Microarray expression studies in the model plant Arabidopsis thaliana infected with the bacterial pathogen Ralstonia solanacearum

Ralstonia solanaearum, a soil borne pathogen infects several important crops causing wilting. In 2000-2001, two eucalyptus isolates, BCCF 401 and BCCF 402 were isolated from plantations in Kwa-Zulu Natal and the Democratic Republic of Congo, respectively. Arabidopsis has been recognised as a host for R. solanacearum and as such has been adopted as a model to understand the plant defence response against this pathogen. The aim of this study was to use microarray expression profiling techniques to elucidate the plant defence response and to identify candidate genes possibly contributing towards resistance against the pathogen. As a means to optimise microarray expression profiling, the differential expression in an Arabidopsis mutant, cir1 (constitutively induced resistance 1) and wild-type plants was investigated using a custom 500-probe microarray. Several genes were found to be induced in cir1 at a significance threshold of –log10(p) equal to 3 (p D559/gmThesis (PhD)--University of Pretoria, 2008.Plant Scienceunrestricte

Microarray experiments: Considerations for experimental design

Microarrays are useful tools to investigate the expression of thousands of genes rapidly. Some researchers remain reluctant to use the technology, however, largely because of its expense. Careful design of a microarray experiment is key to generating cost-effective results. This article explores issues that researchers face when embarking on a microarray experiment for the first time. These include decisions about which microarray platform is available for the organism of interest, the degree of replication (biological and technical) needed and which design (direct or indirect, loop or balanced block) is suitable

The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) and Related Family: Mechanistic Insights in Plant Disease Resistance

The NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1) and related NPR1-like proteins are a functionally similar, yet surprisingly diverse family of transcription co-factors. Initially, NPR1 in Arabidopsis was identified as a positive regulator of systemic acquired resistance (SAR), paralogs NPR3 and NPR4 were later shown to be negative SAR regulators. The mechanisms involved have been the subject of extensive research and debate over the years, during which time a lot has been uncovered. The known roles of this protein family have extended to include influences over a broad range of systems including circadian rhythm, endoplasmic reticulum (ER) resident proteins and the development of lateral organs. Recently, important advances have been made in understanding the regulatory relationship between members of the NPR1-like protein family, providing new insight regarding their interactions, both with each other and other defense-related proteins. Most importantly the influence of salicylic acid (SA) on these interactions has become clearer with NPR1, NPR3, and NPR4 being considered bone fide SA receptors. Additionally, post-translational modification of NPR1 has garnered attention during the past years, adding to the growing regulatory complexity of this protein. Furthermore, growing interest in NPR1 overexpressing crops has provided new insights regarding the role of NPR1 in both biotic and abiotic stresses in several plant species. Given the wealth of information, this review aims to highlight and consolidate the most relevant and influential research in the field to date. In so doing, we attempt to provide insight into the mechanisms and interactions which underly the roles of the NPR1-like proteins in plant disease responses

Transcriptome and hormone profiling reveals Eucalyptus grandis defence responses against Chrysoporthe austroafricana

BACKGROUND : Eucalyptus species and interspecific hybrids exhibit valuable growth and wood properties that make them a highly desirable commodity. However, these trees are challenged by a wide array of biotic stresses during their lifetimes. The Eucalyptus grandis reference genome sequence provides a resource to study pest and pathogen defence mechanisms in long-lived woody plants. E. grandis trees are generally susceptible to Chrysoporthe austroafricana, a causal agent of stem cankers on eucalypts. The aim of this study was to characterize the defence response of E. grandis against C. austroafricana. RESULTS : Hormone profiling of susceptible and moderately resistant clonal E. grandis genotypes indicated a reduction in salicylic acid and gibberellic acid levels at 3 days post inoculation. We hypothesized that these signaling pathways may facilitate resistance. To further investigate other defence mechanisms at this time point, transcriptome profiling was performed. This revealed that cell wall modifications and response to oxidative stress form part of the defence responses common to both genotypes, whilst changes in the hormone signaling pathways may contribute to resistance. Additionally the expression of selected candidate defence response genes was induced earlier in moderately resistant trees than in susceptible trees, supporting the hypothesis that a delayed defence response may occur in the susceptible interaction. CONCLUSION : The ability of a host to fine-tune its defence responses is crucial and the responses identified in this study extends our understanding of plant defence, gained from model systems, to woody perennials.Additional file 1: Table S1. Summary of statistics obtained for transcriptome profiling of TAG5 and ZG14 challenged with C. austroafricana.Additional file 2: Table S2. Summary of significantly differentially expressed genes and their annotations identified from Eucalyptus grandis TAG5 and ZG14.Additional file 3: Figure S1. Molecular function GO terms that are over-represented in TAG5 and ZG14. a – GO terms within the upregulated dataset. b – GO terms within the down-regulated dataset (all terms for this dataset are shown). The y-axis represents the –log2(q-value) and the x-axis represents the GO terms within the datasets. Light and dark grey bars are ZG14 and TAG5 respectively.Additional file 4: Figure S2. Cellular component GO terms that are over-represented in TAG5 and ZG14. a – GO terms within the upregulated dataset. b – GO terms within the down-regulated dataset. The y-axis represents the –log2(q-value) and the x-axis represents the GO terms within the datasets. Light and dark grey bars are ZG14 and TAG5 respectively.Additional file 5: Table S3. List of differentially expressed genes that are common between the susceptible (ZG14) and moderately resistant (TAG5) host.This work was supported by the Genomics Research Institute (GRI) at the University of Pretoria; the National Research Foundation of South Africa (Grant number NBIG 86936); Thuthuka funding (UID:76225); the Forest Molecular Genetics Programme by Mondi and Sappi and the Technology and Human Resources for Industry Programme (UID:80118).http://www.biomedcentral.com/bmcgenomicsam201

eCALIBRATOR : a comparative tool to identify key genes and pathways for eucalyptus defense against biotic stressors

Many pests and pathogens threaten Eucalyptus plantations. The study of defense responses in this economically important wood and fiber crop enables the discovery of novel pathways and genes, which may be adopted to improve resistance. Various functional genomics experiments have been conducted in Eucalyptus-biotic stress interactions following the availability of the Eucalyptus grandis genome, however, comparisons between these studies were limited largely due to a lack of comparative tools. To this end, we developed eCALIBRATOR http://ecalibrator.bi.up.ac.za, a tool for the comparison of Eucalyptus biotic stress interaction. The tool, which is not limited to Eucalyptus, allows the comparison of various datasets, provides a visual output in the form of Venn diagrams and clustering and extraction of lists for gene ontology enrichment analyses. We also demonstrate the usefulness of the tool in revealing pathways and key gene targets to further functionally characterize. We identified 708 differentially expressed E. grandis genes in common among responses to the insect pest Leptocybe invasa, oomycete pathogen Phytophthora cinnamomi and fungus Chrysoporthe austroafricana. Within this set of genes, one of the Gene Ontology terms enriched was “response to organonitrogen compound,” with NITRATE TRANSPORTER 2.5 (NRT2.5) being a key gene, up-regulated under susceptible interactions and downregulated under resistant interactions. Although previous functional genetics studies in Arabidopsis thaliana support a role in nitrate acquisition and remobilization under long-term nitrate starvation, the importance of NRT2.5 in plant defense is unclear. The T-DNA mutants of AtNRT2.5 were more resistant to Pseudomonas syringae pv. tomato pv tomato DC3000 inoculation than the wild-type counterpart, supporting a direct role for NRT2.5 in plant defense. Future studies will focus on characterizing the Eucalyptus ortholog of NRT2.5

Mechanisms of systemic resistance to pathogen infection in plants and their potential application in forestry

BACKGROUND : The complex systemic responses of tree species to fight pathogen infection necessitate attention due to the potential for yield protection in forestry. RESULTS : In this paper, both the localized and systemic responses of model plants, such as Arabidopsis and tobacco, are reviewed. These responses were compared to information available that investigates similar responses in woody plant species and their key differences were highlighted. In addition, tree-specific responses that have been documented were summarised, with the critical responses still relying on certain systemic acquired resistance pathways. Importantly, coniferous species have been shown to utilise phenolic compounds in their immune responses. Here we also highlight the lack of focus on systemic induced susceptibility in trees, which can be important to forest health. CONCLUSIONS : This review highlights the possible mechanisms of systemic response to infection in woody plant species, their potential applications, and where research may be best focused in future.The Department of Science and Innovation, the Technology Innovation Agency of South Africa and the National Research Foundation (NRF).https://bmcplantbiol.biomedcentral.comam2024BiochemistryGeneticsMicrobiology and Plant PathologySDG-15:Life on lan

Insect gallers and their plant hosts : From omics data to systems biology

Gall-inducing insects are capable of exerting a high level of control over their hosts’ cellular machinery to the extent that the plant’s development,metabolism,chemistry,and physiology are all altered in favour of the insect. Many gallers are devastating pests in global agriculture and the limited understanding of their relationship with their hosts prevents the development of robust management strategies. Omics technologies are proving to be important tools in elucidating the mechanisms involved in the interaction as they facilitate analysis of plant hosts and insect effectors for which little or no prior knowledge exists. In this review,we examine the mechanisms behind insect gall development using evidence from omics-level approaches. The secretion of effector proteins and induced phytohormonal imbalances are highlighted as likely mechanisms involved in gall development. However,understanding how these components function within the system is far from complete and a number of questions need to be answered before this information can be used in the development of strategies to engineer or breed plants with enhanced resistance

The expression of the NPR1-dependent defense response pathway genes in Persea americana (Mill.) following infection with Phytophthora cinnamomi

AVAILABILITY OF DATA AND MATERIALS : The raw datasets supporting the conclusions of this article are available in the Sequence Read Archive of NCBI Genbank repository, PRJNA675400 (https:// www. ncbi. nlm. nih. gov/ biopr oject/ PRJNA 675400/). In addition, the processed datasets supporting the conclusions of this article are included within the article (and its additional file(s)).SUPPLEMENTARY INFORMATION : TABLE S1. Plant proteomes obtained as input for orthologue identification using OrthoFinder v2.5.4. TABLE S2. Candidate NPR1 pathway-associated genes in Persea americana. Putative functional descriptions are the result of a combined annotation approach by using original functional annotations (Avocado Genome Consortium) and eggNOG-mapper, InterProScan and BLASTp descriptions. Candidates with no expression data, determined using baseMean following DeSeq2 analyses, were not assigned descriptors. TABLE S3. Protein-protein BLAST of identified Persea americana NPR1-dependent defense response pathway proteins. The NCBI non-redundant protein sequences database was used and limited by entrez entry Viridiplantae with an Expected (E) value cutoff 0.05, word size 3, BLOSUM 62, Gap cost (existence 11, extension 1), max hits per sequence 5. TABLE S4. Differentially expressed Persea americana NPR1- pathway-associated genes (log2(fold change; log2FC) > 0.58 | 0.58 | < -0.58, adjusted p-value (FDR; p-adj) < 0.05) comparing the expression of uninoculated (Control) sample libraries or various Phytophthora cinnamomi inoculated libraries, of the partially resistant rootstock Dusa ® with the respective libraries in the susceptible rootstock R0.12. lfcSE - standard error of log2FC.A plant’s defense against pathogens involves an extensive set of phytohormone regulated defense signaling pathways. The salicylic acid (SA)-signaling pathway is one of the most well-studied in plant defense. The bulk of SA-related defense gene expression and the subsequent establishment of systemic acquired resistance (SAR) is dependent on the nonexpressor of pathogenesis-related genes 1 (NPR1). Therefore, understanding the NPR1 pathway and all its associations has the potential to provide valuable insights into defense against pathogens. The causal agent of Phytophthora root rot (PRR), Phytophthora cinnamomi, is of particular importance to the avocado (Persea americana) industry, which encounters considerable economic losses on account of this pathogen each year. Furthermore, P. cinnamomi is a hemibiotrophic pathogen, suggesting that the SA-signaling pathway plays an essential role in the initial defense response. Therefore, the NPR1 pathway which regulates downstream SA-induced gene expression would be instrumental in defense against P. cinnamomi. Thus, we identified 92 NPR1 pathway-associated orthologs from the P. americana West Indian pure accession genome and interrogated their expression following P. cinnamomi inoculation, using RNA-sequencing data. In total, 64 and 51 NPR1 pathway-associated genes were temporally regulated in the partially resistant (Dusa®) and susceptible (R0.12) P. americana rootstocks, respectively. Furthermore, 42 NPR1 pathway-associated genes were differentially regulated when comparing Dusa® to R0.12. Although this study suggests that SAR was established successfully in both rootstocks, the evidence presented indicated that Dusa® suppressed SA-signaling more effectively following the induction of SAR. Additionally, contrary to Dusa®, data from R0.12 suggested a substantial lack of SA- and NPR1-related defense gene expression during some of the earliest time-points following P. cinnamomi inoculation. This study represents the most comprehensive investigation of the SA-induced, NPR1-dependent pathway in P. americana to date. Lastly, this work provides novel insights into the likely mechanisms governing P. cinnamomi resistance in P. americana.The Hans Merensky Foundation.https://bmcplantbiol.biomedcentral.comam2024BiochemistryGeneticsMicrobiology and Plant PathologySDG-15:Life on lan