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    Research

    One of the major challenges facing humankind in the 21st century is how to feed a growing population that may exceed 9.5 billion people by 2050. This needs to be done using the same or even less natural resources, because water and land are used in the increasing urbanisation of the world. This implies that plant productivity needs to increase dramatically and that preventing crop losses from diseases will therefore be crucial to ensuring global food security.
    Plant diseases, caused by pathogenic microorganisms, reduce the yield of the world’s most important food crops, causing loss up to 40% of their annual production. One of the main reasons that plant diseases continue to cause such damage is that disease resistance introduced by plant breeding, in some cases is rapidly overcome by newly virulent pathogens. This problem is amplified by intensive crop cultivation techniques and mono-culture. Likewise, the loss of the genomic diversity during the transition from wild to cultivated crop populations, enhances this problem. In order to minimize crop losses due to plant diseases we need new knowledge regarding the mechanisms underpinning microbe recognition by plants. This requires, from one hand, to understand the biology of microbial pathogenesis and the virulence proteins they target into host cells to cause disease. From the other hand, to elucidate the mechanisms by which the resistant plants successfully defend themselves from attack.
    To understand plant and animal diseases, the most important challenge is to characterize the molecular mechanisms that underlie both disease susceptibility and host immunity. Only in this way can host immunity mechanisms be predictably manipulated to provide durable disease control.

    Pathogen virulence effector proteins: Pathogenic microorganisms have evolved sophisticated strategies to exploit the attractive nutritional menu provided by their plant and animal hosts. The majority of these pathogens are highly specialized and attack only a limited number of eukaryotic host organisms. However, some strains are capable of infecting a wide range of hosts that includes both plants and animals. Plant and animal pathogens (including bacteria, fungi, oomycetes, nematodes and some insect species), translocate pathogenicity proteins (effectors), into host cells, which facilitate colonisation of susceptible hosts. Effectors have generally evolved to enable parasitism by suppressing host immunity and/or by modifying host physiology to support growth and spread of the parasite. These responses are collectively known as effector-triggered susceptibility (ETS) and are achieved through the perturbation of a set of host processes that defined as effector-targeted pathways (ETPs). It has been shown that in plants a subset of pathogen effectors suppresses innate immune responses. However, in recent years, research has uncovered effector functions distinct from direct immune suppression. These include modulation of plant hormone signalling, metabolism or organelle function. These functions, may contribute to the modulation of plant cells in order to promote pathogen survival and nutrient release leading to pathogen replication and dissemination.

    However, the molecular mechanisms of function and the host targets for the vast majority of the pathogen effectors are largely unknown. While, their activities mean that the effector proteins can be used as tools to identify important components of plant innate immunity and physiology that could potentially lead to innovative strategies for crop improvement.

    Sarris et al., Cell, 2015. Sarris & Jones, Oncotarget, 2015.

    Plant innate immunity:

    The innate immune system protects multicellular organisms against pathogens via specialised immune receptors that activate immunity upon detection of pathogen invasion-associated molecules. Intracellular immune receptors, called NLRs (Nucleotide-binding domain and Leucine-rich Repeat-containing), mediate innate immunity in plants and animals. In animals, NLRs typically detect conserved pathogen-associated molecular patterns (PAMPs) or damage-associated molecular patterns (DAMPs).

    Plant and animal NLRs recognise pathogen-secreted pathogenicity proteins, called ‘effectors’, which promote virulence. The first characterised effectors were called ‘avirulence (AVR) proteins’ because they were recognised by an NLR encoded by a specific Resistance (R) gene allele, resulting in disease resistance, and the loss of pathogen virulence. The requirement of a specific host gene and a cognate pathogen gene for resistance led Harold Flor to postulate the ‘gene-for-gene’ hypothesis, which has acted as a framework for plant-pathogen interaction studies ever since. Upon detection of a pathogen, NLRs rapidly initiate a chain of events leading to an immune response that often culminates in programmed cell death, termed pyroptosis in animals and the hypersensitive response (HR) in plants.

    Animal and plant NLRs are structurally similar: both have a nucleotide binding domain (a NACHT domain in animals and an NB-ARC domain in plants), a leucine-rich repeat domain (LRR), and an N-terminal putative signalling domain. They form part of a structural class termed signal transduction ATPases with numerous domains (STAND). Animal NLRs usually signal via either an N-terminal PYRIN domain (PYD) or caspase recruitment domain (CARD), while plant NLRs usually carry either an N-terminal TIR (Toll/Interleukin-1 receptor/Resistance protein) or CC (coiled-coil) domain.

    Duxbury, et al., Bioessays, 2016.

     

    Plants are able to defend themselves, even if (unlike mammals), they lack mobile immune cells and a somatic adaptive immune system. Plant cells are exquisitely sensitive to colonization attempts by pathogens. They rapidly perceive and respond to potential pathogen threats in a measured manner and most infections are thwarted. To understand and manipulate disease resistance in plants (and animals), we need to understand pathogens recognition by potential hosts, and how this recognition is converted into effective host defence.

           The first level of defence in both plants and animals is initiated by host-encoded Pattern-Recognition Receptors (PRRs) that recognize pathogen-derived components referred to as Microbe- or Pathogen-Associated Molecular Patterns (MAMPs or PAMPs). Plants sense PAMPs and, in turn, differentially regulate a large set of immune responses. This is known as PAMP Triggered Immunity (PTI), or basal defence. However, in susceptible hosts, basal defence is inhibited by translocated/secreted pathogen effector proteins into host cells in order to facilitate spreading and onset of disease.

           The second level of plant defence response, common to plants and animals, engages intracellular immune receptors. In resistant plants intracellular receptors are encoded by Resistance (R) genes. Recent genomic studies reveal that some plants carry a repertoire of up to 100-600 different R genes. These genes mostly encode intra-cellular nucleotide-binding, leucine-rich repeat NLR (Nod-like immune receptors) proteins that resemble mammalian NLR receptors. Plant NLRs recognize specific pathogen effectors, either through direct NLR/effector binding or indirectly through the perception of effector’s function or alteration of a specific host process. R proteins activate a strong immune response known as “Effector-Triggered Immunity” (ETI). ETI in plants often leads to programmed hypersensitive cell death response (HR), which prevents further pathogen growth and spread to neighbouring tissues and other plants. These immune mechanisms have been successfully described in what has become known as the “zigzag” model. However, how perception leads to defence activation and HR induction is largely unknown. This constitutes a general problem for the predictive manipulation of immunity and in immune receptors function.

    Huh, et al., Plos Pathogens, 2017

    Recent findings from our group and others, show that some plant NLRs and host proteins involved in indirect recognition can be fused together. Specifically, NLR receptors can carry an additional protein domain, enabling perception of pathogen effectors. Such recognition mode is known as “The Integrated Decoy/Sensor” model and is based on three examples of NLRs with integrated domains (NLR-IDs) and mechanistic insights into their activity: Arabidopsis NLR protein RRS1 carries an additional WRKY domain; and rice RGA5 and Pik-1 proteins are fused to heavy metal-associated (HMA, also known as RATX1) domains.

    These finding and the availability of sequenced plant genomes allowed us to test if integration of new domains in NLRs is wide-spread in angiosperms. We examined NLR-some domain architectures from publicly available plant predicted proteomes, and identified a number of NLR-IDs that involved both recently formed and conserved or recurrent fusions. We screened 40 plant genomes, including mosses and flowering plants (monocots and dicots), to discover 265 unique NLR integrated-domains (IDs). Our analysis revealed that extraneous domains have repeatedly integrated into NLR proteins across all plant lineages. Some of the integrated domains are already known to be implicated in pathogen defense; for example, RIN4, NPR1. Other integrated domains originated from host proteins that may function in pathogen interactions, and are prime candidates for functional analysis to engineer disease-resistant plants.

    The identification of host subcellular components that are targeted by pathogens is a major advance in understanding “host susceptibility” and the successful manipulation of host immunity by pathogens of both plants and animals.

    The identification of effectors that target the ID domains will help to resolve the molecular mechanisms underlying pathogens virulence and ID function. This will greatly enhance our understanding of host resistance and susceptibility. Furthermore, the elucidation of the mechanistic insights and the molecular architecture of NLR-ISDs will allow predictive capacity and the potential to engineer novel immune receptors with new recognition capacities.

    Targeted re-engineering of NLR-ISDs has potential to greatly reduce crop losses due to disease by generating new resistances to important pathogens.

    Research Fields of Interest:

    • Molecular Plant-Microbe Interactions
    • Molecular Biology and Biotechnology of disease resistance in plants
    • Microbial Molecular Genomics/Proteomics
    • Microbial Comparative Genomics and Phylogeny

    We work on the following topics:

    1. What are the mechanisms of intracellular NLR immune receptors’ activation? and how do these receptors function to activate the plant innate immunity?
    2. What is the diversity of pathogen effector proteins, and how effectors diversity is connected to the limited key host cell targets?
    3. Can we genetic engineer durable disease resistance in plant?