Like animals, plants are made up of many different types of cells, which descend from undifferentiated cells called stem cells. Thanks to these cells, plants are able to grow and develop throughout their lives. Stem cells live at the tips of the plant’s shoots and roots. They constantly divide to produce new cells to self-renew or replace specific plant cells in need of repair. Over time, they change – or differentiate – to go on to become part of tissues like leaves, roots, stems, shoots, flowers or fruits.

To maintain a continuous pool of undifferentiated stem cells and to make sure that stem cells divide at the correct pace, neighbouring cells emit signals that control the activity of stem cells. The new stem cells that remain close to these ‘maintenance signals’ continue to behave like stem cells, but those displaced away begin to differentiate. Stem cells can receive many different types of signals, but how are these signals filtered and passed onto different places within the cell?

To test this, Je, Xu et al. created maize plants that contained mutations in a number of known signalling molecules to see if these molecules used the same communication pathway. The results showed that stem cells could integrate the different signals. Even if the signals pass through the same receiver (a receptor protein called FASCIATED EAR2), each signal exits the receptor as a different message, and attaches to a different messenger protein to relay specific information about stem cell maintenance to the cell.

A next step will be to test if other plants use the same signalling pathways in the same ways to send messages between cells. A better knowledge about stem cell signals in plants could help to develop more productive crops. Previous work has found that precise control of stem cell pathways can help breed crops with more seeds or bigger fruits. These kinds of changes have been selected naturally by humans since the dawn of civilization, but we need to accelerate these advances to help meet the needs of the growing world population and improve agricultural sustainability.

Stem cell proliferation and differentiation throughout plant life is regulated by a feedback loop between the homeodomain transcription factor WUS and CLV ligand-receptor signaling (Mayer et al., 1998; Brand et al., 2000; Schoof et al., 2000; Yadav et al., 2011; Daum et al., 2014). The secretion of the diffusible glycopeptide CLV3 from the central zone (CZ) stem cells of the SAM is believed to initiate signaling through LRR receptors (Fletcher et al., 1999; Rojo et al., 2002; Kondo et al., 2006; Ohyama et al., 2009; Nimchuk et al., 2011b), which transmits the signal to restrict the expression of WUS in the organizing center (OC) cells. To balance this system, WUS non-cell-autonomously promotes stem cell fate by activation of CLV3 expression (Yadav et al., 2011; Daum et al., 2014). CLV3 is thought to be perceived by multiple receptor kinase and receptor like proteins, including the CLV1 LRR receptor-like kinase (Clark et al., 1993; Clark et al., 1997; Brand et al., 2000; Ogawa et al., 2008) and the related BAM receptors (DeYoung et al., 2006; Deyoung and Clark, 2008; Nimchuk et al., 2015; Shinohara and Matsubayashi, 2015), or by a heterodimer of the receptor like protein CLV2 and the transmembrane pseudokinase CRN (Kayes and Clark, 1998; Jeong et al., 1999; Miwa et al., 2008; Müller et al., 2008; Bleckmann et al., 2010; Zhu et al., 2010; Nimchuk et al., 2011a), or by the receptor-like kinase RPK2 (Mizuno et al., 2007; Nodine et al., 2007; Kinoshita et al., 2010). The relationship between CLV1 and CLV2 is not clear- CLV1 can form homodimers, or higher order complexes with CLV2/CRN, to signal co-operatively in the SAM (Guo et al., 2010; Somssich et al., 2015), but it seems that CLV2/CRN is not essential for CLV3 perception or for CLV1 signaling (Müller et al., 2008; Nimchuk et al., 2011b; Nimchuk, 2017). In contrast to CLV1, CLV2 does not bind CLV3 peptide directly (Shinohara and Matsubayashi, 2015), and its expression is not restricted to the SAM, suggesting that it might function as a co-receptor in additional pathways beyond CLV3 signaling. Indeed, CLV2 appears to be involved in signaling by several CLE peptides (Fiers et al., 2005; Meng and Feldman, 2010; Hazak et al., 2017) and in biotic interactions (Replogle et al., 2011; Hanemian et al., 2016), suggesting it plays diverse functions in plant development and immunity (Pan et al., 2016). The multiple roles of CLV2 promote the question of how it confers signal specificity. Two candidate downstream effectors of CLV2 have been identified. One is the transmembrane pseudokinase CRN, discovered in Arabidopsis, and the second is COMPACT PLANT2 (CT2), the heterotrimeric G protein alpha subunit, discovered in maize (Bommert et al., 2013a). However, since CRN and CT2 were identified in different species, their molecular and genetic interactions remain unknown.

The CLV-WUS pathway is widely conserved (Somssich et al., 2016; Soyars et al., 2016). In maize, THICK TASSEL DWARF1 (TD1) and FEA2 are CLV1 and CLV2 orthologs, and function similarly to restrict inflorescence shoot meristem proliferation (Taguchi-Shiobara et al., 2001; Bommert et al., 2005). Two maize WUS orthologs, ZmWUS1 and ZmWUS2, have been predicted by phylogenetic analysis, and a ZmWUS1 reporter is expressed in the presumptive organizing center of the inflorescence shoot meristem (Je et al., 2016), but these genes have not been functionally characterized (Nardmann and Werr, 2006). In rice, FLORAL ORGAN NUMBER 1 (FON1), the CLV1 ortholog, and FON2, the CLV3 ortholog, similarly function in floral development in a common pathway, as expected (Suzaki et al., 2004; Chu et al., 2006; Suzaki et al., 2006; Suzaki et al., 2008; Suzaki et al., 2009), whereas a second rice CLE peptide gene, FON2-LIKE CLE PROTEIN1 (FCP1) controls stem cell proliferation independent of FON1 (Suzaki et al., 2008). The rice WUS homolog, TILLERS ABSENT1/MONOCULM3 functions in axillary shoot meristem formation (Tanaka et al., 2015; Lu et al., 2015), and WUS function in the shoot apical meristems appears to have been taken over by the WUSCHEL RELATED HOMEOBOX4 (WOX4) gene (Ohmori et al., 2013).

How specificity is achieved is a common question in signal transduction pathways. Recently, we identified a distinct CLV receptor, FASCIATED EAR3 (FEA3) in maize and Arabidopsis, and found that FEA3 controls responses to the maize FCP1 (ZmFCP1) CLE peptide (Je et al., 2016). Here, we show that the maize CLV2 ortholog FEA2 also participates in ZmFCP1 signaling, in addition to controlling responses to the maize CLV3 ortholog, ZmCLE7 (Je et al., 2016). To ask how specificity from these different CLE peptide inputs is achieved, we first isolated mutant alleles of the maize CRN gene. Consistent with results in Arabidopsis (Miwa et al., 2008; Müller et al., 2008; Bleckmann et al., 2010; Zhu et al., 2010; Nimchuk et al., 2011a), we found that fea2 was epistatic to Zmcrn in control of meristem size, but Zmcrn;ct2 double mutants showed an additive enhanced phenotype, suggesting they act in parallel pathways, despite the fact that FEA2 binds both ZmCRN and CT2 in co-immunoprecipitation (co-IP) experiments. Strikingly, ct2 and Zmcrn mutants were resistant to different CLE peptides, ZmCLE7 and ZmFCP1, respectively, but fea2 was resistant to both, suggesting that FEA2 controls responses to different CLE peptides by acting through different downstream effectors.

A major question in signal transduction is how multiple inputs can be translated into distinct outputs. CLV-WUS feedback signaling is the central regulatory pathway in shoot meristem development, and perception of CLV3 peptide involves the CLV1 receptor-like kinase and the CLV2 receptor-like protein together with the CRN pseudokinase (Brand et al., 2000; Schoof et al., 2000; Miwa et al., 2008; Müller et al., 2008; Bleckmann et al., 2010; Zhu et al., 2010; Nimchuk et al., 2011a). However, genetic evidence in both maize and Arabidopsis suggests these receptors function independently, and CLV2, and its maize ortholog FEA2, respond to multiple CLE peptides (Bommert et al., 2005; Fiers et al., 2005; Müller et al., 2008; Guo et al., 2010; Meng and Feldman, 2010; Je et al., 2016; Hazak et al., 2017). So how is the information conferred by these different signals kept separate during transmission through a common receptor?

To address this question and further decipher the FEA2 signaling pathway, we isolated mutants in the maize CRN ortholog, ZmCRN, by reverse genetics and by cloning a newly identified fasciated ear mutant fea*148. ZmCRN was predicted to encode a membrane localize pseudokinase, like CRN in Arabidopsis (Nimchuk et al., 2011a), and characterization of the mutants indicated that ZmCRN similarly functioned as a negative regulator of stem cell proliferation. We found that fea2 was epistatic to Zmcrn and that FEA2 and ZmCRN interacted directly, using Co-IP and BiFC assays of proteins transiently overexpressed in N. benthamiana, suggesting that ZmCRN is a signaling component in the FEA2 pathway. Natural variation in the CLV-WUS pathway underlies yield improvements in different crop species including tomato, maize and mustard (Bommert et al., 2013b; Fan et al., 2014; Xu et al., 2015; Je et al., 2016), and FEA2 is a quantitative trait locus (QTL) for kernel row number (KRN) (Bommert et al., 2013b). In this study, we used a maize association panel of 368 diverse inbred lines to show that ZmCRN also had significant association with KRN under multiple environments (Li et al., 2013; Liu et al., 2015), suggesting that ZmCRN contributes to quantitative variation in this trait. Therefore, ZmCRN could be manipulated for maize yield enhancement.

Previously, we identified the alpha subunit of the heterotrimeric G protein, CT2, as an additional interactor of FEA2. fea2 is epistatic to ct2 in meristem regulation, similar to its genetic interaction with Zmcrn, and FEA2 interacts with CT2 in vivo, revealing that CT2, like ZmCRN, is a candidate downstream signaling component of FEA2 (Bommert et al., 2013a). Although fea2 was epistatic both to ct2 and to Zmcrn, we found that ct2; Zmcrn double mutants had an additive interaction, suggesting they function in parallel, and that the FEA2 signaling pathway branches into these two different downstream signaling components. This idea was supported by peptide assays in different mutants, which suggested that ZmCRN and CT2 function specifically in ZmFCP1 or ZmCLE7 signaling, respectively, while FEA2 is involved in both. Although we used high peptide concentrations, the activity of CLE peptides is known to be enhanced by triarabinosylation (Ohyama et al., 2009; Matsubayashi, 2011; Xu et al., 2015; Corcilius et al., 2017), and indeed we found that similarly modified ZmCLE7 peptide was about 10 fold more potent than the non-modified form (Figure 5—figure supplement 2).

Consistently with our findings, ZmCRN, CT2 and FEA2 were expressed broadly in the SAM in overlapping domains (Figure 2—figure supplement 5). These data suggest a novel mechanism in plant receptor signaling, where a single receptor, FEA2, can transmit signals from two different CLE peptides, ZmFCP1 and ZmCLE7, through two different downstream components, ZmCRN and CT2. We thereby shed light on how distinct signaling by different peptides can be achieved through a common receptor. As a candidate receptor or co-receptor for different peptides, FEA2 does not have any close homologs in the maize genome (Figure 6—figure supplement 1), similar to CLV2 in Arabidopsis, and the relatively mild phenotype of fea2 mutants may be due to compensation by partially redundant parallel signaling pathways, such as through FEA3 (Je et al., 2016). Our results are largely consistent with findings in Arabidopsis, that CRN is dispensable for CLV3 perception and signaling (Nimchuk, 2017), and that CLV2/CRN can function with other CLE ligand-receptor complexes (Hazak et al., 2017). However, in Arabidopsis CRN is required for CLV2 trafficking to the plasma membrane (Bleckmann et al., 2010). Our results suggest that the maize CLV2 ortholog FEA2 still functions (with CT2) in a crn mutant, so is presumably on the plasma membrane even in the absence of ZmCRN.

How then can a single receptor recognize different signals and transmit them differentially? The most obvious answer depends on the hypothesis that FEA2 and CLV2 are co-receptors that function with LRR RLKs, which binds CLE peptides directly (Figure 6). This hypothesis is supported by the finding that CLV1 binds CLV3 with high affinity, but CLV2 is unable to bind CLE peptides (Shinohara and Matsubayashi, 2015), and that CLV2/CRN can function with different CLE ligand-receptor complexes (Hazak et al., 2017). There are conflicting results surrounding the interaction between CLV2 and CLV1; some experiments detect their physical interaction, but many of them use over-expression and are prone to false positive results, and clv2 and clv1 act additively in double mutant combinations (Kayes and Clark, 1998; Müller et al., 2008). This genetic result suggests they act separately, and the same is true for the orthologs FEA2 and TD1 in maize (Bommert et al., 2005). A possible explanation for these conflicting findings is that CLV2 may act with multiple CLE receptor RLKs. This model is supported by the observation that CLV1 homologs, the BAMs, function redundantly with CLV1, so multiple LRR RLKs do indeed function in meristem size control. This also explains why all intermediate and strong clv1 alleles are dominant negative, as they likely interfere with the activity of other receptor kinase(s) that have functional overlap with CLV1 (Diévart et al., 2003; Nimchuk et al., 2015).

Despite not knowing the details of specific CLE-receptor interactions, our data show that FEA2 can transmit different peptide signals through two distinct downstream signaling components that most likely converge on the regulation of ZmWUS expression to regulate stem cell proliferation in meristem development (Figure 6). This suggests a new working model for meristem size regulation, in which ligand binding can be transmitted by a common co-receptor working with different RLKs coupled to distinct signaling proteins. Our model differs from most well-studied ligand-receptor signaling pathways, in which the signaling pathways usually converge (Couto and Zipfel, 2016). For instance, different microbial ligands such as flagellin and Elongation Factor Thermo unstable (EF-Tu) are specifically recognized by the FLAGELLIN-SENSITIVE 2 (FLS2)-BRI1 ASSOCIATED RECEPTOR KINASE (BAK1) or EF-Tu RECEPTOR (EFR)-BAK1 RLK complexes, respectively, while signal transduction requires a shared set of cytosolic kinases, including BOTRYTIS-INDUCED KINASE 1 (BIK1) (Aarts et al., 1998; Lu et al., 2010). Nevertheless, a similar principle can be drawn from the different signaling pathways mediated by BAK1, which functions as a co-receptor for the brassinosteroid (BR) receptor, BR INSENSITIVE 1 (BRI1) or for FLS2. After ligand perception, BR signaling through the BAK1-BRI1 complex is transmitted through the receptor-like cytoplasmic kinase (RLCK) BRASSINOSTEROID-SIGNALING KINASE 1 (BSK1), and flagellin signaling through the BAK1-FLS2 complex is transmitted through a different RLCK, BIK1 (Li et al., 2002; Nam and Li, 2002; Chinchilla et al., 2007; Lu et al., 2010; Wang, 2012; Sun et al., 2013). Our study also reveals another source of variation in meristem receptor signaling, by highlighting the role of an additional CLE peptide, ZmFCP1. The role of FCP1 in meristem maintenance has been characterized in both maize and rice (Suzaki et al., 2008; Je et al., 2016), but not yet in Arabidopsis.

In summary, multiple receptor signaling pathways appear to be required to for the perception of different CLE peptide signals to fine tune meristem development. This complex system of multiple peptides, receptors and downstream components presumably confers robustness on the meristem structure, as well as providing flexibility to control meristem development according to different physiological or developmental cues. For example, meristem size responds to stress and developmental transitions, such as floral induction, and different signaling pathways may confer such responsiveness. Our results help explain how meristem size regulation is orchestrated by multiple CLE peptides and receptors, as observed in many species including Arabidopsis, rice, maize and tomato (Ito et al., 2006; Strabala et al., 2006; Suzaki et al., 2009; Nimchuk et al., 2015; Xu et al., 2015). They also support the idea that meristem signaling components are highly conserved between diverse plant species, and a major challenge is to understand how differential regulation of these common components leads to diversity in meristem organization and size across diverse plant taxa.

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[Editors’ note: a previous version of this study was rejected after peer review, but the authors submitted for reconsideration. The first decision letter after peer review is shown below.]

Thank you for submitting your work entitled "The CLAVATA receptor FASCIATED EAR2 responds to distinct CLE peptides by signaling through two downstream effectors" for consideration by eLife. Your article has been reviewed by three peer reviewers, and the evaluation has been overseen by a Senior/Reviewing Editor.

Our decision has been reached after consultation between the reviewers. Based on these discussions and the individual reviews below, we regret to inform you that your work cannot be considered for publication in eLife without substantial improvements that go much beyond a simple round of revisions.

The reviewers all agree that your manuscript presents an interesting story. The concept emerging from your work is potentially exciting and important, however, in the opinion of the reviewers and editors, it is not yet supported rigorously by the data. To make the strong point you project here, a number of additional, crucial experiments would be required. This includes, for example, expression pattern analyses, double mutant analyses, independent protein-protein interaction verifications, or more realistic physiological conditions, like lower peptide concentrations. If you choose to substantially improve the manuscript along these lines, and comprehensively address the individual reviewer comments pasted below, we are however ready to take another look at a resubmitted manuscript.

Reviewer #1:

An unresolved mystery in plant development concerns the developmental mechanisms whereby functional specificity can arise from the redundancy of receptors involved in controlling stem cell homeostasis in shoot meristems. This well written manuscript addresses this question, to describe how the maize CLV2 gene can interact with two distinct peptide ligands by associating with two distinct effectors, which presumably in different downstream signaling pathways. This makes a novel contribution to the field.

Introduction.

1) The introduction should stipulate that no WUS function is yet demonstrated in maize, and that the CLV1 homolog does not have a demonstrated function in the maize SAM. The manuscript says: "In maize, THICK TASSEL DWARF1 (TD1) and FEA2 are CLV1 and CLV2 orthologs, and function similarly to restrict SAM proliferation" – this is untrue – TD1 mutations affect the inflorescence shoot meristems, but there is no evidence that TD1 restricts vegetative SAM size.

Results.

2) Why is there no demonstration of ZmCRN RNA or protein accumulation in maize shoot meristems?

3) A new maize mutation in ZmCRN is identified and characterized. The genetic data clearly demonstrate that FEA2/CLV2 is epistatic to both ZmCRN and CT2, and that ZmCRN and CT2 function in different pathways.

4) Although the CT2 YFP fusion was shown previously to complement the mutant phenotype, no assays of FEA2 or CRN fusion protein function are provided. Although the data, derived from a heterologous system, are clear and indicate the FEA2/CLV2 can interact with both CT2 and ZmCRN – while CT2 and ZmCRN do not form a complex in tobacco – I wonder why these fusion proteins were not introduced into maize? This is not always trivial due to complex promoter issues, but should be explained.

5) The data clearly show that FEA2 mutants are reduced in sensitivity to both the FCP and CLE7 peptides, CT2 shows reduced sensitivity to its presumptive ligand CLE7 (but not FCP1), and ZmCRN is reduced in sensitivity to FCP1 (its presumptive ligand), but is sensitive to CLE7. However, the legend to Figure 5 describes crn mutants as insensitive to FCP1, whereas the text better describes this interaction as "partially resistant", since FEA3 is presumably intact and should be responding to applied FCP ligand. Best to fix this inconsistency between the descriptions in the legend and the manuscript text.

Reviewer #2:

The manuscript by Je et al. reports genetic and phenotypic characterizations among the mutants of CLAVATA pathway in Maize. The authors isolated a loss-of-function allele of ZmCRN, and characterized its meristem phenotype with fea2, that lacks a functional CLV2 ortholog, fea3, an LRR-RLK previously reported by the same group, and ct2, a mutant in G-α. Together with a series of double mutant analysis, CLE peptide application experiments, and in plant Co-IP experiments in N. benthamiana, the authors conclude that FEA2 form a different receptor complex depending on the CLE peptide.

The manuscript brings an important insight into a key question in receptor signaling, "how could a receptor recognizes and discriminates related yet different signals to activate specific response?". At the same time, however, the data provided are rather slim, and this reviewer feels that such a major claim should come with solid and multi-faceted experimental data of high rigor. Specific comments are as the following:

Role of FEA3: The genetic interactions of FEA3 in FEA2-CT and FEA2-ZmCRN pathways needs to be addressed in order to evaluate the genetic interaction and peptide application data. Both fea2 and fea3 are resistant to ZmFCP1 peptide application (Figure 1). Because of this, partial sensitivity of Zmcrn mutants to ZmFCP1 (Figure 5D) may be mediated through FEA3. Peptide application on fea3 Zmcrn double mutants would clarify this.

ZmCRN expression/localization patterns: Where is ZmCRN expressed? For ZmCRN to function via forming a heterodimer with FEA2, their expression domain should overlap within the SAM. The authors could generate transgenic lines expressing the FP-tagged CRN in maize (which I agree might be very difficult and takes time for maize), or at least the authors must show clear in situ hybridization data long with the FEA2 and CT2.

Subcellular co-localization in N. benthamiana: The authors show that ZmCRN-mCherry localizes to PM in tobacco leaf epidermis. Would ZmFEA2 and/or CT co-localizes with ZmCRN on the plasma membrane in tobacco?

Protein-protein interaction assays: The authors present only one type experiment (Co-IP) to conclude that FEA2 forms a separate complex with ZmCRN and CT2 depending on the ligands. The following experiments would strengthen the conclusion:

a) Reciprocal Co-IP. The authors should reciprocally IP FEA2 and confirm that FEA2 indeed brings down BOTH CT2 and ZmCRN when three proteins are co-expressed. I think this experiment must be performed.

b) Role of different peptides, ZmFCP1 and ZmCLE7, on receptor complex formation. This can be done by treating/infiltrating/co-expressing each peptide to the N. benthamiana leaves along with a pair-wise combination of receptors.

Alternative experimental approach to support the in planta Co-IP experiments. The authors could perform BiFC, split-Ub or other protein-protein interaction assays to strengthen their claim.

Figure 4C. The gel lanes appear spliced. This is not an accepted practice or data presentation.

Discussion, fourth paragraph (discussion about why clv2 phenotype is weaker than clv1). A previous report (Diévart et al., 2003) shows that missense alleles of clv1 act in a dominant-negative manner. Please include this into the Discussion.

Reviewer #3:

The manuscript by Je et al. reports the reverse (and forward) genetic characterization of ZmCRN, the mays ortholog of CORYNE (CRN) in Arabidopsis. The authors provide compelling genetic evidence that, just like in Arabidopsis, CRN acts in a common pathway with the LRR receptor kinase CLV2 (FEA2 in Zm). The novel finding is that FEA2 can form complexes with either ZmCRN or the heterotrimeric G-protein α subunit ZmCT2. The phenotypes of ZmCRN and ZmCT2 are additive, suggesting that FEA2 can signal via two different down-stream components. Peptide resistance assays furthermore suggest that these different signaling complexes may form in response to the sensing of different CLE peptides, ZmCLE7 and ZmFCP1, respectively. Overall this is a well written manuscript which provides some novel insight into the CLE signaling pathway involved in plant stem cell maintenance. Since, I am not a maize geneticist, I will focus my review on a) the biochemical experiments presented in this study and b) on the discussion of these novel findings:

a) I understand that it is very difficult to perform any co-IP experiments in maize and that for this reason a transient system was chosen. I would find it nevertheless appropriate to at least mention in the Discussion that the outlined interactions were assayed not with native-like protein levels but rather by strongly overexpressing CRN, FEA2 and CT2.

b) Why are the peptide resistance assays done with such high peptide concentrations (30 μM)? Do the authors think that the binding affinities of the maize receptor complexes are much lower than in Arabidopsis? Or are there post-translational modifications missing from the synthetic peptides? Or are the peptides poorly taken up by the plant tissue?

c) Based on their findings, the authors suggest FEA2/CLV2 as a co-receptor for several CLE peptide-sensing LRR receptor kinases. In terms of the presented as well as previously established genetics on FEA2/CLV2 this would only make sense, if indeed CLV2 function can be replaced by another co-receptor in vivo. I would appreciate if the authors could present here a sequence alignment of the known receptor-like proteins from maize. Are there sequence homologs for CLV2 in maize (there are no obvious homologs in Arabidopsis)?

[Editors’ note: the author responses to the first round of peer review follow.]

The reviewers all agree that your manuscript presents an interesting story. The concept emerging from your work is potentially exciting and important, however, in the opinion of the reviewers and editors, it is not yet supported rigorously by the data. To make the strong point you project here, a number of additional, crucial experiments would be required. This includes, for example, expression pattern analyses, double mutant analyses, independent protein-protein interaction verifications, or more realistic physiological conditions, like lower peptide concentrations. If you choose to substantially improve the manuscript along these lines, and comprehensively address the individual reviewer comments pasted below, we are however ready to take another look at a resubmitted manuscript.

We appreciate the constructive criticisms and suggestions from the three expert reviewers. We have added new data to address all comments, including expression analysis of ZmCRN, fea3;Zmcrn double mutant analyses, independent protein-protein interaction verification and treatments with different peptide concentrations, to address the issues. This new data further supports our major conclusion, and the manuscript has been substantially revised accordingly.

Reviewer #1:

[…] Introduction.

1) The introduction should stipulate that no WUS function is yet demonstrated in maize, and that the CLV1 homolog does not have a demonstrated function in the maize SAM. The manuscript says: "In maize, THICK TASSEL DWARF1 (TD1) and FEA2 are CLV1 and CLV2 orthologs, and function similarly to restrict SAM proliferation" – this is untrue – TD1 mutations affect the inflorescence shoot meristems, but there is no evidence that TD1 restricts vegetative SAM size.

As suggested, we have added text to clarify that WUS has not been functionally characterized in maize, and also added information about rice WUS function:

“Two maize WUS orthologs, ZmWUS1 and ZmWUS2, were predicted by phylogenetic analysis, and a ZmWUS1 reporter is expressed in the presumptive organizing center of the inflorescence shoot meristem (Je at al., 2016), but these genes have not been functionally characterized (Nardmann and Werr 2006). […] The rice WUS homolog, TILLERS ABSENT1/ MONOCULM3 functions in axillary shoot meristem formation (Tanaka et al., 2015; Lu et al., 2015), and WUS function in the shoot apical meristems appears to have been taken over by the WUSCHEL RELATED HOMEOBOX4 (WOX4) gene (Ohmori et al., 2013)”

As to whether these mutations affect SAM or inflorescence shoot meristems, this is a semantic point, since the inflorescence meristem is also a “SAM”, as it is the shoot meristem at the apex of the inflorescence. In general, the fasciated mutations in maize do enlarge the vegetative SAM, but in a much less dramatic way. However, to clarify, we changed “SAM” to “inflorescence shoot meristem” in the Introduction (“… and function similarly to restrict inflorescence shoot meristem proliferation…”).

Results.

2) Why is there no demonstration of ZmCRN RNA or protein accumulation in maize shoot meristems?

In the revised manuscript, we now show expression of ZmCRN byin situ hybridization in maize shoot meristems. ZmCRN was expressed throughout the SAM and more strongly in the peripheral domain and leaf primordia (Figure 2E). This profile is confirmed by laser capture microdissection RNAseq data for different domains of the SAM (data from Timmermans lab, available from MaizeGDB; https://maizegdb.org/). This new data is added as Figure 2E and Figure 2—figure supplement 4, and new text:

“ZmCRN was expressed throughout the SAM and more strongly in the peripheral domain and leaf primordia (Figure 2E, confirmed by laser capture microdissection RNAseq, Figure 2—figure supplement 4).”

3) A new maize mutation in ZmCRN is identified and characterized. The genetic data clearly demonstrate that FEA2/CLV2 is epistatic to both ZmCRN and CT2, and that ZmCRN and CT2 function in different pathways.

Thanks for the positive comment!

4) Although the CT2 YFP fusion was shown previously to complement the mutant phenotype, no assays of FEA2 or CRN fusion protein function are provided. Although the data, derived from a heterologous system, are clear and indicate the FEA2/CLV2 can interact with both CT2 and ZmCRN – while CT2 and ZmCRN do not form a complex in tobacco – I wonder why these fusion proteins were not introduced into maize? This is not always trivial due to complex promoter issues, but should be explained.

We indeed previously made pFEA2-FEA2-YFP transgenic maize plants, and saw clear FEA2-YFP signal on the plasma membrane in the inflorescence meristem (http://maize.jcvi.org/cellgenomics/geneDB_list.php. However, we didn’t make the ZmCRN transgenic plants, as the reviewer points out this is costly and time consuming. However, as requested by reviewer 2, we have added evidence of the plasma membrane localization of ZmCRN and additional support for protein-protein interactions, by performing reciprocal Co-IP and BiFC. These data were added in the revised manuscript (Figure 4D, Figure supplement 6 and Figure supplement 7). These additional assays give us extra confidence in the plasma membrane localization of ZmCRN and interactions between ZmCRN and FEA2, even though the experiments were carried out in N. benthamiana. Please note that we do not detect FEA2-CT2 direct interaction using BiFC, even though we have confirmed their interaction many times by in vivo co-IP, and we believe another protein is bridging their interaction (Q. Wu and DJ, unpublished).

“FEA2-YFP, ZmCRN-mCherry, CT2-YFP and ZmCRN-mCherry were also co-localized on the plasma membrane when they were co-expressed (Figure 4—figure supplement 1). […] Lastly, as expected, no signal was detected when CT2-NmVen210 was co-expressed with ZmCRN-CmVen210 (Figure 4—figure supplement 2), confirming out co-IP results, and supporting the hypothesis that they do not interact.”

5) The data clearly show that FEA2 mutants are reduced in sensitivity to both the FCP and CLE7 peptides, CT2 shows reduced sensitivity to its presumptive ligand CLE7 (but not FCP1), and ZmCRN is reduced in sensitivity to FCP1 (its presumptive ligand), but is sensitive to CLE7. However, the legend to Figure 5 describes crn mutants as insensitive to FCP1, whereas the text better describes this interaction as "partially resistant", since FEA3 is presumably intact and should be responding to applied FCP ligand. Best to fix this inconsistency between the descriptions in the legend and the manuscript text.

Thanks for catching this inconsistency. We reworded the Figure 5 legend to “Zmcrn was partially resistant only to ZmFCP1 peptide” to make it consistent as suggested.

Reviewer #2:

[…] Role of FEA3: The genetic interactions of FEA3 in FEA2-CT and FEA2-ZmCRN pathways needs to be addressed in order to evaluate the genetic interaction and peptide application data. Both fea2 and fea3 are resistant to ZmFCP1 peptide application (Figure 1). Because of this, partial sensitivity of Zmcrn mutants to ZmFCP1 (Figure 5D) may be mediated through FEA3. Peptide application on fea3 Zmcrn double mutants would clarify this.

We agree with the reviewer that it is important to understand the interaction between FEA3 and ZmCRN, since both factors act to transmit the ZmFCP1 signal. We therefore added new data on the genetic interactions between Zmcrn and fea3 (and also ct2 and fea3) in double mutants. In the segregating double mutant population, the fea3; Zmcrn double mutants SAMs were larger than the single mutants,suggesting that FEA3 and ZmCRN do not function in a common pathway. Similar findings were observed for fea3; ct2 double mutants. Thus, fea3 acts additively with Zmcrn, suggesting that ZmFCP1 signaling is mediated by two parallel pathways, one through FEA3 working through an as yet unknown downstream component(s), and another through FEA2 coupled with ZmCRN. This genetic data largely supports the reviewer’s speculation that the partial sensitivity of Zmcrn mutants to ZmFCP1 is mediated through FEA3. Importantly, our data suggest that CT2 and ZmCRN do not act as downstream components for FEA3.

We have not performed peptide assays with the fea3; Zmcrn double mutants, since we just obtained them and it would take an additional 4-5 months to grow plants to make embryos and complete the treatments. We hope that the new data on fea3; Zmcrn double mutants is sufficient to convince the reviewer that FEA3 and ZmCRN are acting in parallel, thus explaining the partial sensitivity of Zmcrn mutants to ZmFCP1 peptide.

These new data are presented in Figure 5—figure supplement 1,and in the text:

“As FEA3 also acts to transmit the ZmFCP1 signal (Je et al., 2016), we used genetic analysis to ask if ZmCRN also functions downstream of FEA3. […] Thus, ZmFCP1 signaling appears to be mediated by two different pathways, one acting through FEA2 coupled with ZmCRN, and another acting through FEA3 working through as yet unknown downstream component(s).”

ZmCRN expression/localization patterns: Where is ZmCRN expressed? For ZmCRN to function via forming a heterodimer with FEA2, their expression domain should overlap within the SAM. The authors could generate transgenic lines expressing the FP-tagged CRN in maize (which I agree might be very difficult and takes time for maize), or at least the authors must show clear in situ hybridization data long with the FEA2 and CT2.

Thanks for understanding the difficulty and long time to make FP-tagged CRN transgenic plants. As also requested by reviewer 1, we carried out in situ hybridization with maize shoot meristems using a ZmCRN anti-sense probe. ZmCRN was expressed throughout the SAM and more strongly in the peripheral domain and leaf primordia (Figure 2E). This profile was confirmed by laser capture microdissection RNAseq data for different domains of the SAM (data from Timmermans lab, available from MaizeGDB; https://maizegdb.org/). This new data is added as Figure 2E and Figure 2—figure supplement 4. CT2 has been shown previously to express broadly in the SAM using CT2-YFP transgenic plants (Bommert et al., 2013a). In addition, laser capture RNA seq data showed that FEA2, ZmCRN and CT2 are all expressed broadly in all domains of the SAM, suggesting that they are co-expressed (Figure 2—figure supplement 4).

This new data is added as Figure 2E and Figure 2—figure supplement 4, and new text:

“ZmCRN was expressed throughout the SAM and more strongly in the peripheral domain and leaf primordia (Figure 2E, confirmed by laser capture microdissection RNAseq, Figure 2—figure supplement 4).”

Subcellular co-localization in N. benthamiana: The authors show that ZmCRN-mCherry localizes to PM in tobacco leaf epidermis. Would ZmFEA2 and/or CT co-localizes with ZmCRN on the plasma membrane in tobacco?

Yes, we observed that FEA2 were co-localized with ZmCRN on the plasma membrane when these two proteins were co-expressed in N. benthamiana (Figure supplement 6). We also saw co-localization of CT2-YFP with ZmCRN-mCherry on plasma membrane when they are co-expressed (Figure 4—figure supplement 1):

“FEA2-YFP, ZmCRN-mCherry, CT2-YFP and ZmCRN-mCherry were also co-localized on the plasma membrane when they were co-expressed (Figure 4—figure supplement 1).”

Protein-protein interaction assays: The authors present only one type experiment (Co-IP) to conclude that FEA2 forms a separate complex with ZmCRN and CT2 depending on the ligands. The following experiments would strengthen the conclusion:

a) Reciprocal Co-IP. The authors should reciprocally IP FEA2 and confirm that FEA2 indeed brings down BOTH CT2 and ZmCRN when three proteins are co-expressed. I think this experiment must be performed.

Alternative experimental approach to support the in planta Co-IP experiments. The authors could perform BiFC, split-Ub or other protein-protein interaction assays to strengthen their claim.

As suggested, we performed the reciprocal Co-IPs and IPs using 3 co-expressed proteins. We had initially shown that either ZmCRN-mCherry or CT2-YFP could IP FEA2-myc, and now we added new experiments using 3 co-expressed proteins showing that when we reciprocally IP FEA2-myc we pull down CT2-YFP and ZmCRN-mCherry (Figure 4D), confirming that FEA2 indeed brings down both CT2 and ZmCRN when three proteins are co-expressed.

We also used bimolecular fluorescence complementation (BiFC) assays to independently confirm our in planta co-IPs. We used an optimized BiFC system, with monomeric Venus (mVenus) split at residue 210 to reduce background due to false positive interactions (Gookin et al., 2014). We detected YFP signal when FEA2 was fused with the N terminal part of mVenus (NmVen210) and ZmCRN was fused with the C terminal part (CmVen210) (Figure 4—figure supplement 2), confirming a direct interaction between FEA2 and ZmCRN. Similar results were reported in Arabidopsis using BiFC to detect CRN-CLV2 interactions (Zhu et al., 2010). However, we failed to detect a YFP signal when FEA2-NmVen210 was co-expressed with CT2-CmVen210 (Figure 4—figure supplement 2). The interaction between FEA2 and CT2 is well documented in N. benthamiana as well as in maize by in vivo Co-IP experiments (Figure 4C and 4D, Bommert et al., 2013a). A failure to detect the same interaction using BiFC suggests that their interaction might be indirect (Figure 6). Our lab has extensively studied FEA2-CT2 interactions and repeated the in vivo co-IP many times, however in other experiments using FRET or BiFC we did not detect the interaction, suggesting the interaction is indirect, i.e. another protein or proteins bridges the interaction – we are currently working on a candidate for this bridging protein.

Lastly, as expected, no signal was detected when CT2-NmVen210 was co-expressed with ZmCRN-CmVen210 (Figure 4—figure supplement 2), confirming out co-IP results, and supporting the hypothesis that they do not interact. This is described in the new text:

“To validate these interactions, a reciprocal Co-IP experiment was carried out, in which all three proteins were co-expressed, and we again found that FEA2-Myc could IP CT2-YFP or ZmCRN-mCherry (Figure 4D), further confirming that FEA2 formed complexes with both CT2 and ZmCRN. […] Lastly, as expected, no signal was detected when CT2-NmVen210 was co-expressed with ZmCRN-CmVen210 (Figure 4—figure supplement 2), confirming out co-IP results, and supporting the hypothesis that they do not interact.”

b) Role of different peptides, ZmFCP1 and ZmCLE7, on receptor complex formation. This can be done by treating/infiltrating/co-expressing each peptide to the N. benthamiana leaves along with a pair-wise combination of receptors.

As suggested, we co-infiltrated ZmFCP1 or ZmCLE7 along with the expression of FEA2-Myc, CT2-YFP and CRN-mCherry, and performed the co-IP experiment. However, adding CLE peptides didn’t affect the interaction between FEA2-myc and CT2-YFP or CRN-mCherry (Figure 4—figure supplement 3). This negative result is difficult to interpret, but we note that similar experiments have not been performed even in Arabidopsis, so there is no precedent to believe that the CLE ligands should lead to change in receptor complex formation. The results are described in the new text:

“Indeed, these interactions appeared to be quite stable, and they were not affected by co-infiltration of CLE peptides (Figure 4—figure supplement 3).”

Figure 4C. The gel lanes appear spliced. This is not an accepted practice or data presentation.

We apologize for the oversight, and inserted lines as suggested. The western blots are now presented in the correct way.

Discussion, fourth paragraph (discussion about why clv2 phenotype is weaker than clv1). A previous report (Diévart et al., 2003) shows that missense alleles of clv1 act in a dominant-negative manner. Please include this into the Discussion.

Thanks. We added this information into the Discussion:

“This also explains why all intermediate and strong clv1 alleles are dominant negative, as they likely interfere with the activity of other receptor kinase(s) that have functional overlap with CLV1 (Dievart et al., 2003; Nimchuk et al., 2015).”

Reviewer #3:

[…] Overall this is a well written manuscript which provides some novel insight into the CLE signaling pathway involved in plant stem cell maintenance. Since, I am not a maize geneticist, I will focus my review on a) the biochemical experiments presented in this study and b) on the discussion of these novel findings:

a) I understand that it is very difficult to perform any co-IP experiments in maize and that for this reason a transient system was chosen. I would find it nevertheless appropriate to at least mention in the Discussion that the outlined interactions were assayed not with native-like protein levels but rather by strongly overexpressing CRN, FEA2 and CT2.

Thanks for the suggestion, we now mentioned in the Discussion part the caveat that the interaction between ZmCRN and FEA2 was carried out in a transiently overexpression system:

“…and that FEA2 and ZmCRN interacted directly, using Co-IP and BiFC assays of proteins transiently overexpressed in N. benthamiana, suggesting that ZmCRN is a signaling component in the FEA2 pathway.”

In addition, in the revised manuscript, we provided more evidence on the interactions between ZmCRN and FEA2 using reciprocal Co-IP and BiFC in N. benthamiana (Figure 4D and Figure 4—figure supplement 2). These data further confirm the interaction between FEA2 and ZmCRN. For the interaction between CT2 and FEA2, we also confirmed the interaction in N. benthamiana by reciprocal Co-IP experiments – this interaction has been previously demonstrated using native expression in CT2-YFP transgenic maize (Bommert et al., 2013a). These new experiments are described in detail in the comments to reviewer 2, above.

b) Why are the peptide resistance assays done with such high peptide concentrations (30 μM)? Do the authors think that the binding affinities of the maize receptor complexes are much lower than in Arabidopsis? Or are there post-translational modifications missing from the synthetic peptides? Or are the peptides poorly taken up by the plant tissue?

As in our previous publications (Bommert et al., 2013a, Je et al., 2016), 5 – 30 μM peptide have been routinely used for maize root and embryo assays, respectively. Of course, we cannot know how much peptide penetrates the tissues. One reason why such a high concentration is needed might be that the synthetic peptides lack necessary post-translational modifications; in Arabidopsis, CLV3 is arabinosylated on a hydroxyproline modified residue (Matsubayashi, 2011), and this post-translational modification is critical for its high-affinity binding to its receptor, CLV1 (Ohyama et al., 2009). In tomato, a mutant in a hydroxyproline O-arabinosyltransferase has enlarged shoot meristems, and the mutant can be rescued with arabinosylated CLV3 (Xu et al., 2015). Thus, CLE peptides with arabinosylated hydroxyproline modifications have higher activity than the non-modified peptides.

The tri-arabinosylated CLE peptides are not commercially available, and the group that first published them were not able to provide it to us because they are very difficult to produce. However, very recently we obtained some hydroxyproline-triarabinosyl modified ZmCLE7 peptide from a collaborator (similar to ones published in Corcilius et al., 2017). We compared maize root and SAM growth following treatment with modified or non-modified peptides. As predicted, the arabinosylated ZmCLE7 peptide was more potent than the non-modified version, we estimate by ~ 10 fold. However, our collaborator could only provide a small amount of the arabinosylated CLE7 peptide and it is not enough to repeat all of the assays in the manuscript. Therefore, we propose the following modification to the manuscript:

“Although we used high peptide concentrations, the activity of CLE peptides is known to be enhanced by triarabinosylation (Ohyama et al., 2009; Matsubayashi 2011; Xu et al., 2015; Corcilius et al., 2017), and indeed we found that similarly modified ZmCLE7 peptide was about 10 fold more potent than the non-modified form (Figure 5—figure supplement 2).”

c) Based on their findings, the authors suggest FEA2/CLV2 as a co-receptor for several CLE peptide-sensing LRR receptor kinases. In terms of the presented as well as previously established genetics on FEA2/CLV2 this would only make sense, if indeed CLV2 function can be replaced by another co-receptor in vivo. I would appreciate if the authors could present here a sequence alignment of the known receptor-like proteins from maize. Are there sequence homologs for CLV2 in maize (there are no obvious homologs in Arabidopsis)?

We included a phylogenetic analysis supporting the idea that similar to CLV2 in Arabidopsis, FEA2 does not have any close homolog that could function redundantly in maize (Figure 6—figure supplement 1). We think the reviewer is asking why then are fea2 phenotypes not stronger. We believe this is because of other redundant pathways, such as fea3, as also discussed in our response to reviewer 2.

“As a candidate receptor or co-receptor for different peptides, FEA2 does not to have any close homologs in the maize genome (Figure 6—figure supplement 1), similar to CLV2 in Arabidopsis, and its relatively modest phenotype may be due to compensation by partially redundant parallel signaling pathways, such as through FEA3 (Je at al., 2016) in fea2 mutants.”

Author details

1. Byoung Il Je

   1. Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
   2. Department of Horticultural Bioscience, College of Natural Resource and Life Science, Pusan National University, Miryang, Republic of Korea

   Contribution

   Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Writing—original draft, Writing—review and editing

   Contributed equally with

   Fang Xu

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-6661-5855

2. Fang Xu

   Cold Spring Harbor Laboratory, Cold Spring Harbor, United States

   Contribution

   Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Writing—review and editing

   Contributed equally with

   Byoung Il Je

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0003-0767-1272

3. Qingyu Wu

   Cold Spring Harbor Laboratory, Cold Spring Harbor, United States

   Contribution

   Data curation, Methodology

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0003-3064-2445

4. Lei Liu

   Cold Spring Harbor Laboratory, Cold Spring Harbor, United States

   Contribution

   Data curation, Methodology

   Competing interests

   No competing interests declared

5. Robert Meeley

   DuPont Pioneer, Agricultural Biotechnology, Johnston, United States

   Contribution

   Conceptualization, Formal analysis, Methodology

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-4496-1888

6. Joseph P Gallagher

   University of Massachusetts Amherst, Amherst, United States

   Contribution

   Conceptualization, Methodology

   Competing interests

   No competing interests declared

7. Leo Corcilius

   The University of Sydney, Camperdown, Australia

   Contribution

   Conceptualization, Methodology

   Competing interests

   No competing interests declared

8. Richard J Payne

   The University of Sydney, Camperdown, Australia

   Contribution

   Conceptualization, Methodology

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-3618-9226

9. Madelaine E Bartlett

   University of Massachusetts Amherst, Amherst, United States

   Contribution

   Conceptualization, Methodology

   Competing interests

   No competing interests declared

10. David Jackson

    Cold Spring Harbor Laboratory, Cold Spring Harbor, United States

    Contribution

    Conceptualization, Data curation, Formal analysis, Supervision, Funding acquisition, Investigation, Methodology, Writing—original draft, Writing—review and editing

    For correspondence

    jacksond@cshl.edu

    Competing interests

    No competing interests declared

    "This ORCID iD identifies the author of this article:" 0000-0002-4269-7649

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