The role of COP1 in repression of Arabidopsis photomorphogenic development

Regulated proteolysis and plant development

Eukaryotes use the ubiquitin-proteasome system to control the abundance of regulatory proteins such as cell-cycle proteins and transcription factors. Over 5% of the Arabidopsis genome encodes for proteins with an apparent functional homology to components of the ubiquitin-proteasome system. This suggests that ubiquitin-mediated proteolysis has a major role in plant growth and development. Consistent with this notion, various processes, including most phytohormone responses and photomorphogenesis, have already been shown to require protein degradation in one way or another. In this review, we provide an overview of the plant ubiquitin-proteasome system and its role during Arabidopsis development. Since we consider auxin response and photomorphogenesis as particularly instructive examples, these processes are reviewed in greater detail.

The COP9 signalosome (CSN): an evolutionary conserved proteolysis regulator in eukaryotic development

The COP9 signalosome (CSN) is a multiprotein complex of the ubiquitin-proteasome pathway. CSN is typically composed of eight subunits, each of which is related to one of the eight subunits that form the lid of the 26S proteasome regulatory particle. CSN was first identified in Arabidopsis where it is required for the repression of photomorphogenic seedling development in the dark. CSN or CSN-related complexes have by now been reported from most eukaryotic model organisms and CSN has been implicated in a vast array of biological processes. It is widely accepted that CSN directly interacts with cullin-containing E3 ubiquitin ligases, and that CSN is required for their proper function. The requirement of CSN for proper E3 function may at least in part be explained by the observation that CSN subunit 5 (CSN5) is the isopeptidase that deconjugates the essential ubiquitin-like Nedd8 modification from the E3 cullin subunit. In addition to its interaction with E3s, CSN may also regulate proteolysis by its association with protein kinases and deubiquitylating enzymes. This review provides a summary of the role of CSN in regulating protein degradation and in eukaryotic development.

Flowering of Arabidopsis cop1 mutants in darkness

To elucidate the role of the COP1 gene in flowering, we analyzed flowering of cop1 mutant lines in darkness. When grown in the presence of 1% (w/v) sucrose, the cop1-6 mutant flowered in darkness, but cop1-1 and cop1-4 did not. However, cop1-1 and cop1-4 flowered in darkness when grown in the presence of 5% (w/v) sucrose. Therefore, the COP1 gene represses not only photomorphogenesis in seedlings but also flowering in darkness. Comparison of mRNAs levels of floral identity genes in cop1-6 and wild-type plants grown in darkness revealed increased mRNA levels of genes that act downstream of CO and reduced FLC mRNA level in cop1-6. Double mutants of cop1-6 and each of the late-flowering mutations cry2-1, gi-2, co-1, and ld-1 flowered in darkness. All of the double mutants except cry2-1 cop1-6 flowered later than cop1-6, demonstrating that cop1-6 is epistatic to cry2-1 for early flowering. The ld-1 cop1-6 double mutant flowered much earlier than the ld-1 mutant. The delay in flowering in the double mutants was not strongly influenced by the light conditions, whereas that of the gi-2 cop1-6 double mutant was reduced in darkness.

Ddb1 is required for the proteolysis of the Schizosaccharomyces pombe replication inhibitor Spd1 during S phase and after DNA damage

Recently we showed that the Schizosaccharomyces pombe ddb1 gene plays a role in S phase progression. A mutant S. pombe strain lacking expression of the ddb1 gene exhibited slow replication through both early and late regions causing a slow S phase phenotype. We attributed the phenotypes in the ddb1 strain to an increased activity of the replication checkpoint kinase Cds1. However, the basis for a high basal Cds1 activity in the ddb1 strain was not clear. It was shown that Ddb1 associates with the Cop9/signalosome. Moreover, the phenotypes of the Deltaddb1 strain are remarkably similar to the Deltacsn1 (or Deltacsn2) strain that lacks expression of the Csn1 (or Csn2) subunit of the Cop9/signalosome. Cop9/signalosome cooperates with Pcu4 to induce proteolysis of Spd1, which inhibits DNA replication by inhibiting ribonucleotide reductase. Therefore, we investigated whether Ddb1 is required for the proteolysis of Spd1. Here we show that a S. pombe strain lacking expression of Ddb1 fails to induce proteolysis of Spd1 in S phase and after DNA damage. Moreover, deletion of the spd1 gene attenuates the Cds1 kinase activity in cells lacking the expression of ddb1, suggesting that an accumulation of Spd1 results in the increase of Cds1 activity in the Deltaddb1 strain. In addition, the double mutant lacking spd1 and ddb1 no longer exhibits the growth defects and DNA damage sensitivity observed in the Deltaddb1 strain. Our results establish an essential role of Ddb1 in the proteolysis of Spd1. In addition, the observation provides evidence for a functional link between Ddb1 and the Cop9/signalosome.

The COP9 signalosome: an assembly and maintenance platform for cullin ubiquitin ligases?

The COP9 signalosome (CSN) is a highly conserved protein complex implicated in diverse biological functions that involve ubiquitin-mediated proteolysis. Paradoxically, conserved enzymatic activities associated with CSN inhibit cullin ubiquitin ligase activity in vitro, whereas mutational analysis suggests that CSN promotes cullin-dependent proteolysis in vivo. This apparent paradox can be resolved in a model that proposes CSN-mediated cullin inhibition is a prerequisite for the proper assembly and maintenance of active cullin ubiquitin ligase complexes.

JAMM: a metalloprotease-like zinc site in the proteasome and signalosome

The JAMM (JAB1/MPN/Mov34 metalloenzyme) motif in Rpn11 and Csn5 underlies isopeptidase activities intrinsic to the proteasome and signalosome, respectively. We show here that the archaebacterial protein AfJAMM possesses the key features of a zinc metalloprotease, yet with a distinct fold. The histidine and aspartic acid of the conserved EX_nHS/THX₇SXXD motif coordinate a zinc, whereas the glutamic acid hydrogen-bonds an aqua ligand. By analogy to the active site of thermolysin, we predict that the glutamic acid serves as an acid-base catalyst and the second serine stabilizes a tetrahedral intermediate. Mutagenesis of Csn5 confirms these residues are required for Nedd8 isopeptidase activity. The active site-like architecture specified by the JAMM motif motivates structure-based approaches to the study of JAMM domain proteins and the development of therapeutic proteasome and signalosome inhibitors.

Protein structure studies suggest that deubiquitination in the proteasome is carried out by a protein with features of a zinc metalloprotease

The COP9 Signalosome

The COP9 signalosome (CSN) is composed of eight distinct subunits and is highly homologous to the lid sub-complex of the 26S proteasome. CSN was initially defined as a repressor of photomorphogenesis in Arabidopsis, and it has now been found to participate in diverse cellular and developmental processes in various eukaryotic organisms. Recently, CSN was revealed to have a metalloprotease activity centered in the CSN5/Jab1 subunit, which removes the post-translational modification of a ubiquitin-like protein, Nedd8/Rub1, from the cullin component of SCF ubiquitin E3 ligase (i.e., de-neddylation). In addition, CSN is associated with de-ubiquitination activity and protein kinase activities capable of phosphorylating important signaling regulators. The involvement of CSN in a number of cellular and developmental processes has been attributed to its control over ubiquitin-proteasome-mediated protein degradation.

COP9 Signalosome

COP9 Signalosome (CSN) is a fascinating protein complex whose biochemical and physiological functions are only beginning to be understood. It is conserved throughout eukaryotes and is critical to the proper development of all multicellular organisms in which its function has been explored. Recent work suggests that CSN plays a key role in sustaining the activity of SCF and other cullin-based ubiquitin ligases, which may account for its essential roles in development. Here, we summarize what is known about CSN, and discuss hypotheses for how CSN promotes the activity of SCF ubiquitin ligases.

The SPA1-like proteins SPA3 and SPA4 repress photomorphogenesis in the light

Suppressor of phyA-105 (SPA1) is a phytochrome A-specific signaling intermediate that acts as a light-dependent repressor of photomorphogenesis in Arabidopsis seedlings. SPA1 is part of a small gene family comprising three genes: SPA1-related 2 (SPA2), SPA1-related 3 (SPA3), and SPA1-related 4 (SPA4). Here, we investigate the functions of SPA3 and SPA4, two very closely related genes coding for proteins with 74% identical amino acids. Seedlings with mutations in SPA3 or SPA4 exhibit enhanced photomorphogenesis in the light, but show no phenotype in darkness. While there are small differences between the effects of spa3 and spa4 mutations, it is apparent that SPA3 and SPA4 function to inhibit light responses in continuous far-red, red, and blue light. Phytochrome A is necessary for all aspects of the spa4 mutant phenotype, suggesting that SPA4, like SPA1, acts specifically in phytochrome A signaling. Enhanced photoresponsiveness of spa3 mutants is also fully dependent on phytochrome A in far-red and blue light, but not in red light. Hence, SPA3 function in red light may be dependent on other phytochromes in addition to phytochrome A. Using yeast two-hybrid and in vitro interaction assays, we further show that SPA3 as well as SPA4 can physically interact with the constitutive repressor of light signaling COP1. Deletion analyses suggest that SPA3 and SPA4, like SPA1, bind to the coiled-coil domain of COP1. Taken together, our results have identified two new loci coding for negative regulators that may be involved in fine tuning of light responses by interacting with COP1.

Characterization of human constitutive photomorphogenesis protein 1, a RING finger ubiquitin ligase that interacts with Jun transcription factors and modulates their transcriptional activity

RING finger proteins have been implicated in many fundamental cellular processes, including the control of gene expression. A key regulator of light-dependent development in Arabidopsis thaliana is the constitutive photomorphogenesis protein 1 (atCOP1), a RING finger protein that plays an essential role in translating light/dark signals into specific changes in gene transcription. atCOP1 binds the basic leucine zipper factor HY5 and suppresses its transcriptional activity through a yet undefined mechanism that results in HY5 degradation in response to darkness. Furthermore, the pleiotropic phenotype of atCOP1 mutants indicates that atCOP1 may be a central regulator of several transcriptional pathways. Here we report the cloning and characterization of the human orthologue of atCOP1. Human COP1 (huCOP1) distributes both to the cytoplasm and the nucleus of cells and shows a striking degree of sequence conservation with atCOP1, suggesting the possibility of a functional conservation as well. In co-immunoprecipitation assays huCOP1 specifically binds basic leucine zipper factors of the Jun family. As a functional consequence of this interaction, expression of huCOP1 in mammalian cells down-regulates c-Jun-dependent transcription and the expression of the AP-1 target genes, urokinase and matrix metalloproteinase 1. The RING domain of huCOP1 displays ubiquitin ligase activity in an autoubiquitination assay in vitro; however, suppression of AP-1-dependent transcription by huCOP1 occurs in the absence of changes in c-Jun protein levels, suggesting that this inhibitory effect is independent of c-Jun degradation. Our findings indicate that huCOP1 is a novel regulator of AP-1-dependent transcription sharing the important properties of Arabidopsis COP1 in the control of gene expression.

Fission Yeast COP9/Signalosome Suppresses Cullin Activity through Recruitment of the Deubiquitylating Enzyme Ubp12p

The COP9/signalosome (CSN) is known to remove the stimulatory NEDD8 modification from cullins. The activity of the fission yeast cullins Pcu1p and Pcu3p is dramatically stimulated when retrieved from csn mutants but inhibited by purified CSN. This inhibition is independent of cullin deneddylation but mediated by the CSN-associated deubiquitylating enzyme Ubp12p, which forms a complex with Pcu3p in a CSN-dependent manner. In ubp12 mutants, as in csn mutants, Pcu3p activity is stimulated. CSN is required for efficient targeting of Ubp12p to the nucleus, where both cullins reside. Finally, the CSN/Ubp12p pathway maintains the stability of the Pcu1p-associated substrate-specific adaptor protein Pop1p. We propose that CSN/Ubp12p-mediated deubiquitylation creates an environment for the safe de novo assembly of cullin complexes by counteracting the autocatalytic destruction of adaptor proteins.

Analysis of the mutational effects of the COP/DET/FUS loci on genome expression profiles reveals their overlapping yet not identical roles in regulating Arabidopsis seedling development

Microarray gene expression profiling was used to examine the role of pleiotropic COP/DET/FUS loci as well as other partially photomorphogenic loci during Arabidopsis seedling development and genome expression regulation. Four types of lethal, pleiotropic cop/det/fus mutants exhibit qualitatively similar gene expression profiles, yet each has specific differences. Mutations in COP1 and DET1 show the most similar genome expression profiles, while the mutations in the COP9 signalosome (CSN) and COP10 exhibit increasingly diverged genome expression profiles in both darkness and light. The genome expression profiles of the viable mutants of COP1 and DET1 in darkness mimic those of the physiological light-regulated genome expression profiles, whereas the genome expression profiles of representative lethal mutants belong to another clade and significantly diverge from the normal light control of genome expression. Instead, these lethal pleiotropic mutants show genome expression profiles similar to those from seedlings growth under high light intensity stress. Distinct lethal pleiotropic cop/det/fus mutants also result in distinct expression profiles in the small portion of genes examined and exhibit similar relatedness in both light and darkness. The partial cop/det/fus mutants affected expression of both light regulated and non-light regulated genes. Our results suggest that pleiotropic COP/DET/FUS loci control is largely overlapping but also has separable roles in plant development. The partially photomorphogenic loci regulate a subset of photomorphogenic responses as well as other non-light regulated processes.

The COP9 signalosome: regulating plant development through the control of proteolysis

The COP9 signalosome (CSN) is a multiprotein complex that was initially identified in plants as a repressor of photomorphogenesis. It is now known to play major roles in several other developmental pathways, from auxin response to flower development. Furthermore, the COP9 signalosome shares homologies with the lid sibcomplex of the proteasome and is evolutionarily conserved from fission yeast to humans. It is important for the proper development of virtually all higher eukaryotes. In recent years, significant progress has been made in unraveling the molecular, cellular, and physiological mode of action of the COP9 signalosome. This review discusses our current understanding of the COP9 signalosome function with particular emphasis on its recently defined role in modulating a wide variety of cellular processes by regulating specific protein degradation events.

Genomic evidence for COP1 as a repressor of light-regulated gene expression and development in Arabidopsis

Microarray gene expression profiling was used to examine the role of COP1 in the light control of Arabidopsis genome expression. Qualitatively similar gene expression profiles were observed between wild-type seedlings grown in white light and multiple cop1 mutant alleles grown in the dark. Furthermore, overexpression of the dominant-negative-acting N terminus of COP1 (N282) in darkness produced a genome expression profile similar to those produced by white light and the cop1 mutations. Different cop1 mutant alleles, N282, and light treatment also resulted in distinct expression profiles in a small fraction of the genes examined. In the light, the genome expression of cop1 mutations displayed an exaggerated light response. COP1-regulated genes in the dark were estimated to account for >20% of the genome. Analysis of these COP1-regulated genes revealed that >28 cellular pathways are coordinately but antagonistically regulated by light and COP1. Interestingly, the gene expression regulation attributable to HY5 in the light is included largely within those genes regulated by COP1 in the dark. Thus, this genomic study supports the hypothesis that COP1 acts as a repressor of photomorphogenesis, possibly by controlling the degradation of transcription factors and their target gene expression. The majority of light-controlled genome expression could be accounted for by the negative regulation of COP1 activity.

De-etiolated 1 and damaged DNA binding protein 1 interact to regulate Arabidopsis photomorphogenesis

BACKGROUND

Plant development is exquisitely sensitive to light. Seedlings grown in the dark have a developmentally arrested etiolated phenotype, whereas in the light they develop leaves and complete their life cycle. Arabidopsis de-etiolated 1 (det1) mutants develop like light-grown seedlings even when grown in the dark. DET1 encodes a nuclear protein that appears to act downstream from multiple photoreceptors to regulate morphogenesis and gene expression in response to light. However, its function has remained unknown.

RESULTS

We used microarrays to examine defects in transcription in dark-grown det1 seedlings. We found extensive changes in gene expression, including many of the transcriptional responses observed in light-treated wild-type seedlings. We used an epitope-tagging approach to determine the basis of DET1 function. GFP-DET1 rescues the det1 phenotype, is localized to the nucleus, and forms an approximately 350 kDa complex, which is required for full DET1 activity. We affinity-purified the DET1 complex and identified an approximately 120 kDa copurifying protein that is the plant homolog of UV-Damaged DNA Binding Protein 1 (DDB1), a protein implicated in the human disease xeroderma pigmentosa. A null mutation in Arabidopsis DDB1A results in no obvious phenotype on its own, yet it enhances the phenotype of a weak det1 allele.

CONCLUSIONS

DET1 and DDB1 interact both biochemically and genetically. In animal cells, DDB1 interacts with histone acetyltransferase complexes. The DET1/DDB1 complex may regulate gene expression in response to light via recruitment of HAT activity. Thus, DET1, whose sequence is conserved in both animals and plants, may play a direct role in the regulation of many genes.

Conservation of the COP9/signalosome in budding yeast

BACKGROUND

The COP9/signalosome (CSN), a multiprotein complex consisting of eight subunits, is implicated in a wide variety of regulatory processes including cell cycle control, signal transduction, transcriptional activation, and plant photomorphogenesis. Some of these functions have been linked to CSN-associated enzymes, including kinases and an activity that removes the ubiquitin-like protein NEDD8/Rub1p from the cullin subunit of E3 ligases. CSN is highly conserved across species from fission yeast to humans, but sequence comparison has failed to identify the complex in budding yeast, except for a putative CSN5 subunit called Rri1p.

RESULTS

We show that disruption of four budding yeast genes, PCI8 and three previously uncharacterized ORFs, which encode proteins interacting with Rrr1p/Csn5p, each results in the accumulation of the cullin Cdc53p exclusively in the Rub1p-modified state. This phenotype, which resembles that of fission yeast csn mutants, is due to a biochemical defect in deneddylation that is complemented by wild-type cell lysate and by purified human CSN in vitro. Although three of the four genes encode proteins with PCI domains conserved in metazoan CSN proteins, their disruption does not confer the DNA damage sensitivity described in some fission yeast csn mutants.

CONCLUSIONS

Our studies present unexpected evidence for the conservation of a functional homologue of the metazoan CSN, which mediates control of cullin neddylation in budding yeast.

Integrin-dependent regulation of gene expression in leukocytes

In addition to their role in strengthening intercellular adhesion, leukocyte integrins transduce signals which affect genetic programs, consequently defining cell phenotype and function. These signals can be independently sufficient, or can cooperate with other environmental stimuli to affect gene expression regulation. In the past several years, there has been an emergence of mechanistic data which contribute to our understanding of these critical integrin roles. In this review, we describe anchorage-dependent T lymphocyte proliferation and, in particular, how leukocyte integrin engagement overcomes the G1 to S cell cycle restriction point in antigen-activated T cells. The related role of alphaLbeta2 integrin (LFA-1) as a T cell co-stimulatory molecule is discussed. This includes defining mechanisms whereby LFA-1 engagement enhances transcriptional activation of numerous genes by regulating its association with transcription modulators such as JAB-1, and through interaction with other gene-activating signaling complexes such as JAK-STATs. Evidence is presented to support that leukocyte integrin engagement provides potent signals which stabilize otherwise labile activation mRNA transcripts, including those encoding cytokine and extracellular matrix degrading proteins. These integrin-dependent mechanisms, all described recently, play important roles in T cell differentiation and proliferation, immune surveillance and inflammatory responses.

Auxin-responsive gene expression: genes, promoters and regulatory factors

A molecular approach to investigate auxin signaling in plants has led to the identification of several classes of early/primary auxin response genes. Within the promoters of these genes, cis elements that confer auxin responsiveness (referred to as auxin-response elements or AuxREs) have been defined, and a family of trans-acting transcription factors (auxin-response factors or ARFs) that bind with specificity to AuxREs has been characterized. A family of auxin regulated proteins referred to as Aux/IAA proteins also play a key role in regulating these auxin-response genes. Auxin may regulate transcription on early response genes by influencing the types of interactions between ARFs and Aux/IAAs.

Two interacting bZIP proteins are direct targets of COP1-mediated control of light-dependent gene expression in Arabidopsis

Arabidopsis COP1 acts to repress photomorphogenesis in the absence of light. It was shown that in the dark, COP1 directly interacts with the bZIP transcription factor HY5, a positive regulator of photomorphogenesis, and promotes its proteasome-mediated degradation. Here we identify a novel bZIP protein HYH, as a new target of COP1. We identify a physical and genetic interaction between HYH and COP1 and show that this interaction results in dark-specific degradation of HYH. Genetic analysis indicates that HYH is predominantly involved in blue-light regulation of development and gene expression, and that the function of HYH in part overlaps with that of HY5. The accumulation of HYH protein, not the mRNA, is dependent on the presence of HY5. Our data suggest that HYH and HY5 can, respectively, act as heterodimers and homodimers, thus mediating light-regulated expression of overlapping as well as distinct target genes. We propose that COP1 mediates light control of gene expression through targeted degradation of multiple photomorphogenesis-promoting transcription factors in the nucleus.

Functional properties and regulatory complexity of a minimal RBCS light-responsive unit activated by phytochrome, cryptochrome, and plastid signals

Light-inducible promoters are able to respond to a wide spectrum of light through multiple photoreceptor systems. Several cis-acting elements have been identified as components of light-responsive promoter elements; however, none of these regulatory elements by itself appears to be sufficient to confer light responsiveness; rather, the combination of at least two elements seems to be required. Using phylogenetic structural analysis, we have identified conserved DNA modular arrays (CMAs) associated with light-responsive promoter regions that have been conserved throughout the evolutionary radiation of angiosperms. Here, we report the functional characterization of CMA5, a native 52-bp fragment of the Nicotiana plumbaginifolia rbcS 8B promoter, which contains an I- and a G-box cis-element. CMA5 behaves as a light-responsive minimal unit capable of activating a heterologous minimal promoter in a phytochrome-, cryptochrome-, and plastid-dependent manner. We also show that CMA5 light induction requires HY5 and that downstream negative regulators COP (constitutive photomorphogenic)/DET (de-etiolated) regulate its activity. Our results show that the simplest light-responsive promoter element from photosynthesis-associated genes described to date is the common target for different signals involved in light regulation. The possible mechanism involved in light-transcriptional regulation and tissue specificity of combinatorial elements units is discussed.

Photosensory perception and signalling in plant cells: new paradigms?

Plants monitor informational light signals using three sensory photoreceptor families: the phototropins, cryptochromes and phytochromes. Recent advances suggest that the phytochromes act transcriptionally by targeting light signals directly to photoresponsive promoters through binding to a transcriptional regulator. By contrast, the cryptochromes appear to act post-translationally, by disrupting extant proteosome-mediated degradation of a key transcriptional activator through direct binding to a putative E3 ubiquitin ligase, thereby elevating levels of the activator and consequently of target gene expression.

Arabidopsis COP10 is a ubiquitin-conjugating enzyme variant that acts together with COP1 and the COP9 signalosome in repressing photomorphogenesis

A group of evolutionarily conserved pleiotropic COP/DET/FUS proteins was initially defined by their ability to repress photomorphogenesis in Arabidopsis. It was proposed that this regulation be mediated by targeting degradation of key cellular regulators that promote photomorphogenesis. Among them, COP1 and the COP9 signalosome have been hypothesized to fulfill the roles as an ubiquitin ligase (E3) and an essential E3 modulator. Here we report that COP10 encodes a protein similar to ubiquitin-conjugating enzyme (E2) variant proteins (UEV). COP10 is part of a nuclear protein complex and capable of directly interacting with both COP1 and the COP9 signalosome. Our data indicates that COP10 defines a possible E2 activity, thus validating the working hypothesis that the pleiotropic COP/DET/FUS group of proteins defined a protein ubiquitination pathway.

The COP9 signalosome: at the interface between signal transduction and ubiquitin-dependent proteolysis

Recently the COP9 signalosome (CSN) has become a focus of interest for many researchers, because of its function at the interface between signal transduction and ubiquitin-dependent proteolysis. It is required for the proper progression of the cell cycle in Schizosaccharomyces pombe and is essential for development in plants and Drosophila. However, its function in mammalian cells remains obscure. Although the CSN shares structural similarities with the 26S proteasome lid complex (LID), its functions seem to be different from that of the LID. A variety of CSN-specific protein-protein interactions have been described in mammalian cells. However,it is currently unclear how many reflect true functions of the complex. Two activities associated with the CSN have been identified so far: a protein kinase and a deneddylase. The CSN-associated kinase phosphorylates transcription factors, which determines their stability towards the ubiquitin system. The associated deneddylase regulates the activity of specific SCF E3 ubiquitin ligases. The CSN thus appears to be a platform connecting signalling with proteolysis.

Phytochrome photosensory signalling networks

Light is life for plants. To continuously assess and adapt to fluctuations in the quality and quantity of this essential commodity, plants deploy sensory photoreceptors, including the phytochromes. Having captured an incoming photon, the activated phytochrome molecule must relay this information to nuclear genes that are poised to respond by directing appropriate adjustments in growth and development. Defining the intricate intracellular signalling networks through which this sensory information is transduced is an area of intense research activity.

Drosophila JAB1/CSN5 acts in photoreceptor cells to induce glial cells

Different classes of photoreceptor neurons (R cells) in the Drosophila compound eye form connections in different optic ganglia. The R1-R6 subclass connects to the first optic ganglion, the lamina, and relies upon glial cells as intermediate targets. Conversely, R cells promote glial cell development including migration of glial cells into the target region. Here, we show that the JAB1/CSN5 subunit of the COP9 signalosome complex is expressed in R cells, accumulates in the developing optic lobe neuropil, and through the analysis of a unique set of missense mutations, is required in R cells to induce lamina glial cell migration. In these CSN5 alleles, R1-R6 targeting is disrupted. Genetic analysis of protein null alleles further revealed that the COP9 signalosome is required at an earlier stage of development for R cell differentiation.

Charting the protein complexome in yeast by mass spectrometry

It has become evident over the past few years that many complex cellular processes, including control of the cell cycle and ubiquitin-dependent proteolysis, are carried out by sophisticated multisubunit protein machines that are dynamic in abundance, post-translational modification state, and composition. To understand better the nature of the macromolecular assemblages that carry out the cell cycle and ubiquitin-dependent proteolysis, we have used mass spectrometry extensively over the past few years to characterize both the composition of various protein complexes and the modification states of their subunits. In this article we review some of our recent efforts, and describe a promising new approach for using mass spectrometry to dissect protein interaction networks.

Direct interaction of Arabidopsis cryptochromes with COP1 in light control development

Arabidopsis seedling photomorphogenesis involves two antagonistically acting components, COP1 and HY5. COP1 specifically targets HY5 for degradation via the 26S proteasome in the dark through their direct physical interaction. Little is known regarding how light signals perceived by photoreceptors are transduced to regulate COP1. Arabidopsis has two related cryptochromes (cry1 and cry2) mediating various blue/ultraviolet-A light responses. Here we show that both photoactivated cryptochromes repress COP1 activity through a direct protein-protein contact and that this direct regulation is primarily responsible for the cryptochrome-mediated blue light regulation of seedling photomorphogenic development and genome expression profile.

The fission yeast COP9/signalosome is involved in cullin modification by ubiquitin-related Ned8p

BACKGROUND

The function of the fission yeast cullins Pcu1p and Pcu4p requires modification by the ubiquitin-related peptide Ned8p. A recent report by Lyapina et al. shows that the COP9/signalosome (CSN), a multifunctional eight subunit complex, regulates Ned8p modification of Pcu1p. Disruption of caa1/csn1, which encodes subunit 1 of the putative S. pombe CSN, results in accumulation of Pcu1p exclusively in the modified form. However, it remained unclear whether this reflects global control of all cullins by the entire CSN complex.

RESULTS

We demonstrate that multiple CSN subunits control Ned8p modification of Pcu3p, another fission yeast cullin, which, in complex with the RING domain protein Pip1p, forms a ubiquitin ligase that functions in cellular stress response. Pcu3p is modified by Ned8p on Lys 729 and accumulates exclusively in the neddylated form in cells lacking the CSN subunits 1, 3, 4, and 5. These CSN subunits co-elute with Pcu3p in gel filtration fractions corresponding to approximately 550 kDa and specifically bind both native and Ned8p-modified Pcu3p in vivo. While CSN does not influence the subcellular localization of Pcu3p, Pcu3p-associated in vitro ubiquitin ligase activity is stimulated in the absence of CSN.

CONCLUSIONS

Taken together, our data suggest that CSN is a global regulator of Ned8p modification of multiple cullins and potentially other proteins involved in cellular regulation.

Proteases and cellular regulation in plants

Protein degradation is accomplished by a diverse collection of proteases. Recent studies have illustrated the importance of proteolysis in the control of many aspects of cellular regulation from photosynthesis to photomorphogenesis. In addition, new results point to a role for proteolysis in programmed cell death, circadian rhythm, and defense response in plants.

Identification of a structural motif that confers specific interaction with the WD40 repeat domain of Arabidopsis COP1

Arabidopsis COP1 is a photomorphogenesis repressor capable of directly interacting with the photomorphogenesis-promoting factor HY5. This interaction between HY5 and COP1 results in targeted deg radation of HY5 by the 26S proteasome. Here we characterized the WD40 repeat domain-mediated interactions of COP1 with HY5 and two new proteins. Mutational analysis of those interactive partners revealed a conserved motif responsible for the interaction with the WD40 domain. This novel motif, with the core sequence V-P-E/D-φ-G (φ = hydrophobic residue) in conjunction with an upstream stretch of 4-5 negatively charged residues, interacts with a defined surface area of the ss-propeller assembly of the COP1 WD40 repeat domain through both hydrophobic and ionic interactions. Several residues in the COP1 WD40 domain that are critical for the interaction with this motif have been revealed. The fact that point mutations either in the COP1 WD40 domain or in the HY5 motif that abolish the interaction between COP1 and HY5 in yeast result in a dramatic reduction of HY5 degradation in transgenic plants validates the biological significance of this defined interaction.

PML and COP1--two proteins with much in common

The recent discovery that the RING-finger domain is involved in mediating ubiquitin transfer from ubiquitin-conjugating enzymes to substrates have highlighted the importance of protein degradation through the ubiquitin-proteasome pathway in the regulation of different cellular processes. Two RING-finger-containing proteins, the promyelocytic leukemia protein (PML) from mammals and the constitutive photomorphogenic protein (COP1) from plants, show conspicuous similarities in their cellular distribution, dynamics and structure, indicating that they share a related function. Comparison of these two proteins suggests that they are involved in regulating the targeting of nuclear proteins to specific nuclear compartments for degradation through the ubiquitin-proteasome pathway.

Interaction between interferon consensus sequence-binding protein and COP9/signalosome subunit CSN2 (Trip15). A possible link between interferon regulatory factor signaling and the COP9/signalosome

Interferon consensus sequence-binding protein (ICSBP) is a member of the interferon regulatory factors (IRF) that has a pivotal role in mediating resistance to pathogenic infections in mice and in promoting the differentiation of myeloid cells. ICSBP exerts some of its transcriptional activities via association with other factors that enable its binding to a variety of promoters containing DNA composite elements. These interactions are mediated through a specific COOH-terminal domain termed IAD (IRF association domain). To gain a broader insight of the capacity of ICSBP to interact with other factors, yeast two-hybrid screens were performed using ICSBP-IAD as a bait against a B-cell cDNA library. Trip15 was identified as a specific interacting factor with ICSBP in yeast cells, which was also confirmed by in vitro glutathione S-transferase pull-down assays and by coimmunoprecipitation studies in COS7 cells. Trip15 was recently identified as a component of the COP9/signalosome (CSN) complex composed of eight evolutionary conserved subunits and thus termed CSN2. This complex has a role in cell-signaling processes, which is manifested by its associated novel kinase activity and by the involvement of its subunits in regulating multiple cell-signaling pathways and cell-cycle progression. We show that in vitro association of ICSBP with the CSN leads to phosphorylation of ICSBP at a unique serine residue within its IAD. The phosphorylated residue is essential for efficient association with IRF-1 and thus for the repressor activity of ICSBP exerted on IRF-1. This suggests that the CSN has a role in integrating incoming signals that affect the transcriptional activity of ICSBP.

Nucleo-cytoplasmic partitioning of the plant photoreceptors phytochromes

Phytochromes in harmony with blue light photoreceptors play a major role in controlling plant growth and development from germination to seed maturation. Light absorption by phytochromes triggers a signaling cascade, phototransduction, which culminates in regulated gene expression. A major regulatory step at the cellular level, which affects specificities of light-induced physiological responses, seems to be the light-quality and light-quantity dependent nuclear import of the phytochromes themselves. The correlations found between the nuclear import of phytochromes (phyA and phyB) and various physiological responses regulated by these photoreceptors provides strong support for this hypothesis.

Control of nuclear import and phytochromes

The past year has brought significant changes in our understanding of the molecular mechanism of photoreceptor-regulated gene expression in higher plants. The light-quantity- and light-quality-dependent nuclear import of phytochromes, followed by the conformation-dependent direct interaction of these phytochromes with transcription factors, seems to play a major role in light-modulated plant growth and development.

The genetics of phytochrome signalling in Arabidopsis

The application of Arabidopsis genetics to research into the responses of plants to light has enabled rapid recent advances in this field. The plant photoreceptor phytochrome mediates well-defined responses that can be exploited to provide elegant and specific genetic screens. By this means, not only have mutants affecting the phytochromes themselves been isolated, but also mutants affecting the transduction of phytochrome signals. The genes involved in these processes have now begun to be characterized by using this genetic approach to isolate signal transduction components. Most of the components characterized so far are capable of being translocated to the cell nucleus, and they may help to define a new system of regulation of gene expression. This review summarises the ongoing contribution made by genetics to our understanding of light perception and signal transduction by the phytochrome system.

The COP9 signalosome: from light signaling to general developmental regulation and back

The COP9 signalosome has eight core subunits that are highly conserved between plants and animals. Some of the subunits in Arabidopsis are found in forms that are independent of the complex. The COP9 complex is essential for animal development. The COP9 signalosome may have both an evolutionary and a physical relationship with both the regulatory lid of the proteasome and eIF3.

HY5 stability and activity in arabidopsis is regulated by phosphorylation in its COP1 binding domain

Arabidopsis HY5 is a bZIP transcription factor that promotes photomorphogenesis. Previous studies suggested that COP1, a negative regulator of photomorphogenesis, directly interacts with nuclear HY5 and targets it for proteasome-mediated degradation. Light negatively regulates the nuclear level of COP1 and thus permits HY5 accumulation. Here we report that HY5 abundance peaks in early seedling development, consistent with its role in promoting photomorphogenesis. HY5 acts exclusively within a complex and exists in two isoforms, resulting from phosphorylation within its COP1 binding domain by a light- regulated kinase activity. Unphosphorylated HY5 shows stronger interaction with COP1, is the preferred substrate for degradation, has higher affinity to target promoters and is physiologically more active than the phosphorylated version. Therefore, HY5 phosphorylation provides an added level of light-mediated regulation of HY5 stability and activity besides nuclear COP1 levels. Regulated HY5 phosphorylation not only provides abundant and physiologically more active unphosphorylated HY5 in the light, but also helps to maintain a small pool of less active phosphorylated HY5 in the dark, which could be essential for a rapid initial response during dark-to-light transition.

FIN219, an auxin-regulated gene, defines a link between phytochrome A and the downstream regulator COP1 in light control of Arabidopsis development

Light signals perceived by photoreceptors are transduced to negatively regulate COP1, a key repressor of photomorphogenic development. To identify genes involved in light inactivation of COP1, a genetic screen was employed to identify extragenic modifier mutations of a temperature-sensitive cop1 allele. One suppressor mutation isolated also exhibited a far-red-specific long hypocotyl phenotype in a wild-type background. Further phenotypic analyses of this new mutation, named fin219, suggested that it defines a novel phytochrome A signaling component. Genetic analysis indicated that FIN219 interacts closely with another phytochrome A signaling component, FHY1. Molecular characterization of FIN219 indicated that it encodes a cytoplasmic localized protein highly similar to the GH3 family of proteins and its expression is rapidly induced by auxin. In contrast to its loss-of-function mutant phenotype, overexpression of FIN219 results in a far-red-specific hyperphotomorphogenic response. Our data suggest that FIN219 may define a critical link for phytochrome A-mediated far-red inactivation of COP1 and a possible cross-talk juncture between auxin regulation and phytochrome signaling.

Electron microscopy and subunit-subunit interaction studies reveal a first architecture of COP9 signalosome

The COP9 signalosome is involved in signal transduction, whereas the 26 S proteasome lid is a regulatory subcomplex of the 26 S proteasome responsible for degradation of ubiquitinated proteins. COP9 signalosome and lid possess significant sequence homologies among their eight core subunits and are likely derived from a common ancestor. Surprisingly, from our two-dimensional electron microscopy data, a common architectural plan for the two complexes could not be deduced. None-the-less, the two particles have structural features in common. Both COP9 signalosome and lid lack any symmetry in subunit arrangement and exhibit a central groove, possibly qualified for scaffolding functions.Filter-binding assays with recombinant COP9 signalosome components revealed a multitude of subunit-subunit interactions, supporting the asymmetrical appearance of the complex in electron microscopy. On the basis of two-dimensional images and subunit interaction studies, a first architectural model of COP9 signalosome was created. The fact that four distinct classes of particle views were identified and that only 50 % of the selected particles could be classified indicates a high degree of heterogeneity in electron microscopic images. Different orientations with respect to the viewing axis and conformational variety, presumably due to different grades of phosphorylation, are possible reasons for the heterogeneous appearance of the complex. Our biochemical data show that recombinant COP9 signalosome subunits 2 and 7 are phosphorylated by the associated kinase activity. The modification of COP9 signalosome subunit 2 might be essential for c-Jun phosphorylation. Dephosphorylation does not inactivate the associated kinase activity. Although substrate phosphorylation by COP9 signalosome is significantly decreased by lambda protein phosphatase treatment, "autophosphorylation" is increased.

Targeted destabilization of HY5 during light-regulated development of Arabidopsis

Arabidopsis seedlings display contrasting developmental patterns depending on the ambient light. Seedlings grown in the light develop photomorphogenically, characterized by short hypocotyls and expanded green cotyledons. In contrast, seedlings grown in darkness become etiolated, with elongated hypocotyls and dosed cotyledons on an apical hook. Light signals, perceived by multiple photoreceptors and transduced to downstream regulators, dictate the extent of photomorphogenic development in a quantitative manner. Two key downstream components, COP1 and HY5, act antagonistically in regulating seedling development. HY5 is a bZIP transcription factor that binds directly to the promoters of light-inducible genes, promoting their expression and photomorphogenic development. COP1 is a RING-finger protein with WD-40 repeats whose nuclear abundance is negatively regulated by light. COP1 interacts directly with HY5 in the nucleus to regulate its activity negatively. Here we show that the abundance of HY5 is directly correlated with the extent of photomorphogenic development, and that the COP1-HY5 interaction may specifically target HY5 for proteasome-mediated degradation in the nucleus.

COP9 signalosome-directed c-Jun activation/stabilization is independent of JNK

The basic region-leucine zipper transcription factor c-Jun regulates gene expression and cell function. It participates in the formation of homo- or heterodimeric complexes that specifically bind to DNA sequences called activating protein 1 (AP-1) sites. The stability and activity of c-Jun is regulated by phosphorylation within the N-terminal activation domain. Mitogen- and stress-activated c-Jun N-terminal kinases (JNKs) were previously the only described enzymes phosphorylating c-Jun at the N terminus in vivo. In this report we demonstrate a JNK-independent activation of c-Jun in vivo directed by the constitutive photomorphogenesis (COP9) signalosome. The overexpression of signalosome subunit 2 (Sgn2), a subunit of the COP9 signalosome, leads to de novo assembly of the complex with a partial incorporation of the overexpressed subunit. The de novo formation of COP9 signalosome parallels an increase of c-Jun protein resulting in elevated AP-1 transcriptional activity. The c-Jun activation caused by Sgn2 overexpression is independent of JNK and mitogen-activated protein kinase kinase 4. The data demonstrate the existence of a novel COP9 signalosome-directed c-Jun activation pathway.

Short communication: the N-terminal fragment of Arabidopsis photomorphogenic repressor COP1 maintains partial function and acts in a concentration-dependent manner

Arabidopsis seedlings exhibit distinct developmental patterns according to their light environment: photomorphogenesis in the light and etiolation or skotomorphogenesis in darkness. COP1 acts within the nucleus to repress photomorphogenesis in darkness, while light depletes COP1 from nucleus and abrogates this repression. COP1 contains three structural modules: a RING finger followed by a coiled-coil domain, and a WD40 repeat domain at the C-terminus. By introducing various domain deletion mutants of COP1 into cop1 null mutant backgrounds, we show that all three domains are essential for the function of COP1 in vivo. Interestingly, a fragment containing the N-terminal 282 amino acids of COP1 (N282) with both the RING finger and coiled-coil modules is sufficient to rescue the lethality of the cop1 null mutations at low expression level. However, high expression levels of the N282 fragment result in a phenocopy of the cop1 null mutation. The sensitivity of the seedling to levels of N282 could reflect the importance of the abundance of COP1 for the appropriate regulation of photomorphogenic development.

Phytochromes are Pr-ipatetic kinases

A series of new studies reveal how the red/far-red light photoreceptors called phytochromes act. Phytochrome A and phytochrome B each move to the nucleus when activated by light, and phytochrome A is a kinase. Phytochrome-interacting proteins provide candidate signal transduction components and a recent physiological study suggests how phyA may mediate responses to far-red light. Regulation of phytochrome nuclear localization and kinase activities creates multiple phytochrome species, which may each have different regulatory activities.

Evidence for functional conservation of a mammalian homologue of the light-responsive plant protein COP1

Identified in Arabidopsis as a repressor of light-regulated development, the COP1 (constitutively photomorphogenic 1) protein is characterized by a RING-finger motif and a WD40 repeat domain [1]. The subcellular localization of COP1 is light-dependent. COP1 acts within the nucleus to repress photomorphogenic development, but light inactivates COP1 and diminishes its nuclear abundance [2]. Here, we report the identification of a mammalian COP1 homologue that contains all the structural features present in Arabidopsis COP1 (AtCOP1). When expressed in plant cells, a fusion protein comprising mammalian COP1 and beta-glucuronidase (GUS) responded to light by changing its subcellular localization pattern in a manner similar to AtCOP1. Whereas the mammalian COP1 was unable to rescue the defects of Arabidopsis cop1 mutants, expression of the amino-terminal half of mammalian COP1 in Arabidopsis interfered with endogenous COP1 function, resulting in a hyperphotomorphogenic phenotype. Therefore, the regulatory modules in COP1 proteins that are responsible for the signal-dependent subcellular localization are functionally conserved between higher plants and mammals, suggesting that mammalian COP1 may share a common mode of action with its plant counterpart in regulating development and cellular signaling.