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The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis

A Publisher Correction to this article was published on 12 June 2020

This article has been updated

Abstract

Directional intercellular transport of the phytohormone auxin mediated by PIN-FORMED (PIN) efflux carriers has essential roles in both coordinating patterning processes and integrating multiple external cues by rapidly redirecting auxin fluxes. PIN activity is therefore regulated by multiple internal and external cues, for which the underlying molecular mechanisms are not fully elucidated. Here, we demonstrate that 3′-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE1 (PDK1), which is conserved in plants and mammals, functions as a molecular hub that perceives upstream lipid signalling and modulates downstream substrate activity through phosphorylation. Using genetic analysis, we show that the loss-of-function Arabidopsis pdk1.1pdk1.2 mutant exhibits a plethora of abnormalities in organogenesis and growth due to defective polar auxin transport. Further cellular and biochemical analyses reveal that PDK1 phosphorylates D6 protein kinase, a well-known upstream activator of PIN proteins. We uncover a lipid-dependent phosphorylation cascade that connects membrane-composition-based cellular signalling with plant growth and patterning by regulating morphogenetic auxin fluxes.

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Fig. 1: Loss of function of PDK1.1 and PDK1.2 attenuates Arabidopsis growth and development.
Fig. 2: PDK1.1 and PDK1.2 regulate auxin distribution through PIN-mediated auxin transport.
Fig. 3: PDK1.1 and PDK1.2 bind to phospholipids and localize to both the cytoplasm and the basal side of the PM in root cells.
Fig. 4: PDK1.1 and PDK1.2 regulate plant growth and development through D6PK/D6PKLs.
Fig. 5: PDK1.1 and PDK1.2 regulate plant growth and development by phosphorylating D6PK/D6PKLs.
Fig. 6: A phospholipid–PDK1–D6PK cascade regulates PIN-dependent polar auxin transport and plant growth.

Data availability

Source data for Figs. 16, and Extended Figs. 24, 7, 9 and 10 are provided with the paper. Sequencing data from this Article is provided in the Arabidopsis Genome Initiative databases under the following accession numbers: PIN1 (AT1G73590), PIN2 (AT5G57090), PIN3 (AT1G70940), PIN4 (AT2G01420), PIN7 (AT1G23080), PDK1.1 (AT5G04510), PDK1.2 (AT3G10540), D6PK (AT5G55910), D6PKL1 (AT4G26610), D6PKL2 (AT5G47750), D6PKL3 (AT3G27580), PID (AT2G34650), WAG1 (AT1G53700) and WAG2 (AT3G14370). All data necessary to evaluate the conclusions in the paper or the Supplementary Information are available from the corresponding authors on request.

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Acknowledgements

We thank C. Schwechheimer and B. Scheres for sharing published materials; M. Glanc for providing pET28a-PIN2/3 plasmids; X. Gao for help with SEM imaging, L. Rodriguez for advice on co-IP; staff at the bioimaging and life science facilities of IST Austria for continuous service and assistance; and the Nottingham Arabidopsis Stock Centre (NASC) and the Arabidopsis Biological Resource Centre (ABRC) for providing T-DNA insertional mutants. J.P. acknowledges the support from imaging facility of IEB CAS. The research leading to these results has received funding from Chinese Ten-Thousand Talent Program (to H.-W.X.) and the European Union’s Horizon2020 program (ERC grant agreement no. 742985, to J.F.). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723–2015). X.Z. was supported by a PhD scholarship from China Scholarship Council.

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Authors and Affiliations

Authors

Contributions

S.T., J.F. and H.-W.X. designed experiments. S.T., X.Z., W.K. and X.-L.Y. performed experiments. G.M. provided [32P]ATP and helped with kinase assays. J.P., Z.V. and R.F. performed experiments in BY-2 cells. S.T., J.F. and H.-W.X. analysed and interpreted the data. S.T., J.F. and H.-W.X. wrote the manuscript with input from other co-authors, and all of the authors read and revised the manuscript.

Corresponding authors

Correspondence to Jiří Friml or Hong-Wei Xue.

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Extended data

Extended Data Fig. 1 Expression pattern of PDK1.1 and PDK1.2.

GUS staining of pPDK1.1::GUS and pPDK1.2::GUS lines indicated that PDK1.1 and PDK1.2 were expressed in the vascular tissues in both roots and shoots at various developmental stages, including young seedlings (a, f; 7 days), root stele (b, g; 7 days), columella cells (c, h, only with expression detected for PDK1.1; 7 days), lateral root primordia (d, i; 12 days), and dark-grown seedlings (e, j; 4 days). Representative images of three independent homozygous lines were shown. Scale bars, 1 mm.

Extended Data Fig. 2 Identification of Arabidopsis pdk1.1 and pdk1.2 T-DNA insertional mutants.

a, Schematic representation of PDK1.1 and PDK1.2 genes and positions of T-DNA insertions for pdk1.1 and pdk1.2. Introns, exons, and non-coding regions are indicated by lines, black, or blank boxes respectively. Positions of primers are indicated. b, Identification of homozygous pdk1.1 and pdk1.2 mutants. Genomic DNA of pdk1.1 and pdk1.2 mutants was used as templates for PCR amplification. Homozygous lines have a single amplified DNA fragment when using LBa1/pdk1.1-RP or LBa1/pdk1.2-RP primers. n = 5 biologically independent experiments, with similar results obtained. c, qRT-PCR analysis confirmed the deficient expression of PDK1.1 and PDK1.2 genes in pdk1.1 and pdk1.2 mutants, respectively. Total RNA of 7-day-old WT, pdk1.1 and pdk1.2 seedlings was extracted, reversely transcribed, and then used for analysis. ACTIN7 was amplified and used as an internal reference to normalize the expression of PDK1.1 and PDK1.2, and the mean value in Col-0 was set as “1”. The experiments were biologically repeated for 3 times. Dots represent individual samples, and lines indicate mean ± s.d.. P values were calculated by a Welch’s two-tailed t-test.

Source Data

Extended Data Fig. 3 Deficiency of PDK1.1 and PDK1.2 impaired the hypocotyl gravitropism under dark and phototropism towards directional light.

a, Deficiency of PDK1.1 and PDK1.2 promoted the radial growth in the root columella cell region. Transverse view of the root columella cells by CLSM. Left, a schematic image to show the positon for the transverse view; middle, Col-0; right, pdk1.1 pdk1.2. Scale bars, 20 µm. n = 3 biologically independent experiments, with similar results obtained. b, Deficiency of PDK1.1 and PDK1.2 gave rise to more columns, but not layers of, root columella cells. Quantification is based on CLSM images of PI-stained roots. Layer numbers were counted for both undifferentiated and differentiated columella cells. Dots represent individual plants, and lines indicate mean ± s.d.. n = 18, 26, 18, and 26, from left to right, respectively. P values were calculated by a Welch’s two-tailed t-test. ce, Deficiency of PDK1.1 and PDK1.2 impaired root and shoot gravitropic response in the dark. Etiolated seedlings of Col-0, pdk1.1, pdk1.2, and pdk1.1 pdk1.2 were grown under dark for 90 h and a representative photo was shown (c). Scale bar, 5 mm. n = 5 biologically independent experiments, with similar results obtained (c). (d), Root tip angles are shown as polar bar charts. n = 61, 62, 69, and 71, respectively. (e), Hypocotyl angles are shown as polar bar charts. n = 51, 50, 59, and 68, respectively. fg, pdk1.1 pdk1.2 showed defects in phototropism. Seedlings of Col-0, pdk1.1, pdk1.2, and pdk1.1 pdk1.2 were grown under dark for 90 h, exposed to white light for 24 h, and were then subjected to directional white light in a box covered with aluminium foil from the other sides. A representative photo is shown (f). Scale bar, 5 mm. n = 3 biologically independent experiments, with similar results obtained (f). (g), hypocotyl angles are shown by polar bar charts. n = 56, 62, 67, and 62, respectively. P values were calculated by a Welch’s two-tailed t-test, and also by a further F-test to indicate differences of variances (d, e, and g).

Source Data

Extended Data Fig. 4 Deficiency of PDK1.1 and PDK1.2 impaired the normal development of the apical hook and high temperature-induced hypocotyl elongation.

a, b, Observation (a, scale bar, 5 mm) and quantification (b) showed that etiolated seedlings (90 h) of pdk1.1 pdk1.2 exhibited less tight apical hooks. n = 5 biologically independent experiments, with similar results obtained (a). n = 14, 18, 12 and 17 seedlings for Col-0, pdk1.1, pdk1.2, and pdk1.1 pdk1.2 respectively (b). c, Etiolated seedlings of pdk1.1 pdk1.2 exhibited comparably long hypocotyls to Col-0. Seedlings were grown under dark for 90 h. n = 20, 21, 20 and 17 seedlings for Col-0, pdk1.1, pdk1.2, and pdk1.1 pdk1.2 respectively. d, Etiolated seedlings of pdk1.1 pdk1.2 did not form exaggerated apical hooks in the presence of ACC. Seedlings of Col-0, pdk1.1, pdk1.2, and pdk1.1 pdk1.2 were grown under dark for 90 h in the absence or presence of ACC (10 µM). Scale bars, 500 µm. n = 3 biologically independent experiments, with similar results obtained. ef, pdk1.1 pdk1.2 showed defects in high temperature-induced hypocotyl elongation. Seedlings of Col-0, pdk1.1, pdk1.2 and pdk1.1 pdk1.2 were grown under light at 22 °C (n = 16, 20, 18 and 22 respectively) or 29 °C (n = 20, 21, 17 and 18) for 5 days, and hypocotyl elongation was observed (e, scale bar, 1 cm) and quantified (e). Hypocotyl length was measured by the Image J program and shown as mean ± s.d. (left) or relative length by setting the hypocotyl length of Col-0 and pdk1.1 pdk1.2 at 22 °C as “1”, respectively (right). Dots represent individual plants, and lines indicate mean ± s.d.. Different letters represent significant difference, P < 0.05, by one-way ANOVA with a Tukey multiple comparison test, and P values are shown for each genotype compared with Col-0 (b, c, and f).

Source Data

Extended Data Fig. 5 Loss of function of PDK1.1 and PDK1.2 impaired auxin distribution.

Observation of the auxin responsive reporter DR5rev::GFP by CLSM indicated a dramatic decrease of the auxin maxima in pdk1.1 pdk1.2 (eh) compared with Col-0 (ad). Fused cotyledon exhibiting two sites of auxin maxima in light-grown 7-day-old seedlings of pdk1.1 pdk1.2 (e) compared with one of Col-0 (a); roots of light-grown 10-day-old seedlings (b and f); apical hooks of 10 µM ACC treated 4-day-old etiolated seedlings (c and g); roots of 10 µM ACC treated 4-day-old etiolated seedlings (d and h). Scale bars, 200 µm. n = 3 biologically independent experiments, with similar results obtained.

Extended Data Fig. 6 Deficiency of PDK1.1 and PDK1.2 did not affect the polarity of PIN proteins.

a, Deficiency of PDK1.1 and PDK1.2 did not change the polarity of PIN1-YFP. Four-day-old seedlings of pPIN1::PIN1-YFP in Col-0 and pPIN1::PIN1-YFP in pdk1.1 pdk1.2 were imaged by CLSM. Scale bars, 20 µm. n = 2 biologically independent experiments, with similar results obtained (a-g). b, Deficiency of PDK1.1 and PDK1.2 did not change the polarity of PIN2-GFP. Four-day-old seedlings of pPIN2::PIN2-GFP in Col-0 and pPIN2::PIN2-GFP in pdk1.1 pdk1.2 were imaged by CLSM. Scale bars, 20 µm. cf, Deficiency of PDK1.1 and PDK1.2 did not change the polarity of PIN3-GFP. Four-day-old seedlings of pPIN3::PIN3-GFP in Col-0 and pPIN3::PIN3-GFP in pdk1.1 pdk1.2 were imaged by CLSM. (c) subcellular localisation of PIN3-GFP; (d) an amplified view of PIN3-GFP in the root stele; (e) a close view of PIN3-GFP in root columella cells; (f) a 3D-projection of PIN3-GFP localisation in root columella cells. The “Green Fire Blue” LUT was used for photo visualization based on fluorescence intensity by Fiji. Scale bars, 20 µm. g, A transverse view of the root columella cells revealed the overproliferation, with an enlarged region expressing PIN3-GFP. Four-day-old seedlings of pPIN3::PIN3-GFP in Col-0 and pPIN3::PIN3-GFP in pdk1.1 pdk1.2 were stained with PI, and imaged by CLSM, at the position as marked in the left image. Scale bars, 20 µm.

Extended Data Fig. 7 Analysis of PDK1 transgenic lines.

a, Expression of PDK1.1 or PDK1.2 (p35S::Venus-PDK1.1, p35S::Venus-PDK1.2, p35S::mCherry-PDK1.1 and p35S::mCherry-PDK1.2) rescued the growth defects of pdk1.1 pdk1.2. Adult plants (25-day-old) were observed and representative photos were shown. Scale bar, 2 cm. b, Western blot analysis verified the PDK1.1 or PDK1.2 expression (p35S::Venus-PDK1.1 and p35S::Venus-PDK1.2) in pdk1.1 pdk1.2, respectively. Seven-day-old T3 homozygous seedlings were used for protein extraction and subjected to analysis. Upper panel, anti-GFP (1:2000); lower panel, Ponceau staining. c, Western blot verified the PDK1.1 or PDK1.2 expression (p35S::mCherry-PDK1.1 and p35S::mCherry-PDK1.2) in pdk1.1 pdk1.2, respectively. Seven-day-old T3 homozygous seedlings were used for protein extraction and subjected to analysis. Upper panel, anti-RFP (1:2000); lower panel, Ponceau staining. de, mCherry-fused PDK1.1 (d) and PDK1.2 (e) localised to both cytoplasm and the basal side of PM. Four-day-old seedlings of p35S::mCherry-PDK1.1 and p35S::mCherry-PDK1.2 were imaged by CLSM. Open arrowheads indicated the basal polar localisation. Scale bar, 10 µm. fi, Subcellular localisation of Venus-fused PDK1.1N (f, cytoplasm), Venus-fused PDK1.1C (g, both cytoplasm and nucleus), Venus-fused PDK1.2N (h, cytoplasm), and Venus-fused PDK1.2C (i, both cytoplasm and nucleus). Four-day-old seedlings expressing corresponding fusion proteins were imaged by CLSM. Scale bar, 10 µm. n = 4, 2, 3, and 3 biologically independent experiments for (a), (b), (c), and (d) respectively, with similar results obtained.

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Extended Data Fig. 8 Functional pPDK1.1::Venus-PDK1.1 localised at both cytoplasm and the basal side of PM.

a, pPDK1.1::Venus-PDK1.1 rescued the growth defects of pdk1.1 pdk1.2. 25-day-old adult plants were observed and representative photos are shown. Scale bar, 2 cm. b, pPDK1.1::Venus-PDK1.1 rescued the lateral root defects of pdk1.1 pdk1.2. 10-day-old seedlings were observed and representative photos are shown. Scale bar, 2 cm. c, pPDK1.1::Venus-PDK1.1 rescued the defects of pdk1.1 pdk1.2 in the hypocotyl gravitropic response. 4-day-old etiolated seedlings were observed and representative photos are shown. Scale bar, 2 cm. d, Venus-fused PDK1.1 localised to both cytoplasm and PM, especially with a predominant presence at the basal side of PM. Four-day-old seedlings of pPDK1.1::Venus-PDK1.1 were imaged by CLSM. Open arrowheads indicate the basal polar localisation. The “Green Fire Blue” LUT was used for photo visualization based on fluorescence intensity by Fiji. Scale bar, 20 µm. e, Venus-PDK1.1 localized to cytoplasm (upper image) in interphase tobacco BY-2 cells, and the association with PM was obvious only during cytokinesis (arrow in lower image). An XVE>>Venus-PDK1.1 line was induced for 48 h with 1 μM β-estradiol and were then imaged by spinning disk confocal microscope. Scale bar, 10 μm. n = 3, 3, 2, 3, and 2 biologically independent experiments for (a), (b), (c), (d), and (e) respectively, with similar results obtained.

Extended Data Fig. 9 mCherry-D6PKs co-localised with Venus-PDK1.1 at the basal side of PM.

a, mCherry-fused D6PKs localised to the basal side of PM. Four-day-old seedlings of p35S::mCherry-D6PK/D6PKLs (short as D0 to D3) were imaged by CLSM. The “mpl-inferno” LUT was used for photo visualization based on fluorescence intensity by Fiji. Scale bars, 10 µm. b, Western blot verified the mCherry-D0~D3 protein level (35S::mCherry-D0~D3) in Col-0, respectively. Seven-day-old T3 homozygous seedlings were used for protein extraction and subjected to Western blot analysis. Upper panel, anti-RFP (1:1000), short exposure (0.5 sec); medium panel, anti-RFP (1:1000), long exposure (5 sec, for low expression of mCherry-D3); lower panel, Ponceau staining. c, Venus-PDK1.1 co-localised with mCherry-D6PKL2 and mCherry-D6PKL3 at the basal side of PM. Four-day-old seedlings of p35S::mCherry-D6PKL2/ p35S::Venus-PDK1.1 and p35S::mCherry-D6PKL3/ p35S::Venus-PDK1.1 were imaged by CLSM. Scale bar, 10 µm. d, In vitro kinase assay with [32P]-ATP revealed that GST-PDK1.2-conducted phosphorylation of D6PK facilitates its activity towards PIN-HL phosphorylation. Upper panel, autoradiography; lower panel, CBB staining. e, In vitro kinase assay with [32P]-ATP revealed that GST-PDK1.2-conducted full phosphorylation and activation of D6PK, towards His-PIN1-HL phosphorylation, required the phosphorylation at S345 for D6PK. Upper panel, autoradiography of 32P; lower panel, CBB staining. n = 3, 2, 2, 3, and 3 biologically independent experiments for (a), (b), (c), (d), and (e) respectively, with similar results obtained.

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Extended Data Fig. 10 Overexpression of Venus-D6PKS345D rescued the defects of lateral root formation and hypocotyl gravitropism in pdk1.1 pdk1.2.

a, b, 35S::Venus-D6PKS345D (L3 as a representative line) rescued the lateral root defects of pdk1.1 pdk1.2. Nine-day-old seedlings were observed. n = 3 biologically independent experiments, with similar results obtained. A representative photo is shown in (a, scale bar, 2 cm), and the lateral root number was quantified (b). Dots represent individual plants, and lines indicate mean ± s.d.. n = 15, 15, 14 and 14 individual seedlings for Col-0, pdk1.1 pdk1.2, 35S::Venus-D6PKS345D in pdk1.1 pdk1.2 (L3), and 35S::Venus-D6PKS345D in pdk1.1 pdk1.2 (L5), respectively. Different letters represent significant difference, P < 0.05, by one-way ANOVA with a Tukey multiple comparison test, and P values are shown for each genotype compared with Col-0. c, The subcellular localisations of Venus-D6PK, Venus-D6PKS345A, and Venus-D6PKS345D exhibit difference in PM targeting, but not show difference in the basal polarity. Four-day-old seedlings of p35S::Venus-D6PK, p35S::Venus-D6PKS345A, and p35S::Venus-D6PKS345D, in Col-0 and pdk1.1 pdk1.2 respectively, were imaged by CLSM. The “Green Fire Blue” LUT was used for photo visualization based on fluorescence intensity by Fiji. Representative photos of at least three independent transgenic lines were shown. Scale bars, 10 µm. n = 2 biologically independent experiments, with similar results obtained.

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Tan, S., Zhang, X., Kong, W. et al. The lipid code-dependent phosphoswitch PDK1–D6PK activates PIN-mediated auxin efflux in Arabidopsis. Nat. Plants 6, 556–569 (2020). https://doi.org/10.1038/s41477-020-0648-9

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