PIF4–Mediated Activation of YUCCA8 Expression Integrates Temperature into the Auxin Pathway in Regulating Arabidopsis Hypocotyl Growth

1Higher plants continually sense environmental conditions to adapt their growth and development. To a large extent, this is achieved through integrating environmental cues into the growth-regulating hormonal pathways. Exposure of Arabidopsis thaliana plants to high temperature (29°C) results in dramatic plant architecture changes including rapid hypocotyl elongation, leaf hyponasty, and early flowering –. High temperature-induced hypocotyl elongation of Arabidopsis plants provides an ideal model system to investigate the regulatory mechanisms underlying adaptive growth of plants to their ever-changing environments. Among the endogenous cues involved in the regulation of high temperature-induced hypocotyl elongation is the plant hormone auxin. An early observation revealed a correlation between high temperature-induced hypocotyl elongation and high temperature-induced elevation of endogenous free indole-3-acetic acid (IAA) levels. Genetic analyses found that high temperature-induced hypocotyl elongation is sharply reduced in Arabidopsis mutants defective in auxin biosynthesis, transport or signaling. Together, these data attribute an essential role of the auxin pathway in mediating high temperature-induced hypocotyl elongation.

2It is long-recognized that auxin has profound effects on plant growth and development. A combination of physiological, biochemical, pharmacological and molecular genetic studies provide an ever-growing body of insights on our understanding of the auxin biosynthesis pathway,. It is generally believed that, IAA, the main auxin in higher plants, can be synthesized from tryptophan (Trp)-dependent and -independent pathways. Among the best-characterized enzymes involved in the Trp-dependent auxin biosynthetic pathway are the YUCCA (YUC) family of flavin-containing monooxygenases, – and the TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1/TRYPTOPHAN AMINOTRANSFERASE-RELATED (TAA1/TAR) family of aminotransferases,,. A wealth of genetic evidence indicated that, while inactivating members of the YUC family genes causes dramatic developmental defects,, overexpression of the YUC family genes leads to auxin overproduction and long hypocotyl phenotype in Arabidopsis. Although mutation of TAA1 or its close homologs (TAR genes) leads to developmental defects similar to those of the yuc mutants,, overexpression of TAA1/TAR does not cause obvious developmental phenotype, suggesting that TAA1/TAR probably do not catalyze a rate-limiting step in IAA biosynthesis,. Interestingly, recent studies provide evidence that TAA1/TARs and YUCs may act in a common linear biosynthetic pathway for auxin production,,.

3In addition to auxin, a family of phytochrome-interacting factors (PIFs), which encode basic helix-loop-helix (bHLH) transcription factors, have been shown to be central integrators of versatile environmental and hormonal signals during plant adaptive growth,. Among the PIF family of transcriptional regulators, a selective function of PIF4 in high temperature-induced hypocotyl elongation has recently been reported,. These studies revealed that high temperature induced a rapid elevation of PIF4 transcript levels and that the pif4 mutant largely lost the robust enhancement of hypocotyl elongation induced by high temperature.

4In the context that both the transcription factor PIF4 and the phytohormone auxin are required for high temperature-induced hypocotyl elongation, a fascinating hypothesis is that PIF4 may directly link the auxin pathway in regulating plant adaptation growth to high temperature. We provide here evidence that, in response to high temperature, PIF4 directly activates YUC8 expression and thus elevates endogenous free IAA levels. We also show that the SHY2/IAA3 protein is a downstream component of the PIF4-auxin signaling pathway in regulating high temperature-induced hypocotyl elongation. Our results exemplify how a transcriptional regulator integrates environmental cues with endogenous hormonal signaling to mediate specialized developmental changes in regulating plant adaptive growth.

5It has been shown that high temperature activates the expression of the transcription factor PIF4, and elevates endogenous free IAA levels in Arabidopsis. To explore the possible molecular linkage between PIF4 and the auxin pathway in regulating high temperature-mediated adaptation growth, we examined high temperature-induced expression of PIF4 and the YUCCA (YUC) family of auxin biosynthetic genes. Consistent with previous reports,, when wild type (WT) seedlings grown at 22°C for 6 days were transferred to 29°C in continuous light over a 24 h time course, PIF4 transcript abundance was transiently elevated to a peak level at 3 h after transfer (Figure 1A). Correlating with an increased expression of PIF4, high temperature also markedly increased transcript abundance of YUC8 with a peak at 3 h in WT seedlings (Figure 1B). Closer observation with a narrower range of time points revealed that high temperature-mediated induction of YUC8 expression occurred generally later than that of PIF4 (Figure S1). Parallel experiments indicated that high temperature did not upregulate the expression of other YUCCA family genes tested (Figure S2). We then compared high temperature-induced YUC8 expression between WT and the pif4 mutant, which has been shown to be defective in high temperature-induced adaptations in plant architecture (Figure 1B). As shown in Figure 1B, the basal expression levels of YUC8 were already low in pif4 seedlings and, significantly, high temperature-induced upregulation of YUC8 expression was largely abolished in this mutant, indicating that the function of PIF4 is important for the basal- and high temperature-induced expression of YUC8.

6The pif4 mutation impairs high temperature-induced upregulation of YUC8 expression suggests that this mutation may also affect high temperature-induced elevation of free IAA levels. To test this, we compared high temperature-induced elevation of free IAA levels in WT and pif4 seedlings. For these experiments, we grew seedlings at 22°C or 29°C in continuous light for 6 days and collected hypocotyls for IAA measurement. Consistent with a previous report, high temperature increased free IAA levels of WT seedlings by around 50% (Figure 1C). As expected, high temperature-induced elevation of free IAA levels was abolished in the pif4 mutant (Figure 1C), indicating that PIF4 is also required for high temperature-induced elevation of auxin biosynthesis. Together, these results suggest that PIF4 and YUC8 may function in linking temperature and auxin pathway in regulating hypocotyl elongation.

7As a first step to test the possibility that PIF4 may directly regulate YUC8 expression during high temperature-induced adaptation growth, we examined YUC8 expression in transgenic plants overexpressing PIF4 (35S-PIF4). Like the reported yucca mutants which contain increased endogenous auxin levels, 35S-PIF4 plants show a long hypocotyl phenotype that resembles high temperature-grown WT seedlings (Figure S3). As revealed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) assays, the expression of YUC8 (Figure 2A), but not that of TAA1 (Figure S4), was substantially increased in 35S-PIF4 seedlings as compared to WT. We also generated PIF4-overexpression plants (pMDC7:PIF4) using the chemical inducible vector pMDC7. In the presence of the chemical inducer estradiol, pMDC7:PIF4 seedlings show increased expression of PIF4 (Figure 2B) and display a long hypocotyl phenotype like 35S-PIF4 seedlings (Figure S5). As expected, YUC8 expression was considerably elevated following estradiol induction (Figure 2C). Consistently, measurement of auxin revealed that the free IAA levels in 35S-PIF4 plants were increased by 50% as compared to those in WT plants (Figure 2D). In line with increased free IAA levels in 35S-PIF4 plants, the expression of the auxin responsive DR5:GUS, a widely used reporter of auxin response, was clearly enhanced in the basal region of 35S-PIF4 hypocotyls (Figure S6). These data together indicate that overexpression of PIF4 leads to increased expression of the auxin biosynthetic gene YUC8 and, as a result, elevated endogenous free IAA levels in planta.

8Three lines of evidence support a scenario that the PIF4 transcription factor may directly regulate YUC8 expression during high temperature-induced adaptation growth. First, underlying high temperature-induced hypocotyl elongation, high temperature upregulates the expression of PIF4 in a similar fasion to that of YUC8. Second, high temperature-induced upregulation of YUC8 expression requires the function of PIF4. Third, overexpression of PIF4 leads to increased expression of YUC8 and elevated free IAA levels in planta. Given that PIF4 specifically binds to a core DNA G-box motif (CACGTG) of its target gene promoters, we searched for the presence of G-box motifs in the promoter regions of the 11 YUC family genes present in the Arabidopsis genome. As shown in Figure 3A, G-box motifs were found not only in the promoter of YUC8, whose expression was significantly induced by high temperature (Figure 1), but also in the promoters of YUC5, YUC9 and YUC10, whose expression was not or slightly induced by high temperature (Figure S2). To test the idea that PIF4 may actually bind to the G-box-containing regions of these YUC genes, we performed chromatin immuno-precipitaiton (ChIP) assays using a previously reported transgenic line expressing a fusion of PIF4 to the haemagglutinin (HA) antigen (PIF4-HA) and anti-HA antibody (Abcam). PCR amplification of the promoter regions of the four YUC genes showed that PIF4-HA specifically bound to the G-box-containing promoter region of YUC8, but not to the G-box-containing promoter regions of YUC5, YUC9 and YUC10 (Figure 3B). These results suggest that PIF4 associates with the G-box DNA motifs in the promoter region of YUC8 in vivo. Further evidence supporting this conclusion came from electrophoretic mobility-shift assays (EMSA) using PIF4 protein expressed in vitro. As shown in Figure 3C, PIF4 bound to the G-box-containing DNA fragments present in the promoter region of YUC8 and, this binding could be effectively competed by the addition of excess amount of unlabeled G-box-containing DNA probes (Figure 3C). As a control, we showed that DNA probes containing a mutated G-box motif (CACGGG) failed to compete the binding of PIF4 to the G-box-containing DNA fragments (Figure 3C). Together, these results support that the PIF4 transcription factor regulates YUC8 expression by directly binding to its promoter region.

9Next, using the well-established transient expression assay of Nicotiana benthamiana leaves, we verified the activation effect of PIF4 on the expression of a reporter containing the YUC8 promoter fused with the firefly luciferase (LUC) gene. When the pYUC8:LUC reporter was infiltrated into N. benthamiana, the LUC activity could be detected at lower level (Figure 4A, B). Coexpression of pYUC8:LUC with the 35S:PIF4 construct led to an obvious induction in luminescence intensity (Figure 4A, 4B), suggesting that ectopic expression of PIF4 can activate pYUC8:LUC expression in this transient expression assay. In a parallel experiment, pYUC8(mut):LUC, in which the two G-boxes of the YUC8 promoter were deleted and fused with LUC, togehter with 35S:PIF4 were co-infiltrated into N. benthamiana leaves. As shown in Figure 4, the activation effect of PIF4 on pYUC8(mut):LUC expression was abolished. Together, our transient expression assays in N. benthamiana leaves confirmed that PIF4 directly activates YUC8 expression in vivo.

10To determine the genetic relationship between PIF4 and YUC8, we identified a yuc8 mutant (SALK_096110) which harbors a T-DNA insertion that markedly reduced the expression levels of the YUC8 gene (Figure S7). We show that the yuc8 mutant is defective in high temperature-induced hypocotyl growth (Figure 5A). We then introduced the above-described 35S-PIF4 construct into the genetic background of the yuc8 mutant through genetic crossing. As shown in Figure 5B, the yuc8 mutation substantially suppressed the long-hypocotyl phenotype of the 35S-PIF4 plants, supporting that YUC8 acts genetically downstream of PIF4 in regulating high temperature-induced hypocotyl elongation.

11Several elegant observations have demonstrated the involvement of PIF4 and auxin in regulating adaptive growth of plants to high temperature,. Our data presented here further revealed that, through directly activating of the YUC8 expression, PIF4 integrates its action into the auxin pathway in regulating high temperature-mediated hypocotyl elongation. To further identify auxin signaling components involved in this process, we employed a genetic approach to search for auxin-related mutations that can suppress the long-hypocotyl phenotype of the 35S-PIF4 plants. It has been shown that the shy2-2 mutant, which harbors a stabilized mutant form of the SHY2/IAA3 protein, displays a short hypocotyl phenotype, suggesting a role of SHY2/IAA3 in regulating auxin-mediated hypocotyl growth. We showed that shy2-2 seedlings are defective in high temperature-induced hypocotyl growth (Figure S3). Importantly, like the auxin signaling mutant axr1-12 (Figure S8), shy2-2 genetically suppressed the long-hypocotyl phenotype of 35S-PIF4 (Figure 6). In contrast, other gain-of-function mutations in different IAA proteins –, including slr-1 (contains a gain-of-function mutation in IAA14), axr2-1 (contains a gain-of-function mutation in IAA7), axr5-1 (contains a gain-of-function mutation in IAA1) and iaa28-1, did not affect hypocotyl elongation in response to high temperature and failed to suppress the long-hypocotyl phenotype of 35S-PIF4 seedlings (Figure S9). These results demonstrate that the auxin signaling repressor SHY2/IAA3 is selectively involved in high temperature-induced hypocotyl growth.

12As sessile organisms, plants have evolved remarkable ability to adapt their development to the ever-changing environmental conditions. Exposure of plants to high temperature results in dramatic changes in plant architecture, including elongation responses and leaf hyponasty. High temperatures can also considerably reduce plant biomass, raising concerns over future crop productivity and food security. Therefore, the modulation of plant architecture by high temperature is a subject of considerable agricultural significance, particularly with regard to global climate change. An ever-growing body of evidence in Arabidopsis has implicated that high temperature-induced plant architecture remodeling relies on the interplays between multiple external and internal cues including light, circadian clock, auxin, gibberellin and others,. Particularly, recent studies reveal that a group of bHLH transcription factors play a central role in modulating developmental responses to both light and temperature,,, –.

13In this study, we discovered that, as a molecular integrator, the PIF4 transcription factor links high temperature to the auxin pathway in regulating high temperature-induced hypocotyl elongation. Several lines of evidence support this finding: First, underlying the long-standing observation that high temperature induces a dramatic elongation of the hypocotyl, we showed that high temperature triggers an elevation of the transcript abundance of both PIF4 and YUC8 (Figure 1). Second, high temperature-induced upregulation of YUC8 expression largely depends on the function of PIF4 (Figure 1). Third, overexpression of PIF4 leads to increased expression of YUC8 and elevated endogenous free IAA levels (Figure 2). Fourth, as revealed by ChIP and EMSA assays, PIF4 specifically binds to a core DNA G-box motif (CACGTG) present in the promoter of the YUC8 gene (Figure 3). Fifth, transactivation assays in N. benthamiana leaves support that PIF4 stimulates the activity of the YUC8 promoter fused with a reporter (Figure 4). Finally, the yuc8 mutation, which is defective in high temperature-induced hypocotyl elongation, is able to partially suppress the long-hypocotyl phenotype of the 35S-PIF4 plants (Figure 5). Together, these data support that, PIF4 selectively activates the expression of the auxin biosynthetic gene YUC8, thus integrates high temperature to the auxin pathway in regulating adaptive hypocotyl growth.

14It is worthy of note that the yuc8 mutant still retains some response to high temperature in hypocotyl elongation and that this mutation fails to completely suppress the long-hypocotyl phenotype of 35S-PIF4 plants (Figure 5). A plausible explanation for this is that the yuc8 mutant used in this study shows reduced, but not loss of, YUC8 expression (Figure S7). Alternatively, we could not rule out the possibility that PIF4 may activate auxin biosynthetic genes other than YUC8, which act weakly in PIF4-mediated hypocotyl growth in response to high temperature. A very recent report hints that the PIF4 transcription factor could target TAA1, which acts genetically upstream of the YUC family genes in IAA production,. Considering that overexpression of TAA1 does not lead to any obvious developmental phenotype, and that TAA1 and YUCs act in a common linear biosynthetic pathway for auxin production,,, it is reasonable to propose that TAA1 acts together with other auxin biosynthesis genes such as YUC8 to mediate high temperature-induced and PIF4-mediated hypocotyl elongation. However, our gene expression analyses reveal that overexpression of PIF4 alone fails to elevate TAA1 transcription (Figure S4).

15PIF4-mediated activation of YUC8 expression in response to high temperature exemplifies a mechanism by which environmental cues manipulate auxin, the key endogenous modulator of plant architecture. Another known physiological process in which both PIF4 and auxin are involved is shade avoidance syndrome (SAS), plant adaptive growth responses to the light signal,,. PIF4 is therefore emerging as a molecular “hub” to integrate both temperature and light signals to regulate plant architecture remodeling. Accumulating evidence reveals that, unlike shade avoidance, where PIF4 acts redundantly with its homolog, PIF5, to regulate elongation growth, PIF4 appears to perform a dominant role in driving high temperature-induced adaptive growth,,, –. These studies suggest that, PIF4, and possibly other PIF family members, have specialized and overlapping functions in regulating plant adaptive growth to different environmental stimuli.

16Our results support a scenario in which the auxin pathway acts downstream of the PIF4 transcriptional regulator in regulating high temperature-induced hypocotyl elongation. Supporting evidence for this hypothesis came from our genetic analysis showing that the axr1-12 mutation, which contains a mutation in a subunit of the heterodimeric RUB-E1 enzyme required for auxin signaling, completely suppressed the long-hypocotyl phenotype of 35S-PIF4 seedlings (Figure S8). Based on our current knowledge of the auxin signaling pathway, auxin mediates the expression of auxin responsive genes through the inactivation of AUX/IAA transcriptional repressors that negatively control the activity of AUXIN REPONSE FACTOR (ARF) transcription factors. In the context that many gain-of-function aux/iaa mutations are associated with reduced response to exogenous auxin, but developmental defects among these mutants are frequently more specific, it is reasonable to speculate that specific Aux/IAA-ARF pair(s) may function in the PIF4-auxin pathway to mediate the specialized hypocotyl elongation process triggered by high temperature. In our genetic efforts to identify new components involved in the PIF4-auxin pathway in regulating high temperature-mediated hypocotyl elongation, we determined that SHY2/IAA3, but not other IAA proteins tested, has a specialized function in mediating high temperature-induced hypocotyl elongation. It is of interest in future studies to identify the ARF transcription factor(s) interacting with SHY2/IAA3 in regulating high temperature-induced hypocotyl elongation.

17Arabidopsis thaliana ecotypes Columbia (Col-0), Ler and WS were used as wild types. The pif4 mutant used in this study was the reported null allele pif4-2. Other plant materials used in this study were previously described: DR5:GUS, 35S-PIF4, 35S:PIF4-HA, yucca, axr1-12, shy2-2 [2019], slr-1, axr2-1, axr5-1 and iaa28-1. yuc8 (SALK_096110) was identified from the SIGnAL T-DNA collection.

18All molecular manipulations were performed according to standard methods. The PIF4 coding fragment was amplified by PCR and cloned into the AscI/PacI sites of the binary vector pMDC7, resulting in a chemical-inducible PIF4 expression construct. The construct was then transformed into Agrobacterium tumefaciens strain GV3101 (pMP90), which was used for transformation of Arabidopsis plants by vacuum infiltration.

19Seeds were surface-sterilized for 15 min in 10% bleach, washed four times with sterile water, and plated on half-strength Murashige and Skoog (MS) medium. Plants were stratified at 4°C for 2 d in darkness and then transferred to a phytotrone set at 22°C with a 16-h light/8-h dark photoperiod or in continuous light for specific experiments. For high temperature treatment, plants were directly grown at 29°C in continuous light or young seedlings were transferred to 29°C in continuous light for different times.

20For qRT-PCR analysis, seedling were harvested and frozen in liquid nitrogen for RNA extraction. RNA extraction and qRT-PCR analysis were performed as previously described. Primers used to quantify gene expression levels are listed in Table S1. The GUS activity assays were performed as previously described.

21One gram of 6-d-old seedlings of 35S:PIF4-HA transgenic plants and the anti-HA antibody (Abcam) were used in ChIP experiments. Chromatin immunoprecipitation (ChIP) assays were performed as previously described. The enrichment of DNA fragments was determined by semi-quantitative PCR analysis. Three independent biological repeats were performed.

22PIF4 and Luciferase (Luc) were synthesized by using the Rabbit Reticulocyte TNT system (Promega),. The 60-bp YUC8 promoter probes containing G-box motifs were synthesized and labeled with biotin at the 3′ end (Invitrogen). Cold competitor probes were generated from dimerized oligos of the YUC8 promoter region containing the wt-G-box (CACGTG) or mut-G-box (CACGGG) motifs, respectively. DNA gel-shift assays were performed as described,. Probe sequences are shown in Table S1.

23The transient expression assays were performed in N. benthamiana leaves as previously described. The YUC8 promoter was amplified with the primer pairs 5-CACCATCCGATATGATAACGAT-3 and 5-TGGAAGTTGTATTGGAAA-3 and cloned into pENTR using the pENTR Directional TOPO cloning kit (Invitrogen). To generate YUC8 promoter with mutations, site-directed mutagenesis was used to delete the two G-boxes in the YUC8 promoter (Figure 3) using the TaKaRa MutanBEST kit. Then, the two YUC8 promoter versions were fused with the luciferase reporter gene LUC through the Gateway reactions into the plant binary vector pGWB35 to generate the reporter constructs pYUC8:LUC and pYUC8(mut):LUC. The PIF4 effector construct was the 35S:PIF4. For this construct, the PIF4 coding fragment was amplified by PCR with the primer pairs 5-CACCATGGAACACCAAGGTTGGAG-3 and 5-GTGGTCCAAACGAGAACCGT-3. Five independent determinations were assessed. Error bars represent SD. The experiments were repeated at least five times with similar results.

24For measurement of free IAA levels in wild-type and pif4 mutant hypocotyls in response to high temperature treatment, the hypocotyls of 6-d-old wild-type and pif4 mutant seedlings grown at 22°C and 29°C in continuous light, respectively, were harvested for free IAA measurement. For the wild-type seedlings grown at 29°C, the 2 mm length parts for each hypocotyl (above the junction between hypocotyl and root) were harvested for free IAA measurement. Eight-d-old seedlings of wild-type and 35S-PIF4 grown at 22°C in continuous light were harvested for free IAA measurement. Approximately 200 mg (fresh weight) of tissues were used for IAA extraction and measurement as previously described.