Genetic diversity and differentiation within and between cultivated (Vitis vinifera L. ssp. sativa) and wild (Vitis vinifera L. ssp. sylvestris) grapes

Genetic characterization of 502 diverse grape accessions including 342 cultivated (V. vinifera ssp. sativa) and 160 wild (V. vinifera ssp. sylvestris) grapes showed considerable genetic diversity among accessions. A total of 117 alleles were detected across eight SSR loci with the average of 14 alleles per locus. The genetic diversity of wild grapes was slightly lower than that observed in the cultivated grapes probably due to small populations and severe natural selection leading to drift and loss of alleles and heterozygosity in wild grapes. The distance cluster analysis (CA) supported the classical ecogeographic groups with moderate genetic differentiation among them. There was a greater affinity of Occidentalis grape to wild grape from the Caucasus than other groups. However, a number of low to moderate frequency alleles that are present in the cultivated grape are not represented in the wild grape.

Arabidopsis TAO1 is a TIR-NB-LRR protein that contributes to disease resistance induced by the Pseudomonas syringae effector AvrB

The type III effector protein encoded by avirulence gene B (AvrB) is delivered into plant cells by pathogenic strains of Pseudomonas syringae. There, it localizes to the plasma membrane and triggers immunity mediated by the Arabidopsis coiled-coil (CC)-nucleotide binding (NB)-leucine-rich repeat (LRR) disease resistance protein RPM1. The sequence unrelated type III effector avirulence protein encoded by avirulence gene Rpm1 (AvrRpm1) also activates RPM1. AvrB contributes to virulence after delivery from P. syringae in leaves of susceptible soybean plants, and AvrRpm1 does the same in Arabidopsis rpm1 plants. Conditional overexpression of AvrB in rpm1 plants results in leaf chlorosis. In a genetic screen for mutants that lack AvrB-dependent chlorosis in an rpm1 background, we isolated TAO1 (target of AvrB operation), which encodes a Toll-IL-1 receptor (TIR)-NB-LRR disease resistance protein. In rpm1 plants, TAO1 function results in the expression of the pathogenesis-related protein 1 (PR-1) gene, suggestive of a defense response. In RPM1 plants, TAO1 contributes to disease resistance in response to Pto (P. syringae pathovars tomato) DC3000(avrB), but not against Pto DC3000(avrRpm1). The tao1–5 mutant allele, a stop mutation in the LRR domain of TAO1, posttranscriptionally suppresses RPM1 accumulation. These data provide evidence of genetically separable disease resistance responses to AvrB and AvrRpm1 in Arabidopsis. AvrB activates both RPM1, a CC-NB-LRR protein, and TAO1, a TIR-NB-LRR protein. These NB-LRR proteins then act additively to generate a full disease resistance response to P. syringae expressing this type III effector

The Arabidopsis thaliana RPM1 disease resistance gene product is a peripheral plasma membrane protein that is degraded coincident with the hypersensitive response

Disease resistance in plants is often controlled by a gene-for-gene mechanism in which avirulence (avr) gene products encoded by pathogens are specifically recognized, either directly or indirectly, by plant disease resistance (R) gene products. Members of the NBS-LRR class of R genes encode proteins containing a putative nucleotide binding site (NBS) and carboxyl-terminal leucine-rich repeats (LRRs). Generally, NBS-LRR proteins do not contain predicted transmembrane segments or signal peptides, suggesting they are soluble cytoplasmic proteins. RPM1 is an NBS-LRR protein from Arabidopsis thaliana that confers resistance to Pseudomonas syringae expressing either avrRpm1 or avrB. RPM1 protein was localized by using an epitope tag. In contrast to previous suggestions, RPM1 is a peripheral membrane protein that likely resides on the cytoplasmic face of the plasma membrane. Furthermore, RPM1 is degraded coincident with the onset of the hypersensitive response, suggesting a negative feedback loop controlling the extent of cell death and overall resistance response at the site of infection

What a Difference a Dalton Makes: Bacterial Virulence Factors Modulate Eukaryotic Host Cell Signaling Systems via Deamidation

Pathogenic bacteria commonly deploy enzymes to promote virulence. These enzymes can modulate the functions of host cell targets. While the actions of some enzymes can be very obvious (e.g., digesting plant cell walls), others have more subtle activities. Depending on the lifestyle of the bacteria, these subtle modifications can be crucially important for pathogenesis. In particular, if bacteria rely on a living host, subtle mechanisms to alter host cellular function are likely to dominate. Several bacterial virulence factors have evolved to use enzymatic deamidation as a subtle posttranslational mechanism to modify the functions of host protein targets. Deamidation is the irreversible conversion of the amino acids glutamine and asparagine to glutamic acid and aspartic acid, respectively. Interestingly, all currently characterized bacterial deamidases affect the function of the target protein by modifying a single glutamine residue in the sequence. Deamidation of target host proteins can disrupt host signaling and downstream processes by either activating or inactivating the target. Despite the subtlety of this modification, it has been shown to cause dramatic, context-dependent effects on host cells. Several crystal structures of bacterial deamidases have been solved. All are members of the papain-like superfamily and display a cysteine-based catalytic triad. However, these proteins form distinct structural subfamilies and feature combinations of modular domains of various functions. Based on the diverse pathogens that use deamidation as a mechanism to promote virulence and the recent identification of multiple deamidases, it is clear that this enzymatic activity is emerging as an important and widespread feature in bacterial pathogenesis

Pseudomonas syringae type III effector HopAF1 suppresses plant immunity by targeting methionine recycling to block ethylene induction

Pseudomonas syringae is a Gram-negative bacterium that uses a type III secretion system to inject type III effector (T3E) proteins into the host to cause disease in plants. Multiple P. syringae T3Es promote virulence by targeting immune system signaling pathways using diverse biochemical mechanisms. We provide evidence for a molecular function of the P. syringae T3E HopAF1. We demonstrate that the C-terminal region of HopAF1 has structural homology to deamidases. We demonstrate that an enzyme important for production of the gaseous signaling hormone ethylene is a target for HopAF1 and show that HopAF1 targets methylthioadenosine nucleosidase proteins MTN1 and MTN2 to dampen ethylene production during bacterial infection

Pivoting the Plant Immune System from Dissection to Deployment

Diverse and rapidly evolving pathogens cause plant diseases and epidemics that threaten crop yield and food security around the world. Research over the last 25 years has led to an increasingly clear conceptual understanding of the molecular components of the plant immune system. Combined with ever-cheaper DNA-sequencing technology and the rich diversity of germ plasm manipulated for over a century by plant breeders, we now have the means to begin development of durable (long-lasting) disease resistance beyond the limits imposed by conventional breeding and in a manner that will replace costly and unsustainable chemical controls

A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528

<p>Abstract</p> <p>Background</p> <p><it>Pseudomonas syringae </it>is a widespread bacterial pathogen that causes disease on a broad range of economically important plant species. Pathogenicity of <it>P. syringae </it>strains is dependent on the type III secretion system, which secretes a suite of up to about thirty virulence 'effector' proteins into the host cytoplasm where they subvert the eukaryotic cell physiology and disrupt host defences. <it>P. syringae </it>pathovar <it>tabaci </it>naturally causes disease on wild tobacco, the model member of the Solanaceae, a family that includes many crop species as well as on soybean.</p> <p>Results</p> <p>We used the 'next-generation' Illumina sequencing platform and the Velvet short-read assembly program to generate a 145X deep 6,077,921 nucleotide draft genome sequence for <it>P. syringae </it>pathovar <it>tabaci </it>strain 11528. From our draft assembly, we predicted 5,300 potential genes encoding proteins of at least 100 amino acids long, of which 303 (5.72%) had no significant sequence similarity to those encoded by the three previously fully sequenced <it>P. syringae </it>genomes. Of the core set of Hrp Outer Proteins that are conserved in three previously fully sequenced <it>P. syringae </it>strains, most were also conserved in strain 11528, including AvrE1, HopAH2, HopAJ2, HopAK1, HopAN1, HopI, HopJ1, HopX1, HrpK1 and HrpW1. However, the <it>hrpZ1 </it>gene is partially deleted and <it>hopAF1 </it>is completely absent in 11528. The draft genome of strain 11528 also encodes close homologues of HopO1, HopT1, HopAH1, HopR1, HopV1, HopAG1, HopAS1, HopAE1, HopAR1, HopF1, and HopW1 and a degenerate HopM1'. Using a functional screen, we confirmed that <it>hopO1, hopT1, hopAH1</it>, <it>hopM1'</it>, <it>hopAE1</it>, <it>hopAR1</it>, and <it>hopAI1' </it>are part of the virulence-associated HrpL regulon, though the <it>hopAI1' </it>and <it>hopM1' </it>sequences were degenerate with premature stop codons. We also discovered two additional HrpL-regulated effector candidates and an HrpL-regulated distant homologue of <it>avrPto1</it>.</p> <p>Conclusion</p> <p>The draft genome sequence facilitates the continued development of <it>P. syringae </it>pathovar <it>tabaci </it>on wild tobacco as an attractive model system for studying bacterial disease on plants. The catalogue of effectors sheds further light on the evolution of pathogenicity and host-specificity as well as providing a set of molecular tools for the study of plant defence mechanisms. We also discovered several large genomic regions in <it>Pta </it>11528 that do not share detectable nucleotide sequence similarity with previously sequenced <it>Pseudomonas </it>genomes. These regions may include horizontally acquired islands that possibly contribute to pathogenicity or epiphytic fitness of <it>Pta </it>11528.</p

New Horizons for Plant Translational Research

The world’s human population continues to expand and is predicted to reach ~9 billion by 2040, up from its current level of just over 7 billion. Some estimate that with this rate of population growth, accommodating the increased demand for food will require the world’s agricultural production to increase 50% by 2030. The planet’s water resources are also under pressure. As Pamela Ronald highlights in her accompanying Essay, the amount of fresh water available per person has decreased 4-fold in the last 60 years and of the water that is available ~70% is already used for agriculture. Thus, agricultural production must be intensified to feed more people with less water on the same amount of land (given that little undeveloped arable land remains and what does is being lost to urbanization, desertification, and environmental damage). Furthermore, pathogens that cause devastating crop losses continue to spread in the face of increased global commerce and climate change. Given these challenges, there is a pressing need for plant research to produce solutions to ensure food security in a sustainable and safe way. The need is acute in both developed countries and in the less developed parts of the world, where many people endure chronic malnutrition and suffer the long term consequences on their health and well being. Plant scientists, therefore, urgently need to increase the productivity, pathogen resistance, and sustainability of existing crops, and are challenged to domesticate new crops

Programmed cell death in the plant immune system

Cell death has a central role in innate immune responses in both plants and animals. Besides sharing striking convergences and similarities in the overall evolutionary organization of their innate immune systems, both plants and animals can respond to infection and pathogen recognition with programmed cell death. The fact that plant and animal pathogens have evolved strategies to subvert specific cell death modalities emphasizes the essential role of cell death during immune responses. The hypersensitive response (HR) cell death in plants displays morphological features, molecular architectures and mechanisms reminiscent of different inflammatory cell death types in animals (pyroptosis and necroptosis). In this review, we describe the molecular pathways leading to cell death during innate immune responses. Additionally, we present recently discovered caspase and caspase-like networks regulating cell death that have revealed fascinating analogies between cell death control across both kingdoms