Small RNAs in Tomato: from defence to development

RNA silencing is a major regulator of gene expression in plants, controlling from development to transposable element silencing and stress responses. As part of the silencing machinery, micro (mi)RNAs orchestrate silencing of their targets, either directly or through cascades of secondary small interfering (si)RNAs. To investigate the role of RNA silencing in plant immunity, I chose to focus on the miR482/2118 family, because of its diversity and presence in many plant species since the appearance of seed plants, with most genomes containing several copies, and because its members target sequences conserved in a family of disease resistance genes known Nucleotide biding site leucine-rich repeat (NLR) genes. In this dissertation, I wanted to address the extent to which the miRNA family and its derived phasiRNAs regulate expression of defence genes as well as contribute to quantitative resistance in crops. I explore the structural differences of miR482/2118 members in Solanum lycopersicum and show that they are functionally significant and affect their target preferences. My approach was based on small RNA sequencing and degradome data to characterize targets of these miRNAs, including the recently discovered tomato TAS5 locus. I also generated transgenic tomatoes constitutively expressing target mimic RNAs that sequester different miR482/2118 members. These tomato mimic RNA lines were less susceptible than their non-transgenic precursors to pathogens Phytophthora infestans and Pseudomonas syringae. Additionally, I investigated the role of small RNAs and their effector proteins during vegetative and reproductive development in tomato. I employed transcript and small RNA sequencing and CRISPR-Cas9 techniques of gene editing to investigate the impact of these factors in gamete viability and transposable element silencing in vegetative meristems. The results presented here provide new evidence about the extent that RNA silencing contributes to the regulation of vital processes in plants. My study primarily explores the extent to which structural differences between the members of the miR482/2118 family affect their range of action, and the use of target mimics against these miRNAs as biotechnological approach for enhancing disease resistance in highly bred cultivars.My work on this thesis was supported by the European Research Council Advanced Investigator Grant ERC-2013-AdG 340642 awarded to Professor David Baulcomb

A novel DCL2-dependent miRNA pathway in tomato affects susceptibility to RNA viruses.

Tomato Dicer-like2 (slDCL2) is a key component of resistance pathways against potato virus X (PVX) and tobacco mosaic virus (TMV). It is also required for production of endogenous small RNAs, including miR6026 and other noncanonical microRNAs (miRNAs). The slDCL2 mRNAs are targets of these slDCL2-dependent RNAs in a feedback loop that was disrupted by target mimic RNAs of miR6026. In lines expressing these RNAs, there was correspondingly enhanced resistance against PVX and TMV. These findings illustrate a novel miRNA pathway in plants and a crop protection strategy in which miRNA target mimicry elevates expression of defense-related mRNAs

Enhanced resistance to bacterial and oomycete pathogens by short tandem target mimic RNAs in tomato

Nucleotide binding site leucine-rich repeat (NLR) proteins of the plant innate immune system are negatively regulated by the miR482/2118 family microRNAs (miRNAs) that are in a distinct 22nt class of miRNAs with a double mode of action. First they cleave the target RNA, as with the canonical 21nt miRNAs, and second they trigger secondary siRNA production using the target RNA as a template. Here we address the extent to which the miR482/2118 family affects expression of NLR mRNAs and disease resistance. First we show that structural differences of miR482/2118 family members in tomato (Solanum lycopersicum) are functionally significant. The predicted target of the miR482 subfamily is conserved motif in multiple NLR mRNAs whereas, for miR2118b, it is a novel non-coding RNA target formed by rearrangement of several different NLR genes. From RNA sequencing and degradome data in lines expressing short tandem target mimic (STTM) RNAs of miR482/2118 we confirm the different targets of these miRNAs. The effect on NLR mRNA accumulation is slight but, nevertheless, the tomato STTM lines display enhanced resistance to infection with the oomycete and bacterial pathogens. These data implicate an RNA cascade of miRNAs and secondary siRNAs in the regulation of NLR RNAs and show that the encoded NLR proteins have a role in quantitative disease resistance in addition to dominant gene resistance that has been well characterized elsewhere. We also illustrate the use of STTM RNA in a biotechnological approach for enhancing quantitative disease resistance in highly bred cultivars.This work was supported by the Balzan Foundation and the European Research Council Advanced Investigator Grant ERC-2013-AdG 340642, Royal Society Edward Penley Abraham Research Professor, Gatsby Foundation Fellowship GAT3395/GLD and a Royal Society University Research Fellowship UF160413

Enhanced resistance to bacterial and oomycete pathogens by short tandem target mimic RNAs in tomato

Nucleotide binding site leucine-rich repeat (NLR) proteins of the plant innate immune system are negatively regulated by the miR482/2118 family miRNAs that are in a distinct 22-nt class of miRNAs with a double mode of action. First, they cleave the target RNA, as with the canonical 21-nt miRNAs, and second, they trigger secondary siRNA production using the target RNA as a template. Here, we address the extent to which the miR482/2118 family affects expression of NLR mRNAs and disease resistance. We show that structural differences of miR482/2118 family members in tomato (Solanum lycopersicum) are functionally significant. The predicted target of the miR482 subfamily is a conserved motif in multiple NLR mRNAs, whereas for miR2118b, it is a noncoding RNA target formed by rearrangement of several different NLR genes. From RNA sequencing and degradome data in lines expressing short tandem target mimic (STTM) RNAs of miR482/2118, we confirm the different targets of these miRNAs. The effect on NLR mRNA accumulation is slight, but nevertheless, the tomato STTM lines display enhanced resistance to infection with the oomycete and bacterial pathogens. These data implicate an RNA cascade of miRNAs and secondary siRNAs in the regulation of NLR RNAs and show that the encoded NLR proteins have a role in quantitative disease resistance in addition to dominant gene resistance that has been well characterized elsewhere. We also illustrate the use of STTM RNA in a biotechnological approach for enhancing quantitative disease resistance in highly bred cultivars.This work was supported by the Balzan Foundation and European Research Council Advanced Investigator Grant ERC-2013-AdG 340642. S.S. is funded by Gatsby Foundation Fellowship GAT3395/GLD and Royal Society University Research Fellowship UF160413. D.C.B. is the Royal Society Edward Penley Abraham Research Professor

Innovation, conservation, and repurposing of gene function in root cell type development

Plant species have evolved myriads of solutions, including complex cell type development and regulation, to adapt to dynamic environments. To understand this cellular diversity, we profiled tomato root cell type translatomes. Using xylem differentiation in tomato, examples of functional innovation, repurposing, and conservation of transcription factors are described, relative to the model plant Arabidopsis. Repurposing and innovation of genes are further observed within an exodermis regulatory network and illustrate its function. Comparative translatome analyses of rice, tomato, and Arabidopsis cell populations suggest increased expression conservation of root meristems compared with other homologous populations. In addition, the functions of constitutively expressed genes are more conserved than those of cell type/tissue-enriched genes. These observations suggest that higher order properties of cell type and pan-cell type regulation are evolutionarily conserved between plants and animals

Innovation, conservation, and repurposing of gene function in root cell type development

Plant species have evolved myriads of solutions, including complex cell type development and regulation, to adapt to dynamic environments. To understand this cellular diversity, we profiled tomato root cell type translatomes. Using xylem differentiation in tomato, examples of functional innovation, repurposing, and conservation of transcription factors are described, relative to the model plant Arabidopsis. Repurposing and innovation of genes are further observed within an exodermis regulatory network and illustrate its function. Comparative translatome analyses of rice, tomato, and Arabidopsis cell populations suggest increased expression conservation of root meristems compared with other homologous populations. In addition, the functions of constitutively expressed genes are more conserved than those of cell type/tissue-enriched genes. These observations suggest that higher order properties of cell type and pan-cell type regulation are evolutionarily conserved between plants and animals