Protein Termini and Their Modifications Revealed by Positional Proteomics

Marino, Giada; Eckhard, Ulrich; Overall, Christopher M.

doi:10.1021/acschembio.5b00189

Cited by 89 publications

(102 citation statements)

References 102 publications

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“…In addition, single molecule long-read sequencing has become a powerful method to get full-length transcripts for gene model re-annotation and subsequent AS analysis. Coupling with other techniques such as ribosome sequencing (Brar and Weissman, 2015), positional proteomics (Marino et al, 2015), and peptidome (Tavormina et al, 2015) may further increase our understanding on genome coding ability and its regulation during rice grain filling.…”

Section: Discussionmentioning

confidence: 99%

SWATH-MS Quantitative Analysis of Proteins in the Rice Inferior and Superior Spikelets during Grain Filling

Zhu

Chen

et al. 2016

Front. Plant Sci.

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Modern rice cultivars have large panicle but their yield potential is often not fully achieved due to poor grain-filling of late-flowering inferior spikelets (IS). Our earlier work suggested a broad transcriptional reprogramming during grain filling and showed a difference in gene expression between IS and earlier-flowering superior spikelets (SS). However, the links between the abundances of transcripts and their corresponding proteins are unclear. In this study, a SWATH-MS (sequential window acquisition of all theoretical spectra-mass spectrometry) -based quantitative proteomic analysis has been applied to investigate SS and IS proteomes. A total of 304 proteins of widely differing functionality were observed to be differentially expressed between IS and SS. Detailed gene ontology analysis indicated that several biological processes including photosynthesis, protein metabolism, and energy metabolism are differentially regulated. Further correlation analysis revealed that abundances of most of the differentially expressed proteins are not correlated to the respective transcript levels, indicating that an extra layer of gene regulation which may exist during rice grain filling. Our findings raised an intriguing possibility that these candidate proteins may be crucial in determining the poor grain-filling of IS. Therefore, we hypothesize that the regulation of proteome changes not only occurs at the transcriptional, but also at the post-transcriptional level, during grain filling in rice.

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Section: Discussionmentioning

confidence: 99%

SWATH-MS Quantitative Analysis of Proteins in the Rice Inferior and Superior Spikelets during Grain Filling

Zhu

Chen

et al. 2016

Front. Plant Sci.

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“…A total of 1,508 of these sequences harbor the C-terminal lysine residue that could in principle be acetylated and consequently serve as the DD1-specific substrate of HDAC6 (the distribution of C-terminal Xxx-Lys dipeptides is given in Supplemental Table S1). We note, however, that experimental identification of C-terminal acetyl-lysines would require the development of specific mass spectrometry protocols because the currently used approaches are only marginally suitable for this purpose (27,33).…”

Section: The Dd1 Catalytic Domain Fails To Deacetylate Peptides On Thmentioning

confidence: 99%

The unraveling of substrate specificity of histone deacetylase 6 domains using acetylome peptide microarrays and peptide libraries

et al. 2018

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Histone deacetylase 6 (HDAC6) is a multidomain cytosolic hydrolase acting mostly on nonhistone protein substrates. Investigations of the substrate specificity of HDAC6 are confounded by the presence of 2 catalytically active deacetylase domains (DD1 and DD2). In this study, acetylome peptide microarrays and peptide libraries were used to map the substrate specificity of DD1 and DD2 of human HDAC6. The results show that DD1 is solely responsible for the deacetylation of substrates harboring the acetyllysine at their C terminus, whereas DD2 exclusively deacetylates peptides with an internal acetyllysine residue. Also, statistical analysis of the deacetylation data revealed amino acid preferences at individual positions flanking the acetyllysine, where glycine and arginine residues are favored at positions N‐terminal to the central acetyllysine; negatively charged glutamate is strongly disfavored throughout the sequence. Finally, the deacylation activity of HDAC6 was profiled by using a panel of acyl derivatives of the optimized peptide substrate and showed that HDAC6 acts as a proficient deformylase. Our data thus offer a detailed insight into the substrate preferences of the individual HDAC6 domains at the peptide level, and these findings can in turn help in elucidating the biologic roles of the enzyme and facilitate the development of new domain‐specific inhibitors as research tools or therapeutic agents.—Kutil, Z., Skultetyova, L., Rauh, D., Meleshin, M., Snajdr, I., Novakova, Z., Mikesova, J., Pavlicek, J., Hadzima, M., Baranova, P., Havlinova, B., Majer, P., Schutkowski, M., Barinka, C. The unraveling of substrate specificity of histone deacetylase 6 domains using acetylome peptide microarrays and peptide libraries. FASEB J. 33,4035–4045 (2019). http://www.fasebj.org

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“…Proteolysis is an important post‐translational modification that can terminate protein function through their degradation, whereas proteolytic processing specifically alters protein structure, localization, and function through precise and measured cleavage events leading to stable cleavage fragments (Lange & Overall, ; Marino et al , ). To further explore whether protein fragments generated after cleavage accumulate or are depleted, and thus behave differently than suggested by the whole protein averages, we employed the Shannon index (Shannon & Weaver, ; Bent & Forney, ) to globally assess peptide chromatogram diversity and evenness.…”

Section: Resultsmentioning

confidence: 99%

Interactome disassembly during apoptosis occurs independent of caspase cleavage

Scott

Rogers

Prudova

et al. 2017

Molecular Systems Biology

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Protein–protein interaction networks (interactomes) define the functionality of all biological systems. In apoptosis, proteolysis by caspases is thought to initiate disassembly of protein complexes and cell death. Here we used a quantitative proteomics approach, protein correlation profiling (PCP), to explore changes in cytoplasmic and mitochondrial interactomes in response to apoptosis initiation as a function of caspase activity. We measured the response to initiation of Fas‐mediated apoptosis in 17,991 interactions among 2,779 proteins, comprising the largest dynamic interactome to date. The majority of interactions were unaffected early in apoptosis, but multiple complexes containing known caspase targets were disassembled. Nonetheless, proteome‐wide analysis of proteolytic processing by terminal amine isotopic labeling of substrates (TAILS) revealed little correlation between proteolytic and interactome changes. Our findings show that, in apoptosis, significant interactome alterations occur before and independently of caspase activity. Thus, apoptosis initiation includes a tight program of interactome rearrangement, leading to disassembly of relatively few, select complexes. These early interactome alterations occur independently of cleavage of these protein by caspases.

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Protein Termini and Their Modifications Revealed by Positional Proteomics

Cited by 89 publications

References 102 publications

SWATH-MS Quantitative Analysis of Proteins in the Rice Inferior and Superior Spikelets during Grain Filling

SWATH-MS Quantitative Analysis of Proteins in the Rice Inferior and Superior Spikelets during Grain Filling

The unraveling of substrate specificity of histone deacetylase 6 domains using acetylome peptide microarrays and peptide libraries

Interactome disassembly during apoptosis occurs independent of caspase cleavage

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