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A bioinformatic analysis of genes involved in stress responses in Arabidopsis thaliana

By Linda Karen Hughes


Hyaloperonospora arabidopsidis is an obligate biotrophic oomycete shown to cause\ud downy mildew in Arabidopsis thaliana. The main focus of this project is examining\ud plant stress response and the strategies employed by H. arabidopsidis to infect\ud Arabidopsis and evade plant stress responses. Two regions of the H. arabidopsidis\ud genome containing genes expressed in planta during infection were bioinformatically\ud annotated. The results indicated the genes were involved in regulatory processes\ud associated with the pathogenicity of H. arabidopsidis but not a direct role in\ud pathogenicity. H. arabidopsidis infects its host by secreting effector proteins into the\ud cytoplasm and apoplastic space of the host. The secretome of H. arabidopsidis was\ud analysed to identify classes of cysteine rich apoplastic effectors. This identified 15\ud candidate elicitin (ELI) and elicitin-like (ELL) sequences, three Kazal-like serine\ud protease inhibitors and four candidates similar to the protein sequences of Ppats 14\ud and 24, expressed during infection.\ud A second set of aims was to identify potential signalling networks up activated\ud during plant defence responses to infection by H. arabidopsidis using a new model\ud developed by Beal et al (Beal, Falciani et al. 2005) to eventually engineer\ud transcriptional networks. Unfortunately this failed due to problems with the\ud experiment. However, it was still possible to identify signalling networks from a\ud second microarray time course experimental data set centred on signalling networks\ud up regulated in response to the onset of senescence, as they share overlapping\ud signalling pathways. The modelling methodology was used to model the\ud anthocyanin biosynthesis pathway. The model predicted the presence of AtMYB15\ud as a positive regulator of anthocyanin biosynthesis along with AtMYB90. Research\ud carried out by Nichola Warner (Warner 2008) suggested that AtMYB90 was not\ud essential for anthocyanin biosynthesis during senescence based on by comparing the\ud phenotype of the MYB90 knock out, IM28, with the wild type (WT) Col-0 using a\ud time course microarray. Models of networks of transcriptional regulation of the\ud anthocyanin biosynthesis pathway for IM28 and WT implicate AtMYB29 as a\ud positive regulator of anthocyanin biosynthesis

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  2. (2006). A catalogue of the effector secretome of plant pathogenic oomycetes."
  3. (1998). A comparison of the expression patterns of several senescence-associated genes in response to stress and hormone treatment."
  4. (2009). A Critical Role for the TIFY Motif in Repression of Jasmonate Signaling by a Stabilized Splice Variant of the JASMONATE ZIM-Domain Protein JAZ10 in Arabidopsis."
  5. (2002). A dual role for microbial pathogenderived effector proteins in plant disease and resistance."
  6. (1997). A gene encoding a protein elicitor of Phytophthora infestans is down-regulated during infection of potato."
  7. (2002). A gene encoding an acyl hydrolase is involved in leaf senescence in Arabidopsis."
  8. (2007). A high-resolution root spatiotemporal map reveals dominant expression patterns."
  9. (2004). A host-targeting signal in virulence proteins reveals a secretome in malarial infection."
  10. (2004). A Kazal-like extracellular serine protease inhibitor from Phytophthora infestans targets the tomato pathogenesis-related protease P69B."
  11. (2000). A loss of resistance to avirulent bacterial pathogens in tobacco is associated with the attenuation of a salicylic acid-potentiated oxidative burst."
  12. (2003). A mating-induced protein of Phytophthora infestans is a member of a family of elicitors with divergent structures and stage-specific patterns of expression."
  13. (2006). A multivariate empirical Bayes statistic for replicated microarray time course data."
  14. (1960). A new approach to linear filtering and prediction problems."
  15. (2001). A novel protein elicitor (PaNie) from Pythium aphanidermatum induces multiple defense responses in carrot, Arabidopsis, and tobacco."
  16. (1994). A Proposed Superfamily of Transposase Genes - Transposon-Like Elements in Ciliated Protozoa and a Common D35e Motif."
  17. (2006). A R2R3 type MYB transcription factor is involved in the cold regulation of CBF genes and in acquired freezing tolerance."
  18. (2005). A second kazal-like protease inhibitor from Phytophthora infestans inhibits and interacts with the apoplastic pathogenesis-related protease P69B of tomato."
  19. (2007). A translocation signal for delivery of oomycete effector proteins into host plant cells."
  20. (1999). A unifying review of linear gaussian models."
  21. (2005). ACT: the Artemis comparison tool."
  22. (2000). Activation tagging identifies a conserved MYB regulator of phenylpropanoid biosynthesis."
  23. (2005). An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm."
  24. (1982). An approach to time series smoothing and forecasting using the EM algorithm."
  25. (2001). An extensive class of small RNAs in Caenorhabditis elegans."
  26. (2007). Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome."
  27. (2006). Ancient origin of elicitin gene clusters in Phytophthora genomes."
  28. (2006). Application of phylogenetic networks in evolutionary studies."
  29. (2002). Arabidopsis onset of leaf death mutants identify a regulatory pathway controlling leaf senescence."
  30. (2000). Arabidopsis thaliana EDS4 contributes to salicylic acid (SA)-dependent expression of defense responses: Evidence for inhibition of jasmonic acid signaling by SA."
  31. (1998). Arabidopsis thaliana: A model plant for genome analysis."
  32. (2003). AraCyc: A biochemical pathway database for Arabidopsis."
  33. (2000). Artemis: sequence visualization and annotation."
  34. (2006). AtNAP, a NAC family transcription factor, has an important role in leaf senescence."
  35. (2005). Bayesian coclustering of Anopheles gene expression time series: Study of immune defense response to multiple experimental challenges."
  36. (1998). Biological sequence analysis: probabilistic models of proteins and nucleic acids."
  37. (2007). CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes."
  38. (2003). CATMA: a complete Arabidopsis GST database."
  39. (2000). Cell sampling and analysis (SiCSA): metabolites measured at single cell resolution. Annual Meeting of the Society-forExperimental-Biology,
  40. (1997). Changes of ethylene evolution, ACC content, ethylene forming enzyme activity and respiration in fruits of highbush blueberry."
  41. (2003). Characterization of 1,3-beta-glucanase and 1,3;1,4-beta-glucanase genes from Phytophthora infestans."
  42. (2006). Characterization of alternative oxidase (AOX) gene expression in response to methyl salicylate and methyl jasmonate pretreatment and low temperature in tomatoes."
  43. (1999). Characterization of elicitin-like phospholipases isolated from Phytophthora capsici culture filtrate."
  44. (2002). Chromosome rearrangements and transposable elements."
  45. (1994). Clustal-W - Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, PositionSpecific Gap Penalties and Weight Matrix Choice."
  46. (2000). Comparative analysis of expressed sequences in Phytophthora sojae."
  47. (2006). Comparative analysis of Phytophthora genes encoding secreted proteins reveals conserved synteny and lineage-specific gene duplications and deletions." Molecular Plant-Microbe Interactions
  48. (2005). Comparative transcriptome analysis reveals significant differences in gene expression and signalling pathways between developmental and dark/starvation-induced senescence in Arabidopsis."
  49. (1998). Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization."
  50. (1997). Compromising early salicylic acid accumulation delays the hypersensitive response and increases viral dispersal during lesion establishment in TMV-infected tobacco."
  51. (2000). Coordinated plant defense responses in Arabidopsis revealed by microarray analysis."
  52. (1996). Cosegregation of Avr4 and Avr6 in Phytophthora sojae."
  53. (2006). Cytokinin-mediated control of leaf longevity by AHK3 through phosphorylation of ARR2 in Arabidopsis."
  54. (2005). Differential recognition of highly divergent downy mildew avirulence gene alleles by RPP1 resistance genes from two Arabidopsis lines."
  55. (2000). Direct interaction of resistance gene and avirulence gene products confers rice blast resistance." Embo Journal
  56. (2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data."
  57. (2003). Downy mildew of Arabidopsis thaliana caused by Hyaloperonospora parasitica (formerly Peronospora parasitica)."
  58. (2000). Effector proteins of phytopathogenic bacteria: bifunctional signals in virulence and host recognition."
  59. (2005). Elicitin genes in Phytophthora infestans are clustered and interspersed with various transposon-like elements."
  60. (1998). Elicitins, proteinaceous elicitors of plant defense, are a new class of sterol carrier proteins."
  61. (2007). Elucidating signaling pathways that control Arabidopsis leaf senescence."
  62. (2000). EMBOSS: The European molecular biology open software suite."
  63. (2006). Endogenous and synthetic microRNAs stimulate simultaneous, efficient, and localized regulation of multiple targets in diverse species."
  64. (2009). Epigenetic programming via histone methylation at WRKY53 controls leaf senescence in Arabidopsis thaliana."
  65. (1997). Ethylene and vegetative development."
  66. (2005). Ethylene-induced leaf senescence depends on age-related changes and OLD genes in Arabidopsis."
  67. (2001). Eugène, an eukaryotic gene finder that combines several sources of evidence."
  68. (2005). Evaluating eukaryotic secreted protein prediction."
  69. (2007). Expression of a nitric oxide degrading enzyme induces a senescence programme in Arabidopsis."
  70. (2002). Expression of a Phytophthora sojae necrosisinducing protein occurs during transition from biotrophy to necrotrophy."
  71. (2004). Expression patterns of defense-related genes in different types of arbuscular mycorrhizal development in wild-type and mycorrhiza-defective mutant tomato."
  72. (2002). Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses."
  73. (2001). Flavonoid biosynthesis. A colorful model for genetics, biochemistry, cell biology, and biotechnology."
  74. (2007). Flax rust resistance gene specificity is based on direct resistance-avirulence protein interactions."
  75. (1998). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs."
  76. (1990). Gene-Expression in Response to Abscisic-Acid and Osmotic-Stress."
  77. (2005). GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses."
  78. (2001). Genes controlling expression of defense responses in Arabidopsis -
  79. (1999). Genetic and physical mapping of the RPP13 locus, in arabidopsis, responsible for specific recognition of several Peronospora 201 parasitica (downy mildew) isolates."
  80. (1998). Genetic mapping of Ph-2, a single locus controlling partial resistance to Phytophthora infestans in tomato."
  81. (2008). Genome-wide identification of in vivo proteinDNA binding sites from ChIP-Seq data."
  82. (2006). Genomewide analysis of phospholipid signaling genes in Phytophthora spp.: Novelties and a missing link." Molecular Plant-Microbe Interactions
  83. (2008). Gibberellins, jasmonate and abscisic acid modulate the sucrose-induced expression of anthocyanin biosynthetic genes in Arabidopsis."
  84. (2003). Glycosylphosphatidylinositol lipid anchoring of plant proteins. Sensitive prediction from sequence- and genome-wide studies for arabidopsis and rice."
  85. (2004). GOstat: find statistically overrepresented Gene Ontologies within a group of genes."
  86. (2006). Graph-based analysis and visualization of experimental results with ONDEX."
  87. (2008). HAG2/MYB76 and HAG3/MYB29 exert a specific and coordinated control on the regulation of aliphatic glucosinolate biosynthesis in Arabidopsis thaliana."
  88. (2008). Highly integrated single-base resolution maps of the epigenome in Arabidopsis."
  89. (2006). Highly specific gene silencing by artificial microRNAs in Arabidopsis."
  90. (2008). Hormonal changes during salinityinduced leaf senescence in tomato (Solanum lycopersicum L.)."
  91. (2004). Host-parasite coevolutionary conflict between Arabidopsis and downy mildew."
  92. (1999). Hot papers - Bioinformatics - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs by
  93. (2008). Identification and characterization of COI1-dependent transcription factor genes involved in JA-mediated response to wounding in Arabidopsis plants."
  94. (1999). Identification of genetic networks from a small number of gene expression patterns under the Boolean network model." Pac Symp Biocomput:
  95. (1997). Identification of three genetic loci controlling leaf senescence in Arabidopsis thaliana."
  96. (1999). Improved microbial gene identification with GLIMMER."
  97. (2004). Improved prediction of signal peptides: SignalP 3.0."
  98. (1988). Induction of 33-Kd and 60-Kd Peroxidases During Ethylene-Induced Senescence of Cucumber Cotyledons."
  99. (1992). Inheritance and Race Reaction of a New Soybean Rps1 Allele."
  100. (1999). Initial assessment of gene diversity for the oomycete pathogen Phytophthora infestans based on expressed sequences."
  101. (2000). Interplay of signaling pathways in plant disease resistance."
  102. (2006). Interpreting experimental results using gene ontologies.
  103. (1998). Intragenic recombination and diversifying selection contribute to the evolution of downy mildew resistance at the RPP8 locus of arabidopsis."
  104. (2003). Intraspecific comparative genomics to identify avirulence genes from Phytophthora."
  105. (1980). Isolation and Identification of a Senescence-Promoting Substance from Wormwood (Artemisia-Absinthium L)."
  106. (2005). Jasmonate-regulated Arabidopsis stress signalling network."
  107. (2000). JunD protects cells from p53-dependent senescence and apoptosis."
  108. (2007). Leaf senescence."
  109. (2004). Linking sequence to phenotype in Phytophthora-plant interactions."
  110. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq."
  111. (2001). Mapping Genes Conferring Resistance to Phytophthora Root Rot of Soybean, Rps1a and Rps7."
  112. (2001). Mapping of avirulence genes in Phytophthora infestans with amplified fragment length polymorphism markers selected by bulked segregant analysis."
  113. (2008). Mapping short DNA sequencing reads and calling variants using mapping quality scores."
  114. (2004). MicroRNA regulation of gene expression in plants."
  115. (2004). Modeling T-cell activation using gene expression profiling and state-space models."
  116. (2002). Molecular basis of recognition between Phytophthora pathogens and their hosts."
  117. (2002). Molecular cloning and characterization of glucanase inhibitor proteins: Coevolution of a counterdefense mechanism by plant pathogens."
  118. (2006). Necrosis- and ethylene-inducing peptide from Fusarium oxysporum induces a complex cascade of transcripts associated with signal transduction and cell death in arabidopsis."
  119. (2005). NEP1 orthologs encoding necrosis and ethylene inducing proteins exist as a multigene family in Phytophthora megakarya, causal agent of black pod disease on cacao."
  120. (2007). Network inference, analysis, and modeling in systems biology." Plant Cell
  121. (2007). Networks of WRKY transcription factors in defense signaling."
  122. (2002). Novel protein kinase induced during sporangial cleavage in the oomycete Phytophthora infestans."
  123. (2005). Novel quorum-sensing-control led genes in Erwinia carotovora subsp carotovora: Identification of a fungal elicitor homologue in a soft-rotting bacterium."
  124. (2002). NPP1, a Phytophthora-associated trigger of plant defense in parsley and Arabidopsis."
  125. (2003). Oomycetes and fungi: similar weaponry to attack plants."
  126. (2001). Organization of genes controlling disease resistance in the potato genome."
  127. (2006). Overexpression of the wounding-responsive gene AtMYB15 activates the shikimate pathway in Arabidopsis."
  128. (2002). Ozone-induced ethylene production is dependent on salicylic acid, and both salicylic acid and ethylene act in concert to regulate ozone-induced cell death."
  129. (1996). Pathogen-induced systemic activation of a plant defensin gene in Arabidopsis follows a salicylic acid-independent pathway."
  130. (2005). Pathogen-induced, NADPH oxidasederived reactive oxygen intermediates suppress spread of cell death in Arabidopsis thaliana."
  131. (2005). Patterns of diversifying selection in the phytotoxin-like scr74 gene family of Phytophthora infestans (vol 22, pg 659,
  132. (2004). Patterns of gene expression upon infection of soybean plants by Phytophthora sojae."
  133. (2003). PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods).
  134. (2003). PcF protein from Phytophthora cactorum and its recombinant homologue elicit phenylalanine ammonia lyase activation in tomato."
  135. (2009). PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls."
  136. (2002). Pep-13, a plant defense-inducing pathogenassociated pattern from Phytophthora transglutaminases."
  137. (1995). Peptide Elicitor Recognition and SignalTransduction in Plant Defense."
  138. (2006). Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis."
  139. (2005). Phytophthora ramorum: Integrative research and management of an emerging pathogen in California and Oregon forests."
  140. (1995). Phytophthora sojae avirulence genes, RAPD, and RFLP markers used to construct a detailed genetic linkage map."
  141. (2007). Phytophthora sojae: root rot pathogen of soybean and model oomycete."
  142. (1997). Pollination-induced ethylene in carnation - Role of stylar ethylene in corolla senescence."
  143. (2001). Production of extracellular matrices during development of infection structures by the downy mildew Peronospora parasitica."
  144. (2005). Quantitative inference of dynamic regulatory pathways via microarray data."
  145. (2008). Regulation of the anthocyanin biosynthetic pathway by the TTG1/bHLH/Myb transcriptional complex in Arabidopsis seedlings."
  146. (1998). Resistance of Nicotiana benthamiana to Phytophthora infestans is mediated by the recognition of the elicitor protein INF1."
  147. (1999). Resistance to oomycetes: a general role for the hypersensitive response?"
  148. (2001). Resistance to Pseudomonas syringae conferred by an Arabidopsis thaliana coronatine-insensitive (coi1) mutation occurs through two distinct mechanisms."
  149. (2000). Resistance to turnip crinkle virus in Arabidopsis is regulated by two host genes and is salicylic acid dependent but NPR1, ethylene, and jasmonate independent."
  150. (2001). RNA interference is mediated by 21-and 22-nucleotide RNAs."
  151. (2007). RXLR effectors of plant pathogenic oomycetes."
  152. (2000). Salicylic acid has a role in regulating gene expression during leaf senescence."
  153. (2004). Seeing the unseen: Microarray-based gene expression profiling in vision."
  154. (2005). Selection on glycine beta-1,3-endoglucanase genes differentially inhibited by a phytophthora glucanase inhibitor protein."
  155. (2006). Senescence-promoting effect of arabidopside A."
  156. (2003). Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks." Bioinformatics
  157. (1998). Separate jasmonate-dependent and salicylate-dependent defense-response pathways in Arabidopsis are essential for resistance to distinct microbial pathogens."
  158. (2000). Signal transduction cascades regulating fungal development and virulence."
  159. (1998). SOSUI: classification and secondary structure prediction system for membrane proteins."
  160. (2009). Stay-green regulates chlorophyll and chlorophyll-binding protein degradation during senescence."
  161. (2002). Structural basis for the guanine nucleotidebinding activity of tissue transglutaminase and its regulation of transamidation activity."
  162. (2008). Structure of the glucanase inhibitor protein (GIP) family from Phytophthora species suggests coevolution with plant endo-beta-1,3-glucanases."
  163. (1997). Symbiology of mouse-ear cress (Arabidopsis thaliana) and oomycetes.
  164. (2006). Synergistic interactions of the plant cell death pathways induced by Phytophthora infestans Nep1-like protein PiNPP1.1 and INF1 elicitin."
  165. (2002). Targets of AtWRKY6 regulation during plant senescence and pathogen defense."
  166. (2004). Targets of the WRKY53 transcription factor and its role during leaf senescence in Arabidopsis."
  167. (1997). The Arabidopsis downy mildew resistance gene RPP5 shares similarity to the toll and interleukin-1 receptors with N and L6."
  168. (2003). The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community."
  169. (2008). The Arabidopsis Information Resource (TAIR): gene structure and function annotation."
  170. (2004). The Avr1b locus of Phytophthora sojae encodes an elicitor and a regulator required for avirulence on soybean plants carrying resistance gene Rps1b." Molecular Plant-Microbe Interactions
  171. (2002). The bioperl toolkit: Perl modules for the life sciences."
  172. (2004). The CBEL elicitor of Phytophthora parasitica var. nicotianae activates defence in Arabidopsis thaliana via three different signalling pathways."
  173. (2002). The CBEL glycoprotein of Phytophthora parasitica var. nicotianae is involved in cell wall deposition and adhesion to cellulosic substrates."
  174. (2001). The cell biology behind Phytophthora pathogenicity. 2nd Australasian Soilborne Diseases Symposium,
  175. (1997). The fungal elicitor cryptogein is a sterol carrier protein."
  176. (1931). The Generalization of Student's Ratio."
  177. (2004). The maintenance of extreme amino acid diversity at the disease resistance gene, RPP13, in Arabidopsis thaliana."
  178. (2006). The malarial host-targeting signal is conserved in the Irish potato famine pathogen."
  179. (2007). The nature of systems biology."
  180. (2004). The Nep1-like proteins - a growing family of microbial elicitors of plant necrosis."
  181. (2004). The Pfam protein families database."
  182. (2001). The physiology of ozone induced cell death."
  183. (2002). The pipg 1 gene of the oomycete Phytophthora infestans encodes a fungal-like endopolygalacturonase."
  184. (2006). The plant immune system."
  185. (2002). The PROSITE database, its status in 2002."
  186. (2003). The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003."
  187. (2002). The variational Bayesian EM algorithm for incomplete data: With application to scoring graphical model structures. 7th Valencia International Meeting on Bayesian Statistics,
  188. (1998). Three genes of the arabidopsis RPP1 complex resistance locus recognize distinct Peronospora parasitica avirulence determinants."
  189. (1997). Three-dimensional solution structure of beta cryptogein, a beta elicitin secreted by a phytopathogenic fungus Phytophthora cryptogea."
  190. (2008). Timing is everything: regulatory overlap in plant cell death."
  191. (2006). Trafficking arms: oomycete effectors enter host plant cells."
  192. (2006). Transcription analysis of arabidopsis membrane transporters and hormone pathways during developmental and induced leaf senescence."
  193. (2009). Transcription factors and regulation of photosynthetic and related metabolism under environmental stresses."
  194. (2002). Transcription factors in plant defense and stress responses."
  195. (2008). Transcriptional regulation of plant senescence: from functional genomics to systems biology."
  196. (2003). Transcriptional regulation of secondary metabolism."
  197. (1997). Transposable element-host interactions: Regulation of insertion and excision."
  198. (1996). TreeView: An application to display phylogenetic trees on personal computers."
  199. (2004). Type III secretion system effector proteins: Double agents in bacterial disease and plant defense."
  200. (2008). Unravelling the roles of two senescent enhanced MYB transcription factors in the regulation of anthocyanin biosynthesis in Arabidopsis thaliana. Warwick HRI.
  201. (2003). Use of suppression subtractive hybridization to identify downy mildew genes expressed during infection of Arabidopsis thaliana."
  202. (2000). Using Bayesian networks to analyze expression data.
  203. (1988). Vacuolar H+ pyrophosphatases: from the evolutionary backwaters into the mainstream."
  204. (2003). Variation in structure and activity among elicitins from Phytophthora sojae."
  205. (2008). VirtualPlant: A software platform to support systems biology research in the post-genomic era." Plant Biology (Rockville)
  206. (2007). Within-plant signaling by volatiles leads to induction and priming of an indirect plant defense in nature."

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