Molecular cloning and characterisation of SlAGO family in tomato

Resistance gene Ty-1 restricts TYLCV infection in tomato by increasing RNA silencing

A major antiviral mechanism in plants is mediated by RNA silencing through the action of DICER-like (DCL) proteins, which cleave dsRNA into discrete small RNA fragments, and ARGONAUTE (AGO) proteins, which use the small RNAs to target single-stranded RNA. RNA silencing can also be amplified through the action of RNA-dependent RNA polymerases (RDRs), which use single stranded RNA to generate dsRNA that in turn is targeted by DCL proteins. As a counter-defense, plant viruses encode viral suppressors of RNA silencing (VSRs) that target different components in the RNA silencing pathway. The tomato Ty-1 gene confers resistance to the DNA virus tomato yellow leaf curl virus (TYLCV) and has been reported to encode an RDRγ protein. However, the molecular mechanisms by which Ty-1 controls TYLCV infection, including whether Ty-1 is involved in RNA silencing, are unknown. Here, by using a transient expression assay, we have confirmed that Ty-1 shows antiviral activity against TYLCV in Nicotiana benthamiana. Also, in transient expression-based silencing assays, Ty-1 augmented systemic transgene silencing in GFP transgenic N. benthamiana plants. Furthermore, co-expression of Ty-1 or other RDRγ proteins from N. benthamiana or Arabidopsis with various proteins resulted in lower protein expression. These results are consistent with a model wherein Ty-1-mediated resistance to TYLCV is due, at least in part, to an increase in RNA silencing activity.

Function and regulation of plant ARGONAUTE proteins in response to environmental challenges: a review

Environmental stresses diversely affect multiple processes related to the growth, development, and yield of many crops worldwide. In response, plants have developed numerous sophisticated defense mechanisms at the cellular and subcellular levels to react and adapt to biotic and abiotic stressors. RNA silencing, which is an innate immune mechanism, mediates sequence-specific gene expression regulation in higher eukaryotes. ARGONAUTE (AGO) proteins are essential components of the RNA-induced silencing complex (RISC). They bind to small noncoding RNAs (sRNAs) and target complementary RNAs, causing translational repression or triggering endonucleolytic cleavage pathways. In this review, we aim to illustrate the recently published molecular functions, regulatory mechanisms, and biological roles of AGO family proteins in model plants and cash crops, especially in the defense against diverse biotic and abiotic stresses, which could be helpful in crop improvement and stress tolerance in various plants.

Tomato MicroRNAs and Their Functions

MicroRNAs (miRNAs) define an essential class of non-coding small RNAs that function as posttranscriptional modulators of gene expression. They are coded by MIR genes, several hundreds of which exist in the genomes of Arabidopsis and rice model plants. The functional analysis of Arabidopsis and rice miRNAs indicate that their miRNAs regulate a wide range of processes including development, reproduction, metabolism, and stress. Tomato serves as a major model crop for the study of fleshy fruit development and ripening but until recently, information on the identity of its MIR genes and their coded miRNAs was limited and occasionally contradictory. As a result, the majority of tomato miRNAs remained uncharacterized. Recently, a comprehensive annotation of tomato MIR genes has been carried out by several labs and us. In this review, we curate and organize the resulting partially overlapping MIR annotations into an exhaustive and non-redundant atlas of tomato MIR genes. There are 538 candidate and validated MIR genes in the atlas, of which, 169, 18, and 351 code for highly conserved, Solanaceae-specific, and tomato-specific miRNAs, respectively. Furthermore, a critical review of functional studies on tomato miRNAs is presented, highlighting validated and possible functions, creating a useful resource for future tomato miRNA research.

Tomato salt tolerance mechanisms and their potential applications for fighting salinity: A review

One of the most significant environmental factors affecting plant growth, development and productivity is salt stress. The damage caused by salt to plants mainly includes ionic, osmotic and secondary stresses, while the plants adapt to salt stress through multiple biochemical and molecular pathways. Tomato (Solanum lycopersicum L.) is one of the most widely cultivated vegetable crops and a model dicot plant. It is moderately sensitive to salinity throughout the period of growth and development. Biotechnological efforts to improve tomato salt tolerance hinge on a synthesized understanding of the mechanisms underlying salinity tolerance. This review provides a comprehensive review of major advances on the mechanisms controlling salt tolerance of tomato in terms of sensing and signaling, adaptive responses, and epigenetic regulation. Additionally, we discussed the potential application of these mechanisms in improving salt tolerance of tomato, including genetic engineering, marker-assisted selection, and eco-sustainable approaches.

RNAi-Based Antiviral Innate Immunity in Plants

Multiple antiviral immunities were developed to defend against viral infection in hosts. RNA interference (RNAi)-based antiviral innate immunity is evolutionarily conserved in eukaryotes and plays a vital role against all types of viruses. During the arms race between the host and virus, many viruses evolve viral suppressors of RNA silencing (VSRs) to inhibit antiviral innate immunity. Here, we reviewed the mechanism at different stages in RNAi-based antiviral innate immunity in plants and the counteractions of various VSRs, mainly upon infection of RNA viruses in model plant Arabidopsis. Some critical challenges in the field were also proposed, and we think that further elucidating conserved antiviral innate immunity may convey a broad spectrum of antiviral strategies to prevent viral diseases in the future.

Genome-wide identification of Argonautes in Solanaceae with emphasis on potato

Regulatory small RNAs (sRNAs) play important roles in many fundamental processes in plant biology such as development, fertilization and stress responses. The AGO protein family has here a central importance in gene regulation based on their capacity to associate with sRNAs followed by mRNA targeting in a sequence-complementary manner. The present study explored Argonautes (AGOs) in the Solanaceae family, with emphasis on potato, Solanum tuberosum (St). A genome-wide monitoring was performed to provide a deeper insight into gene families, genomic localization, gene structure and expression profile against the potato late blight pathogen Phytophthora infestans. Among 15 species in the Solanaceae family we found a variation from ten AGOs in Nicotiana obtusifolia to 17 in N. tabacum. Comprehensive analyses of AGO phylogeny revealed duplication of AGO1, AGO10 and AGO4 paralogs during early radiation of Solanaceae. Fourteen AGOs were identified in potato. Orthologs of AGO8 and AGO9 were missing in the potato genome. However, AGO15 earlier annotated in tomato was identified. StAGO15 differs from the other paralogs having residues of different physico-chemical properties at functionally important amino acid positions. Upon pathogen challenge StAGO15 was significantly activated and hence may play a prominent role in sRNA-based regulation of potato defense.

miR168 targets Argonaute1A mediated miRNAs regulation pathways in response to potassium deficiency stress in tomato

BACKGROUND

Potassium (K⁺) is an essential ion for most plants, as it is involved in the regulation of growth and development. K⁺ homeostasis in plant cells has evolved to facilitate plant adaptation to K⁺-deficiency stress. Argonaute1 (AGO1) is regulated by miR168 to modulate the small RNA regulatory pathway by RNA silencing complex (RISC) in tomatoes. However, the role of miR168-mediated regulation of AGO1 in the context of K⁺ deficiency stress in tomatoes has not been elucidated yet.

RESULTS

SlmiR168 and its target gene SlAGO1A were differentially expressed among low-K⁺-tolerant JZ34 and low-K⁺-sensitive JZ18 tomato plants. Transgenic tomato plants constitutively expressing pri-SlmiR168a showed stronger root system growth, better leaves development, and higher K⁺ contents in roots under K⁺-deficiency stress than those of the transgenic tomato lines expressing rSlAGO1A (SlmiR168-resistant) and the wild type (WT). Deep sequencing analysis showed that 62 known microRNAs (miRNAs) were up-regulated in 35S:rSlAGO1 compared with WT tomatoes. The same miRNAs were down-regulated in 35S:SlmiR168a compared with WT plants. The integrated analysis found 12 miRNA/mRNA pairs from the 62 miRNAs, including the root growth and cytokinin (CTK)/abscisic acid (ABA) pathways.

CONCLUSIONS

The regulation mediated by SlmiR168 of SlAGO1A contributes to the plant development under low-K⁺ stress. Moreover, this regulation mechanism may influence downstream miRNA pathways in response to low-K⁺ stress through the CTK/ABA and root growth modulation pathways.

New insights into tomato microRNAs

Cultivated tomato, Solanum lycopersicum, is one of the most common fruits in the global food industry. Together with the wild tomato Solanum pennellii, it is widely used for developing better cultivars. MicroRNAs affect mRNA regulation, inhibiting its translation and/or promoting its degradation. Important proteins involved in these processes are ARGONAUTE and DICER. This study aimed to identify and characterize the genes involved in the miRNA processing pathway, miRNA molecules and target genes in both species. We validated the presence of pathway genes and miRNA in different NGS libraries and 6 miRNA families using quantitative RT-PCR. We identified 71 putative proteins in S. lycopersicum and 108 in S. pennellii likely involved in small RNAs processing. Of these, 29 and 32 participate in miRNA processing pathways, respectively. We identified 343 mature miRNAs, 226 pre-miRNAs in 87 families, including 192 miRNAs, which were not previously identified, belonging to 38 new families in S. lycopersicum. In S. pennellii, we found 388 mature miRNAs and 234 pre-miRNAs contained in 85 families. All miRNAs found in S. pennellii were unpublished, being identified for the first time in our study. Furthermore, we identified 2471 and 3462 different miRNA target in S. lycopersicum and S. pennellii, respectively.

Cloning and Characterization of Argonaute Genes in Tomato

Argonaute (AGO) proteins are core elements in plant posttranscriptional RNA silencing pathways. The identification and functional characterization of tomato (Solanum lycopersicum) AGOs will help to better understand RNA silencing-based posttranscriptional regulation in fleshy fruits. Here we describe how to identify and clone SlAGO genes, as well as the methodology for their functional characterization.

Generation of an integrated Hieracium genomic and transcriptomic resource enables exploration of small RNA pathways during apomixis initiation

Background

Application of apomixis, or asexual seed formation, in crop breeding would allow rapid fixation of complex traits, economizing improved crop delivery. Identification of apomixis genes is confounded by the polyploid nature, high genome complexity and lack of genomic sequence integration with reproductive tissue transcriptomes in most apomicts.

Results

A genomic and transcriptomic resource was developed for Hieracium subgenus Pilosella (Asteraceae) which incorporates characterized sexual, apomictic and mutant apomict plants exhibiting reversion to sexual reproduction. Apomicts develop additional female gametogenic cells that suppress the sexual pathway in ovules. Disrupting small RNA pathways in sexual Arabidopsis also induces extra female gametogenic cells; therefore, the resource was used to examine if changes in small RNA pathways correlate with apomixis initiation. An initial characterization of small RNA pathway genes within Hieracium was undertaken, and ovary-expressed ARGONAUTE genes were identified and cloned. Comparisons of whole ovary transcriptomes from mutant apomicts, relative to the parental apomict, revealed that differentially expressed genes were enriched for processes involved in small RNA biogenesis and chromatin silencing. Small RNA profiles within mutant ovaries did not reveal large-scale alterations in composition or length distributions; however, a small number of differentially expressed, putative small RNA targets were identified.

Conclusions

The established Hieracium resource represents a substantial contribution towards the investigation of early sexual and apomictic female gamete development, and the generation of new candidate genes and markers. Observed changes in small RNA targets and biogenesis pathways within sexual and apomictic ovaries will underlie future functional research into apomixis initiation in Hieracium.

Electronic supplementary material

The online version of this article (doi:10.1186/s12915-016-0311-0) contains supplementary material, which is available to authorized users.

Ectopic expression of SlAGO7 alters leaf pattern and inflorescence architecture and increases fruit yield in tomato

ARGONAUTE7 (AGO7), a key regulator of the trans-acting small interfering RNAs (ta-siRNA) pathway, plays a conserved role in controlling leaf pattern among species. However, little is known about the ta-siRNA pathway in regulating inflorescence architecture and fruit yield. In this study, we characterized the expression pattern, subcellular localization and developmental functions of SlAGO7 in tomato (Solanum lycopersicum). Overexpressing SlAGO7 in tomato exhibited pleiotropic phenotypes, including improved axillary bud formation, altered leaf morphology and inflorescence architecture, and increased fruit yield. Cross-sectioning of leaves showed that the number of vascular bundles was significantly increased in 35:SlAGO7 lines. Overexpression of SlAGO7 increased the production of ta-siRNA, and repressed the expression ta-siRNA-targeted genes (SlARF2a, SlARF2b, SlARF3 and SlARF4). Further analysis showed that overexpression of SlAGO7 alters the expression of key genes implicated in leaf morphology, inflorescence architecture, auxin transport and signaling. In addition, the altered auxin response of 35:SlAGO7 lines were also investigated. These results suggested that SlAGO7 plays a positive role in determining inflorescence architecture and fruit yield though the ta-siRNA pathway. Therefore, SlAGO7 represents a useful gene that can be incorporated in tomato breeding programs for developing cultivars with yield potential.

Suppress to Survive-Implication of Plant Viruses in PTGS

In higher plants, evolutionarily conserved processes playing an essential role during gene expression rely on small noncoding RNA molecules (sRNA). Within a wide range of sRNA-dependent cellular events, there is posttranscriptional gene silencing, the process that is activated in response to the presence of double-stranded RNAs (dsRNAs) in planta. The sequence-specific mechanism of silencing is based on RNase-mediated trimming of dsRNAs into translationally inactive short molecules. Viruses invading and replicating in host are also a source of dsRNAs and are recognized as such by cellular posttranscriptional silencing machinery leading to degradation of the pathogenic RNA. However, viruses are not totally defenseless. In parallel with evolving plant defense strategies, viruses have managed a wide range of multifunctional proteins that efficiently impede the posttranscriptional gene silencing. These viral counteracting factors are known as suppressors of RNA silencing. The aim of this review is to summarize the role and the mode of action of several functionally characterized RNA silencing suppressors encoded by RNA viruses directly involved in plant-pathogen interactions. Additionally, we point out that the widely diverse functions, structures, and modes of action of viral suppressors can be performed by different proteins, even in related viruses. All those adaptations have been evolved to achieve the same goal: to maximize the rate of viral genetic material replication by interrupting the evolutionary conserved plant defense mechanism of posttranscriptional gene silencing.

miR168 influences phase transition, leaf epinasty, and fruit development via SlAGO1s in tomato

In Arabidopsis thaliana, Argonaute1 (AGO1) interacts with miR168 to modulate the small RNA regulatory pathway. However, the underlying mechanism of regulation and relationship between AGO1 and miR168 is poorly understood in the cash crop Solanum lycopersicum (tomato). We previously found that SlAGO1A and SlAGO1B were cleaved by miR168 in tomato. In this study, we show that SlAGO1A and SlAGO1B accumulate in miR168-sponge transgenic plants, and that expression of miR168-resistant SlAGO1A (4m-SlAGO1A) and SlAGO1B (4m-SlAGO1B) in tomato results in a series of defects affecting growth rate, floral timing, leaves, and fruit. Accumulation of miR156 was found when 4m-SlAGO1A was at an early developmental stage compared to the wild type and original SlAGO1A transgenic plants, and miR172 was highly expressed in adult 4m-SlAGO1A compared to the controls. In addition, the expression of multiple small RNAs was altered in 4m-SlAGO1A. Taken together, our data provide novel insights into the interaction between SlAGO1s and miR168 in determining growth rate, phase change, leaf epinasty, fruit initiation and expansion, and other developmental processes in tomato.

Identification and functional analysis of novel and conserved microRNAs in tomato

MicroRNAs are ~22 nt non-coding endogenous RNAs which play important regulation roles in various species. By using homology-based computational research, 14 novel and conserved tomato miRNAs belonging to ten families were identified from EST, GSS, and nucleotide sequences. Real-time PCR analysis of these miRNAs demonstrated their expression in tomato afterwards. Meanwhile, a total of 36 potential targets were predicted for the ten miRNAs using psRNATarget. The target genes were mainly involved in metabolism, transmembrane transport, stress response, and transcription regulation. According to our experiment, miR398 was down-regulated on different levels under biotic and abiotic stresses, suggesting that miR398 might be involved in tomato stress regulatory network. Our results supplement the findings of tomato miRNAs and also suggest crucial regulatory functions of miRNAs in stress responses.