Article
Biochemistry & Molecular Biology
Jose-Luis Garcia-Gimenez, Concepcion Garces, Carlos Roma-Mateo, Federico Pallardo
Summary: Epigenetic regulation of gene expression plays a crucial role in cellular response to environmental changes, but cellular imbalance can lead to pathological conditions. Oxidative stress and free radicals can influence histone modifications, affecting gene expression.
FREE RADICAL BIOLOGY AND MEDICINE
(2021)
Review
Cell Biology
Faith M. Joseph, Nicolas L. Young
Summary: Post-translational modifications (PTMs) of histones play a key role in DNA-based processes and contribute to cell differentiation and gene function by adding an extra layer of regulation. Variations in histone sequences within each family of histones expand the chromatin repertoire and provide further mechanisms for regulation and signaling. However, much remains unknown about variant-specific PTMs and their role in regulating chromatin due to limited technologies and appropriate reagents.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Sarah R. Rommelfanger, Mowei Zhou, Henna Shaghasi, Shin-Cheng Tzeng, Bradley S. Evans, Ljiljana Pasa-Toli, James G. Umen, James J. Pesavento
Summary: An updated analysis of linker and core histone proteins in the green microalga Chlamydomonas reinhardtii was conducted using top-down mass spectrometry, revealing 86 proteoforms. Variants with high levels of acetylation were identified among the canonical histones, emphasizing the presence of diverse protein forms in this organism.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Biochemical Research Methods
Elizabeth A. Mojica, Dietmar Kultz
Summary: This study developed a workflow for analyzing histone post-translational modifications (PTMs) in nonmodel organisms, and validated it in Mozambique tilapia. By using mass spectrometry methods, 214 biologically relevant histone PTMs were reliably quantified. The study found that 91.59% of histone PTMs were tissue-dependent. The developed workflow and tools are now publicly available for investigating the influence of environmental stress on histone PTMs in nonmodel organisms.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Jennifer S. Brodbelt
Summary: Post-translational modifications (PTMs) create diversity in proteins and affect their function and regulation. Mass spectrometry analysis allows identification and analysis of PTMs, providing a comprehensive catalog of protein forms. The top-down approach enables in-depth exploration of the impact of combinatorial PTMs on proteins.
CURRENT OPINION IN CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Kuo-Feng Hsu, Sarah E. Wilkins, Richard J. Hopkinson, Rok Sekirnik, Emily Flashman, Akane Kawamura, James S. O. McCullagh, Louise J. Walport, Christopher J. Schofield
Summary: Hypoxia affects histone modifications, but synthetic hypoxia mimetics may not accurately replicate these effects. Liquid chromatography-mass spectrometry is a simple and robust method for investigating potential drug effects on histone modifications. The findings suggest caution should be used in interpreting data from chemically-induced hypoxia.
Review
Biochemistry & Molecular Biology
Irene Messana, Barbara Manconi, Tiziana Cabras, Mozhgan Boroumand, Maria Teresa Sanna, Federica Iavarone, Alessandra Olianas, Claudia Desiderio, Diana Valeria Rossetti, Federica Vincenzoni, Cristina Contini, Giulia Guadalupi, Antonella Fiorita, Gavino Faa, Massimo Castagnola
Summary: In this review, the main post-translational modifications leading to multiple proteoforms in the human salivary proteome are extensively described, along with their potential role. The majority of the data reported in this review were obtained through over twenty-five years of research on human saliva, primarily using a top-down strategy. Various proteolytic cleavage products, salivary protein families, phospho-proteome, sulfo-proteomes, glycation, enzymatic glycosylation, citrullination, N- and C-terminal post-translational modifications, and miscellaneous other modifications are discussed in different sections of the manuscript. Furthermore, the impact and relevance of these findings in the development of new diagnostic biomarkers for clinical practice are emphasized.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Van-An Duong, Onyou Nam, EonSeon Jin, Jong-Moon Park, Hookeun Lee
Summary: Emiliania huxleyi, a cosmopolitan coccolithophore, was studied for the global discovery of post-translational modifications (PTMs) using a three-dimensional separation method combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Methylation was found to be the most frequent PTM, with lysine being the most frequently modified amino acid. The number of identified proteins increased by 22.5% after the PTM search, with some proteins showing a significant increase in intensity.
Article
Multidisciplinary Sciences
Nathalie Kyalu Ngoie Zola, Clemence Balty, Sebastien Pyr dit Ruys, Axelle A. T. Vanparys, Nicolas D. G. Huyghe, Gaetan Herinckx, Manuel Johanns, Emilien Boyer, Pascal Kienlen-Campard, Mark H. Rider, Didier Vertommen, Bernard J. Hanseeuw
Summary: Tau isoforms in insoluble aggregates differ between tauopathies, but not in soluble brain extracts. This study characterizes the post-translational modifications of aggregated and soluble tau protein in various tauopathies, revealing specific soluble signatures for each tauopathy.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Samuel S. Porter, Jennifer C. Liddle, Kristen Browne, Diana Pastrana, Benjamin A. Garcia, Christopher B. Buck, Matthew D. Weitzman, Alison A. McBride
Summary: Papillomaviruses package their genomes with host histones into virions, with specific histone modifications being acquired late in infection that benefit viral replication and gene expression. The viral minichromosome is enriched in posttranslational modifications associated with active chromatin, potentially aiding in evasion of detection and promoting early infection stages.
Review
Biochemistry & Molecular Biology
Gengjun Zhu, Lifang Jin, Wanchun Sun, Shuang Wang, Ning Liu
Summary: This review highlights the importance of post-translational modifications (PTMs) in colorectal cancer (CRC) and discusses their role in diagnosis, prognosis, and treatment. The review summarizes the proteomic profiling strategies for key PTMs and describes the methods used to delineate the global landscapes of each PTM. The review also discusses the current status of PTM research in CRC and provides future perspectives on the role of PTM regulation in translational medicine for CRC.
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER
(2022)
Review
Immunology
Hengwei Wu, He Huang, Yanmin Zhao
Summary: Cellular metabolism plays a crucial role in determining cell fate and function, and metabolic reprogramming has a complex impact on cellular activities. In quiescent T cells, oxidative phosphorylation (OXPHOS) is the primary survival pathway, but upon antigen activation, T cells undergo rapid metabolic reprogramming characterized by increased glycolysis and OXPHOS. This review focuses on the metabolic reprogramming of T cells, explores the interplay between lactate and the immune system, highlights the impact of lactylation on cellular function, and elucidates the intersection of metabolic reprogramming and epigenetics.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Bethany C. Taylor, Nicolas L. Young
Summary: Histone post-translational modifications (PTMs) play a crucial role in regulating the genome by storing and transmitting complex signals about the genome state. Different PTM sites on the same histone molecule or nucleosome work in concert, supported by 'readers' structures, to transduce signals in specific cellular contexts.
BIOCHEMICAL JOURNAL
(2021)
Review
Biochemistry & Molecular Biology
Juliane Hermann, Leon Schurgers, Vera Jankowski
Summary: Post-translational modifications play a key role in protein function and disease progression, but their reliable detection and quantification remain a challenge in clinical diagnosis. Mass spectrometry offers a solution, but its clinical translation still faces challenges.
MOLECULAR ASPECTS OF MEDICINE
(2022)
Article
Biotechnology & Applied Microbiology
Assaf Kacen, Aaron Javitt, Matthias P. Kramer, David Morgenstern, Tomer Tsaban, Merav D. Shmueli, Guo Ci Teo, Felipe da Veiga Leprevost, Eilon Barnea, Fengchao Yu, Arie Admon, Lea Eisenbach, Yardena Samuels, Ora Schueler-Furman, Yishai Levin, Alexey Nesvizhskii, Yifat Merbl
Summary: This study describes an antigen discovery pipeline that analyzes different post-translational modifications (PTMs) of antigens, expands the antigen landscape, and reveals disease-specific modified targets, which have important implications for T cell-mediated therapies in cancer and other fields.
NATURE BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Tatjana Petojevic, James J. Pesavento, Alessandro Costa, Jingdan Liang, Zhijun Wang, James M. Berger, Michael R. Botchan
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2015)
Article
Biochemistry & Molecular Biology
Ruedi Aebersold, Jeffrey N. Agar, I. Jonathan Amster, Mark S. Baker, Carolyn R. Bertozzi, Emily S. Boja, Catherine E. Costello, Benjamin F. Cravatt, Catherine Fenselau, Benjamin A. Garcia, Ying Ge, Jeremy Gunawardena, Ronald C. Hendrickson, Paul J. Hergenrother, Christian G. Huber, Alexander R. Ivanov, Ole N. Jensen, Michael C. Jewett, Neil L. Kelleher, Laura L. Kiessling, Nevan J. Krogan, Martin R. Larsen, Joseph A. Loo, Rachel R. Ogorzalek Loo, Emma Lundberg, Michael J. MacCoss, Parag Mallick, Vamsi K. Mootha, Milan Mrksich, Tom W. Muir, Steven M. Patrie, James J. Pesavento, Sharon J. Pitteri, Henry Rodriguez, Alan Saghatelian, Wendy Sandoval, Hartmut Schluter, Salvatore Sechi, Sarah A. Slavoff, Lloyd M. Smith, Michael P. Snyder, Paul M. Thomas, Mathias Uhlen, Jennifer E. Van Eyk, Marc Vidal, David R. Walt, Forest M. White, Evan R. Williams, Therese Wohlschlager, Vicki H. Wysocki, Nathan A. Yates, Nicolas L. Young, Bing Zhang
NATURE CHEMICAL BIOLOGY
(2018)
Article
Chemistry, Analytical
Ari M. Frank, James J. Pesavento, Craig A. Mizzen, Neil L. Kelleher, Pavel A. Pevzner
ANALYTICAL CHEMISTRY
(2008)
Article
Biochemistry & Molecular Biology
Hongbo Yang, James J. Pesavento, Taylor W. Starnes, Diane E. Cryderman, Lori L. Wallrath, Neil L. Kelleher, Craig A. Mizzen
JOURNAL OF BIOLOGICAL CHEMISTRY
(2008)
Article
Biochemistry & Molecular Biology
James J. Pesavento, Courtney R. Bullock, Richard D. LeDuc, Craig A. Mizzen, Neil L. Kelleher
JOURNAL OF BIOLOGICAL CHEMISTRY
(2008)
Article
Cell Biology
Yupeng Zheng, Sam John, James J. Pesavento, Jennifer R. Schultz-Norton, R. Louis Schiltz, Sonjoon Baek, Ann M. Nardulli, Gordon L. Hager, Neil L. Kelleher, Craig A. Mizzen
JOURNAL OF CELL BIOLOGY
(2010)
Article
Biochemistry & Molecular Biology
Ivar Ilves, Tatjana Petojevic, James J. Pesavento, Michael R. Botchan
Article
Biology
Alessandro Costa, Ludovic Renault, Paolo Swuec, Tatjana Petojevic, James J. Pesavento, Ivar Ilves, Kirsty MacLellan-Gibson, Roland A. Fleck, Michael R. Botchan, James M. Berger
Article
Biochemical Research Methods
Amanda L. Wong, Nicholas N. Totah, Anthony T. Iavarone, James J. Pesavento
Article
Biochemical Research Methods
Sarah R. Rommelfanger, Mowei Zhou, Henna Shaghasi, Shin-Cheng Tzeng, Bradley S. Evans, Ljiljana Pasa-Toli, James G. Umen, James J. Pesavento
Summary: An updated analysis of linker and core histone proteins in the green microalga Chlamydomonas reinhardtii was conducted using top-down mass spectrometry, revealing 86 proteoforms. Variants with high levels of acetylation were identified among the canonical histones, emphasizing the presence of diverse protein forms in this organism.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Biochemical Research Methods
James J. Pesavento, Benjamin A. Garcia, James A. Streeky, Neil L. Kelleher, Craig A. Mizzen
MOLECULAR & CELLULAR PROTEOMICS
(2007)
Article
Biochemical Research Methods
Benjamin A. Garcia, James J. Pesavento, Craig A. Mizzen, Neil L. Kelleher
Article
Chemistry, Analytical
James J. Pesavento, Craig A. Mizzen, Neil L. Kelleher
ANALYTICAL CHEMISTRY
(2006)
Article
Biochemistry & Molecular Biology
James J. Pesavento, Hongbo Yang, Neil L. Kelleher, Craig A. Mizzen
MOLECULAR AND CELLULAR BIOLOGY
(2008)