microRNA-mediated <Emphasis Type="Italic">R</Emphasis> gene regulation: molecular scabbards for double-edged swords

Plant resistance (R) proteins are immune receptors that recognize pathogen effectors and trigger rapid defense responses, namely effector-triggered immunity. R protein-mediated pathogen resistance is usually race specific. During plant-pathogen coevolution, plant genomes accumulated large numbers of R genes. Even though plant R genes provide important natural resources for breeding disease-resistant crops, their presence in the plant genome comes at a cost. Misregulation of R genes leads to developmental defects, such as stunted growth and reduced fertility. In the past decade, many microRNAs (miRNAs) have been identified to target various R genes in plant genomes. miRNAs reduce R gene levels under normal conditions and allow induction of R gene expression under various stresses. For these reasons, we consider R genes to be double-edged “swords” and miRNAs as molecular “scabbards”. In the present review, we summarize the contributions and potential problems of these “swords” and discuss the features and production of the “scabbards”, as well as the mechanisms used to pull the “sword” from the “scabbard” when needed.     

Suppression of NB-LRR genes by miRNAs promotes nitrogen-fixing nodule development in Medicago truncatula

Plant genomes contain two major classes of innate immune receptors to recognize different pathogens. The pattern recognition receptors perceive conserved pathogen-associated molecular patterns and the resistance genes with nucleotide-binding (NB) and leucine-rich repeat (LRR) domains recognize specific pathogen effectors. The precise regulation of resistance genes is important since the unregulated expression of NB-LRR genes can inhibit growth and may result in autoimmunity in the absence of pathogen infection. It was shown that a subset of miRNAs could target NB-LRR genes and act as an important regulator of plant immunity in the absence of pathogens. Plants not only interact with pathogens, but they can also establish symbiotic interactions with microbes. Nitrogen-fixing symbiotic interaction and nodule formation of legumes may also require the suppression of host defence to prevent immune responses. We found that upon symbiotic interactions, miRNAs repressing NB-LRR expression are upregulated in the developing nodules of Medicago truncatula. Furthermore, we show that the suppression of the activity of the NB-LRR genes targeted by these miRNAs is important during nodule development. Our results suggest that the downregulation of NB-LRR resistance genes in the developing nodule produces a suitable niche that facilitates bacterial colonization and the development of an N-fixing nodule.     

Conservation and divergence in plant microRNAs

MicroRNAs (miRNAs) are a class of small, non-coding RNAs that regulate gene expression in eukaryotic cells. The past decade has seen an explosion in our understanding of the sets of miRNA genes encoded in the genomes in different species of plants and the mechanisms by which miRNAs interact with target RNAs. A subset of miRNA families (and their binding sites in target RNAs) are conserved between angiosperms and basal plants, suggesting they predate the divergence of existing lineages of plants. However, the majority of miRNA families expressed by any given plant species have a narrow phylogenetic distribution. As a group, these "young" miRNAs genes appear to be evolutionarily fluid and lack clearly understood biological function. The goal of this review is to summarize our understanding of the sets of miRNA genes and miRNA targets that exist in various plant species and to discuss hypotheses that explain the patterns of conservation and divergence observed among microRNAs in plants.     

寄主植物与病原菌免疫反应的分子遗传基础

近年来,大量的植物抗病基因和病原菌无毒基因被克隆,抗病基因和无毒基因的结构、功能及其互作关系的研究也取得重大进展。在植物中,由病原菌模式分子(pathogen-associated molecular patterns, PAMPs)引发的免疫反应(PAMP-triggered immunity, PTI)和由效应因子引发的免疫反应(effector-triggered immunity, ETI)是植物在长期进化过程中形成的两类抵抗病原物的机制。PTI反应主要通过细胞表面受体(patternrecognition receptors, PRRs)识别并结合PAMPs从而激活下游免疫反应,而在ETI反应中,则通过植物R基因(resistance gene,R)与病原菌无毒基因(avirulence gene, Avr)产物间的直接或间接相互作用来完成免疫反应。本文对植物PTI反应和ETI反应分别进行了概述,重点探讨了植物R基因与病原菌Avr基因之间的互作遗传机理,并对目前植物抗性分子遗传机制研究和抗病育种中的问题进行了探讨和展望。     

Comparative genetics of disease resistance within the solanaceae

Genomic positions of phenotypically defined disease resistance genes (R genes) and R gene homologues were analyzed in three solanaceous crop genera, Lycopersicon (tomato), Solanum (potato), and Capsicum (pepper). R genes occurred at corresponding positions in two or more genomes more frequently than expected by chance; however, in only two cases, both involving Phytophthora spp., did genes at corresponding positions have specificity for closely related pathogen taxa. In contrast, resistances to Globodera spp., potato virus Y, tobacco mosaic virus, and tomato spotted wilt virus were mapped in two or more genera and did not occur in corresponding positions. Without exception, pepper homologues of the cloned R genes Sw-5, N, Pto, Prf, and I2 were found in syntenous positions in other solanaceous genomes and in some cases also mapped to additional positions near phenotypically defined solanaceous R genes. This detailed analysis and synthesis of all available data for solanaceous R genes suggests a working hypothesis regarding the evolution of R genes. Specifically, while the taxonomic specificity of host R genes may be evolving rapidly, general functions of R alleles (e.g., initiation of resistance response) may be conserved at homologous loci in related plant genera.     

Identification of miR414 and expression analysis of conserved miRNAs from Stevia rebaudiana

MicroRNAs (miRNAs) usually contain 19-24 nucleotides and have been identified as important eukaryotic gene regulators. Applications of various computational approaches have simplified the task by predicting miRNAs from available sequence data sources. In this study, we identified a conserved miR414 from a computational analysis of EST sequence data available from Stevia rebaudiana. In addition, we also identified six conserved miRNAs namely miR169, miR319, miR414, miR164, miR167 and miR398 using stem-loop RT-PCR analysis. Hence, miR414 was commonly identified using both methods. The expression analysis of these miRNAs documented their roles in growth and development of Stevia. Furthermore, the detected miRNAs were found to target genes involved in plant growth, development, metabolism and signal transduction. This is the first study reporting these conserved miRNAs and their expression in Stevia.     

Genomes, diversity and resistance gene analogues in Musa species

Resistance genes (R genes) in plants are abundant and may represent more than 1% of all the genes. Their diversity is critical to the recognition and response to attack from diverse pathogens. Like many other crops, banana and plantain face attacks from potentially devastating fungal and bacterial diseases, increased by a combination of worldwide spread of pathogens, exploitation of a small number of varieties, new pathogen mutations, and the lack of effective, benign and cheap chemical control. The challenge for plant breeders is to identify and exploit genetic resistances to diseases, which is particularly difficult in banana and plantain where the valuable cultivars are sterile, parthenocarpic and mostly triploid so conventional genetic analysis and breeding is impossible. In this paper, we review the nature of R genes and the key motifs, particularly in the Nucleotide Binding Sites (NBS), Leucine Rich Repeat (LRR) gene class. We present data about identity, nature and evolutionary diversity of the NBS domains of Musa R genes in diploid wild species with the Musa acuminata (A), M. balbisiana (B), M. schizocarpa (S), M. textilis (T), M. velutina and M. ornata genomes, and from various cultivated hybrid and triploid accessions, using PCR primers to isolate the domains from genomic DNA. Of 135 new sequences, 75% of the sequenced clones had uninterrupted open reading frames (ORFs), and phylogenetic UPGMA tree construction showed four clusters, one from Musa ornata, one largely from the B and T genomes, one from A and M. velutina, and the largest with A, B, T and S genomes. Only genes of the coiled-coil (non-TIR) class were found, typical of the grasses and presumably monocotyledons. The analysis of R genes in cultivated banana and plantain, and their wild relatives, has implications for identification and selection of resistance genes within the genus which may be useful for plant selection and breeding and also for defining relationships and genome evolution patterns within the genus using the multi-copy and variable resistance genes.     

miRNA在植物响应高温胁迫中的研究进展

microRNA(miRNA)是一类由20-24个核苷酸组成的小的非编码RNA,通常通过序列互补降解或抑制其靶标基因转录后的翻译过程,从而在转录后水平上调控基因的表达。miRNA在植物基因组中普遍存在,作为一类重要的调节因子参与到植物的生长发育与逆境响应中。目前,已有研究表明高温除了诱导植物编码基因表达发生改变之外,一些非编码RNA的表达也发生了显著改变,其中miRNA作为重要的非编码RNA,参与了植物的高温胁迫响应。对植物miRNA的合成途径,作用机制以及主要功能进行了扼要阐述,重点阐述了高温胁迫下植物miRNA的作用机制,旨在为mi RNA在植物抵抗高温胁迫中的研究与应用提供新的思路。     

Balancing selection at the tomato RCR3 Guardee gene family maintains variation in strength of pathogen defense

Coevolution between hosts and pathogens is thought to occur between interacting molecules of both species. This results in the maintenance of genetic diversity at pathogen antigens (or so-called effectors) and host resistance genes such as the major histocompatibility complex (MHC) in mammals or resistance (R) genes in plants. In plant-pathogen interactions, the current paradigm posits that a specific defense response is activated upon recognition of pathogen effectors via interaction with their corresponding R proteins. According to the "Guard-Hypothesis," R proteins (the "guards") can sense modification of target molecules in the host (the "guardees") by pathogen effectors and subsequently trigger the defense response. Multiple studies have reported high genetic diversity at R genes maintained by balancing selection. In contrast, little is known about the evolutionary mechanisms shaping the guardee, which may be subject to contrasting evolutionary forces. Here we show that the evolution of the guardee RCR3 is characterized by gene duplication, frequent gene conversion, and balancing selection in the wild tomato species Solanum peruvianum. Investigating the functional characteristics of 54 natural variants through in vitro and in planta assays, we detected differences in recognition of the pathogen effector through interaction with the guardee, as well as substantial variation in the strength of the defense response. This variation is maintained by balancing selection at each copy of the RCR3 gene. Our analyses pinpoint three amino acid polymorphisms with key functional consequences for the coevolution between the guardee (RCR3) and its guard (Cf-2). We conclude that, in addition to coevolution at the "guardee-effector" interface for pathogen recognition, natural selection acts on the "guard-guardee" interface. Guardee evolution may be governed by a counterbalance between improved activation in the presence and prevention of auto-immune responses in the absence of the corresponding pathogen.     

Plants and pathogenic agents, a refined and dangerous relationship: the example of fungi

Plant-fungus interactions are highly diverse, either being beneficial to the host plant such as those leading to mycorhizal symbiosis, or very detrimental when leading to severe diseases. Since the beginning of agriculture, improvement of plant resistance to pathogens has remained a major challenge. Breeding for resistance, first conducted empirically in the past centuries, was then performed on a more theoretical basis after the statement of heredity laws by Mendel at the end of the XIXth century. As a result, most cultivated species contain various cultivars whose resistance or susceptibility to a given pathogen species depend on their interaction with various races of that pathogen. Such highly specific race-cultivar systems are particularly suited for understanding the molecular dialogue which underlies compatible (host susceptible/pathogen virulent) or incompatible (host resistant/pathogen avirulent) interactions. During the twentieth century, one of the major events that paved the way for future research was the statement by Flor [1946, 1947] of the gene-for-gene concept. Studying inheritance of the disease phenotype in the interaction between flax and Melampsora lini he showed that resistance in the host and avirulence in the pathogen are dictated by single dominant genes which correspond one to one, i.e. one resistance gene for one avirulence gene. The fact that incompatibility may depend on the presence of only one resistance (R) gene in the host and one avirulence (Avr) gene in the pathogen was fully confirmed about 40 years later. Molecular genetics and complementation experiments have allowed to isolate numerous R and Avr genes from various plant-pathogen systems, and to verify the gene-for-gene concept. These studies have enlightened the elicitor/receptor concept, formerly introduced to account for the specificity of the compatible and incompatible interactions. The present knowledge of R and Avr genes also allows to predict how such genes have evolved and how they could be used to improve disease resistance. At the beginning of the twenty first century, this remains a major challenge in view of the severe losses caused by pests and pathogens to most crops on the earth.     

Gene expression profile of the plant pathogen Xylella fastidiosa during biofilm formation in vitro

A biofilm is a community of microorganisms attached to a solid surface. Cells within biofilms differ from planktonic cells, showing higher resistance to biocides, detergent, antibiotic treatments and host defense responses. Even though there are a number of gene expression studies in bacterial biofilm formation, limited information is available concerning plant pathogen. It was previously demonstrated that the plant pathogen Xylella fastidiosa could grow as a biofilm, a possibly important factor for its pathogenicity. In this study we utilized analysis of microarrays to specifically identify genes expressed in X. fastidiosa cells growing in a biofilm, when compared to planktonic cells. About half of the differentially expressed genes encode hypothetical proteins, reflecting the large number of ORFs with unknown functions in bacterial genomes. However, under the biofilm condition we observed an increase in the expression of some housekeeping genes responsible for metabolic functions. We also found a large number of genes from the pXF51 plasmid being differentially expressed. Some of the overexpressed genes in the biofilm condition encode proteins involved in attachment to surfaces. Other genes possibly confer advantages to the bacterium in the environment that it colonizes. This study demonstrates that the gene expression in the biofilm growth condition of the plant pathogen X. fastidiosa is quite similar to other characterized systems.     

The R1 gene for potato resistance to late blight (Phytophthora infestans) belongs to the leucine zipper/NBS/LRR class of plant resistance genes

Late blight caused by the oomycete Phytophthora infestans is the most destructive disease in potato cultivation worldwide. New, more virulent P. infestans strains have evolved which overcome the genetic resistance that has been introgressed by conventional breeding from wild potato species into commercial varieties. R genes (for single-gene resistance) and genes for quantitative resistance to late blight are present in the germplasm of wild and cultivated potato. The molecular basis of single-gene and quantitative resistance to late blight is unknown. We have cloned R1, the first gene for resistance to late blight, by combining positional cloning with a candidate gene approach. The R1 gene is member of a gene family. It encodes a protein of 1293 amino acids with a molecular mass of 149.4 kDa. The R1 gene belongs to the class of plant genes for pathogen resistance that have a leucine zipper motif, a putative nucleotide binding domain and a leucine-rich repeat domain. The most closely related plant resistance gene (36% identity) is the Prf gene for resistance to Pseudomonas syringae of tomato. R1 is located within a hot spot for pathogen resistance on potato chromosome V. In comparison to the susceptibility allele, the resistance allele at the R1 locus represents a large insertion of a functional R gene.