelengths and intensity of light. This form of photomorphogenesis is known as chromatic acclimation and has been widely studied. Recent insights into the photosensory photoreceptors found in cyanobacteria and developments in our understanding of the molecular mechanisms initiated by light sensing to affect the changes characteristic of chromatic acclimation are discussed. I consider cyanobacterial responses to light, the broad diversity of photoreceptors encoded by these organisms, specific mechanisms of photomorphogenesis, and associated fitness implications in chromatically acclimating cyanobacteria.

In the Limelight: Photoreceptors in Cyanobacteria

Certain cyanobacteria look green if grown in red light and vice versa. This dramatic color change, called complementary chromatic adaptation (CCA), is caused by alterations of the major colored light-harvesting proteins. A major controller of CCA is the cyanobacteriochrome (CBCR) RcaE, a red-green reversible photoreceptor that triggers a complex signal transduction pathway. Now, a new study demonstrates that CCA is also modulated by DpxA, a CBCR that senses yellow and teal (greenish blue) light. DpxA acts to expand the range of wavelengths that can impact CCA, by fine-tuning the process. This dual control of CCA might positively impact the fitness of cells growing in the shade of competing algae or in a water column where light levels and spectral quality change gradually with depth. This discovery adds to the growing number of light-responsive phenomena controlled by multiple CBCRs. Furthermore, the diverse CBCRs which are exclusively found in cyanobacteria have significant biotechnological potential.