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Proteomes
Special Issues
Tools for understanding PTM crosstalk
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Tools for understanding PTM crosstalk

A special issue of Proteomes (ISSN 2227-7382).

Deadline for manuscript submissions: closed (30 August 2018) | Viewed by 19302

Special Issue Editors

Dr. Frederique Lisacek

E-Mail Website
Guest Editor
Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Switzerland
Interests: bioinformatics; proteomics; glycomics
Dr. Lydie Lane

E-Mail Website
Guest Editor
Calipho Group, Swiss Institute of Bioinformatics, Geneva, Switzerland
Interests: bioinformatics; proteomics; biocuration

Special Issue Information

Dear Colleagues,

It is now well established that posttranslational modifications (PTMs) act in combination on proteins for modulation and regulation purposes. The next challenge is to identify the constraints that rule their cooperative and/or antagonist effects. This is illustrated in attempts to decipher the “histone code” that would explain the combined effects of methylation, acetylation, ADP-ribosylation, ubiquitination, citrullination and phosphorylation of histone tails. In fact, the elucidation of PTM crosstalk requires dedicated effort not only in improving detection and characterization methods but also in apprehending the interplay between modified proteins and modifying enzymes.

This special issue will reflect the variety of methods and expertise needed to take on this challenge. It will cover PTM detection methods mostly using mass spectrometry (MS) technology, particularly top down strategies that have been successful in characterizing modified histones, along with innovative bioinformatics tools supporting data analysis as well as PTM prediction. Furthermore, since detection and prediction are necessary but not sufficient to understand PTM crosstalk; this Special Issue welcomes manuscripts reflecting current research on how PTM combinations are generated and affect protein function and interactions. This covers studies in protein science in the broadest sense and is equally applicable to prokaryotic or eukaryotic species.

Sincerely,

Dr. Frederique Lisacek
Dr. Lydie Lane
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Proteomes is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • posttranslational modification (PTM)
  • PTM crosstalk
  • mass spectrometry
  • functional assay
  • protein-protein interactions,
  • detection method
  • prediction
  • bioinformatics

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Published Papers (3 papers)

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14 pages, 1486 KiB  
Article
Utilizing Optimized Tools to Investigate PTM Crosstalk: Identifying Potential PTM Crosstalk of Acetylated Mitochondrial Proteins
by Henrick Horita, Andy Law and Kim Middleton
Proteomes 2018, 6(2), 24; https://doi.org/10.3390/proteomes6020024 - 22 May 2018
Cited by 10 | Viewed by 5191
Abstract
Post-translational modification (PTM) crosstalk is recognized as a major cell-regulatory mechanism, and studies of several proteins have validated the premise that PTMs work in concert. Previous work by our group investigated the potential PTM crosstalk on proteins in the EGFR-Ras-c-Fos axis by utilizing [...] Read more.
Post-translational modification (PTM) crosstalk is recognized as a major cell-regulatory mechanism, and studies of several proteins have validated the premise that PTMs work in concert. Previous work by our group investigated the potential PTM crosstalk on proteins in the EGFR-Ras-c-Fos axis by utilizing a comprehensive set of PTM reagents termed Signal-Seeker toolkits. In this study, these tools were used to investigate the potential PTM crosstalk that occurs in acetylated mitochondrial proteins in response to a mitochondrial stress-inducing agent hydrogen peroxide (H2O2). Mitochondrial protein acetylation has been shown to participate in PTM crosstalk as exemplified by the regulation of the pyruvate dehydrogenase complex via kinase, phosphatase, acetyltransferase, and deacetylase activities. Changes in the acetylated state of mitochondrial proteins were investigated, in response to H2O2, using a novel anti acetyl lysine (Ac-K) antibody. Signal-Seeker PTM detection tools were used to validate the acetylation state of ten mitochondrial targets, as well as their endogenous acetylation state in response to H2O2. Importantly, the endogenous acetylation, ubiquitination, SUMOylation 2/3, and tyrosine phosphorylation state of four target mitochondrial proteins were also investigated with the toolkit. Each of the four proteins had unique PTM profiles, but diverging acetylation and ubiquitin or SUMO 2/3 signals appeared to be a common theme. This proof-of-concept study identifies the Signal-Seeker toolkits as a useful tool to investigate potential PTM crosstalk. Full article
(This article belongs to the Special Issue Tools for understanding PTM crosstalk)
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16 pages, 3064 KiB  
Review
Proteomic Analysis of Histone Variants and Their PTMs: Strategies and Pitfalls
by Sara El Kennani, Marion Crespo, Jérôme Govin and Delphine Pflieger
Proteomes 2018, 6(3), 29; https://doi.org/10.3390/proteomes6030029 - 21 Jun 2018
Cited by 32 | Viewed by 8038
Abstract
Epigenetic modifications contribute to the determination of cell fate and differentiation. The molecular mechanisms underlying histone variants and post-translational modifications (PTMs) have been studied in the contexts of development, differentiation, and disease. Antibody-based assays have classically been used to target PTMs, but these [...] Read more.
Epigenetic modifications contribute to the determination of cell fate and differentiation. The molecular mechanisms underlying histone variants and post-translational modifications (PTMs) have been studied in the contexts of development, differentiation, and disease. Antibody-based assays have classically been used to target PTMs, but these approaches fail to reveal combinatorial patterns of modifications. In addition, some histone variants are so similar to canonical histones that antibodies have difficulty distinguishing between these isoforms. Mass spectrometry (MS) has progressively developed as a powerful technology for the study of histone variants and their PTMs. Indeed, MS analyses highlighted exquisitely complex combinations of PTMs, suggesting “crosstalk” between them, and also revealed that PTM patterns are often variant-specific. Even though the sensitivity and acquisition speed of MS instruments have considerably increased alongside the development of computational tools for the study of multiple PTMs, it remains challenging to correctly describe the landscape of histone PTMs, and in particular to confidently assign modifications to specific amino acids. Here, we provide an inventory of MS-based strategies and of the pitfalls inherent to histone PTM and variant characterization, while stressing the complex interplay between PTMs and histone sequence variations. We will particularly illustrate the roles played by MS-based analyses in identifying and quantifying histone variants and modifications. Full article
(This article belongs to the Special Issue Tools for understanding PTM crosstalk)
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10 pages, 2277 KiB  
Communication
Inhibiting Arginine Methylation as a Tool to Investigate Cross-Talk with Methylation and Acetylation Post-Translational Modifications in a Glioblastoma Cell Line
by Sabrina Francesca Samuel, Alistair James Marsden, Srihari Deepak, Francisco Rivero, John Greenman and Pedro Beltran-Alvarez
Proteomes 2018, 6(4), 44; https://doi.org/10.3390/proteomes6040044 - 20 Oct 2018
Cited by 8 | Viewed by 5080
Abstract
Glioblastomas (GBM) are the most common grade 4 brain tumours; patients have very poor prognosis with an average survival of 15 months after diagnosis. Novel research lines have begun to explore aberrant protein arginine methylation (ArgMe) as a possible therapeutic target in GBM [...] Read more.
Glioblastomas (GBM) are the most common grade 4 brain tumours; patients have very poor prognosis with an average survival of 15 months after diagnosis. Novel research lines have begun to explore aberrant protein arginine methylation (ArgMe) as a possible therapeutic target in GBM and ArgMe inhibitors are currently in clinical trials. Enzymes known as protein arginine methyltransferases (PRMT1-9) can lead to mono- or di-ArgMe, and in the latter case symmetric or asymmetric dimethylation (SDMA and ADMA, respectively). Using the most common GBM cell line, we have profiled the expression of PRMTs, used ArgMe inhibitors as tools to investigate post-translational modifications cross-talk and measured the effect of ArgMe inhibitors on cell viability. We have identified novel SDMA events upon inhibition of ADMA in GBM cells and spheroids. We have observed cross-talk between ADMA and lysine acetylation in GBM cells and platelets. Treatment of GBM cells with furamidine, a PRMT1 inhibitor, reduces cell viability in 2D and 3D models. These data provide new molecular understanding of a disease with unmet clinical needs. Full article
(This article belongs to the Special Issue Tools for understanding PTM crosstalk)
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