A methodology for carbamate post-translational modification discovery and its application in Escherichia coli

2021 ◽  
Vol 11 (2) ◽  
pp. 20200028
Author(s):  
Victoria L. Linthwaite ◽  
Martin J. Cann
Keyword(s):  
Escherichia Coli ◽  
Carbon Dioxide ◽  
Arabidopsis Thaliana ◽  
Protein Interactions ◽  
Signalling Pathways ◽  
Post Translational Modification ◽  
Cellular Targets ◽  
Biologically Relevant ◽  
Cellular Processes ◽  
Cell Phenotypes

Carbon dioxide can influence cell phenotypes through the modulation of signalling pathways. CO 2 regulates cellular processes as diverse as metabolism, cellular homeostasis, chemosensing and pathogenesis. This diversity of regulated processes suggests a broadly conserved mechanism for CO 2 interactions with diverse cellular targets. CO 2 is generally unreactive but can interact with neutral amines on protein under normal intracellular conditions to form a carbamate post-translational modification (PTM). We have previously demonstrated the presence of this PTM in a subset of protein produced by the model plant species Arabidopsis thaliana . Here, we describe a detailed methodology for identifying new carbamate PTMs in an extracted soluble proteome under biologically relevant conditions. We apply this methodology to the soluble proteome of the model prokaryote Escherichia coli and identify new carbamate PTMs . The application of this methodology, therefore, supports the hypothesis that the carbamate PTM is both more widespread in biology than previously suspected and may represent a broadly relevant mechanism for CO 2 –protein interactions.

scholarly journals The Protein Interactome of Glycolysis in Escherichia coli

Proteomes ◽  
2021 ◽  
Vol 9 (2) ◽  
pp. 16
Author(s):  
Shomeek Chowdhury ◽  
Stephen Hepper ◽  
Mudassir K. Lodi ◽  
Milton H. Saier ◽  
Peter Uetz
Keyword(s):  
Escherichia Coli ◽  
Protein Interactions ◽  
Allosteric Regulation ◽  
Glycolytic Enzymes ◽  
Protein Protein Interactions ◽  
Post Translational Modification ◽  
Interacting Protein ◽  
E Coli ◽  
Protein Interactome ◽  
The Impact

Glycolysis is regulated by numerous mechanisms including allosteric regulation, post-translational modification or protein-protein interactions (PPI). While glycolytic enzymes have been found to interact with hundreds of proteins, the impact of only some of these PPIs on glycolysis is well understood. Here we investigate which of these interactions may affect glycolysis in E. coli and possibly across numerous other bacteria, based on the stoichiometry of interacting protein pairs (from proteomic studies) and their conservation across bacteria. We present a list of 339 protein-protein interactions involving glycolytic enzymes but predict that ~70% of glycolytic interactors are not present in adequate amounts to have a significant impact on glycolysis. Finally, we identify a conserved but uncharacterized subset of interactions that are likely to affect glycolysis and deserve further study.

Applications of Mass Spectrometry in Proteomics

2013 ◽  
Vol 66 (7) ◽  
pp. 721 ◽  
Author(s):  
Izabela Sokolowska ◽  
Armand G. Ngounou Wetie ◽  
Alisa G. Woods ◽  
Costel C. Darie
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Protein Identification ◽  
Protein Protein Interactions ◽  
Post Translational Modification ◽  
Cellular Processes ◽  
Physiological Processes ◽  
Protein Functions ◽  
Instruments And Techniques ◽  
Accurate Mass Spectrometry

Characterisation of proteins and whole proteomes can provide a foundation to our understanding of physiological and pathological states and biological diseases or disorders. Constant development of more reliable and accurate mass spectrometry (MS) instruments and techniques has allowed for better identification and quantification of the thousands of proteins involved in basic physiological processes. Therefore, MS-based proteomics has been widely applied to the analysis of biological samples and has greatly contributed to our understanding of protein functions, interactions, and dynamics, advancing our knowledge of cellular processes as well as the physiology and pathology of the human body. This review will discuss current proteomic approaches for protein identification and characterisation, including post-translational modification (PTM) analysis and quantitative proteomics as well as investigation of protein–protein interactions (PPIs).

scholarly journals Molecular basis for specificity of the Met1-linked polyubiquitin signal

2016 ◽  
Vol 44 (6) ◽  
pp. 1581-1602 ◽  
Author(s):  
Paul R. Elliott
Keyword(s):  
Molecular Mechanisms ◽  
Cellular Responses ◽  
Signalling Pathways ◽  
Post Translational Modification ◽  
Polyubiquitin Chains ◽  
Cellular Processes ◽  
Protein Ubiquitination ◽  
Ubiquitin Binding ◽  
Inflammatory Signalling ◽  
Unique Ability

The post-translational modification of proteins provides a rapid and versatile system for regulating all signalling pathways. Protein ubiquitination is one such type of post-translational modification involved in controlling numerous cellular processes. The unique ability of ubiquitin to form polyubiquitin chains creates a highly complex code responsible for different subsequent signalling outcomes. Specialised enzymes (‘writers’) generate the ubiquitin code, whereas other enzymes (‘erasers’) disassemble it. Importantly, the ubiquitin code is deciphered by different ubiquitin-binding proteins (‘readers’) functioning to elicit particular cellular responses. Ten years ago, the methionine1 (Met1)-linked (linear) polyubiquitin code was first identified and the intervening years have witnessed a seismic shift in our understanding of Met1-linked polyubiquitin in cellular processes, particularly inflammatory signalling. This review will discuss the molecular mechanisms of specificity determination within Met1-linked polyubiquitin signalling.

scholarly journals Ubiquitin-Specific Proteases: Players in Cancer Cellular Processes

2021 ◽  
Vol 14 (9) ◽  
pp. 848
Author(s):  
Lucas Cruz ◽  
Paula Soares ◽  
Marcelo Correia
Keyword(s):  
Protein Function ◽  
Deubiquitinating Enzymes ◽  
Post Translational Modification ◽  
Cellular Functions ◽  
Cellular Targets ◽  
Cellular Processes ◽  
Protein Ubiquitination ◽  
Damage Repair ◽  
Ubiquitin Molecule

Ubiquitination represents a post-translational modification (PTM) essential for the maintenance of cellular homeostasis. Ubiquitination is involved in the regulation of protein function, localization and turnover through the attachment of a ubiquitin molecule(s) to a target protein. Ubiquitination can be reversed through the action of deubiquitinating enzymes (DUBs). The DUB enzymes have the ability to remove the mono- or poly-ubiquitination signals and are involved in the maturation, recycling, editing and rearrangement of ubiquitin(s). Ubiquitin-specific proteases (USPs) are the biggest family of DUBs, responsible for numerous cellular functions through interactions with different cellular targets. Over the past few years, several studies have focused on the role of USPs in carcinogenesis, which has led to an increasing development of therapies based on USP inhibitors. In this review, we intend to describe different cellular functions, such as the cell cycle, DNA damage repair, chromatin remodeling and several signaling pathways, in which USPs are involved in the development or progression of cancer. In addition, we describe existing therapies that target the inhibition of USPs.

Computer Analysis of Phytochrome Sequences from Five Species: Implications for the Mechanism of Action

1990 ◽  
Vol 45 (9-10) ◽  
pp. 987-998 ◽  
Author(s):  
Michael D. Partis ◽  
Rudolf Grimm
Keyword(s):  
Arabidopsis Thaliana ◽  
Amino Acid ◽  
Lipid Bilayers ◽  
Protein Interactions ◽  
Avena Sativa ◽  
Sequence Similarity ◽  
Amino Acid Sequences ◽  
Amino Acid Sequence Similarity ◽  
Post Translational Modification ◽  
C Terminus

Abstract The amino acid sequences of phytochrome from Avena sativa, Oryza sativa, Curcurbita pepo, Pisum sativum and Arabidopsis thaliana have been analyzed with a variety of computer programs, with a view to identifying areas of the protein which contribute to the properties of this photoreceptor. A region at the C-terminus has been shown to be amphiphilic, and by ana­logy with surface-seeking peptides, may be responsible for interaction of phytochrome with lipid bilayers. Possible targeting sequences in phytochromes have been identified, including a series of four basic residues which correspond to those responsible for transport of nuclear-located proteins. Sites capable of post-translational modification have been found in monocot sequences, but not in dicot sequences. Areas of the phytochrome molecule which are exposed on the surface of the portein, and which are therefore capable of interaction with other cellular macromolecules, have been identified. Analogies with other biliproteins have been used to define minimum chromophore-protein interactions. Possible enzymic activities associated with phytochromes have been discussed with respect to local amino acid sequence similarity with enzymes.

scholarly journals Regulation of Protein Post-Translational Modifications on Metabolism of Actinomycetes

Biomolecules ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1122
Author(s):  
Chen-Fan Sun ◽  
Yong-Quan Li ◽  
Xu-Ming Mao
Keyword(s):  
Protein Interactions ◽  
Protein Protein Interactions ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
Cellular Processes ◽  
Structure Activity ◽  
Variable Environments ◽  
Metabolic States ◽  
Metabolite Synthesis ◽  
External Stimuli

Protein post-translational modification (PTM) is a reversible process, which can dynamically regulate the metabolic state of cells through regulation of protein structure, activity, localization or protein–protein interactions. Actinomycetes are present in the soil, air and water, and their life cycle is strongly determined by environmental conditions. The complexity of variable environments urges Actinomycetes to respond quickly to external stimuli. In recent years, advances in identification and quantification of PTMs have led researchers to deepen their understanding of the functions of PTMs in physiology and metabolism, including vegetative growth, sporulation, metabolite synthesis and infectivity. On the other hand, most donor groups for PTMs come from various metabolites, suggesting a complex association network between metabolic states, PTMs and signaling pathways. Here, we review the mechanisms and functions of PTMs identified in Actinomycetes, focusing on phosphorylation, acylation and protein degradation in an attempt to summarize the recent progress of research on PTMs and their important role in bacterial cellular processes.

scholarly journals Machine learning empowers phosphoproteome prediction in cancers

2019 ◽  
Vol 36 (3) ◽  
pp. 859-864 ◽  
Author(s):  
Hongyang Li ◽  
Yuanfang Guan
Keyword(s):  
Signaling Pathways ◽  
Cancer Patients ◽  
Protein Interactions ◽  
Supplementary Information ◽  
Protein Protein Interactions ◽  
Post Translational Modification ◽  
Cellular Processes ◽  
Testing Dataset ◽  
Protein Functions ◽  
Cancer Tissues

Abstract Motivation Reversible protein phosphorylation is an essential post-translational modification regulating protein functions and signaling pathways in many cellular processes. Aberrant activation of signaling pathways often contributes to cancer development and progression. The mass spectrometry-based phosphoproteomics technique is a powerful tool to investigate the site-level phosphorylation of the proteome in a global fashion, paving the way for understanding the regulatory mechanisms underlying cancers. However, this approach is time-consuming and requires expensive instruments, specialized expertise and a large amount of starting material. An alternative in silico approach is predicting the phosphoproteomic profiles of cancer patients from the available proteomic, transcriptomic and genomic data. Results Here, we present a winning algorithm in the 2017 NCI-CPTAC DREAM Proteogenomics Challenge for predicting phosphorylation levels of the proteome across cancer patients. We integrate four components into our algorithm, including (i) baseline correlations between protein and phosphoprotein abundances, (ii) universal protein–protein interactions, (iii) shareable regulatory information across cancer tissues and (iv) associations among multi-phosphorylation sites of the same protein. When tested on a large held-out testing dataset of 108 breast and 62 ovarian cancer samples, our method ranked first in both cancer tissues, demonstrating its robustness and generalization ability. Availability and implementation Our code and reproducible results are freely available on GitHub: https://github.com/GuanLab/phosphoproteome_prediction. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Poly(ADP-ribosyl)ation reactions in the regulation of nuclear functions

1999 ◽  
Vol 342 (2) ◽  
pp. 249-268 ◽  
Author(s):  
Damien d'AMOURS ◽  
Serge DESNOYERS ◽  
Icy d'SILVA ◽  
Guy G. POIRIER
Keyword(s):  
Dna Repair ◽  
Protein Interactions ◽  
Physiological Role ◽  
Polymer Chains ◽  
Protein Protein Interactions ◽  
Post Translational Modification ◽  
Strand Breaks ◽  
Cellular Processes ◽  
Dna Strand

Poly(ADP-ribosyl)ation is a post-translational modification of proteins. During this process, molecules of ADP-ribose are added successively on to acceptor proteins to form branched polymers. This modification is transient but very extensive in vivo, as polymer chains can reach more than 200 units on protein acceptors. The existence of the poly(ADP-ribose) polymer was first reported nearly 40 years ago. Since then, the importance of poly(ADP-ribose) synthesis has been established in many cellular processes. However, a clear and unified picture of the physiological role of poly(ADP-ribosyl)ation still remains to be established. The total dependence of poly(ADP-ribose) synthesis on DNA strand breaks strongly suggests that this post-translational modification is involved in the metabolism of nucleic acids. This view is also supported by the identification of direct protein-protein interactions involving poly(ADP-ribose) polymerase (113 kDa PARP), an enzyme catalysing the formation of poly(ADP-ribose), and key effectors of DNA repair, replication and transcription reactions. The presence of PARP in these multiprotein complexes, in addition to the actual poly(ADP-ribosyl)ation of some components of these complexes, clearly supports an important role for poly(ADP-ribosyl)ation reactions in DNA transactions. Accordingly, inhibition of poly(ADP-ribose) synthesis by any of several approaches and the analysis of PARP-deficient cells has revealed that the absence of poly(ADP-ribosyl)ation strongly affects DNA metabolism, most notably DNA repair. The recent identification of new poly(ADP-ribosyl)ating enzymes with distinct (non-standard) structures in eukaryotes and archaea has revealed a novel level of complexity in the regulation of poly(ADP-ribose) metabolism.

scholarly journals Androgen signaling uses a writer and a reader of ADP-ribosylation to regulate protein complex assembly

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chun-Song Yang ◽  
Kasey Jividen ◽  
Teddy Kamata ◽  
Natalia Dworak ◽  
Luke Oostdyk ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Interactions ◽  
Prostate Cancer Cells ◽  
Protein Protein Interactions ◽  
Post Translational Modification ◽  
Complex Assembly ◽  
Adp Ribosylation ◽  
Signaling Axis ◽  
Regulate Protein ◽  
Protein Complex Assembly

AbstractAndrogen signaling through the androgen receptor (AR) directs gene expression in both normal and prostate cancer cells. Androgen regulates multiple aspects of the AR life cycle, including its localization and post-translational modification, but understanding how modifications are read and integrated with AR activity has been difficult. Here, we show that ADP-ribosylation regulates AR through a nuclear pathway mediated by Parp7. We show that Parp7 mono-ADP-ribosylates agonist-bound AR, and that ADP-ribosyl-cysteines within the N-terminal domain mediate recruitment of the E3 ligase Dtx3L/Parp9. Molecular recognition of ADP-ribosyl-cysteine is provided by tandem macrodomains in Parp9, and Dtx3L/Parp9 modulates expression of a subset of AR-regulated genes. Parp7, ADP-ribosylation of AR, and AR-Dtx3L/Parp9 complex assembly are inhibited by Olaparib, a compound used clinically to inhibit poly-ADP-ribosyltransferases Parp1/2. Our study reveals the components of an androgen signaling axis that uses a writer and reader of ADP-ribosylation to regulate protein-protein interactions and AR activity.

Sign in / Sign up

Export Citation Format

Share Document