Puccinia striiformis f. sp. tritici microRNA-like RNA 1 (Pst-milR1), an important pathogenicity factor of Pst, impairs wheat resistance to Pst by suppressing the wheat pathogenesis-related 2 gene

Trichoderma as a Model to Study Effector-Like Molecules

Plants are capable of perceiving microorganisms by coordinating processes to establish different forms of plant-microbe relationships. Plant colonization is governed in fungal and bacterial systems by secreted effector molecules, suppressing plant defense responses and modulating plant physiology to promote either virulence or compatibility. Proteins, secondary metabolites, and small RNAs have been described as effector molecules that use different mechanisms to establish the interaction. Effector molecules have been studied in more detail due to their involvement in harmful interactions, leading to a negative impact on agriculture. Recently, research groups have started to study the effectors in symbiotic interactions. Interestingly, most symbiotic effectors are members of the same families present in phytopathogens. Nevertheless, the quantity and ratio of secreted effectors depends on the microorganism and the host, suggesting a complex mechanism of recognition between the plant and their associated microorganisms. Fungi belonging to Trichoderma genus interact with plants by inducing their defense system and promoting plant growth. Research suggests that some of these effects are associated with effector molecules that Trichoderma delivers during the association with the plant. In this review, we will focus on the main findings concerning the effector molecules reported in Trichoderma spp. and their role during the interaction with plants, mainly in the molecular dialogue that takes place between them.

Wheat TaLr35PR2 gene is required for Lr35-mediated adult plant resistance against leaf rust fungus

In this study we analysed the expression patterns of TaLr35PR2 and confirmed its role in Lr35-mediated adult resistance to leaf rust fungus. β-1,3-glucanase, a pathogenesis-related protein, has a critical function in plant defence response against fungal pathogens. We previously described the full-length gene TaLr35PR2, which encodes a protein exhibiting amino acid and structural similarity to β-1,3-glucanase, in the wheat near-isogenic line TcLr35 (GenBank accession number DQ294235.1). This work aimed to further assess TaLr35PR2 expression patterns and function in Lr35-mediated adult resistance to Puccinia triticina. Immunoblot was performed to demonstrate that TaLr35PR2 expression was triggered early by P. triticina, with expression levels markedly elevated in incompatible interaction compared with those in compatible one. Additionally, TaLr35PR2 accumulation steadily increased and overtly peaked after challenge with P. triticina through the various developmental stages of TcLr35 wheat, and remaining at similar levels after mock inoculation. Furthermore, TaLr35PR2 expression was significantly reduced in barley stripe mosaic virus (BSMV)-induced gene knockdown plants, in which pathological assessment revealed that TaLr35PR2-silenced plants was obviously susceptible to leaf rust fungus compared with wild-type TcLr35, indicating that Lr35-mediated resistance to leaf rust was diminished. These findings strongly suggest that TaLr35PR2 is involved in Lr35-mediated wheat defence against the leaf rust pathogen.

Further Elucidation of the Argonaute and Dicer Protein Families in the Model Grass Species Brachypodium distachyon

RNA interference (RNAi) is a biological process in which small RNAs regulate gene silencing at the transcriptional or posttranscriptional level. The trigger for gene silencing is double-stranded RNA generated from an endogenous genomic locus or a foreign source, such as a transgene or virus. In addition to regulating endogenous gene expression, RNAi provides the mechanistic basis for small RNA-mediated communication between plant hosts and interacting pathogenic microbes, known as cross-kingdom RNAi. Two core protein components, Argonaute (AGO) and Dicer (DCL), are central to the RNAi machinery of eukaryotes. Plants encode for several copies of AGO and DCL genes; in Arabidopsis thaliana, the AGO protein family contains 10 members, and the DCL family contains four. Little is known about the conservation and specific roles of these proteins in monocotyledonous plants, which account for the most important food staples. Here, we utilized in silico tools to investigate the structure and related functions of AGO and DCL proteins from the model grass Brachypodium distachyon. Based on the presence of characteristic domains, 16 BdAGO- and 6 BdDCL-predicted proteins were identified. Phylogenetic analysis showed that both protein families were expanded in Brachypodium as compared with Arabidopsis. For BdDCL proteins, both plant species contain a single copy of DCL1 and DCL4; however, Brachypodium contains two copies each of DCL2 and DCL3. Members of the BdAGO family were placed in all three functional clades of AGO proteins previously described in Arabidopsis. The greatest expansion occurred in the AtAGO1/5/10 clade, which contains nine BdAGOs (BdAGO5/6/7/9/10/11/12/15/16). The catalytic tetrad of the AGO P-element-induced wimpy testis domain (PIWI), which is required for endonuclease activity, is conserved in most BdAGOs, with the exception of BdAGO1, which lacks the last D/H residue. Three-dimensional modeling of BdAGO proteins using tertiary structure prediction software supported the phylogenetic classification. We also predicted a provisional interactome network for BdAGOs, their localization within the cell, and organ/tissue-specific expression. Exploring the specifics of RNAi machinery proteins in a model grass species can serve as a proxy for agronomically important cereals such as barley and wheat, where the development of RNAi-based plant protection strategies is of great interest.

A novel miRNA negatively regulates resistance to Glomerella leaf spot by suppressing expression of an NBS gene in apple

Glomerella leaf spot (GLS) of apple (Malus×domestica Borkh.), caused by Glomerella cingulata, is an emerging fungal epidemic threatening the apple industry. Little is known about the molecular mechanism underlying resistance to this devastating fungus. In this study, high-throughput sequencing technology was used to identify microRNAs (miRNAs) involved in GLS resistance in apple. We focused on miRNAs that target genes related to disease and found that expression of a novel miRNA, Md-miRln20, was higher in susceptible apple varieties than in resistant ones. Furthermore, its target gene Md-TN1-GLS exhibited the opposite expression pattern, which suggested that the expression levels of Md-miRln20 and its target gene are closely related to apple resistance to GLS. Furthermore, downregulation of Md-miRln20 in susceptible apple leaves resulted in upregulation of Md-TN1-GLS and reduced the disease incidence. Conversely, overexpression of Md-miRln20 in resistant apple leaves suppressed Md-TN1-GLS expression, with increased disease incidence. We demonstrated that Md-miRln20 negatively regulates resistance to GLS by suppressing Md-TN1-GLS expression and showed, for the first time, a crucial role for miRNA in response to GLS in apple.

Functional characterization of the Wrab17 gene in the interaction process between wheat and Puccinia triticina

In the interaction between wheat and Puccinia triticina, wheat resists the invasion of P. triticina by producing hypersensitive reaction-programmed cell death (HR-PCD). To better understand the mechanism of wheat resistance to P. triticina, it is important to identify the defensive genes involved in wheat resistance to leaf rust. This paper systematically presented the role of Wrab17 in the HR-PCD process in wheat after infection by P. triticina. The subcellular location analysis is performed using the full length of Wrab17 coding sequences and Wrab17 is found to be localized in cell nucleus and cytoplasm. Quantitative RT-PCR (RT-qPCR) and western blot analysis showed that expression of Wrab17 at both mRNA and protein levels increased by P. triticina infection, indicating that the Wrab17 gene participated in the interaction between wheat and P. triticina. Wrab17 knockdown plants were generated by RNA-mediated gene silencing technology (RNA interference, RNAi) and confirmed by southern blot. Further analysis with P. triticina inoculation found that knockdown of Wrab17 exhibited decreased HR expansion area in incompatible combination (L10×260) and significant higher sensitivity to the compatible pathogen P. triticina race 165. In all, this work reports that Wrab17 is a new defensive gene playing a role in wheat resistance to leaf rust.

Small RNA trafficking at the forefront of plant-pathogen interactions

Plants and pathogenic microbes are engaged in constant attacks and counterattacks at the interface of the interacting organisms. Much of the molecular warfare involves cross-kingdom trafficking of proteins, nucleic acids, lipids, and metabolites that act as toxins, inhibitors, lytic enzymes, and signaling molecules. How various molecules are transported across the boundaries of plants and pathogens has remained largely unknown until now. Extracellular vesicles have emerged as likely carriers of molecular ammunition for both plants and pathogens. Recent advances are beginning to show how extracellular vesicles serve as powerful vehicles that transfer small RNAs from plants to fungal cells to diminish pathogen virulence and from fungi to plant cells to dampen host immunity.

A Bioinformatics Pipeline for the Analysis and Target Prediction of RNA Effectors in Bidirectional Communication During Plant-Microbe Interactions

Small RNA (sRNA) molecules are key factors in the communication between hosts and their interacting pathogens, where they function as effectors that can modulate both host defense and microbial virulence/pathogenicity through a mechanism termed cross-kingdom RNA interference (ck-RNAi). Consistent with this recent knowledge, sRNAs and their double-stranded RNA precursor have been adopted to control diseases in crop plants, demonstrating a straight forward application of the new findings to approach agricultural problems. Despite the great interest in natural ck-RNAi, it is astonishing to find just a few additional examples in the literature since the first report was published in 2013. One reason might be that the identification of sRNA effectors is hampered both by technical challenges and lack of routine bioinformatics application strategies. Here, we suggest a practical procedure to find, characterize, and validate sRNA effectors in plant-microbe interaction. The aim of this review is not to present and discuss all possible tools, but to give guidelines toward the best established software available for the analysis.

Plant MicroRNAs in Cross-Kingdom Regulation of Gene Expression

MicroRNAs (miRNAs) are a class of noncoding small RNAs, which play a crucial role in post-transcriptional gene regulation. Recently, various reports revealed that miRNAs could be transmitted between species to mediate cross-kingdom regulation by integrating into a specific target gene-mediated regulatory pathway to exert relevant biological functions. Some scholars and researchers have observed this as an attractive hypothesis that may provide a foundation for novel approaches in the diagnosis, prognosis, and treatment of disease. Meanwhile, others deem the mentioned results were obtained from a “false positive effect” of performed experiments. Here, we focus on several current studies concerning plant miRNA-mediated cross-kingdom regulation (from both fronts) and discuss the existing issues that need further consideration. We also discuss possible miRNA horizontal transfer mechanisms from one species to another and analyze the relationship between miRNA-mediated cross-kingdom regulation and coevolution during a long-term specific host–pathogen interaction.

Cross-kingdom RNA trafficking and environmental RNAi-nature's blueprint for modern crop protection strategies

In plants, small RNA (sRNA)-mediated RNA interference (RNAi) is critical for regulating host immunity against bacteria, fungi, oomycetes, viruses, and pests. Similarly, sRNAs from pathogens and pests also play an important role in modulating their virulence. Strikingly, recent evidence supports that some sRNAs can travel between interacting organisms and induce gene silencing in the counter party, a mechanism termed cross-kingdom RNAi. Exploiting this new knowledge, host-induced gene silencing (HIGS) by transgenic expression of pathogen gene-targeting double-stranded (ds)RNA has the potential to become an important disease-control method. To circumvent transgenic approaches, direct application of dsRNAs or sRNAs (environmental RNAi) onto host plants or post-harvest products leads to silencing of the target microbe/pest gene (referred to spray-induced gene silencing, SIGS) and confers efficient disease control. This review summarizes the current understanding of cross-kingdom RNA trafficking and environmental RNAi and how these findings can be developed into novel effective strategies to fight diseases caused by microbial pathogens and pests.

TaMAPK4 Acts as a Positive Regulator in Defense of Wheat Stripe-Rust Infection

Highly conserved mitogen-activated protein kinase (MAPK) cascades regulate numerous plant processes, including hormonal responses, stress, and innate immunity. In this research, TaMAPK4 was predicted to be a target of tae-miR164. We verified the binding and suppression of TaMAPK4 by co-expression in Nicotiana benthamiana. Moreover, we found TaMAPK4 was localized in the cytoplasm and nucleus using transient expression analyses. TaMAPK4 transcripts increased following salicylic acid (SA) treatment and when host plants were infected with an avirulent race of the stripe-rust pathogen. Silencing of TaMAPK4 by virus-induced gene silencing permitted increased colonization by the avirulent pathogen race. Detailed histological results showed increased Puccinia striiformis (Pst) hyphal length, hyphal branches, and infection uredinial size compared to the non-silenced control. SA accumulation and the transcript levels of TaPR1, TaPR2, and TaPR5 were significantly down-regulated in TaMAPK4 knockdown plants. Overall, these results suggest that TaMAPK4 plays an important role in signaling during the wheat-Pst interaction. These results present new insights into MAPK signaling in wheat defense to rust pathogen.