Sample Preparation Protocols for Protein Abundance, Acetylome, and Phosphoproteome Profiling of Plant Tissues

Song, Gaoyuan; McReynolds, Maxwell R; Walley, Justin W.

doi:10.1007/978-1-4939-7003-2_9

Cited by 6 publications

(7 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Total protein was extracted from the samples, and tryptic peptides were labeled with iTRAQ (SCIEX) reagents to quantify protein abundance ( 39 ). In parallel, we enriched for acetylated peptides with a pan–acetyl-lysine antibody and then quantified the immunopurified peptides using spectral counting ( 14 , 40 , 41 ). We compared the levels of 3,636 nonenriched proteins and 2,791 acetylation sites originating from 912 acetylated proteins ( Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Peptide preparation and protein abundance profiling by mass spectrometry were based on previously described methods ( 41 , 63 , 84 , 85 ). Quantification of total nonenriched protein abundance was conducted by labeling peptides before acetyl enrichment with iTRAQ reagent, which labels primary amines and lysine side chains ( 39 , 86 ).…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Fungal-induced protein hyperacetylation in maize identified by acetylome profiling

Walley

Shen

McReynolds

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

SignificanceHow pathogens manipulate host cellular machinery to enable infection is a major question in biology. The ability of Cochliobolus carbonum race 1 to infect susceptible corn plants relies on production of HC-toxin (HCT). While it is known that HC-toxin is a histone deacetylase inhibitor, knowledge of how HCT actually promotes virulence has remained elusive. Here, we use mass spectrometry to quantify protein abundance and levels of protein acetylation in HCT-treated or pathogen-infected plants. These analyses revealed that the activity of plant-encoded enzymes can be modulated to alter both histone and nonhistone protein acetylation during a susceptible interaction and suggest that virulent C. carbonum utilizes HCT to reprogram the transcriptional response to infection, resulting in an ineffective defense response.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Fungal-induced protein hyperacetylation in maize identified by acetylome profiling

Walley

Shen

McReynolds

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

View full text Add to dashboard Cite

show abstract

“…Proteins were then subjected to four rounds of acetone precipitation with probe sonication between each round. Pelleted protein was solubilized in UA buffer (8 M urea, 50 mM Tris-HCl, pH 7, and 5 mM TCEP) and processed using the filter-aided sample preparation method ( Wiśniewski et al, 2009 ; Song et al, 2017 ) with microcon YM-30 centrifugal filters (Millipore). Proteins were digested on the filter overnight with 1 µg trypsin (Roche) at 37°C.…”

Section: Methodsmentioning

confidence: 99%

Maize defective kernel5 is a bacterial TamB homologue required for chloroplast envelope biogenesis

Zhang

Boehlein

et al. 2019

Journal of Cell Biology

Self Cite

View full text Add to dashboard Cite

Chloroplasts are of prokaryotic origin with a double-membrane envelope separating plastid metabolism from the cytosol. Envelope membrane proteins integrate chloroplasts with the cell, but envelope biogenesis mechanisms remain elusive. We show that maize defective kernel5 (dek5) is critical for envelope biogenesis. Amyloplasts and chloroplasts are larger and reduced in number in dek5 with multiple ultrastructural defects. The DEK5 protein is homologous to rice SSG4, Arabidopsis thaliana EMB2410/TIC236, and Escherichia coli tamB. TamB functions in bacterial outer membrane biogenesis. DEK5 is localized to the envelope with a topology analogous to TamB. Increased levels of soluble sugars in dek5 developing endosperm and elevated osmotic pressure in mutant leaf cells suggest defective intracellular solute transport. Proteomics and antibody-based analyses show dek5 reduces levels of Toc75 and chloroplast envelope transporters. Moreover, dek5 chloroplasts reduce inorganic phosphate uptake with at least an 80% reduction relative to normal chloroplasts. These data suggest that DEK5 functions in plastid envelope biogenesis to enable transport of metabolites and proteins.

show abstract

“…The advances in LC separation and MS instrumentation are providing more and more high analytical reproducibility, speed in acquisition, high-resolution and sensitivity up to femtomoles [ 57 , 58 , 59 ]. The improvement of these aspects, coupled with sample preparation protocols [ 60 ] and advanced bioinformatic tools [ 61 ], may be translated into higher plant proteome coverage, including post-translational modifications (PTMs) and PPIs [ 62 ]; PTMs identification often requires specific enrichment steps, like in the case of phosphorylation or glycosylation, which complexify sample preparation procedure as well as protein quantitation [ 63 ]. To reach these purposes, a key factor is the massive application of the high-throughput genomic technologies in order to increase the number of sequenced genomes, including that of the crop species [ 64 ].…”

Section: Omic Technologies In the Plant World: From Genomics To Mementioning

confidence: 99%

Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World

et al. 2018

View full text Add to dashboard Cite

The investigation of plant organisms by means of data-derived systems biology approaches based on network modeling is mainly characterized by genomic data, while the potential of proteomics is largely unexplored. This delay is mainly caused by the paucity of plant genomic/proteomic sequences and annotations which are fundamental to perform mass-spectrometry (MS) data interpretation. However, Next Generation Sequencing (NGS) techniques are contributing to filling this gap and an increasing number of studies are focusing on plant proteome profiling and protein-protein interactions (PPIs) identification. Interesting results were obtained by evaluating the topology of PPI networks in the context of organ-associated biological processes as well as plant-pathogen relationships. These examples foreshadow well the benefits that these approaches may provide to plant research. Thus, in addition to providing an overview of the main-omic technologies recently used on plant organisms, we will focus on studies that rely on concepts of module, hub and shortest path, and how they can contribute to the plant discovery processes. In this scenario, we will also consider gene co-expression networks, and some examples of integration with metabolomic data and genome-wide association studies (GWAS) to select candidate genes will be mentioned.

show abstract

Sample Preparation Protocols for Protein Abundance, Acetylome, and Phosphoproteome Profiling of Plant Tissues

Cited by 6 publications

References 27 publications

Fungal-induced protein hyperacetylation in maize identified by acetylome profiling

Fungal-induced protein hyperacetylation in maize identified by acetylome profiling

Maize defective kernel5 is a bacterial TamB homologue required for chloroplast envelope biogenesis

Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World

Contact Info

Product

Resources

About