Logo of pnasPNASInfo for AuthorsSubscriptionsAboutThis Article
Proc Natl Acad Sci U S A. May 5, 2009; 106(18): 7654–7659.
Published online Apr 20, 2009. doi:  10.1073/pnas.0811684106
PMCID: PMC2678601
Plant Biology

PIF3 is a repressor of chloroplast development

Abstract

The phytochrome-interacting factor PIF3 has been proposed to act as a positive regulator of chloroplast development. Here, we show that the pif3 mutant has a phenotype that is similar to the pif1 mutant, lacking the repressor of chloroplast development PIF1, and that a pif1pif3 double mutant has an additive phenotype in all respects. The pif mutants showed elevated protochlorophyllide levels in the dark, and etioplasts of pif mutants contained smaller prolamellar bodies and more prothylakoid membranes than corresponding wild-type seedlings, similar to previous reports of constitutive photomorphogenic mutants. Consistent with this observation, pif1, pif3, and pif1pif3 showed reduced hypocotyl elongation and increased cotyledon opening in the dark. Transfer of 4-d-old dark-grown seedlings to white light resulted in more chlorophyll synthesis in pif mutants over the first 2 h, and analysis of gene expression in dark-grown pif mutants indicated that key tetrapyrrole regulatory genes such as HEMA1 encoding the rate-limiting step in tetrapyrrole synthesis were already elevated 2 d after germination. Circadian regulation of HEMA1 in the dark also showed reduced amplitude and a shorter, variable period in the pif mutants, whereas expression of the core clock components TOC1, CCA1, and LHY was largely unaffected. Expression of both PIF1 and PIF3 was circadian regulated in dark-grown seedlings. PIF1 and PIF3 are proposed to be negative regulators that function to integrate light and circadian control in the regulation of chloroplast development.

Keywords: chlorophyll synthesis, circadian regulation, phytochrome, etioplast, light signaling

Light is a major regulator of growth and development throughout the life cycle of the plant, and this myriad of complex responses is mediated by different photoreceptor families. Responses to blue light are predominantly controlled by the cryptochrome and phototropin photoreceptors, whereas the phytochromes are responsible for regulating growth and development in response to red (R) and far-red (FR) light (1). In Arabidopsis, there are 5 phytochromes (phyA–E) that regulate responses such as germination, seedling and chloroplast development, plant growth and architecture, and flowering. The mechanism by which the phytochromes regulate cellular processes is not yet understood, but remarkable progress has been made in recent years. Phytochromes are dimeric, photoreversible proteins that exist in the dark in the inactive Pr (R-absorbing) form and are converted by light to the active Pfr (FR-absorbing) form (2). After light absorption, phytochromes rapidly relocate to the nucleus, where they control the response to light through 2 main mechanisms. First, they act to exclude the E3-ubiquitin ligase, COP1, from the nucleus, thereby preventing the degradation of the positive signaling factors HY5, HFR1, and LAF1 (3). Second, phytochromes bind and target a family of bHLH proteins for degradation, thus relieving repression of light responses such as inhibition of hypocotyl elongation and germination (4).

The first of these bHLH proteins to be identified as a phytochrome-interacting protein was PIF3 (5), which binds to both phyA and phyB in a light-dependent manner (6), but through different motifs (7, 8). Activation of phytochrome results in PIF3 phosphorylation (8) and subsequent degradation (9, 10) in a mechanism that appears to be common to this class of signaling protein (11, 12). Although there seems to be broad agreement on what is known about the molecular events after phytochrome interaction with PIF3, there is less certainty about how PIF3 is functioning in photomorphogenesis. From the outset, PIF3 was proposed as a positive regulator of light signals, because the hypersensitive poc1 mutant was initially described as a PIF3 overexpressor (13). Subsequent analysis of PIF3 loss-of-function mutants demonstrated that PIF3 promoted hypocotyl elongation, suggesting that PIF3 is a negative regulator of seedling growth (14). In contrast, PIF3 has been described as acting positively in the light regulation of chloroplast development (15), and this has led to the hypothesis that PIF3 has a dual function, acting early and positively as a transcription factor, but acting later to regulate phyB abundance and repress light-induced inhibition of hypocotyl elongation (16, 17). In contrast to the proposal for PIF3, other members of the PIF family appear to function predominantly as negative regulators (3, 4). This is clearly seen for PIF1 (PIL5), which negatively regulates phytochrome-mediated promotion of seed germination (18) through the repression of gibberellin biosynthesis genes (19) and repression of chlorophyll biosynthesis (20).

Given the controversy in the role of PIF3, we have reevaluated the function of PIF3 in chloroplast development through careful examination of the phenotype of pif3 and a pif1pif3 double mutant. Our results show that PIF3 acts similarly and additively to PIF1 to repress chloroplast development and chlorophyll synthesis in the dark. Interestingly, the pif1pif3 double mutant showed a broader range of constitutively photomorphogenic phenotypes, in keeping with roles for the PIF proteins as global repressors of photomorphogenesis.

Results

pif1 and pif3 Accumulate Protochlorophyllide in the Dark.

To further understand the role of PIF3 in early seedling development, we constructed a pif1pif3 double mutant using an independently isolated pif3 T-DNA insertion allele that is identical to pif3-1 (14) and a previously undescribed pif1 allele designated pif1-101 (see SI Text and Fig. S1). The PIF1 protein has been shown to repress chloroplast development and protochlorophyllide (Pchlide) synthesis in the dark (20). To test whether PIF3 might be acting similarly, we followed accumulation of Pchlide in pif1, pif3, and the pif1pif3 double mutant (Fig. 1A). All lines showed an increase in Pchlide. This increase was clearly detectable 2.5 d after germination, and at all time points the response of the pif1pif3 double mutant appeared additive to that of pif1 and pif3. Analysis of Pchlide levels in the pif1-2 and pif3-3 alleles confirmed our results (Fig. S2A). Because the pif3-3 allele contains no detectable transcript (15) or protein (17), this result is consistent with the phenotype of pif3 mutants being due to loss of PIF3 function. In our experiments, seeds were routinely germinated after 2 h of white light (WL), a treatment reported to have no longer-term effects on seedling growth in the dark (21). Nevertheless, we checked whether this short pretreatment contributed to the pif mutant response. As shown in Fig. S3A, Pchlide was also elevated in the pif1pif3 double mutant even after germination in complete darkness. The increase in Pchlide was not simply due to an increased rate of germination, because all genotypes showed at least 95% germination by day 1 in these experiments.

Fig. 1.
Dark-grown phenotype of pif mutant seedlings. (A) Protochlorophyllide accumulation in WT and pif mutant seedlings in darkness. (B) Cotyledons of WT and pif mutant seedlings after 4 d in the dark. (C) Hypocotyl growth of WT and pif mutant seedlings in ...

pif1 and pif3 Mutants Have a Constitutively Photomorphogenic Phenotype.

In addition to the effects on Pchlide accumulation, we also observed that dark-grown pif mutant seedlings had open cotyledons and had lost their apical hook (Fig. 1B). This response was observed in the majority, but not all, of the single mutant seedlings but was more consistent and stronger in the pif1pif3 double mutant. Moreover, it was not due to the WL pretreatment because seedlings germinated completely in the dark showed the same response (Fig. S3B). To test whether pif mutant seedlings showed the full constitutive photomorphogenic phenotype, we also measured hypocotyl lengths of dark-grown seedlings. In all cases, pif mutants were shorter in the dark compared with WT, with the pif1pif3 double mutant again showing an additive phenotype (Fig. 1C). This was also true in the absence of the WL pretreatment (Fig. S3C). Finally, one distinctive feature of constitutively photomorphogenic seedlings such as cop1 is that they show a partially developed chloroplast in the dark that is characterized by a reduced prolamellar body (PLB) and increased prothylakoid membranes (22). We therefore examined etioplasts in dark-grown pif mutant seedlings (Fig. 2 A–D). After 4 d in the dark, WT etioplasts showed a characteristic, highly regular PLB with little prothylakoid development (Fig. 2A). In contrast, both pif1 and pif3 etioplasts showed increased membrane development and PLBs that were generally reduced in size (Fig. 2 B and C). The most significant differences to WT were seen with the pif1pif3 double mutant, where PLB size was severely reduced and prothylakoid membranes were extensive, although no membrane stacking was observed (Fig. 2D). In some cases, no PLB was observed in pif1pif3 double mutant seedlings, although full-size PLBs were detected occasionally.

Fig. 2.
Plastid ultrastructure in pif mutant seedlings. Transmission electron micrographs of plastids from WT (A, E, and I), pif1 (B, F, and J), pif3 (C, G, and K), and pif1pif3 (D, H, and L) seedlings. Seedlings were grown for 4 d in the dark (A–D), ...

Greening of pif1 and pif3 Is Dependent on the Time of Transfer to White Light.

When grown in the dark for 4 d before transfer to WL, pif1pif3 double mutants failed to green over the next 24 h, with pif1 and pif3 showing only moderate greening during this period (Fig. 3A and Fig. S4). An identical result was observed with the pif1-2 and pif3-3 alleles (Fig. S2 B and C) and has been observed for pif1 (20). Interestingly, detailed examination of the time course after transfer to WL showed that at 2 h pif1, pif3, and the pif1pif3 double mutant had more chlorophyll than WT but that this was already reversed after 4 h of WL (Fig. 3B). In contrast to the situation after 4 d in the dark, seedlings transferred to WL after 2 d in the dark were able to green, with the pif1pif3 double mutant accumulating the most chlorophyll (Fig. 3C). The pif1-2 and pif3-3 alleles were also able to green more efficiently under these conditions (Fig. S2 B and C), and this ability was gradually lost as seedlings aged at transfer to WL (Fig. 3C and Fig. S2C). The time course of chlorophyll loss after transfer to WL and the effect of increasing the dark period on subsequent greening ability are consistent with the loss of chlorophyll in the pif mutants being due to photooxidative destruction rather than reduced synthesis. To test this, we examined the effect of different WL fluences on chlorophyll levels in WT and pif mutant seedlings. As shown in Fig. 3D, as the fluence rate increased, the relative loss of chlorophyll in the pif mutants also increased compared with WT, consistent with photooxidation being the primary cause of chlorophyll deficiency in the pif mutants.

Fig. 3.
Light-grown phenotype of pif mutant seedlings. (A) Chlorophyll accumulation in WT and pif mutant seedlings after transfer to WL (110 μmol·m−2·s−1) after 4 d in the dark. (B) Chlorophyll levels in WT and pif mutant ...

We examined chloroplast ultrastructure in WT and pif mutant seedlings after transfer to WL after 2 or 4 d in the dark (Fig. 2 E–L). Wild-type chloroplasts were already well developed 24 h after transfer from 2 d in the dark, with some thylakoid stacking evident at this stage, although in some cases a residual PLB was observed (Fig. 2E). Consistent with the chlorophyll data, there was no evidence of any repression of chloroplast development in pif1, pif3, and pif1pif3 mutants, and in all cases there appeared to be more thylakoid stacking than in WT (Fig. 2 F–H). No residual PLBs were observed in pif1, pif3, or pif1pif3 under these conditions. The situation after transfer to WL from 4 d in the dark was more complex. Development of WT chloroplasts was similar to that seen after transfer from 2 d in the dark (Fig. 2I). In contrast, pif1 and particularly pif1pif3 double mutants contained chloroplasts with poorly defined membrane structure and no evidence of granal stacking (Fig. 2 J and L). The appearance of the chloroplasts was reminiscent of chloroplasts damaged through pigment-induced photooxidative stress (e.g., ref. 23) and was not due to problems of fixation, because other structures in these sections were well defined (for example, the mitochondrion to the right of the chloroplast in Fig. 2L). Chloroplasts in the pif3 mutant were generally more similar to WT in appearance than those for pif1 or pif1pif3 (Fig. 2K), consistent with the higher levels of chlorophyll in pif3 at this time point.

pif1 and pif3 Affect the Expression of Tetrapyrrole Biosynthesis Genes in the Dark.

To understand the basis of the increase in Pchlide, we followed the expression of HEMA1 encoding glutamyl tRNA reductase, the rate-limiting step in tetrapyrrole synthesis (24). Expression was measured at 6 h time points from 1¼ d after germination using real-time PCR. HEMA1 expression was strongly induced in all pif mutants relative to WT at 2 and 3 d after germination, with the response severely diminished or lost at days 4 and 5 (Fig. 4A). The response in the pif1pif3 double mutant was again equivalent to both single mutants combined. We also analyzed 2 additional genes shown to be key regulatory targets in the tetrapyrrole pathway, CHLH encoding the H subunit of Mg chelatase and the chelatase regulator GUN4 (2527). Both genes showed a similar pattern, with the strongest peak 3 d after germination, high expression after 2 d, and little induction if any after 4 d (Fig. 4B). Analysis of GUN4 expression in the pif1-2 and pif3-3 alleles gave similar results when measured 3 and 4 d after germination (Fig. S2D). Examination of glutamyl tRNA reductase protein levels showed an increase in pif1, pif3, and the pif1pif3 double mutant by 2 d in the dark (Fig. 4C).

Fig. 4.
Expression of tetrapyrrole synthesis genes in pif mutant seedlings. (A) Real-time PCR data showing expression of HEMA1 in dark-grown pif mutant seedlings. Data are presented as the fold difference from WT after normalizing to the control gene YLS8. ( ...

The profile of the relative induction of HEMA1 in the pif mutants is quite unusual, with sharp peaks 2 and 3 d after germination but no induction at 2½ d. To understand the basis for this, we plotted the normalized level of HEMA1 mRNA (relative to YLS8) for WT and the pif mutants independently (Fig. 4D). This analysis revealed 2 main observations. First, HEMA1 expression was generally higher at early time points in pif1, pif3, and pif1pif3 compared with WT. Second, and most strikingly, HEMA1 expression was out of circadian phase in the pif mutants compared with WT seedlings. Although expression of HEMA1 oscillated with a period close to 24 h in WT seedlings, pif1, pif3, and pif1pif3 showed a reduction in the amplitude of oscillation and a period of oscillation that was variable ranging from ≈12 to 22 h for pif1pif3 (Fig. 4D). To test whether the circadian clock is functioning normally in dark-grown pif mutant seedlings, we examined the expression of the central clock genes CCA1, TOC1, and LHY in the same samples (Fig. S5 A–C). No major changes in expression were observed for all 3 genes, indicating that the clock is still functional in etiolated pif mutants. We also examined the expression of another circadian-regulated gene, CAX1, that is not involved in chloroplast development. Circadian expression of this output gene was unaffected in the pif mutants (Fig. S5D), indicating that pif1 and pif3 might specifically affect circadian regulation of chloroplast-related genes. Finally, we investigated the circadian regulation of PIF1 and PIF3 at this developmental stage. PIF1 and PIF3 showed a robust circadian rhythm in dark-grown seedlings, with a similar phase to that of HEMA1 (Fig. 4E).

pif Mutants Still Show Light Induction of Tetrapyrrole Biosynthesis Genes.

Because PIF3 has been proposed to function positively in the light induction of nuclear-encoded chloroplast genes, we followed gene expression after transfer to 24 h of WL, a time at which chlorophyll levels are severely reduced in the mutants. Although, as noted previously, expression was higher in the dark for HEMA1, CHLH, and GUN4 in all pif mutant lines, all 3 genes were light induced to a similar degree, and the final expression levels of these genes in the light were still higher in pif1, pif3, and pif1pif3 than in WT (Fig. 4F and Fig. S6). We also tested whether pif mutants could respond to monochromatic lights sources and over shorter time periods. As shown in Fig. S2, induction of GUN4 was still apparent in pif1-2 and pif3-3 after 4 h FR and 8 h R light treatments.

Discussion

PIF3 Is a Negative Regulator of Chloroplast Development.

The data presented here are consistent with PIF3 functioning as a repressor of chloroplast development in the dark. Pchlide synthesis was higher in pif3 than WT seedlings (Fig. 1A), and initial rates of chlorophyll synthesis were also greater (Fig. 3 B and C). pif3 seedlings also showed more advanced development of etioplasts and chloroplasts (Fig. 2). In these respects, the pif3 mutant behaved identically to the pif1 mutant, which has been identified as a negative regulator of chloroplast development (20). Consistent with these observations, the pif1pif3 double mutant showed an additive phenotype. Previously, the pif3 mutant had been described as showing inhibition of chloroplast development (15), and the hypothesis that PIF3 acts positively early in signal transduction (and negatively in the longer term) is still current (16, 17). Our data suggest that for the earliest stages of chloroplast development and for the target genes that we have analyzed (Fig. 4) that this is not the case. As discussed later, there are possible explanations for the previously reported loss of induction of chloroplast genes in pif3 (15, 17), but the observations that the overexpression of PIF3 is not sufficient for the induction of phytochrome-regulated genes and that DNA binding of PIF3 in the dark is required (17) are certainly consistent with a role for PIF3 as a repressor. Moreover, the phytochrome-interacting PIF proteins have generally been shown to be acting as repressors not activators of photomorphogenic responses (3, 4, 28), and our results are therefore consistent with a common molecular mechanism for this class of signaling protein.

The reason for the previous misinterpretation of the pif3 mutant phenotype is that seedlings transferred to WL after 4 d in the dark showed a reduced level of chlorophyll compared with WT (Fig. 3). This response, which is identical for pif1 and exaggerated in a pif1pif3 double mutant, is most likely due to photooxidative destruction of chlorophyll. Our results are entirely consistent with this explanation, because the loss of chlorophyll is dependent on the length of the dark period before transfer (and therefore the degree of excess Pchlide production), the fluence rate of WL, and the time of WL exposure. Misregulation of the tetrapyrrole synthesis pathway commonly leads to a photobleaching phenotype (e.g., refs. 29 and 30), and overaccumulation of Pchlide is well established as leading to photooxidative damage (29), for example, in the FR block of greening response (31).

The pif1pif3 Double Mutant Shows a Constitutively Photomorphogenic Phenotype.

One interesting phenotype that we observed for the pif1pif3 double mutant was that it showed a moderate constitutive photomorphogenic response in dark-grown seedlings (Fig. 1). This response was seen even when seeds were kept in complete darkness postimbibition (Fig. S3). Further investigation demonstrated that both pif1 and pif3 single mutants showed a similar, but less pronounced, response. A shorter hypocotyl in the dark has been seen for pif3 (14, 18) and pif1 (32), and a similar phenotype with expanded cotyledons, hook opening, and hypocotyl inhibition was recently observed for pif1, pif3, and a pif1pif3 double mutant (28). In this case, the authors reported a synergistic interaction between PIF1 and PIF3 in contrast to the additive phenotype reported here. A constitutive photomorphogenic phenotype of the pif1pif3 double mutant is expected based on the stronger, dominant negative phenotype of overexpressed truncated PIF1 (12). Presumably, in this case, the PIF1 protein is interfering with the function of additional PIFs, including PIF4 and PIF5 (28). Interestingly, constitutive activation of phytochromes in the dark also results in this phenotype, which could result from Pfr-mediated degradation of multiple PIFs (33). However, whether the pif1pif3 double mutant still requires the presence of seed Pfr (produced during seed set) to reveal the response remains to be seen. In our assays, we saw all aspects of the phenotype in seedlings that had only seen light during seed plating, before the seeds had fully imbibed, and Leivar et al. (28) were unable to block the pif1 and pif1pif3 response, even with a FR light treatment immediately after plating.

PIF1 and PIF3 Repress the Expression of key Chlorophyll Synthesis Genes.

The rate-limiting step for Pchlide (and chlorophyll) synthesis is the enzyme glutamyl tRNA reductase (24). Light regulation of this step is mediated through changes in expression of the HEMA1 gene (34), and HEMA1 is one of a small group of highly regulated tetrapyrrole genes including CHLH and GUN4 (25, 27). The substantial increase in HEMA1 expression and consequent increase in glutamyl tRNA reductase protein can fully account for the observed increase in Pchlide levels in the pif1 and pif3 mutants. The increase in tetrapyrrole synthesis in pif1 was previously suggested to be due to a subtle down-regulation of the ferrochelatase gene (FCII) and a concomitant up-regulation of the heme oxygenase HO3, resulting in less free heme and less inhibition of glutamyl tRNA reductase activity (35), the opposite of the phenotype of the phytochrome-chromophore-deficient mutants in which the heme branch of the pathway is almost completely blocked (36). We have not tested these genes directly, but because HO3 has exceptionally low expression in seedlings and its loss has no impact on chromophore synthesis in the presence of HO1 (37), these changes are unlikely to make more than a minor contribution compared with the substantial increase in levels of the rate-limiting enzyme of the pathway. One reason that previous studies did not observe the changes seen here is that microarrays using dark-grown pif1 (35) and pif3 (15) and their follow-up analyses were performed using seedlings that had been grown for 4 d in the dark. As is clear from our current studies (Fig. 4 and Fig. S2D) differences between WT and the pif mutants are minor at this time.

PIF1 and PIF3 may Function in the Output from the Circadian Clock.

We observed that both the pif1 and pif3 mutations affected circadian regulation of HEMA1, CHLH, and GUN4. HEMA1 and CHLH have been shown to be circadian regulated in the light (25), but circadian regulation for GUN4 has not been reported previously. The altered clock regulation of HEMA1 was not due to a major defect in the circadian clock, because the pif mutants did not have a strong effect on the expression of the core clock components CCA1, LHY, and TOC1. The control output gene CAX1, a H+/Ca2+ antiporter (38) unrelated to chloroplast function, was also unaffected, suggesting that PIF1 and PIF3 function specifically in circadian control of genes involved in chloroplast development. A circadian clock has been shown to be functional in dark-grown Arabidopsis seedlings, with entrainment initiated through changes in temperature or imbibition (39), and can be observed just 2 d after imbibition (39) or even earlier (40). Moreover, the importance of this clock in controlling chloroplast development is supported by the observation that a range of clock mutants fail to green normally after transfer to WL (40). We therefore propose that PIF1 and PIF3 function in circadian control of chloroplast development as shown in the model in Fig. 5. Furthermore, we favor a role for the PIF proteins in the output from the clock. Although phytochrome has a major role in the entrainment of the circadian clock by light (41), PIF3 does not play a significant role in controlling light input or function of the clock (15, 42, 43). Although we cannot completely rule out a role in entrainment, the apparent specificity of the response for chloroplast development genes suggests otherwise.

Fig. 5.
Model for regulation of tetrapyrrole synthesis genes and chloroplast development in pif mutant seedlings.

In our experiments, PIF1 and PIF3 showed robust circadian regulation in dark-grown seedlings, suggesting that clock regulation of PIF function is via circadian control of expression. Analysis of multiple circadian microarray experiments suggests that PIF1, but not PIF3, expression is under circadian control (44). However, a low-amplitude circadian rhythm has also been observed for PIF3 using a PIF3:LUC+ reporter construct (43). Within the resolution of our experiments, the PIF genes appear to cycle in the same circadian phase as HEMA1, precluding a simple mechanism of circadian-regulated PIF repression of HEMA1 expression. However, a small difference in phase could still permit such a mechanism. Alternatively, because both PIF1 and PIF3 have been shown to interact directly with TOC1 (45), a model in which the clock controls PIF function through direct protein interaction is also plausible.

In summary, our results show that both PIF1 and PIF3 are negative regulators of chloroplast development that function to integrate light and circadian control of this critical process. Exactly how they achieve this will be the focus of future studies.

Experimental Procedures

Plant Growth Conditions.

Arabidopsis (Arabidopsis thaliana L.) seeds were imbibed at 4 °C for 2 d in darkness, followed by 2 h of WL (110 μmol·m−2·s−1), and returned to darkness at 23 °C, indicating the start of the respective experiment (unless otherwise stated).

Phenotypic Analyses.

For hypocotyl measurements, 15 Arabidopsis seedlings were measured, and the longest 10 were averaged for 1 biological repeat. For Pchlide measurements, 100 μg of seedling material was extracted twice in acetone/0.1 M NH4OH, 90:10 (vol/vol) as described in ref. 36. Chlorophyll was measured as described in ref. 27. Cotyledon samples for transmission electron microscopy were prepared and examined as described in ref. 36. Numerous plastids in at least 2 independent samples were viewed for each genotype and experimental condition and photographs were taken of representative plastids.

Gene Expression Analyses.

RNA extraction and real-time PCR methods were exactly as described in ref. 27, with one exception (see SI Text). To assess the expression of genes between genotypes at different time points, the absolute C(t) value of the YLS8 control gene was subtracted from the absolute value of the experimental gene for each biological replicate, and the average C(t) value for all biological replicates was used for comparison between genotypes. For primers, see SI Text. Protein extraction and immunoblotting were conducted exactly as described in refs. 27 and 36, with 50 seedlings extracted in 100 μL of SDS extraction buffer.

Supplementary Material

Supporting Information:

Acknowledgments.

We thank Anton Page (Biomedical Imaging Unit, University of Southampton) for help with electron microscopy and Dieter Söll (Yale University) for the polyclonal antibody to glutamyl tRNA reductase. We also thank Patricia Hornitschek, Paula Duek, and Séverine Lorrain for generating the mutants used in this study. P.G.S. was supported by a studentship from the Biotechnology and Biological Sciences Research Council, and work in the C.F. laboratory was supported by Swiss National Science Foundation Grant 3100A0-112638.

Footnotes

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at www.pnas.org/cgi/content/full/0811684106/DCSupplemental.

References

1. Chen M, Chory J, Fankhauser C. Light signal transduction in higher plants. Annu Rev Genet. 2004;38:87–117. [PubMed]
2. Rockwell NC, Su Y-S, Lagarias JC. Phytochrome structure and signaling mechanisms. Annu Rev Plant Biol. 2006;57:837–858. [PMC free article] [PubMed]
3. Bae G, Choi G. Decoding of light signals by plant phytochromes and their interacting proteins. Annu Rev Plant Biol. 2008;59:281–311. [PubMed]
4. Duek PD, Fankhauser C. bHLH class transcription factors take centre stage in phytochrome signalling. Trends Plants Sci. 2005;10:51–54. [PubMed]
5. Ni M, Tepperman JM, Quail PH. PIF3, a phytochrome-interacting factor necessary for normal photoinduced signal transduction, is a novel basic helix-loop-helix protein. Cell. 1998;95:657–667. [PubMed]
6. Zhu Y, Tepperman JM, Fairchild CD, Quail PH. Phytochrome B binds with greater apparent affinity than phytochrome A to the basic helix-loop-helix factor PIF3 in a reaction requiring the PAS domain of PIF3. Proc Natl Acad Sci USA. 2000;97:13419–13424. [PMC free article] [PubMed]
7. Khanna R, et al. A novel molecular recognition motif necessary for targeting photoactivated phytochrome signaling to specific basic helix-loop-helix transcription factors. Plant Cell. 2004;16:3033–3044. [PMC free article] [PubMed]
8. Al-Sady B, Ni W, Kircher S, Schäfer E, Quail PH. Photoactivated phytochrome induces rapid PIF3 phosphorylation prior to proteasome-mediated degradation. Mol Cell. 2006;23:439–446. [PubMed]
9. Bauer D, et al. Constitutive photomorphogenesis 1 and multiple photoreceptors control degradation of phytochrome interacting factor 3, a transcription factor required for light signaling in Arabidopsis. Plant Cell. 2004;16:1433–1445. [PMC free article] [PubMed]
10. Park E, et al. Degradation of phytochrome interacting factor 3 in phytochrome-mediated light signaling. Plant Cell Physiol. 2004;136:968–975. [PubMed]
11. Lorrain S, Allen T, Duek PD, Whitelam GC, Fankhauser C. Phytochrome-mediated inhibition of shade avoidance involves degradation of growth-promoting bHLH transcription factors. Plant J. 2008;53:312–323. [PubMed]
12. Shen H, et al. Light-indicated phosphorylation and degradation of the negative regulator PHYTOCHROME INTERACTING FACTOR 1 from Arabidopsis depend upon its direct physical interactions with photoactivated phytochromes. Plant Cell. 2008;20:1586–1602. [PMC free article] [PubMed]
13. Halliday KJ, Hudon M, Ni M, Qin M, Quail PH. poc1: An Arabidopsis mutant perturbed in phytochrome signaling because of a T DNA insertion in the promoter of PIF3, a gene encoding a phytochrome-interacting bHLH protein. Proc Natl Acad Sci USA. 1999;96:5832–5837. [PMC free article] [PubMed]
14. Kim J, et al. Functional characterization of phytochrome interacting factor 3 in phytochrome-mediated light signal transduction. Plant Cell. 2003;15:2399–2407. [PMC free article] [PubMed]
15. Monte E, et al. The phytochrome-interacting transcription factor, PIF3, acts early, selectively, and positively in light-induced chloroplast development. Proc Natl Acad Sci USA. 2004;101:16091–16098. [PMC free article] [PubMed]
16. Monte E, Al-Sady B, Leivar P, Quail PH. Out of the dark: How the PIFs are unmasking a dual temporal mechanism of phytochrome signalling. J Exp Bot. 2007;58:3125–3133. [PubMed]
17. Al-Sady B, Kikis EA, Monte E, Quail PH. Mechanistic duality of transcription factor function in phytochrome signaling. Proc Natl Acad Sci USA. 2008;105:2232–2237. [PMC free article] [PubMed]
18. Oh E, et al. PIL5, a phytochrome-interacting basic helix-loop-helix protein, is a key negative regulator of seed germination in Arabidopsis thaliana. Plant Cell. 2004;16:3045–3058. [PMC free article] [PubMed]
19. Oh E, et al. Light activates the degradation of PIL5 protein to promote seed germination through gibberellin in Arabidopsis. Plant J. 2006;47:124–139. [PubMed]
20. Huq E, et al. Phytochrome-interacting factor 1 is a critical bHLH regulator of chlorophyll biosynthesis. Science. 2004;305:1937–1941. [PubMed]
21. Magliano TA, Casal JJ. Pre-germination seed-phytochrome signals control stem extension in dark-grown Arabidopsis seedlings. Photochem Photobiol Sci. 2004;3:612–616. [PubMed]
22. McNellis TW, et al. Genetic and molecular analysis of an allelic series of cop1 mutants suggests functional roles for the multiple protein domains. Plant Cell. 1994;6:487–500. [PMC free article] [PubMed]
23. McCormac AC, Terry MJ. The nuclear genes Lhcb and HEMA1 are differentially sensitive to plastid signals and suggest distinct roles for GUN1 and GUN5 plastid-signalling pathways during de-etiolation. Plant J. 2004;40:672–685. [PubMed]
24. Tanaka R, Tanaka A. Tetrapyrrole biosynthesis in higher plants. Annu Rev Plant Biol. 2007;58:321–346. [PubMed]
25. Matsumoto F, et al. Gene expression profiling of the tetrapyrrole metabolic pathway in Arabidopsis with a mini-array system. Plant Physiol. 2004;135:2379–2391. [PMC free article] [PubMed]
26. Larkin RM, Alonso JM, Ecker JR, Chory J. GUN4, a regulator of chlorophyll synthesis and intracellular signaling. Science. 2003;299:902–906. [PubMed]
27. Stephenson PG, Terry MJ. Light signalling pathways regulating the Mg-chelatase branchpoint of chlorophyll synthesis during de-etiolation in Arabidopsis thaliana. Photochem Photobiol Sci. 2008;7:1243–1252. [PubMed]
28. Leivar P, et al. Multiple phytochrome-interacting bHLH transcription factors repress premature seedling photomorphogenesis in darkness. Curr Biol. 2008;18:1815–1823. [PMC free article] [PubMed]
29. Meskauskiene R, et al. FLU: A negative regulator of chlorophyll biosynthesis in Arabidopsis thaliana. Proc Natl Acad Sci USA. 2001;98:12826–12831. [PMC free article] [PubMed]
30. Franklin KA, et al. Misregulation of tetrapyrrole biosynthesis in transgenic tobacco seedlings expressing mammalian biliverdin reductase. Plant J. 2003;35:717–728. [PubMed]
31. McCormac AC, Terry MJ. Loss of nuclear gene expression during the phytochrome A-mediated far-red block of greening response. Plant Physiol. 2002;130:402–414. [PMC free article] [PubMed]
32. Shen H, Moon J, Huq E. PIF1 is regulated by light-mediated degradation through the ubiquitin-26S proteasome pathway to optimize photomorphogenesis of seedlings in Arabidopsis. Plant J. 2005;44:1023–1035. [PubMed]
33. Su YS, Lagarias JC. Light-independent phytochrome signaling mediated by dominant GAF domain tyrosine mutants of Arabidopsis phytochromes in transgenic plants. Plant Cell. 2007;19:2124–2139. [PMC free article] [PubMed]
34. McCormac AC, Terry MJ. Light-signalling pathways leading to the co-ordinated expression of HEMA1 and Lhcb during chloroplast development in Arabidopsis thaliana. Plant J. 2002;32:549–559. [PubMed]
35. Moon J, Zhu L, Shen H, Huq E. PIF1 directly and indirectly regulates chlorophyll biosynthesis to optimize the greening process in Arabidopsis. Proc Natl Acad Sci USA. 2008;105:9433–9438. [PMC free article] [PubMed]
36. Terry MJ, Ryberg M, Raitt CE, Page AM. Altered etioplast development in phytochrome chromophore-deficient mutants. Planta. 2001;214:314–325. [PubMed]
37. Emborg TJ, Walker JM, Noh B, Vierstra RD. Multiple heme oxygenase family members contribute to the biosynthesis of the phytochrome chromophore in Arabidopsis. Plant Physiol. 2006;140:856–868. [PMC free article] [PubMed]
38. Hirschi KD, Zhen RG, Cunningham KW, Rea PA, Fink GR. CAX1, an H+/Ca2+ antiporter from Arabidopsis. Proc Natl Acad Sci USA. 1996;93:8782–8786. [PMC free article] [PubMed]
39. Salomé PA, Xie Q, McClung CR. Circadian timekeeping during early Arabidopsis development. Plant Physiol. 2008;147:1110–1125. [PMC free article] [PubMed]
40. Kato T, et al. Mutants of circadian-associated PRR genes display a novel and visible phenotype as to light responses during de-etiolation of Arabidopsis thaliana seedlings. Biosci Biotechnol Biochem. 2007;71:834–839. [PubMed]
41. Fankhauser C, Staiger D. Photoreceptors in Arabidopsis thaliana: Light perception, signal transduction and entrainment of the endogenous clock. Planta. 2002;216:1–16. [PubMed]
42. Oda A, Fujiwara S, Kamada H, Goupland G, Mizoguchi T. Antisense suppression of the Arabidopsis PIF3 gene does not affect circadian rhythms but causes early flowering and increases FT expression. FEBS Lett. 2004;557:259–264. [PubMed]
43. Viczián A, et al. Functional characterization of phytochrome interacting factor 3 for the Arabidopsis thaliana circadian clockwork. Plant Cell Physiol. 2005;46:1591–1602. [PubMed]
44. Covington MF, Maloof JN, Straume M, Kay SA, Harmer SL. Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome Biol. 2008;9:R130. [PMC free article] [PubMed]
45. Yamashino T, et al. A link between circadian-controlled bHLH factors and the APRR1/TOC1 quintet in Arabidopsis thaliana. Plant Cell Physiol. 2003;44:619–629. [PubMed]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences
PubReader format: click here to try

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • Compound
    Compound
    PubChem Compound links
  • Gene
    Gene
    Gene links
  • GEO Profiles
    GEO Profiles
    Related GEO records
  • MedGen
    MedGen
    Related information in MedGen
  • Protein
    Protein
    Published protein sequences
  • PubMed
    PubMed
    PubMed citations for these articles
  • Substance
    Substance
    PubChem Substance links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...