Role of small RNAs in host-microbe interactions

Identification of Arabidopsis thaliana small RNAs responsive to the fungal pathogen Botrytis cinerea at an early stage of interaction

In plants, small RNAs (sRNAs), mainly microRNAs (miRNAs) and small interfering RNAs (siRNAs), have been described as key regulators of plant development, growth, and abiotic and biotic responses. Despite reports indicating the involvement of certain sRNAs in regulating the interaction between Botrytis cinerea (a major necrotrophic fungal phytopathogen) and host plants, there remains a lack of analysis regarding the potential regulatory roles of plant sRNAs during early stages of the interaction despite early immune responses observed then during infection. We present the first transcriptome-wide analysis of small RNA expression on the early interaction between the necrotrophic fungus Botrytis cinerea and the model plant Arabidopsis thaliana. We found that evolutionary conserved A. thaliana miRNAs were the sRNAs that accumulated the most in the presence of B. cinerea. The upregulation of miR167, miR159 and miR319 was of particular interest because these, together with their target transcripts, are involved in the fine regulation of the plant hormone signaling pathways. We also describe that miR173, which triggers the production of secondary siRNAs from TAS1 and TAS2 loci, as well as secondary siRNAs derived from these loci, is upregulated in response to B. cinerea. Thus, at an early stage of the interaction there are transcriptional changes of sRNA-guided silencing pathway genes and of a subset of sRNAs that targeted genes from the PPR gene superfamily, and these may be important mechanisms regulating the interaction between A. thaliana and B. cinerea. This work provides the basis for a better understanding of the regulation mediated by sRNAs during early B. cinerea-plant interaction and may help in the development of more effective strategies for its control.

miR394 modulates brassinosteroid signaling to regulate hypocotyl elongation in Arabidopsis

The interplay between microRNAs (miRNAs) and phytohormones allows plants to integrate multiple internal and external signals to optimize their survival of different environmental conditions. Here, we report that miR394 and its target gene LEAF CURLING RESPONSIVENESS (LCR), which are transcriptionally responsive to BR, participate in BR signaling to regulate hypocotyl elongation in Arabidopsis thaliana. Phenotypic analysis of various transgenic and mutant lines revealed that miR394 negatively regulates BR signaling during hypocotyl elongation, whereas LCR positively regulates this process. Genetically, miR394 functions upstream of BRASSINOSTEROID INSENSITIVE2 (BIN2), BRASSINAZOLEs RESISTANT1 (BZR1), and BRI1-EMS-SUPPRESSOR1 (BES1), but interacts with BRASSINOSTEROID INSENSITIVE1 (BRI1) and BRI1 SUPRESSOR PROTEIN (BSU1). RNA-sequencing analysis suggested that miR394 inhibits BR signaling through BIN2, as miR394 regulates a significant number of genes in common with BIN2. Additionally, miR394 increases the accumulation of BIN2 but decreases the accumulation of BZR1 and BES1, which are phosphorylated by BIN2. MiR394 also represses the transcription of PACLOBUTRAZOL RESISTANCE1/5/6 and EXPANSIN8, key genes that regulate hypocotyl elongation and are targets of BZR1/BES1. These findings reveal a new role for a miRNA in BR signaling in Arabidopsis.

Identification of microRNAs and their target genes associated with chasmogamous and cleistogamous flower development in Viola prionantha

MAIN CONCLUSION

Differentially expressed microRNAs were found associated with the development of chasmogamous and cleistogamous flowers in Viola prionantha, revealing potential roles of microRNAs in the developmental evolution of dimorphic flowers. In Viola prionantha, chasmogamous (CH) flowers are induced by short daylight, while cleistogamous (CL) flowers are triggered by long daylight. How environmental factors and microRNAs (miRNAs) affect dimorphic flower formation remains unknown. In this study, small RNA sequencing was performed on CH and CL floral buds at different developmental stages in V. prionantha, differentially expressed miRNAs (DEmiRNAs) were identified, and their target genes were predicted. In CL flowers, Viola prionantha miR393 (vpr-miR393a/b) and vpr-miRN3366 were highly expressed, while in CH flowers, vpr-miRN2005, vpr-miR172e-2, vpr-miR166m-3, vpr-miR396f-2, and vpr-miR482d-2 were highly expressed. In the auxin-activated signaling pathway, vpr-miR393a/b and vpr-miRN2005 could target Vpr-TIR1/AFB and Vpr-ARF2, respectively, and other DEmiRNAs could target genes involved in the regulation of transcription, e.g., Vpr-AP2-7. Moreover, Vpr-UFO and Vpr-YAB5, the main regulators in petal and stamen development, were co-expressed with Vpr-TIR1/AFB and Vpr-ARF2 and showed lower expression in CL flowers than in CH flowers. Some V. prionantha genes relating to the stress/defense responses were co-expressed with Vpr-TIR1/AFB, Vpr-ARF2, and Vpr-AP2-7 and highly expressed in CL flowers. Therefore, in V. prionantha, CH-CL flower development may be regulated by the identified DEmiRNAs and their target genes, thus providing the first insight into the formation of dimorphic flowers in Viola.

The grapevine miR827a regulates the synthesis of stilbenes by targeting VqMYB14 and gives rise to susceptibility in plant immunity

Grapevine (Vitis vinifera L.) is an economically important fruit crop cultivated worldwide. In China, grapevine cultivation is very extensive, and a few Vitis grapes have excellent pathogen and stress resistance, but the molecular mechanisms underlying the grapevine response to stress remain unclear. In this study, a microRNA (miRNA; miR827a), which negatively regulates its target gene VqMYB14, a key regulatory role in the synthesis of stilbenes, was identified in Vitis quinquangularis (V. quinquangularis) using transcriptome sequencing. Using overexpression and silencing approaches, we found that miR827a regulates the synthesis of stilbenes by targeting VqMYB14. We used flagellin N-terminal 22-amino-acid peptide (flg22), the representative elicitor in plant basal immunity, as the elicitor to verify whether miR827a is involved in the basal immunity of V. quinquangularis. Furthermore, the promoter activity of miR827a was alleviated in transgenic grape protoplasts and Arabidopsis thaliana following treatment with flg22 and Pseudomonas syringae pv. Tomato DC3000 (Pst DC3000), respectively. In addition, yeast one-hybrid and dual luciferase reporter assay revealed that the ethylene transcription factor VqERF057 acted as a key regulator in the inhibition of miR827a transcription. These results will contribute to the understanding of the biological functions of miR827a in grapevine and clarify the molecular mechanism of the interaction between miR827a and VqMYB14.

Potato miR394 targets StA/N-INVE and StLCR to negatively regulate late blight resistance

MicroRNAs (miRNAs) are small noncoding RNAs in eukaryotes. Plant endogenous miRNAs play pivotal roles in regulating plant development and defense responses. MicroRNA394 (miR394) has been reported to regulate plant development, abiotic stresses and defense responses. Previous reports showed that miR394 responded to P. infestans inoculation in potato, indicating that miR394 may be involved in defense responses. In this study, we further investigated its role in potato defense against P. infestans. Stable expression of miR394 in tobacco and potato enhances the susceptibility to P. infestans, which is accompanied with the reduced accumulation of ROS and down-regulation of the PTI (pattern-triggered immunity) marker genes. Besides well-known target StLCR, miR394 also targets StA/N-INVE, which encodes a chloroplast Alkaline/Neutral Invertases (A/N-INVE). Both StLCR and StA/N-INVE positively regulate late blight resistance, while miR394 degrades them. Interestingly, StA/N-INVE is located in the chloroplast, indicating that miR394 may manipulate chloroplast immunity. Degradation of StA/N-INVE may affect the chloroplast function and hence lead to the compromised ROS (reactive oxygen species) burst and reduced retrograde signaling from the chloroplast to the nucleus and cytoplasm. In summary, this study provides new information that miR394 targets and degrades StA/N-INVE and StLCR, which are positive regulators, to enhance potato susceptibility to P. infestans.

Identification of Tomato microRNAs in Late Response to Trichoderma atroviride

The tomato (Solanum lycopersicum) is an important crop worldwide and is considered a model plant to study stress responses. Small RNAs (sRNAs), 21-24 nucleotides in length, are recognized as a conserved mechanism for regulating gene expression in eukaryotes. Plant endogenous sRNAs, such as microRNA (miRNA), have been involved in disease resistance. High-throughput RNA sequencing was used to analyze the miRNA profile of the aerial part of 30-day-old tomato plants after the application of the fungus Trichoderma atroviride to the seeds at the transcriptional memory state. Compared to control plants, ten differentially expressed (DE) miRNAs were identified in those inoculated with Trichoderma, five upregulated and five downregulated, of which seven were known (miR166a, miR398-3p, miR408, miR5300, miR6024, miR6027-5p, and miR9471b-3p), and three were putatively novel (novel miR257, novel miR275, and novel miR1767). miRNA expression levels were assessed using real-time quantitative PCR analysis. A plant sRNA target analysis of the DE miRNAs predicted 945 potential target genes, most of them being downregulated (84%). The analysis of KEGG metabolic pathways showed that most of the targets harbored functions associated with plant-pathogen interaction, membrane trafficking, and protein kinases. Expression changes of tomato miRNAs caused by Trichoderma are linked to plant defense responses and appear to have long-lasting effects.

Identification of nitric oxide mediated defense signaling and its microRNA mediated regulation during Phytophthora capsici infection in black pepper

Nitric oxide plays a significant role in the defense signaling during pathogen interaction in plants. Quick wilt disease is a devastating disease of black pepper, and leads to sudden mortality of pepper vines in plantations. In this study, the role of nitric oxide was studied during Phytophthora capsici infection in black pepper variety Panniyur-1. Nitric oxide was detected from the different histological sections of P. capsici infected leaves. Furthermore, the genome-wide transcriptome analysis characterized typical domain architect and structural features of nitrate reductase (NR) and nitric oxide associated 1 (NOA1) gene that are involved in nitric oxide biosynthesis in black pepper. Despite the upregulation of nitrate reductase (Pn1_NR), a reduced expression of Pn1_NOA1 was detected in the P. capsici infected black pepper leaf. Subsequent sRNAome-assisted in silico analysis revealed possible microRNA mediated regulation of Pn1_NOA mRNAs. Furthermore, sRNA/miRNA mediated cleavage on Pn1_NOA1 mRNA was validated through modified 5' RLM RACE experiments. Several hormone-responsive cis-regulatory elements involved in stress response was detected from the promoter regions of Pn_NOA1, Pn_NR1 and Pn_NR2 genes. Our results revealed the role of nitric oxide during stress response of P. capsici infection in black pepper, and key genes involved in nitric oxide biosynthesis and their post-transcriptional regulatory mechanisms.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01414-z.

Trichoderma harzianum Cellulase Gene thph2 Affects Trichoderma Root Colonization and Induces Resistance to Southern Leaf Blight in Maize

Trichoderma, widely distributed all over the world, is commonly found in soil and root ecosystems. It is a group comprising beneficial fungi that improve plant disease resistance and promote plant growth. Studies have shown that Trichoderma cellulases can also improve plant disease resistance. Based on previous studies, we reported that a C6 zinc finger protein (Thc6) regulates two cellulase genes, thph1 and thph2, to induce ISR responses in plants. Therefore, in this study, we focused on the role of thph2 in the colonization of maize roots by T. harzianum and the induction of systemic resistance against southern leaf blight. The results showed that thph2 had a positive regulatory effect on the Trichoderma colonization of maize roots. After the root was treated with Trichoderma, the leaf defense genes AOS, LOX5, HPL, and OPR1 were expressed to resist the attack of Cochliobolus heterostrophus. The pure Thph2 protein also resulted in a similar induction activity of the AOS, LOX5, HPL, and OPR1 expression in maize roots, further demonstrating that thph2 can induce plant defense responses and that signal transduction occurs mainly through the JA signaling pathway.

Osa-miR11117 Targets OsPAO4 to Regulate Rice Immunity against the Blast Fungus Magnaporthe oryzae

The intricate regulatory process governing rice immunity against the blast fungus Magnaporthe oryzae remains a central focus in plant-pathogen interactions. In this study, we investigated the important role of Osa-miR11117, an intergenic microRNA, in regulating rice defense mechanisms. Stem-loop qRT-PCR analysis showed that Osa-miR11117 is responsive to M. oryzae infection, and overexpression of Osa-miR11117 compromises blast resistance. Green fluorescent protein (GFP)-based reporter assay indicated OsPAO4 is one direct target of Osa-miR11117. Furthermore, qRT-PCR analysis showed that OsPAO4 reacts to M. oryzae infection and polyamine (PA) treatment. In addition, OsPAO4 regulates rice resistance to M. oryzae through the regulation of PA accumulation and the expression of the ethylene (ETH) signaling genes. Taken together, these results suggest that Osa-miR11117 is targeting OsPAO4 to regulate blast resistance by adjusting PA metabolism and ETH signaling pathways.

Osa-miR162a Enhances the Resistance to the Brown Planthopper via α-Linolenic Acid Metabolism in Rice (Oryza sativa)

The brown planthopper (BPH) is the most serious pest causing yield losses in rice. MicroRNAs (miRNAs) are emerging as key modulators of plant-pest interactions. In the study, we found that osa-miR162a is induced in response to BPH attack in the seedling stage and tunes rice resistance to the BPH via the α-linolenic acid metabolism pathway as indicated by gas chromatography/liquid chromatography-mass spectrometry analysis. Overexpression of osa-miR162a inhibited the development and growth of the BPH and simultaneously reduced the release of 3-hexenal and 3-hexen-1-ol to block host recognition in the BPH. Moreover, knockdown of OsDCL1, which is targeted by osa-miR162a, inhibited α-linolenic acid metabolism to enhance the resistance to the BPH, which was similar to that in miR162a-overexpressing plants. Our study revealed a novel defense mechanism mediated by plant miRNAs developed during the long-term evolution of plant-host interaction, provided new ideas for the identification of rice resistance resources, and promoted a better understanding of pest control.

RNA-Based Control of Fungal Pathogens in Plants

Our duty to conserve global natural ecosystems is increasingly in conflict with our need to feed an expanding population. The use of conventional pesticides not only damages the environment and vulnerable biodiversity but can also still fail to prevent crop losses of 20-40% due to pests and pathogens. There is a growing call for more ecologically sustainable pathogen control measures. RNA-based biopesticides offer an eco-friendly alternative to the use of conventional fungicides for crop protection. The genetic modification (GM) of crops remains controversial in many countries, though expression of transgenes inducing pathogen-specific RNA interference (RNAi) has been proven effective against many agronomically important fungal pathogens. The topical application of pathogen-specific RNAi-inducing sprays is a more responsive, GM-free approach to conventional RNAi transgene-based crop protection. The specific targeting of essential pathogen genes, the development of RNAi-nanoparticle carrier spray formulations, and the possible structural modifications to the RNA molecules themselves are crucial to the success of this novel technology. Here, we outline the current understanding of gene silencing pathways in plants and fungi and summarize the pioneering and recent work exploring RNA-based biopesticides for crop protection against fungal pathogens, with a focus on spray-induced gene silencing (SIGS). Further, we discuss factors that could affect the success of RNA-based control strategies, including RNA uptake, stability, amplification, and movement within and between the plant host and pathogen, as well as the cost and design of RNA pesticides.

Small RNAs: Efficient and miraculous effectors that play key roles in plant-microbe interactions

Plants' response to pathogens is highly complex and involves changes at different levels, such as activation or repression of a vast array of genes. Recently, many studies have demonstrated that many RNAs, especially small RNAs (sRNAs), are involved in genetic expression and reprogramming affecting plant-pathogen interactions. The sRNAs, including short interfering RNAs and microRNAs, are noncoding RNA with 18-30 nucleotides, and are recognized as key genetic and epigenetic regulators. In this review, we summarize the new findings about defence-related sRNAs in the response to pathogens and our current understanding of their effects on plant-pathogen interactions. The main content of this review article includes the roles of sRNAs in plant-pathogen interactions, cross-kingdom sRNA trafficking between host and pathogen, and the application of RNA-based fungicides for plant disease control.

Overexpression of Sly-miR398b Compromises Disease Resistance against Botrytis cinerea through Regulating ROS Homeostasis and JA-Related Defense Genes in Tomato

MicroRNAs (miRNAs) have been shown to be critical components in plant immunity. MicroRNA398 (miR398) is a highly conserved miRNA in all land plants and plays crucial roles in diverse biotic stress responses. However, the role of miR398 has not yet been characterized in tomato resistance against Botrytis cinerea. In this report, the transcript levels of sly-miR398b were strongly decreased in B. cinerea-infected leaves and the overexpression of sly-miR398b resulted in enhanced susceptibility. The attenuated expression of cytosol Cu/Zn-SOD (CSD1), chloroplast Cu/Zn-SOD (CSD2), and guaiacol peroxidase (GPOD), as well as the decreased activities of superoxide dismutase (SOD) and GPOD, collectively led to increased hydrogen peroxide (H₂O₂) accumulation in sly-miR398b overexpressing plants. Furthermore, sly-miR398b was induced by methyl jasmonate (MeJA) treatment. The overexpression of sly-miR398b suppressed the expression of TomLoxD, LapA, and PR-STH2 in response to B. cinerea and MeJA treatment. Our data demonstrate that sly-miR398b overexpression negatively regulates the resistance to B. cinerea in tomato by inducing the accumulation of reactive oxygen species (ROS) and downregulating the expression of MeJA-responsive defense genes.

Extracellular vesicles: cross-organismal RNA trafficking in plants, microbes, and mammalian cells

Extracellular vesicles (EVs) are membrane-enclosed nanometer-scale particles that transport biological materials such as RNAs, proteins, and metabolites. EVs have been discovered in nearly all kingdoms of life as a form of cellular communication across different cells and between interacting organisms. EV research has primarily focused on EV-mediated intra-organismal transport in mammals, which has led to the characterization of a plethora of EV contents from diverse cell types with distinct and impactful physiological effects. In contrast, research into EV-mediated transport in plants has focused on inter-organismal interactions between plants and interacting microbes. However, the overall molecular content and functions of plant and microbial EVs remain largely unknown. Recent studies into the plant-pathogen interface have demonstrated that plants produce and secrete EVs that transport small RNAs into pathogen cells to silence virulence-related genes. Plant-interacting microbes such as bacteria and fungi also secrete EVs which transport proteins, metabolites, and potentially RNAs into plant cells to enhance their virulence. This review will focus on recent advances in EV-mediated communications in plant-pathogen interactions compared to the current state of knowledge of mammalian EV capabilities and highlight the role of EVs in cross-kingdom RNA interference.

The Biological Roles of Puccinia striiformis f. sp. tritici Effectors during Infection of Wheat

Puccinia striiformis f. sp. tritici (Pst) is the causative agent of wheat stripe rust, which can lead to a significant loss in annual wheat yields. Therefore, there is an urgent need for a deeper comprehension of the basic mechanisms underlying Pst infection. Effectors are known as the agents that plant pathogens deliver into host tissues to promote infection, typically by interfering with plant physiology and biochemistry. Insights into effector activity can significantly aid the development of future strategies to generate disease-resistant crops. However, the functional analysis of Pst effectors is still in its infancy, which hinders our understanding of the molecular mechanisms of the interaction between Pst and wheat. In this review, we summarize the potential roles of validated and proposed Pst effectors during wheat infection, including proteinaceous effectors, non-coding RNAs (sRNA effectors), and secondary metabolites (SMs effectors). Further, we suggest specific countermeasures against Pst pathogenesis and future research directions, which may promote our understanding of Pst effector functions during wheat immunity attempts.

Treatment with benznidazole and pentoxifylline regulates microRNA transcriptomic profile in a murine model of Chagas chronic cardiomyopathy

Chronic Chagas cardiomyopathy (CCC) is one of the leading causes of morbidity and mortality due to cardiovascular disorders in endemic areas of Chagas disease (CD), a neglected tropical illness caused by the protozoan parasite Trypanosoma cruzi. CCC is characterized by parasite persistence and inflammatory response in the heart tissue, which occur parallel to microRNA (miRNA) alterations. Here, we investigated the miRNA transcriptome profiling in the cardiac tissue of chronically T. cruzi-infected mice treated with a suboptimal dose of benznidazole (Bz), the immunomodulator pentoxifylline alone (PTX), or the combination of both (Bz+PTX), following the CCC onset. At 150 days post-infection, Bz, PTX, and Bz+PTX treatment regimens improved electrocardiographic alterations, reducing the percentage of mice afflicted by sinus arrhythmia and second-degree atrioventricular block (AVB2) when compared with the vehicle-treated animals. miRNA Transcriptome profiling revealed considerable changes in the differential expression of miRNAs in the Bz and Bz+PTX treatment groups compared with the control (infected, vehicle-treated) group. The latter showed pathways related to organismal abnormalities, cellular development, skeletal muscle development, cardiac enlargement, and fibrosis, likely associated with CCC. Bz-Treated mice exhibited 68 differentially expressed miRNAs related to signaling pathways like cell cycle, cell death and survival, tissue morphology, and connective tissue function. Finally, the Bz+PTX-treated group revealed 58 differentially expressed miRNAs associated with key signaling pathways related to cellular growth and proliferation, tissue development, cardiac fibrosis, damage, and necrosis/cell death. The T. cruzi-induced upregulation of miR-146b-5p, previously shown in acutely infected mice and in vitro T. cruzi-infected cardiomyocytes, was reversed upon Bz and Bz+PTX treatment regimens when further experimentally validated. Our results further our understanding of molecular pathways related to CCC progression and evaluation of treatment response. Moreover, the differentially expressed miRNAs may serve as drug targets, associated molecular therapy, or biomarkers of treatment outcomes.

Small Talk: On the Possible Role of Trans-Kingdom Small RNAs during Plant-Virus-Vector Tritrophic Communication

Small RNAs (sRNAs) are the hallmark and main effectors of RNA silencing and therefore are involved in major biological processes in plants, such as regulation of gene expression, antiviral defense, and plant genome integrity. The mechanisms of sRNA amplification as well as their mobile nature and rapid generation suggest sRNAs as potential key modulators of intercellular and interspecies communication in plant-pathogen-pest interactions. Plant endogenous sRNAs can act in cis to regulate plant innate immunity against pathogens, or in trans to silence pathogens' messenger RNAs (mRNAs) and impair virulence. Likewise, pathogen-derived sRNAs can act in cis to regulate expression of their own genes and increase virulence towards a plant host, or in trans to silence plant mRNAs and interfere with host defense. In plant viral diseases, virus infection alters the composition and abundance of sRNAs in plant cells, not only by triggering and interfering with the plant RNA silencing antiviral response, which accumulates virus-derived small interfering RNAs (vsiRNAs), but also by modulating plant endogenous sRNAs. Here, we review the current knowledge on the nature and activity of virus-responsive sRNAs during virus-plant interactions and discuss their role in trans-kingdom modulation of virus vectors for the benefit of virus dissemination.

Fungal Secondary Metabolites and Small RNAs Enhance Pathogenicity during Plant-Fungal Pathogen Interactions

Fungal plant pathogens use proteinaceous effectors as well as newly identified secondary metabolites (SMs) and small non-coding RNA (sRNA) effectors to manipulate the host plant's defense system via diverse plant cell compartments, distinct organelles, and many host genes. However, most molecular studies of plant-fungal interactions have focused on secreted effector proteins without exploring the possibly equivalent functions performed by fungal (SMs) and sRNAs, which are collectively known as "non-proteinaceous effectors". Fungal SMs have been shown to be generated throughout the plant colonization process, particularly in the early biotrophic stages of infection. The fungal repertoire of non-proteinaceous effectors has been broadened by the discovery of fungal sRNAs that specifically target plant genes involved in resistance and defense responses. Many RNAs, particularly sRNAs involved in gene silencing, have been shown to transmit bidirectionally between fungal pathogens and their hosts. However, there are no clear functional approaches to study the role of these SM and sRNA effectors. Undoubtedly, fungal SM and sRNA effectors are now a treasured land to seek. Therefore, understanding the role of fungal SM and sRNA effectors may provide insights into the infection process and identification of the interacting host genes that are targeted by these effectors. This review discusses the role of fungal SMs and sRNAs during plant-fungal interactions. It will also focus on the translocation of sRNA effectors across kingdoms, the application of cross-kingdom RNA interference in managing plant diseases and the tools that can be used to predict and study these non-proteinaceous effectors.

The Impact of Deleting Stem-Loop 1 of Epstein-Barr Virus-Encoded RNA 1 on Cell Proliferation

Epstein-Barr virus-encoded RNAs (EBERs) are two small, noncoding, structurally conserved transcripts, constitutively expressed at >10⁶ copies per EBV-infected cell. They have been shown to drive cell growth. However, the mechanism(s) involved in EBER-induced proliferation is not clear. In this study, we investigated the molecular mechanisms and structural impact of EBER1. Sequences of EBER1 stem-loops (SL) 1, 3, and 4 were deleted, creating three mutants: ∆SL1, ∆SL3, and ∆SL4. These mutants were cloned into pHebo plasmids and expressed in Jurkat cell lines. Cells transfected with wildtype EBER1 and pHebo were used as controls. Cell proliferation was monitored by microscopy and flow cytometry. Microarray, qPCR, and Western blotting were used to investigate the cell cycle markers. We found significantly higher cell proliferation in wildtype EBER1 cells compared to pHebo, ∆SL1, and ∆SL3, but not ∆SL4 mutants. There was also significant upregulation of S-phase and G2/M phase markers in wildtype EBER1 and ∆SL4 mutant. Furthermore, CDT1, a factor for DNA replication, was upregulated in wildtype EBER1 and ∆SL4 mutant. However, in ∆SL1 mutant, CDT1 was significantly downregulated and translocated to the cytoplasm. These data indicate that the structure of EBER1 is important in cell proliferation.

Integrated High-Throughput Sequencing, Microarray Hybridization and Degradome Analysis Uncovers MicroRNA-Mediated Resistance Responses of Maize to Pathogen Curvularia lunata

Curvularia lunata (Wakker) Boed, the causal agent of leaf spot in maize, is prone to mutation, making it difficult to control. RNAi technology has proven to be an important tool of genetic engineering and functional genomics aimed for crop improvement. MicroRNAs (miRNAs), which act as post-transcriptional regulators, often cause translational repression and gene silencing. In this article, four small RNA (sRNA) libraries were generated from two maize genotypes inoculated by C. lunata; among these, ltR1 and ltR2 were from the susceptible variety Huangzao 4 (HZ), ltR3 and ltR4, from the resistant variety Luyuan (LY), and 2286, 2145, 1556 and 2504 reads were annotated as miRNA in these four sRNA libraries, respectively. Through the combined analysis of high-throughput sequencing, microarray hybridization and degradome, 48 miRNAs were identified as being related to maize resistance to C. lunata. Among these, PC-732 and PC-169, two new maize miRNAs discovered, were predicted to cleave mRNAs of metacaspase 1 (AMC1) and thioredoxin family protein (Trx), respectively, possibly playing crucial roles in the resistance of maize to C. lunata. To further confirm the role of PC-732 in the interaction of maize and C. lunata, the miRNA was silenced through STTM (short tandem target mimic) technology, and we found that knocking down PC-732 decreased the susceptibility of maize to C. lunata. Precisely speaking, the target gene of PC-732 might inhibit the expression of disease resistance-related genes during the interaction between maize and C. lunata. Overall, the findings of this study indicated the existence of miRNAs involved in the resistance of maize to C. lunata and will contribute to rapidly clarify the resistant mechanism of maize to C. lunata.

Do small RNAs unlock the below ground microbiome-plant interaction mystery?

Over the past few decades, regulatory RNAs, such as small RNAs (sRNAs), have received increasing attention in the context of host-microbe interactions due to their diverse roles in controlling various biological processes in eukaryotes. In addition, studies have identified an increasing number of sRNAs with novel functions across a wide range of bacteria. What is not well understood is why cells regulate gene expression through post-transcriptional mechanisms rather than at the initiation of transcription. The finding of a multitude of sRNAs and their identified associated targets has allowed further investigation into the role of sRNAs in mediating gene regulation. These foundational data allow for further development of hypotheses concerning how a precise control of gene activity is accomplished through the combination of transcriptional and post-transcriptional regulation. Recently, sRNAs have been reported to participate in interkingdom communication and signalling where sRNAs originating from one kingdom are able to target or control gene expression in another kingdom. For example, small RNAs of fungal pathogens that silence plant genes and vice-versa plant sRNAs that mediate bacterial gene expression. However, there is currently a lack of evidence regarding sRNA-based inter-kingdom signalling across more than two interacting organisms. A habitat that provides an excellent opportunity to investigate interconnectivity is the plant rhizosphere, a multifaceted ecosystem where plants and associated soil microbes are known to interact. In this paper, we discuss how the interconnectivity of bacteria, fungi, and plants within the rhizosphere may be mediated by bacterial sRNAs with a particular focus on disease suppressive and non-suppressive soils. We discuss the potential roles sRNAs may play in the below-ground world and identify potential areas of future research, particularly in reference to the regulation of plant immunity genes by bacterial and fungal communities in disease-suppressive and non-disease-suppressive soils.

Distinguishing friends from foes: Can smRNAs modulate plant interactions with beneficial and pathogenic organisms?

In their agro-ecological habitats, plants are constantly challenged by fungal interactions that might be pathogenic or beneficial in nature, and thus, plants need to exhibit appropriate responses to discriminate between them. Such interactions involve sophisticated molecular mechanism of signal exchange, signal transduction and regulation of gene expression. Small RNAs (smRNAs), including the microRNAs (miRNAs), form an essential layer of regulation in plant developmental processes as well as in plant adaptation to environmental stresses, being key for the outcome during plant-microbial interactions. Further, smRNAs are mobile signals that can go across kingdoms from one interacting partner to the other and hence can be used as communication as well as regulatory tools not only by the host plant but also by the colonising fungus. Here, largely with a focus on plant-fungal interactions and miRNAs, we will discuss the role of smRNAs, and how they might help plants to discriminate between friends and foes.

Development of plant systemic resistance by beneficial rhizobacteria: Recognition, initiation, elicitation and regulation

A plant growing in nature is not an individual, but it holds an intricate community of plants and microbes with relatively stable partnerships. The microbial community has recently been demonstrated to be closely linked with plants since their earliest evolution, to help early land plants adapt to environmental threats. Mounting evidence has indicated that plants can release diverse kinds of signal molecules to attract beneficial bacteria for mediating the activities of their genetics and biochemistry. Several rhizobacterial strains can promote plant growth and enhance the ability of plants to withstand pathogenic attacks causing various diseases and loss in crop productivity. Beneficial rhizobacteria are generally called as plant growth-promoting rhizobacteria (PGPR) that induce systemic resistance (ISR) against pathogen infection. These ISR-eliciting microbes can mediate the morphological, physiological and molecular responses of plants. In the last decade, the mechanisms of microbial signals, plant receptors, and hormone signaling pathways involved in the process of PGPR-induced ISR in plants have been well investigated. In this review, plant recognition, microbial elicitors, and the related pathways during plant-microbe interactions are discussed, with highlights on the roles of root hair-specific syntaxins and small RNAs in the regulation of the PGPR-induced ISR in plants.

MicroRNA-mediated host defense mechanisms against pathogens and herbivores in rice: balancing gains from genetic resistance with trade-offs to productivity potential

BACKGROUND

Rice (Oryza sativa L.) is the major source of daily caloric intake for more than 30% of the human population. However, the sustained productivity of this staple food crop is continuously threatened by various pathogens and herbivores. Breeding has been successful in utilizing various mechanisms of defense by gene pyramiding in elite cultivars, but the continuous resurgence of highly resistant races of pathogens and herbivores often overcomes the inherent capacity of host plant immunity. MicroRNAs (miRNAs) are endogenous, short, single-stranded, non-coding RNA molecules that regulate gene expression by sequence-specific cleavage of target mRNA or suppressing target mRNA translation. While miRNAs function as upstream regulators of plant growth, development, and host immunity, their direct effects on growth and development in the context of balancing defenses with agronomic potential have not been extensively discussed and explored as a more viable strategy in breeding for disease and pest resistant cultivars of rice with optimal agronomic potentials.

RESULTS

Using the available knowledge in rice and other model plants, this review examines the important roles of miRNAs in regulating host responses to various fungal, bacterial, and viral pathogens, and insect pests, in the context of gains and trade-offs to crop yield. Gains from R-gene-mediated resistance deployed in modern rice cultivars are often undermined by the rapid breakdown of resistance, negative pleiotropic effects, and linkage drags with undesirable traits. In stark contrast, several classes of miRNAs are known to efficiently balance the positive gains from host immunity without significant costs in terms of losses in agronomic potentials (i.e., yield penalty) in rice. Defense-related miRNAs such as Osa-miR156, Osa-miR159, Osa-miR162, Osa-miR396, Osa-530, Osa-miR1432, Osa-miR1871, and Osa-miR1873 are critical in fine-tuning and integrating immune responses with physiological processes that are necessary to the maintenance of grain yield. Recent research has shown that many defense-related miRNAs regulate complex and agronomically important traits.

CONCLUSIONS

Identification of novel immune-responsive miRNAs that orchestrate physiological processes critical to the full expression of agronomic potential will facilitate the stacking of optimal combinations of miRNA-encoding genes to develop high-yielding cultivars with durable resistance to disease and insect pests with minimal penalties to yield.

miR398b and AtC2GnT form a negative feedback loop to regulate Arabidopsis thaliana resistance against Phytophthora parasitica

Oomycetes are diploid eukaryotic microorganisms that seriously threaten sustainable crop production. MicroRNAs (miRNAs) and corresponding natural antisense transcripts (NATs) are important regulators of multiple biological processes. However, little is known about their roles in plant immunity against oomycete pathogens. In this study, we report the identification and functional characterization of miR398b and its cis-NAT, the core-2/I-branching beta-1,6-N-acetylglucosaminyltransferase gene (AtC2GnT), in plant immunity. Gain- and loss-of-function assays revealed that miR398b mediates Arabidopsis thaliana susceptibility to Phytophthora parasitica by targeting Cu/Zn-Superoxidase Dismutase1 (CSD1) and CSD2, leading to suppressed expression of CSD1 and CSD2 and decreased plant disease resistance. We further showed that AtC2GnT transcripts could inhibit the miR398b-CSDs module via inhibition of pri-miR398b expression, leading to elevated plant resistance to P. parasitica. Furthermore, quantitative reverse transcription PCR, RNA ligase-mediated 5'-amplification of cDNA ends (RLM-5' RACE), and transient expression assays indicated that miR398b suppresses the expression of AtC2GnT. We generated AtC2GnT-silenced A. thaliana plants by CRISPR/Cas9 or RNA interference methods, and the Nicotiana benthamiana NbC2GnT-silenced plants by virus-induced gene silencing. Pathogenicity assays showed that the C2GnT-silenced plants were more susceptible, while AtC2GnT-overexpressing plants exhibited elevated resistance to P. parasitica. AtC2GnT encodes a Golgi-localized protein, and transient expression of AtC2GnT enhanced N. benthamiana resistance to Phytophthora pathogens. Taken together, our results revealed a positive role of AtC2GnT and a negative regulatory loop formed by miR398b and AtC2GnT in regulating plant resistance to P. parasitica.

The small RNA-mediated gene silencing machinery is required in Arabidopsis for stimulation of growth, systemic disease resistance, and suppression of the nitrile-specifier gene NSP4 by Trichoderma atroviride

Trichoderma atroviride is a root-colonizing fungus that confers multiple benefits to plants. In plants, small RNA (sRNA)-mediated gene silencing (sRNA-MGS) plays pivotal roles in growth, development, and pathogen attack. Here, we explored the role of core components of Arabidopsis thaliana sRNA-MGS pathways during its interaction with Trichoderma. Upon interaction with Trichoderma, sRNA-MGS-related genes paralleled the expression of Arabidopsis defense-related genes, linked to salicylic acid (SA) and jasmonic acid (JA) pathways. SA- and JA-related genes were primed by Trichoderma in leaves after the application of the well-known pathogen-associated molecular patterns flg22 and chitin, respectively. Defense-related genes were primed in roots as well, but to different extents and behaviors. Phenotypical characterization of mutants in AGO genes and components of the RNA-dependent DNA methylation (RdDM) pathway revealed that different sets of sRNA-MGS-related genes are essential for (i) the induction of systemic acquired resistance against Botrytis cinerea, (ii) the activation of the expression of plant defense-related genes, and (iii) root colonization by Trichoderma. Additionally, plant growth induced by Trichoderma depends on functional RdDM. Profiling of DNA methylation and histone N-tail modification patterns at the Arabidopsis Nitrile-Specifier Protein-4 (NSP4) locus, which is responsive to Trichoderma, showed altered epigenetic modifications in RdDM mutants. Furthermore, NSP4 is required for the induction of systemic acquired resistance against Botrytis and avoidance of enhanced root colonization by Trichoderma. Together, our results indicate that RdDM is essential in Arabidopsis to establish a beneficial relationship with Trichoderma. We propose that DNA methylation and histone modifications are required for plant priming by the beneficial fungus against B. cinerea.

Induced Systemic Resistance for Improving Plant Immunity by Beneficial Microbes

Plant beneficial microorganisms improve the health and growth of the associated plants. Application of beneficial microbes triggers an enhanced resistance state, also termed as induced systemic resistance (ISR), in the host, against a broad range of pathogens. Upon the activation of ISR, plants employ long-distance systemic signaling to provide protection for distal tissue, inducing rapid and strong immune responses against pathogens invasions. The transmission of ISR signaling was commonly regarded to be a jasmonic acid- and ethylene-dependent, but salicylic acid-independent, transmission. However, in the last decade, the involvement of both salicylic acid and jasmonic acid/ethylene signaling pathways and the regulatory roles of small RNA in ISR has been updated. In this review, the plant early recognition, responsive reactions, and the related signaling transduction during the process of the plant-beneficial microbe interaction was discussed, with reflection on the crucial regulatory role of small RNAs in the beneficial microbe-mediated ISR.

RIR1 represses plant immunity by interacting with mitochondrial complex I subunit in rice

We previously observed decreased expression of rice OsmiR159a.1 on infection with the bacterial blight-causing pathogen Xanthomonas oryzae pv. oryzae (Xoo), and identified the OsLRR_RLK (leucine-rich repeat_ receptor like kinase) gene as an authentic target of OsmiR159a.1. Here, we found that a Tos17 insertion mutant of LRR_RLK displayed increasing temporal resistance to Xoo, whereas the LRR_RLK overexpression lines were susceptible to the pathogen early on in the infection, indicating that LRR_RLK encodes a repressor of rice resistance to Xoo infection, and it was renamed as RIR1 (Rice Immunity Repressor 1). RIR1 overexpression plants were more susceptible to Xoo at late growth stage, suggesting that RIR1 mRNA levels are negatively correlated with the resistance of rice against Xoo. We discovered that OsmiR159a.1 repression in Xoo-infected plants was largely dependent on the pathogen's type III secretion system. Co-immunoprecipitation, bimolecular fluoresence complementation, and pull-down assays indicated that RIR1 interacted with the NADH-ubiquinone oxidoreductase (NUO) 51-kDa subunit of the mitochondrial complex I through its kinase domain. Notably, impairment of RIR1 or overexpression of NUO resulted in reactive oxygen species accumulation and enhanced expression of pathogen-resistance genes, including jasmonic acid pathway genes. We propose that pathogens may inhibit OsmiR159 to interfere with the RIR1-NUO interaction, and subsequently depression of rice immune signalling pathways. The resistance genes manipulated by Xoo can be a probe to explore the regulatory network during host-pathogen interactions.

Use of deep sequencing to profile small RNAs derived from tomato spotted wilt orthotospovirus and hippeastrum chlorotic ringspot orthotospovirus in infected Capsicum annuum

Virus-derived small RNAs are one of the key factors of RNA silencing in plant defence against viruses. We obtained virus-derived small interfering RNA profiles from Tomato spotted wilt orthotospovirus and Hippeastrum chlorotic ringspot orthotospovirus infected Capsicum annuum XX19 and XY11 by deep sequencing one day after inoculation. The vsiRNAs data were mapped to the TSWV and HCRV genomes, and the results showed that the vsiRNAs measured 19-24 nucleotides in length. Most of the vsiRNAs were mapped to the S segment of the viral genome. For XX19 and XY11 infected with HCRV, the distribution range of vsiRNAs in S RNA was 52.06-55.20%, while for XX19 and XY11 infected with TSWV, the distribution range of vsiRNAs in S RNA was 87.76-89.07%. The first base at the 5' end of the siRNA from TSWV and HCRV was primarily biased towards A, U, or C. Compared with mock-inoculated XX19 and XY11, the expression level of CaRDR1 was upregulated in TSWV- and HCRV-inoculated XX19 and XY11. CaAGO2 and CaAGO5 were upregulated in XY11 against HCRV infection, and CaRDR2 was downregulated in TSWV-infected XY11 and XX19. The profile of HCRV and TSWV vsiRNA verified in this study could be useful for selecting key vsiRNA such as those in disease-resistant varieties by artificially synthesizing amiRNA.

Application of CRISPR-Cas9 in plant-plant growth-promoting rhizobacteria interactions for next Green Revolution

Agriculture's beginnings resulted in the domestication of numerous plant species as well as the use of natural resources. Food grain production took about 10,000 years to reach a billion tonnes in 1960, however, it took only 40 years to achieve 2 billion tonnes in year 2000. The creation of genetically modified crops, together with the use of enhanced agronomic practices, resulted in this remarkable increase, dubbed the "Green Revolution". Plants and bacteria that interact with each other in nature are co-evolving, according to Red Queen dynamics. Plant microorganisms, also known as plant microbiota, are an essential component of plant life. Plant-microbe (PM) interactions can be beneficial or harmful to hosts, depending on the health impact. The significance of microbiota in plant growth promotion (PGP) and stress resistance is well known. Our understanding of the community composition of the plant microbiome and important driving forces has advanced significantly. As a result, utilising the plant microbiota is a viable strategy for the next Green Revolution for meeting food demand. The utilisation of newer methods to understand essential genetic and molecular components of the multiple PM interactions is required for their application. The use of clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-mediated genome editing (GE) techniques to investigate PM interactions is of tremendous interest. The implementation of GE techniques to boost the ability of microorganisms or plants for agronomic trait development will be enabled by a comprehensive understanding of PM interactions. This review focuses on using GE approaches to investigate the principles of PM interactions, disease resistance, PGP activity, and future implications in agriculture in plants or associated microbiota.

Tr-milRNA1 Contributes to Lignocellulase Secretion under Heat Stress by Regulating the Lectin-Type Cargo Receptor Gene Trvip36 in Trichoderma guizhouence NJAU 4742

Background: MicroRNA plays an important role in multifarious biological processes by regulating their corresponding target genes. However, the biological function and regulatory mechanism of fungal microRNA-like RNAs (milRNAs) remain poorly understood. Methods: In this study, combined with deep sequencing and bioinformatics analysis, milRNAs and their targets from Trichoderma guizhouence NJAU 4742 were isolated and identified under solid-state fermentation (SSF) by using rice straw as the sole carbon source at 28 °C and 37 °C, respectively. Results: A critical milRNA, TGA1_S04_31828 (Tr-milRNA1), was highly expressed under heat stress (37 °C) and adaptively regulated lignocellulase secretion. Overexpression of Tr-milRNA1 (OE-Tr-milRNA1) did not affect vegetative growth, but significantly increased lignocellulose utilization under heat stress. Based on the bioinformatics analysis and qPCR validation, a target of Tr-milRNA1 was identified as Trvip36, a lectin-type cargo receptor. The expression of Tr-milRNA1 and Trvip36 showed a divergent trend under SSF when the temperature was increased from 28 °C to 37 °C. In addition, the expression of Trvip36 was suppressed significantly in Tr-milRNA1 overexpression strain (OE-Tr-milRNA1). Compared with the wild type, deletion of Trvip36 (ΔTrvip36) significantly improved the secretion of lignocellulases by reducing the retention of lignocellulases in the ER under heat stress. Conclusions: Tr-milRNA1 from NJAU 4742 improved lignocellulose utilization under heat stress by regulating the expression of the corresponding target gene Trvip36. These findings might open avenues for exploring the mechanism of lignocellulase secretion in filamentous fungi.

Expression Patterns of miR398, miR167, and miR159 in the Interaction between Bread Wheat (Triticum aestivum L.) and Pathogenic Fusarium culmorum and Beneficial Trichoderma Fungi

Bread wheat (Triticum aestivum L.) is an agronomically significant cereal cultivated worldwide. Wheat breeding is limited by numerous abiotic and biotic stresses. One of the most deleterious factors is biotic stress provoked by the Fusarium culmorum fungus. This pathogen is a causative agent of Fusarium root rot and Fusarium head blight. Beneficial fungi Trichoderma atroviride and T. cremeum are strong antagonists of mycotoxigenic Fusarium spp. These fungi promote plant growth and enhance their tolerance of negative environmental conditions. The aim of the study was to determine and compare the spatial (in above- and underground organs) and temporal (early: 6 and 22 hpi; and late: 5 and 7 dpi reactions) expression profiles of three mature miRNAs (miR398, miR167, and miR159) in wheat plants inoculated with two strains of F. culmorum (KF846 and EW49). Moreover, the spatial expression patterns in wheat response between plants inoculated with beneficial T. atroviride (AN35) and T. cremeum (AN392) were assessed. Understanding the sophisticated role of miRNAs in wheat-fungal interactions may initiate a discussion concerning the use of this knowledge to protect wheat plants from the harmful effects of fungal pathogens. With the use of droplet digital PCR (ddPCR), the absolute quantification of the selected miRNAs in the tested material was carried out. The differential accumulation of miR398, miR167, and miR159 in the studied groups was observed. The abundance of all analyzed miRNAs in the roots demonstrated an increase in the early and reduction in late wheat response to F. culmorum inoculation, suggesting the role of these particles in the initial wheat reaction to the studied fungal pathogen. The diverse expression patterns of the studied miRNAs between Trichoderma-inoculated or F. culmorum-inoculated plants and control wheat, as well as between Trichoderma-inoculated and F. culmorum-inoculated plants, were noticed, indicating the need for further analysis.

Rice miR1432 Fine-Tunes the Balance of Yield and Blast Disease Resistance via Different Modules

microRNAs act as fine-tuners in the regulation of plant growth and resistance against biotic and abiotic stress. Here we demonstrate that rice miR1432 fine-tunes yield and blast disease resistance via different modules. Overexpression of miR1432 leads to compromised resistance and decreased yield, whereas blocking miR1432 using a target mimic of miR1432 results in enhanced resistance and yield. miR1432 suppresses the expression of LOC_Os03g59790, which encodes an EF-hand family protein 1 (OsEFH1). Overexpression of OsEFH1 leads to enhanced rice resistance but decreased grain yield. Further study revealed that miR1432 and OsEFH1 are differentially responsive to chitin, a fungus-derived pathogen/microbe-associated molecular pattern (PAMP/MAMP). Consistently, blocking miR1432 or overexpression of OsEFH1 improves chitin-triggered immunity responses. In contrast, overexpression of ACOT, another target gene regulating rice yield traits, has no significant effects on rice blast disease resistance. Altogether, these results indicate that miR1432 balances yield and resistance via different target genes, and blocking miR1432 can simultaneously improve yield and resistance.

Fol-milR1, a pathogenicity factor of Fusarium oxysporum, confers tomato wilt disease resistance by impairing host immune responses

Although it is well known that miRNAs play crucial roles in multiple biological processes, there is currently no evidence indicating that milRNAs from Fusarium oxysporum f. sp. lycopersici (Fol) interfere with tomato resistance during infection. Here, using sRNA-seq, we demonstrate that Fol-milR1, a trans-kingdom small RNA, is exported into tomato cells after infection. The knockout strain ∆Fol-milR1 displays attenuated pathogenicity to the susceptible tomato cultivar 'Moneymaker'. On the other hand, Fol-milR1 overexpression strains exhibit enhanced virulence against the resistant cultivar 'Motelle'. Several tomato mRNAs are predicted targets of Fol-milR1. Among these genes, Solyc06g007430 (encoding the CBL-interacting protein kinase, SlyFRG4) is regulated at the posttranscriptional level by Fol-milR1. Furthermore, SlyFRG4 loss-of-function alleles created using CRISPR/Cas9 in tomato ('Motelle') exhibit enhanced disease susceptibility to Fol, further supporting the idea that SlyFRG4 is essential for tomato wilt disease resistance. Notably, our results using immunoprecipitation with specific antiserum suggest that Fol-milR1 interferes with the host immunity machinery by binding to tomato ARGONAUTE 4a (SlyAGO4a). Furthermore, virus-induced gene silenced (VIGS) knock-down SlyAGO4a plants exhibit reduced susceptibility to Fol. Together, our findings support a model in which Fol-milR1 is an sRNA fungal effector that suppresses host immunity by silencing a disease resistance gene, thus providing a novel virulence strategy to achieve infection.

Extracellular Vesicles: Emerging Players in Plant Defense Against Pathogens

Communication between plants and interacting microorganisms requires functional molecule trafficking, which is essential for host defense and pathogen virulence. Extracellular vesicles (EVs) are single membrane-bound spheres that carry complex cargos, including lipids, proteins, and nucleic acids. They mediate cell-to-cell communication via the transfer of molecules between cells. Plant EVs have been isolated from many plant species and play a prominent role in immune system modulation and plant defense response. Recent studies have shown that plant EVs are emerging players in cross-kingdom regulation and contribute to plant immunity by mediating the trafficking of regulatory small RNA into pathogens, leading to the silencing of pathogen virulence-related genes. This review summarizes the current understanding of plant EV isolation technologies, the role of plant EVs in plant immunity, and the mechanism of plant EV biogenesis, as well as approaches for how these findings can be developed into innovative strategies for crop protection.

Molecular virulence determinants of Magnaporthe oryzae: disease pathogenesis and recent interventions for disease management in rice plant

Magnaporthe oryzae, causative agent of the rice blast disease, is a major concern for the loss in yield of rice crop across the globe. It is known for its characteristic melanised dome-shaped appressorium containing a dense melanin layer. The melanised layer is of considerable importance as it is required to generate turgor pressure for initiating peg formation, consequently rupturing the plant cuticle. Various virulence factors play an important role in the disease progression as well as pathogenesis of the fungus. Some of the proteins encoded by virulence genes are associated with signalling, secondary metabolism, protein deprivation, defence responses and conidiation. The purpose of this review is to describe various fungal virulence determinants and provide insights into the molecular mechanisms that are involved in progression of the disease. Besides, the recent molecular approaches being employed to combat the rice blast have also been elaborated.

Laccase Directed Lignification Is One of the Major Processes Associated With the Defense Response Against Pythium ultimum Infection in Apple Roots

Apple replant disease (ARD), incited by a pathogen complex including Pythium ultimum, causes stunted growth or death of newly planted trees at replant sites. Development and deployment of resistant or tolerant rootstocks offers a cost-effective, ecologically friendly, and durable approach for ARD management. Maximized exploitation of natural resistance requires integrated efforts to identify key regulatory mechanisms underlying resistance traits in apple. In this study, miRNA profiling and degradome sequencing identified major miRNA pathways and candidate genes using six apple rootstock genotypes with contrasting phenotypes to P. ultimum infection. The comprehensive RNA-seq dataset offered an expansive view of post-transcriptional regulation of apple root defense activation in response to infection from P. ultimum. Several pairs of miRNA families and their corresponding targets were identified for their roles in defense response in apple roots, including miR397-laccase, miR398-superoxide dismutase, miR10986-polyphenol oxidase, miR482-resistance genes, and miR160-auxin response factor. Of these families, the genotype-specific expression patterns of miR397 indicated its fundamental role in developing defense response patterns to P. ultimum infection. Combined with other identified copper proteins, the importance of cellular fortification, such as lignification of root tissues by the action of laccase, may critically contribute to genotype-specific resistance traits. Our findings suggest that quick and enhanced lignification of apple roots may significantly impede pathogen penetration and minimize the disruption of effective defense activation in roots of resistant genotypes. The identified target miRNA species and target genes consist of a valuable resource for subsequent functional analysis of their roles during interaction between apple roots and P. ultimum.

Roles of small RNAs in crop disease resistance

Small RNAs (sRNAs) are a class of short, non-coding regulatory RNAs that have emerged as critical components of defense regulatory networks across plant kingdoms. Many sRNA-based technologies, such as host-induced gene silencing (HIGS), spray-induced gene silencing (SIGS), virus-induced gene silencing (VIGS), artificial microRNA (amiRNA) and synthetic trans-acting siRNA (syn-tasiRNA)-mediated RNA interference (RNAi), have been developed as disease control strategies in both monocot and dicot plants, particularly in crops. This review aims to highlight our current understanding of the roles of sRNAs including miRNAs, heterochromatic siRNAs (hc-siRNAs), phased, secondary siRNAs (phasiRNAs) and natural antisense siRNAs (nat-siRNAs) in disease resistance, and sRNAs-mediated trade-offs between defense and growth in crops. In particular, we focus on the diverse functions of sRNAs in defense responses to bacterial and fungal pathogens, oomycete and virus in crops. Further, we highlight the application of sRNA-based technologies in protecting crops from pathogens. Further research perspectives are proposed to develop new sRNAs-based efficient strategies to breed non-genetically modified (GMO), disease-tolerant crops for sustainable agriculture.

Regulatory non-coding RNAs: a new frontier in regulation of plant biology

Beyond the most crucial roles of RNA molecules as a messenger, ribosomal, and transfer RNAs, the regulatory role of many non-coding RNAs (ncRNAs) in plant biology has been recognized. ncRNAs act as riboregulators by recognizing specific nucleic acid targets through homologous sequence interactions to regulate plant growth, development, and stress responses. Regulatory ncRNAs, ranging from small to long ncRNAs (lncRNAs), exert their control over a vast array of biological processes. Based on the mode of biogenesis and their function, ncRNAs evolved into different forms that include microRNAs (miRNAs), small interfering RNAs (siRNAs), miRNA variants (isomiRs), lncRNAs, circular RNAs (circRNAs), and derived ncRNAs. This article explains the different classes of ncRNAs and their role in plant development and stress responses. Furthermore, the applications of regulatory ncRNAs in crop improvement, targeting agriculturally important traits, have been discussed.

Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions

The microbiome, by virtue of its interactions with the host, is implicated in various host functions including its influence on nutrition and homeostasis. Many chronic diseases such as diabetes, cancer, inflammatory bowel diseases are characterized by a disruption of microbial communities in at least one biological niche/organ system. Various molecular mechanisms between microbial and host components such as proteins, RNAs, metabolites have recently been identified, thus filling many gaps in our understanding of how the microbiome modulates host processes. Concurrently, high-throughput technologies have enabled the profiling of heterogeneous datasets capturing community level changes in the microbiome as well as the host responses. However, due to limitations in parallel sampling and analytical procedures, big gaps still exist in terms of how the microbiome mechanistically influences host functions at a system and community level. In the past decade, computational biology and machine learning methodologies have been developed with the aim of filling the existing gaps. Due to the agnostic nature of the tools, they have been applied in diverse disease contexts to analyze and infer the interactions between the microbiome and host molecular components. Some of these approaches allow the identification and analysis of affected downstream host processes. Most of the tools statistically or mechanistically integrate different types of -omic and meta -omic datasets followed by functional/biological interpretation. In this review, we provide an overview of the landscape of computational approaches for investigating mechanistic interactions between individual microbes/microbiome and the host and the opportunities for basic and clinical research. These could include but are not limited to the development of activity- and mechanism-based biomarkers, uncovering mechanisms for therapeutic interventions and generating integrated signatures to stratify patients.

Deciphering the role of microRNAs during Pi54 gene mediated Magnaporthe oryzae resistance response in rice

The broad-spectrum resistance gene Pi54 confers resistance to multiple isolates of Magnaporthe oryzae in rice. In order to decipher the molecular mechanism underlying the Pi54 mediated resistance in rice line Taipei309 ^Pi54 (carrying Pi54), miRNAome study was performed at 24 h post-inoculation (hpi) with M. oryzae. A total of 222 known miRNAs representing 101 miRNA families were found in this study. Of these, 29 and 24 miRNAs were respectively up- and down-regulated in the resistant Taipei309 ^Pi54 . Defence response (DR) genes, like, NBSGO35, and OsWAK129b, and genes related to transcription factors were up-regulated in Taipei309 ^Pi54 line. The vast array of miRNA candidates identified here are miR159c, miR167c, miR2100, miR2118o, miR2118l, miR319a, miR393, miR395l, miR397a, miR397b, miR398, miR439g, miR531b, miR812f, and miR815c, and they manifest their role in balancing the interplay between various DR genes during Pi54 mediated resistance. We also validated miRNA/target gene pairs involved in hormone signalling, and cross-talk among hormone pathways regulating the rice immunity. This study suggests that the Pi54 gene mediated blast resistance is influenced by several microRNAs through PTI and ETI components in the rice line Taipei309 ^Pi54 , leading to incompatible host-pathogen interaction.

Contribution of Small RNA Pathway to Interactions of Rice with Pathogens and Insect Pests

Small RNAs (sRNAs) are mainly classified into microRNAs (miRNAs) and small interfering RNAs (siRNAs) according to their origin. miRNAs originate from single-stranded RNA precursors, whereas siRNAs originate from double-stranded RNA precursors that are synthesized by RNA-dependent RNA polymerases. Both of single-stranded and double-stranded RNA precursors are processed into sRNAs by Dicer-like proteins. Then, the sRNAs are loaded into ARGONAUTE proteins, forming RNA-induced silencing complexes (RISCs). The RISCs repress the expression of target genes with sequences complementary to the sRNAs through the cleavage of transcripts, the inhibition of translation or DNA methylation. Here, we summarize the recent progress of sRNA pathway in the interactions of rice with various parasitic organisms, including fungi, viruses, bacteria, as well as insects. Besides, we also discuss the hormone signal in sRNA pathway, and the emerging roles of circular RNAs and long non-coding RNAs in rice immunity. Obviously, small RNA pathway may act as a part of rice innate immunity to coordinate with growth and development.

Vm-milR37 contributes to pathogenicity by regulating glutathione peroxidase gene VmGP in Valsa mali

MicroRNAs play important roles in various biological processes by regulating their corresponding target genes. However, the function and regulatory mechanism of fungal microRNA-like RNAs (milRNAs) are still largely unknown. In this study, a milRNA (Vm-milR37) was isolated and identified from Valsa mali, which causes the most serious disease on the trunk of apple trees in China. Based on the results of deep sequencing and quantitative reverse transcription PCR, Vm-milR37 was found to be expressed in the mycelium, while it was not expressed during the V. mali infection process. Overexpression of Vm-milR37 did not affect vegetative growth, but significantly decreased pathogenicity. Based on degradome sequencing, the target of Vm-milR37 was identified as VmGP, a glutathione peroxidase. The expression of Vm-milR37 and VmGP showed a divergent trend in V. mali-apple interaction samples and Vm-milR37 overexpression transformants. The expression of VmGP could be suppressed significantly by Vm-milR37 when coexpressed in tobacco leaves. Deletion of VmGP showed significantly reduced pathogenicity compared with the wild type. VmGP deletion mutants showed more sensitivity to hydrogen peroxide. Apple leaves inoculated with Vm-milR37 overexpression transformants and VmGP deletion mutant displayed increased accumulation of reactive oxygen species compared with the wild type. Thus, Vm-milR37 plays a critical role in pathogenicity by regulating VmGP, which contributes to the oxidative stress response during V. mali infection. These results provide important evidence to define the roles of milRNAs and their corresponding target genes in pathogenicity.

A novel antisense long non-coding RNA participates in asexual and sexual reproduction by regulating the expression of GzmetE in Fusarium graminearum

Fusarium graminearum is an important worldwide pathogen that causes Fusarium head blight in wheat, barley, maize and other grains. LncRNAs play important roles in many biological processes, but little is known about their functions and mechanisms in filamentous fungi. Here, we report that a natural antisense RNA, GzmetE-AS, is transcribed from the opposite strand of GzmetE. GzmetE encodes a homoserine O-acetyltransferase, which is important for sexual development and plant infection. The expression of GzmetE-AS was increased significantly during the conidiation stage, while GzmetE was upregulated in the late stage of sexual reproduction. Overexpression of GzmetE-AS inhibited the transcription of GzmetE. In contrast, the expression of GzmetE was significantly increased in GzmetE-AS transcription termination strain GzmetE-AS-T. Furthermore, GzmetE-AS-T produced more perithecia and facilitated the ascospore discharge, resembling the phenotype of GzmetE overexpressing strains. However, overexpression of GzmetE-AS in ∆dcl1/2 strain cannot inhibit the expression of GzmetE, and the GzmetE nat-siRNA is also significantly reduced in ∆dcl1/2 mutant. Taken together, we have identified a novel antisense lncRNA GzmetE-AS, which is involved in asexual and sexual reproduction by regulating its antisense gene GzmetE through RNAi pathway. Our findings reveal that the lncRNA plays critical roles in the development of F. graminearum.

Blocking miR530 Improves Rice Resistance, Yield, and Maturity

MicroRNAs fine-tune plant growth and resistance against multiple biotic and abiotic stresses. The trade-off between biomass and resistance can penalize crop yield. In this study, we have shown that rice miR530 regulates blast disease resistance, yield, and growth period. While the overexpression of miR530 results in compromised blast disease resistance, reduced grain yield, and late maturity, blocking miR530 using a target mimic (MIM530) leads to enhanced resistance, increased grain yield, and early maturity. Further study revealed that the accumulation of miR530 was decreased in both leaves and panicles along with the increase of age. Such expression patterns were accordant with the enhanced resistance from seedlings to adult plants, and the grain development from panicle formation to fully-filled seeds. Divergence analysis of miR530 precursor with upstream 1,000-bp promoter sequence in 11 rice species revealed that miR530 was diverse in Oryza sativa japonica and O. sativa indica group, which was consistent with the different accumulation of miR530 in japonica accessions and indica accessions. Altogether, our results indicate that miR530 coordinates rice resistance, yield, and maturity, thus providing a potential regulatory module for breeding programs aiming to improve yield and disease resistance.

Integrated Analysis of MicroRNA and Target Genes in Brachypodium distachyon Infected by Magnaporthe oryzae by Small RNA and Degradome Sequencing

Rice blast caused by Magnaporthe oryzae is one of the most important diseases that seriously threaten rice production. Brachypodium distachyon is a grass species closely related to grain crops, such as rice, barley, and wheat, and has become a new model plant of Gramineae. In this study, 15 small RNA samples were sequenced to examine the dynamic changes in microRNA (miRNA) expression in B. distachyon infected by M. oryzae at 0, 24, and 48 h after inoculation. We identified 432 conserved miRNAs and 288 predicted candidate miRNAs in B. distachyon. Additionally, there were 7 and 19 differentially expressed miRNAs at 24 and 48 h post-inoculation, respectively. Furthermore, using degradome sequencing, we identified 2,126 genes as targets for 308 miRNAs; using quantitative real-time PCR (qRT-PCR), we validated five miRNA/target regulatory units involved in B. distachyon-M. oryzae interactions. Moreover, using co-transformation technology, we demonstrated that BdNAC21 was negatively regulated by miR164c. This study provides a new approach for identifying resistance genes in B. distachyon by mining the miRNA regulatory network of host-pathogen interactions.

A Comprehensive Analysis of MicroRNAs Expressed in Susceptible and Resistant Rice Cultivars during Rhizoctonia solani AG1-IA Infection Causing Sheath Blight Disease

MicroRNAs regulate plant responses to fungal infections and immunity. In this study, miRNAs were identified in six rice cultivars during a Rhizoctonia solani Kühn AG1-IA infection using a deep sequencing approach. Known and novel miRNAs were analyzed in these rice cultivars, and a set of fungal infection/immunity-associated miRNAs and target genes were quantified by reverse transcription (RT)-qPCR in six rice cultivars. Additionally, the relative expression of these miRNAs was analyzed in different time points of the infection, wild species of rice, and in response to different strains of R. solani. Osa-miR1320-5p showed preferential expression during the fungal infection in all the six rice genotypes, while Osa-miR156d, Osa-miR159b, Osa-miR820c, and Osa-miR1876 were differentially regulated in susceptible and resistant genotypes. A greater degree of downregulation of miRNAs was observed during the initial time points of infection (24-72 h), suggesting a maximum molecular activity of rice-R. solani interaction and resistance response of the host during the early phase of infection. After R. solani infection, the expression of Osa-miR820c and Osa-miR156d was downregulated in Oryza rufipogon, O. alta, O. latifolia, and O. minuta, while Osa-miR397b was downregulated in all the wild rice species except O. officinalis. This study provided comprehensive information on the repertoire of miRNAs expressed in six sheath blight disease-susceptible and resistant indica and aus rice cultivars.

Barley microRNAs as metabolic sensors for soil nitrogen availability

Barley (Hordeum vulgare) is one of the most important crops in the world, ranking 4th in the worldwide production. Crop breeders are facing increasing environmental obstacles in the field, such as drought, salinity but also toxic over fertilization which not only impacts quality of the grain but also an yield. One of the most prevalent mechanisms of gene expression regulation in plants is microRNA-mediated silencing of target genes. We identified 13 barley microRNAs and 2 microRNAs* that are nitrogen excess responsive. Four microRNAs respond only in root, eight microRNAs only in shoot and one displays broad response in roots and shoots. We demonstrate that 2 microRNAs* are induced in barley shoot by nitrogen excess. For all microRNAs we identified putative target genes and confirmed microRNA-guided cleavage sites for ten out of thirteen mRNAs. None of the identified microRNAs or their target genes is known as nitrogen excess responsive. Analysis of expression pattern of thirteen target mRNAs and their cognate microRNAs showed expected correlations of their levels. The plant microRNAs analyzed are also known to respond to nitrogen deprivation and exhibit the opposite expression pattern when nitrogen excess/deficiency conditions are compared. Thus, they can be regarded as metabolic sensors of the regulation of nitrogen homeostasis in plants.

Overexpression of Arabidopsis microRNA167 induces salicylic acid-dependent defense against Pseudomonas syringae through the regulation of its targets ARF6 and ARF8

microRNAs are powerful regulators of growth, development, and stress responses in plants. The Arabidopsis thaliana microRNA miR167 was previously found to regulate diverse processes including flower development, root development, and response to osmotic stress by controlling the patterns of expression of its target genes AUXIN RESPONSE FACTOR 6 (ARF6), ARF8, and IAA-Ala RESISTANT 3. Here, we report that miR167 also modulates defense against pathogens through ARF6 and ARF8. miR167 is differentially expressed in response to the bacterial pathogen Pseudomonas syringae, and overexpression of miR167 confers very high levels of resistance. This resistance appears to be due to suppression of auxin responses and is partially dependent upon salicylic acid signaling, and also depends upon altered stomatal behavior in these plants. Closure of stomata upon the detection of P. syringae is an important aspect of the basal defense response, as it prevents bacterial cells from entering the leaf interior and causing infection. Plants overexpressing miR167 constitutively maintain small stomatal apertures, resulting in very high resistance when the pathogen is inoculated onto the leaf surface. Additionally, the systemic acquired resistance (SAR) response is severely compromised in plants overexpressing miR167, in agreement with previous work showing that the activation of SAR requires intact auxin signaling responses. This work highlights a new role for miR167, and also emphasizes the importance of hormonal balance in short- and long-term defense and of stomata as an initial barrier to pathogen entry.