Similarity of a chromatic adaptation sensor to phytochrome and ethylene receptors

Structure of the biliverdin cofactor in the Pfr state of bathy and prototypical phytochromes

Phytochromes act as photoswitches between the red- and far-red absorbing parent states of phytochromes (Pr and Pfr). Plant phytochromes display an additional thermal conversion route from the physiologically active Pfr to Pr. The same reaction pattern is found in prototypical biliverdin-binding bacteriophytochromes in contrast to the reverse thermal transformation in bathy bacteriophytochromes. However, the molecular origin of the different thermal stabilities of the Pfr states in prototypical and bathy bacteriophytochromes is not known. We analyzed the structures of the chromophore binding pockets in the Pfr states of various bathy and prototypical biliverdin-binding phytochromes using a combined spectroscopic-theoretical approach. For the Pfr state of the bathy phytochrome from Pseudomonas aeruginosa, the very good agreement between calculated and experimental Raman spectra of the biliverdin cofactor is in line with important conclusions of previous crystallographic analyses, particularly the ZZEssa configuration of the chromophore and its mode of covalent attachment to the protein. The highly homogeneous chromophore conformation seems to be a unique property of the Pfr states of bathy phytochromes. This is in sharp contrast to the Pfr states of prototypical phytochromes that display conformational equilibria between two sub-states exhibiting small structural differences at the terminal methine bridges A-B and C-D. These differences may mainly root in the interactions of the cofactor with the highly conserved Asp-194 that occur via its carboxylate function in bathy phytochromes. The weaker interactions via the carbonyl function in prototypical phytochromes may lead to a higher structural flexibility of the chromophore pocket opening a reaction channel for the thermal (ZZE → ZZZ) Pfr to Pr back-conversion.

Fluorescence properties of the chromophore-binding domain of bacteriophytochrome from Deinococcus radiodurans

Fluorescent proteins are versatile tools for molecular imaging. In this study, we report a detailed analysis of the absorption and fluorescence properties of the chromophore-binding domain from Deinococcus radiodurans and its D207H mutant. Using single photon counting and transient absorption techniques, the average excited state lifetime of both studied systems was about 370 ps. The D207H mutation slightly changed the excited state decay profile but did not have a considerable effect on the average decay time of the system or the shape of the absorption and emission spectra of the biliverdin chromophore. We confirmed that the fluorescence properties of both samples are very similar in vivo and in vitro. However, we found that the paraformaldehyde fixation of the Escherichia coli cells containing the recombinant phytochrome protein significantly changed the fluorescence properties of the chromophore-binding domain. The biliverdin fluorescence was diminished almost completely, and the fluorescence originated only from the protoporphyrin molecules. Our results emphasize that the effect of protoporphyrin IXa should not be ignored in the fluorescence experiments with phytochrome systems while designing better red fluorescence markers for cellular imaging.

Green/red cyanobacteriochromes regulate complementary chromatic acclimation via a protochromic photocycle

Cyanobacteriochromes (CBCRs) are cyanobacterial members of the phytochrome superfamily of photosensors. Like phytochromes, CBCRs convert between two photostates by photoisomerization of a covalently bound linear tetrapyrrole (bilin) chromophore. Although phytochromes are red/far-red sensors, CBCRs exhibit diverse photocycles spanning the visible spectrum and the near-UV (330-680 nm). Two CBCR subfamilies detect near-UV to blue light (330-450 nm) via a "two-Cys photocycle" that couples bilin 15Z/15E photoisomerization with formation or elimination of a second bilin-cysteine adduct. On the other hand, mechanisms for tuning the absorption between the green and red regions of the spectrum have not been elucidated as of yet. CcaS and RcaE are members of a CBCR subfamily that regulates complementary chromatic acclimation, in which cyanobacteria optimize light-harvesting antennae in response to green or red ambient light. CcaS has been shown to undergo a green/red photocycle: reversible photoconversion between a green-absorbing 15Z state ((15Z)P(g)) and a red-absorbing 15E state ((15E)P(r)). We demonstrate that RcaE from Fremyella diplosiphon undergoes the same photocycle and exhibits light-regulated kinase activity. In both RcaE and CcaS, the bilin chromophore is deprotonated as (15Z)P(g) but protonated as (15E)P(r). This change of bilin protonation state is modulated by three key residues that are conserved in green/red CBCRs. We therefore designate the photocycle of green/red CBCRs a "protochromic photocycle," in which the dramatic change from green to red absorption is not induced by initial bilin photoisomerization but by a subsequent change in bilin protonation state.

Structures of cyanobacteriochromes from phototaxis regulators AnPixJ and TePixJ reveal general and specific photoconversion mechanism

Cyanobacteriochromes are cyanobacterial tetrapyrrole-binding photoreceptors that share a bilin-binding GAF domain with photoreceptors of the phytochrome family. Cyanobacteriochromes are divided into many subclasses with distinct spectral properties. Among them, putative phototaxis regulators PixJs of Anabaena sp. PCC 7120 and Thermosynechococcus elongatus BP-1 (denoted as AnPixJ and TePixJ, respectively) are representative of subclasses showing red-green-type and blue/green-type reversible photoconversion, respectively. Here, we determined crystal structures for the AnPixJ GAF domain in its red-absorbing 15Z state (Pr) and the TePixJ GAF domain in its green-absorbing 15E state (Pg). The overall structure of these proteins is similar to each other and also similar to known phytochromes. Critical differences found are as follows: (i) the chromophore of AnPixJ Pr is phycocyanobilin in a C5-Z,syn/C10-Z,syn/C15-Z,anti configuration and that of TePixJ Pg is phycoviolobilin in a C10-Z,syn/C15-E,anti configuration, (ii) a side chain of the key aspartic acid is hydrogen bonded to the tetrapyrrole rings A, B and C in AnPixJ Pr and to the pyrrole ring D in TePixJ Pg, (iii) additional protein-chromophore interactions are provided by subclass-specific residues including tryptophan in AnPixJ and cysteine in TePixJ. Possible structural changes following the photoisomerization of the chromophore between C15-Z and C15-E are discussed based on the X-ray structures at 1.8 and 2.0-Å resolution, respectively, in two distinct configurations.

Sensing and responding to UV-A in cyanobacteria

Ultraviolet (UV) radiation can cause stresses or act as a photoregulatory signal depending on its wavelengths and fluence rates. Although the most harmful effects of UV on living cells are generally attributed to UV-B radiation, UV-A radiation can also affect many aspects of cellular processes. In cyanobacteria, most studies have concentrated on the damaging effect of UV and defense mechanisms to withstand UV stress. However, little is known about the activation mechanism of signaling components or their pathways which are implicated in the process following UV irradiation. Motile cyanobacteria use a very precise negative phototaxis signaling system to move away from high levels of solar radiation, which is an effective escape mechanism to avoid the detrimental effects of UV radiation. Recently, two different UV-A-induced signaling systems for regulating cyanobacterial phototaxis were characterized at the photophysiological and molecular levels. Here, we review the current understanding of the UV-A mediated signaling pathways in the context of the UV-A perception mechanism, early signaling components, and negative phototactic responses. In addition, increasing evidences supporting a role of pterins in response to UV radiation are discussed. We outline the effect of UV-induced cell damage, associated signaling molecules, and programmed cell death under UV-mediated oxidative stress.

Red/green cyanobacteriochromes: sensors of color and power

Phytochromes are red/far-red photoreceptors using cysteine-linked linear tetrapyrrole (bilin) chromophores to regulate biological responses to light. Light absorption triggers photoisomerization of the bilin between the 15Z and 15E photostates. The related cyanobacteriochromes (CBCRs) extend the photosensory range of the phytochrome superfamily to shorter wavelengths of visible light. Several subfamilies of CBCRs have been described. Representatives of one such subfamily, including AnPixJ and NpR6012g4, exhibit red/green photocycles in which the 15Z photostate is red-absorbing like that of phytochrome but the 15E photoproduct is instead green-absorbing. Using recombinant expression of individual CBCR domains in Escherichia coli, we fully survey the red/green subfamily from the cyanobacterium Nostoc punctiforme. In addition to 14 new photoswitching CBCRs, one apparently photochemically inactive protein exhibiting intense red fluorescence was observed. We describe a novel orange/green photocycle in one of these CBCRs, NpF2164g7. Dark reversion varied in this panel of CBCRs; some examples were stable as the 15E photoproduct for days, while others reverted to the 15Z dark state in minutes or even seconds. In the case of NpF2164g7, dark reversion was so rapid that reverse photoconversion of the green-absorbing photoproduct was not significant in restoring the dark state, resulting in a broadband response to light. Our results demonstrate that red/green CBCRs can thus act as sensors for the color or intensity of the ambient light environment.

Light-induced alteration of c-di-GMP level controls motility of Synechocystis sp. PCC 6803

Cph2 from the cyanobacterium Synechocystis sp. PCC 6803 is a hybrid photoreceptor that comprises an N-terminal module for red/far-red light reception and a C-terminal module switching between a blue- and a green-receptive state. This unusual photoreceptor exerts complex, light quality-dependent control of the motility of Synechocystis sp. PCC 6803 cells by inhibiting phototaxis towards blue light. Cph2 perceives blue light by its third GAF domain that bears all characteristics of a cyanobacteriochrome (CBCR) including photoconversion between green- and blue-absorbing states as well as formation of a bilin species simultaneously tethered to two cysteines, C994 and C1022. Upon blue light illumination the CBCR domain activates the subsequent C-terminal GGDEF domain, which catalyses formation of the second messenger c-di-GMP. Accordingly, expression of the CBCR-GGDEF module in Δcph2 mutant cells restores the blue light-dependent inhibition of motility. Additional expression of the N-terminal Cph2 fragment harbouring a red/far-red interconverting phytochrome fused to a c-di-GMP degrading EAL domain restores the complex behaviour of the intact Cph2 photosensor. c-di-GMP was shown to regulate flagellar and pili-based motility in several bacteria. Here we provide the first evidence that this universal bacterial second messenger is directly involved in the light-dependent regulation of cyanobacterial phototaxis.

Light Quantity Affects the Regulation of Cell Shape in Fremyella diplosiphon

In some cyanobacteria, the color or prevalent wavelengths of ambient light can impact the protein or pigment composition of the light-harvesting complexes. In some cases, light color or quality impacts cellular morphology. The significance of changes in pigmentation is associated strongly with optimizing light absorption for photosynthesis, whereas the significance of changes in light quality-dependent cellular morphology is less well understood. In natural aquatic environments, light quality and intensity change simultaneously at varying depths of the water column. Thus, we hypothesize that changes in morphology that also have been attributed to differences in the prevalent wavelengths of available light may largely be associated with changes in light intensity. Fremyella diplosiphon shows highly reproducible light-dependent changes in pigmentation and morphology. Under red light (RL), F. diplosiphon cells are blue-green in color, due to the accumulation of high levels of phycocyanin, a RL-absorbing pigment in the light-harvesting complexes or phycobilisomes (PBSs), and the shape of cells are short and rounded. Conversely, under green light (GL), F. diplosiphon cells are red in color due to accumulation of GL-absorbing phycoerythrin in PBSs, and are longer and brick-shaped. GL is enriched at lower depths in the water column, where overall levels of light also are reduced, i.e., to 10% or less of the intensity found at the water surface. We hypothesize that longer cells under low light intensities at increasing depths in the water column, which are generally also enriched in green wavelengths, are associated with greater levels of total photosynthetic pigments in the thylakoid membranes. To test this hypothesis, we grew F. diplosiphon under increasing intensities of GL and observed whether the length of cells diminished due to reduced pressure to maintain larger cells and the associated increased photosynthetic membrane capacity under high light intensity, independent of whether it is light of green wavelengths.

Emerging perspectives on the mechanisms, regulation, and distribution of light color acclimation in cyanobacteria

Chromatic acclimation (CA) provides many cyanobacteria with the ability to tailor the properties of their light-harvesting antennae to the spectral distribution of ambient light. CA was originally discovered as a result of its dramatic cellular phenotype in red and green light. However, discoveries over the past decade have revealed that many pairs of light colors, ranging from blue to infrared, can trigger CA responses. The capacity to undergo CA is widespread geographically, occurs in most habitats around the world, and is found within all major cyanobacterial groups. In addition, many other cellular activities have been found to be under CA control, resulting in distinct physiological and morphological states for cells under different light-color conditions. Several types of CA appear to be the result of convergent evolution, where different strategies are used to achieve the final goal of optimizing light-harvesting antenna composition to maximize photon capture. The regulation of CA has been found to occur primarily at the level of RNA abundance. The CA-regulatory pathways uncovered thus far are two-component systems that use phytochrome-class photoreceptors with sensor-kinase domains to control response regulators that function as transcription factors. However, there is also at least one CA-regulatory pathway that operates at the post-transcriptional level. It is becoming increasingly clear that large numbers of cyanobacterial species have the capacity to acclimate to a wide variety of light colors through the use of a range of different CA processes.

Convergence and divergence of the photoregulation of pigmentation and cellular morphology in Fremyella diplosiphon

Photosynthetic pigment accumulation and cellular and filament morphology are regulated reversibly by green light (GL) and red light (RL) in the cyanobacterium Fremyella diplosiphon during complementary chromatic adaptation (CCA). The photoreceptor RcaE (regulator of chromatic adaptation), which appears to function as a light-responsive sensor kinase, controls both of these responses. Recent findings indicate that downstream of RcaE, the signaling pathways leading to light-dependent changes in morphology or pigment synthesis and/or accumulation branch, and utilize distinct molecular components. We recently reported that the regulation of the accumulation of the GL-absorbing photosynthetic accessory protein phycoerythrin (PE) and photoregulation of cellular morphology are largely independent, as many mutants with severe PE accumulation defects do not have major disruptions in the regulation of cellular morphology. Furthermore, morphology can be disrupted under GL without impacting GL-dependent PE accumulation. Most recently, however, we determined that the disruption of the cpeR gene, which encodes a protein that is known to function as an activator of PE synthesis under GL, results in disruption of cellular morphology under GL and RL. Thus, apart from RcaE, CpeR is only the second known regulator to impact morphology under both light conditions in F. diplosiphon.

Light-dependent attenuation of phycoerythrin gene expression reveals convergent evolution of green light sensing in cyanobacteria

The colorful process of chromatic acclimation allows many cyanobacteria to change their pigmentation in response to ambient light color changes. In red light, cells produce red-absorbing phycocyanin (PC), whereas in green light, green-absorbing phycoerythrin (PE) is made. Controlling these pigment levels increases fitness by optimizing photosynthetic activity in different light color environments. The light color sensory system controlling PC expression is well understood, but PE regulation has not been resolved. In the filamentous cyanobacterium Fremyella diplosiphon UTEX 481, two systems control PE synthesis in response to light color. The first is the Rca pathway, a two-component system controlled by a phytochrome-class photoreceptor, which transcriptionally represses cpeCDESTR (cpeC) expression during growth in red light. The second is the Cgi pathway, which has not been characterized. We determined that the Cgi system also regulates PE synthesis by repressing cpeC expression in red light, but acts posttranscriptionally, requiring the region upstream of the CpeC translation start codon. cpeC RNA stability was comparable in F. diplosiphon cells grown in red and green light, and a short transcript that included the 5' region of cpeC was detected, suggesting that the Cgi system operates by transcription attenuation. The roles of four predicted stem-loop structures within the 5' region of cpeC RNA were analyzed. The putative stem-loop 31 nucleotides upstream of the translation start site was required for Cgi system function. Thus, the Cgi system appears to be a unique type of signal transduction pathway in which the attenuation of cpeC transcription is regulated by light color.

Phytochrome structure and photochemistry: recent advances toward a complete molecular picture

Phytochromes are nature's primary photoreceptors dedicated to detecting the red and far-red regions of the visible light spectrum, a region also essential for photosynthesis and thus crucial to the survival of plants and other photosynthetic organisms. Given their roles in measuring competition and diurnal/seasonal light fluctuations, understanding how phytochromes work at the molecular level would greatly aid in engineering crop plants better suited to specific agricultural settings. Recently, scientists have determined the three-dimensional structures of prokaryotic phytochromes, which now provide clues as to how these modular photoreceptors might work at the atomic level. The models point toward a largely unifying mechanism whereby novel knot, hairpin, and dimeric interfaces transduce photoreversible bilin isomerization into protein conformational changes that alter signal output.

Temporal responses of wild-type pigmentation and RcaE-deficient strains of Fremyella diplosiphon during light transitions

A temporal study was conducted to evaluate the dynamic complementary chromatic adaptation (CCA) response of two Fremyella diplosiphon strains-wild-type pigmentation strain SF33 and an RcaE-deficient (ΔrcaE) strain, which lacks the photosensor that regulates CCA. SF33 and ΔrcaE cultures were monitored for 15 days after transition of green-light (GL) acclimated cultures to red light (RL) and vice versa. SF33 showed similar growth irrespective of the external light quality; however, a ΔrcaE strain grew slower than SF33 under both RL and GL. Chlorophyll a (chla) content increased in both strains over time and was not much different under RL and GL indicating that chla biosynthesis is not affected significantly by light quality or RcaE function. Phycoerythrin is the sole pigment to absorb GL, whereas several pigments, i.e., allophycocyanin, phycocyanin and chla, function under RL to drive photosynthesis. SF33 compensates for this by synthesizing a higher percentage of PE under GL. The final pigment distribution in the ΔrcaE mutant was found to be more different from SF33 under GL than under RL indicating that RcaE is needed for a transitional response to RL and RL-dependent repression of PE accumulation, yet RcaE is virtually critical for both transitioning to and a full adaptation to GL.

Phytochrome signaling mechanisms

Phytochromes are red (R)/far-red (FR) light photoreceptors that play fundamental roles in photoperception of the light environment and the subsequent adaptation of plant growth and development. There are five distinct phytochromes in Arabidopsis thaliana, designated phytochrome A (phyA) to phyE. phyA is light-labile and is the primary photoreceptor responsible for mediating photomorphogenic responses in FR light, whereas phyB-phyE are light stable, and phyB is the predominant phytochrome regulating de-etiolation responses in R light. Phytochromes are synthesized in the cytosol in their inactive Pr form. Upon light irradiation, phytochromes are converted to the biologically active Pfr form, and translocate into the nucleus. phyB can enter the nucleus by itself in response to R light, whereas phyA nuclear import depends on two small plant-specific proteins FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). Phytochromes may function as light-regulated serine/threonine kinases, and can phosphorylate several substrates, including themselves in vitro. Phytochromes are phosphoproteins, and can be dephosphorylated by a few protein phosphatases. Photoactivated phytochromes rapidly change the expression of light-responsive genes by repressing the activity of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), an E3 ubiquitin ligase targeting several photomorphogenesis-promoting transcription factors for degradation, and by inducing rapid phosphorylation and degradation of Phytochrome-Interacting Factors (PIFs), a group of bHLH transcription factors repressing photomorphogenesis. Phytochromes are targeted by COP1 for degradation via the ubiquitin/26S proteasome pathway.

Regulation of phycoerythrin synthesis and cellular morphology in Fremyella diplosiphon green mutants

Light-dependent modification of photosynthetic pigmentation and cellular growth responses is commonly associated with increased fitness in photosynthetic organisms, including cyanobacteria. Prior analyses of pigmentation mutants in the freshwater cyanobacterium Fremyelladiplosiphon has resulted in the observation that RcaE is a photosensor responsible for regulating organismal responses to changes in red light (RL) and green light (GL). RcaE regulates both pigmentation and cellular morphology, yet previous investigations and the analysis of additional pigmentation mutants here show that the signaling pathways regulating pigmentation and morphology appear to branch downstream of RcaE. We provide evidence that a ΔcpeR mutant has altered regulation of cellular morphology in addition to a known disruption in phycoerythrin synthesis. This marks the first description of the association of a regulator with the control of cellular morphology under both RL and GL in F.diplosiphon, apart from RcaE. In addition to providing a link between CpeR and the photoregulation of morphology in F.diplosiphon, the isolation of a ΔcpeR::IS66 mutant in the UTEX 481 strain represents both the first isolation of an IS66-based gene disruption and verification of the existence of an IS66-related element in F. diplosiphon.

Phytochrome signaling: solving the Gordian knot with microbial relatives

Phytochromes encompass a diverse collection of biliproteins that regulate numerous photoresponses in plants and microorganisms. Whereas the plant versions have proven experimentally intractable for structural studies, the microbial forms have recently provided important insights into how these photoreceptors work at the atomic level. Here, we review the current understanding of these microbial phytochromes, which shows that they have a modular dimeric architecture that propagates light-driven rotation of the bilin to distal contacts between adjacent signal output domains. Surprising features underpinning this signaling include: a deeply buried chromophore; a knot and hairpin loop that stabilizes the photosensing domain; and an extended helical spine that translates conformational changes in the photosensing domain to the output domain. Conservation within the superfamily both in modular construction and sequence strongly suggests that higher plant phytochromes work similarly as light-regulated toggle switches.

Diverse two-cysteine photocycles in phytochromes and cyanobacteriochromes

Phytochromes are well-known as photoactive red- and near IR-absorbing chromoproteins with cysteine-linked linear tetrapyrrole (bilin) prosthetic groups. Phytochrome photoswitching regulates adaptive responses to light in both photosynthetic and nonphotosynthetic organisms. Exclusively found in cyanobacteria, the related cyanobacteriochrome (CBCR) sensors extend the photosensory range of the phytochrome superfamily to shorter wavelengths of visible light. Blue/green light sensing by a well-studied subfamily of CBCRs proceeds via a photolabile thioether linkage to a second cysteine fully conserved in this subfamily. In the present study, we show that dual-cysteine photosensors have repeatedly evolved in cyanobacteria via insertion of a second cysteine at different positions within the bilin-binding GAF domain (cGMP-specific phosphodiesterases, cyanobacterial adenylate cyclases, and formate hydrogen lyase transcription activator FhlA) shared by CBCRs and phytochromes. Such sensors exhibit a diverse range of photocycles, yet all share ground-state absorbance of near-UV to blue light and a common mechanism of light perception: reversible photoisomerization of the bilin 15,16 double bond. Using site-directed mutagenesis, chemical modification and spectroscopy to characterize novel dual-cysteine photosensors from the cyanobacterium Nostoc punctiforme ATCC 29133, we establish that this spectral diversity can be tuned by varying the light-dependent stability of the second thioether linkage. We also show that such behavior can be engineered into the conventional phytochrome Cph1 from Synechocystis sp. PCC6803. Dual-cysteine photosensors thus allow the phytochrome superfamily in cyanobacteria to sense the full solar spectrum at the earth surface from near infrared to near ultraviolet.

Bacterial phytochromes: more than meets the light

Phytochromes are environmental sensors, historically thought of as red/far-red photoreceptors in plants. Their photoperception occurs through a covalently linked tetrapyrrole chromophore, which undergoes a light-dependent conformational change propagated through the protein to a variable output domain. The phytochrome composition is modular, typically consisting of a PAS-GAF-PHY architecture for the N-terminal photosensory core. A collection of three-dimensional structures has uncovered key features, including an unusual figure-of-eight knot, an extension reaching from the PHY domain to the chromophore-binding GAF domain, and a centrally located, long α-helix hypothesized to be crucial for intramolecular signaling. Continuing identification of phytochromes in microbial systems has expanded the assigned sensory abilities of this family out of the red and into the yellow, green, blue, and violet portions of the spectrum. Furthermore, phytochromes acting not as photoreceptors but as redox sensors have been recognized. In addition, architectures other than PAS-GAF-PHY are known, thus revealing phytochromes to be a varied group of sensory receptors evolved to utilize their modular design to perceive a signal and respond accordingly. This review focuses on the structures of bacterial phytochromes and implications for signal transmission. We also discuss the small but growing set of bacterial phytochromes for which a physiological function has been ascertained.

Determining cell shape: adaptive regulation of cyanobacterial cellular differentiation and morphology

Similar to other bacteria, cyanobacteria exist in a wide-ranging diversity of shapes and sizes. However, three general shapes are observed most frequently: spherical, rod and spiral. Bacteria can also grow as filaments of cells. Some filamentous cyanobacteria have differentiated cell types that exhibit distinct morphologies: motile hormogonia, nitrogen-fixing heterocysts, and spore-like akinetes. Cyanobacterial cell shapes, which are largely controlled by the cell wall, can be regulated by developmental and/or environmental cues, although the mechanisms of regulation and the selective advantage(s) of regulating cellular shape are still being elucidated. In this review, recent insights into developmental and environmental regulation of cell shape in cyanobacteria and the relationship(s) of cell shape and differentiation to organismal fitness are discussed.

Characterization of complementary chromatic adaptation in Gloeotrichia UTEX 583 and identification of a transposon-like insertion in the cpeBA operon

Many cyanobacteria are able to alter the pigment composition of the phycobilisome in a process called complementary chromatic adaptation (CCA). The regulatory mechanisms of CCA have been identified in Fremyella diplosiphon, which regulates both phycoerythrin and phycocyanin levels, and Nostoc punctiforme, which regulates only phycoerythrin production. Recent studies show that these species use different regulatory proteins for CCA. We chose to study the CCA response of Gloeotrichia UTEX 583 in an effort to expand our knowledge about CCA and its regulation. We found that Gloeotrichia 583 has a CCA pigment response more similar to that of N. punctiforme rather than F. diplosiphon and exhibits none of the CCA-regulated morphological responses seen in F. diplosiphon. Preliminary experiments suggest that Gloeotrichia 583 contains a homolog to the CCA photoreceptor from N. punctiforme but not the CCA photoreceptor from F. diplosiphon. Additionally, two spontaneous mutants lacking phycoerythrin production were identified. Analysis has shown that these mutants contain a transposon-like insertion in the cpeA gene, which encodes the α subunit of phycoerythrin. These results suggest that CCA in Gloeotrichia UTEX 583 is more similar to that of N. punctiforme than it is to F. diplosiphon, a closely related species.

Lights on and action! Controlling microbial gene expression by light

Light-mediated control of gene expression and thus of any protein function and metabolic process in living microbes is a rapidly developing field of research in the areas of functional genomics, systems biology, and biotechnology. The unique physical properties of the environmental factor light allow for an independent photocontrol of various microbial processes in a noninvasive and spatiotemporal fashion. This mini review describes recently developed strategies to generate photo-sensitive expression systems in bacteria and yeast. Naturally occurring and artificial photoswitches consisting of light-sensitive input domains derived from different photoreceptors and regulatory output domains are presented and individual properties of light-controlled expression systems are discussed.

Purification and characterization of a recombinant bacteriophytochrome of Xanthomonas oryzae pathovar oryzae

Phytochrome-like proteins have been recently identified in prokaryotes but their features and functions are not clear. We cloned a gene encoding the phytochrome-like protein (XoBphP) in a pathogenic bacteria, Xanthomonas oryzae pv. oryzae (Xoo) and investigated characteristics of the protein using a recombinant XoBphP. The N-terminal region of XoBphP containing the PAS/GAF/PHY domains is highly similar to most bacteriophytochromes, but Cys4, corresponding to Cys24 of DrBphP, isn't involved in chromophore attachment. Recombinant XoBphP could bind a bilin molecule and a differential spectrum from Pr/Pfr shows that XoBphP has similar characteristics of known bacteriophytochromes with shifted absorption maxima of 683 and 757 nm for the Pr and Pfr forms. Unlike other bacteriophytochromes, XoBphP has no histidine kinase domain at C-terminus. The domain was predicted from amino-acid 279 to 342 with less significance than the required threshold. This result suggests that XoBphP probably has different signal transduction mechanisms for its intracellular function.

Fungi, hidden in soil or up in the air: light makes a difference

Light is one of the most important environmental factors for orientation of almost all organisms on Earth. Whereas light sensing is of crucial importance in plants to optimize light-dependent energy conservation, in nonphotosynthetic organisms, the synchronization of biological clocks to the length of a day is an important function. Filamentous fungi may use the light signal as an indicator for the exposure of hyphae to air and adapt their physiology to this situation or induce morphogenetic pathways. Although a yes/no decision appears to be sufficient for the light-sensing function in fungi, most species apply a number of different, wavelength-specific receptors. The core of all receptor types is a chromophore, a low-molecular-weight organic molecule, such as flavin, retinal, or linear tetrapyrrols for blue-, green-, or red-light sensing, respectively. Whereas the blue-light response in fungi is one of the best-studied light responses, all other light-sensing mechanisms are less well studied or largely unknown. The discovery of phytochrome in bacteria and fungi in recent years not only advanced the scientific field significantly, but also had great impact on our view of the evolution of phytochrome-like photoreceptors.

Characterization of green mutants in Fremyella diplosiphon provides insight into the impact of phycoerythrin deficiency and linker function on complementary chromatic adaptation

Functions of phycobiliprotein (PBP) linkers are less well studied than other PBP polypeptides that are structural components or required for the synthesis of the light-harvesting phycobilisome (PBS) complexes. Linkers serve both structural and functional roles in PBSs. Here, we report the isolation of a phycoerythrin (PE) rod-linker mutant and a novel PE-deficient mutant in Fremyella diplosiphon. We describe their phenotypic characterization, including light-dependent photosynthetic pigment accumulation and photoregulation of cellular morphology. PE-linker protein CpeE and a novel protein impact PE accumulation, and thus PBS function, primarily under green light conditions.

Functional characterization of a cyanobacterial OmpR/PhoB class transcription factor binding site controlling light color responses

Complementary chromatic acclimation (CCA) allows many cyanobacteria to change the composition of their light-harvesting antennae for maximal absorption of different wavelengths of light. In the freshwater species Fremyella diplosiphon, this process is controlled by the ratio of red to green light and allows the differential regulation of two subsets of genes in the genome. This response to ambient light color is controlled in part by a two-component system that includes a phytochrome class photoreceptor and a response regulator with an OmpR/PhoB class DNA binding domain called RcaC. During growth in red light, RcaC is able to simultaneously activate expression of red light-induced genes and repress expression of green light-induced genes through binding to the L box promoter element. Here we investigate how the L box functions as both an activator and a repressor under the same physiological conditions by analyzing the effects of changing the position, orientation, and sequence of the L box. We demonstrate that changes in the local sequences surrounding the L box affect the strength of its activity and that the activating and repressing functions of the L box are orientation dependent. Also, the spacing between the L box and the transcription start site is critical for it to work as an activator, while its repressing role during light regulation requires additional upstream and downstream DNA sequence elements. The latter result suggests that the repressing function of RcaC requires it to operate in association with multiple additional DNA binding proteins, at least one of which is functioning as an activator.

Exploiting the autofluorescent properties of photosynthetic pigments for analysis of pigmentation and morphology in live Fremyella diplosiphon cells

Fremyella diplosiphon is a freshwater, filamentous cyanobacterium that exhibits light-dependent regulation of photosynthetic pigment accumulation and cellular and filament morphologies in a well-known process known as complementary chromatic adaptation (CCA). One of the techniques used to investigate the molecular bases of distinct aspects of CCA is confocal laser scanning microscopy (CLSM). CLSM capitalizes on the autofluorescent properties of cyanobacterial phycobiliproteins and chlorophyll a. We employed CLSM to perform spectral scanning analyses of F. diplosiphon strains grown under distinct light conditions. We report optimized utilization of CLSM to elucidate the molecular basis of the photoregulation of pigment accumulation and morphological responses in F. diplosiphon.

A brief history of phytochromes

Photosensory proteins enable living things to detect the quantity and quality of the light environment and to transduce that physical signal into biochemical outputs which entrain their metabolism with the ambient light environment. Phytochromes, which photoconvert between red-absorbing P(r) and far-red-absorbing P(fr) states, are the most extensively studied of these interesting proteins. Critical regulators of a number of key adaptive processes in higher plants, including photomorphogenesis and shade avoidance, phytochromes are widespread in photosynthetic and nonphotosynthetic bacteria, and even in fungi. Cyanobacterial genomes also possess a plethora of more distant relatives of phytochromes known as cyanobacteriochromes (CBCRs). Biochemical characterization of representative CBCRs has demonstrated that this class of photosensors exhibits a broad range of wavelength sensitivities, spanning the entire visible spectrum. Distinct protein-bilin interactions are responsible for this astonishing array of wavelength sensitivities. Despite this spectral diversity, all members of the extended family of phytochrome photosensors appear to share a common photochemical mechanism for light sensing: photoisomerization of the 15/16 double bond of the bilin chromophore.

A framework for classification of prokaryotic protein kinases

BACKGROUND

Overwhelming majority of the Serine/Threonine protein kinases identified by gleaning archaeal and eubacterial genomes could not be classified into any of the well known Hanks and Hunter subfamilies of protein kinases. This is owing to the development of Hanks and Hunter classification scheme based on eukaryotic protein kinases which are highly divergent from their prokaryotic homologues. A large dataset of prokaryotic Serine/Threonine protein kinases recognized from genomes of prokaryotes have been used to develop a classification framework for prokaryotic Ser/Thr protein kinases.

METHODOLOGY/PRINCIPAL FINDINGS

We have used traditional sequence alignment and phylogenetic approaches and clustered the prokaryotic kinases which represent 72 subfamilies with at least 4 members in each. Such a clustering enables classification of prokaryotic Ser/Thr kinases and it can be used as a framework to classify newly identified prokaryotic Ser/Thr kinases. After series of searches in a comprehensive sequence database we recognized that 38 subfamilies of prokaryotic protein kinases are associated to a specific taxonomic level. For example 4, 6 and 3 subfamilies have been identified that are currently specific to phylum proteobacteria, cyanobacteria and actinobacteria respectively. Similarly subfamilies which are specific to an order, sub-order, class, family and genus have also been identified. In addition to these, we also identify organism-diverse subfamilies. Members of these clusters are from organisms of different taxonomic levels, such as archaea, bacteria, eukaryotes and viruses.

CONCLUSION/SIGNIFICANCE

Interestingly, occurrence of several taxonomic level specific subfamilies of prokaryotic kinases contrasts with classification of eukaryotic protein kinases in which most of the popular subfamilies of eukaryotic protein kinases occur diversely in several eukaryotes. Many prokaryotic Ser/Thr kinases exhibit a wide variety of modular organization which indicates a degree of complexity and protein-protein interactions in the signaling pathways in these microbes.

Cyanobacteriochrome CcaS regulates phycoerythrin accumulation in Nostoc punctiforme, a group II chromatic adapter

Responding to green and red light, certain cyanobacteria change the composition of their light-harvesting pigments, phycoerythrin (PE) and phycocyanin (PC). Although this phenomenon-complementary chromatic adaptation-is well known, the green light-sensing mechanism for PE accumulation is unclear. The filamentous cyanobacterium Nostoc punctiforme ATCC 29133 (N. punctiforme) regulates PE synthesis in response to green and red light (group II chromatic adaptation). We disrupted the green/red-perceiving histidine-kinase gene (ccaS) or the cognate response regulator gene (ccaR), which are clustered with several PE and PC genes (cpeC-cpcG2-cpeR1 operon) in N. punctiforme. Under green light, wild-type cells accumulated a significant amount of PE upon induction of cpeC-cpcG2-cpeR1 expression, whereas they accumulated little PE with suppression of cpeC-cpcG2-cpeR1 expression under red light. Under both green and red light, the ccaS mutant constitutively accumulated some PE with constitutively low cpeC-cpcG2-cpeR1 expression, whereas the ccaR mutant accumulated little PE with suppression of cpeC-cpcG2-cpeR1 expression. The results of an electrophoretic mobility shift assay suggest that CcaR binds to the promoter region of cpeC-cpcG2-cpeR1, which contains a conserved direct-repeat motif. Taken together, the results suggest that CcaS phosphorylates CcaR under green light and that phosphorylated CcaR then induces cpeC-cpcG2-cpeR1 expression, leading to PE accumulation. In contrast, CcaS probably represses cpeC-cpcG2-cpeR1 expression by dephosphorylation of CcaR under red light. We also found that the cpeB-cpeA operon is partially regulated by green and red light, suggesting that the green light-induced regulatory protein CpeR1 activates cpeB-cpeA expression together with constitutively induced CpeR2.

Stress sensors and signal transducers in cyanobacteria

In living cells, the perception of environmental stress and the subsequent transduction of stress signals are primary events in the acclimation to changes in the environment. Some molecular sensors and transducers of environmental stress cannot be identified by traditional and conventional methods. Based on genomic information, a systematic approach has been applied to the solution of this problem in cyanobacteria, involving mutagenesis of potential sensors and signal transducers in combination with DNA microarray analyses for the genome-wide expression of genes. Forty-five genes for the histidine kinases (Hiks), 12 genes for serine-threonine protein kinases (Spks), 42 genes for response regulators (Rres), seven genes for RNA polymerase sigma factors, and nearly 70 genes for transcription factors have been successfully inactivated by targeted mutagenesis in the unicellular cyanobacterium Synechocystis sp. PCC 6803. Screening of mutant libraries by genome-wide DNA microarray analysis under various stress and non-stress conditions has allowed identification of proteins that perceive and transduce signals of environmental stress. Here we summarize recent progress in the identification of sensory and regulatory systems, including Hiks, Rres, Spks, sigma factors, transcription factors, and the role of genomic DNA supercoiling in the regulation of the responses of cyanobacterial cells to various types of stress.

Molecular Genetics of Emericella nidulans Sexual Development

Many aspergilli that belongs to ascomycetes have sexuality. In a homothallic or self-fertile fungus, a number of fruiting bodies or cleistothecia are formed in a thallus grown from a single haploid conidia or ascospores. Genome-sequencing project revealed that two mating genes (MAT) encoding the regulatory proteins that are necessary for controlling partner recognition in heterothallic fungi were conserved in most aspergilli. The MAT gene products in some self-fertile species were not required for recognition of mating partner at pheromone-signaling stage but required at later stages of sexual development. Various environmental factors such as nutritional status, culture conditions and several stresses, influence the decision or progression of sexual reproduction. A large number of genes are expected to be involved in sexual development of Emericella nidulans (anamorph: Aspergillus nidulans), a genetic and biological model organism in aspergilli. The sexual development process can be grouped into several development stages, including the decision of sexual reproductive cycle, mating process, growth of fruiting body, karyogamy followed by meiosis, and sporulation process. Complicated regulatory networks, such as signal transduction pathways and gene expression controls, may work in each stage and stage-to-stage linkages. In this review, the components joining in the regulatory pathways of sexual development, although they constitute only a small part of the whole regulatory networks, are briefly mentioned. Some of them control sexual development positively and some do negatively. Regarding the difficulties for studying sexual differentiation compare to asexual one, recent progresses in molecular genetics of E. nidulans enlarge the boundaries of understanding sexual development in the non-fertile species as well as in fertile fungi.

Cyanochromes are blue/green light photoreversible photoreceptors defined by a stable double cysteine linkage to a phycoviolobilin-type chromophore

Phytochromes are a collection of bilin-containing photoreceptors that regulate a diverse array of processes in microorganisms and plants through photoconversion between two stable states, a red light-absorbing Pr form, and a far red light-absorbing Pfr form. Recently, a novel set of phytochrome-like chromoproteins was discovered in cyanobacteria, designated here as cyanochromes, that instead photoconvert between stable blue and green light-absorbing forms Pb and Pg, respectively. Here, we show that the distinctive absorption properties of cyanochromes are facilitated through the binding of phycocyanobilin via two stable cysteine-based thioether linkages within the cGMP phosphodiesterase/adenyl cyclase/FhlA domain. Absorption, resonance Raman and infrared spectroscopy, and molecular modeling of the Te-PixJ GAF (cGMP phosphodiesterase/adenyl cyclase/FhlA) domain assembled with phycocyanobilin are consistent with attachments to the C3(1) carbon of the ethylidene side chain and the C4 or C5 carbons in the A-B methine bridge to generate a double thioether-linked phycoviolobilin-type chromophore. These spectroscopic methods combined with NMR data show that the bilin is fully protonated in the Pb and Pg states and that numerous conformation changes occur during Pb --> Pg photoconversion. Also identified were a number of photochromically inactive mutants with strong yellow or red fluorescence that may be useful for fluorescence-based cell biological assays. Phylogenetic analyses detected cyanochromes capable of different signaling outputs in a wide range of cyanobacterial species. One unusual case is the Synechocystis cyanochrome Etr1 that also binds ethylene, suggesting that it works as a hybrid receptor to simultaneously integrate light and hormone signals.

Light-dependent and light-independent protochlorophyllide oxidoreductases in the chromatically adapting cyanobacterium Fremyella diplosiphon UTEX 481

The cyanobacterium Fremyella diplosiphon can alternate its light-harvesting pigments, a process called comple-mentary chromatic adaptation (CCA), allowing it to photosynthesize in green light (GL) and in fluctuating light conditions. Nevertheless, F. diplosiphon requires chlorophylls for photosynthesis under all light conditions. Two alternative enzymes catalyze the penultimate step of chlorophyll synthesis, light-dependent protochlorophyllide oxidoreductase (LPOR) and dark-operative protochlo-rophyllide oxidoreductase (DPOR). DPOR enzymatic activity is light independent, while LPOR requires light. Therefore, we hypothesize that F. diplosiphon up-regulates DPOR gene expression in GL, so that DPOR is more abundant when LPOR is less functional. We cloned the genes encoding the three subunits of DPOR, chlL, chlN and chlB, and the LPOR gene, por, to determine the abundance of the transcripts under red light (RL), GL and dark conditions. We found that F. diplosiphon chlL and chlN genes are transcribed as parts of a single operon, a gene structure that is conserved within cyanobacteria. Tran-scripts levels of all DPOR genes are up-regulated approximately 2-fold in GL relative to levels in RL, whereas LPOR transcript levels are reduced in GL. Moreover, mutations in CCA regulators, RcaE and CpeR, modify DPOR and LPOR transcript levels under specific light conditions. Finally, both DPOR and LPOR transcripts are down-regulated 2- to 5-fold in the dark. These results provide the first evidence that light quality and CCA affect the genetic regulation of chlorophyll biosynthesis in freshwater cyanobacteria, ecologically important photosynthetic organisms.

Shedding new light on the regulation of complementary chromatic adaptation

Complementary chromatic adaptation (CCA) is a light-dependent acclimation process that occurs in cyanobacteria and likely is related to increased fitness of these organisms in natural environments. Although CCA has been studied for over 40 years, significant advances in our understanding of the molecular foundations of CCA are still emerging. In this minireview, I explore recently reported developments that include novel insights into the molecular mechanisms utilized in the photoregulation of pigmentation and the molecular basis of light-dependent changes in cellular morphology, which are central elements of the process of CCA. I also discuss future avenues of study that are expected to lead to additional progress in our understanding of CCA and our general appreciation of light sensing and photomorphogenesis in cyanobacteria.

Discovering functional novelty in metagenomes: examples from light-mediated processes

The emerging coverage of diverse habitats by metagenomic shotgun data opens new avenues of discovering functional novelty using computational tools. Here, we apply three different concepts for predicting novel functions within light-mediated microbial pathways in five diverse environments. Using phylogenetic approaches, we discovered two novel deep-branching subfamilies of photolyases (involved in light-mediated repair) distributed abundantly in high-UV environments. Using neighborhood approaches, we were able to assign seven novel functional partners in luciferase synthesis, nitrogen metabolism, and quorum sensing to BLUF domain-containing proteins (involved in light sensing). Finally, by domain analysis, for RcaE proteins (involved in chromatic adaptation), we predict 16 novel domain architectures that indicate novel functionalities in habitats with little or no light. Quantification of protein abundance in the various environments supports our findings that bacteria utilize light for sensing, repair, and adaptation far more widely than previously thought. While the discoveries illustrate the opportunities in function discovery, we also discuss the immense conceptual and practical challenges that come along with this new type of data.

Abundance changes of the response regulator RcaC require specific aspartate and histidine residues and are necessary for normal light color responsiveness

RcaC is a large, complex response regulator that controls transcriptional responses to changes in ambient light color in the cyanobacterium Fremyella diplosiphon. The regulation of RcaC activity has been shown previously to require aspartate 51 and histidine 316, which appear to be phosphorylation sites that control the DNA binding activity of RcaC. All available data suggest that during growth in red light, RcaC is phosphorylated and has relatively high DNA binding activity, while during growth in green light RcaC is not phosphorylated and has less DNA binding activity. RcaC has also been found to be approximately sixfold more abundant in red light than in green light. Here we demonstrate that the light-controlled abundance changes of RcaC are necessary, but not sufficient, to direct normal light color responses. RcaC abundance changes are regulated at both the RNA and protein levels. The RcaC protein is significantly less stable in green light than in red light, suggesting that the abundance of this response regulator is controlled at least in part by light color-dependent proteolysis. We provide evidence that the regulation of RcaC abundance does not depend on any RcaC-controlled process but rather depends on the presence of the aspartate 51 and histidine 316 residues that have previously been shown to control the activity of this protein. We propose that the combination of RcaC abundance changes and modification of RcaC by phosphorylation may be necessary to provide the dynamic range required for transcriptional control of RcaC-regulated genes.

The phytochrome red/far-red photoreceptor superfamily

The phytochrome protein superfamily reveals a diversity of mechanisms of action.

Proteins of the phytochrome superfamily of red/far-red light receptors have a variety of biological roles in plants, algae, bacteria and fungi and demonstrate a diversity of spectral sensitivities and output signaling mechanisms. Over the past few years the first three-dimensional structures of phytochrome light-sensing domains from bacteria have been determined.

Cyanobacteriochromes: a new superfamily of tetrapyrrole-binding photoreceptors in cyanobacteria

A new group of photoreceptors has been experimentally revealed in cyanobacteria. They are phototaxis regulator SyPixJ1, TePixJ and AnPixJ, chromatic acclimation regulator SyCcaS, circadian input kinase homolog SyCikA and many other candidates, which have been found only in cyanobacteria to date. These new photoreceptors are now proposed to be "cyanobacteriochromes". They are characterized by the presence of a chromophore-binding GAF domain that is homologous to the tetrapyrrole-binding GAF domain of the phytochrome. Here, we summarized unique features of those representatives: (1) only the GAF domain is sufficient for full photoconversion, (2) the GAF domain is homologous to but distinct from the phytochrome GAF, (3) the GAF domain binds a linear tetrapyrrole pigment such as phycoviolobilin or phycocyanobilin, (4) spectral properties are very diverse from near ultra-violet to red region. We also discussed the functionality of the other candidate GAFs, structure and evolution.