Biology subjects

Lipscombe, R.

Publications and source records attributed to Lipscombe, R..

3 recordsLinked to original sources

bioRxiv2022

Proteomic analysis revealed that the oomyceticide phosphite exhibits multi-modal action in an oomycete pathosystem.

BACKGROUNDPhytopathogenic oomycetes constitute some of the most devastating plant pathogens that cause significant crop and horticultural loss. Phytophthora cinnamomi is a phytopathogenic oomycete that causes dieback disease in native vegetation and a variety of crops. This pathogen can survive through harsh environmental conditions which gives it an advantage over its susceptible hosts. The only implemented chemical used to control P. cinnamomi is the oomyceticide phosphite. Despite its widespread use, the mode of action of phosphite is not well understood and it is unclear whether it works directly on the pathogen or through the host. Additionally, resistance to phosphite is emerging in P. cinnamomi isolates and other oomycete phytopathogens. RESULTSThe mode of action of phosphite on the pathogen and through a model host was investigated using label-free quantitative proteomics. In vitro treatment of P. cinnamomi with phosphite hinders growth by interfering with metabolism, signalling and gene expression, traits that are not observed in the tolerant isolate. When the model host L. angustifolius was treated with phosphite, enrichment of proteins that are associated with photosynthesis, carbon fixation and lipid metabolism in the host was observed. An increase in the production of a range of defence-related proteins was observed. CONCLUSIONWe hypothesise direct and indirect models of the multi-modal action of phosphite that directly targets the pathogen as well as alters plant metabolism and immune response.

biochemistry↗

bioRxiv2022

Comparative sub-cellular proteome analyses reveals metabolic differentiation and production of effector-like molecules in the dieback phytopathogen Phytophthora cinnamomi.

Phytopathogenic oomycetes pose a significant threat to global biodiversity and food security. The proteomes of these oomycetes likely contain important factors that contribute to their pathogenic success, making their discovery crucial for elucidating pathogenicity. Oomycetes secrete effector proteins that overcome or elicit a defence response in susceptible hosts. Phytophthora cinnamomi is a root pathogen that causes dieback in a wide variety of crops and a range of native vegetation world-wide. Virulence proteins produced by P. cinnamomi are not well defined and a large-scale approach to understand the biochemistry of this pathogen has not been documented. Here, soluble mycelial, zoospore and secreted proteomes were obtained and label-free quantitative proteomics was used to compare the composition of protein content of the three sub-proteomes by matching the MS/MS data to a sequenced P. cinnamomi genome. Mass spectra matched to a total of 4635 proteins, validating 17.7% of the predicted gene set of the P. cinnamomi genome. The mycelia were abundant in transporters for nutrient acquisition, metabolism and cellular proliferation. The zoospores had less metabolic related ontologies than the mycelia but were abundant in energy generating, motility and signalling associated proteins. Virulence-associated proteins were identified in the secretome such as candidate effector and effector-like proteins, which interfere with the host immune system. These include hydrolases, cell wall degrading enzymes, putative necrosis-inducing proteins and elicitins. The secretome elicited a hypersensitive response on the roots of a model host and thus suggests evidence of effector activity. SignificancePhytophthora cinnamomi is a phytopathogenic oomycete that causes dieback disease in native vegetation and several horticultural crops such as avocado, pineapple and macadamia. Whilst this pathogen has significance world-wide, its pathogenicity and virulence have not been described in depth. We carried out comparative label-free proteomics of the mycelia, zoospores and secretome of P. cinnamomi. This study highlights the differential metabolism and cellular processes between the sub-proteomes. Proteins associated with metabolism, nutrient transport and cellular proliferation were over represented in the mycelia. The zoospores have a specialised proteome showing increased energy generation geared towards motility. Candidate effectors and effector-like secreted proteins were also identified, which can be exploited for genetic resistance. This demonstrates a better understanding of the biology and pathogenicity of P. cinnamomi infection that can subsequently be used to develop effective methods of disease management

biochemistry↗

bioRxiv2020

Gene validation and remodelling using proteogenomics of Phytophthora cinnamomi, the causal agent of Dieback.

Phytophthora cinnamomi is a pathogenic oomycete that causes plant dieback disease across a range of natural ecosystems and in many agriculturally important crops on a global scale. An annotated draft genome sequence and annotation is publicly available (JGI Mycocosm) and suggests 26,131 gene models. In this study, soluble mycelial, extracellular (secretome) and zoospore proteins of P. cinnamomi were exploited to refine the genome by correcting gene annotations and discovering novel genes. By implementing the diverse set of sub-proteomes into a generated proteogenomics pipeline, we were able to improve the P. cinnamomi genome. Liquid chromatography mass spectrometry was used to obtain high confidence peptides with spectral matching to both the annotated genome and a generated 6-frame translation. 2,764 annotations from the draft genome were confirmed by spectral matching. Using a proteogenomic pipeline, mass spectra were used to edit the P. cinnamomi genome and allowed identification of 23 new gene models and 60 edited gene features using high confidence peptides obtained by mass spectrometry, suggesting a rate of incorrect annotations of 3% of the detectable proteome. The novel features were further validated by total peptide support, alongside functional analysis including the use of Gene Ontology and functional domain identification. We demonstrated the use of spectral data in combination with our proteogenomics pipeline can be used to improve the genome of important plant diseases and identify biologically relevant missed genes. This study presents the first use of spectral data to edit and manually annotate an oomycete pathogen.

genomics↗