Barry Saville | Trent University (original) (raw)
Papers by Barry Saville
Research Square (Research Square), Oct 16, 2023
Phytopathology, Jun 1, 2015
Additional file 9:Pt unigenes were compared to sets of known or predicted (small) secreted protei... more Additional file 9:Pt unigenes were compared to sets of known or predicted (small) secreted proteins (SSPs). This file reveals families of likely paralogous proteins and their matches to orthologous and homeologous predicted SSPs in various in rust fungi and U. maydis. It includes representation of ESTs over the sampled stages. (XLS 929 KB)
Additional file 7:Pt non-redundant unigene sequences specific for and shared between spore stages... more Additional file 7:Pt non-redundant unigene sequences specific for and shared between spore stages as presented in the Venn diagram (supporting Figure 3) with annotation results. (XLS 197 KB)
U. maydis detected antisense and putative orthologs with detected antisense. (XLSX 386 kb)
Trinotate results for S. reilianum intergenic transcripts. (XLSX 242 kb)
Trinotate results for U. hordei intergenic transcripts. (XLSX 247 kb)
U. maydis RNA-seq based predicted gene models. (XLSX 661 kb)
RNA-seq based detected gene models using different FPKM cut-off values. (XLSX 239 kb)
International Microbiology, Jan 2, 2024
Research Square (Research Square), Oct 15, 2023
Fungal Genetics and Biology, 2020
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Frontiers in Environmental Science, Mar 15, 2022
Mercury contamination in aquatic systems poses a serious environmental stress to phototrophic pla... more Mercury contamination in aquatic systems poses a serious environmental stress to phototrophic plankton. We used Euglena gracilis to gain an understanding of the physiochemical changes resulting from mercury stress across the transcriptome and metabolome. Using a combination of Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) and RNA-sequencing, we identified metabolomic and transcriptomic changes both within and outside cellular space after mercury exposure. Metabolic profiles of E. gracilis were less diverse after mercury exposure, highlighting an overall refinement of metabolites produced. Significant fold changes in cysteine, glutathione, and amino acid-based metabolites were significantly higher (p < 0.05) within the mercury exposed cells and in extracellular space than in untreated cultures. Using integrated omics analyses, a significant upregulation of transcripts and metabolites involved in amino acid synthesis, cellular responses to chemical stress, reactive oxygen species detoxification, and electron transport were identified. Together the enrichment of these pathways highlights mechanisms that E. gracilis harness to mitigate oxidative stress at sublethal concentrations of mercury exposure and give rise to new biomarkers of environmental stress in the widely distributed E. gracilis.
Current Genetics, Apr 5, 2005
When fungi interact with plants as pathogens or as symbionts, there are often changes in fungal c... more When fungi interact with plants as pathogens or as symbionts, there are often changes in fungal cell morphology and nuclear state. This study establishes the use of cDNA microarrays to detect gene expression changes in Ustilago maydis cells that differ in structure and nuclear content. Categorizing differentially expressed genes on the basis of function indicated that U. maydis cell types vary most in the expression of genes related to metabolism. We also observed that more genes are up-regulated in the filamentous dikaryon than in the filamentous diploid, relative to non-pathogenic budding cells. Our comparison of pathogenic development indicated that the dikaryon is more virulent than the diploid. Other identified expression patterns suggest a cell-specific difference in nutrient acquisition, cell metabolism and signal transduction. The relevance of gene expression change to cell type biology is discussed.
Molecular Microbiology, May 30, 2013
Plant Pathology, Nov 8, 2016
Fungal derived cytokinins are necessary for normal Ustilago maydis infection of corn.
Molecular Microbiology, Jul 12, 2012
SummaryFungi are models for investigating many eukaryotic molecular processes. The identification... more SummaryFungi are models for investigating many eukaryotic molecular processes. The identification of natural antisense transcripts (NATs) in fungi led to the discovery of mechanisms for controlling gene expression through transcriptional interference, chromatin remodelling and dsRNA formation. An overview of these mechanisms and the description of specific NAT functions is provided to give context for a broader discussion of fungal NATs. Transcriptome analyses have revealed a large number of NATs in a divergent group of fungi. The timing of NAT expression suggests roles in core life functions, such as responding to the environment and sexual reproduction. The transcriptome studies also uncover a large number of NATs whose functions remain elusive. These could provide novel control of gene expression, targeted responses to stimuli, or other functions. The goal of this review is provide background for this expanding field of research while highlighting opportunities for future discoveries.
Plant Physiology, Sep 1, 1987
The organization of the three structural nitrogen fixation (ni) genes that encode nitrogenase (ni... more The organization of the three structural nitrogen fixation (ni) genes that encode nitrogenase (nif K and nif D) and nitrogenase reductase (nif H) have been examined in a number of cyanobacteria. Hybridization of Anabaena 7120 nif gene probes to restriction endonuclease-digested genomic DNA has shown (a) that cyanobacteria incapable of N2 fixation have no regions of DNA with significant homology to the three nif probes, (b) that Pseudanabaena sp., a nonheterocystous cyanobacterium, has a contiguous nif KDH gene cluster, and (c) that in contrast with other heterocystous cyanobacteria, Fiwherella sp. has a contiguous nif KDH gene cluster.
PLOS ONE, Jun 24, 2015
Ustilago maydis is the causative agent of common smut of corn. Early studies noted its ability to... more Ustilago maydis is the causative agent of common smut of corn. Early studies noted its ability to synthesize phytohormones and, more recently these growth promoting substances were confirmed as cytokinins (CKs). Cytokinins comprise a group of phytohormones commonly associated with actively dividing tissues. Lab analyses identified variation in virulence between U. maydis dikaryon and solopathogen infections of corn cob tissue. Samples from infected cob tissue were taken at sequential time points post infection and biochemical profiling was performed using high performance liquid chromatography-electrospray ionization tandem mass spectrometry (HPLC-ESI MS/MS). This hormone profiling revealed that there were altered levels of ABA and major CKs, with a marked reduction in CK glucosides, increases in methylthiol CKs and a particularly dramatic increase in cisZ CK forms, in U. maydis infected tissue. These changes were more pronounced in the more virulent dikaryon relative to the solopathogenic strain suggesting a role for cytokinins in moderating virulence during biotrophic infection. These findings highlight the fact that U. maydis does not simply mimic a fertilized seed but instead reprograms the host tissue. Results underscore the suitability of the Ustilago maydis-Zea mays model as a basis for investigating the control of phytohormone dynamics during biotrophic infection of plants.
Molecular Microbiology, Jan 9, 2017
The basidiomycete smut fungus Ustilago maydis causes common smut of corn. This disease is spread ... more The basidiomycete smut fungus Ustilago maydis causes common smut of corn. This disease is spread through the production of teliospores, which are thick-walled dormant structures characterized by low rates of respiration and metabolism. Teliospores are formed when the fungus grows within the plant, and the morphological steps involved in their formation have been described, but the molecular events leading to dormancy are not known. In U. maydis, natural antisense transcripts (NATs) can function to alter gene expression and many NATs have increased levels in the teliospore. One such NAT is as-ssm1 which is complementary to the gene for the mitochondrial seryl-tRNA synthetase (ssm1), an enzyme important to mitochondrial function. The disruption of ssm1 leads to cell lysis, indicating it is also essential for cellular viability. To assess the function of as-ssm1, it was ectopically expressed in haploid cells, where it is not normally present. This expression led to reductions in growth rate, virulence, mitochondrial membrane potential and oxygen consumption. It also resulted in the formation of as-ssm1/ssm1 doublestranded RNA and increased ssm1 transcript levels, but no change in Ssm1 protein levels was detected. Together, these findings suggest a role for as-ssm1 in facilitating teliospore dormancy through dsRNA formation and reduction of mitochondrial function.
Research Square (Research Square), Oct 16, 2023
Phytopathology, Jun 1, 2015
Additional file 9:Pt unigenes were compared to sets of known or predicted (small) secreted protei... more Additional file 9:Pt unigenes were compared to sets of known or predicted (small) secreted proteins (SSPs). This file reveals families of likely paralogous proteins and their matches to orthologous and homeologous predicted SSPs in various in rust fungi and U. maydis. It includes representation of ESTs over the sampled stages. (XLS 929 KB)
Additional file 7:Pt non-redundant unigene sequences specific for and shared between spore stages... more Additional file 7:Pt non-redundant unigene sequences specific for and shared between spore stages as presented in the Venn diagram (supporting Figure 3) with annotation results. (XLS 197 KB)
U. maydis detected antisense and putative orthologs with detected antisense. (XLSX 386 kb)
Trinotate results for S. reilianum intergenic transcripts. (XLSX 242 kb)
Trinotate results for U. hordei intergenic transcripts. (XLSX 247 kb)
U. maydis RNA-seq based predicted gene models. (XLSX 661 kb)
RNA-seq based detected gene models using different FPKM cut-off values. (XLSX 239 kb)
International Microbiology, Jan 2, 2024
Research Square (Research Square), Oct 15, 2023
Fungal Genetics and Biology, 2020
This is a PDF file of an article that has undergone enhancements after acceptance, such as the ad... more This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
Frontiers in Environmental Science, Mar 15, 2022
Mercury contamination in aquatic systems poses a serious environmental stress to phototrophic pla... more Mercury contamination in aquatic systems poses a serious environmental stress to phototrophic plankton. We used Euglena gracilis to gain an understanding of the physiochemical changes resulting from mercury stress across the transcriptome and metabolome. Using a combination of Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) and RNA-sequencing, we identified metabolomic and transcriptomic changes both within and outside cellular space after mercury exposure. Metabolic profiles of E. gracilis were less diverse after mercury exposure, highlighting an overall refinement of metabolites produced. Significant fold changes in cysteine, glutathione, and amino acid-based metabolites were significantly higher (p < 0.05) within the mercury exposed cells and in extracellular space than in untreated cultures. Using integrated omics analyses, a significant upregulation of transcripts and metabolites involved in amino acid synthesis, cellular responses to chemical stress, reactive oxygen species detoxification, and electron transport were identified. Together the enrichment of these pathways highlights mechanisms that E. gracilis harness to mitigate oxidative stress at sublethal concentrations of mercury exposure and give rise to new biomarkers of environmental stress in the widely distributed E. gracilis.
Current Genetics, Apr 5, 2005
When fungi interact with plants as pathogens or as symbionts, there are often changes in fungal c... more When fungi interact with plants as pathogens or as symbionts, there are often changes in fungal cell morphology and nuclear state. This study establishes the use of cDNA microarrays to detect gene expression changes in Ustilago maydis cells that differ in structure and nuclear content. Categorizing differentially expressed genes on the basis of function indicated that U. maydis cell types vary most in the expression of genes related to metabolism. We also observed that more genes are up-regulated in the filamentous dikaryon than in the filamentous diploid, relative to non-pathogenic budding cells. Our comparison of pathogenic development indicated that the dikaryon is more virulent than the diploid. Other identified expression patterns suggest a cell-specific difference in nutrient acquisition, cell metabolism and signal transduction. The relevance of gene expression change to cell type biology is discussed.
Molecular Microbiology, May 30, 2013
Plant Pathology, Nov 8, 2016
Fungal derived cytokinins are necessary for normal Ustilago maydis infection of corn.
Molecular Microbiology, Jul 12, 2012
SummaryFungi are models for investigating many eukaryotic molecular processes. The identification... more SummaryFungi are models for investigating many eukaryotic molecular processes. The identification of natural antisense transcripts (NATs) in fungi led to the discovery of mechanisms for controlling gene expression through transcriptional interference, chromatin remodelling and dsRNA formation. An overview of these mechanisms and the description of specific NAT functions is provided to give context for a broader discussion of fungal NATs. Transcriptome analyses have revealed a large number of NATs in a divergent group of fungi. The timing of NAT expression suggests roles in core life functions, such as responding to the environment and sexual reproduction. The transcriptome studies also uncover a large number of NATs whose functions remain elusive. These could provide novel control of gene expression, targeted responses to stimuli, or other functions. The goal of this review is provide background for this expanding field of research while highlighting opportunities for future discoveries.
Plant Physiology, Sep 1, 1987
The organization of the three structural nitrogen fixation (ni) genes that encode nitrogenase (ni... more The organization of the three structural nitrogen fixation (ni) genes that encode nitrogenase (nif K and nif D) and nitrogenase reductase (nif H) have been examined in a number of cyanobacteria. Hybridization of Anabaena 7120 nif gene probes to restriction endonuclease-digested genomic DNA has shown (a) that cyanobacteria incapable of N2 fixation have no regions of DNA with significant homology to the three nif probes, (b) that Pseudanabaena sp., a nonheterocystous cyanobacterium, has a contiguous nif KDH gene cluster, and (c) that in contrast with other heterocystous cyanobacteria, Fiwherella sp. has a contiguous nif KDH gene cluster.
PLOS ONE, Jun 24, 2015
Ustilago maydis is the causative agent of common smut of corn. Early studies noted its ability to... more Ustilago maydis is the causative agent of common smut of corn. Early studies noted its ability to synthesize phytohormones and, more recently these growth promoting substances were confirmed as cytokinins (CKs). Cytokinins comprise a group of phytohormones commonly associated with actively dividing tissues. Lab analyses identified variation in virulence between U. maydis dikaryon and solopathogen infections of corn cob tissue. Samples from infected cob tissue were taken at sequential time points post infection and biochemical profiling was performed using high performance liquid chromatography-electrospray ionization tandem mass spectrometry (HPLC-ESI MS/MS). This hormone profiling revealed that there were altered levels of ABA and major CKs, with a marked reduction in CK glucosides, increases in methylthiol CKs and a particularly dramatic increase in cisZ CK forms, in U. maydis infected tissue. These changes were more pronounced in the more virulent dikaryon relative to the solopathogenic strain suggesting a role for cytokinins in moderating virulence during biotrophic infection. These findings highlight the fact that U. maydis does not simply mimic a fertilized seed but instead reprograms the host tissue. Results underscore the suitability of the Ustilago maydis-Zea mays model as a basis for investigating the control of phytohormone dynamics during biotrophic infection of plants.
Molecular Microbiology, Jan 9, 2017
The basidiomycete smut fungus Ustilago maydis causes common smut of corn. This disease is spread ... more The basidiomycete smut fungus Ustilago maydis causes common smut of corn. This disease is spread through the production of teliospores, which are thick-walled dormant structures characterized by low rates of respiration and metabolism. Teliospores are formed when the fungus grows within the plant, and the morphological steps involved in their formation have been described, but the molecular events leading to dormancy are not known. In U. maydis, natural antisense transcripts (NATs) can function to alter gene expression and many NATs have increased levels in the teliospore. One such NAT is as-ssm1 which is complementary to the gene for the mitochondrial seryl-tRNA synthetase (ssm1), an enzyme important to mitochondrial function. The disruption of ssm1 leads to cell lysis, indicating it is also essential for cellular viability. To assess the function of as-ssm1, it was ectopically expressed in haploid cells, where it is not normally present. This expression led to reductions in growth rate, virulence, mitochondrial membrane potential and oxygen consumption. It also resulted in the formation of as-ssm1/ssm1 doublestranded RNA and increased ssm1 transcript levels, but no change in Ssm1 protein levels was detected. Together, these findings suggest a role for as-ssm1 in facilitating teliospore dormancy through dsRNA formation and reduction of mitochondrial function.