Dicarbonyl derived post-translational modifications: chemistry bridging biology and aging-related disease

2020 ◽  
Vol 64 (1) ◽  
pp. 97-110
Author(s):  
Christian Sibbersen ◽  
Mogens Johannsen
Keyword(s):  
Mass Spectrometry ◽  
Future Research ◽  
Amino Acid Residues ◽  
Post Translational Modification ◽  
Dicarbonyl Compounds ◽  
Protein Targets ◽  
Post Translational Modifications ◽  
Reactive Protein ◽  
Glycation End Products ◽  
Direct Mass Spectrometry

Abstract In living systems, nucleophilic amino acid residues are prone to non-enzymatic post-translational modification by electrophiles. α-Dicarbonyl compounds are a special type of electrophiles that can react irreversibly with lysine, arginine, and cysteine residues via complex mechanisms to form post-translational modifications known as advanced glycation end-products (AGEs). Glyoxal, methylglyoxal, and 3-deoxyglucosone are the major endogenous dicarbonyls, with methylglyoxal being the most well-studied. There are several routes that lead to the formation of dicarbonyl compounds, most originating from glucose and glucose metabolism, such as the non-enzymatic decomposition of glycolytic intermediates and fructosyl amines. Although dicarbonyls are removed continuously mainly via the glyoxalase system, several conditions lead to an increase in dicarbonyl concentration and thereby AGE formation. AGEs have been implicated in diabetes and aging-related diseases, and for this reason the elucidation of their structure as well as protein targets is of great interest. Though the dicarbonyls and reactive protein side chains are of relatively simple nature, the structures of the adducts as well as their mechanism of formation are not that trivial. Furthermore, detection of sites of modification can be demanding and current best practices rely on either direct mass spectrometry or various methods of enrichment based on antibodies or click chemistry followed by mass spectrometry. Future research into the structure of these adducts and protein targets of dicarbonyl compounds may improve the understanding of how the mechanisms of diabetes and aging-related physiological damage occur.

SUMO: getting it on

2007 ◽  
Vol 35 (6) ◽  
pp. 1409-1413 ◽  
Author(s):  
J. Anckar ◽  
L. Sistonen
Keyword(s):  
Biological Processes ◽  
Amino Acid Residues ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
Sumo Conjugation ◽  
Lysine Residues ◽  
Ubiquitin Conjugating Enzyme ◽  
Specificity Determinants ◽  
Conjugating Enzyme

Post-translational modification of cellular proteins by the SUMO (small ubiquitin-related modifier) is involved in numerous modes of regulation in widely different biological processes. In contrast with ubiquitination, SUMO conjugation is highly specific in terms of target lysine residues, but many aspects of substrate and lysine selection by the SUMO conjugating machinery are still poorly understood. SUMOylation events usually occur on the ΨKXE SUMO consensus motifs, which mediate binding to Ubc9 (ubiquitin-conjugating enzyme 9), the SUMO E2 conjugating enzyme. Although most, if not all, SUMO conjugations are catalysed by Ubc9, far from all ΨKXE tetrapeptides are modified, demonstrating a need for additional specificity determinants in SUMOylation. Recent results intimately link regulation of SUMOylation to other post-translational modifications, including phosphorylation and acetylation and reveal that certain lysine residues are marked for SUMOylation by negatively charged amino acid residues or phosphorylation events immediately downstream of the consensus site. In the present review, we explore the intriguing role of extended motifs in the regulation of SUMO conjugation.

scholarly journals Identification of novel protein lysine acetyltransferases inEscherichia coli

2018 ◽  
Author(s):  
David G. Christensen ◽  
Jesse G. Meyer ◽  
Jackson T. Baumgartner ◽  
Alexandria K. D’Souza ◽  
William C. Nelson ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Substrate Specificity ◽  
Lysine Acetylation ◽  
Acetyl Phosphate ◽  
Protein Acetylation ◽  
Active Site Residues ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
E Coli ◽  
Enzymatic Mechanism

AbstractPost-translational modifications, such as Nε-lysine acetylation, regulate protein function. Nε-lysine acetylation can occur either non-enzymatically or enzymatically. The non-enzymatic mechanism uses acetyl phosphate (AcP) or acetyl coenzyme A (AcCoA) as acetyl donors to modify an Nε-lysine residue of a protein. The enzymatic mechanism uses Nε-lysine acetyltransferases (KATs) to specifically transfer an acetyl group from AcCoA to Nε-lysine residues on proteins. To date, only one KAT (YfiQ, also known as Pka and PatZ) has been identified inE. coli. Here, we demonstrate the existence of 4 additionalE. coliKATs: RimI, YiaC, YjaB, and PhnO. In a genetic background devoid of all known acetylation mechanisms (most notably AcP and YfiQ) and one deacetylase (CobB), overexpression of these putative KATs elicited unique patterns of protein acetylation. We mutated key active site residues and found that most of them eliminated enzymatic acetylation activity. We used mass spectrometry to identify and quantify the specificity of YfiQ and the four novel KATs. Surprisingly, our analysis revealed a high degree of substrate specificity. The overlap between KAT-dependent and AcP-dependent acetylation was extremely limited, supporting the hypothesis that these two acetylation mechanisms play distinct roles in the post-translational modification of bacterial proteins. We further showed that these novel KATs are conserved across broad swaths of bacterial phylogeny. Finally, we determined that one of the novel KATs (YiaC) and the known KAT (YfiQ) can negatively regulate bacterial migration. Together, these results emphasize distinct and specific non-enzymatic and enzymatic protein acetylation mechanisms present in bacteria.ImportanceNε-lysine acetylation is one of the most abundant and important post-translational modifications across all domains of life. One of the best-studied effects of acetylation occurs in eukaryotes, where acetylation of histone tails activates gene transcription. Although bacteria do not have true histones, Nε-lysine acetylation is prevalent; however, the role of these modifications is mostly unknown. We constructed anE. colistrain that lacked both known acetylation mechanisms to identify four new Nε-lysine acetyltransferases (RimI, YiaC, YjaB, and PhnO). We used mass spectrometry to determine the substrate specificity of these acetyltransferases. Structural analysis of selected substrate proteins revealed site-specific preferences for enzymatic acetylation that had little overlap with the preferences of the previously reported acetyl-phosphate non-enzymatic acetylation mechanism. Finally, YiaC and YfiQ appear to regulate flagellar-based motility, a phenotype critical for pathogenesis of many organisms. These acetyltransferases are highly conserved and reveal deeper and more complex roles for bacterial post-translational modification.

scholarly journals Breaking the Histone Code with Two-Dimensional Partial Covariance Mass Spectrometry

2020 ◽  
Author(s):  
Taran Driver ◽  
Ruediger Pipkorn ◽  
Vitali Averbukh ◽  
Leszek Frasinski ◽  
Jon P. Marangos ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Large Body ◽  
Active Role ◽  
Repeated Measurements ◽  
Charge Ratio ◽  
Two Dimensional ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
Single Fragment ◽  
The Individual

<div> <p>A large body of research points to the biological importance of combinatorial post-translational modifications in proteins, such as the active role played by histone modification patterns in the development of cancers, neurodevelopmental disorders, neurodegenerative and other diseases. Nonetheless, our understanding of the precise biological function of different modification patterns is limited by the difficulty of identifying and quantifying different combinatorial isomers in their mixtures as they naturally occur. Tandem mass spectrometry, which infers primary structure from the mass-to-charge ratios of biomolecular fragments, is the preferred method of analysis for proteins and their post-translational modifications. However, the information contained in the mass-to-charge ratios of the individual fragments is frequently insufficient to identify the correct set of modification patterns present in a mixture of combinatorial isomers. This is because no possible single fragment of a combinatorially modified sequence is unique to that sequence in its mass-to-charge ratio. Here we show that the combinatorial post-translational modification problem can be solved by the recently introduced technique of two-dimensional partial covariance mass spectrometry, which provides information about fragment connectivity in a biomolecule by quantifying correlations between the random intensity fluctuations of its fragments, across repeated measurements. Unique fragment-fragment correlations provide the missing link between the non-unique individual fragments to produce unambiguous fingerprints of co-occurring combinatorial isomers, enabling the discovery of biomolecular combinatorial modification patterns by mass spectrometry.</p> </div>

Post-translational modification-derived products are associated with frailty status in elderly subjects

2019 ◽  
Vol 57 (8) ◽  
pp. 1153-1161
Author(s):  
Rachid Mahmoudi ◽  
Stéphane Jaisson ◽  
Sarah Badr ◽  
Yacine Jaidi ◽  
Laurie-Anne Bertholon ◽  
...  
Keyword(s):  
Elderly Subjects ◽  
Post Translational Modification ◽  
Term Care ◽  
Logistic Regression Models ◽  
Frailty Status ◽  
Reactive Protein ◽  
Frail Patients ◽  
Glycation End Products ◽  
Protein Aging

Abstract Background Identifying frail elderly subjects is of paramount importance in order to conduct a tailored care. The characterization of frailty status is currently based on the collection of clinical data and on the use of various tools such as Fried’s criteria, which constitutes a difficult and time-consuming process. Up to now, no biological markers have been described as reliable tools for frailty characterization. We tested the hypothesis that a link between frailty and protein molecular aging existed. This study aimed therefore at determining whether post-translational modification derived products (PTMDPs), recognized as biomarkers of protein aging, were associated with frailty status in elderly subjects. Methods Frailty status was determined according to Fried’s criteria in 250 elderly patients (>65 years old) hospitalized in a short-term care unit. Serum concentrations of protein-bound PTMDPs, including carboxymethyllysine (CML), pentosidine, methylglyoxal-hydroimidazolone-1 and homocitrulline (HCit), were determined by liquid chromatography coupled with tandem mass spectrometry, and tissue content of advanced glycation end-products was assessed by skin autofluorescence (SAF) measurement. Associations between PTMDPs and frailty status were analyzed using logistic regression models. Results Frail patients had significantly (p<0.01) higher CML, HCit, and SAF values compared to non-frail and pre-frail subjects. By multivariate analysis, only HCit concentrations and SAF values remained associated with frailty status (p=0.016 and p=0.002, respectively), independently of age, comorbidities, renal function, C-reactive protein and albumin concentrations. Conclusions HCit and SAF are significantly associated with frailty status in elderly subjects. This study suggests that PTMDPs constitute promising biomarkers for identifying frail patients and guiding personalized patient care.

scholarly journals Molecular Characterization of Collagen Hydroxylysine O-Glycosylation by Mass Spectrometry: Current Status

2013 ◽  
Vol 66 (7) ◽  
pp. 760 ◽  
Author(s):  
Irina Perdivara ◽  
Mitsuo Yamauchi ◽  
Kenneth B. Tomer
Keyword(s):  
Mass Spectrometry ◽  
Type I Collagen ◽  
Molecular Mapping ◽  
Biological Significance ◽  
The Body ◽  
Current Status ◽  
Future Research ◽  
Type I ◽  
Post Translational Modifications

The most abundant proteins in vertebrates – the collagen family proteins – play structural and biological roles in the body. The predominant member, type I collagen, provides tissues and organs with structure and connectivity. This protein has several unique post-translational modifications that take place intra- and extra-cellularly. With growing evidence of the relevance of such post-translational modifications in health and disease, the biological significance of O-linked collagen glycosylation has recently drawn increased attention. However, several aspects of this unique modification – the requirement for prior lysyl hydroxylation as a substrate, involvement of at least two distinct glycosyl transferases, its involvement in intermolecular crosslinking – have made its molecular mapping and quantitative characterization challenging. Such characterization is obviously crucial for understanding its biological significance. Recent progress in mass spectrometry has provided an unprecedented opportunity for this type of analysis. This review summarizes recent advances in the area of O-glycosylation of fibrillar collagens and their characterization using state-of-the-art liquid chromatography–mass spectrometry-based methodologies, and perspectives on future research. The analytical characterization of collagen crosslinking and advanced glycation end-products are not addressed here.

scholarly journals Protein Lipoxidation: Basic Concepts and Emerging Roles

Antioxidants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 295
Author(s):  
Álvaro Viedma-Poyatos ◽  
Patricia González-Jiménez ◽  
Ophélie Langlois ◽  
Idoia Company-Marín ◽  
Corinne M. Spickett ◽  
...  
Keyword(s):  
Cell Signalling ◽  
Stress Protein ◽  
Cytoskeletal Proteins ◽  
Detailed Knowledge ◽  
Post Translational Modification ◽  
Complex Interplay ◽  
Protein Targets ◽  
Post Translational Modifications ◽  
Lipid Species ◽  
Functionally Diverse

Protein lipoxidation is a non-enzymatic post-translational modification that consists of the covalent addition of reactive lipid species to proteins. This occurs under basal conditions but increases in situations associated with oxidative stress. Protein targets for lipoxidation include metabolic and signalling enzymes, cytoskeletal proteins, and transcription factors, among others. There is strong evidence for the involvement of protein lipoxidation in disease, including atherosclerosis, neurodegeneration, and cancer. Nevertheless, the involvement of lipoxidation in cellular regulatory mechanisms is less understood. Here we review basic aspects of protein lipoxidation and discuss several features that could support its role in cell signalling, including its selectivity, reversibility, and possibilities for regulation at the levels of the generation and/or detoxification of reactive lipids. Moreover, given the great structural variety of electrophilic lipid species, protein lipoxidation can contribute to the generation of multiple structurally and functionally diverse protein species. Finally, the nature of the lipoxidised proteins and residues provides a frameshift for a complex interplay with other post-translational modifications, including redox and redox-regulated modifications, such as oxidative modifications and phosphorylation, thus strengthening the importance of detailed knowledge of this process.

scholarly journals Breaking the Histone Code with Two-Dimensional Partial Covariance Mass Spectrometry

2020 ◽  
Author(s):  
Taran Driver ◽  
Vitali Averbukh ◽  
Leszek Frasinski ◽  
Jon P. Marangos ◽  
Marina Edelson-Averbukh
Keyword(s):  
Mass Spectrometry ◽  
Large Body ◽  
Active Role ◽  
Repeated Measurements ◽  
Charge Ratio ◽  
Two Dimensional ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
Single Fragment ◽  
The Individual

<div> <p>A large body of research points to the biological importance of combinatorial post-translational modifications in proteins, such as the active role played by histone modification patterns in the development of cancers, neurodevelopmental disorders, neurodegenerative and other diseases. Nonetheless, our understanding of the precise biological function of different modification patterns is limited by the difficulty of identifying and quantifying different combinatorial isomers in their mixtures as they naturally occur. Tandem mass spectrometry, which infers primary structure from the mass-to-charge ratios of biomolecular fragments, is the preferred method of analysis for proteins and their post-translational modifications. However, the information contained in the mass-to-charge ratios of the individual fragments is frequently insufficient to identify the correct set of modification patterns present in a mixture of combinatorial isomers. This is because no possible single fragment of a combinatorially modified sequence is unique to that sequence in its mass-to-charge ratio. Here we show that the combinatorial post-translational modification problem can be solved by the recently introduced technique of two-dimensional partial covariance mass spectrometry, which provides information about fragment connectivity in a biomolecule by quantifying correlations between the random intensity fluctuations of its fragments, across repeated measurements. Unique fragment-fragment correlations provide the missing link between the non-unique individual fragments to produce unambiguous fingerprints of co-occurring combinatorial isomers, enabling the discovery of biomolecular combinatorial modification patterns by mass spectrometry.</p> </div>

scholarly journals Comparison of Predicted Amino Acid Sequences of Allatotropin/Allatostatin Receptors from Solitary to Eusocial Bee Species (Hymenoptera, Apoidea)

2019 ◽  
Vol 63 (2) ◽  
pp. 267-279
Author(s):  
Huipeng Yang ◽  
Jie Wu
Keyword(s):  
Amino Acid ◽  
Juvenile Hormone ◽  
Amino Acid Sequences ◽  
Amino Acid Residues ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
Specific Amino Acid ◽  
Hormone Synthesis ◽  
Evolution Of Eusociality ◽  
Coupling Characteristics

AbstractAn increasingly amount of evidence supports that the evolution of eusociality is accompanies by shifts in ancient molecular and physiological pathways. The juvenile hormone, one of the most important hormones in the post-embryonic development of insects, attracts the most attention in the context of social organization. Allatoregulatory neuropeptides (Allatotropin, Allatostatin-A and Allatostatin-C) are known to regulate juvenile hormone synthesis and release in insects. In order to clarify the transitions of juvenile hormone synthesis involved in eusocial evolution, the substitutions of amino acid residues and the complexity of post-translational modifications in allatoregulatory neuropeptide receptors were characterized. Both allatotropin and allatostatin receptors are identified in all examined bee species regardless if they are solitary or eusocial. Although the amino acid sequences are highly conserved, phylogenetic results are consistent with the eusocial status. The abundance of predicted post-translational modifications correlates with social complexity except for that in allatostatin-C receptors. Even though the consequences of these specific amino acid substitutions and various post-translational modification complexity have not been studied, they likely contribute to the localizing, binding and coupling characteristics of the receptor groups.

scholarly journals Clinically Relevant Post-Translational Modification Analyses—Maturing Workflows and Bioinformatics Tools

2018 ◽  
Vol 20 (1) ◽  
pp. 16 ◽  
Author(s):  
Dana Pascovici ◽  
Jemma X. Wu ◽  
Matthew J. McKay ◽  
Chitra Joseph ◽  
Zainab Noor ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Data Interpretation ◽  
Label Free ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
Data Independent Acquisition ◽  
Bioinformatics Tools ◽  
Functional Understanding ◽  
Health And Disease ◽  
Regulate Protein

Post-translational modifications (PTMs) can occur soon after translation or at any stage in the lifecycle of a given protein, and they may help regulate protein folding, stability, cellular localisation, activity, or the interactions proteins have with other proteins or biomolecular species. PTMs are crucial to our functional understanding of biology, and new quantitative mass spectrometry (MS) and bioinformatics workflows are maturing both in labelled multiplexed and label-free techniques, offering increasing coverage and new opportunities to study human health and disease. Techniques such as Data Independent Acquisition (DIA) are emerging as promising approaches due to their re-mining capability. Many bioinformatics tools have been developed to support the analysis of PTMs by mass spectrometry, from prediction and identifying PTM site assignment, open searches enabling better mining of unassigned mass spectra—many of which likely harbour PTMs—through to understanding PTM associations and interactions. The remaining challenge lies in extracting functional information from clinically relevant PTM studies. This review focuses on canvassing the options and progress of PTM analysis for large quantitative studies, from choosing the platform, through to data analysis, with an emphasis on clinically relevant samples such as plasma and other body fluids, and well-established tools and options for data interpretation.

scholarly journals MoMo: Discovery of post-translational modification motifs

2017 ◽  
Author(s):  
Alice Cheng ◽  
Charles E. Grant ◽  
Timothy L. Bailey ◽  
William Stafford Noble
Keyword(s):  
Mass Spectrometry ◽  
Source Code ◽  
Software Tool ◽  
Mass Spectrometry Data ◽  
Supplementary Information ◽  
Biological Functions ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
Sequence Patterns ◽  
Supplementary Material

AbstractMotivationPost-translational modifications (PTMs) of proteins are associated with many significant biological functions and can be identified in high throughput using tandem mass spectrometry. Many PTMs are associated with short sequence patterns called “motifs” that help localize the modifying enzyme. Accordingly, many algorithms have been designed to identify these motifs from mass spectrometry data.ResultsMoMo is a software tool for identifying motifs among sets of PTMs. The program re-implements two previously described algorithms, Motif-X and MoDL, packaging them in a web-accessible user interface. In addition to reading sequence files in FASTA format, MoMo is capable of directly parsing output files produced by commonly used mass spectrometry search engines. The resulting motifs are presented to the user in an HTML summary with motif logos and linked text files in MEME motif format.AvailabilitySource code and web server available at http://[email protected] and [email protected] informationSupplementary figures are available at Bioinformatics online.

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