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Biomolecules
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Exploring the Dynamics of Protein Lysine Methylation and Its Implication...
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Exploring the Dynamics of Protein Lysine Methylation and Its Implication in Disease

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Biomacromolecules: Proteins".

Deadline for manuscript submissions: closed (1 August 2024) | Viewed by 5086

Special Issue Editor

Dr. Kyle K. Biggar

E-Mail Website
Guest Editor
Institute of Biochemistry, Carleton University, Ottawa, ON, Canada
Interests: the discovery and characterization of how proteins coordinate and work; functional proteomics; how proteins dynamically interact with each other; how PTM-modifying enzymes select substrates; changes in protein signaling or regulatory networks that accompany disease progression or resistance to treatment

Special Issue Information

Dear Colleagues,

This Special Issue delves into the dynamic world of protein lysine methylation within the realm of functional proteomics, aiming to illuminate its crucial roles in both normal biology and disease progression. Lysine methylation, a pivotal post-translational modification, orchestrates a multitude of cellular functions by regulating protein–protein interactions, enzymatic activities, and signaling pathways. This compilation of articles endeavors to unravel the complexities of lysine methylation, exploring its impact on protein dynamics, enzymatic substrate selection, and alterations in regulatory networks associated with various diseases.

From the nuanced understanding of lysine methylation's role in protein coordination to its implications in disease pathogenesis and therapy resistance, this issue showcases cutting-edge research from international researchers. The insights gained from these studies promise to advance our understanding of basic biology regulated by protein lysine methylation and its impact on disease mechanisms, paving the way for innovative interventions targeting protein lysine methylation in diverse pathological conditions.

Dr. Kyle K. Biggar
Guest Editor

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. Biomolecules is an international peer-reviewed open access monthly 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 2700 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

  • protein regulation
  • disease mechanisms
  • biomarkers and therapeutic targets
  • cellular signaling
  • mass spectrometry

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Published Papers (4 papers)

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Research

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13 pages, 1739 KiB  
Article
Reversible Histone Modifications Contribute to the Frozen and Thawed Recovery States of Wood Frog Brains
by Tighe Bloskie, Olawale O. Taiwo and Kenneth B. Storey
Biomolecules 2024, 14(7), 839; https://doi.org/10.3390/biom14070839 - 12 Jul 2024
Viewed by 1151
Abstract
Epigenetic regulation, notably histone post-translational modification (PTM), has emerged as a major transcriptional control of gene expression during cellular stress adaptation. In the present study, we use an acid extraction method to isolate total histone protein and investigate dynamic changes in 23 well-characterized [...] Read more.
Epigenetic regulation, notably histone post-translational modification (PTM), has emerged as a major transcriptional control of gene expression during cellular stress adaptation. In the present study, we use an acid extraction method to isolate total histone protein and investigate dynamic changes in 23 well-characterized histone methylations/acetylations in the brains of wood frogs subject to 24-h freezing and subsequent 8-h thawed recovery conditions. Our results identify four histone PTMs (H2BK5ac, H3K14ac, H3K4me3, H3K9me2) and three histone proteins (H1.0, H2B, H4) that were significantly (p < 0.05) responsive to freeze-thaw in freeze-tolerant R. sylvatica brains. Two other permissive modifications (H3R8me2a, H3K9ac) also trended downwards following freezing stress. Together, these data are strongly supportive of the proposed global transcriptional states of hypometabolic freeze tolerance and rebounded thawed recovery. Our findings shed light on the intricate interplay between epigenetic regulation, gene transcription and energy metabolism in wood frogs’ adaptive response to freezing stress. Full article
(This article belongs to the Special Issue Exploring the Dynamics of Protein Lysine Methylation and Its Implication in Disease)
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15 pages, 2301 KiB  
Article
Protein Thermal Stability Changes Induced by the Global Methylation Inhibitor 3-Deazaneplanocin A (DZNep)
by Christine A. Berryhill, Emma H. Doud, Jocelyne N. Hanquier, Whitney R. Smith-Kinnaman, Devon L. McCourry, Amber L. Mosley and Evan M. Cornett
Biomolecules 2024, 14(7), 817; https://doi.org/10.3390/biom14070817 - 9 Jul 2024
Viewed by 929
Abstract
DZNep (3-deazaneplanocin A) is commonly used to reduce lysine methylation. DZNep inhibits S-adenosyl-l-homocysteine hydrolase (AHCY), preventing the conversion of S-adenosyl-l-homocysteine (SAH) into L-homocysteine. As a result, the SAM-to-SAH ratio decreases, an indicator of the methylation potential within a cell. [...] Read more.
DZNep (3-deazaneplanocin A) is commonly used to reduce lysine methylation. DZNep inhibits S-adenosyl-l-homocysteine hydrolase (AHCY), preventing the conversion of S-adenosyl-l-homocysteine (SAH) into L-homocysteine. As a result, the SAM-to-SAH ratio decreases, an indicator of the methylation potential within a cell. Many studies have characterized the impact of DZNep on histone lysine methylation or in specific cell or disease contexts, but there has yet to be a study looking at the potential downstream impact of DZNep treatment on proteins other than histones. Recently, protein thermal stability has provided a new dimension for studying the mechanism of action of small-molecule inhibitors. In addition to ligand binding, post-translational modifications and protein–protein interactions impact thermal stability. Here, we sought to characterize the protein thermal stability changes induced by DZNep treatment in HEK293T cells using the Protein Integral Solubility Alteration (PISA) assay. DZNep treatment altered the thermal stability of 135 proteins, with over half previously reported to be methylated at lysine residues. In addition to thermal stability, we identify changes in transcript and protein abundance after DZNep treatment to distinguish between direct and indirect impacts on thermal stability. Nearly one-third of the proteins with altered thermal stability had no changes at the transcript or protein level. Of these thermally altered proteins, CDK6 had a stabilized methylated peptide, while its unmethylated counterpart was unaltered. Multiple methyltransferases were among the proteins with thermal stability alteration, including DNMT1, potentially due to changes in the SAM/SAH levels. This study systematically evaluates DZNep’s impact on the transcriptome, the proteome, and the thermal stability of proteins. Full article
(This article belongs to the Special Issue Exploring the Dynamics of Protein Lysine Methylation and Its Implication in Disease)
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Review

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13 pages, 903 KiB  
Review
Biological Relevance of Dual Lysine and N-Terminal Methyltransferase METTL13
by Mullen Boulter and Kyle K. Biggar
Biomolecules 2024, 14(9), 1112; https://doi.org/10.3390/biom14091112 - 3 Sep 2024
Viewed by 836
Abstract
The dual methyltransferase methyltransferase-like protein 13, also referred to as METTL13, or formerly known as FEAT (faintly expressed in healthy tissues, aberrantly overexpressed in tumors), has garnered attention as a significant enzyme in various cancer types, as evidenced by prior literature reviews. Recent [...] Read more.
The dual methyltransferase methyltransferase-like protein 13, also referred to as METTL13, or formerly known as FEAT (faintly expressed in healthy tissues, aberrantly overexpressed in tumors), has garnered attention as a significant enzyme in various cancer types, as evidenced by prior literature reviews. Recent studies have shed light on new potential roles for METTL13, hinting at its promise as a therapeutic target. This review aims to delve into the multifaceted biology of METTL13, elucidating its proposed mechanisms of action, regulatory pathways, and its implications in disease states, as supported by the current body of literature. Furthermore, the review will highlight emerging trends and gaps in our understanding of METTL13, paving the way for future research efforts. By contextualizing METTL13 within the broader landscape of cancer biology and therapeutics, this study serves as an introductory guide to METTL13, aiming to provide readers with a thorough understanding of its role in disease phenotypes. Full article
(This article belongs to the Special Issue Exploring the Dynamics of Protein Lysine Methylation and Its Implication in Disease)
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21 pages, 2364 KiB  
Review
Roles of Lysine Methylation in Glucose and Lipid Metabolism: Functions, Regulatory Mechanisms, and Therapeutic Implications
by Zhen Wang and Huadong Liu
Biomolecules 2024, 14(7), 862; https://doi.org/10.3390/biom14070862 - 19 Jul 2024
Cited by 1 | Viewed by 1793
Abstract
Glucose and lipid metabolism are essential energy sources for the body. Dysregulation in these metabolic pathways is a significant risk factor for numerous acute and chronic diseases, including type 2 diabetes (T2DM), Alzheimer’s disease (AD), obesity, and cancer. Post-translational modifications (PTMs), which regulate [...] Read more.
Glucose and lipid metabolism are essential energy sources for the body. Dysregulation in these metabolic pathways is a significant risk factor for numerous acute and chronic diseases, including type 2 diabetes (T2DM), Alzheimer’s disease (AD), obesity, and cancer. Post-translational modifications (PTMs), which regulate protein structure, localization, function, and activity, play a crucial role in managing cellular glucose and lipid metabolism. Among these PTMs, lysine methylation stands out as a key dynamic modification vital for the epigenetic regulation of gene transcription. Emerging evidence indicates that lysine methylation significantly impacts glucose and lipid metabolism by modifying key enzymes and proteins. This review summarizes the current understanding of lysine methylation’s role and regulatory mechanisms in glucose and lipid metabolism. We highlight the involvement of methyltransferases (KMTs) and demethylases (KDMs) in generating abnormal methylation signals affecting these metabolic pathways. Additionally, we discuss the chemical biology and pharmacology of KMT and KDM inhibitors and targeted protein degraders, emphasizing their clinical implications for diseases such as diabetes, obesity, neurodegenerative disorders, and cancers. This review suggests that targeting lysine methylation in glucose and lipid metabolism could be an ideal therapeutic strategy for treating these diseases. Full article
(This article belongs to the Special Issue Exploring the Dynamics of Protein Lysine Methylation and Its Implication in Disease)
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