Showing papers by "Pamela C. Ronald published in 2012"

Top 10 plant pathogenic bacteria in molecular plant pathology

Abstract: Many plant bacteriologists, if not all, feel that their particular microbe should appear in any list of the most important bacterial plant pathogens. However, to our knowledge, no such list exists. The aim of this review was to survey all bacterial pathologists with an association with the journal Molecular Plant Pathology and ask them to nominate the bacterial pathogens they would place in a 'Top 10' based on scientific/economic importance. The survey generated 458 votes from the international community, and allowed the construction of a Top 10 bacterial plant pathogen list. The list includes, in rank order: (1) Pseudomonas syringae pathovars; (2) Ralstonia solanacearum; (3) Agrobacterium tumefaciens; (4) Xanthomonas oryzae pv. oryzae; (5) Xanthomonas campestris pathovars; (6) Xanthomonas axonopodis pathovars; (7) Erwinia amylovora; (8) Xylella fastidiosa; (9) Dickeya (dadantii and solani); (10) Pectobacterium carotovorum (and Pectobacterium atrosepticum). Bacteria garnering honourable mentions for just missing out on the Top 10 include Clavibacter michiganensis (michiganensis and sepedonicus), Pseudomonas savastanoi and Candidatus Liberibacter asiaticus. This review article presents a short section on each bacterium in the Top 10 list and its importance, with the intention of initiating discussion and debate amongst the plant bacteriology community, as well as laying down a benchmark. It will be interesting to see, in future years, how perceptions change and which bacterial pathogens enter and leave the Top 10.

Reference genome sequence of the model plant Setaria

Abstract: We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ~400-Mb assembly covers ~80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).

Plant Innate Immunity: Perception of Conserved Microbial Signatures

Abstract: Plants and animals sense conserved microbial signatures through receptors localized to the plasma membrane and cytoplasm. These receptors typically carry or associate with non-arginine-aspartate (non-RD) kinases that initiate complex signaling networks cumulating in robust defense responses. In plants, coregulatory receptor kinases have been identified that not only are critical for the innate immune response but also serve an essential function in other regulatory signaling pathways.

XAX1 from glycosyltransferase family 61 mediates xylosyltransfer to rice xylan

Abstract: Xylan is the second most abundant polysaccharide on Earth and represents an immense quantity of stored energy for biofuel production. Despite its importance, most of the enzymes that synthesize xylan have yet to be identified. Xylans have a backbone of β-1,4–linked xylose residues with substitutions that include α-(1→2)–linked glucuronosyl, 4-O-methyl glucuronosyl, and α-1,2- and α-1,3-arabinofuranosyl residues. The substitutions are structurally diverse and vary by taxonomy, with grass xylan representing a unique composition distinct from dicots and other monocots. To date, no enzyme has yet been identified that is specific to grass xylan synthesis. We identified a xylose-deficient loss-of-function rice mutant in Os02g22380, a putative glycosyltransferase in a grass-specific subfamily of family GT61. We designate the mutant xax1 for xylosyl arabinosyl substitution of xylan 1. Enzymatic fingerprinting of xylan showed the specific absence in the mutant of a peak, which was isolated and determined by 1H-NMR to be (β-1,4-Xyl)4 with a β-Xylp-(1→2)-α-Araf-(1→3). Rice xax1 mutant plants are deficient in ferulic and coumaric acid, aromatic compounds known to be attached to arabinosyl residues in xylan substituted with xylosyl residues. The xax1 mutant plants exhibit an increased extractability of xylan and increased saccharification, probably reflecting a lower degree of diferulic cross-links. Activity assays with microsomes isolated from tobacco plants transiently expressing XAX1 demonstrated xylosyltransferase activity onto endogenous acceptors. Our results provide insight into grass xylan synthesis and how substitutions may be modified for increased saccharification for biofuel generation.

The Rice Oligonucleotide Array Database: an atlas of rice gene expression

Abstract: Microarray technologies facilitate high-throughput gene expression analysis. However, the diversity of platforms for rice gene expression analysis hinders efficient analysis. Tools to broadly integrate microarray data from different platforms are needed. In this study, we developed the Rice Oligonucleotide Array Database (ROAD, http://www.ricearray.org ) to explore gene expression across 1,867 publicly available rice microarray hybridizations. The ROAD’s user-friendly web interface and variety of visualization tools facilitate the extraction of gene expression profiles using gene and microarray element identifications. The ROAD supports meta-analysis of genes expressed in different tissues and at developmental stages. Co-expression analysis tool provides information on co-regulation between genes under general, abiotic and biotic stress conditions. Additionally, functional analysis tools, such as Gene Ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology, are embedded in the ROAD. These tools facilitate the identification of meaningful biological patterns in a list of query genes. The Rice Oligonucleotide Array Database provides comprehensive gene expression profiles for all rice genes, and will be a useful resource for researchers of rice and other grass species.

Loss of Cellulose Synthase-Like F6 Function Affects Mixed-Linkage Glucan Deposition, Cell Wall Mechanical Properties, and Defense Responses in Vegetative Tissues of Rice

Abstract: Mixed-linkage glucan (MLG) is a cell wall polysaccharide containing a backbone of unbranched (1,3)- and (1,4)-linked β-glucosyl residues. Based on its occurrence in plants and chemical characteristics, MLG has primarily been associated with the regulation of cell wall expansion due to its high and transient accumulation in young, expanding tissues. The Cellulose synthase-like F (CslF) subfamily of glycosyltransferases has previously been implicated in mediating the biosynthesis of this polymer. We confirmed that the rice (Oryza sativa) CslF6 gene mediates the biosynthesis of MLG by overexpressing it in Nicotiana benthamiana. Rice cslf6 knockout mutants show a slight decrease in height and stem diameter but otherwise grew normally during vegetative development. However, cslf6 mutants display a drastic decrease in MLG content (97% reduction in coleoptiles and virtually undetectable in other tissues). Immunodetection with an anti-MLG monoclonal antibody revealed that the coleoptiles and leaves retain trace amounts of MLG only in specific cell types such as sclerenchyma fibers. These results correlate with the absence of endogenous MLG synthase activity in mutant seedlings and 4-week-old sheaths. Mutant cell walls are weaker in mature stems but not seedlings, and more brittle in both stems and seedlings, compared to wild type. Mutants also display lesion mimic phenotypes in leaves, which correlates with enhanced defense-related gene expression and enhanced disease resistance. Taken together, our results underline a weaker role of MLG in cell expansion than previously thought, and highlight a structural role for MLG in nonexpanding, mature stem tissues in rice.

Cleavage and nuclear localization of the rice XA21 immune receptor

Abstract: The rice pattern recognition receptor—XA21—confers immunity against the Gram-negative bacterial pathogen, Xanthomonas oryzae pv. oryzae. This study shows that the intracellular kinase domain of XA21 translocates to the nucleus and that this translocation is essential for the XA21-mediated immune response.

Protein phosphorylation in plant immunity: insights into the regulation of pattern recognition receptor-mediated signaling.

Abstract: Plants are continuously challenged by pathogens including viruses, bacteria, and fungi The plant immune system recognizes invading pathogens and responds by activating an immune response These responses occur rapidly and often involve post-translational modifications (PTMs) within the proteome Protein phosphorylation is a common and intensively studied form of these PTMs and regulates many plant processes including plant growth, development, and immunity Most well-characterized pattern recognition receptors (PRRs), including Xanthomonas resistance 21 (XA21), flagellin sensitive 2 (FLS2), and elongation factor (EF)-Tu receptor (EFR), possess intrinsic protein kinase activity and regulate downstream signaling through phosphorylation events Here, we focus on the phosphorylation events of plant PRRs that play important roles in the immune response We also discuss the role of phosphorylation in regulating mitogen-associated protein kinase (MAPK) cascades and transcription factors in plant immune signaling

Tyrosine sulfation in a Gram-negative bacterium

Abstract: Tyrosine sulfation, a well-characterized post-translation modification in eukaryotes, has not previously been reported in prokaryotes. Here, we demonstrate that the RaxST protein from the Gram-negative bacterium, Xanthomonas oryzae pv. oryzae, is a tyrosine sulfotransferase. We used a newly developed sulfotransferase assay and ultraviolet photodissociation mass spectrometry to demonstrate that RaxST catalyses sulfation of tyrosine 22 of the Xoo Ax21 (activator of XA21-mediated immunity) protein. These results demonstrate a previously undescribed post-translational modification in a prokaryotic species with implications for studies of host immune responses and bacterial cell-cell communication systems.

A Genome-Wide Survey of Switchgrass Genome Structure and Organization

Abstract: The perennial grass, switchgrass (Panicum virgatum L.), is a promising bioenergy crop and the target of whole genome sequencing. We constructed two bacterial artificial chromosome (BAC) libraries from the AP13 clone of switchgrass to gain insight into the genome structure and organization, initiate functional and comparative genomic studies, and assist with genome assembly. Together representing 16 haploid genome equivalents of switchgrass, each library comprises 101,376 clones with average insert sizes of 144 (HindIII-generated) and 110 kb (BstYI-generated). A total of 330,297 high quality BAC-end sequences (BES) were generated, accounting for 263.2 Mbp (16.4%) of the switchgrass genome. Analysis of the BES identified 279,099 known repetitive elements, >50,000 SSRs, and 2,528 novel repeat elements, named switchgrass repetitive elements (SREs). Comparative mapping of 47 full-length BAC sequences and 330K BES revealed high levels of synteny with the grass genomes sorghum, rice, maize, and Brachypodium. Our data indicate that the sorghum genome has retained larger microsyntenous regions with switchgrass besides high gene order conservation with rice. The resources generated in this effort will be useful for a broad range of applications.

Genome-wide identification and analysis of early heat stress responsive genes in rice

Abstract: To overcome the challenges presented by predicted climate change, it is important to understand how crops perceive and respond to high temperatures. In this paper, we performed genome-wide transcriptome analysis of rice to identify immediate early genes strongly induced by high temperature. We compared the effects of high temperature (37°C) treatments (for 0.5 or 1h) of seedlings relative to untreated controls (28°C) using the NSF45K array. We then identified 710 genes exhibiting at least 2-fold up-regulation at both time points. From the comparison of this dataset with other publicly available rice datasets under heat stress [i.e., for 10 and 30 min (early heat response), and 10 h at 42°C (late heat response)], we identified 244 genes and 238 genes at least 2 fold upregulated during the early and late heat responses, respectively. We defined 244 genes as early heat stress responsive group and 238 genes as prolonged heat stress responsive group. Gene ontology (GO) enrichment analysis revealed that a chaperone-mediated protein folding cofactor was the most significantly over-represented GO term associated with the prolonged heat response. Processes involved in cellular protein metabolism, protein folding, response to stress, small GTPase mediated signal transduction, and glycolysis are enriched in both early and prolonged heat responses, suggesting a role for these genes in the general heat stress response. Enrichment of processes involved in cell redox homeostasis, intracellular protein transport, electron transport chain, and regulation of transcription (DNA-dependent) were only identified in the early heat response. In addition, we observed that a large portion of the genes relating to the prolonged heat response were also associated with responses to other abiotic stresses such as drought, salt, cold, and submergence. Our data contribute to a better understanding the molecular mechanism of heat stress response in rice.

A rice transient assay system identifies a novel domain in NRR required for interaction with NH1/OsNPR1 and inhibition of NH1-mediated transcriptional activation.

Abstract: Background: Arabidopsis NPR1 is a master regulator of systemic acquired resistance. NPR1 binds to TGA transcription factors and functions as a transcriptional co-activator. In rice, NH1/OsNPR1 functions to enhance innate immunity. NRR disrupts NH1 function, when over-expressed. Results: We have established a rice transient protoplast assay to demonstrate that NH1 is a transcriptional coactivator and that NRR represses NH1-mediated activation. We identified three NRR homologues (RH1, RH2, and RH3). RH1 and RH3, but not RH2, also effectively repress NH1-mediated transcriptional activation. NRR, RH1, RH2, and RH3 share sequence similarity in a region beyond the previously identified NPR1-interacting domain. This region is required for strong interaction with NH1. A double point mutation, W66A/F70A, in this novel NH1interacting domain severely reduces interaction with NH1. Mutation W66A/F70A also greatly reduces the ability of NRR to repress NH1-mediated activation. RH2 carries a deviation (amino acids AV) in this region as compared to consensus sequences (amino acids ED) among NRR, RH1, and RH3. A substitution (AV to ED) in RH2 results in strong binding of mutant RH2ED to NH1 and effective repression of NH1-mediated activation. Conclusions: The protoplast-based transient system can be used to dissect protein domains associated with their functions. Our results demonstrate that the ability of NRR and its homologues to repress NH1-mediated transcriptional activation is tightly correlated with their ability to bind to NH1. Furthermore, a sequence is identified as a novel NH1-interacting domain. Importantly, this novel sequence is widely present in plant species, from cereals to castor bean plants, to poplar trees, to Arabidopsis, indicating its significance in plants.

Top 10 plant pathogenic bacteria in molecular plant pathology. - eScholarship

Abstract: Many plant bacteriologists, if not all, feel that their particular microbe should appear in any list of the most important bacterial plant pathogens. However, to our knowledge, no such list exists. The aim of this review was to survey all bacterial pathologists with an association with the journal Molecular Plant Pathology and ask them to nominate the bacterial pathogens they would place in a 'Top 10' based on scientific/economic importance. The survey generated 458 votes from the international community, and allowed the construction of a Top 10 bacterial plant pathogen list. The list includes, in rank order: (1) Pseudomonas syringae pathovars; (2) Ralstonia solanacearum; (3) Agrobacterium tumefaciens; (4) Xanthomonas oryzae pv. oryzae; (5) Xanthomonas campestris pathovars; (6) Xanthomonas axonopodis pathovars; (7) Erwinia amylovora; (8) Xylella fastidiosa; (9) Dickeya (dadantii and solani); (10) Pectobacterium carotovorum (and Pectobacterium atrosepticum). Bacteria garnering honourable mentions for just missing out on the Top 10 include Clavibacter michiganensis (michiganensis and sepedonicus), Pseudomonas savastanoi and Candidatus Liberibacter asiaticus. This review article presents a short section on each bacterium in the Top 10 list and its importance, with the intention of initiating discussion and debate amongst the plant bacteriology community, as well as laying down a benchmark. It will be interesting to see, in future years, how perceptions change and which bacterial pathogens enter and leave the Top 10.

Establishment of Glucocorticoid-Mediated Transcriptional Induction of the Rice XA21 Pattern Recognition Receptor

Abstract: The rice pattern recognition receptor, XA21, confers robust resistance to the bacterial pathogen Xantho- monas oryzae pv. oryzae (Xoo). We have generated transgenic plants that express Xa21 only in the presence of the glucocorticoid hormone, dexamethasone (DEX). DEX-mediated transcriptional induction of Xa21 is accom- panied by upregulation of pathogenesis-related 1 gene expression and restriction of Xoo multiplication. The DEX- inducible system can be used to synchronize the XA21- mediated response to infection throughout the entire leaf, facilitating the study of innate immunity.

FLS2-Mediated Responses to Ax21-Derived Peptides: Response to the Mueller et al. Commentary

Abstract: In [Danna et al. (2011)][1], we reported the surprising result that sulfated synthetic peptide preparations, corresponding to derivatives of the Xanthomonas oryzae pv oryzae axYS22 peptide, activate a variety of FLAGELLIN-SENSITIVE2 (FLS2)–dependent defense-related responses in Arabidopsis

Ligand induced cleavage and nuclear localization of the rice XA21 immune receptor

Abstract: The rice XA21 receptor confers immunity to the Gram-negative bacterial pathogen, Xanthomonas oryzae pv. oryzae (Xoo) upon recognition of the conserved microbial signature AxY^S^22. Here, we demonstrate that the intracellular kinase domain of XA21 translocates to the nucleus upon AxY^S^22-mediated perception and that this translocation event is required for XA21-mediated immunity.

Genes involved in stress response in plants

Abstract: Provided herein are genes involved in stress resistance ( e . g ., resistance to a pathogen), genetically modified plants with elevated or reduced expression of these genes, and methods of making genetically modified plants with enhanced stress resistance.

The Rice Xa21 Immune Receptor Recognizes a Novel Bacterial Quorum Sensing Factor

Abstract: During the course of evolution, plants and animals have acquired the capability to perceive microbes and respond with robust defense responses. Plant diseases were mentioned in 750 BCE in the Hebrew Bible and again in the writings of Democritus, around 470 BCE (Agrios 1997). Theophrastus made plants and plant disease a subject of systematic studies in 300 BCE. He and his contemporaries believed that plant diseases were a manifestation of the wrath of God (Agrios 1997). Very little useful knowledge about plant diseases was gained for another 2000 years. The devastating late blight of potatoes, an epidemic that began in 1845 and destroyed the principal food source for millions of people in Ireland, launched the first serious investigations into the basis of plant disease. Although some scientists believed that the causal agent was a microbe (Kelman and Peterson 2002), this hypothesis flew in the face of the prevailing scientific view that microbes commonly found in diseased plant tissues were the products rather than the cause of disease. In 1853, through studies of rusts and smut fungi infection of cereal crops, De Bary conclusively demonstrated that microbes are the causal agents of infectious disease (Agrios 1997). A quarter century later, the causal role of microorganisms in animal diseases was demonstrated by Koch (1876), who studied anthrax in cattle, using the mouse as a model host. Koch’s postulates, developed in the course of these studies, applied equally thereafter to work with plant and animal pathogens. Biffen (1894–1949), a British geneticist and plant breeder, speculated that resistance to disease would be inherited in Mendelian ratios, and in 1905 he demonstrated that this was true for resistance to yellow rust, a fungal disease of wheat (http://www.answers.com/topic/rowland-biffen). In 1946, Flor (1942, 1971) working with the rust disease of flax proposed the gene-for-gene hypothesis based on genetic analyses of the variation within host and pathogen populations. He used the terms “host resistance genes” and “pathogen avirulence (avr) genes.” The presence of corresponding avr-R genes in each organism leads to recognition and the activation of defense responses, limiting infection. Flor’s hypothesis suggested that specific sensors for microbial molecules were present in their hosts. Although some resistance genes conferred broad-spectrum resistance, others did not, specifying resistance to only some races of a particular pathogen species.