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Proteome of the wood decay fungus Fomitopsis pinicola is altered by substrate

ABSTRACT: The brown rot fungus, Fomitopsis pinicola strain FP-58527, was cultivated in media containing ground Populus tremuloides, Pinus taeda or Picea glauca wood as sole carbon source. Mass spectrometry analyses identified proteins likely involved in the degradation of lignocellulose. Patterns of enzymes detected varied with substrate.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Fomitopsis Pinicola

TISSUE(S): Cell Suspension Culture, Extracellular Space

SUBMITTER: Greg Sabat

LAB HEAD: Dr. Daniel Cullen

PROVIDER: PXD028833 | Pride | 2021-09-29

REPOSITORIES: Pride

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			Action	DRS
	1_Aspen-1_Cullen_adj.raw	Raw
	1_Aspen-1_Cullen_adj__F002438_.mzid.gz	Mzid
	1_Aspen-1_Cullen_adj__F002438_.mzid.gz_1_Aspen-1_Cullen_adj__F002438_.MGF	Mzid
	2_Aspen-2_Cullen_adj.raw	Raw
	2_Aspen-2_Cullen_adj__F002439_.mzid.gz	Mzid

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Proteome of the wood decay fungus Fomitopsis pinicola is altered by substrate

Project description:The brown rot fungus, Fomitopsis pinicola strain FP-58527, was cultivated in media containing ground Populus tremuloides, Pinus taeda or Picea glauca wood as sole carbon source. Mass spectrometry analyses identified proteins likely involved in the degradation of lignocellulose. Patterns of enzymes detected varied with substrate.

2022-06-08 | PXD033887 | Pride

Proteomic analysis in transgenic hybrid aspen (Populus tremula x tremuloides) trees overexpression of vesicle-associated membrane protein PttVAP27-17

Project description:In this study we report on transgenic hybrid aspen (Populus tremula x P. tremuloides) lines that showed potential to increase biomass production both in the greenhouse and after five years of growth in the field. The transgenic lines carried an overexpression construct for Populus tremula x tremuloides vesicle-associated membrane protein (VAMP)-associated protein PttVAP27-17 (Potri.019G116400) that was selected from a gene-mining program for novel regulators of wood formation. A proteomic analysis was performed to characterize the overall effect of the overexpression of PttVAP27-17 on plant metabolic pathways. 20 mg of xylem sample for the selected wild type (WT) and three transgenic lines (lines 1,2 and 3) was collected in the following manner from two-months-old, greenhouse grown trees: The frozen bottom-part of the stem (10-17 cm portion from the base of the stem) was peeled, and the surface of the secondary xylem consisting of living vessels and fibers (into the depth of approximately one mm from the surface) was scraped. The xylem scrapings were ground to fine powder in liquid nitrogen and stored at -80oC. The analyses included 3-5 biological replicates for each of the transgenic lines, and seven replicates for the wild type.

2021-09-10 | PXD023826 | Pride

A proteomics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of Populus trees

Project description:Secretory Carrier-Associated Membrane Proteins (SCAMPs) are highly conserved 32–38 kDa proteins that are involved in membrane trafficking. A proteomics approach was taken to elucidate function of the SCAMPs in wood formation of transgenic Populus trees carrying an RNAi construct for Populus tremula x tremuloides SCAMP3 (PttSCAMP3; Potri.019G104000). Secondary xylem tissues were run on a SynaptTM G2 HDMS mass spectrometer equipped with a nanoflow electrospray ionization interface. Multivariate OnPLS (orthogonal projections to latent structures) modeling was applied to identify consistent changes in the proteomes of the transgenic lines compared to the wild type trees. The woody tissues of the transgenic trees displayed increased amounts of both polysaccharides and lignin oligomers, indicating increased deposition of both the carbohydrate and lignin components of the secondary cell walls. This coincided with slightly increased wood density as well as significantly increased thickness of the suberized cork in the transgenic lines. The OnPLS model identified a rather large number of proteins that were more abundant in the transgenic lines than in the wild type. Several of these were related to secretion and/or endocytosis as well as both primary and secondary cell wall biosynthesis, suggesting function of the Populus SCAMP proteins in membrane trafficking to fine-tune the abundance of cell wall precursors and/or proteins involved in cell wall biosynthesis and transport. The data provides a multi-level source of information for future studies on the function of the SCAMP proteins in plant stem tissues.

2018-01-10 | PXD008266 | Pride

Proteomes of wood decay Basiomycetes Phanerochaete chrysosporium RP78 [Taxon ID 273507], Rhodonia placenta MAD-698-R-SB12 [Taxon ID 670580] and Jaapia argillacea MUCL33604 [Taxon ID 933084]

Project description:Culture filtrates from three wood decay fungi were analyzed after five- and 10-days growth in submerged cultures containing 0.75 % (w/v) finely ground lodgepole pine (Pinus contorta). Significant differences in proteome profiles were observed among the species.

2022-09-27 | PXD037036 | Pride

Interplay between Two Paralogous Human Silencing Hub (HuSH) Complexes in Regulating LINE-1 Element Silencing

Project description:The Human Silencing Hub (HuSH) complex is a complex that silences retrotransposable elements invertebrates. Here, we identify a second HuSH complex, designated HuSH2, which is centered aroundTASOR2, a paralog of the core TASOR protein in HuSH. Our findings reveal that HuSH and HuSH2 localize todistinct and non-overlapping genomic loci. Specifically, HuSH localizes to and represses LINE-1retrotransposons, whereas HuSH2 targets and represses KRAB-ZNFs and interferon signaling and responsegenes. We use in silico protein structure predictions to simulate MPP8 interactions with TASOR paralogs,guiding amino acid substitutions that disrupted binding to HuSH complexes. These MPP8 transgenes andother constructs reveal the importance of HuSH complex quantities in regulating LINE-1 activity. Furthermore,our results suggest that dynamic changes in TASOR and TASOR2 expression enable cells to finely tuneHuSH-mediated silencing. This study offers insights into the interplay of HuSH complexes, highlighting theirvital role in retrotransposon regulation.

2024-09-24 | PXD049085 | Pride

Cleavage of hemagglutinin from influenza A, at varying pH and over a twenty-four hour time period in the presence of cathepsin B, H and S

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Identity of Neisseria gonorrhoeae MS11 membrane associated proteins in supernatant

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Altered PtAIL1 expression is accompanied by significant transcriptome changes during adventitious rooting induction

Project description:Oligoarray analysis was used to identify genes differentially expressed in 2 mm sections of the basal stem region of wild type T89, PtAIL1 over-expressing or PtAIL1 RNAi lines of P. tremula x Populus tremuloides 24h and 72h after adventitious rooting induction. The Populus trichocarpa custom-exon expression array (12x135K) manufactured by Roche NimbleGen Systems Limited (Madison, WI) (http://www.nimblegen.com/products/exp/index.html) contained three independent, nonidentical, 60-mer probes per gene model coding sequence. Included in the oligoarray were 43,929 annotated gene models (Populus trichocarpa genome v2 ; Phytozome 5.0), 5,859 random 60-mer control probes and labelling controls. We performed 27 hybridizations from wildtype, PtAIL1 over-expressing or PtAIL1 RNAi lines of P. tremula x Populus tremuloides at time 0, 24h and 72h after adventitious rooting induction. For each timepoint we performed three biological replicates.

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Mitochondria-rough-ER Contacts in The Liver Regulate Systemic Lipid Homeostasis

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