Dataset Information

Multi-omics driven metabolic network reconstruction and analysis of lignocellulosic carbon utilization in Rhodosporidium toruloides

ABSTRACT: Global proteomics datasets to study lignocellulosic carbon utilization in Rhodosporidium Toruloides

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Rhodotorula Toruloides

TISSUE(S): Fungus Form

SUBMITTER: Matthew Monroe

LAB HEAD: Jon K Magnuson

PROVIDER: PXD022377 | Pride | 2021-09-09

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	Dataset_Replicate_Information.csv	Csv
	Sporid_Cell_A_40H_1_P_005_A_12Apr18_Merry_18-02-04.mzML.gz	Mzml
	Sporid_Cell_A_40H_1_P_005_A_12Apr18_Merry_18-02-04.raw	Raw
	Sporid_Cell_A_40H_1_P_005_A_12Apr18_Merry_18-02-04_msgfplus.mzid.gz	Mzid
	Sporid_Cell_A_40H_1_P_005_B_12Apr18_Merry_18-02-04.mzML.gz	Mzml

Items per page:

1 - 5 of 199

Publications

Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in Rhodosporidium toruloides.

Kim Joonhoon J Coradetti Samuel T ST Kim Young-Mo YM Gao Yuqian Y Yaegashi Junko J Zucker Jeremy D JD Munoz Nathalie N Zink Erika M EM Burnum-Johnson Kristin E KE Baker Scott E SE Simmons Blake A BA Skerker Jeffrey M JM Gladden John M JM Magnuson Jon K JK

Frontiers in bioengineering and biotechnology 20210108

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 w ...[more]

PMID: 33585414

Similar Datasets

Project description:Cells must sense and respond to available nutrients to utilize available resources and establish fungal colonies. Saprophytic microbes harvest carbon from plant biomass, which contain insoluble, complex carbohydrates that must be degraded extracellularly prior to import into the cell. Filamentous fungi can degrade these complex carbohydrates. However, while many single cellular microbes can utilize the building blocks of these insoluble polysaccharides, they frequently are unable to degrade insoluble carbohydrates. Cellobiose is a disaccharide breakdown product of cellulose, the most abundant component of plant biomass. We investigated the genetic regulation of cellobiose utilization in the oleaginous, basidiomycete yeast Rhodotorula (Rhodosporidium) toruloides using a combination of phylogenetic, genetic, and genomic approaches. We tested the closest R. toruloides homolog of the cellulose degradation regulator CLR-2/ClrB for a role in cellobiose utilization. Deletion of this transcription factor, which we named Cbr1, eliminated the ability of cells to grow on media containing cellobiose as the sole carbon source. Although, the role of CLR-2/ClrB is limited to regulating the expression of genes involved in the utilization of cellulose and hemicellulose, Cbr1 plays a role not only in cellobiose utilization, but also utilization of tricarboxylic acid (TCA) cycle intermediates. Transcriptional profiling revealed that the genes activated by Cbr1 included genes encoding beta-glucosidases and transporters. These beta-glucosidases are secreted and are necessary and sufficient for cellobiose utilization, while one of the transporters is required for utilization of the TCA cycle intermediate, citrate. Additionally, Cbr1 inhibits carbon catabolite repression, specifically during utilization of disaccharides, which may have evolved to limit the repression of genes encoding secreted proteins that cleave disaccharides into glucose extracellularly. The co-regulation of cellobiose and TCA cycle utilization with carbon catabolite repression may shed light on alternative methods of the regulation of carbon catabolite repression in fungi.

Project description:The oleaginous red yeast species Rhodotorula toruloides, a prominent environmental basidiomycetous yeast, has garnered significant interest for its remarkable capacity to utilize main carbon sources present in lignocellulosic hydrolysates, such as glucose, xylose, and acetic acid, and to efficiently produce lipids and carotenoids. This species can also efficiently use other less usual and difficult-to-catabolize C-sources, as is the case of the acid sugar D-galacturonic acid and the neutral sugar L-arabinose, present in hydrolysates from pectin-rich agro-industrial residues. Strain R. toruloides IST536 (alias PYCC 5615) was previously selected in our laboratory for sugar beet pulp valorization based on its ability to produce lipids and carotenoids through the complete catabolism of the major C-sources present in the hydrolysates (1). This strain, whose genome has been recently sequenced in our laboratory, is a conjugated strain derived from IFO 0559 (isolated from wood-pulp; GCA_000988805.1) × IFO 0880 (isolated from air; GCA_001255795.1) (2). Despite its potential, the metabolism of this promising strain can be limited by the presence of acetic acid in the hydrolysates as well as other inhibitors present in lignocellulosic hydrolysates. To increase IST536 (PYCC 5615) strain robustness, an adaptive laboratory evolution (ALE) strategy was used. The selected evolved strain IST536 MM15 exhibits increased tolerance to several inhibitors of biotechnological relevance: methanol and the four main inhibitors present in lignocellulosic hydrolysates: acetic and formic acids, hydroxymethylfurfural (HMF), and furfural (3). The superior performance of this evolved multi-stress tolerant strain for lipid production from non-detoxified lignocellulosic biomass hydrolysates was confirmed. To obtain mechanistic insights underlying such multi-tolerant phenotype, the genomes of the original and the evolved strains, IST536 (PYCC 5615) and IST536 MM15, respectively, were sequenced and the transcriptomic profiling of both strains under non-stressing conditions was performed. References: 1. Martins LC, et, al. Journal of Fungi. 2021; 7(3):215. https://doi.org/10.3390/jof7030215 2. Banno, I. (1967). The Journal of General and Applied Microbiology, 13(2), 167-196. https://doi.org/10.2323/jgam.13.167 3. Fernandes, M. A., Mota, M. N., et al, Journal of Fungi, 2023, 9(11), 1073 https://doi.org/10.3390/jof9111073

Dataset Information

Multi-omics driven metabolic network reconstruction and analysis of lignocellulosic carbon utilization in Rhodosporidium toruloides

Dataset's files

Publications

Multi-Omics Driven Metabolic Network Reconstruction and Analysis of Lignocellulosic Carbon Utilization in <i>Rhodosporidium toruloides</i>.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets