ORCID Profile
0000-0001-5085-3106
Current Organisation
Pacific Northwest National Laboratory
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Publisher: American Society for Microbiology
Date: 26-12-2018
Abstract: Many yeasts undergo a morphological transition from yeast-to-hyphal growth in response to environmental conditions. We used forward and reverse genetic techniques to identify genes regulating this transition in Yarrowia lipolytica . We confirmed that the transcription factor Yl msn2 is required for the transition to hyphal growth and found that signaling by the histidine kinases Yl chk1 and Yl nik1 as well as the MAP kinases of the HOG pathway (Yl ssk2 , Yl pbs2 , and Yl hog1 ) regulates the transition to hyphal growth. These results suggest that Y. lipolytica transitions to hyphal growth in response to stress through multiple kinase pathways. Intriguingly, we found that a repetitive portion of the genome containing telomere-like and rDNA repeats may be involved in the transition to hyphal growth, suggesting a link between this region and the general stress response.
Publisher: Springer Science and Business Media LLC
Date: 03-2010
DOI: 10.1038/NATURE08850
Publisher: American Society for Microbiology
Date: 02-2005
DOI: 10.1128/EC.4.2.443-454.2005
Abstract: Redox sensing is a ubiquitous mechanism regulating cellular activity. Fungal pathogens face reactive oxygen species produced by the host plant's oxidative burst in addition to endogenous reactive oxygen species produced during aerobic metabolism. An array of preformed and induced detoxifying enzymes, including superoxide dismutase, catalases, and peroxidases, could allow fungi to infect plants despite the oxidative burst. We isolated a gene ( CHAP1 ) encoding a redox-regulated transcription factor in Cochliobolus heterostrophus , a fungal pathogen of maize. CHAP1 is a bZIP protein that possesses two cysteine-rich domains structurally and functionally related to Saccharomyces cerevisiae YAP1. Deletion of CHAP1 in C. heterostrophus resulted in decreased resistance to oxidative stress caused by hydrogen peroxide and menadione, but the virulence of chap1 mutants was unaffected. Upon activation by oxidizing agents or plant signals, a green fluorescent protein (GFP)-CHAP1 fusion protein became localized in the nucleus. Expression of genes encoding antioxidant proteins was induced in the wild type but not in chap1 mutants. Activation of CHAP1 occurred from the earliest stage of plant infection, in conidial germ tubes on the leaf surface, and persisted during infection. Late in the course of infection, after extensive necrotic lesions were formed, GFP-CHAP1 redistributed to the cytosol in hyphae growing on the leaf surface. Localization of CHAP1 to the nucleus may, through changes in the redox state of the cell, provide a mechanism linking extracellular cues to transcriptional regulation during the plant-pathogen interaction.
Publisher: Springer New York
Date: 2018
DOI: 10.1007/978-1-4939-7877-9_22
Abstract: The author's family name were incorrectly published in the original version. This has been corrected to read as.
Publisher: Springer New York
Date: 2018
DOI: 10.1007/978-1-4939-7877-9_10
Abstract: Cellulases and other enzymes are needed for saccharification of plant biomass in the biorefinery industry. Expression, characterization, and eventual large-scale production of known and novel cellulases requires the ability to express and secrete heterologous enzymes in relevant protein production platforms like Aspergillus niger. A method for cloning and expression of genes for these desirable enzymes in A. niger is presented in this Chapter.
Publisher: Public Library of Science (PLoS)
Date: 27-12-2017
Publisher: Springer Science and Business Media LLC
Date: 04-2011
Abstract: Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea / Trichoderma . Here we report an analysis of the genome sequences of the two biocontrol species Trichoderma atroviride (teleomorph Hypocrea atroviridis ) and Trichoderma virens (formerly Gliocladium virens , teleomorph Hypocrea virens ), and a comparison with Trichoderma reesei (teleomorph Hypocrea jecorina ). These three Trichoderma species display a remarkable conservation of gene order (78 to 96%), and a lack of active mobile elements probably due to repeat-induced point mutation. Several gene families are expanded in the two mycoparasitic species relative to T. reesei or other ascomycetes, and are overrepresented in non-syntenic genome regions. A phylogenetic analysis shows that T. reesei and T. virens are derived relative to T. atroviride . The mycoparasitism-specific genes thus arose in a common Trichoderma ancestor but were subsequently lost in T. reesei . The data offer a better understanding of mycoparasitism, and thus enforce the development of improved biocontrol strains for efficient and environmentally friendly protection of plants.
Publisher: Proceedings of the National Academy of Sciences
Date: 24-06-2021
Abstract: Lignocellulose-based biorefinery relies on plant cell wall degrading enzymes. Current genome editing methods can create fungal enzyme hypersecreter strains by design. However, the identification of candidate genes for targeted engineering of this trait remains a bottleneck, and the necessity of specific inducer molecules further complicates production. By the resequencing of a classical hypersecreting Neurospora crassa mutant, we uncovered that mutation of a gene encoding an F-box protein ( exo - 1 ) causes inducer-independent hypersecretion of amylases, invertase, and pectinases. Systems biology and genetic studies of Δ exo - 1 shed light on the regulation of enzyme secretion in filamentous fungi, allowing targeted reverse engineering of industrially employed fungi, such as Myceliophthora thermophila , demonstrating the power of classical mutants in combination with modern sequencing and omics technologies.
Publisher: Springer Science and Business Media LLC
Date: 06-01-2018
Publisher: American Society for Microbiology
Date: 30-04-2015
Abstract: We report the elucidation of the complete genome of the Neurospora crassa (Shear and Dodge) strain FGSC 73, a mat-a , trp-3 mutant strain. The genome sequence around the idiotypic mating type locus represents the only publicly available sequence for a mat-a strain. 40.42 Megabases are assembled into 358 scaffolds carrying 11,978 gene models.
Publisher: Springer Science and Business Media LLC
Date: 27-02-2020
DOI: 10.1038/S41467-019-14051-Y
Abstract: Section Flavi encompasses both harmful and beneficial Aspergillus species, such as Aspergillus oryzae , used in food fermentation and enzyme production, and Aspergillus flavus , food spoiler and mycotoxin producer. Here, we sequence 19 genomes spanning section Flavi and compare 31 fungal genomes including 23 Flavi species. We reassess their phylogenetic relationships and show that the closest relative of A. oryzae is not A. flavus , but A. minisclerotigenes or A. aflatoxiformans and identify high genome ersity, especially in sub-telomeric regions. We predict abundant CAZymes (598 per species) and prolific secondary metabolite gene clusters (73 per species) in section Flavi . However, the observed phenotypes (growth characteristics, polysaccharide degradation) do not necessarily correlate with inferences made from the predicted CAZyme content. Our work, including genomic analyses, phenotypic assays, and identification of secondary metabolites, highlights the genetic and metabolic ersity within section Flavi .
Publisher: Proceedings of the National Academy of Sciences
Date: 09-01-2018
Abstract: The genus of Aspergillus holds fungi relevant to plant and human pathology, food biotechnology, enzyme production, model organisms, and a selection of extremophiles. Here we present six whole-genome sequences that represent unexplored branches of the Aspergillus genus. The comparison of these genomes with previous genomes, coupled with extensive chemical analysis, has allowed us to identify genes for toxins, antibiotics, and anticancer compounds, as well as show that Aspergillus novofumigatus is potentially as pathogenic as Aspergillus fumigatus , and has an even more erse set of secreted bioactive compounds. The findings are of interest to industrial biotechnology and basic research, as well as medical and clinical research.
Publisher: Frontiers Media SA
Date: 08-01-2021
DOI: 10.3389/FBIOE.2020.612832
Abstract: An oleaginous yeast Rhodosporidium toruloides is a promising host for converting lignocellulosic biomass to bioproducts and biofuels. In this work, we performed multi-omics analysis of lignocellulosic carbon utilization in R. toruloides and reconstructed the genome-scale metabolic network of R. toruloides . High-quality metabolic network models for model organisms and orthologous protein mapping were used to build a draft metabolic network reconstruction. The reconstruction was manually curated to build a metabolic model using functional annotation and multi-omics data including transcriptomics, proteomics, metabolomics, and RB-TDNA sequencing. The multi-omics data and metabolic model were used to investigate R. toruloides metabolism including lipid accumulation and lignocellulosic carbon utilization. The developed metabolic model was validated against high-throughput growth phenotyping and gene fitness data, and further refined to resolve the inconsistencies between prediction and data. We believe that this is the most complete and accurate metabolic network model available for R. toruloides to date.
Publisher: Elsevier BV
Date: 06-2016
Publisher: Springer Science and Business Media LLC
Date: 10-2011
DOI: 10.1038/NBT.1976
Abstract: Thermostable enzymes and thermophilic cell factories may afford economic advantages in the production of many chemicals and biomass-based fuels. Here we describe and compare the genomes of two thermophilic fungi, Myceliophthora thermophila and Thielavia terrestris. To our knowledge, these genomes are the first described for thermophilic eukaryotes and the first complete telomere-to-telomere genomes for filamentous fungi. Genome analyses and experimental data suggest that both thermophiles are capable of hydrolyzing all major polysaccharides found in biomass. Examination of transcriptome data and secreted proteins suggests that the two fungi use shared approaches in the hydrolysis of cellulose and xylan but distinct mechanisms in pectin degradation. Characterization of the biomass-hydrolyzing activity of recombinant enzymes suggests that these organisms are highly efficient in biomass decomposition at both moderate and high temperatures. Furthermore, we present evidence suggesting that aside from representing a potential reservoir of thermostable enzymes, thermophilic fungi are amenable to manipulation using classical and molecular genetics.
Publisher: Public Library of Science (PLoS)
Date: 17-01-2019
Location: United States of America
Location: United States of America
No related grants have been discovered for Scott Baker.