CLE Peptides Research Articles

Genome-Wide Identification and Expression Analysis of the CLAVATA3/ESR-Related Gene Family in Tiger Nut

CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (ESR)-related (CLE) genes encode a group of peptide hormones, which coordinate cell proliferation and differentiation in plants. Tiger nut (Cyperus esculentus L.) is a perennial monocot plant that produces oil-rich tubers. However, the mechanisms regulating tuber development in tiger nut are poorly understood, and nothing is known about CLE genes in tiger nut. In this study, we identified 34 CLE genes in the genomes, proteomes, and transcriptomes of C. esculentus (CeCLE). We analyzed their gene structures and expression profiles in different parts of the plant, at three stages of tuber development and in roots in response to dehydration stress. We found a relatively high expression level of CeCLE13 in growing tuber and suggested that the corresponding CLE peptide could be involved in the regulation of tuberization. We also analyzed CeCLE gene sequences in the genome of the most productive K-17 variety in the N. I. Vavilov All-Russian Institute of Plant Genetic Resources collection and found many single nucleotide polymorphisms, insertions, and deletions. Our data provides fundamental information for future research on tiger nut growth and tuberization.

A novel toolbox to record CLE peptide signaling.

A novel toolbox to record CLE peptide signaling.

The Defective in Autoregulation (DAR) gene of Medicago truncatula encodes a protein involved in regulating nodulation and arbuscular mycorrhiza

BackgroundLegumes utilize a long-distance signaling feedback pathway, termed Autoregulation of Nodulation (AON), to regulate the establishment and maintenance of their symbiosis with rhizobia. Several proteins key to this pathway have been discovered, but the AON pathway is not completely understood.ResultsWe report a new hypernodulating mutant, defective in autoregulation, with disruption of a gene, DAR (Medtr2g450550/MtrunA17_Chr2g0304631), previously unknown to play a role in AON. The dar-1 mutant produces ten-fold more nodules than wild type, similar to AON mutants with disrupted SUNN gene function. As in sunn mutants, suppression of nodulation by CLE peptides MtCLE12 and MtCLE13 is abolished in dar. Furthermore, dar-1 also shows increased root length colonization by an arbuscular mycorrhizal fungus, suggesting a role for DAR in autoregulation of mycorrhizal symbiosis (AOM). However, unlike SUNN which functions in the shoot to control nodulation, DAR functions in the root.ConclusionsDAR encodes a membrane protein that is a member of a small protein family in M. truncatula. Our results suggest that DAR could be involved in the subcellular transport of signals involved in symbiosis regulation, but it is not upregulated during symbiosis. DAR gene family members are also present in Arabidopsis, lycophytes, mosses, and microalgae, suggesting the AON and AOM may use pathway components common to other plants, even those that do not undergo either symbiosis.

Macromolecular tool box to elucidate CLAVATA3/EMBRYO SURROUNDING REGION-RELATED-RLK binding, signaling, and downstream effects.

Plant peptides communicate by binding to a large family of receptor-like kinases (RLKs), and they share a conserved binding mechanism, which may account for their promiscuous interaction with several RLKs. In order to understand the in vivo binding specificity of the CLAVATA3/EMBRYO SURROUNDING REGION-RELATED peptide family in Arabidopsis, we have developed a novel set of CLAVATA3 (CLV3)-based peptide tools. After carefully evaluating the CLE peptide binding characteristics, using solid phase synthesis process, we modified the CLV3 peptide and attached a fluorophore and a photoactivable side group. We observed that the labeled CLV3 shows binding specificity within the CLAVATA1 clade of RLKs while avoiding the distantly related PEP RECEPTOR clade, thus resolving the contradictory results obtained previously by many in vitro methods. Furthermore, we observed that the RLK-bound CLV3 undergoes clathrin-mediated endocytosis and is trafficked to the vacuole via ARA7 (a Rab GTPase)-labeled endosomes. Additionally, modifying CLV3 for light-controlled activation enabled spatial and temporal control over CLE signaling. Hence, our CLV3 macromolecular toolbox can be used to study rapid cell specific down-stream effects. Given the conserved binding properties, in the future our toolbox can also be used as a template to modify other CLE peptides.

GmNLP1 and GmNLP4 activate nitrate-induced CLE peptides NIC1a/b to mediate nitrate-regulated root nodulation.

Symbiotic nitrogen fixation is an energy-intensive process, to maintain the balance between growth and nitrogen fixation, high concentrations of nitrate inhibit root nodulation. However, the precise mechanism underlying the nitrate inhibition of nodulation in soybean remains elusive. In this study, CRISPR-Cas9-mediated knockout of GmNLP1 and GmNLP4 unveiled a notable nitrate-tolerant nodulation phenotype. GmNLP1b and GmNLP4a play a significant role in the nitrate-triggered inhibition of nodulation, as the expression of nitrate-responsive genes was largely suppressed in Gmnlp1b and Gmnlp4a mutants. Furthermore, we demonstrated that GmNLP1b and GmNLP4a can bind to the promoters of GmNIC1a and GmNIC1b and activate their expression. Manipulations targeting GmNIC1a and GmNIC1b through knockdown or overexpression strategies resulted in either increased or decreased nodule number in response to nitrate. Additionally, transgenic roots that constitutively express GmNIC1a or GmNIC1b rely on both NARK and hydroxyproline O-arabinosyltransferase RDN1 to prevent the inhibitory effects imposed by nitrate on nodulation. In conclusion, this study highlights the crucial role of the GmNLP1/4-GmNIC1a/b module in mediating high nitrate-induced inhibition of nodulation.

Mutation of BAM2 rescues the sunn hypernodulation phenotype in Medicago truncatula, suggesting that a signaling pathway like CLV1/BAM in Arabidopsis affects nodule number.

The unique evolutionary adaptation of legumes for nitrogen-fixing symbiosis leading to nodulation is tightly regulated by the host plant. The autoregulation of nodulation (AON) pathway negatively regulates the number of nodules formed in response to the carbon/nitrogen metabolic status of the shoot and root by long-distance signaling to and from the shoot and root. Central to AON signaling in the shoots of Medicago truncatula is SUNN, a leucine-rich repeat receptor-like kinase with high sequence similarity with CLAVATA1 (CLV1), part of a class of receptors in Arabidopsis involved in regulating stem cell populations in the root and shoot. This class of receptors in Arabidopsis includes the BARELY ANY MERISTEM family, which, like CLV1, binds to CLE peptides and interacts with CLV1 to regulate meristem development. M. truncatula contains five members of the BAM family, but only MtBAM1 and MtBAM2 are highly expressed in the nodules 48 hours after inoculation. Plants carry mutations in individual MtBAMs, and several double BAM mutant combinations all displayed wild-type nodule number phenotypes. However, Mtbam2 suppressed the sunn-5 hypernodulation phenotype and partially rescued the short root length phenotype of sunn-5 when present in a sunn-5 background. Grafting determined that bam2 suppresses supernodulation from the roots, regardless of the SUNN status of the root. Overexpression of MtBAM2 in wild-type plants increases nodule numbers, while overexpression of MtBAM2 in some sunn mutants rescues the hypernodulation phenotype, but not the hypernodulation phenotypes of AON mutant rdn1-2 or crn. Relative expression measurements of the nodule transcription factor MtWOX5 downstream of the putative bam2 sunn-5 complex revealed disruption of meristem signaling; while both bam2 and bam2 sunn-5 influence MtWOX5 expression, the expression changes are in different directions. We propose a genetic model wherein the specific root interactions of BAM2/SUNN are critical for signaling in nodule meristem cell homeostasis in M. truncatula.

Putative molecular pathways of autoregulation of nodulation activated by CLE peptides in pea

Legume plants are important for ecosystems due to their ability to form root nodules in symbiosis with rhizobia, where nitrogen fixation takes place. The number of symbiotic nodules is regulated by the CLE peptides inhibiting excessive nodule formation. Previously, we have identified four genes encoding CLE peptides, activated in response to rhizobia inoculation in pea. Three of them, PsCLE13, PsCLE12 and PsNIC-like, were also activated by nitrate, and, therefore, they could mediate nitrate-dependent inhibition of nodulation [1]. Overexpression of PsCLE13 and PsCLE12 inhibited nodulation on transgenic roots: however, the role of PsNIC-like and PsCLE12-like have not been investigated.
 In this study, we constructed vectors for overexpression of the PsCLE12-like and PsNIC-like genes to study their possible role in nodulation, and also analyzed the expression levels of nodulation-related genes in transgenic roots overexpressing four PsCLEs genes. Moreover, vectors for CRISPR-Cas9-mediated gene editing of the PsCLE12 and PsCLE13 genes were constructed to further explore the role of these genes in nodulation. Overexpression of PsCLE12-like, PsCLE13 and PsCLE12 resulted in increased expression levels of TOO MUCH LOVE (PsTMLs) genes known as root-acting regulators of nodule number. In addition, in the roots overexpressing four PsCLEs genes, down regulation of the PsSYM37 gene (encoding the receptor for Nod-factors) was observed, suggesting that the CLE peptides might inhibit the development of symbiotic nodules at the earliest stages of symbiosis development upon Nod-factor perception.

The search for inhibitors of somatic embryogenesis in Medicago truncatula

The success of protocols for the genetic transformation of legumes is limited by their low ability to regenerate. Plant regeneration can occur both along the path of shoot regeneration and their further rooting, and along the path of somatic embryogenesis (SE). SE is similar to zygotic embryogenesis (ZE). It is a method of asexual reproduction, in which the somatic cell, due to its totipotency, switches on the embryogenesis program.
 SE and ZE involve common participants in transcriptional, hormonal, and epigenetic control. Like many processes in the plant organism, SE is controlled by the activity of various stimulants or repressors.
 As a result of transcriptional analysis of embryogenic and non-embryogenic calli ofMedicago truncatulaat different stages of development, putative genes-inhibitors of SE were found. Using the Golden Gate system, we created vectors for agrobacterial transformation to overexpress genes of interest in embryogenic calli and evaluate their effect on SE. Overexpression of two genes encoding the transcription factors from WRKY and Homobox-WOX families had a significant inhibitory effect on SE (the average number of somatic embryos per callus decreased).
 TheMtCLE16,a previously found SE inhibitor from the CLE peptides group, was edited and heterozygous frameshift mutants were obtained. The impact of loss of its function on the SE capacity remains to be analyzed.
 This research was supported by the Sirius University of Science and Technology, project PBB-RND-2243.

Laser Capture Microdissection Transcriptome Reveals Spatiotemporal Tissue Gene Expression Patterns of Medicago truncatula Roots Responding to Rhizobia.

We report a public resource for examining the spatiotemporal RNA expression of 54,893 Medicago truncatula genes during the first 72 h of response to rhizobial inoculation. Using a methodology that allows synchronous inoculation and growth of more than 100 plants in a single media container, we harvested the same segment of each root responding to rhizobia in the initial inoculation over a time course, collected individual tissues from these segments with laser capture microdissection, and created and sequenced RNA libraries generated from these tissues. We demonstrate the utility of the resource by examining the expression patterns of a set of genes induced very early in nodule signaling, as well as two gene families (CLE peptides and nodule specific PLAT-domain proteins) and show that despite similar whole-root expression patterns, there are tissue differences in expression between the genes. Using a rhizobial response dataset generated from transcriptomics on intact root segments, we also examined differential temporal expression patterns and determined that, after nodule tissue, the epidermis and cortical cells contained the most temporally patterned genes. We circumscribed gene lists for each time and tissue examined and developed an expression pattern visualization tool. Finally, we explored transcriptomic differences between the inner cortical cells that become nodules and those that do not, confirming that the expression of 1-aminocyclopropane-1-carboxylate synthases distinguishes inner cortical cells that become nodules and provide and describe potential downstream genes involved in early nodule cell division. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Characterization of the CLE Family in Three Nicotiana Species and Potential Roles of CLE Peptides in Osmotic and Salt Stress Responses

The CLE family (CLAVATA3/embryo surrounding region-related), a class of small secreted proteins, play important roles in plant development and stress responses. Members of the CLE family have been characterized in a number of plant species, including Arabidopsis and rice. However, limited information is available about CLE peptides in tobacco (Nicotiana tabacum) and related Nicotiana species. Here we report the identification of 84 CLE family members in three Nicotiana species based on sequence similarity. The newly identified CLE members, including 41 from N. tabacum, 19 from N. sylvestris, and 24 from N. tomentosiformis, together with 32 CLEs from Arabidopsis and 52 CLEs from tomato, formed 9 subgroups in a phylogenic tree. The unbalanced distribution of the Nicotiana CLEs in the subgroups suggested potential preferential gene family expansion during evolution. Expression of the NtCLE genes was analyzed and a number of the NtCLEs showed induced expression upon abiotic stress treatments. Synthetic peptides of several NtCLEs, when applied to detached tobacco leaf discs, were able to increase plants’ tolerance to osmotic and salinity stresses, suggesting potential roles of CLE peptides in the stress responses of tobacco.

A phosphoinositide hub connects CLE peptide signaling and polar auxin efflux regulation

Auxin efflux through plasma-membrane-integral PIN-FORMED (PIN) carriers is essential for plant tissue organization and tightly regulated. For instance, a molecular rheostat critically controls PIN-mediated auxin transport in developing protophloem sieve elements of Arabidopsis roots. Plasma-membrane-association of the rheostat proteins, BREVIS RADIX (BRX) and PROTEIN KINASE ASSOCIATED WITH BRX (PAX), is reinforced by interaction with PHOSPHATIDYLINOSITOL-4-PHOSPHATE-5-KINASE (PIP5K). Genetic evidence suggests that BRX dampens autocrine signaling of CLAVATA3/EMBRYO SURROUNDING REGION-RELATED 45 (CLE45) peptide via its receptor BARELY ANY MERISTEM 3 (BAM3). How excess CLE45-BAM3 signaling interferes with protophloem development and whether it does so directly or indirectly remains unclear. Here we show that rheostat polarity is independent of PIN polarity, but interdependent with PIP5K. Catalytically inactive PIP5K confers rheostat polarity without reinforcing its localization, revealing a possible PIP5K scaffolding function. Moreover, PIP5K and PAX cooperatively control local PIN abundance. We further find that CLE45-BAM3 signaling branches via RLCK-VII/PBS1-LIKE (PBL) cytoplasmic kinases to destabilize rheostat localization. Our data thus reveal antagonism between CLE45-BAM3-PBL signaling and PIP5K that converges on auxin efflux regulation through dynamic control of PAX polarity. Because second-site bam3 mutation suppresses root as well as shoot phenotypes of pip5k mutants, CLE peptide signaling likely modulates phosphoinositide-dependent processes in various developmental contexts.

PH-dependent CLE peptide perception permits phloem differentiation in Arabidopsis roots

The plant vasculature delivers phloem sap to the growth apices of sink organs, the meristems, via the interconnected sieve elements of the protophloem.1,2,3 In the A.thaliana root meristem, the stem cells form two files of protophloem sieve elements (PPSEs), whose timely differentiation requires a set of positive genetic regulators. In corresponding loss-of-function mutants, signaling of secreted CLAVATA3/EMBRYO SURROUNDING REGION 45 (CLE45) peptide through the BARELY ANY MERISTEM 3 (BAM3) receptor is hyperactive and interferes with PPSE differentiation. This can be mimicked by an external CLE45 application to wild type. Because developing PPSEs express CLE45-BAM3 pathway components from early on until terminal differentiation, it remains unclear how they escape the autocrine inhibitory CLE45 signal. Here, we report that the wild type becomes insensitive to CLE45 treatment on neutral to alkaline pH media, as well as upon simultaneous treatment with a specific proton pump inhibitor at a standard pH of 5.7. We find that these observations can be explained by neither pH-dependent CLE45 uptake nor pH-dependent CLE45 charge. Moreover, pH-dependent perception specifically requires the CLE45 R4 residue and is not observed for the redundant PPSE-specific CLE25 and CLE26 peptides. Finally, pH-dependent CLE45 response in developing PPSEs as opposed to pH-independent response in neighboring cell files indicates that late-developing PPSEs can no longer sense CLE45. This is consistent with an apoplastic acidic to alkaline pH gradient we observed along developing PPSE cell files. In summary, we conclude that developing PPSEs self-organize their transition to differentiation by desensitizing themselves against autocrine CLE45 signaling through an apoplastic pH increase.

CLE3 and its homologs share overlapping functions in the modulation of lateral root formation through CLV1 and BAM1 in Arabidopsis thaliana.

Lateral roots are important for a wide range of processes, including uptake of water and nutrients. The CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION-RELATED (CLE) 1 ~ 7 peptide family and their cognate receptor CLV1 have been shown to negatively regulate lateral root formation under low-nitrate conditions. However, little is known about how CLE signaling regulates lateral root formation. A persistent obstacle in CLE peptide research is their functional redundancies, which makes functional analyses difficult. To address this problem, we generate the cle1 ~ 7 septuple mutant (cle1 ~ 7-cr1, cr stands for mutant allele generated with CRISPR/Cas9). cle1 ~ 7-cr1 exhibits longer lateral roots under normal conditions. Specifically, in cle1 ~ 7-cr1, the lateral root density is increased, and lateral root primordia initiation is found to be accelerated. Further analysis shows that cle3 single mutant exhibits slightly longer lateral roots. On the other hand, plants that overexpress CLE2 and CLE3 exhibit decreased lateral root lengths. To explore cognate receptor(s) of CLE2 and CLE3, we analyze lateral root lengths in clv1 barely any meristem 1(bam1) double mutant. Mutating both the CLV1 and BAM1 causes longer lateral roots, but not in each single mutant. In addition, genetic analysis reveals that CLV1 and BAM1 are epistatic to CLE2 and CLE3. Furthermore, gene expression analysis shows that the LATERAL ORGAN BOUNDARIES DOMAIN/ASYMMETRIC LEAVES2-LIKE (LBD/ASL) genes, which promote lateral root formation, are upregulated in cle1 ~ 7-cr1 and clv1 bam1. We therefore propose that CLE2 and CLE3 peptides are perceived by CLV1 and BAM1 to mediate lateral root formation through LBDs regulation.

MtCLE08, MtCLE16, and MtCLE18 Transcription Patterns and Their Possible Functions in the Embryogenic Calli of Medicago truncatula.

CLE peptides are well-known hormonal regulators of plant development, but their role in somatic embryogenesis remains undetermined. CLE genes are often regulated by WOX transcription factors and, in their turn, regulate the expression level of WOX genes. In this study, we used in vitro cultivation, as well as qPCR and transcriptomic analysis, to find CLE peptides which could regulate the MtWOX9-1 gene, stimulating somatic embryogenesis in Medicago truncatula. Three CLE peptides were found which could probably be such regulators, but none of them was found to influence MtWOX9-1 expression in the embryogenic calli. Nevertheless, overexpression of one of CLE genes under study, MtCLE16, decreased somatic embryogenesis intensity. Additionally, overexpression of MtCLE08 was found to suppress expression of MtWOX13a, a supposed antagonist of somatic embryo development. Our findings can be helpful for the search for new regeneration regulators which could be used for plant transformation.

A Review on Plant-parasitic Nematode Mimics Acting as a Smart Tool for Establishing Parasitism in Host

Molecular mimics are an excellent example of nature’s survival tool adopted by different pathogens. Plant-parasitic nematodes especially the sedentary endoparasites like Cyst nematodes and Root-knot nematodes are one such dangerous pathogens which were mastered in mimicking their host proteins crucial for cell growth and development. At the time of infection, a nematode fight against the host immune response with simultaneously establishing its feeding site. Thus, this parallel reprograming of plants cell growth and development at the feeding site is what make these pathogens the most dangerous and at the same time intrigued pathogen to study. Plethora of studies have demonstrated that different effector proteins like CLE peptide, AUX1, PHAN, WRKY, RALFs, LBD16, SPRYSEC etc. secreted by nematode mimicking genes playing role in lateral root development; growth hormone regulators; shoot meristem; procambium development; and in immune responses. This review is a brief focusing on genes that are mimics in nematode and can be utilized for biotechnological strategies of plant disease control.

The <i>MtWOX</i> and <i>MtCLE</i> genes in the regulation of <i>Medicago truncatula</i> somatic embryogenesis

Plant somatic cells can be reprogrammed into totipotent embryonic cells that are able to form differentiated embryos in a process called somatic embryogenesis (SE). SE can occur naturally in various plant species and it is widely used for clonal propagation, transformation and regeneration of different crops. This process is regulated by hormone treatment and many proteins, among which WUSCHEL-related homeobox (WOX) transcription factors are believed to play crucial roles. The WOX family is involved in the regulation of a wide range of key developmental programs in different plant organs and tissues. CLE peptides are well-known hormonal regulators of plant development. WOX and CLE genes can be related to each other through feedback regulatory loops.
 Our previous studies have shown that MtWOX9-1 stimulates SE in Medicago truncatula [1] and overexpression of the MtWOX9-1 gene increases the expression level of the MtCLE08, MtCLE16, MtCLE18 genes in SE. In this study, we examine the overexpression effect of MtCLE08, 16, and 18 on the expression level of MtWOX9-1 gene and a number of other MtWOX genes, which were shown to change expression in SE according to the transcriptomic data. No significant impact of MtCLE overexpression on any MtWOX gene under study was found.
 Our findings could be a helpful point for searching and studying new morphogenetic regulators controlling SE and could have a positive impact on plant biotechnology in improving the transformation and regeneration capacity for other legumes.
 The research was supported by grant from the Russian Foundation for Basic Research No. 20-016-00124.

Deeper genomic insights into tomato CLE genes repertoire identify new active peptides

BackgroundIn eukaryotes, cell-to-cell communication relies on the activity of small signaling peptides. In plant genomes, many hundreds of genes encode for such short peptide signals. However, only few of them are functionally characterized and due to the small gene size and high sequence variability, the comprehensive identification of such peptide-encoded genes is challenging. The CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION-RELATED (CLE) gene family encodes for short peptides that have a role in plant meristem maintenance, vascular patterning and responses to environment. The full repertoire of CLE genes and the role of CLE signaling in tomato (Solanum lycopersicum)- one of the most important crop plants- has not yet been fully studied.ResultsBy using a combined approach, we performed a genome-wide identification of CLE genes using the current tomato genome version SL 4.0. We identified 52 SlCLE genes, including 37 new non annotated before. By analyzing publicly available RNAseq datasets we could confirm the expression of 28 new SlCLE genes. We found that SlCLEs are often expressed in a tissue-, organ- or condition-specific manner. Our analysis shows an interesting gene diversification within the SlCLE family that seems to be a result of gene duplication events. Finally, we could show a biological activity of selected SlCLE peptides in the root growth arrest that was SlCLV2-dependent.ConclusionsOur improved combined approach revealed 37 new SlCLE genes. These findings are crucial for better understanding of the CLE signaling in tomato. Our phylogenetic analysis pinpoints the closest homologs of Arabidopsis CLE genes in tomato genome and can give a hint about the function of newly identified SlCLEs. The strategy described here can be used to identify more precisely additional short genes in plant genomes. Finally, our work suggests that the mechanism of root-active CLE peptide perception is conserved between Arabidopsis and tomato. In conclusion, our work paves the way to further research on the CLE-dependent circuits modulating tomato development and physiological responses.

RsCLE22a regulates taproot growth through an auxin signaling-related pathway in radish (Raphanus sativus L.).

CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) peptides are a class of small molecules involved in plant growth and development. Although radish (Raphanus sativus) is an important root vegetable crop worldwide, the functions of CLE peptides in its taproot formation remain elusive. Here, a total of 48 RsCLE genes were identified from the radish genome. RNA in situ hybridization showed that RsCLE22a gene was highly expressed in the vascular cambium. Overexpression of RsCLE22a inhibited root growth by impairing stem cell proliferation in Arabidopsis, and radish plants with exogenous supplementation of RsCLE22 peptide (CLE22p) showed a similar phenotype. The vascular cambial activity was increased in RsCLE22a-silenced plants. Transcriptome analysis revealed that CLE22p altered the expression of several genes involved in meristem development and hormone signal transduction in radish. Immunolocalization results showed that CLE22p increased auxin accumulation in vascular cambium. Yeast one-hybrid and dual-luciferase assays showed that the WUSCHEL-RELATED HOMEOBOX 4 (RsWOX4) binds to RsCLE22a promoter and activates its transcription. The expression level of RsWOX4 was related to vascular cambial activity and was regulated by auxin. Furthermore, a RsCLE22a-RsWOX4 module is proposed to regulate taproot vascular cambium activity through an auxin signaling-related pathway in radish. These findings provide novel insights into the regulation of root growth in a horticultural crop.

CLE peptides join the plant longevity club.

Leaf senescence, the final step of leaf development, is an essential adaptive process that involves intricate regulatory networks mediated by various developmental and environmental clues. Two recent reports, by Zhang Z. et al. and Zhang Y. et al., shed light on how CLE peptides recruit reactive oxygen species (ROS) and ethylene signaling to promote plant leaf longevity.

Transcriptomic Analysis of Radish (Raphanus sativus L.) Roots with CLE41 Overexpression.

The CLE41 peptide, like all other TRACHEARY ELEMENT DIFFERENTIATION INHIBITORY FACTOR (TDIF) family CLE peptides, promotes cell division in (pro-)cambium vascular meristem and prevents xylem differentiation. In this work, we analyzed the differential gene expression in the radish primary-growing P35S:RsCLE41-1 roots using the RNA-seq. Our analysis of transcriptomic data revealed a total of 62 differentially expressed genes between transgenic radish roots overexpressing the RsCLE41-1 gene and the glucuronidase (GUS) gene. For genes associated with late embryogenesis, response to abscisic acid and auxin-dependent xylem cell fate determination, an increase in the expression in P35S:RsCLE41-1 roots was found. Among those downregulated, stress-associated genes prevailed. Moreover, several genes involved in xylem specification were also downregulated in the roots with RsCLE41-1 overexpression. Unexpectedly, none of the well-known targets of TDIFs, such as WOX4 and WOX14, were identified as DEGs in our experiment. Herein, we discuss a suggestion that the activation of pathways associated with desiccation resistance, which are more characteristic of late embryogenesis, in roots with RsCLE41-overexpression may be a consequence of water deficiency onset due to impaired vascular specification.