The sequence flanking the N-terminus of the CLV3 peptide is critical for its cleavage and activity in stem cell regulation in Arabidopsis

Pull the fuzes: Processing protein precursors to generate apoplastic danger signals for triggering plant immunity

The apoplast is one of the first cellular compartments outside the plasma membrane encountered by phytopathogenic microbes in the early stages of plant tissue invasion. Plants have developed sophisticated surveillance mechanisms to sense danger events at the cell surface and promptly activate immunity. However, a fine tuning of the activation of immune pathways is necessary to mount a robust and effective defense response. Several endogenous proteins and enzymes are synthesized as inactive precursors, and their post-translational processing has emerged as a critical mechanism for triggering alarms in the apoplast. In this review, we focus on the precursors of phytocytokines, cell wall remodeling enzymes, and proteases. The physiological events that convert inactive precursors into immunomodulatory active peptides or enzymes are described. This review also explores the functional synergies among phytocytokines, cell wall damage-associated molecular patterns, and remodeling, highlighting their roles in boosting extracellular immunity and reinforcing defenses against pests.

Stem Cells: Engines of Plant Growth and Development

The development of both animals and plants relies on populations of pluripotent stem cells that provide the cellular raw materials for organ and tissue formation. Plant stem cell reservoirs are housed at the shoot and root tips in structures called meristems, with the shoot apical meristem (SAM) continuously producing aerial leaf, stem, and flower organs throughout the life cycle. Thus, the SAM acts as the engine of plant development and has unique structural and molecular features that allow it to balance self-renewal with differentiation and act as a constant source of new cells for organogenesis while simultaneously maintaining a stem cell reservoir for future organ formation. Studies have identified key roles for intercellular regulatory networks that establish and maintain meristem activity, including the KNOX transcription factor pathway and the CLV-WUS stem cell feedback loop. In addition, the plant hormones cytokinin and auxin act through their downstream signaling pathways in the SAM to integrate stem cell activity and organ initiation. This review discusses how the various regulatory pathways collectively orchestrate SAM function and touches on how their manipulation can alter stem cell activity to improve crop yield.

Identification and comprehensive analysis of the CLV3/ESR-related (CLE) gene family in Brassica napus L

The CLE (CLAVATA3/ESR) gene family, encoding a group of small secretory peptides, plays important roles in cell-to-cell communication, thereby controlling a broad spectrum of development processes. The CLE family has been systematically characterized in some plants, but not in Brassica napus. In the present study, 116 BnCLE genes were identified in the B. napus genome, including seven unannotated, six incorrectly predicted and five multi-CLE domain-encoding genes. These BnCLE members were separated into seven distinct groups based on phylogenetic analysis, which might facilitate the functional characterization of the peptides. Further characterization of CLE pre-propeptides revealed 31 unique CLE peptides from 45 BnCLE genes, which may give rise to distinct roles of BnCLE and expansion of the gene family. The biological activity of these unique CLE dodecamer peptides was tested further through in vitro peptide assays. Variations in several important residues were identified as key contributors to the functional differentiation of BnCLE and expansion of the gene family in B. napus. Expression profile analysis helped to characterize possible functional redundancy and sub-functionalization among the BnCLE members. This study presents a comprehensive overview of the CLE gene family in B. napus and provides a foundation for future evolutionary and functional studies.

Comparative Mapping Combined With Map-Based Cloning of the Brassica juncea Genome Reveals a Candidate Gene for Multilocular Rapeseed

Multilocular traits exist in a variety of plants and exert important effects on plant yield. Previous genetic studies have shown that multilocular trait of the Brassica juncea cultivar Duoshi is controlled by two recessive genes, Bjln1 and Bjln2. In previous studies, the Bjln1 gene is located on chromosome A07, and the Bjln1 candidate gene is BjuA07.CLV1. In this study, a BC4 mapping population for the Bjln2 gene was generated. This population was used to construct genetic linkage maps of the Bjln2 gene using amplified fragment length polymorphism (AFLP), intron length polymorphism (IP) and simple sequence repeat (SSR) methodology. The results showed that the Bjln2 gene was restricted to a 0.63 cM interval. BLAST alignment with B. juncea revealed the Bjln2 gene was located within a 11.81-16.65 Mb region on chromosome B07. Moreover, the candidate gene BjuB07.CLV1 (equivalent to Bjln2) was cloned by comparing mapping and map-based cloning, and BjuB07.CLV1 gene was shown to have the ability to restore the bilocular traits in a genetic complementation experiment. The sequencing revealed that a 4961 bp insertion interrupted the coding sequence of the BjuB07.CLV1 gene, resulting in an increase in locule number. Expression analysis revealed that BjuB07.CLV1 was expressed in all tissues and the expression level in bilocular plants was significantly higher than that in multilocular plants. In addition, markers closely linked to the Bjln2 gene were developed and used for molecular marker-assisted breeding of multilocular traits.

Expression of CLAVATA3 fusions indicates rapid intracellular processing and a role of ERAD

The 12 amino acid peptide derived from the Arabidopsis soluble secretory protein CLAVATA3 (CLV3) acts at the cell surface in a signalling system that regulates the size of apical meristems. The subcellular pathway involved in releasing the peptide from its precursor is unknown. We show that a CLV3-GFP fusion expressed in transfected tobacco protoplasts or transgenic tobacco plants has very short intracellular half-life that cannot be extended by the secretory traffic inhibitors brefeldin A and wortmannin. The fusion is biologically active, since the incubation medium of protoplasts from CLV3-GFP-expressing tobacco contains the CLV3 peptide and inhibits root growth. The rapid disappearance of intact CLV3-GFP requires the signal peptide and is inhibited by the proteasome inhibitor MG132 or coexpression with a mutated CDC48 that inhibits endoplasmic reticulum-associated protein degradation (ERAD). The synthesis of CLV3-GFP is specifically supported by the endoplasmic reticulum chaperone endoplasmin in an in vivo assay. Our results indicate that processing of CLV3 starts intracellularly in an early compartment of the secretory pathway and that ERAD could play a regulatory or direct role in the active peptide synthesis.

Dual CLAVATA3 Peptides in Arabidopsis Shoot Stem Cell Signaling

Plant shoot stem cell pool is constantly maintained by a negative feedback loop through peptide-receptor mediated signaling pathway. CLAVATA3 (CLV3) encode a 96 amino-acid protein which is processed to 12-amino-acid or arabinosylated 13-amino-acid peptides, acting as a ligand signal to regulate stem cell homeostasis in the shoot apical meristem (SAM). Although arabinosylated 13-amino-acid CLV3 peptide (CLV3p) shows more significant binding affinity to its receptors and biological activities in the SAM, the physiological function of two mature forms of CLV3p remained an unresolved puzzle in the past decade due to the technical difficulties of arabinosylation modification in the peptide synthesis. Here, we analyzed the role of two mature CLV3 peptides with newly synthesized arabinosylated peptide. Beside shoot meristem phenotypes, arabinosylated CLV3p showed the conventional trait of CLV2-dependent root growth inhibition. Moreover, both 12-amino-acid and arabinosylated 13-amino-acid CLV3 peptides have analogous activities in shoot stem cell signaling. Notably, we demonstrated that non-arabinosylated 12-amino acid CLV3p can affect shoot stem cell signaling at the physiological level unlike previously suggested (Ohyama et al., 2009; Shinohara and Matsubayashi, 2013; Shinohara and Matsubayashi, 2015). Therefore, these results support the physiological role of the 12-amino-acid CLV3p in shoot stem cell signaling in the deficient condition of arabinosylated 13-amino-acid CLV3p in Arabidopsis thaliana.

Comparative Transcriptome Analysis of SE initial dedifferentiation in cotton of different SE capability

Somatic embryogenesis (SE) is a critical transition from vegetative to embryogenic growth in higher plants; however, few studies have investigated the mechanism that regulates SE initial differentiation. Most cotton varieties have not undergone regeneration by SE, so only a few varieties can be used in genetic engineering. Here, two varieties of cotton with different SE capabilities (HD, higher differentiation and LD, lower differentiation) were analyzed by high throughout RNA-Seq at the pre-induction stage (0h) and two induction stages (3h and 3d) under callus-induction medium (CIM). About 1150 million clean reads were obtained from 98.21% raw data. Transcriptomic analysis revealed that "protein kinase activity" and "oxidoreductase activity" were highly represented GO terms during the same and different treatment stages among HD and LD. Moreover, several stress-related transcription factors might play important roles in SE initiation. The SE-related regulation genes (SERKs) showed different expression patterns between HD and LD. Furthermore, the complex auxin and ethylene signaling pathway contributes to initiation of differentiation in SE. Thus, our RNA-sequencing of comparative transcriptome analysis will lay a foundation for future studies to better define early somatic formation in cotton with different SE capabilities.

Recent advances in the research for the homolog of breast cancer associated gene AtROW1 in higher plants

BARD1 (BRCA1 associated RING domain protein 1), as an important animal tumor suppressor gene associated with many kinds of cancers, has been intensively studied for decades. Surprisingly, homolog of BARD1 was found in plants and it was renamed AtROW1 (repressor of Wuschel-1) according to its extremely important function with regard to plant stem cell homeostasis. Although great advances have been made in human BARD1, the function of this animal tumor-suppressor like gene in plant is not well studied and need to be further elucidated. Here, we review and summarize past and present work regarding this protein. Apart from its previously proposed role in DNA repair, recently it is found essential for shoot and root stem cell development and differentiation in plants. The study of AtROW1 in plant may provide an ideal model for further elucidating the functional mechanism of BARD1 in mammals.

Expanding the Regulatory Network for Meristem Size in Plants

The remarkable plasticity of post-embryonic plant development is due to groups of stem-cell-containing structures called meristems. In the shoot, meristems continuously produce organs such as leaves, flowers, and stems. Nearly two decades ago the WUSCHEL/CLAVATA (WUS/CLV) negative feedback loop was established as being essential for regulating the size of shoot meristems by maintaining a delicate balance between stem cell proliferation and cell recruitment for the differentiation of lateral primordia. Recent research in various model species (Arabidopsis, tomato, maize, and rice) has led to discoveries of additional components that further refine and improve the current model of meristem regulation, adding new complexity to a vital network for plant growth and productivity.

Identification and characterization of the Populus trichocarpa CLE family

Background

The CLE (CLAVATA3/Endosperm Surrounding Region-related) gene family encodes small signaling peptides that are primarily involved in coordinating stem cell fate in different types of plant meristems. Their roles in vascular cambium have highlighted their potential function in wood formation. Apart from recent advances on identification and characterization of CLE genes, little is known about this gene family in a tree species.

Results

Fifty PtCLE genes were identified from the Populus trichocarpa genome and were classified into four major groups based on sequence similarity. Analysis of the genomic organization of PtCLE genes indicates that genome duplication, as well as the diversity in the CLE motif, have contributed to the expansion of CLE gene family in poplar. A comparison with functionally characterized Arabidopsis CLE protein sequences showed that many PtCLE proteins are closely related to their predicted Arabidopsis counterparts. Particularly, PtCLE3, PtCLE12, PtCLE14 and PtCLE38 comprised an identical CLE motif to AtCLE41/TDIF, which is known as a regulator of vascular cambium homeostasis, strongly supporting the idea that similar signaling pathways exist in both species to regulate wood formation and secondary growth. Transcriptome profiling revealed that PtCLE genes generally were differentially expressed while some PtCLE genes exhibited tissue-specific expression patterns. Moreover, compared to their Arabidopsis counterparts, PtCLE genes showed either similar or distinct expression patterns, implying functional conservation in some cases and functional divergence in others.

Conclusions

Our study provides a genome-wide analysis of the CLE gene family in poplar, and highlights the potential roles of key PtCLE genes in the regulation of secondary growth and wood formation. The comparative analysis revealed that functional conservation may exist between PtCLEs and their AtCLE orthologues, which was further supported by transcriptomic analysis. Transcriptional profiling provided further insights into possible functional divergence, evidenced by differential expression patterns of various PtCLE genes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2504-x) contains supplementary material, which is available to authorized users.

A cascade of arabinosyltransferases controls shoot meristem size in tomato

Shoot meristems of plants are composed of stem cells that are continuously replenished through a classical feedback circuit involving the homeobox WUSCHEL (WUS) gene and the CLAVATA (CLV) gene signaling pathway. In CLV signaling, the CLV1 receptor complex is bound by CLV3, a secreted peptide modified with sugars. However, the pathway responsible for modifying CLV3 and its relevance for CLV signaling are unknown. Here we show that tomato inflorescence branching mutants with extra flower and fruit organs due to enlarged meristems are defective in arabinosyltransferase genes. The most extreme mutant is disrupted in a hydroxyproline O-arabinosyltransferase and can be rescued with arabinosylated CLV3. Weaker mutants are defective in arabinosyltransferases that extend arabinose chains, indicating that CLV3 must be fully arabinosylated to maintain meristem size. Finally, we show that a mutation in CLV3 increased fruit size during domestication. Our findings uncover a new layer of complexity in the control of plant stem cell proliferation.

Biologically active and antimicrobial peptides from plants

Bioactive peptides are part of an innate response elicited by most living forms. In plants, they are produced ubiquitously in roots, seeds, flowers, stems, and leaves, highlighting their physiological importance. While most of the bioactive peptides produced in plants possess microbicide properties, there is evidence that they are also involved in cellular signaling. Structurally, there is an overall similarity when comparing them with those derived from animal or insect sources. The biological action of bioactive peptides initiates with the binding to the target membrane followed in most cases by membrane permeabilization and rupture. Here we present an overview of what is currently known about bioactive peptides from plants, focusing on their antimicrobial activity and their role in the plant signaling network and offering perspectives on their potential application.