Modulation of plant innate immune signaling by small peptides

The plant signal peptide CLE7 induces plant defense response against viral infection in Nicotiana benthamiana

In plants, small peptides are important players in the plant stress response, yet their function in plant antiviral responses remains poorly understood. Here, we identify that the plant small peptide, CLAVATA3/ESR-RELATED 7 (CLE7), enhances plant resistance to Chinese wheat mosaic virus infection in Nicotiana (N.) benthamiana. Subsequent investigations demonstrate that CLE7 recognizes receptor kinase NbPXC3 to control the plant antiviral response. Moreover, CLE7-NbPXC3 signaling induces NbMKK2-controlled NbMPK4 phosphorylation, resulting in phosphorylation of the transcription factor NbEDT1. NbEDT1 phosphorylation is involved in the transcriptional activity of NbNCED3, which is a rate-limiting enzyme in abscisic acid (ABA) biosynthesis. Moreover, CLE7 activates broad-spectrum disease resistance to multiple RNA viral infections. Our study indicates that CLE7 induces a plant antiviral response through a series of immune signal transductions in N. benthamiana and provides a foundation for the exploration of efficient viral disease management methods based on plant small peptides.

Subfamily C7 Raf-like kinases MRK1, RAF26, and RAF39 regulate immune homeostasis and stomatal opening in Arabidopsis thaliana

The calcium-dependent protein kinase CPK28 regulates several stress pathways in multiple plant species. Here, we aimed to discover CPK28-associated proteins in Arabidopsis thaliana. We used affinity-based proteomics and identified several potential CPK28 binding partners, including the C7 Raf-like kinases MRK1, RAF26, and RAF39. We used biochemistry, genetics, and physiological assays to gain insight into their function. We define redundant roles for these kinases in stomatal opening, immune-triggered reactive oxygen species (ROS) production, and resistance to a bacterial pathogen. We report that CPK28 associates with and trans-phosphorylates RAF26 and RAF39, and that MRK1, RAF26, and RAF39 are active kinases that localize to endomembranes. Although Raf-like kinases share some features with mitogen-activated protein kinase kinase kinases (MKKKs), we found that MRK1, RAF26, and RAF39 are unable to trans-phosphorylate any of the 10 Arabidopsis mitogen-activated protein kinase kinases (MKKs). Overall, our study suggests that C7 Raf-like kinases associate with and are phosphorylated by CPK28, function redundantly in stomatal opening and immunity, and possess substrate specificities distinct from canonical MKKKs.

Immunity priming and biostimulation by airborne nonanal increase yield of field-grown common bean plants

Introduction

Stress-induced volatile organic compounds (VOCs) that induce plant immunity bear potential for biocontrol. Here, we explore the potential of nonanal to enhance the seed yield of common bean (Phaseolus vulgaris) under open field conditions that are realistic for smallholder farmers.

Methods and results

Using plastic cups with a nonanal-containing lanolin paste as low-cost dispensers, we observed that exposure of Flor de Junio Marcela (FJM) plants over 48h to airborne nonanal was followed by a 3-fold higher expression of pathogenesis-related (PR) genes PR1 and PR4. Both genes further increased their expression in response to subsequent challenge with the fungal pathogen Colletotrichum lindemuthianum. Therefore, we conclude that nonanal causes resistance gene priming. This effect was associated with ca. 2.5-fold lower infection rates and a 2-fold higher seed yield. Offspring of nonanal-exposed FJM plants exhibited a 10% higher emergence rate and a priming of PR1- and PR4-expression, which was associated with decreased infection by C. lindemuthianum and, ultimately, a ca. 3-fold increase in seed yield by anthracnose-infected offspring of nonanal-exposed plants. Seeds of nonanal-exposed and of challenged plants contained significantly more phenolic compounds (increase by ca 40%) and increased antioxidant and radical scavenging activity. Comparative studies including five widely used bean cultivars revealed 2-fold to 3-fold higher seed yield for nonanal-exposed plants. Finally, a cost-benefit analysis indicated a potential economic net profit of nonanal exposure for some, but not all cultivars.

Outlook

We consider nonanal as a promising candidate for an affordable tool that allows low-income smallholder farmers to increase the yield of an important staple-crop without using pesticides.

Comparative Genomics Screens Identify a Novel Small Secretory Peptide, SlSolP12, which Activates Both Local and Systemic Immune Response in Tomatoes and Exhibits Broad-Spectrum Activity

Small secreted peptides (SSPs) are essential for defense mechanisms in plant-microbe interactions, acting as danger-associated molecular patterns (DAMPs). Despite the first discovery of SSPs over three decades ago, only a limited number of SSP families, particularly within Solanaceae plants, have been identified due to inefficient approaches. This study employed comparative genomics screens with Solanaceae proteomes (tomato, tobacco, and pepper) to discover a novel SSP family, SolP. Bioinformatics analysis suggests that SolP may serve as an endogenous signal initiating the plant PTI response. Interestingly, SolP family members from tomato, tobacco, and pepper share an identical sequence (VTSNALALVNRFAD), named SlSolP12 (also referred to as NtSolP15 or CaSolP1). Biochemical and phenotypic analyses revealed that synthetic SlSolP12 peptide triggers multiple defense responses: ROS burst, MAPK activation, callose deposition, stomatal closure, and expression of immune defense genes. Furthermore, SlSolP12 enhances systemic resistance against Botrytis cinerea infection in tomato plants and interferes with classical peptides, flg22 and Systemin, which modulate the immune response. Remarkably, SolP12 activates ROS in diverse plant species, such as Arabidopsis thaliana, soybean, and rice, showing a broad spectrum of biological activities. This study provides valuable approaches for identifying endogenous SSPs and highlights SlSolP12 as a novel DAMP that could serve as a useful target for crop protection.

Intricacies of plants' innate immune responses and their dynamic relationship with fungi: A review

The role of the plant innate immune system in the defense and symbiosis processes becomes integral in a complex network of interactions between plants and fungi. An understanding of the molecular characterization of the plant innate immune system is crucial because it constitutes plants' self-defense shield against harmful fungi, while creating mutualistic relationships with beneficial fungi. Due to the plant-induced awareness and their complexity of interaction with fungi, sufficient assessment of the participation of the plant innate immune system in ecological balance, agriculture, and maintenance of an infinite ecosystem is mandatory. Given the current global challenge, such as the surge of plant-infectious diseases, and pursuit of sustainable forms of agriculture; it is imperative to understand the molecular language of communication between plants and fungi. That knowledge can be practically used in diverse areas, e.g., in agriculture, new tactics may be sought after to try new methods that boost crop receptiveness against fungal pathogens and reduce the dependence on chemical management. Also, it could boost sustainable agricultural practices via enhancing mycorrhizal interactions that promote nutrient absorption and optimum cropping with limited exposure of environmental contamination. Moreover, this review offers insights that go beyond agriculture and can be manipulated to boost plant conservation, environmental restoration, and quality understanding of host-pathogen interactions. Consequently, this specific review paper has offered a comprehensive view of the complex plant innate immune-based responses with fungi and the mechanisms in which they interact.

Genome-wide Characterization of Small Secreted Peptides in Nicotiana tabacum and Functional Assessment of NtLTP25 in Plant Immunity

Small secreted peptides (SSPs), serving as signaling molecules for intercellular communication, play significant regulatory roles in plant growth, development, pathogen immunity, and responses to abiotic stress. Despite several SSPs, such as PIP, PSK, and PSY having been identified to participate in plant immunity, the majority of SSPs remain understudied, necessitating the exploration and identification of SSPs regulating plant immunity from vast genomic resources. Here we systematically characterized 756 putative SSPs across the genome of Nicotiana tabacum. 173 SSPs were further annotated as established SSPs, such as nsLTP, CAPE, and CEP. Furthermore, we detected the expression of 484 putative SSP genes in five tissues, with 83 SSPs displaying tissue-specific expression. Transcriptomic analysis of tobacco roots under plant defense hormones revealed that 46 SSPs exhibited specific responsiveness to salicylic acid (SA), and such response was antagonistically regulated by methyl jasmonate. It's worth noting that among these 46 SSPs, 16 members belong to nsLTP family, and one of them, NtLTP25, was discovered to enhance tobacco's resistance against Phytophthora nicotianae. Overexpression of NtLTP25 in tobacco enhanced the expression of ICS1, subsequently stimulating the biosynthesis of SA and the expression of NPR1 and pathogenesis-related genes. Concurrently, NtLTP25 overexpression activated genes associated with ROS scavenging, consequently mitigating the accumulation of ROS during the subsequent phases of pathogenesis. These discoveries indicate that these 46 SSPs, especially the 16 nsLTPs, might have a vital role in governing plant immunity that relies on SA signaling. This offers a valuable source for pinpointing SSPs involved in regulating plant immunity.

Research Progress of Small Plant Peptides on the Regulation of Plant Growth, Development, and Abiotic Stress

Small peptides in plants are typically characterized as being shorter than 120 amino acids, with their biologically active variants comprising fewer than 20 amino acids. These peptides are instrumental in regulating plant growth, development, and physiological processes, even at minimal concentrations. They play a critical role in long-distance signal transduction within plants and act as primary responders to a range of stress conditions, including salinity, alkalinity, drought, high temperatures, and cold. This review highlights the crucial roles of various small peptides in plant growth and development, plant resistance to abiotic stress, and their involvement in long-distance transport. Furthermore, it elaborates their roles in the regulation of plant hormone biosynthesis. Special emphasis is given to the functions and mechanisms of small peptides in plants responding to abiotic stress conditions, aiming to provide valuable insights for researchers working on the comprehensive study and practical application of small peptides.

Small but mighty: Peptides regulating abiotic stress responses in plants

Throughout evolution, plants have developed strategies to confront and alleviate the detrimental impacts of abiotic stresses on their growth and development. The combat strategies involve intricate molecular networks and a spectrum of early and late stress-responsive pathways. Plant peptides, consisting of fewer than 100 amino acid residues, are at the forefront of these responses, serving as pivotal signalling molecules. These peptides, with roles similar to phytohormones, intricately regulate plant growth, development and facilitate essential cell-to-cell communications. Numerous studies underscore the significant role of these small peptides in coordinating diverse signalling events triggered by environmental challenges. Originating from the proteolytic processing of larger protein precursors or directly translated from small open reading frames, including microRNA (miRNA) encoded peptides from primary miRNA, these peptides exert their biological functions through binding with membrane-embedded receptor-like kinases. This interaction initiates downstream cellular signalling cascades, often involving major phytohormones or reactive oxygen species-mediated mechanisms. Despite these advances, the precise modes of action for numerous other small peptides remain to be fully elucidated. In this review, we delve into the dynamics of stress physiology, mainly focusing on the roles of major small signalling peptides, shedding light on their significance in the face of changing environmental conditions.

Intrinsically disordered Prosystemin discloses biologically active repeat motifs

The in-depth studies over the years on the defence barriers by tomato plants have shown that the Systemin peptide controls the response to a wealth of environmental stress agents. This multifaceted stress reaction seems to be related to the intrinsic disorder of its precursor protein, Prosystemin (ProSys). Since latest findings show that ProSys has biological functions besides Systemin sequence, here we wanted to assess if this precursor includes peptide motifs able to trigger stress-related pathways. Candidate peptides were identified in silico and synthesized to test their capacity to trigger defence responses in tomato plants against different biotic stressors. Our results demonstrated that ProSys harbours several repeat motifs which triggered plant immune reactions against pathogens and pest insects. Three of these peptides were detected by mass spectrometry in plants expressing ProSys, demonstrating their effective presence in vivo. These experimental data shed light on unrecognized functions of ProSys, mediated by multiple biologically active sequences which may partly account for the capacity of ProSys to induce defense responses to different stress agents.

S-acylation of a non-secreted peptide controls plant immunity via secreted-peptide signal activation

Small peptides modulate multiple processes in plant cells, but their regulation by post-translational modification remains unclear. ROT4 (ROTUNDIFOLIA4) belongs to a family of Arabidopsis non-secreted small peptides, but knowledge on its molecular function and how it is regulated is limited. Here, we find that ROT4 is S-acylated in plant cells. S-acylation is an important form of protein lipidation, yet so far it has not been reported to regulate small peptides in plants. We show that this modification is essential for the plasma membrane association of ROT4. Overexpression of S-acylated ROT4 results in a dramatic increase in immune gene expression. S-acylation of ROT4 enhances its interaction with BSK5 (BRASSINOSTEROID-SIGNALING KINASE 5) to block the association between BSK5 and PEPR1 (PEP RECEPTOR1), a receptor kinase for secreted plant elicitor peptides (PEPs), thereby activating immune signaling. Phenotype analysis indicates that S-acylation is necessary for ROT4 functions in pathogen resistance, PEP response, and the regulation of development. Collectively, our work reveals an important role for S-acylation in the cross-talk of non-secreted and secreted peptide signaling in plant immunity.

Influences of Ipomoea batatas Anti-Cancer Peptide on Tomato Defense Genes

AIMS

This study investigates the impact of IbACP (Ipomoea batatas anti-cancer peptide) on defense-related gene expression in tomato leaves, focusing on its role in plant defense mechanisms.

BACKGROUND

Previously, IbACP was isolated from sweet potato leaves, and it was identified as a peptide capable of inducing an alkalinization response in tomato suspension culture media. Additionally, IbACP was found to regulate the proliferation of human pancreatic adenocarcinoma cells.

OBJECTIVE

Elucidate IbACP's molecular influence on defense-related gene expression in tomato leaves using next-generation sequencing analysis.

METHODS

To assess the impact of IbACP on defense-related gene expression, transcriptome data were analyzed, encompassing various functional categories such as photosynthesis, metabolic processes, and plant defense. Semi-quantitative reverse-transcription polymerase chain reaction analysis was employed to verify transcription levels of defense-related genes in tomato leaves treated with IbACP for durations ranging from 0 h (control) to 24 h.

RESULTS

IbACP induced jasmonic acid-related genes (LoxD and AOS) at 2 h, with a significant up-regulation of salicylic acid-dependent gene NPR1 at 24 h. This suggested a temporal antagonistic effect between jasmonic acid and salicylic acid during the early hours of IbACP treatment. Downstream ethylene-responsive regulator genes (ACO1, ETR4, and ERF1) were consistently down-regulated by IbACP at all times. Additionally, IbACP significantly up-regulated the gene expressions of suberization-associated anionic peroxidases (TMP1 and TAP2) at all time points, indicating enhanced suberization of the plant cell wall to prevent pathogen invasion.

CONCLUSION

IbACP enhances the synthesis of defense hormones and up-regulates downstream defense genes, improving the plant's resistance to biotic stresses.

A papain-like cysteine protease-released small signal peptide confers wheat resistance to wheat yellow mosaic virus

Wheat yellow mosaic virus (WYMV), a soil-borne pathogen, poses a serious threat to global wheat production. Here, we identify a WYMV resistance gene, TaRD21A, that belongs to the papain-like cysteine protease family. Through genetic manipulation of TaRD21A expression, we establish its positive role in the regulation of wheat to WYMV resistance. Furthermore, our investigation shows that the TaRD21A-mediated plant antiviral response relies on the release of a small peptide catalyzed by TaRD21A protease activity. To counteract wheat resistance, WYMV-encoded nuclear inclusion protease-a (NIa) suppress TaRD21A activity to promote virus infection. In resistant cultivars, a natural variant of TaRD21A features a glycine-to-threonine substitution and this substitution enables the phosphorylation of threonine, thereby weakening the interaction between NIa and TaRD21A, reinforcing wheat resistance against WYMV. Our study not only unveils a WYMV resistance gene but also offers insights into the intricate mechanisms underpinning resistance against WYMV.

RALF22 promotes plant immunity and amplifies the Pep3 immune signal

Rapid alkalinization factors (RALFs) in plants have been reported to dampen pathogen-associated molecular pattern (PAMP)-triggered immunity via suppressing PAMP-induced complex formation between the pattern recognition receptor (PRR) and its co-receptor BAK1. However, the direct and positive role of RALFs in plant immunity remains largely unknown. Herein, we report the direct and positive roles of a typical RALF, RALF22, in plant immunity. RALF22 alone directly elicited a variety of typical immune responses and triggered resistance against the devastating necrotrophic fungal pathogen Sclerotinia sclerotiorum in a FERONIA (FER)-dependent manner. LORELEI (LRE)-like glycosylphosphatidylinositol (GPI)-anchored protein 1 (LLG1) and NADPH oxidase RBOHD were required for RALF22-elicited reactive oxygen species (ROS) generation. The mutation of cysteines conserved in the C terminus of RALFs abolished, while the constitutive formation of two disulfide bridges between these cysteines promoted the RALF22-elicited ROS production and resistance against S. sclerotiorum, demonstrating the requirement of these cysteines in the functions of RALF22 in plant immunity. Furthermore, RALF22 amplified the Pep3-induced immune signal by dramatically increasing the abundance of PROPEP3 transcript and protein. Supply with RALF22 induced resistance against S. sclerotiorum in Brassica crop plants. Collectively, our results reveal that RALF22 triggers immune responses and augments the Pep3-induced immune signal in a FER-dependent manner, and exhibits the potential to be exploited as an immune elicitor in crop protection.

Shining in the dark: the big world of small peptides in plants

Small peptides represent a subset of dark matter in plant proteomes. Through differential expression patterns and modes of action, small peptides act as important regulators of plant growth and development. Over the past 20 years, many small peptides have been identified due to technical advances in genome sequencing, bioinformatics, and chemical biology. In this article, we summarize the classification of plant small peptides and experimental strategies used to identify them as well as their potential use in agronomic breeding. We review the biological functions and molecular mechanisms of small peptides in plants, discuss current problems in small peptide research and highlight future research directions in this field. Our review provides crucial insight into small peptides in plants and will contribute to a better understanding of their potential roles in biotechnology and agriculture.

Rapid alkalinization factor: function, regulation, and potential applications in agriculture

Rapid alkalinization factor (RALF) is widespread throughout the plant kingdom and controls many aspects of plant life. Current studies on the regulatory mechanism underlying RALF function mainly focus on Arabidopsis, but little is known about the role of RALF in crop plants. Here, we systematically and comprehensively analyzed the relation between RALF family genes from five important crops and those in the model plant Arabidopsis thaliana. Simultaneously, we summarized the functions of RALFs in controlling growth and developmental behavior using conservative motifs as cues and predicted the regulatory role of RALFs in cereal crops. In conclusion, RALF has considerable application potential in improving crop yields and increasing economic benefits. Using gene editing technology or taking advantage of RALF as a hormone additive are effective way to amplify the role of RALF in crop plants.

Dietary Methionine Increased the Growth Performances and Immune Function of Partridge Shank Broilers after Challenged with Coccidia

The present study investigated the effects of methionine (Met) on growth, immune function, and antioxidant capacity in partridge shank broilers, which were treated with either an anticoccidial drug or a coccidia vaccine. Chickens were fed five graded levels of Met (0.33%, 0.39%, 0.45%, 0.51%, or 0.57%) for 21 days in combination with the drug or vaccine. The results revealed that an optimal level of Met supplementation (1) increased ADFI (average daily feed intake), ADG (average daily gain), and F/G values (feed-to-gain ratio), indicating improved production; (2) increased OPG levels (oocysts per gram feces), intestinal lesion scores, bursa of Fabricius and thymus indexes, and sIgA content; (3) improved GSH-Px activities, and increased content levels of T-protein, albumin, and urea nitrogen. In addition, birds in the anticoccidial drug group had higher final weights, higher ADFI and ADG values, as well as lower F/G values, compared with birds in the vaccine group, indicating that coccidia vaccine reduces the performance of broilers. In conclusion, we found that an optimal level of dietary Met improved the production of partridge shank broilers, and this result might be related to immune function and antioxidant capacity. Optimal levels of digestible Met in terms of production performance (ADG and F/G) and immune function (sIgA in ileum mucosa) in partridge shank broilers (1-21 days) were found to be 0.418, 0.451, and 0.451 of diet, respectively, when birds were given anticoccidial drug treatment, with corresponding figures of 0.444, 0.455, and 0.452% when the coccidia vaccine was administered.

The Essentials on microRNA-Encoded Peptides from Plants to Animals

Primary transcripts of microRNAs (pri-miRNAs) were initially defined as long non-coding RNAs that host miRNAs further processed by the microRNA processor complex. A few years ago, however, it was discovered in plants that pri-miRNAs actually contain functional open reading frames (sORFs) that translate into small peptides called miPEPs, for microRNA-encoded peptides. Initially detected in Arabidopsis thaliana and Medicago truncatula, recent studies have revealed the presence of miPEPs in other pri-miRNAs as well as in other species ranging from various plant species to animals. This suggests that miPEP numbers remain largely underestimated and that they could be a common signature of pri-miRNAs. Here we present the most recent advances in miPEPs research and discuss how their discovery has broadened our vision of the regulation of gene expression by miRNAs, and how miPEPs could be interesting tools in sustainable agriculture or the treatment of certain human diseases.

RGI-GOLVEN signaling promotes cell surface immune receptor abundance to regulate plant immunity

Plant immune responses must be tightly controlled for proper allocation of resources for growth and development. In plants, endogenous signaling peptides regulate developmental and growth‐related processes. Recent research indicates that some of these peptides also have regulatory functions in the control of plant immune responses. This classifies these peptides as phytocytokines as they show analogies with metazoan cytokines. However, the mechanistic basis for phytocytokine‐mediated regulation of plant immunity remains largely elusive. Here, we identify GOLVEN2 (GLV2) peptides as phytocytokines in Arabidopsis thaliana. GLV2 signaling enhances sensitivity of plants to elicitation with immunogenic bacterial elicitors and contributes to resistance against virulent bacterial pathogens. GLV2 is perceived by ROOT MERISTEM GROWTH FACTOR 1 INSENSITIVE (RGI) receptors. RGI mutants show reduced elicitor sensitivity and enhanced susceptibility to bacterial infection. RGI3 forms ligand‐induced complexes with the pattern recognition receptor (PRR) FLAGELLIN SENSITIVE 2 (FLS2), suggesting that RGIs are part of PRR signaling platforms. GLV2‐RGI signaling promotes PRR abundance independent of transcriptional regulation and controls plant immunity via a previously undescribed mechanism of phytocytokine activity.

RGI-GOLVEN signaling promotes cell surface immune receptor abundance to regulate plant immunity

Plant immune responses must be tightly controlled for proper allocation of resources for growth and development. In plants, endogenous signaling peptides regulate developmental and growth-related processes. Recent research indicates that some of these peptides also have regulatory functions in the control of plant immune responses. This classifies these peptides as phytocytokines as they show analogies with metazoan cytokines. However, the mechanistic basis for phytocytokine-mediated regulation of plant immunity remains largely elusive. Here, we identify GOLVEN2 (GLV2) peptides as phytocytokines in Arabidopsis thaliana. GLV2 signaling enhances sensitivity of plants to elicitation with immunogenic bacterial elicitors and contributes to resistance against virulent bacterial pathogens. GLV2 is perceived by ROOT MERISTEM GROWTH FACTOR 1 INSENSITIVE (RGI) receptors. RGI mutants show reduced elicitor sensitivity and enhanced susceptibility to bacterial infection. RGI3 forms ligand-induced complexes with the pattern recognition receptor (PRR) FLAGELLIN SENSITIVE 2 (FLS2), suggesting that RGIs are part of PRR signaling platforms. GLV2-RGI signaling promotes PRR abundance independent of transcriptional regulation and controls plant immunity via a previously undescribed mechanism of phytocytokine activity.

Small signaling peptides mediate plant adaptions to abiotic environmental stress

Peptide-receptor complexes activate distinct downstream regulatory networks to mediate plant adaptions to abiotic environmental stress. Plants are constantly exposed to various adverse environmental factors; thus they must adjust their growth accordingly. Plants recruit small secretory peptides to adapt to these detrimental environments. These small peptides, which are perceived by their corresponding receptors and/or co-receptors, act as local- or long-distance mobile signaling molecules to establish cell-to-cell regulatory networks, resulting in optimal cellular and physiological outputs. In this review, we highlight recent advances on the regulatory role of small peptides in plant abiotic responses and nutrients signaling.

Virtual 2D mapping of the viral proteome reveals host-specific modality distribution of molecular weight and isoelectric point

A proteome-wide study of the virus kingdom based on 1.713 million protein sequences from 19,128 virus proteomes was conducted to construct an overall proteome map of the virus kingdom. Viral proteomes encode an average of 386.214 amino acids per protein with the variation in the number of protein-coding sequences being host-specific. The proteomes of viruses of fungi hosts (882.464) encoded the greatest number of amino acids, while the viral proteome of bacterial host (210.912) encoded the smallest number of amino acids. Viral proteomes were found to have a host-specific amino acid composition. Leu (8.556%) was the most abundant and Trp (1.274%) the least abundant amino acid in the collective proteome of viruses. Viruses were found to exhibit a host-dependent molecular weight and isoelectric point of encoded proteins. The isoelectric point (pI) of viral proteins was found in the acidic range, having an average pI of 6.89. However, the pI of viral proteins of algal (pI 7.08) and vertebrate (pI 7.09) hosts was in the basic range. The virtual 2D map of the viral proteome from different hosts exhibited host-dependent modalities. The virus proteome from algal hosts and archaea exhibited a bimodal distribution of molecular weight and pI, while the virus proteome of bacterial host exhibited a trimodal distribution, and the virus proteome of fungal, human, land plants, invertebrate, protozoa, and vertebrate hosts exhibited a unimodal distribution.

Emerging roles of pathogen-secreted host mimics in plant disease development

Plant pathogens and parasites use multiple virulence factors to successfully infect plants. While most plant-pathogen interaction studies focus on pathogen effectors and their functions in suppressing plant immunity or interfering with normal cellular processes, other virulence factors likely also contribute. Here we highlight another important strategy used by pathogens to promote virulence: secretion of mimics of host molecules, including peptides, phytohormones, and small RNAs, which play diverse roles in plant development and stress responses. Pathogen-secreted mimics hijack the host endogenous signaling pathways, thereby modulating host cellular functions to the benefit of the pathogen and promoting infection. Understanding the mechanisms of pathogen-secreted host mimics will expand our knowledge of host-pathogen coevolution and interactions, while providing new targets for plant disease control.

MAMP and DAMP signaling contributes resistance to Fusarium graminearum in Arabidopsis

Plants perceive externally produced microbe-associated molecular patterns (MAMPs) and endogenously produced danger-associated molecular patterns (DAMPs) to activate inducible immunity. While several inducible immune responses have been observed during Fusarium graminearum infection, the identity of the signaling pathways involved is only partly known. We screened 227 receptor kinase and innate immune response genes in Arabidopsis to identify nine genes with a role in F. graminearum resistance. Resistance-promoting genes included the chitin receptors LYK5 and CERK1, and the reactive oxygen species (ROS)-producing NADPH oxidase RbohF, which were required for full inducible immune responses during infection. Two of the genes identified in our screen, APEX and the PAMP-induced peptide 1 (PIP1) DAMP receptor RLK7, repressed F. graminearum resistance. Both RbohF and RLK7 were required for full chitin-induced immune responses and PIP1 precursor expression was induced by chitin and F. graminearum infection. Together, this indicates that F. graminearum resistance is mediated by MAMP and DAMP signaling pathways and that chitin-induced signaling is enhanced by PIP1 perception and ROS production.

Phytohormone signaling and crosstalk in regulating drought stress response in plants

Phytohormones are ubiquitously involved in plant biological processes and regulate cellular signaling pertaining to unheralded environmental cues, such as salinity, drought, extreme temperature and nutrient deprivation. The association of phytohormones to nearly all the fundamental biological processes epitomizes the phytohormone syndicate as a candidate target for consideration during engineering stress endurance in agronomically important crops. The drought stress response is essentially driven by phytohormones and their intricate network of crosstalk, which leads to transcriptional reprogramming. This review is focused on the pivotal role of phytohormones in water deficit responses, including their manipulation for mitigating the effect of the stressor. We have also discussed the inherent complexity of existing crosstalk accrued among them during the progression of drought stress, which instigates the tolerance response. Therefore, in this review, we have highlighted the role and regulatory aspects of various phytohormones, namely abscisic acid, auxin, gibberellic acid, cytokinin, brassinosteroid, jasmonic acid, salicylic acid, ethylene and strigolactone, with emphasis on drought stress tolerance.

The sequenced genomes of non-flowering land plants reveal the innovative evolutionary history of peptide signaling

An understanding of land plant evolution is a prerequisite for in-depth knowledge of plant biology. Here we extract and explore information hidden in the increasing number of sequenced plant genomes, from bryophytes to angiosperms, to elucidate a specific biological question - how peptide signaling evolved. To conquer land and cope with changing environmental conditions, plants have gone through transformations that must have required innovations in cell-to-cell communication. We discuss peptides mediating endogenous and exogenous changes by interaction with receptors activating intracellular molecular signaling. Signaling peptides were discovered in angiosperms and operate in tissues and organs such as flowers, seeds, vasculature, and 3D meristems that are not universally conserved across land plants. Nevertheless, orthologs of angiosperm peptides and receptors have been identified in non-angiosperms. These discoveries provoke questions regarding co-evolution of ligands and their receptors, and whether de novo interactions in peptide signaling pathways may have contributed to generate novel traits in land plants. The answers to such questions will have profound implications for the understanding of the evolution of cell-to-cell communication and the wealth of diversified terrestrial plants. Under this perspective we have generated, analyzed, and reviewed phylogenetic, genomic, structural, and functional data to elucidate the evolution of peptide signaling.

Advances and perspectives in discovery and functional analysis of small secreted proteins in plants

Small secreted proteins (SSPs) are less than 250 amino acids in length and are actively transported out of cells through conventional protein secretion pathways or unconventional protein secretion pathways. In plants, SSPs have been found to play important roles in various processes, including plant growth and development, plant response to abiotic and biotic stresses, and beneficial plant-microbe interactions. Over the past 10 years, substantial progress has been made in the identification and functional characterization of SSPs in several plant species relevant to agriculture, bioenergy, and horticulture. Yet, there are potentially a lot of SSPs that have not been discovered in plant genomes, which is largely due to limitations of existing computational algorithms. Recent advances in genomics, transcriptomics, and proteomics research, as well as the development of new computational algorithms based on machine learning, provide unprecedented capabilities for genome-wide discovery of novel SSPs in plants. In this review, we summarize known SSPs and their functions in various plant species. Then we provide an update on the computational and experimental approaches that can be used to discover new SSPs. Finally, we discuss strategies for elucidating the biological functions of SSPs in plants.

The novel peptide NbPPI1 identified from Nicotiana benthamiana triggers immune responses and enhances resistance against Phytophthora pathogens

In plants, recognition of small secreted peptides, such as damage/danger-associated molecular patterns (DAMPs), regulates diverse processes, including stress and immune responses. Here, we identified an SGPS (Ser-Gly-Pro-Ser) motif-containing peptide, Nicotiana tabacum NtPROPPI, and its two homologs in Nicotiana benthamiana, NbPROPPI1 and NbPROPPI2. Phytophthora parasitica infection and salicylic acid (SA) treatment induced NbPROPPI1/2 expression. Moreover, SignalP predicted that the 89-amino acid NtPROPPI includes a 24-amino acid N-terminal signal peptide and NbPROPPI1/2-GFP fusion proteins were mainly localized to the periplasm. Transient expression of NbPROPPI1/2 inhibited P. parasitica colonization, and NbPROPPI1/2 knockdown rendered plants more susceptible to P. parasitica. An eight-amino-acid segment in the NbPROPPI1 C-terminus was essential for its immune function and a synthetic 20-residue peptide, NbPPI1, derived from the C-terminus of NbPROPPI1 provoked significant immune responses in N. benthamiana. These responses led to enhanced accumulation of reactive oxygen species, activation of mitogen-activated protein kinases, and up-regulation of the defense genes Flg22-induced receptor-like kinase (FRK) and WRKY DNA-binding protein 33 (WRKY33). The NbPPI1-induced defense responses require Brassinosteroid insensitive 1-associated receptor kinase 1 (BAK1). These results suggest that NbPPI1 functions as a DAMP in N. benthamiana; this novel DAMP provides a potentially useful target for improving plant resistance to Pytophthora pathogens.

Comprehensive analysis of structural, functional, and evolutionary dynamics of Leucine Rich Repeats-RLKs in Thinopyrum elongatum

Leucine Rich Repeats-receptor-like protein kinases (LRR-RLKs) regulate several critical biological processes ranging from growth and development to stress response. Thinopyrum elongatum harbours many desirable traits such as biotic and abiotic stress resistance and therefore commonly used by wheat breeders. In the present investigation, in-silico analysis of LRR-RLKs yielded 589 genes of which 431 were membrane surface RLKs and 158 were receptor like cytoplasmic kinases. An insight into the gene and protein structure revealed quite a conserved nature of these proteins within subgroups. A large expansion in LRR-RLKs was due to tandem and segmental duplication event. Maximum number of tandem and segmentally duplicated pairs was observed in LRR-VI and LRR-XII subfamily, respectively. Furthermore, syntenic analyses revealed that chromosome 6 harboured more (48) tandem duplicated genes while chromosome 7 possessed more (47) segmentally duplicated genes. A detailed analysis about the gene duplication events coupled with expression profiles during Fusarium graminearum infection and water deficiency unravelled the expansion of the gene family with sub functionalization and neofunctionalization. Interaction network analysis showed that LRR-RLKs can heterodimerize upon ligand binding to perform various plant functional attributes.

Identification of Ipomoea batatas anti-cancer peptide (IbACP)-responsive genes in sweet potato leaves

IbACP, Ipomoea batatas anti-cancer peptide, a sixteen-amino-acid peptide isolated from sweet potato leaves, is capable of mediating a rapid alkalinization of growth media in plant suspension cells. However, the biological roles of IbACP as a defense peptide have not been studied. The objective of this study was to investigate the effect of IbACP on the accumulation of reactive oxygen species (ROS) and the expression of the defense-related genes. IbACP treatment of sweet potato leaves resulted in marked accumulation of both superoxide ion (O₂^-) and hydrogen peroxide (H₂O₂). The activity of peroxidase (POD) was significantly enhanced by IbACP treatment, suggesting that high levels of POD antioxidant activity may be used to scavenge the excess H₂O₂ in sweet potato plants. The IbACP-related genes were identified by suppression subtractive hybridization (SSH), and were then classified and assigned to the following categories: defense, development, metabolism, signaling, gene expression, and abiotic stress. H₂O₂ acts as a second messenger for gene activation in some of the IbACP-triggered gene expressions. These results demonstrated that IbACP is part of an integrated strategy for genetic regulation in sweet potato. Our work highlights the function of IbACP and its potential use for enhancing stress tolerance in sweet potato, in an effort to improve our understanding of defense-response mechanisms.

Virtual 2-D map of the fungal proteome

The molecular weight and isoelectric point (pI) of the proteins plays important role in the cell. Depending upon the shape, size, and charge, protein provides its functional role in different parts of the cell. Therefore, understanding to the knowledge of their molecular weight and charges is (pI) is very important. Therefore, we conducted a proteome-wide analysis of protein sequences of 689 fungal species (7.15 million protein sequences) and construct a virtual 2-D map of the fungal proteome. The analysis of the constructed map revealed the presence of a bimodal distribution of fungal proteomes. The molecular mass of individual fungal proteins ranged from 0.202 to 2546.166 kDa and the predicted isoelectric point (pI) ranged from 1.85 to 13.759 while average molecular weight of fungal proteome was 50.98 kDa. A non-ribosomal peptide synthase (RFU80400.1) found in Trichoderma arundinaceum was identified as the largest protein in the fungal kingdom. The collective fungal proteome is dominated by the presence of acidic rather than basic pI proteins and Leu is the most abundant amino acid while Cys is the least abundant amino acid. Aspergillus ustus encodes the highest percentage (76.62%) of acidic pI proteins while Nosema ceranae was found to encode the highest percentage (66.15%) of basic pI proteins. Selenocysteine and pyrrolysine amino acids were not found in any of the analysed fungal proteomes. Although the molecular weight and pI of the protein are of enormous important to understand their functional roles, the amino acid compositions of the fungal protein will enable us to understand the synonymous codon usage in the fungal kingdom. The small peptides identified during the study can provide additional biotechnological implication.

Full-Length Transcriptome Analysis of Plasmodium falciparum by Single-Molecule Long-Read Sequencing

Malaria, an infectious disease caused by Plasmodium parasites, still accounts for amounts of deaths annually in last decades. Despite the significance of Plasmodium falciparum as a model organism of malaria parasites, our understanding of gene expression of this parasite remains largely elusive since lots of progress on its genome and transcriptome are based on assembly with short sequencing reads. Herein, we report the new version of transcriptome dataset containing all full-length transcripts over the whole asexual blood stages by adopting a full-length sequencing approach with optimized experimental conditions of cDNA library preparation. We have identified a total of 393 alternative splicing (AS) events, 3,623 long non-coding RNAs (lncRNAs), 1,555 alternative polyadenylation (APA) events, 57 transcription factors (TF), 1,721 fusion transcripts in P. falciparum. Furthermore, the shotgun proteome was performed to validate the full-length transcriptome of P. falciparum. More importantly, integration of full-length transcriptomic and proteomic data identified 160 novel small proteins in lncRNA regions. Collectively, this full-length transcriptome dataset with high quality and accuracy and the shotgun proteome analyses shed light on the complex gene expression in malaria parasites and provide a valuable resource for related functional and mechanistic researches on P. falciparum genes.

A novel allele of the Arabidopsis thaliana MACPF protein CAD1 results in deregulated immune signaling

Immune recognition in plants is governed by two major classes of receptors: pattern recognition receptors (PRRs) and nucleotide-binding leucine-rich repeat receptors (NLRs). Located at the cell surface, PRRs bind extracellular ligands originating from microbes (indicative of "non-self") or damaged plant cells (indicative of "infected-self"), and trigger signaling cascades to protect against infection. Located intracellularly, NLRs sense pathogen-induced physiological changes and trigger localized cell death and systemic resistance. Immune responses are under tight regulation in order to maintain homeostasis and promote plant health. In a forward-genetic screen to identify regulators of PRR-mediated immune signaling, we identified a novel allele of the membrane-attack complex and perforin (MACPF)-motif containing protein CONSTITUTIVE ACTIVE DEFENSE 1 (CAD1) resulting from a missense mutation in a conserved N-terminal cysteine. We show that cad1-5 mutants display deregulated immune signaling and symptoms of autoimmunity dependent on the lipase-like protein ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1), suggesting that CAD1 integrity is monitored by the plant immune system. We further demonstrate that CAD1 localizes to both the cytosol and plasma membrane using confocal microscopy and subcellular fractionation. Our results offer new insights into immune homeostasis and provide tools to further decipher the intriguing role of MACPF proteins in plants.

The RGF/GLV/CLEL Family of Short Peptides Evolved Through Lineage-Specific Losses and Diversification and Yet Conserves Its Signaling Role Between Vascular Plants and Bryophytes

Short secreted plant peptides act as key signaling molecules and control a plethora of developmental and physiological processes. The ROOT GROWTH FACTOR (RGF)/GOLVEN (GLV)/CLE-Like (CLEL) family of peptides was discovered to be involved in root development in Arabidopsis thaliana. In contrast to active research efforts, which have been revealing receptors and downstream signaling components, little attention has been paid to evolutionary processes that shaped the RGF signaling system as we know it in angiosperms today. As a first step toward understanding how RGF signaling emerged and evolved, this study aimed to elucidate the phylogenetic distribution and functional conservation of RGF-like sequences. Using publicly available, genome and transcriptome data, RGF-like sequences were searched in 27 liverworts, 22 mosses, 8 hornworts, 23 lycophytes, 23 ferns, 38 gymnosperms, and 8 angiosperms. This led to the identification of more than four hundreds of RGF-like sequences in all major extant land plant lineages except for hornworts. Sequence comparisons within and between taxonomic groups identified lineage-specific characters. Notably, one of the two major RGF subgroups, represented by A. thaliana RGF6/GLV1/CLEL6, was found only in vascular plants. This subgroup, therefore, likely emerged in a common ancestor of vascular plants after its divergence from bryophytes. In bryophytes, our results infer independent losses of RGF-like sequences in mosses and hornworts. On the other hand, a single, highly similar RGF-like sequence is conserved in liverworts, including Marchantia polymorpha, a genetically tractable model species. When constitutively expressed, the M. polymorpha RGF-like sequence (MpRGF) affected plant development and growth both in A. thaliana and M. polymorpha. This suggests that MpRGF can exert known RGF-like effects and that MpRGF is under transcriptional control so that its potent activities are precisely controlled. These data suggest that RGFs are conserved as signaling molecules in both vascular plants and bryophytes and that lineage-specific diversification has increased sequence variations of RGFs. All together, our findings form a basis for further studies into RGF peptides and their receptors, which will contribute to our understandings of how peptide signaling pathways evolve.

Differential activities of maize plant elicitor peptides as mediators of immune signaling and herbivore resistance

Plant elicitor peptides (Peps) are conserved regulators of defense responses and models for the study of damage-associated molecular pattern-induced immunity. Although present as multigene families in most species, the functional relevance of these multigene families remains largely undefined. While Arabidopsis Peps appear largely redundant in function, previous work examining Pep-induced responses in maize (Zm) implied specificity of function. To better define the function of individual ZmPeps and their cognate receptors (ZmPEPRs), activities were examined by assessing changes in defense-associated phytohormones, specialized metabolites and global gene expression patterns, in combination with heterologous expression assays and analyses of CRISPR/Cas9-generated knockout plants. Beyond simply delineating individual ZmPep and ZmPEPR activities, these experiments led to a number of new insights into Pep signaling mechanisms. ZmPROPEP and other poaceous precursors were found to contain multiple active Peps, a phenomenon not previously observed for this family. In all, seven new ZmPeps were identified and the peptides were found to have specific activities defined by the relative magnitude of their response output rather than by uniqueness. A striking correlation was observed between individual ZmPep-elicited changes in levels of jasmonic acid and ethylene and the magnitude of induced defense responses, indicating that ZmPeps may collectively regulate immune output through rheostat-like tuning of phytohormone levels. Peptide structure-function studies and ligand-receptor modeling revealed structural features critical to the function of ZmPeps and led to the identification of ZmPep5a as a potential antagonist peptide able to competitively inhibit the activity of other ZmPeps, a regulatory mechanism not previously observed for this family.

Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives

For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.

Plant Immune Mechanisms: From Reductionistic to Holistic Points of View

After three decades of the amazing progress made on molecular studies of plant-microbe interactions (MPMI), we have begun to ask ourselves "what are the major questions still remaining?" as if the puzzle has only a few pieces missing. Such an exercise has ultimately led to the realization that we still have many more questions than answers. Therefore, it would be an impossible task for us to project a coherent "big picture" of the MPMI field in a single review. Instead, we provide our opinions on where we would like to go in our research as an invitation to the community to join us in this exploration of new MPMI frontiers.

Physico-chemical characterization and topological analysis of pathogenesis-related proteins from Arabidopsis thaliana and Oryza sativa using in-silico approaches

Plants are constantly under the threat of various biotic and abiotic stress conditions and to overcome these stresses, they have evolved multiple mechanisms including systematic accumulation of different phytohormones, phytoalexins and pathogenesis related (PR) proteins. PR proteins are cluster of proteins with low molecular weight which get incited in plants under different stresses. In this paper, in-silico approaches are used to compare the physico-chemical properties of 6 PR proteins (PR1, PR2, PR5, PR9, PR10, PR12) of Arabidopsis thaliana and Oryza sativa. Topological analysis revealed the presence of transmembrane localization of PR2 and absence of transmembrane domain in PR10 of both model plants studied. Amino acid composition shows the dominance of small aliphatic amino acids i.e. alanine, glycine and serine in both plants studied. These results highlights the similarities and differences between PRs of both model plants, which provides clue towards their diversified roles in plants.

Wheat Encodes Small, Secreted Proteins That Contribute to Resistance to Septoria Tritici Blotch

During plant-pathogen interactions, pathogens secrete many rapidly evolving, small secreted proteins (SSPs) that can modify plant defense and permit pathogens to colonize plant tissue. The fungal pathogen Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB), one of the most important foliar diseases of wheat, globally. Z. tritici is a strictly apoplastic pathogen that can secrete numerous proteins into the apoplast of wheat leaves to promote infection. We sought to determine if, during STB infection, wheat also secretes small proteins into the apoplast to mediate the recognition of pathogen proteins and/or induce defense responses. To explore this, we developed an SSP-discovery pipeline to identify small, secreted proteins from wheat genomic data. Using this pipeline, we identified 6,998 SSPs, representing 2.3% of all proteins encoded by the wheat genome. We then mined a microarray dataset, detailing a resistant and susceptible host response to STB, and identified 141 Z. tritici- responsive SSPs, representing 4.7% of all proteins encoded by Z. tritici - responsive genes. We demonstrate that a subset of these SSPs have a functional signal peptide and can interact with Z. tritici SSPs. Transiently silencing two of these wheat SSPs using virus-induced gene silencing (VIGS) shows an increase in susceptibility to STB, confirming their role in defense against Z. tritici.

The role of peptides cleaved from protein precursors in eliciting plant stress reactions

As sessile organisms, plants are exposed to diverse abiotic and biotic stresses, and thus have developed complex signaling mechanisms that orchestrate multiple stress responses. Plant peptides have recently emerged as key signaling molecules of stress responses, not only to mechanical wounding and pathogen infection but also to nutrient imbalance, drought and high salinity. The currently identified stress-related signaling peptides in plants are derived from proteolytic processing of protein precursors. Here, we review these protein-derived peptides and the evidence for their functions in stress signaling. We recommend potential research directions that could clarify their roles in stress biology, and propose possible crosstalk with regard to the physiological outcome. The stress-centric perspective allows us to highlight the crucial roles of peptides in regulating the dynamics of stress physiology. Inspired by historic and recent findings, we review how peptides initiate complex molecular interactions to coordinate biotic and abiotic stress responses in plants.

The Lifecycle of the Plant Immune System

Throughout their life span, plants confront an endless barrage of pathogens and pests. To successfully defend against biotic threats, plants have evolved a complex immune system responsible for surveillance, perception, and the activation of defense. Plant immunity requires multiple signaling processes, the outcome of which vary according to the lifestyle of the invading pathogen(s). In short, these processes require the activation of host perception, the regulation of numerous signaling cascades, and transcriptome reprograming, all of which are highly dynamic in terms of temporal and spatial scales. At the same time, the development of a single immune event is subjective to the development of plant immune system, which is co-regulated by numerous processes, including plant ontogenesis and the host microbiome. In total, insight into each of these processes provides a fuller understanding of the mechanisms that govern plant-pathogen interactions. In this review, we will discuss the "lifecycle" of plant immunity: the development of individual events of defense, including both local and distal processes, as well as the development and regulation of the overall immune system by ontogenesis regulatory genes and environmental microbiota. In total, we will integrate the output of recent discoveries and theories, together with several hypothetical models, to present a dynamic portrait of plant immunity.