- Email: [email protected]
Light perception in plants: cytokinins and red light join forces to keep phytochrome B active
Research Update
TRENDS in Plant Science Vol.7 No.4 April 2002
143
Research News
Light perception in plants: cytokinins and red light join forces to keep phytochrome B active Christian Fankhauser Plant growth and development is modulated by internal cues such as the hormonal balance and external factors. Plants are particularly sensitive to their light environment, which they scrutinize with at least three classes of photoreceptors. In recent years, it has become increasingly clear that light and hormonal signaling interact at several levels. A cytokinin receptor was recently identified together with several elements acting in this signaling pathway. ARR4, a response regulator working downstream of a cytokinin receptor, has been shown to modulate phytochrome B-mediated light signaling. Published online: 20 February 2002
The phytochromes are most sensitive to red and far-red light. They are synthesized in their red-light-absorbing form (Pr) in the dark and get converted into their far-red absorbing form (Pfr) upon absorption of red light. Far-red light will convert Pfr back into Pr [1,2]. Because many physiological responses correlate with the amount of Pfr, phytochromes can be regarded as light-regulated switches or rheostats [1,2]. Phytochromes are encoded by small gene families in plants (PHYA–PHYE in Arabidopsis). They are soluble homodimeric proteins that are cytoplasmic in the dark. Light activation triggers their accumulation in the nucleus [2,3]. Phytochromes control various processes throughout the life cycle of a plant, in the natural environment their most important role is probably the shade avoidance response [4,5]. Genetic analysis of light perception in Arabidopsis has shown that phyB mutants are impaired in numerous processes including seed germination, seedling de-etiolation in red light, shade avoidance and the transition to flowering [1,2]. Photoperception by phytochromes is well understood. It requires covalent attachment of a chromophore, called phytochromobilin in plants, to a cysteine residue in the bilin lyase domain [6] (Fig. 1). http://plants.trends.com
Pr is the ground state of phytochromes. The stability of the photo-activated Pfr state depends on the particular species of phytochrome. Important remodeling of the protein backbone accompanies this phototransformation [6]. Pfr reverts into Pr upon absorption of far-red light, or spontaneously in the absence of light in a process known as dark reversion [6] (Fig. 1). Dark reversion can have an important physiological implication because the rate of dark reversion directly affects the Pr:Pfr ratio particularly during the night period. If dark reversion is rapid, shortly after sunset all the phytochrome is reverted to Pr and therefore phytochrome-mediated responses are relieved during most of the night. Several years ago it was discovered that purified recombinant Arabidopsis phyB has fast dark reversion rates compared with those measured for phyA [7]. The physiological importance of this phenomenon was highlighted by the
finding that phyB-101 a hypomorphic allele of phyB has accelerated darkreversion rates [7]. Phytochrome B meets the ARR4 response regulator
An interesting and recently published study by Uta Sweere and colleagues proposes that one way to increase the pool of active PfrB (Pfr form of phyB) in plants, is by stabilization of PfrB [8]. They have identified a response regulator known as ARR4, which interacts with the amino-terminal extension of phyB (Fig. 1). This interaction is specific because several other response regulators do not interact with phyB [8]. To confirm the relevance of this finding in vivo, ARR4 was overexpressed in Arabidopsis. These plants are more sensitive to red light suggesting that they have more effective phyBmediated light perception [8]. Additional experiments show that ARR4 inhibits dark reversion of phyB when co-expressed
CK
HH
Amino-terminal extension PAS-related domain Bilin lyase domain Histidine kinase-related domain Histidine kinase domain Histidine phospho transfer domain Receiver domain Output domain CHASE domain CK: Cytokinin
CRE1/WOL/AHK4 AHK3 AHK2
DD
H AHP
phyB responses
P
ARR4
D
PφB C C
ARR4
D
PfrB active
PφB
P
FR R Dark reversion
Light
P
ARR4
D
PφB C C
ARR4
D
PrB inactive
PφB
P TRENDS in Plant Science
Fig. 1. The ARR4 response regulator inhibits dark-reversion of phytochrome B. The ARR4 response regulator works in a phospho-relay signaling cascade downstream of the CRE1/WOL/AHK4 cytokinin receptor. Interaction of the ARR4 response regulator with the amino-terminal extension of phyB inhibits dark reversion of PfrB. This interaction inhibits the conversion of the active PfrB into the inactive PrB, therefore increasing phyB responses. Abbreviations: PrB, red light absorbing phytochrome B; PfrB, far-red light absorbing phytochrome B; R, red light; FR, far-red light; PφB, phytochromobilin.
1360-1385/02/$ – see front matter © 2002 Elsevier Science Ltd. All rights reserved. PII S1360-1385(02)02228-8
144
Research Update
with phyB in yeast and in planta [8]. The accentuated response to red light can therefore be explained because the slower dark-reversion rate leads to a bigger pool of the active PfrB [8]. The rapid rate of dark reversion of phyB in vivo is another important finding of this work. This contrasts with the stable Pfr form measured for phyA in Arabidopsis [9]. Two-component signaling in plants
The stabilization of PfrB by ARR4 is interesting by itself but it also raises another important point. The ARR4 protein is a member of a large family of response regulators found in Arabidopsis [10]. In bacteria, response regulators play crucial functions in signaling in response to various stimuli [11]. Typically, a sensor kinase, composed of a sensor domain and a histidine kinase domain, will phosphorylate a conserved aspartate of a cognate response regulator. Response regulators are composed of a receiver domain (containing the conserved aspartate residue) and an output domain (e.g. a DNA binding domain). This simple scheme enables gene expression to be modulated with only two proteins and is therefore known as a two-component system [11]. This mode of signaling is prevalent in prokaryotes but not common in eukaryotes. However, in Arabidopsis, there are more than ten sensor histidine kinases [12]. The best understood ones are the ethylene receptors, which have been characterized extensively, genetically and biochemically [13]. The receptor for the cytokinins is also a member of the sensor histidine kinase class [12,14–17]. Remarkably, plant phytochromes themselves have a histidine kinaserelated domain. However, several crucial residues in this domain are lacking and there is no evidence that plant phytochromes possess histidine kinase activity [18]. Biochemical evidence has shown that oat phyA is a light-regulated Ser/Thr kinase [19]. However, bacteriophytochromes are true histidine kinases with a light-modulated activity [20,21]. Cytokinin control of PfrB stability?
It might have been expected that response regulators such as ARR4 interact with the histidine kinase-related domain of phytochromes. However, the study by Sweere et al. shows that ARR4 interacts with the amino-terminal extension of http://plants.trends.com
TRENDS in Plant Science Vol.7 No.4 April 2002
phyB, which is not found in the other Arabidopsis phytochromes (except phyD, which is closely related to phyB) [8]. Moreover, rather than placing ARR4 downstream of this histidine kinase-like light sensor, current data suggest that ARR4 acts downstream of a true histidine kinase, possibly the cytokinin receptor CRE1 (also known as WOL or AHK4), and modulates phyB activity [8,22] (Fig. 1). Cytokinin-mediated signaling probably does not occur via a simple two-component system but rather through a so-called phosphorelay mechanism that requires up to four components and has been encountered in bacteria but also in fungi [11,22,23] (Fig. 1). Two recent papers indicate that ARR4 and the closely related ARR6 protein are early targets of this cytokinin-modulated phosphorelay [22,24]. The work by Ildoo Hwang and Jen Sheen indicates that ARR4 is a transcriptional repressor involved in a negative feedback loop that inhibits CRE1/WOL/AHK4-mediated signaling [22]. The studies of Sweere et al. and Hwang and Sheen taken together suggest that cytokinin and light signaling converge at the level of ARR4 and phyB [8,22] (Fig. 1). Phytochrome B control of cytokinin signaling?
The phytochromes are translocated into the nucleus upon light activation (as PfrB for phyB), and PfrB physically interacts with the bHLH class transcription factor PIF3, forming a complex on DNA [2,25]. How this interaction modulates the activity of the PIF3 transcription factor remains to be solved, but these findings suggest a short signaling route for phytochrome-mediated gene expression. The interaction of phyB with ARR4 presumably also occurs in the nucleus, and ARR4 appears to be a transcriptional repressor [8,22]. Therefore, can this interaction be regarded as phyB control of ARR4-modulated transcriptional repression in addition to a cytokinin control of phyB signaling? In this context, it might be worth pointing out that ARR4 is rapidly induced in response to exogenously applied cytokinin and in response to red light in a phyB-dependent manner [8,26]. It might be interesting to test if cytokinin induction of ARR4 is phyB dependent. What is the connection between light and cytokinin-mediated signaling?
Several recent publications show that light and hormonal signals have points of convergence. The most direct evidence has been obtained for hormones such as auxins, gibberellins and brassinosteroids [27–30]. The link between light and cytokinins is not as well documented, but several reports suggest that it exists [31]. Moreover, it has long been recognized that cytokinins mediate certain aspects of light-mediated development, such as chloroplast differentiation. With these recent findings, we now begin to have the molecular players in hand to address these issues directly. Acknowledgements
I thank Nicolas Roggli for artwork, Patricia Lariguet, Isabelle Schepens and Michel Goldschmidt-Clermont for comments on the manuscript. Work in my laboratory is supported by the Swiss National Science Foundation (Grant 631-58 151.99). References 1 Quail, P.H. et al. (1995) Phytochromes: photosensory perception and signal transduction. Science 268, 675–680 2 Smith, H. (2000) Phytochromes and light signal perception by plants – an emerging synthesis. Nature 407, 585–591 3 Nagy, F. and Schaefer, E. (2000) Nuclear and cytosolic events of light-induced, phytochromeregulated signaling in higher plants. EMBO J. 19, 157–163 4 Smith, H. (1995) Physiological and ecological function within the phytochrome family. Annu. Rev. Plant Physiol. Plant Mol. Biol. 46, 289–315 5 Maloof, J.N. et al. (2000) Natural variation in phytochrome signaling. Semin. Cell Dev. Biol. 11, 523–530 6 Park, C.M. et al. (2000) Inter-domain crosstalk in the phytochrome molecules. Semin. Cell Dev. Biol. 11, 449–456 7 Elich, T.D. and Chory, J. (1997) Biochemical characterization of Arabidopsis wild-type and mutant phytochrome B holoproteins. Plant Cell 9, 2271–2280 8 Sweere, U. et al. (2001) Interaction of the response regulator ARR4 with phytochrome b in modulating red light signaling. Science 294, 1108–1111 9 Hennig, L. et al. (1999) Dynamic properties of endogenous phytochrome A in Arabidopsis seedlings. Plant Physiol. 121, 571–577 10 Urao, I. et al. (2000) Two-component systems in plant signal transduction. Trends Plant Sci. 5, 67–74 11 Stock, A.M. et al. (2000) Two-component signal transduction. Annu. Rev. Biochem. 69, 183–215 12 Inoue, T. et al. (2001) Identification of CRE1 as a cytokinin receptor from Arabidopsis. Nature 409, 1060–1063 13 Stepanova, A.N. and Ecker, J.R. (2000) Ethylene signaling: from mutants to molecules. Curr. Opin. Plant Biol. 3, 353–360
Research Update
TRENDS in Plant Science Vol.7 No.4 April 2002
14 Mahonen, A.P. et al. (2000) A novel twocomponent hybrid molecule regulates vascular morphogenesis of the Arabidopsis root. Genes Dev. 14, 2938–2943 15 Yamada, H. et al. (2001) The Arabidopsis AHK4 histidine kinase is a cytokinin-binding receptor that transduces cytokinin signals across the membrane. Plant Cell Physiol. 42, 1017–1023 16 Mougel, C. and Zhulin, I.B. (2001) CHASE: an extracellular sensing domain common to transmembrane receptors from prokaryotes, lower eukaryotes and plants. Trends Biochem. Sci. 26, 582–584 17 Anantharaman, V. and Aravind, L. (2001) The CHASE domain: a predicted ligand-binding module in plant cytokinin receptors and other eukaryotic and bacterial receptors. Trends Biochem. Sci. 26, 579–582 18 Cashmore, A.R. (1998) Higher-plant phytochrome: ‘I used to date histidine, but now I prefer serine’. Proc. Natl. Acad. Sci. U. S. A. 95, 13358–13360 19 Yeh, K.C. and Lagarias, J.C. (1998) Eukaryotic phytochromes: light-regulated serine/threonine protein kinases with histidine kinase ancestry. Proc. Natl. Acad. Sci. U. S. A. 95, 13976–13981
20 Yeh, K.C. et al. (1997) A cyanobacterial phytochrome two-component light sensory system. Science 277, 1505–1508 21 Vierstra, R.D. and Davis, S.J. (2000) Bacteriophytochromes: new tools for understanding phytochrome signal transduction. Semin. Cell Dev. Biol. 11, 511–521 22 Hwang, I. and Sheen, J. (2001) Two-component circuitry in Arabidopsis cytokinin signal transduction. Nature 413, 383–389 23 Schmülling, T. (2001) CREam of cytokinin signalling: receptor identified. Trends Plant Sci. 6, 281–284 24 Sakai, H. et al. (2001) ARR1, a transcription factor for genes immediately responsive to cytokinins. Science 294, 1519–1521 25 Martinez-Garcia, J.F. et al. (2000) Direct targeting of light signals to a promoter element-bound transcription factor. Science 288, 859–863 26 Brandstatter, I. and Kieber, J.J. (1998) Two genes with similarity to bacterial response regulators are rapidly and specifically induced by cytokinin in Arabidopsis. Plant Cell 10, 1009–1019
145
27 Kamiya, Y. and Garcia-Martinez, J.L. (1999) Regulation of gibberellin biosynthesis by light. Curr. Opin. Plant Biol. 2, 398–403 28 Reed, J.W. (2001) Roles and activities of Aux/IAA proteins in Arabidopsis. Trends Plant Sci. 6, 420–425 29 Neff, M.M. et al. (1999) BAS1: a gene regulating brassinosteroid levels and light responsiveness in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 96, 15316–15323 30 Kang, J.G. et al. (2001) Light and brassinosteroid signals are integrated via a dark-induced small G protein in etiolated seedling growth. Cell 105, 625–636 31 Kusnetsov, V. et al. (1999) The assembly of the CAAT-box binding complex at a photosynthesis gene promoter is regulated by light, cytokinin, and the stage of the plastids. J. Biol. Chem. 274, 36009–36014
Christian Fankhauser Dept of Molecular Biology, 30 quai E. Ansermet, CH-1211 Geneva 4, Switzerland. e-mail: [email protected]
GARNet, the Genomic Arabidopsis Resource Network Michael Beale, Paul Dupree, Kathryn Lilley, Jim Beynon, Martin Trick, Jonathan Clarke, Michael Bevan, Ian Bancroft, Jonathan Jones, Sean May, Karin van de Sande and Ottoline Leyser GARNet, the Genomic Arabidopsis Resource Network, was created to establish UK-based facilities for functional genomic research on Arabidopsis thaliana. In addition, GARNet provides a platform for international Arabidopsis research and for research on other plant species. To use the GARNet facilities apply via the website: http://garnet.arabidopsis.org.uk. All GARNet services and resources are publicly available, and data created using the GARNet resources will be freely distributed via databases held at the Nottingham Arabidopsis Stock Centre and the John Innes Centre. Published online: 20 February 2002
GARNet, the Genomic Arabidopsis Resource Network, was created to establish UK-based facilities for functional genomic research on Arabidopsis thaliana and has three years funding from the Biotechnology and Biological Science Research Council (BBSRC). GARNet also provides a platform for international Arabidopsis research and for research on other plant species. A team of nine service providers at http://plants.trends.com
different UK universities and institutes has combined forces to form GARNet to ensure that an extensive range of functional genomics technologies is available on a user-driven basis. Readers who would like to use the GARNet facilities can apply via the website: http://garnet.arabidopsis. org.uk. The GARNet steering committee will evaluate and prioritize your application. All GARNet services and resources are publicly available, and data created using the GARNet resources will be freely distributed via databases designed and held at the Nottingham Arabidopsis Stock Centre (NASC) and the John Innes Centre. Users can choose to impose a three to six month delay on the donation of data
into the databases but we will prioritize experiments that allow immediate release of data. The project components are described here. Metabolite analysis
Analysis of the effect of genetic change and/or the environment on the levels of low molecular weight compounds plays an important role in plant functional genomics. Within the GARNet project, a metabolite analysis service has been established at the Institute of Arable Crops Research (Long Ashton, Bristol). The service is built around gas chromatography (GC)- and liquid chromatography-mass spectrometry (LC-MS) analysis but also includes facilities for nuclear magnetic resonance (NMR). Although much effort is being put into the development of methods for reliable quantitative analysis, ultimately, the service should operate at two levels. On the first level, analysis of relatively crude solvent extracts of Arabidopsis plants or plant parts by GC-MS, LC-MS and NMR should yield information about the status of the major metabolites present. Comparison
1360-1385/02/$ – see front matter © 2002 Elsevier Science Ltd. All rights reserved. PII: S1360-1385(01)02224-5
TRENDS in Plant Science Vol.7 No.4 April 2002
143
Research News
Light perception in plants: cytokinins and red light join forces to keep phytochrome B active Christian Fankhauser Plant growth and development is modulated by internal cues such as the hormonal balance and external factors. Plants are particularly sensitive to their light environment, which they scrutinize with at least three classes of photoreceptors. In recent years, it has become increasingly clear that light and hormonal signaling interact at several levels. A cytokinin receptor was recently identified together with several elements acting in this signaling pathway. ARR4, a response regulator working downstream of a cytokinin receptor, has been shown to modulate phytochrome B-mediated light signaling. Published online: 20 February 2002
The phytochromes are most sensitive to red and far-red light. They are synthesized in their red-light-absorbing form (Pr) in the dark and get converted into their far-red absorbing form (Pfr) upon absorption of red light. Far-red light will convert Pfr back into Pr [1,2]. Because many physiological responses correlate with the amount of Pfr, phytochromes can be regarded as light-regulated switches or rheostats [1,2]. Phytochromes are encoded by small gene families in plants (PHYA–PHYE in Arabidopsis). They are soluble homodimeric proteins that are cytoplasmic in the dark. Light activation triggers their accumulation in the nucleus [2,3]. Phytochromes control various processes throughout the life cycle of a plant, in the natural environment their most important role is probably the shade avoidance response [4,5]. Genetic analysis of light perception in Arabidopsis has shown that phyB mutants are impaired in numerous processes including seed germination, seedling de-etiolation in red light, shade avoidance and the transition to flowering [1,2]. Photoperception by phytochromes is well understood. It requires covalent attachment of a chromophore, called phytochromobilin in plants, to a cysteine residue in the bilin lyase domain [6] (Fig. 1). http://plants.trends.com
Pr is the ground state of phytochromes. The stability of the photo-activated Pfr state depends on the particular species of phytochrome. Important remodeling of the protein backbone accompanies this phototransformation [6]. Pfr reverts into Pr upon absorption of far-red light, or spontaneously in the absence of light in a process known as dark reversion [6] (Fig. 1). Dark reversion can have an important physiological implication because the rate of dark reversion directly affects the Pr:Pfr ratio particularly during the night period. If dark reversion is rapid, shortly after sunset all the phytochrome is reverted to Pr and therefore phytochrome-mediated responses are relieved during most of the night. Several years ago it was discovered that purified recombinant Arabidopsis phyB has fast dark reversion rates compared with those measured for phyA [7]. The physiological importance of this phenomenon was highlighted by the
finding that phyB-101 a hypomorphic allele of phyB has accelerated darkreversion rates [7]. Phytochrome B meets the ARR4 response regulator
An interesting and recently published study by Uta Sweere and colleagues proposes that one way to increase the pool of active PfrB (Pfr form of phyB) in plants, is by stabilization of PfrB [8]. They have identified a response regulator known as ARR4, which interacts with the amino-terminal extension of phyB (Fig. 1). This interaction is specific because several other response regulators do not interact with phyB [8]. To confirm the relevance of this finding in vivo, ARR4 was overexpressed in Arabidopsis. These plants are more sensitive to red light suggesting that they have more effective phyBmediated light perception [8]. Additional experiments show that ARR4 inhibits dark reversion of phyB when co-expressed
CK
HH
Amino-terminal extension PAS-related domain Bilin lyase domain Histidine kinase-related domain Histidine kinase domain Histidine phospho transfer domain Receiver domain Output domain CHASE domain CK: Cytokinin
CRE1/WOL/AHK4 AHK3 AHK2
DD
H AHP
phyB responses
P
ARR4
D
PφB C C
ARR4
D
PfrB active
PφB
P
FR R Dark reversion
Light
P
ARR4
D
PφB C C
ARR4
D
PrB inactive
PφB
P TRENDS in Plant Science
Fig. 1. The ARR4 response regulator inhibits dark-reversion of phytochrome B. The ARR4 response regulator works in a phospho-relay signaling cascade downstream of the CRE1/WOL/AHK4 cytokinin receptor. Interaction of the ARR4 response regulator with the amino-terminal extension of phyB inhibits dark reversion of PfrB. This interaction inhibits the conversion of the active PfrB into the inactive PrB, therefore increasing phyB responses. Abbreviations: PrB, red light absorbing phytochrome B; PfrB, far-red light absorbing phytochrome B; R, red light; FR, far-red light; PφB, phytochromobilin.
1360-1385/02/$ – see front matter © 2002 Elsevier Science Ltd. All rights reserved. PII S1360-1385(02)02228-8
144
Research Update
with phyB in yeast and in planta [8]. The accentuated response to red light can therefore be explained because the slower dark-reversion rate leads to a bigger pool of the active PfrB [8]. The rapid rate of dark reversion of phyB in vivo is another important finding of this work. This contrasts with the stable Pfr form measured for phyA in Arabidopsis [9]. Two-component signaling in plants
The stabilization of PfrB by ARR4 is interesting by itself but it also raises another important point. The ARR4 protein is a member of a large family of response regulators found in Arabidopsis [10]. In bacteria, response regulators play crucial functions in signaling in response to various stimuli [11]. Typically, a sensor kinase, composed of a sensor domain and a histidine kinase domain, will phosphorylate a conserved aspartate of a cognate response regulator. Response regulators are composed of a receiver domain (containing the conserved aspartate residue) and an output domain (e.g. a DNA binding domain). This simple scheme enables gene expression to be modulated with only two proteins and is therefore known as a two-component system [11]. This mode of signaling is prevalent in prokaryotes but not common in eukaryotes. However, in Arabidopsis, there are more than ten sensor histidine kinases [12]. The best understood ones are the ethylene receptors, which have been characterized extensively, genetically and biochemically [13]. The receptor for the cytokinins is also a member of the sensor histidine kinase class [12,14–17]. Remarkably, plant phytochromes themselves have a histidine kinaserelated domain. However, several crucial residues in this domain are lacking and there is no evidence that plant phytochromes possess histidine kinase activity [18]. Biochemical evidence has shown that oat phyA is a light-regulated Ser/Thr kinase [19]. However, bacteriophytochromes are true histidine kinases with a light-modulated activity [20,21]. Cytokinin control of PfrB stability?
It might have been expected that response regulators such as ARR4 interact with the histidine kinase-related domain of phytochromes. However, the study by Sweere et al. shows that ARR4 interacts with the amino-terminal extension of http://plants.trends.com
TRENDS in Plant Science Vol.7 No.4 April 2002
phyB, which is not found in the other Arabidopsis phytochromes (except phyD, which is closely related to phyB) [8]. Moreover, rather than placing ARR4 downstream of this histidine kinase-like light sensor, current data suggest that ARR4 acts downstream of a true histidine kinase, possibly the cytokinin receptor CRE1 (also known as WOL or AHK4), and modulates phyB activity [8,22] (Fig. 1). Cytokinin-mediated signaling probably does not occur via a simple two-component system but rather through a so-called phosphorelay mechanism that requires up to four components and has been encountered in bacteria but also in fungi [11,22,23] (Fig. 1). Two recent papers indicate that ARR4 and the closely related ARR6 protein are early targets of this cytokinin-modulated phosphorelay [22,24]. The work by Ildoo Hwang and Jen Sheen indicates that ARR4 is a transcriptional repressor involved in a negative feedback loop that inhibits CRE1/WOL/AHK4-mediated signaling [22]. The studies of Sweere et al. and Hwang and Sheen taken together suggest that cytokinin and light signaling converge at the level of ARR4 and phyB [8,22] (Fig. 1). Phytochrome B control of cytokinin signaling?
The phytochromes are translocated into the nucleus upon light activation (as PfrB for phyB), and PfrB physically interacts with the bHLH class transcription factor PIF3, forming a complex on DNA [2,25]. How this interaction modulates the activity of the PIF3 transcription factor remains to be solved, but these findings suggest a short signaling route for phytochrome-mediated gene expression. The interaction of phyB with ARR4 presumably also occurs in the nucleus, and ARR4 appears to be a transcriptional repressor [8,22]. Therefore, can this interaction be regarded as phyB control of ARR4-modulated transcriptional repression in addition to a cytokinin control of phyB signaling? In this context, it might be worth pointing out that ARR4 is rapidly induced in response to exogenously applied cytokinin and in response to red light in a phyB-dependent manner [8,26]. It might be interesting to test if cytokinin induction of ARR4 is phyB dependent. What is the connection between light and cytokinin-mediated signaling?
Several recent publications show that light and hormonal signals have points of convergence. The most direct evidence has been obtained for hormones such as auxins, gibberellins and brassinosteroids [27–30]. The link between light and cytokinins is not as well documented, but several reports suggest that it exists [31]. Moreover, it has long been recognized that cytokinins mediate certain aspects of light-mediated development, such as chloroplast differentiation. With these recent findings, we now begin to have the molecular players in hand to address these issues directly. Acknowledgements
I thank Nicolas Roggli for artwork, Patricia Lariguet, Isabelle Schepens and Michel Goldschmidt-Clermont for comments on the manuscript. Work in my laboratory is supported by the Swiss National Science Foundation (Grant 631-58 151.99). References 1 Quail, P.H. et al. (1995) Phytochromes: photosensory perception and signal transduction. Science 268, 675–680 2 Smith, H. (2000) Phytochromes and light signal perception by plants – an emerging synthesis. Nature 407, 585–591 3 Nagy, F. and Schaefer, E. (2000) Nuclear and cytosolic events of light-induced, phytochromeregulated signaling in higher plants. EMBO J. 19, 157–163 4 Smith, H. (1995) Physiological and ecological function within the phytochrome family. Annu. Rev. Plant Physiol. Plant Mol. Biol. 46, 289–315 5 Maloof, J.N. et al. (2000) Natural variation in phytochrome signaling. Semin. Cell Dev. Biol. 11, 523–530 6 Park, C.M. et al. (2000) Inter-domain crosstalk in the phytochrome molecules. Semin. Cell Dev. Biol. 11, 449–456 7 Elich, T.D. and Chory, J. (1997) Biochemical characterization of Arabidopsis wild-type and mutant phytochrome B holoproteins. Plant Cell 9, 2271–2280 8 Sweere, U. et al. (2001) Interaction of the response regulator ARR4 with phytochrome b in modulating red light signaling. Science 294, 1108–1111 9 Hennig, L. et al. (1999) Dynamic properties of endogenous phytochrome A in Arabidopsis seedlings. Plant Physiol. 121, 571–577 10 Urao, I. et al. (2000) Two-component systems in plant signal transduction. Trends Plant Sci. 5, 67–74 11 Stock, A.M. et al. (2000) Two-component signal transduction. Annu. Rev. Biochem. 69, 183–215 12 Inoue, T. et al. (2001) Identification of CRE1 as a cytokinin receptor from Arabidopsis. Nature 409, 1060–1063 13 Stepanova, A.N. and Ecker, J.R. (2000) Ethylene signaling: from mutants to molecules. Curr. Opin. Plant Biol. 3, 353–360
Research Update
TRENDS in Plant Science Vol.7 No.4 April 2002
14 Mahonen, A.P. et al. (2000) A novel twocomponent hybrid molecule regulates vascular morphogenesis of the Arabidopsis root. Genes Dev. 14, 2938–2943 15 Yamada, H. et al. (2001) The Arabidopsis AHK4 histidine kinase is a cytokinin-binding receptor that transduces cytokinin signals across the membrane. Plant Cell Physiol. 42, 1017–1023 16 Mougel, C. and Zhulin, I.B. (2001) CHASE: an extracellular sensing domain common to transmembrane receptors from prokaryotes, lower eukaryotes and plants. Trends Biochem. Sci. 26, 582–584 17 Anantharaman, V. and Aravind, L. (2001) The CHASE domain: a predicted ligand-binding module in plant cytokinin receptors and other eukaryotic and bacterial receptors. Trends Biochem. Sci. 26, 579–582 18 Cashmore, A.R. (1998) Higher-plant phytochrome: ‘I used to date histidine, but now I prefer serine’. Proc. Natl. Acad. Sci. U. S. A. 95, 13358–13360 19 Yeh, K.C. and Lagarias, J.C. (1998) Eukaryotic phytochromes: light-regulated serine/threonine protein kinases with histidine kinase ancestry. Proc. Natl. Acad. Sci. U. S. A. 95, 13976–13981
20 Yeh, K.C. et al. (1997) A cyanobacterial phytochrome two-component light sensory system. Science 277, 1505–1508 21 Vierstra, R.D. and Davis, S.J. (2000) Bacteriophytochromes: new tools for understanding phytochrome signal transduction. Semin. Cell Dev. Biol. 11, 511–521 22 Hwang, I. and Sheen, J. (2001) Two-component circuitry in Arabidopsis cytokinin signal transduction. Nature 413, 383–389 23 Schmülling, T. (2001) CREam of cytokinin signalling: receptor identified. Trends Plant Sci. 6, 281–284 24 Sakai, H. et al. (2001) ARR1, a transcription factor for genes immediately responsive to cytokinins. Science 294, 1519–1521 25 Martinez-Garcia, J.F. et al. (2000) Direct targeting of light signals to a promoter element-bound transcription factor. Science 288, 859–863 26 Brandstatter, I. and Kieber, J.J. (1998) Two genes with similarity to bacterial response regulators are rapidly and specifically induced by cytokinin in Arabidopsis. Plant Cell 10, 1009–1019
145
27 Kamiya, Y. and Garcia-Martinez, J.L. (1999) Regulation of gibberellin biosynthesis by light. Curr. Opin. Plant Biol. 2, 398–403 28 Reed, J.W. (2001) Roles and activities of Aux/IAA proteins in Arabidopsis. Trends Plant Sci. 6, 420–425 29 Neff, M.M. et al. (1999) BAS1: a gene regulating brassinosteroid levels and light responsiveness in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 96, 15316–15323 30 Kang, J.G. et al. (2001) Light and brassinosteroid signals are integrated via a dark-induced small G protein in etiolated seedling growth. Cell 105, 625–636 31 Kusnetsov, V. et al. (1999) The assembly of the CAAT-box binding complex at a photosynthesis gene promoter is regulated by light, cytokinin, and the stage of the plastids. J. Biol. Chem. 274, 36009–36014
Christian Fankhauser Dept of Molecular Biology, 30 quai E. Ansermet, CH-1211 Geneva 4, Switzerland. e-mail: [email protected]
GARNet, the Genomic Arabidopsis Resource Network Michael Beale, Paul Dupree, Kathryn Lilley, Jim Beynon, Martin Trick, Jonathan Clarke, Michael Bevan, Ian Bancroft, Jonathan Jones, Sean May, Karin van de Sande and Ottoline Leyser GARNet, the Genomic Arabidopsis Resource Network, was created to establish UK-based facilities for functional genomic research on Arabidopsis thaliana. In addition, GARNet provides a platform for international Arabidopsis research and for research on other plant species. To use the GARNet facilities apply via the website: http://garnet.arabidopsis.org.uk. All GARNet services and resources are publicly available, and data created using the GARNet resources will be freely distributed via databases held at the Nottingham Arabidopsis Stock Centre and the John Innes Centre. Published online: 20 February 2002
GARNet, the Genomic Arabidopsis Resource Network, was created to establish UK-based facilities for functional genomic research on Arabidopsis thaliana and has three years funding from the Biotechnology and Biological Science Research Council (BBSRC). GARNet also provides a platform for international Arabidopsis research and for research on other plant species. A team of nine service providers at http://plants.trends.com
different UK universities and institutes has combined forces to form GARNet to ensure that an extensive range of functional genomics technologies is available on a user-driven basis. Readers who would like to use the GARNet facilities can apply via the website: http://garnet.arabidopsis. org.uk. The GARNet steering committee will evaluate and prioritize your application. All GARNet services and resources are publicly available, and data created using the GARNet resources will be freely distributed via databases designed and held at the Nottingham Arabidopsis Stock Centre (NASC) and the John Innes Centre. Users can choose to impose a three to six month delay on the donation of data
into the databases but we will prioritize experiments that allow immediate release of data. The project components are described here. Metabolite analysis
Analysis of the effect of genetic change and/or the environment on the levels of low molecular weight compounds plays an important role in plant functional genomics. Within the GARNet project, a metabolite analysis service has been established at the Institute of Arable Crops Research (Long Ashton, Bristol). The service is built around gas chromatography (GC)- and liquid chromatography-mass spectrometry (LC-MS) analysis but also includes facilities for nuclear magnetic resonance (NMR). Although much effort is being put into the development of methods for reliable quantitative analysis, ultimately, the service should operate at two levels. On the first level, analysis of relatively crude solvent extracts of Arabidopsis plants or plant parts by GC-MS, LC-MS and NMR should yield information about the status of the major metabolites present. Comparison
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