Plants perceive various external signals, but how signals interact with the extracellular matrix is poorly understood. Pectin is a heteropolysaccharide, primarily composed of galacturonic acid units, contributing to the mechanical strength and integrity of the cell wall. Pectin (homogalacturonan) plays a vital role in growth control with an emerging role in signalling (Wolf, 2022). In the cell wall, PMEs catalyse the removal of methyl groups from the initially esterified pectin, giving rise to negatively charged carboxylic acid groups and altering the interaction of pectin with various extracellular components (Peaucelle et al., 2008). Here, we address how the methylation status of pectin in the extracellular matrix contributes to the integration of RALFs, which are extracellular cysteine-rich plant peptide hormones. RALF peptides are involved in multiple physiological and developmental processes, ranging from organ and pollen tube growth to the modulation of immune responses (Stegmann et al., 2017; Abarca et al., 2021; Mecchia et al., 2017; Geldner et al., 2009). Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) are transmembrane proteins with an extracellular domain, consisting of two adjacent malectin-like domains, for RALF signal perception and a cytoplasmic kinase domain for intracellular signal transduction (Escobar-Restrepo et al., 2007). Feronia (FER) is currently the best characterized CrRLK1L, contributing to the above-mentioned developmental programs as well as the integration of environmental cues (Feng et al., 2018; Gigli Bisceglia et al., 2022). On a cellular level, RALF binding to FER leads to rapid apoplastic (extracellular) alkalinisation (Haruta et al., 2014), which modulates cell wall properties, ion fluxes, and enzymatic activities, thereby influencing cellular expansion rates (Haruta et al., 2014; Barbez et al., 2017; Dünser et al., 2019; Dünser and Kleine-Vehn, 2015). Besides its role in apoplastic pH, CrRLK1Ls play a role in cell wall sensing (Hématy et al., 2007; Höfte, 2015; Shih et al., 2014) and can bind to extracellular pectin (Feng et al., 2018; Lin et al., 2022; Liu et al., 2024). The FER-dependent cell wall sensing mechanism involves the direct interaction with the extracellular leucine-rich repeat extensinsLRXs in roots (Dünser et al., 2019), suggesting that LRXs provide a physical link between FER and the cell wall (Herger et al., 2019). On the other hand, root, as well as pollen-expressed LRX proteins, also bind to RALF peptides (Mecchia et al., 2017; Dünser et al., 2019; Moussu et al., 2020), but its contribution to mechanochemical sensing and/or growth control is largely unknown in roots. Here, we show that the PME-dependent de-methylesterification status of pectin defines the FER-dependent perception of RALF1, contributing to extracellular regulation of pH, cell wall and plasma membrane remodelling, control of receptor endocytosis as well as organ growth in roots. Our data suggest that negatively charged, de-methylesterified pectin binds to positively charged RALF1 peptides with low affinity but high avidity. Interference with the de-methylesterification of pectin, out-titrating RALF1 with small charged, de-methylesterified pectin fragments, as well as the disruption of the positive charges in RALF1, abolishes the RALF1 activity in roots. We accordingly propose that the RALF interaction with de-methylesterified pectin at the root surface is crucial for its FER-dependent perception in roots. Even though root-expressed LRX proteins are strictly required for the FER-dependent mechano-sensing in roots, the LRX proteins are not essential for RALF perception in roots (Dünser et al., 2019). We moreover show here that LRX proteins do not contribute to the integration of RALF-pectin signalling in roots. In conclusion, we report on the crucial contribution of pectin de-methylesterification, for FER-dependent RALF peptide hormone signalling in root growth control. Our work proposes that pectin acts as a context-dependent extracellular signalling scaffold, contributing to signalling dynamics at the plasma membrane.

The application of RALF1 peptides induces strong repression of main root growth in Arabidopsis thaliana (Haruta et al., 2014; Figure 1A and B), which we initially used here as a bioassay to visualise RALF1 activity. To assess if the de-methylesterification status of pectin may impact peptide signalling, we pharmacologically interfered with the de-methylesterification of pectin, using epigallocatechin gallate (EGCG). EGCG is a natural inhibitor of PME activity (Lewis et al., 2008) and its application lowered main root growth but its co-treatment markedly interfered with the RALF1-induced reduction in root growth (Figure 1A and B). In contrast, the structurally similar epicatechin (EC) is not an inhibitor of PMEs (Lewis et al., 2008) and did not block RALF1-induced root growth repression (Figure 1C and D). In agreement, EGCG but not EC application reduced the labelling of de-methyl esterified pectin in roots (Figure 1E and F) as visualised by the fluorescent probe COS⁴⁸⁸ (Mravec et al., 2014). This set of data suggests that the EGCG-induced interference with PME activity correlates with reduced RALF1 responses in roots. To consolidate this assumption, we employed the overexpression of PECTIN METHYLESTERASE INHIBITOR 3 (PMEI3), which is well characterised to interfere with PME activity (Peaucelle et al., 2008; Xu et al., 2022) and accordingly also reduced the extracellular de-methylesterification of pectin in epidermal root cells (Figure 1G and H). In agreement with the EGCG application, PMEI3, as well as PMEI5, gain-of-function reduced the RALF1-induced root growth repression (Figure 1I and J).

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We accordingly conclude that pharmacological and genetic interference with PME activity leads to the repression of RALF1 effects on root growth. To test the specificity of this effect, we subsequently used the peptide flagellin22 (flg22). The flg22 peptide is derived from the N-terminus of bacterial flagellin and is known to elicit root growth repression via the innate immune receptor flagellin sensitive2 (FLS2) (Chinchilla et al., 2007). EGCG treatments were not able to suppress, but instead additively enhanced the FLG22-induced root growth repression (Figure 1K and L), suggesting a rather specific effect of PME inhibition on balancing RALF1 activity.

Next, we addressed how PME activity affects RALF1-dependent root growth control. FER-dependent perception of RALF peptides may affect cell wall integrity and it is hence conceivable that the pharmacological and genetic interference with extracellular PME activity could counterbalance some extracellular effects of RALF1 signalling. Using electron microscopy, we indeed observed a RALF1-induced effect on cell wall integrity, showing swollen cell walls, but also revealed plasma membrane invaginations (Figure 2A and B). These pronounced RALF effects were, to our knowledge, never reported and hence we confirmed these effects independently, using live cell confocal imaging. RALF1-induced invaginations of plasma membrane markers, such as Low-Temperature inducible protein 6b (LTi6b) (Figure 2C) and Novel Plant SNARE 12 (NPSN12) (Figure 2—figure supplement 1A), were readily detectable. Similarly, confocal imaging of propidium iodide (PI)-stained cell walls of wild-type seedlings also depicted the RALF1-induced swelling of the apoplastic signal and revealed additional ectopic accumulations (Figure 2D and F). These RALF1-induced alterations were absent in PI-stained fer-4 loss-of-function mutants (Figure 2E and F), suggesting that FER activation is required for these cellular effects of RALF1. The pharmacological (Figure 2G and H) as well as genetic (Figure 2J and K) interference with PME activity abolished the RALF1-induced alterations in cell wall labelling, phenocopying fer-4 mutants.

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PME activity could hence either indirectly counterbalance RALF1 effects on the cell wall and/or it could directly define RALF1 signalling output in root cells. Accordingly, we next tested the RALF1 impact on apoplastic pH regulation, which is a primary readout of RALF1 perception by FER (Haruta et al., 2014). We used 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (HPTS) as a fluorescent pH indicator for assessing apoplastic pH in epidermal root cells (Barbez et al., 2017). As expected, the application of RALF1 peptides induced an extracellular pH alkalisation in wild-type epidermal root cells (Barbez et al., 2017; Figure 3A and B). In contrast, EGCG application (Figure 3A and B) as well as the overexpression of PMEI3 (Figure 3C and D), abolished the RALF-induced alkalisation of the apoplastic pH. We accordingly conclude that interference with PME activity disrupts the primary output signalling of RALF1 in root cells.

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Our data suggest that PME inhibition interferes with RALF1 signalling output, ultimately affecting cell wall properties and root growth. To assess if PME activity affects the extracellular perception of RALF1, we next investigated the ligand-induced cellular dynamics of its receptor FER. An early event of receptor-mediated signalling often involves the ligand-induced endocytosis of the receptor as has been previously demonstrated for the RALF1-receptor FER (Yu et al., 2020). Therefore, we next tested whether the RALF1 ligand-induced endocytosis of FER is altered upon changes in the methylation status of pectin. In agreement with previous reports, we observed the RALF1-induced internalisation of functional FER::FER-GFP in epidermal root cells (Figure 3F and G). On the other hand, the ligand-induced internalisation of FER-GFP was abolished when we pharmacologically or genetically suppressed PME activity (Figure 3F–J). These findings propose that the PME activity is required for the earliest events of RALF1 perception by FER in roots.

To test the specificity of this observation, we used another RALF peptide called RALF34, which is a ligand of CrRLK1L theseus1 (THE1) (Gonneau et al., 2018). Similar to RALF1, the application of RALF34 induced the internalisation of FER-GFP, which was fully suppressed when PME activity was inhibited (Figure 3—figure supplement 1). Therefore, we assume that several RALF peptides display the same or similar signalling modalities.

RALF peptides are positively charged (Abarca et al., 2021). Hence, it is hence conceivable that the association of positively charged RALF1 peptides with de-methylesterified, negatively charged pectin is required for its FER-dependent perception. To indirectly assess if RALF1 peptides bind de-methylesterified pectin, we tested if RALF1 peptides bind fragments of de-methylesterified oligogalacturonides (OGs).

We initially assessed potential OG binding to RALF1, using the RALF1 impact on root cells as a bio-assay. The addition of high levels of free, de-methylesterified OGs into the media did not visibly affect the cell wall or FER endocytosis on its own (Figure 4—figure supplement 1A–D). On the other hand, free OGs in the medium strongly interfered with RALF1-induced cell wall swelling and FER receptor endocytosis in roots (Figure 4—figure supplement 1A–D). This effect was concentration-dependent (Figure 4A and B), suggesting that excess of de-methylesterified OGs in the medium can bind and out-titrate RALF1 peptides and thereby limit the RALF1 activity at the root surface.

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To characterise this binding in vitro, we next used biotinylated RALF1 in biolayer interferometry (BLI), which is an optical technique for measuring macromolecular interactions by analyzing interference patterns of white light reflected from the surface of a biosensor tip. The equilibrium dissociation constant (Kd) in the range of 105 nanomolar (nM) (Figure 4C) suggests a physiologically relevant binding affinity. Notably, we, however, observed an initial OG association to RALF1 with a constant (K_on) in the micromolar (µM) range, but the dissociation kinetics revealed a remarkably slow rate (Figure 4C and D). This is indicative of relatively low affinity at the individual RALF1-OG binding event level but multiple intermolecular binding events may eventually lead to a high accumulative binding strength. We hence propose that RALF1 peptides and de-methylesterified OGs undergo low affinity but high avidity binding assemblies. This finding complements recent data, indicating that the binding of RALF peptides and de-methylesterified OGs leads to phase separation in vitro (Liu et al., 2024).

RALF1 contains in total eight positively charged amino acids (three lysine (K) and five arginine (R)) (Figure 4—figure supplement 2A, B). This is reminiscent of the well-characterised de-methylesterified pectin-binding protein polygalacturonase-inhibiting protein (PGIP), which binds to de-methylesterified pectin through a positively charged binding site formed by clustered residues of lysine (K) and arginine (R) (Spadoni et al., 2006). Notably, the LRX8-RALF4 complex binds de-methylesterified OGs in a charge-dependent manner in pollen (Moussu et al., 2023). To address the positive charges in RALF1, we synthesized a RALF1-like peptide by substituting the K and R residues (RALF1^-KR). Thereby, we created a slightly negatively charged peptide in the pH range of the cell wall (Figure 4—figure supplement 2A, C). RALF1^-KR peptides are not bioactive, because they did neither affect root growth, nor cell wall integrity, nor did they induce the ligand-induced endocytosis of FER in epidermal root cells (Figure 4—figure supplement 2D–I). These findings suggest that the positively charged residues in RALF1 are essential for its activity in roots. Even though we cannot rule out that RALF1^-KR affects several characteristics of RALF1 signalling, we used this non-charged peptide to test if these residues affect the RALF1 binding to de-methylesterified pectin. Using our in vitro system, we did not observe RALF1^-KR binding to de-methylesterified OGs (Figure 4—figure supplement 2J), proposing that RALF1 and OGs indeed interact in a charge-dependent manner.

The LRX-RALF complex and its interaction with pectin exert a condensing effect on the cell wall in pollen and root hairs (Moussu et al., 2023; Schoenaers et al., 2024). Moreover, LRX proteins also bind and link FER with a cell wall-sensing mechanism in roots (Dünser et al., 2019). Nevertheless, LRX function in root growth appears to be independent of FER-dependent RALF signalling (Dünser et al., 2019). Hence, we next tested if LRX proteins are required for the joint RALF1/pectin-dependent signalling in roots. We observed that RALF1 applications still induced cell wall alterations in lrx1 lrx2 lrx3 lrx4 lrx5 quintuple mutant roots (Figure 5A–D). Similar to wild-type roots (Figure 5E and F), pharmacological interference with PME activity still repressed RALF1 activity in the lrx1 lrx2 lrx3 lrx4 lrx5 quintuple mutant roots (Figure 5G and H). These findings confirm our previous assumptions that LRX proteins are not essential for the RALF activity in roots (Dünser et al., 2019) and, moreover, reveal that LRX proteins are also not required for the PME-dependent control of RALF1 signalling in roots.

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In conclusion, our data proposes that RALF1 peptides are associated with high avidity to de-methylesterified pectin, which is required for the RALF perception by FER. We hence conclude that the methylation status of pectin provides a conceptualising input to RALF peptide hormone signalling (Figure 5I and J).

Concluding remarks:

Intriguingly, the exogenous application of RALF1 does not only affect cell wall characteristics but also induces prominent plasma membrane protrusions into root epidermal cells. Plasma membrane invagination is a highly controlled process and often relates to plant endosymbiotic events (Su et al., 2023). The developmental importance of this RALF1 effect remains to be addressed but could pinpoint pectin signalling playing a central role in the structural coordination of cell wall and plasma membrane dynamics. Most importantly, we reveal an essential function of the cell wall component pectin for RALF1 peptide signalling (Figure 5I and J). We illustrate that the pharmacological and genetic interference with PME activity specifically abolishes RALF1, but not flg22 peptide, activity in roots. We conclude that PME activity is required for all hallmarks of RALF1 signalling, including the rapid alkalinisation of the cell wall and the ligand-induced endocytosis of FER. We hence propose that the generation of de-methylesterified, negatively charged pectin in the cell wall is required for the FER-dependent perception of positively charged RALF1 at the root cell surface. We show that RALF1 binds in a charge-dependent manner to de-methylesterified OGs in vitro and that the application of free OGs can out-titrate RALF1 peptides in the medium. Our in vitro data proposes low affinity but a high avidity binding of OGs and RALF1. This interaction mechanism could be key in the spatial enrichment of RALF peptides at the root surface because receptor interactions at the plasma membrane could contribute to the accumulated strength of multiple binding interactions. In agreement, after we pre-printed a previous version of this manuscript (Rößling et al., 2023), Moussu and colleagues proposed that the LRX8-RALF4 complex and its charge-dependent binding of de-methylesterified OGs controls extracellular condensations in pollen tubes (Moussu et al., 2023). The contribution of FER signalling remains unknown in this process, but a similar structural mechanism defines root hair growth in a FER-dependent manner (Schoenaers et al., 2024). Within the main root, the RALF peptide binding to de-methylesterified pectin was suggested to be sufficient to lead to its extracellular phase separation, subsequently inducing the clustering of FER receptors in the plasma membrane (Liu et al., 2024). It remained, however, unknown if LRX proteins are implied in this root organ growth response. LRX proteins directly interact with FER and thereby contribute to cell wall sensing in roots (Dünser et al., 2019). Notably, LRX proteins are not required to sense RALF1 in roots (Dünser et al., 2019) and also the inhibition of PMEs still represses RALF1 activity in lrx1 lrx2 lrx3 lrx4 lrx5 quintuple mutant roots. These findings suggest an LRX-independent mode of action in the FER-RALF1-pectin signalling mechanism. Our findings (this study and Dünser et al., 2019) pinpoint distinct FER- and RALF-dependent roles of LRX proteins. Considering that LRX8-RALF4-pectin interaction contributes to wall integrity and pollen tube expansion (Moussu et al., 2023), distinct modes of cell wall integrity control may be also in place in root cells and tip-growing pollen tubes.

Based on our findings, we envision that negatively charged, de-methylesterified pectin could function as a signalling scaffold for positively charged RALF peptides, which seems crucial for its signalling via the FER receptor. It needs to be seen how precisely the RALF binding to homogalacturonan affects its interaction with FER receptors. Here it is noteworthy that the pectin sensing function of FER is physically separated from the RALF binding domain (Gronnier et al., 2022).

The impact of de-methylesterified pectin on RALF signalling could also lead to self-emerging feedback properties because high extracellular PME activity is expected to strongly acidify the apoplast (Wolf et al., 2009), which in turn would be counteracted by the de-methylesterified pectin-induced activation of RALF peptides and its consequences on apoplast alkalinisation (Haruta et al., 2014; Barbez et al., 2017; this study). The here uncovered mechanism links the pectin-related cell wall status with RALF peptide hormone signalling. A scaffold protein can tether signalling components, enhancing the efficiency and specificity of cellular signalling pathways by acting as a structural framework. In analogy, we propose that pectin functions in a PME-dependent manner as a tunable extracellular signalling scaffold.

All data generated or analysed during this study are included in the manuscript and supporting files.

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Author details

1. Ann-Kathrin Rößling

   1. Institute of Biology II, Molecular Plant Physiology (MoPP), University of Freiburg, Freiburg, Germany
   2. Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany

   Contribution

   Conceptualization, Data curation, Validation, Investigation, Visualization, Methodology, Writing – original draft, Writing – review and editing

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-1395-6525

2. Kai Dünser

   1. Institute of Biology II, Molecular Plant Physiology (MoPP), University of Freiburg, Freiburg, Germany
   2. Institute of Molecular Plant Biology (IMPB), Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria

   Contribution

   Conceptualization, Data curation, Formal analysis, Validation, Investigation, Methodology

   Competing interests

   No competing interests declared

3. Chenlu Liu

   1. Institute of Biology II, Molecular Plant Physiology (MoPP), University of Freiburg, Freiburg, Germany
   2. Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany

   Contribution

   Data curation, Investigation, Methodology

   Competing interests

   No competing interests declared

4. Susan Lauw

   1. Core Facility Signalling Factory & Robotics, University of Freiburg, Freiburg im Breisgau, Germany
   2. Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Freiburg im Breisgau, Germany

   Contribution

   Data curation, Investigation

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-0541-2173

5. Marta Rodriguez-Franco

   Institute of Biology II, Cell Biology, University of Freiburg, Freiburg im Breisgau, Germany

   Contribution

   Data curation, Investigation

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0003-1183-2075

6. Lothar Kalmbach

   Institute of Biology II, Molecular Plant Physiology (MoPP), University of Freiburg, Freiburg, Germany

   Contribution

   Supervision, Validation

   Competing interests

   No competing interests declared

7. Elke Barbez

   1. Institute of Biology II, Molecular Plant Physiology (MoPP), University of Freiburg, Freiburg, Germany
   2. Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany

   Contribution

   Conceptualization, Supervision, Funding acquisition, Writing – original draft, Project administration, Writing – review and editing

   For correspondence

   elke.barbez@cibss.uni-freiburg.de

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-5531-7916

8. Jürgen Kleine-Vehn

   1. Institute of Biology II, Molecular Plant Physiology (MoPP), University of Freiburg, Freiburg, Germany
   2. Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
   3. Institute of Molecular Plant Biology (IMPB), Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria

   Contribution

   Conceptualization, Data curation, Supervision, Funding acquisition, Writing – original draft, Project administration, Writing – review and editing

   For correspondence

   juergen.kleine-vehn@biologie.uni-freiburg.de

   Competing interests

   Reviewing editor, eLife

   "This ORCID iD identifies the author of this article:" 0000-0002-4354-3756

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