Browse
Submit Data
Databases
API
Help

Dataset Information

447 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Protein extraction in recalcitrant plant species

ABSTRACT: A possible approach for gel-based proteomic studies in recalcitrant woody plants, using phenol as the most suitable protein extraction method when working with tissues with high interfering compounds

INSTRUMENT(S): 4700 Proteomics Analyzer

ORGANISM(S): Pinus Pinaster (maritime Pine) Quercus Suber (cork Oak) Pisolithus Tinctorius Marx 270 Vitis Vinifera (grape)

SUBMITTER: Andreia Figueiredo

PROVIDER: PXD000224 | Pride | 2013-07-09

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

A possible approach for gel-based proteomic studies in recalcitrant woody plants.

Sebastiana Mónica M Figueiredo Andreia A Monteiro Filipa F Martins Joana J Franco Catarina C Coelho Ana Varela AV Vaz Fátima F Simões Tânia T Penque Deborah D Pais Maria Salomé MS Ferreira Sílvia S

SpringerPlus 20130508 1

Woody plants are particularly difficult to investigate due to high phenolic, resin, and tannin contents and laborious sample preparation. In particular, protein isolation from woody plants for two-dimensional gel electrophoresis (2-DE) is challenging as secondary metabolites negatively interfere with protein extraction and separation. In this study, three protein extraction protocols, using TCA, phenol and ethanol as precipitation or extraction agents, were tested in order to select the more eff ...[more]

PMID: 23724367

Similar Datasets

SILEX: a fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species.

Project description: Not available

| S-EPMC7419208 | biostudies-literature

Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

Project description:The rumen harbors a complex mixture of archaea, bacteria, protozoa and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacteria populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen fauna. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to the initial stages of rumination, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated in nylon bags within the rumen of cannulated dairy cows for 48 hours.

2020-10-14 | PXD017007 | Pride

plant metagenome

Project description:Viromes of perennial woody plants species.

| PRJNA269207 | ENA

An optimised protocol for protein extraction from salt gland-enriched tissues of a mangrove tree species for proteomic analysis

Project description:Preparation of proteins from salt-gland-enriched tissues of mangrove plant is necessary for a systematic study of proteins involved in the plant’s unique desalination mechanism. Extraction of high-quality proteins from the leaves of mangrove tree species, however, is difficult due to the presence of high levels of endogenous phenolic compounds. In our study, preparation of proteins from only a part of the leaf tissues was required, rendering extraction even more challenging. By comparing several extraction methods, we developed a reliable procedure for obtaining sufficient proteins from salt gland-enriched tissues of the mangrove species Avicennia officinalis. Protein extraction was markedly improved using a phenol-based extraction method. Despite the lower protein yield obtained, one-dimensional protein gel profiles with greater resolution could be obtained, with more than twice the number of proteins detected when 1D-LC-MS/MS analyses were compared. Further analysis of proteins that were solely present in each extraction method favoured the phenol-based extraction. Phenol-based extracts contained nearly 10 times more solely-detected proteins than those were detectable in the extracts without using phenol. The protocol established could thus be applied for downstream high-throughput proteomic analyses involving LC-MS/MS or equivalent.

2015-07-17 | PXD001691 | Pride

plant metagenome

Project description:Coarse woody debris metagenomes Biodiversity Exploratory ALB

| PRJNA252423 | ENA

Flexible wood caused by altered lignin, following viral-induced suppression of phenylalanine ammonia lyase (PAL) activity. sRNA-seq

Project description:Woody plant material represents a renewable resource that has the potential to produce biofuels and/or novel materials with greatly reduced CO2 emissions. The study of viral infection in plants has largely focussed on detrimental symptoms, such as leaf yellowing or cell death that result in reduced crop yields. Apple rubbery wood (ARW) disease is the result of a viral infection that causes woody stems to exhibit increased flexibility. Biochemical and histochemical studies suggest the phenotype is a result of reduced lignification, specifically within the fibre cells of woody xylem. Expression analysis and proteomic data suggests that the downregulation of phenylalanine ammonia lyase (PAL) is responsible for decreased lignification. PAL is required for the first committed step in the phenylpropanoid pathway that leads to lignin biosynthesis. This is consistent with a large increase in soluble phenolics, including the lignin precursor phenylalanine, in symptomatic xylem. Downregulation of PAL appears to result from a widespread siRNA induction by the infected host, triggered by the virus. Symptomatic wood exhibited increased digestibility comparable to those seen in genetically engineered plants that alter lignin biosynthesis. To our knowledge this is the first example of a virus that alters lignin metabolism and offers a unique route to address the problem of the recalcitrant nature of plant biomass and a possible route to generating wood with altered mechanical properties.

2023-01-12 | E-MTAB-11409 | biostudies-arrayexpress

Flexible wood caused by altered lignin, following viral-induced suppression of phenylalanine ammonia lyase (PAL) activity. RNA-seq

2023-01-12 | E-MTAB-11410 | biostudies-arrayexpress

Leaf protein extraction method

Project description:We evaluated several approaches for sample processing that are based on popular urea extraction, methanol/chloroform, and phenol methods. Additionally, we examined whether these methods were improved using FASP-based on filter digestion. We found that phenol-FASP and UA-FASP methods enabled the best coverage of protein, peptides, and MS/MS

2018-02-20 | MSV000082080 | MassIVE

Arabidopsis Root Protein Extraction Evaluation

2018-05-15 | MSV000082362 | MassIVE

An efficient method for protein extraction from low protein concentration solutions compatible with the proteomic analysis of latex-producing organelles

Project description:The extraction of high-purity proteins from the washing solution (WS) of rubber tree latex-producing organelles (also termed rubber particles) in laticifers for proteomic analysis is challenging due to the low concentration of proteins in the WS. Recent studies have revealed that proteins in the WS might play crucial roles in natural rubber biosynthesis. To further examine the involvement of these proteins in natural rubber biosynthesis, we designed an efficiency method to extract high-purity WS proteins. We improved our current borax and phenol-based (BPP) method by adding re-extraction steps with phenol (REP) to improve the yield from low-protein concentration samples. With this new method, we extracted WS proteins that were suitable for proteomics. Indeed, compared to the original BPP method, the REP method improved both the quality and quantity of isolated proteins. By repeatedly extracting from low-protein concentration solutions using the same small amount of phenol, the REP method yielded enough protein of sufficiently high-quality from starting samples containing less than 0.02 mg of proteins per mL. This method was successfully applied to extract the rubber particle proteins from the WS of natural rubber latex samples. The REP-extracted WS proteins were resolved by two-dimensional gel electrophoresis (2-DE), and 28 proteins were positively identified by mass spectrometry. This method has the potential to become widely used for the extraction of proteins from low-protein-concentration solutions for proteomic analysis.

2016-10-10 | PXD004156 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data