Similarity of a chromatic adaptation sensor to phytochrome and ethylene receptors

Stoichiometry of the photosynthetic apparatus and phycobilisome structure of the cyanobacterium Plectonema boryanum UTEX 485 are regulated by both light and temperature

The role of growth temperature and growth irradiance on the regulation of the stoichiometry and function of the photosynthetic apparatus was examined in the cyanobacterium Plectonema boryanum UTEX 485 by comparing mid-log phase cultures grown at either 29 degrees C/150 micromol m(-2) s(-1), 29 degrees C/750 micromol m(-2) s(-1), 15 degrees C/150 micromol m(-2) s(-1), or 15 degrees C/10 micromol m(-2) s(-1). Cultures grown at 29 degrees C/750 micromol m(-2) s(-1) were structurally and functionally similar to those grown at 15 degrees C/150 micromol m(-2) s(-1), whereas cultures grown at 29 degrees C/150 micromol m(-2) s(-1) were structurally and functionally similar to those grown at 15 degrees C/10 micromol m(-2) s(-1). The stoichiometry of specific components of the photosynthetic apparatus, such as the ratio of photosystem (PS) I to PSII, phycobilisome size and the relative abundance of the cytochrome b(6)/f complex, the plastoquinone pool size, and the NAD(P)H dehydrogenase complex were regulated by both growth temperature and growth irradiance in a similar manner. This indicates that temperature and irradiance may share a common sensing/signaling pathway to regulate the stoichiometry and function of the photosynthetic apparatus in P. boryanum. In contrast, the accumulation of neither the D1 polypeptide of PSII, the large subunit of Rubisco, nor the CF(1) alpha-subunit appeared to be regulated by the same mechanism. Measurements of P700 photooxidation in vivo in the presence and absence of inhibitors of photosynthetic electron transport coupled with immunoblots of the NAD(P)H dehydrogenase complex in cells grown at either 29 degrees C/750 micromol m(-2) s(-1) or 15 degrees C/150 micromol m(-2) s(-1) are consistent with an increased flow of respiratory electrons into the photosynthetic intersystem electron transport chain maintaining P700 in a reduced state relative to cells grown at either 29 degrees C/150 micromol m(-2) s(-1) or 15 degrees C/10 micromol m(-2) s(-1). These results are discussed in terms of acclimation to excitation pressure imposed by either low growth temperature or high growth irradiance.

Phytochrome ancestry: sensors of bilins and light

Phytochromes were long thought to have evolved in non-motile photosynthetic eukaryotes for adaptation to unfavorable light environments, but recent studies suggest that phytochromes evolved billions of years earlier from a tetrapyrrole sensor protein progenitor. These investigations have identified phytochromes and phytochrome-related proteins in photosynthetic bacteria (cyanobacteria and purple bacteria), nonphotosynthetic eubacteria and fungi - an observation that has opened new avenues for investigating the origins, molecular evolution and biochemical functions of this ecologically important family of plant photoreceptors.

Two independent, light-sensing two-component systems in a filamentous cyanobacterium

Two ORFs, cphA and cphB, encoding proteins CphA and CphB with strong similarities to plant phytochromes and to the cyanobacterial phytochrome Cph1 of Synechocystis sp. PCC 6803 have been identified in the filamentous cyanobacterium Calothrix sp. PCC7601. While CphA carries a cysteine within a highly conserved amino-acid sequence motif, to which the chromophore phytochromobilin is covalently bound in plant phytochromes, in CphB this position is changed into a leucine. Both ORFs are followed by rcpA and rcpB genes encoding response regulator proteins similar to those known from the bacterial two-component signal transduction. In Calothrix, all four genes are expressed under white light irradiation conditions, albeit in low amounts. For heterologous expression and convenient purification, the cloned genes were furnished with His-tag encoding sequences at their 3' end and expressed in Escherichia coli. The two recombinant apoproteins CphA and CphB bound the chromophore phycocyanobilin (PCB) in a covalent and a noncovalent manner, respectively, and underwent photochromic absorption changes reminiscent of the P(r) and P(fr) forms (red and far-red absorbing forms, respectively) of the plant phytochromes and Cph1. A red shift in the absorption maxima of the CphB/PCB complex (lambda(max) = 685 and 735 nm for P(r) and P(fr), respectively) is indicative for a noncovalent incorporation of the chromophore (lambda(max) of P(r), P(fr) of CphA: 663, 700 nm). A CphB mutant generated at the chromophore-binding position (Leu246-->Cys) bound the chromophore covalently and showed absorption spectra very similar to its paralog CphA, indicating the noncovalent binding to be the only cause for the unexpected absorption properties of CphB. The kinetics of the light-induced P(fr) formation of the CphA-PCB chromoprotein, though similar to that of its ortholog from Synechocystis, showed differences in the kinetics of the P(fr) formation. The kinetics were not influenced by ATP (probing for autophosphorylation) or by the response regulator. In contrast, the light-induced kinetics of the CphB-PCB complex was markedly different, clearly due to the noncovalently bound chromophore.

The cell biology of phytochrome signalling

Phytochrome signal transduction has in the past often been viewed as being a nonspatially separated linear chain of events. However, through a combination of molecular, genetic and cell biological approaches, it is becoming increasingly evident that phytochrome signalling constitutes a highly ordered multidimensional network of events. The discovery that some phytochromes and signalling intermediates show light-dependent nucleo-cytoplasmic partitioning has not only led to the suggestion that early signalling events take place in the nucleus, but also that subcellular localization patterns most probably represent an important signalling control point. Moreover, detailed characterization of signalling intermediates has demonstrated that various branches of the signalling network are spatially separated and take place in different cellular compartments including the nucleus, cytosol, and chloroplasts. In addition, proteasome-mediated degradation of signalling intermediates most probably act in concert with subcellular partitioning events as an integrated checkpoint. An emerging view from this is that phytochrome signalling is separated into several subcellular organelles and that these are interconnected in order to execute accurate responses to changes in the light environment. By integrating the available data, both at the cellular and subcellular level, we should be able to construct a solid foundation for further dissection of phytochrome signal transduction in plants. Contents Summary 553 I. Introduction 554 II. Nucleus vs cytoplasm 556 III. The nucleus 562 IV. The cytoplasm 571 V. Interactions with other signalling pathways 577 VI. Conclusions and the future 582 Acknowledgements 583 References 583.

CpeR is an activator required for expression of the phycoerythrin operon (cpeBA) in the cyanobacterium Fremyella diplosiphon and is encoded in the phycoerythrin linker-polypeptide operon (cpeCDESTR)

In the cyanobacteria, phycobilisomes are assembled from (alphabeta)(6) hexamers of the coloured phycobiliproteins, allophycocyanin, phycocyanin and phycoerythrin (PE). The precise architecture of the phycobilisome is determined by the various colourless linker proteins that bind to the biliprotein hexamers. Genes for beta and alpha subunits of PE make up one operon (cpeBA), whereas genes for PE-associated linker polypeptides are in a second operon. In the chromatically adapting cyanobacterium Fremyella diplosiphon green light is required for the transcription of both cpeBA and the operon encoding the PE-associated linkers (cpeCDE). From the genome of F. diplosiphon we have identified an open reading frame, cpeR, which, when expressed from a shuttle plasmid, is capable of suppressing various mutations that cause a decrease in PE synthesis. The introduction of a shuttle plasmid bearing cpeR+ into wild-type F. diplosiphon caused PE expression in red light. Fremyella diplosiphon cpeR-, created by in vitro mutagenesis and in vivo homologous recombination, is fully PE and, in this strain, cpeCDE is transcribed normally whereas the transcript from cpeBA is undetectable. Polymerase chain reaction (PCR) amplification of cDNA showed that cpeR is transcribed as part of the cpeCDE operon on an extended transcript. As CpeR is an activator required for expression of the cpeBA operon, we propose that at the onset of green light the operons cpeCDESTR and cpeBA are expressed in series as a genetic cascade.

Regulation of cAMP-mediated photosignaling by a phytochrome in the cyanobacterium Anabaena cylindrica

Changes in cellular adenosine 3',5'-cyclic monophosphate (cAMP) content induced by monochromatic light of various wavelengths were determined in the cyanobacterium Anabaena cylindrica. Irradiation with monochromatic red light caused a rapid decrease in cAMP content. In contrast, far-red light caused a rapid increase in its content. The effects of red and far-red light were reversible, suggesting the involvement of a prototype phytochrome as the photoreceptor for cAMP-mediated light-responsive signal transduction.

Bacteriophytochrome controls photosystem synthesis in anoxygenic bacteria

Plants use a set of light sensors to control their growth and development in response to changes in ambient light. In particular, phytochromes exert their regulatory activity by switching between a biologically inactive red-light-absorbing form (Pr) and an active far-red-light absorbing form (Pfr). Recently, biochemical and genetic studies have demonstrated the occurrence of phytochrome-like proteins in photosynthetic and non-photosynthetic bacteria--but little is known about their functions. Here we report the discovery of a bacteriophytochrome located downstream from the photosynthesis gene cluster in a Bradyrhizobium strain symbiont of Aeschynomene. The synthesis of the complete photosynthetic apparatus is totally under the control of this bacteriophytochrome. A similar behaviour is observed for the closely related species Rhodopseudomonas palustris, but not for the more distant anoxygenic photosynthetic bacteria of the genus Rhodobacter, Rubrivivax or Rhodospirillum. Unlike other (bacterio)phytochromes, the carboxy-terminal domain of this bacteriophytochrome contains no histidine kinase features. This suggests a light signalling pathway involving direct protein-protein interaction with no phosphorelay cascade. This specific mechanism of regulation may represent an important ecological adaptation to optimize the plant-bacteria interaction.

The cyanobacterial phytochrome Cph2 inhibits phototaxis towards blue light

We analysed the effects of inactivation of the phytochrome genes cph1 and cph2 on the phototactic migration of the cyanobacterium Synechocystis sp. PCC 6803 under different light qualities. Motility towards white, green, red and far red light was not altered in several independently raised cph1, cph2 and cph1/cph2 double mutants. Blue light (lambda = 400-500 nm) did not induce motility in wild-type and cph1 mutant cells, whereas cph2 and cph1/cph2 double mutants moved towards the blue light. Inhibition of the photosynthetic electron transport by DCMU influenced the motility of cph2 mutants under blue light, but not under white, red and far red light. RNA blot hybridizations did not indicate an altered transcript accumulation of the pilin-encoding pilA1 gene under blue light. We propose that the Cph2 protein is part of a light-stimulated signal transduction chain inhibiting the movement of Synechocystis sp. PCC 6803 cells towards blue light.

nblS, a gene involved in controlling photosynthesis-related gene expression during high light and nutrient stress in Synechococcus elongatus PCC 7942

The HliA protein of the cyanobacterium Synechococcus elongatus PCC 7942 is a small, thylakoid-associated protein that appears to play a role in photoprotection; its transcript rapidly accumulates in response to high-intensity light (HL) and the hli gene family is required for survival of cells in high light. In order to discover regulatory factors involved in HL acclimation in cyanobacteria, a screen was performed for chemically generated mutants unable to properly control expression of the hliA gene in response to HL. One such mutant was identified, and complementation analysis led to the identification of the affected gene, designated nblS. Based on its deduced protein sequence, NblS appears to be a membrane-bound, PAS-domain-bearing, sensor histidine kinase of two-component regulatory systems in bacteria. The nblS mutant was unable to properly control light intensity-mediated expression of several other photosynthesis-related genes, including all three psbA genes and the cpcBA genes. The mutant was also unable to control expression of the hliA and psbA genes in response to low-intensity blue/UV-A light, a response that may be related to the HL-mediated regulation of the genes. Additionally, in response to nutrient deprivation, the nblS mutant was unable to properly control accumulation of the nblA transcript and associated degradation of the light-harvesting phycobilisomes. The nblS mutant dies more rapidly than wild-type cells following exposure to HL or nutrient deprivation, likely due to its inability to properly acclimate to these stress conditions. Thus, the NblS protein is involved in the control of a number of processes critical for altering the photosynthetic apparatus in response to both HL and nutrient stress conditions.

Plants compared to animals: the broadest comparative study of development

If the last common ancestor of plants and animals was unicellular, comparison of the developmental mechanisms of plants and animals would show that development was independently invented in each lineage. And if this is the case, comparison of plant and animal developmental processes would give us a truly comparative study of development, which comparisons merely among animals, or merely among plants, do not-because in each of these lineages, the fundamental mechanisms are similar by descent. Evidence from studies of developmental mechanisms in both kingdoms, and data from genome-sequencing projects, indicate that development evolved independently in the lineages leading to plants and to animals.

A turquoise mutant genetically separates expression of genes encoding phycoerythrin and its associated linker peptides

During complementary chromatic adaptation (CCA), cyanobacterial light harvesting structures called phycobilisomes are restructured in response to ambient light quality shifts. Transcription of genes encoding components of the phycobilisome is differentially regulated during this process: red light activates cpcB2A2, whereas green light coordinately activates the cpeCDE and cpeBA operons. Three signal transduction components that regulate CCA have been isolated to date: a sensor-photoreceptor (RcaE) and two response regulators (RcaF and RcaC). Mutations in the genes encoding these components affect the accumulation of both cpcB2A2 and cpeBA gene products. We have isolated and characterized a new pigmentation mutant called Turquoise 1. We demonstrate that this mutant phenotype is due to a dramatic decrease in cpeBA transcript abundance and results from a lesion in the cpeR gene. However, in this mutant cpeCDE RNA levels remain near those found in wild-type cells. Our results show that the coordinate regulation of cpeBA and cpeCDE by green light can be uncoupled by the loss of CpeR, and we furnish the first genetic evidence that different regulatory mechanisms control these two operons. Sequence analysis of CpeR reveals that it shares limited sequence similarity to members of the PP2C class of protein serine/threonine phosphatases. We also demonstrate that cpeBA and cpeCDE retain light quality responsiveness in a mutant lacking the RcaE photoreceptor. This provides compelling evidence for the partial control of CCA through an as-yet-uncharacterized second light quality sensing system.

Revealing the molecular secrets of marine diatoms

Diatoms are unicellular photosynthetic eukaryotes that contribute close to one quarter of global primary productivity. In spite of their ecological success in the world's oceans, very little information is available at the molecular level about their biology. Their most well-known characteristic is the ability to generate a highly ornamented silica cell wall, which made them very popular study organisms for microscopists in the last century. Recent advances, such as the development of a range of molecular tools, are now allowing the dissection of diatom biology, e.g., for understanding the molecular and cellular basis of bioinorganic pattern formation of their cell walls and for elucidating key aspects of diatom ecophysiology. Making diatoms accessible to genomics technologies will potentiate greatly these efforts and may lead to the use of diatoms to construct submicrometer-scale silica structures for the nanotechnology industry.

Bacteriophytochromes are photochromic histidine kinases using a biliverdin chromophore

Phytochromes comprise a principal family of red/far-red light sensors in plants. Although phytochromes were thought originally to be confined to photosynthetic organisms, we have recently detected phytochrome-like proteins in two heterotrophic eubacteria, Deinococcus radiodurans and Pseudomonas aeruginosa. Here we show that these form part of a widespread family of bacteriophytochromes (BphPs) with homology to two-component sensor histidine kinases. Whereas plant phytochromes use phytochromobilin as the chromophore, BphPs assemble with biliverdin, an immediate breakdown product of haem, to generate photochromic kinases that are modulated by red and far-red light. In some cases, a unique haem oxygenase responsible for the synthesis of biliverdin is part of the BphP operon. Co-expression of this oxygenase with a BphP apoprotein and a haem source is sufficient to assemble holo-BphP in vivo. Both their presence in many diverse bacteria and their simplified assembly with biliverdin suggest that BphPs are the progenitors of phytochrome-type photoreceptors.

Phytochrome Cph1 from the cyanobacterium Synechocystis PCC6803. Purification, assembly, and quaternary structure

The phytochrome Cph1 from the cyanobacterium Synechocystis PCC6803 forms holoprotein adducts with close spectral similarity to plant phytochromes when autoassembled in vitro with bilin chromophores. Cph1 is a 85-kDa protein that acts as a light-regulated histidine kinase seemingly involved in 'two-component' signalling. This paper describes the improvement of Cph1 purification, estimation of the extinction coefficient of holo-Cph1, spectral analyses of the assembly procedure and studies on quaternary structure. During assembly with the natural chromophore phycocyanobilin (PCB), a red-shifted intermediate is observed. A similar result was obtained when phycoerythrobilin was used as chromophore. As shown by SDS/PAGE and Zn2+ fluorescence, the covalent attachment of PCB is blocked by 1 mM iodoacetamide, a cysteine-derivatizing agent. When PCB was incubated with blocked apo-Cph1, again a shoulder at longer wavelengths appeared. It is therefore proposed that the long-wavelength-absorbing form represents the protonated, noncovalently bound bilin. Biliverdin, which is neither protonated nor covalently attached, undergoes spectral changes in its blue-absorbing band upon incubation with apo-Cph1. On the basis of these data we therefore propose a three-step model for phytochrome autoassembly. Size-exclusion chromatography revealed different mobilities for the apoprotein, red-absorbing Cph1-PCB and far-red-absorbing Cph1-PCB. The major peaks of both holoprotein adducts had apparent molecular masses approximately 200 kDa, a result in agreement with the notion that autophosphorylation in sensory histidine kinases requires dimerization. When Cph1-PCB was further purified by preparative native electrophoresis, the mobility on size-exclusion chromatography was approximately 100 kDa, and it was found to have lost its kinase activity, results implying that the material had lost its capacity to dimerize.

Light regulation of type IV pilus-dependent motility by chemosensor-like elements in Synechocystis PCC6803

To optimize photosynthesis, cyanobacteria move toward or away from a light source by a process known as phototaxis. Phototactic movement of the cyanobacterium Synechocystis PCC6803 is a surface-dependent phenomenon that requires type IV pili, cellular appendages implicated in twitching and social motility in a range of bacteria. To elucidate regulation of cyanobacterial motility, we generated transposon-tagged mutants with aberrant phototaxis; mutants were either nonmotile or exhibited an "inverted motility response" (negative phototaxis) relative to wild-type cells. Several mutants contained transposons in genes similar to those involved in bacterial chemotaxis. Synechocystis PCC6803 has three loci with chemotaxis-like genes, of which two, Tax1 and Tax3, are involved in phototaxis. Transposons interrupting the Tax1 locus yielded mutants that exhibited an inverted motility response, suggesting that this locus is involved in controlling positive phototaxis. However, a strain null for taxAY1 was nonmotile and hyperpiliated. Interestingly, whereas the C-terminal region of the TaxD1 polypeptide is similar to the signaling domain of enteric methyl-accepting chemoreceptor proteins, the N terminus has two domains resembling chromophore-binding domains of phytochrome, a photoreceptor in plants. Hence, TaxD1 may play a role in perceiving the light stimulus. Mutants in the Tax3 locus are nonmotile and do not make type IV pili. These findings establish links between chemotaxis-like regulatory elements and type IV pilus-mediated phototaxis.

Phosphorylation of proteins in the light-dependent signalling pathway of a filamentous cyanobacterium

The genome of the filamentous cyanobacterium Calothrix sp. PCC7601 contains two genes, cphA and cphB, encoding proteins with similarity to plant phytochromes and bacterial histidine kinases. In vitro, CphA and CphB readily attach a tetrapyrrole chromophore to develop spectrally active holoproteins that are photointerconvertible between a red light-absorbing and a far-red light-absorbing form. Together with the putative response regulators, RcpA and RcpB, the putative histidine kinases, CphA and CphB, are suggested to constitute two two-component systems of light-dependent signal transduction. In this report, we demonstrate the kinase activity of both CphA and CphB. In vitro experiments carried out on the purified proteins show that CphA and CphB are autophosphorylated in the presence of ATP and that phospho-CphA is capable of efficient phosphotransfer to RcpA as is phospho-CphB towards RcpB. The autophosphorylation and the phosphorelay are dependent on light. Both activities are reduced under red light vs. far-red light irradiation. No phosphoryl transfer occurred between phospho-CphA and RcpB or between phospho-CphB and RcpA. The response regulators RcpA and RcpB can receive a phosphoryl moiety also from the small phospho-donor acetyl phosphate. The stability of the phosphorylated regulators is not affected by CphA and CphB or light.

Characterization of the Cph1 holo-phytochrome from Synechocystis sp. PCC 6803

The cph1 gene from the unicellular cyanobacterium Synechoycstis sp. PCC 6803 encodes a protein with the characteristics of plant phytochromes and histidine kinases of two-component phospho-relay systems. Spectral and biochemical properties of Cph1 have been intensely studied in vitro using protein from recombinant systems, but virtually nothing is known about the situation in the natural host. In the present study, His6-tagged Cph1 was isolated from Synechocystis cells. The cph1-his gene was expressed either under the control of the natural cph1 promoter or over-expressed using the strong promoter of the psbA2 gene. Upon purification with nickel affinity chromatography, the presence of Cph1 in extracts was confirmed by immunoblotting and Zn2+-induced fluorescence. The Cph1 extracts exhibited a red/far-red photoactivity characteristic of phytochromes. Difference spectra were identical with those of the phycocyanobilin adduct of recombinant Cph1, implying that phycocyanobilin is the chromophore of Cph1 in Synechocystis.

Phytochrome A mediates blue light and UV-A-dependent chloroplast gene transcription in green leaves

We characterized the photobiology of light-activated chloroplast transcription and transcript abundance in mature primary leaves by using the following two systems: transplastomic promoter-reporter gene fusions in tobacco (Nicotiana tabacum), and phytochrome (phyA, phyB, and hy2) and cryptochrome (cry1) mutants of Arabidopsis. In both dicots, blue light and UV-A radiation were the major signals that activated total chloroplast and psbA, rbcL, and 16S rrn transcription. In contrast, transcription activities in plants exposed to red and far-red light were 30% to 85% less than in blue light/UV-A, depending on the gene and plant species. Total chloroplast, psbA, and 16S rrn transcription were 60% to 80% less in the Arabidopsis phyA mutant exposed to blue light/UV-A relative to wild type, thus definitively linking phyA signaling to these photoresponses. To our knowledge, the major role of phyA in mediating the blue light/UV-A photoresponses is a new function for phyA in chloroplast biogenesis at this stage of leaf development. Although rbcL expression in plants exposed to UV-A was 50% less in the phyA mutant relative to wild type, blue light-induced rbcL expression was not significantly affected in the phyA, phyB, and cry1 mutants. However, rbcL expression in blue light was 60% less in the phytochrome chromophore mutant, hy2, relative to wild type, indicating that another phytochrome species (phyC, D, or E) was involved in blue light-induced rbcL transcription. Therefore, at least two different phytochromes, as well as phytochrome-independent photosensory pathways, mediated blue light/UV-A-induced transcription of chloroplast genes in mature leaves.

Chromatic adaptation in marine Synechococcus strains

Characterization of two genetically distinct groups of marine Synechococcus sp. strains shows that one, but not the other, increases its phycourobilin/phycoerythrobilin chromophore ratio when growing in blue light. This ability of at least some marine Synechococcus strains to chromatically adapt may help explain their greater abundance in particular ocean environments than cyanobacteria of the genus Prochlorococcus.

Novel putative photoreceptor and regulatory genes Required for the positive phototactic movement of the unicellular motile cyanobacterium Synechocystis sp. PCC 6803

Synechocystis: sp. PCC 6803 is a unicellular motile cyanobacterium, which shows positive or negative phototaxis on agar plates under lateral illumination. By gene disruption in a substrain showing of positive phototaxis, it was demonstrated that mutants defective in sll0038, sll0039, sll0041, sll0042 or sll0043 lost positive phototaxis but showed negative phototaxis away from the light source. Mutants of sll0040, which is located within the cluster of these genes, retained the capacity of positive phototaxis but to a lesser extent than the parent cells. These genes are homologous to che genes, which are involved in flagellar switching for bacterial chemotaxis. Interestingly, sll0041 (designated pisJ1) is predicted to have a chromophore-binding motif of phytochrome-like proteins and a signaling motif of chemoreceptors for bacterial chemotaxis. It is strongly suggested that the positive phototactic response was mediated by a phytochrome-like photoreceptor and CheA/CheY-type signal transduction system.

Phytochromes as light-modulated protein kinases

Many phytochrome responses in plants are induced by red light and inhibited by far-red light. To explain the biochemical basis of these observations, it was speculated that plant phytochromes are light-regulated enzymes more than 40 years ago. The search for such an enzymatic activity has a long and rather tumultuous history. Biochemical data in the late 1980s had suggested that oat phytochrome might be a light-regulated protein kinase. The topic was the subject of intense debate, but solid experimental data backing the kinase model has been published recently. Two lines of research played a key role in this finding: the production of biologically active highly purified recombinant phytochrome and the discovery of phytochromes in prokaryotes. This review discusses the key steps of this discovery, and suggests some hypotheses for the role of protein kinase activity in photomorphogenesis.

Bacteriophytochromes: new tools for understanding phytochrome signal transduction

The recent discovery of phytochrome-like photoreceptors, collectively called bacteriophytochromes, in a number of bacteria has greatly expanded our understanding of the origins and modes of action of phytochromes in higher plants. These primitive receptors contain an N-terminal domain homologous to the chromophore-binding pocket of phytochromes, and like phytochromes, they bind a variety of bilins to generate photochromic holoproteins. Following the chromophore pocket is a domain similar to two-component histidine kinases, suggesting that these bacterial photoreceptors function in phosphorelay cascades that respond to the light environment. Their organization and distribution support the views that higher-plant phytochromes evolved from a cyanobacterial precursor and that they act as light-regulated kinases. With the ability to exploit bacterial genetics, these bacteriophytochromes now offer simple models to help unravel the biochemical and biophysical events that initiate phytochrome signal transmission.

Structure of the GAF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor

GAF domains are ubiquitous motifs present in cyclic GMP (cGMP)-regulated cyclic nucleotide phosphodiesterases, certain adenylyl cyclases, the bacterial transcription factor FhlA, and hundreds of other signaling and sensory proteins from all three kingdoms of life. The crystal structure of the Saccharomyces cerevisiae YKG9 protein was determined at 1.9 A resolution. The structure revealed a fold that resembles the PAS domain, another ubiquitous signaling and sensory transducer. YKG9 does not bind cGMP, but the isolated first GAF domain of phosphodiesterase 5 binds with K:(d) = 650 nM. The cGMP binding site of the phosphodiesterase GAF domain was identified by homology modeling and site-directed mutagenesis, and consists of conserved Arg, Asn, Lys and Asp residues. The structural and binding studies taken together show that the cGMP binding GAF domains form a new class of cyclic nucleotide receptors distinct from the regulatory domains of cyclic nucleotide-regulated protein kinases and ion channels.

Phytochromes and light signal perception by plants--an emerging synthesis

For plants, the sensing of light in the environment is as important as vision is for animals. Fluctuations in light can be crucial to competition and survival. One way plants sense light is through the phytochromes, a small family of diverse photochromic protein photoreceptors whose origins have been traced to the photosynthetic prokaryotes. During their evolution, the phytochromes have acquired sophisticated mechanisms to monitor light. Recent advances in understanding the molecular mechanisms of phytochromes and their significance to evolutionary biology make possible an interim synthesis of this rapidly advancing branch of photobiology.

CikA, a bacteriophytochrome that resets the cyanobacterial circadian clock

The circadian oscillator of the cyanobacterium Synechococcus elongatus, like those in eukaryotes, is entrained by environmental cues. Inactivation of the gene cikA (circadian input kinase) shortens the circadian period of gene expression rhythms in S. elongatus by approximately 2 hours, changes the phasing of a subset of rhythms, and nearly abolishes resetting of phase by a pulse of darkness. The CikA protein sequence reveals that it is a divergent bacteriophytochrome with characteristic histidine protein kinase motifs and a cryptic response regulator motif. CikA is likely a key component of a pathway that provides environmental input to the circadian oscillator in S. elongatus.

The phytochrome gene family in tomato and the rapid differential evolution of this family in angiosperms

A reexamination of the genome of the tomato (renamed Solanum lycopersicum L.) indicates that it contains five, or at most perhaps six, phytochrome genes (PHY), each encoding a different apoprotein (PHY). Five previously identified tomato PHY genes have been designated PHYA, PHYB1, PHYB2, PHYE, and PHYF. A molecular phylogenetic analysis is consistent with the hypothesis that the angiosperm PHY family is composed of four subfamilies (A, B, C/F, and E). Southern analyses indicate that the tomato genome does not contain both a PHYC and a PHYF. Molecular phylogenetic analyses presented here, which utilize for the first time full-length PHY sequences from two completely characterized angiosperm gene families, indicate that tomato PHYF is probably an ortholog of Arabidopsis PHYC. They also confirm that the angiosperm PHY family is undergoing relatively rapid differential evolution. Assuming PHYF is an ortholog of PHYC, PHY genes in eudicots are evolving (Ka/site) at 1.52-2.79 times the rate calculated as average for other plant nuclear genes. Again assuming PHYF is an ortholog of PHYC, the rate of evolution of the C and E subfamilies is at least 1.33 times the rate of the A and B subfamilies. PHYA and PHYB in eudicots are evolving at least 1.45 times as fast as their counterparts in the Poaceae. PHY functional domains also exhibit different evolutionary rates. The C-terminal region of angiosperm PHY (codons 800-1105) is evolving at least 2.11 times as fast as the photosensory domain (codons 200-500). The central region of a domain essential for phytochrome signal transduction (codons 652-712) is also evolving rapidly. Nonsynonymous substitutions occur in this region at 2.03-3.75 times the average rate for plant nuclear genes. It is not known if this rapid evolution results from selective pressure or from the absence of evolutionary constraint.

Two-component systems in plant signal transduction

In plants, two-component systems play important roles in signal transduction in response to environmental stimuli and growth regulators. Genetic and biochemical analyses indicate that sensory hybrid-type histidine kinases, ETR1 and its homologs, function as ethylene receptors and negative regulators in ethylene signaling. Two other hybrid-type histidine kinases, CKI1 and ATHK1, are implicated in cytokinin signaling and osmosensing processes, respectively. A data base search of Arabidopsis ESTs and genome sequences has identified many homologous genes encoding two-component regulators. We discuss the possible origins and functions of these two-component systems in plants.

Bacteriophytochromes: phytochrome-like photoreceptors from nonphotosynthetic eubacteria

Phytochromes are a family of photoreceptors used by green plants to entrain their development to the light environment. The distribution of these chromoproteins has been expanded beyond photoautotrophs with the discovery of phytochrome-like proteins in the nonphotosynthetic eubacteria Deinococcus radiodurans and Pseudomonas aeruginosa. Like plant phytochromes, the D. radiodurans receptor covalently binds linear tetrapyrroles autocatalytically to generate a photochromic holoprotein. However, the attachment site is distinct, using a histidine to potentially form a Schiff base linkage. Sequence homology and mutational analysis suggest that D. radiodurans bacteriophytochrome functions as a light-regulated histidine kinase, which helps protect the bacterium from visible light.

The histidine protein kinase superfamily

Signal transduction in microorganisms and plants is often mediated by His-Asp phosphorelay systems. Two conserved families of proteins are centrally involved: histidine protein kinases and phospho-aspartyl response regulators. The kinases generally function in association with sensory elements that regulate their activities in response to environmental signals. A sequence analysis with 348 histidine kinase domains reveals that this family consists of distinct subgroups. A comparative sequence analysis with 298 available receiver domain sequences of cognate response regulators demonstrates a significant correlation between kinase and regulator subfamilies. These findings suggest that different subclasses of His-Asp phosphorelay systems have evolved independently of one another.

Bacterial photoreceptor with similarity to photoactive yellow protein and plant phytochromes

A phytochrome-like protein called Ppr was discovered in the purple photosynthetic bacterium Rhodospirillum centenum. Ppr has a photoactive yellow protein (PYP) amino-terminal domain, a central domain with similarity to phytochrome, and a carboxyl-terminal histidine kinase domain. Reconstitution experiments demonstrate that Ppr covalently attaches the blue light-absorbing chromophore p-hydroxycinnamic acid and that it has a photocycle that is spectrally similar to, but kinetically slower than, that of PYP. Ppr also regulates chalcone synthase gene expression in response to blue light with autophosphorylation inhibited in vitro by blue light. Phylogenetic analysis demonstrates that R. centenum Ppr may be ancestral to cyanobacterial and plant phytochromes.

Light-dependent translocation of a phytochrome B-GFP fusion protein to the nucleus in transgenic Arabidopsis

Phytochrome is a ubiquitous photoreceptor of plants and is encoded by a small multigene family. We have shown recently that a functional nuclear localization signal may reside within the COOH-terminal region of a major member of the family, phytochrome B (phyB) (Sakamoto, K., and A. Nagatani. 1996. Plant J. 10:859-868). In the present study, a fusion protein consisting of full-length phyB and the green fluorescent protein (GFP) was overexpressed in the phyB mutant of Arabidopsis to examine subcellular localization of phyB in intact tissues. The resulting transgenic lines exhibited pleiotropic phenotypes reported previously for phyB overexpressing plants, suggesting that the fusion protein is biologically active. Immunoblot analysis with anti-phyB and anti-GFP monoclonal antibodies confirmed that the fusion protein accumulated to high levels in these lines. Fluorescence microscopy of the seedlings revealed that the phyB-GFP fusion protein was localized to the nucleus in light grown tissues. Interestingly, the fusion protein formed speckles in the nucleus. Analysis of confocal optical sections confirmed that the speckles were distributed within the nucleus. In contrast, phyB-GFP fluorescence was observed throughout the cell in dark-grown seedlings. Therefore, phyB translocates to specific sites within the nucleus upon photoreceptor activation.

Light receptor kinases in plants!

Plants must adapt to a capricious light environment, but the mechanism by which light signals are transmitted to cause changes in development has long eluded us. The search might be over, however, as two photoreceptors, phytochrome and NPH1, have been shown to autophosphorylate in a light-dependent fashion.

A model for early events in the assembly pathway of cyanobacterial phycobilisomes

Biological self-assembly is remarkable in its fidelity and in the efficient production of intricate molecular machines and functional materials from a heterogeneous mixture of macromolecules. The phycobilisome, a light-harvesting structure of cyanobacteria, presents the opportunity to study an in vivo assembly process in detail. The phycobilisome molecular architecture is defined, and crystal structures are available for all major proteins, as are a large sequence database (including a genome sequence) and effective genetic systems exist for some cyanobacteria. Recent studies on subunit interaction, covalent modification, and protein stability suggest a model for the earliest events in the phycobilisome assembly pathway. Partitioning of phycobilisome proteins between degradation and assembly is proposed to be controlled by the interaction equilibria between phycobilisome assembly partners, processing enzymes and chaperones. The model provides plausible explanations for existing observations and makes predictions that are amenable to direct experimental investigation.

The ethylene-receptor family from Arabidopsis: structure and function

The gaseous hormone ethylene regulates many aspects of plant growth and development. Ethylene is perceived by a family of high-affinity receptors typified by the ETR1 protein from Arabidopsis. The ETR1 gene codes for a protein which contains a hydrophobic N-terminal domain that binds ethylene and a C-terminal domain that is related in sequence to histidine kinase-response regulator two-component signal transducers found in bacteria. A structural model for the ethylene-binding domain is presented in which a Cu(I) ion is coordinated within membrane-spanning alpha-helices of the hydrophobic domain. It is proposed that binding of ethylene to the transition metal would induce a conformational change in the sensor domain that would be propagated to the cytoplasmic transmitter domain of the protein. A total of four additional genes that are related in sequence to ETR1 have been identified in Arabidopsis. Specific missense mutations in any one of the five genes leads to ethylene insensitivity in planta. Models for signal transduction that can account for the genetic dominance of these mutations are discussed.

A model for signal transduction during gamete release in the fucoid alga pelvetia compressa

Fucoid algae release gametes into seawater following an inductive light period (potentiation), and gamete expulsion from potentiated receptacles of Pelvetia compressa began about 2 min after a light-to-dark transition. Agitation of the medium reversed potentiation, with an exponential time course completed in about 3 h. Light regulated two signaling pathways during potentiation and gamete expulsion: a photosynthetic pathway and a photosynthesis-independent pathway in which red light was active but blue light was not. Uptake of K+ appears to have an important role in potentiation, because a 50% inhibition of potentiation occurred in the presence of the tetraethylammonium ion, a K+-channel blocker. A central role of anion channels in the maintenance of potentiation is suggested by the premature release of gametes in the light when receptacles were incubated with inhibitors of slow-type anion channels. An inhibitor of tyrosine kinases, tyrphostin A63, also inhibited potentiation. A model for gamete release from P. compressa is presented that proposes that illumination results in the accumulation of ions (e.g. K+) throughout the cells of the receptacle during potentiation, which then move into the extracellular matrix during gamete expulsion to generate osmomechanical force, resulting in gamete release.

A novel gene, pmgA, specifically regulates photosystem stoichiometry in the cyanobacterium Synechocystis species PCC 6803 in response to high light

Previously, we identified a novel gene, pmgA, as an essential factor to support photomixotrophic growth of Synechocystis species PCC 6803 and reported that a strain in which pmgA was deleted grew better than the wild type under photoautotrophic conditions. To gain insight into the role of pmgA, we investigated the mutant phenotype of pmgA in detail. When low-light-grown (20 microE m(-2) s(-1)) cells were transferred to high light (HL [200 microE m(-2) s(-1)]), pmgA mutants failed to respond in the manner typically associated with Synechocystis. Specifically, mutants lost their ability to suppress accumulation of chlorophyll and photosystem I and, consequently, could not modulate photosystem stoichiometry. These phenotypes seem to result in enhanced rates of photosynthesis and growth during short-term exposure to HL. Moreover, mixed-culture experiments clearly demonstrated that loss of pmgA function was selected against during longer-term exposure to HL, suggesting that pmgA is involved in acquisition of resistance to HL stress. Finally, early induction of pmgA expression detected by reverse transcriptase-PCR upon the shift to HL led us to conclude that pmgA is the first gene identified, to our knowledge, as a specific regulatory factor for HL acclimation.

Signal transduction in bacteria: molecular mechanisms of stimulus-response coupling

In bacteria, adaptive responses to changing environmental conditions are mediated by signal transduction systems that involve modular protein domains. Despite great diversity in the integration of domains into different systems, studies of individual components have revealed molecular strategies that are widely applicable. Studies of receptors have advanced our understanding of how information is transmitted across membranes, the determination of three-dimensional structures of domains of histidine protein kinase domains and response regulator proteins has begun to reveal the molecular basis of signaling via two-component phosphoryltransfer pathways, and the description of 'eukaryotic-like' protein domains involved in bacterial signaling has emphasized the universality of intracellular signaling mechanisms.

Computational learning reveals coiled coil-like motifs in histidine kinase linker domains

The recent rapid growth of protein sequence databases is outpacing the capacity of researchers to biochemically and structurally characterize new proteins. Accordingly, new methods for recognition of motifs and homologies in protein primary sequences may be useful in determining how these proteins might function. We have applied such a method, an iterative learning algorithm, to analyze possible coiled coil domains in histidine kinase receptors. The potential coiled coils have not yet been structurally characterized in any histidine kinase, and they appear outside previously noted kinase homology regions. The learning algorithm uses a combination of established sequence patterns in known coiled coil proteins and histidine kinase sequence data to learn to recognize efficiently this coiled coil-like motif in the histidine kinases. The common appearance of the structural motif in a functionally important part of the receptors suggests hypotheses for kinase regulation and signal transduction.