TIR-catalyzed nucleotide signaling molecules in plant defense

Evolutionary and immune-activating character analyses of NLR genes in algae suggest the ancient origin of plant intracellular immune receptors

Nucleotide-binding leucine-rich repeat (NLR) proteins are crucial intracellular immune receptors in plants, responsible for detecting invading pathogens and initiating defense responses. While previous studies on the evolution and function of NLR genes were mainly limited to land plants, the evolutionary trajectory and immune-activating character of NLR genes in algae remain less explored. In this study, genome-wide NLR gene analysis was conducted on 44 chlorophyte species across seven classes and seven charophyte species across five classes. A few but variable number of NLR genes, ranging from one to 20, were identified in five chlorophytes and three charophytes, whereas no NLR gene was identified from the remaining algal genomes. Compared with land plants, algal genomes possess fewer or usually no NLR genes, implying that the expansion of NLR genes in land plants can be attributed to their adaptation to the more complex terrestrial pathogen environments. Through phylogenetic analysis, domain composition analysis, and conserved motifs profiling of the NBS domain, we detected shared and lineage-specific features between NLR genes in algae and land plants, supporting the common origin and continuous evolution of green plant NLR genes. Immune-activation assays revealed that both TNL and RNL proteins from green algae can elicit hypersensitive responses in Nicotiana benthamiana, indicating the molecular basis for immune activation has emerged in the early evolutionary stage of different types of NLR proteins. In summary, the results from this study suggest that NLR proteins may have taken a role as intracellular immune receptors in the common ancestor of green plants.

Arabidopsis PHYTOALEXIN DEFICIENT 4 promotes the maturation and nuclear accumulation of immune-related cysteine protease RD19

Arabidopsis PHYTOALEXIN DEFICIENT 4 (PAD4) has an essential role in pathogen resistance as a heterodimer with ENHANCED DISEASE SUSCEPTIBILITY 1 (EDS1). Here we investigated an additional PAD4 role in which it associates with and promotes the maturation of the immune-related cysteine protease RESPONSIVE TO DEHYDRATION 19 (RD19). We found that RD19 and its paralog RD19c promoted EDS1- and PAD4-mediated effector-triggered immunity to an avirulent Pseudomonas syringae strain, DC3000, expressing the effector AvrRps4 and basal immunity against the fungal pathogen Golovinomyces cichoracearum. Overexpression of RD19, but not RD19 protease-inactive catalytic mutants, in Arabidopsis transgenic lines caused EDS1- and PAD4-dependent autoimmunity and enhanced pathogen resistance. In these lines, RD19 maturation to a pro-form required its catalytic residues, suggesting that RD19 undergoes auto-processing. In transient assays, PAD4 interacted preferentially with the RD19 pro-protease and promoted its nuclear accumulation in leaf cells. Our results lead us to propose a model for PAD4-stimulated defense potentiation. PAD4 promotes maturation and nuclear accumulation of processed RD19, and RD19 then stimulates EDS1-PAD4 dimer activity to confer pathogen resistance. This study highlights potentially important additional PAD4 functions that eventually converge on canonical EDS1-PAD4 dimer signaling in plant immunity.

Systemic analysis of metabolome reconfiguration in Arabidopsis after abiotic stressors uncovers metabolites that modulate defense against pathogens

Understanding plant immune responses is complex because of the high interdependence among biological processes in homeostatic networks. Hence, the integration of environmental cues causes network rewiring that interferes with defense responses. Similarly, plants retain molecular signatures configured under abiotic stress periods to rapidly respond to recurrent stress, and these can alter immunity. Metabolome changes imposed by abiotic stressors are persistent, although their impact on defense remains to be clarified. In this study, we profiled metabolomes of Arabidopsis plants under several abiotic stress treatments applied individually or simultaneously to capture temporal trajectories in metabolite composition during adverse conditions and recovery. Further systemic analysis was performed to address the relevance of metabolome changes and extract central features to be tested in planta. Our results demonstrate irreversibility in major fractions of metabolome changes as a general pattern in response to abiotic stress periods. Functional analysis of metabolomes and co-abundance networks points to convergence in the reconfiguration of organic acid and secondary metabolite metabolism. Arabidopsis mutant lines for components related to these metabolic pathways showed altered defense capacities against different pathogens. Collectively, our data suggest that sustained metabolome changes configured in adverse environments can act as modulators of immune responses and provide evidence for a new layer of regulation in plant defense.

Plant NLR immunity activation and execution: a biochemical perspective

Plants deploy cell-surface and intracellular receptors to detect pathogen attack and trigger innate immune responses. Inside host cells, families of nucleotide-binding/leucine-rich repeat (NLR) proteins serve as pathogen sensors or downstream mediators of immune defence outputs and cell death, which prevent disease. Established genetic underpinnings of NLR-mediated immunity revealed various strategies plants adopt to combat rapidly evolving microbial pathogens. The molecular mechanisms of NLR activation and signal transmission to components controlling immunity execution were less clear. Here, we review recent protein structural and biochemical insights to plant NLR sensor and signalling functions. When put together, the data show how different NLR families, whether sensors or signal transducers, converge on nucleotide-based second messengers and cellular calcium to confer immunity. Although pathogen-activated NLRs in plants engage plant-specific machineries to promote defence, comparisons with mammalian NLR immune receptor counterparts highlight some shared working principles for NLR immunity across kingdoms.

Immunobiodiversity: Conserved and specific immunity across land plants and beyond

Angiosperms represent most plants that humans cultivate, grow, and eat. However, angiosperms are only one of five major land plant lineages. As a whole lineage, plants also include algal groups. All these clades represent a tremendous genetic diversity that can be investigated to reveal the evolutionary history of any given mechanism. In this review, we describe the current model of the plant immune system, discuss its evolution based on the recent literature, and propose future directions for the field. In angiosperms, plant-microbe interactions have been intensively studied, revealing essential cell surface and intracellular immune receptors, as well as metabolic and hormonal defense pathways. Exploring diversity at the genomic and functional levels demonstrates the conservation of these pathways across land plants, some of which are beyond plants. On basis of the conserved mechanisms, lineage-specific variations have occurred, leading to diversified reservoirs of immune mechanisms. In rare cases, this diversity has been harnessed and successfully transferred to other species by integration of wild immune receptors or engineering of novel forms of receptors for improved resistance to pathogens. We propose that exploring further the diversity of immune mechanisms in the whole plant lineage will reveal completely novel sources of resistance to be deployed in crops.

Regulation of plant immunity via small RNA-mediated control of NLR expression

Plants use different receptors to detect potential pathogens: membrane-anchored pattern recognition receptors (PRRs) activated upon perception of pathogen-associated molecular patterns (PAMPs) that elicit pattern-triggered immunity (PTI); and intracellular nucleotide-binding leucine-rich repeat proteins (NLRs) activated by detection of pathogen-derived effectors, activating effector-triggered immunity (ETI). The interconnections between PTI and ETI responses have been increasingly reported. Elevated NLR levels may cause autoimmunity, with symptoms ranging from fitness cost to developmental arrest, sometimes combined with run-away cell death, making accurate control of NLR dosage key for plant survival. Small RNA-mediated gene regulation has emerged as a major mechanism of control of NLR dosage. Twenty-two nucleotide miRNAs with the unique ability to trigger secondary siRNA production from target transcripts are particularly prevalent in NLR regulation. They enhance repression of the primary NLR target, but also bring about repression of NLRs only complementary to secondary siRNAs. We summarize current knowledge on miRNAs and siRNAs in the regulation of NLR expression with an emphasis on 22 nt miRNAs and propose that miRNA and siRNA regulation of NLR levels provides additional links between PTI and NLR defense pathways to increase plant responsiveness against a broad spectrum of pathogens and control an efficient deployment of defenses.

NLR signaling in plants: from resistosomes to second messengers

Nucleotide binding and leucine-rich repeat-containing receptors (NLRs) have a critical role in plant immunity through direct or indirect recognition of pathogen effectors. Recent studies have demonstrated that such recognition induces formation of large protein complexes called resistosomes to mediate NLR immune signaling. Some NLR resistosomes activate Ca2+ influx by acting as Ca2+-permeable channels, whereas others function as active NADases to catalyze the production of nucleotide-derived second messengers. In this review we summarize these studies on pathogen effector-induced assembly of NLR resistosomes and resistosome-mediated production of the second messengers of Ca2+ and nucleotide derivatives. We also discuss downstream events and regulation of resistosome signaling.

Novel Compounds Derived from DFPM Induce Root Growth Arrest through the Specific VICTR Alleles of Arabidopsis Accessions

The small compound [5-(3,4-dichlorophenyl) furan-2-yl]-piperidine-1-ylmethanethione (DFPM) inhibits ABA responses by activating effector-triggered immune signal transduction in Arabidopsis. In addition to the known function of DFPM as an antagonist of ABA signaling, DFPM causes accession-specific root growth arrest in Arabidopsis Columbia-0 via the TIR-NLR protein VICTR (VARIATION IN COMPOUND TRIGGERED ROOT growth response) in an EDS1/PAD4/RAR1/SGT1B-dependent manner. Although DFPM could control the specific steps of various cellular responses, the functional residues for the activity of DFPM or the existence of a stronger version of DFPM modification have not been characterized thoroughly. This study analyzed twenty-two DFPM derivatives during root growth arrest, inhibition of ABA signaling, and induction of biotic signal transduction to determine critical residues that confer the specific activity of DFPM. Furthermore, this study identified two more Arabidopsis accessions that generate significant root growth arrest in response to DFPM derivatives dependent on multiple amino acid polymorphisms in the coding region of VICTR. The isolation of novel compounds, such as DFPM-5, and specific amino acid polymorphisms critical for the compound-induced responses will help determine the detailed regulatory mechanism for how DFPM regulates abiotic and biotic stress signaling interactions.

New Biochemical Principles for NLR Immunity in Plants

While working for the United States Department of Agriculture on the North Dakota Agricultural College campus in Fargo, North Dakota, in the 1940s and 1950s, Harold H. Flor formulated the genetic principles for coevolving plant host-pathogen interactions that govern disease resistance or susceptibility. His 'gene-for-gene' legacy runs deep in modern plant pathology and continues to inform molecular models of plant immune recognition and signaling. In this review, we discuss recent biochemical insights to plant immunity conferred by nucleotide-binding domain/leucine-rich-repeat (NLR) receptors, which are major gene-for-gene resistance determinants in nature and cultivated crops. Structural and biochemical analyses of pathogen-activated NLR oligomers (resistosomes) reveal how different NLR subtypes converge in various ways on calcium (Ca2+) signaling to promote pathogen immunity and host cell death. Especially striking is the identification of nucleotide-based signals generated enzymatically by plant toll-interleukin 1 receptor (TIR) domain NLRs. These small molecules are part of an emerging family of TIR-produced cyclic and noncyclic nucleotide signals that steer immune and cell-death responses in bacteria, mammals, and plants. A combined genetic, molecular, and biochemical understanding of plant NLR activation and signaling provides exciting new opportunities for combatting diseases in crops. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.