keyword
https://read.qxmd.com/read/37723562/analysis-of-a-macrophage-carbamylated-proteome-reveals-a-function-in-post-translational-modification-crosstalk
#1
JOURNAL ARTICLE
Youngki You, Chia-Feng Tsai, Rishi Patel, Soumyadeep Sarkar, Geremy Clair, Mowei Zhou, Tao Liu, Thomas O Metz, Chittaranjan Das, Ernesto S Nakayasu
BACKGROUND: Lysine carbamylation is a biomarker of rheumatoid arthritis and kidney diseases. However, its cellular function is understudied due to the lack of tools for systematic analysis of this post-translational modification (PTM). METHODS: We adapted a method to analyze carbamylated peptides by co-affinity purification with acetylated peptides based on the cross-reactivity of anti-acetyllysine antibodies. We also performed immobilized-metal affinity chromatography to enrich for phosphopeptides, which allowed us to obtain multi-PTM information from the same samples...
September 18, 2023: Cell Communication and Signaling: CCS
https://read.qxmd.com/read/37227083/lysine-trimethylation-in-planktonic-and-pellicle-modes-of-growth-in-acinetobacter-baumannii
#2
JOURNAL ARTICLE
Nicolas Nalpas, Takfarinas Kentache, Emmanuelle Dé, Julie Hardouin
Over the past 30 years, Acinetobacter baumannii has been described as an important nosocomial pathogen due to frequent ventilator-associated infections. Many biological processes of A. baumannii remain elusive, such as the formation of an air-liquid biofilm (pellicle). Several studies demonstrated the importance of post-translational modifications (PTMs) in A. baumannii physiology. Here, we investigated K-trimethylation in A. baumannii ATCC 17978 in planktonic and pellicle modes using proteomic analysis. To identify the most high-confidence K-trimethylated peptides, we compared different sample preparation methods (i...
May 25, 2023: Journal of Proteome Research
https://read.qxmd.com/read/37019596/mechanistic-aspects-of-reversible-methylation-modifications-of-arginine-and-lysine-of-nuclear-histones-and-their-roles-in-human-colon-cancer
#3
JOURNAL ARTICLE
Ankan Roy, Niharika, Subhajit Chakraborty, Jagdish Mishra, Suraj Pratap Singh, Samir Kumar Patra
Developmental proceedings and maintenance of cellular homeostasis are regulated by the precise orchestration of a series of epigenetic events that eventually control gene expression. DNA methylation and post-translational modifications (PTMs) of histones are well-characterized epigenetic events responsible for fine-tuning gene expression. PTMs of histones bear molecular logic of gene expression at chromosomal territory and have become a fascinating field of epigenetics. Nowadays, reversible methylation on histone arginine and lysine is gaining increasing attention as a significant PTM related to reorganizing local nucleosomal structure, chromatin dynamics, and transcriptional regulation...
2023: Progress in Molecular Biology and Translational Science
https://read.qxmd.com/read/36781207/ppict-an-integrated-deep-neural-network-for-predicting-inter-protein-ptm-cross-talk
#4
JOURNAL ARTICLE
Fei Zhu, Lei Deng, Yuhao Dai, Guangyu Zhang, Fanwang Meng, Cheng Luo, Guang Hu, Zhongjie Liang
Post-translational modifications (PTMs) fine-tune various signaling pathways not only by the modification of a single residue, but also by the interplay of different modifications on residue pairs within or between proteins, defined as PTM cross-talk. As a challenging question, less attention has been given to PTM dynamics underlying cross-talk residue pairs and structural information underlying protein-protein interaction (PPI) graph, limiting the progress in this PTM functional research. Here we propose a novel integrated deep neural network PPICT (Predictor for PTM Inter-protein Cross-Talk), which predicts PTM cross-talk by combining protein sequence-structure-dynamics information and structural information for PPI graph...
February 13, 2023: Briefings in Bioinformatics
https://read.qxmd.com/read/36750094/recycling-of-modified-h2a-h2b-provides-short-term-memory-of-chromatin-states
#5
JOURNAL ARTICLE
Valentin Flury, Nazaret Reverón-Gómez, Nicolas Alcaraz, Kathleen R Stewart-Morgan, Alice Wenger, Robert J Klose, Anja Groth
Chromatin landscapes are disrupted during DNA replication and must be restored faithfully to maintain genome regulation and cell identity. The histone H3-H4 modification landscape is restored by parental histone recycling and modification of new histones. How DNA replication impacts on histone H2A-H2B is currently unknown. Here, we measure H2A-H2B modifications and H2A.Z during DNA replication and across the cell cycle using quantitative genomics. We show that H2AK119ub1, H2BK120ub1, and H2A.Z are recycled accurately during DNA replication...
March 2, 2023: Cell
https://read.qxmd.com/read/36607631/sumoylation-regulates-functional-properties-of-the-oocyte-transcription-factors-sohlh1-and-nobox
#6
JOURNAL ARTICLE
Bethany K Patton, Surabhi Madadi, Shawn M Briley, Avery A Ahmed, Stephanie A Pangas
SOHLH1 and NOBOX are oocyte-expressed transcription factors with critical roles in ovary development and fertility. In mice, Sohlh1 and Nobox are essential for fertility through their regulation of the oocyte transcriptional network and cross-talk to somatic cells. Sumoylation is a posttranslational modification that regulates transcription factor function, and we previously showed that mouse oocytes deficient for sumoylation had an altered transcriptional landscape that included significant changes in NOBOX target genes...
February 2023: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://read.qxmd.com/read/36305460/cysmoddb-a-comprehensive-platform-with-the-integration-of-manually-curated-resources-and-analysis-tools-for-cysteine-posttranslational-modifications
#7
JOURNAL ARTICLE
Yanzheng Meng, Lin Zhang, Laizhi Zhang, Ziyu Wang, Xuanwen Wang, Chan Li, Yu Chen, Shipeng Shang, Lei Li
The unique chemical reactivity of cysteine residues results in various posttranslational modifications (PTMs), which are implicated in regulating a range of fundamental biological processes. With the advent of chemical proteomics technology, thousands of cysteine PTM (CysPTM) sites have been identified from multiple species. A few CysPTM-based databases have been developed, but they mainly focus on data collection rather than various annotations and analytical integration. Here, we present a platform-dubbed CysModDB, integrated with the comprehensive CysPTM resources and analysis tools...
October 27, 2022: Briefings in Bioinformatics
https://read.qxmd.com/read/36189113/impairment-strained-analytical-modeling-evaluation-and-cross-talk-analysis-of-symmetric-and-coexistent-channels-for-extended-class-1-ng-pon2-access-network
#8
JOURNAL ARTICLE
Rajendraprasad A Pagare, Abhilasha Mishra, Santosh Kumar
The analytical modeling for linear and non-linear impairments (LNI) for single mode fiber (SMF) and simulative analysis of extended power budget class-1 i.e. E1-class of next generation passive optic network-2 (NG-PON2) is presented in the paper. The proposed power-budget class time and wavelength division multiplexing (TWDM) based NG-PON2 network configuration is delivering symmetric 2.5 point-to-multi point (PtM) representing time and TWDM XGS-PON along with 10 Gbps point-to-point (PtP) wavelength division multiplexing (WDM) symmetric and coexistent channels (Ch) in worst-case scenario...
2022: Optical and Quantum Electronics
https://read.qxmd.com/read/36154077/quantitative-cell-proteomic-atlas-pathway-scale-targeted-mass-spectrometry-for-high-resolution-functional-profiling-of-cell-signaling
#9
JOURNAL ARTICLE
Paolo Cifani, Alex Kentsis
In spite of extensive studies of cellular signaling, many fundamental processes such as pathway integration, cross-talk, and feedback remain poorly understood. To enable integrated and quantitative measurements of cellular biochemical activities, we have developed the Quantitative Cell Proteomics Atlas (QCPA). QCPA consists of panels of targeted mass spectrometry assays to determine the abundance and stoichiometry of regulatory post-translational modifications of sentinel proteins from most known physiologic and pathogenic signaling pathways in human cells...
September 26, 2022: Journal of Proteome Research
https://read.qxmd.com/read/36120045/cross-talk-of-protein-expression-and-lysine-acetylation-in-response-to-tmv-infection-in-nicotiana-benthamiana
#10
JOURNAL ARTICLE
Liyun Song, Huaixu Zhan, Yujie Wang, Zhonglong Lin, Bin Li, Lili Shen, Yubing Jiao, Ying Li, Fenglong Wang, Jinguang Yang
Lysine acetylation (Kac ), a reversible PTM, plays an essential role in various biological processes, including those involving metabolic pathways, pathogen resistance, and transcription, in both prokaryotes and eukaryotes. TMV, the major factor that causes the poor quality of Solanaceae crops worldwide, directly alters many metabolic processes in tobacco. However, the extent and function of Kac during TMV infection have not been determined. The validation test to detect Kac level and viral expression after TMV infection and Nicotinamide (NAM) treatment clarified that acetylation was involved in TMV infection...
September 13, 2022: ACS Omega
https://read.qxmd.com/read/35904007/bidirectional-regulation-between-ap-1-and-sumoylation-pathway-genes-modulates-inflammatory-signaling-during-salmonella-infection
#11
JOURNAL ARTICLE
Pharvendra Kumar, Amarendranath Soory, Salman Ahmad Mustfa, Dipanka Tanu Sarmah, Himadri Devvanshi, Samrat Chatterjee, Guillaume Bossis, Girish S Ratnaparkhi, Chittur V Srikanth
Post-translational modifications (PTMs), such as SUMOylation, are known to modulate fundamental processes of a cell. Infectious agents such as Salmonella Typhimurium (STm), which causes gastroenteritis, utilize the PTM mechanism SUMOylation to hijack the host cell. STm suppresses host SUMO pathway genes UBC9 (also known as UBE2I) and PIAS1 to perturb SUMOylation for an efficient infection. In the present study, the regulation of SUMO pathway genes during STm infection was investigated. A direct binding of c-Fos (encoded by FOS), a component of activator protein-1 (AP-1), to promoters of both UBC9 and PIAS1 was observed...
August 15, 2022: Journal of Cell Science
https://read.qxmd.com/read/35696086/ptm-x-prediction-of-post-translational-modification-crosstalk-within-and-across-proteins
#12
JOURNAL ARTICLE
Yuxuan Li, Yuanhua Huang, Tingting Li
Posttranslational modifications (PTMs), which are processes of adding covalent groups in protein amino acids after the translation, play an important role in regulating proteins' localization, degradation, and functions. Different PTMs both within a single protein and across multiple proteins can work together or regulate reciprocally, known as PTM cross talk. However, high-throughput experimental identifications of PTM cross talk are lack due to technical limitations. In this chapter, we review in silico prediction approaches and illustrate the usage of PTM-X, a suite of recently proposed machine learning methods to predict both intra- and interprotein PTM cross talk...
2022: Methods in Molecular Biology
https://read.qxmd.com/read/35696085/exploration-of-protein-posttranslational-modification-landscape-and-cross-talk-with-crosstalkmapper
#13
JOURNAL ARTICLE
Arthur Grimaud, Frederik Haugaard Holck, Louise Marie Buur, Rebecca Kirsch, Veit Schwämmle
Post-translational modifications (PTMs) of proteins play crucial roles in defining protein function. They often do not occur alone, leading to a large variety of proteoforms that correspond to different combinations of multiple PTMs simultaneously decorating a protein. Changes of these proteoforms can be quantified via middle-down and top-down mass spectrometry experiments where the simultaneous PTM settings are obtained by measuring long peptides or entire proteins. Data from such experiments poses big challenges in identifying relevant features of biological and clinical importance...
2022: Methods in Molecular Biology
https://read.qxmd.com/read/35696079/analysis-of-posttranslational-modifications-in-arabidopsis-proteins-and-metabolic-pathways-using-the-fat-ptm-database
#14
JOURNAL ARTICLE
Madison N Blea, Ian S Wallace
Posttranslational modifications (PTMs) are critical regulators of protein behavior, and over 200 different types of PTMs have been identified. Recent developments in mass spectrometry technology and sample enrichment approaches have led to a massive expansion in the number of identified PTM types and sites within eukaryotic proteins. As these types of data become increasingly available, it is important to develop additional analysis tools and data repositories to investigate PTM cross talk and larger networks of PTMs...
2022: Methods in Molecular Biology
https://read.qxmd.com/read/35577067/prometheusdb-an-in-depth-analysis-of-the-high-quality-human-methyl-proteome
#15
JOURNAL ARTICLE
Enrico Massignani, Roberto Giambruno, Marianna Maniaci, Luciano Nicosia, Avinash Yadav, Alessandro Cuomo, Francesco Raimondi, Tiziana Bonaldi
Protein Arginine (R) methylation is a post-translational modification involved in various biological processes, such as RNA splicing, DNA repair, immune response, signal transduction, and tumour development. Although several advancements were made in the study of this modification by mass spectrometry, researchers still face the problem of a high false discovery rate. We present a dataset of high-quality methylations obtained from several different heavy methyl SILAC (hmSILAC) experiments analysed with a machine learning-based tool and show that this model allows for improved high-confidence identification of real methyl-peptides...
May 13, 2022: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/35544053/a-glance-at-post-translational-modifications-of-human-thyroglobulin-potential-impact-on-function-and-pathogenesis
#16
REVIEW
Laura Tosatto, Francesca Coscia
Thyroid hormones are essential for the metabolism of vertebrates and their synthesis, storage and release in the thyroid gland are orchestrated by their large protein precursor thyroglobulin (Tg). Alterations of Tg structure and localisation often correlate with major thyroid disorders. Namely, Tg is the main antigen in autoimmune thyroid diseases, and mutations in its gene are one of the causes of congenital hypothyroidism. Post-translational modifications (PTMs) are crucial for Tg surface properties and may be affected by the disease microenvironment; yet, their role in thyroid homeostasis and pathogenesis remains elusive...
June 21, 2022: European Thyroid Journal
https://read.qxmd.com/read/35051657/a-dynamic-and-combinatorial-histone-code-drives-malaria-parasite-asexual-and-sexual-development
#17
JOURNAL ARTICLE
Hilde von Grüning, Mariel Coradin, Mariel R Mendoza, Janette Reader, Simone Sidoli, Benjamin A Garcia, Lyn-Marie Birkholtz
Histone post-translational modifications (PTMs) are frequently co-occurring on the same chromatin domains or even the same molecule. It is now established that these 'histone codes' are the result of cross-talk between enzymes that catalyze multiple PTMs with univocal readout as compared to these PTMs in isolation. Here, we performed a comprehensive identification and quantification of histone codes of the malaria parasite, Plasmodium falciparum. We used advanced quantitative middle-down proteomics to identify combinations of PTMs in both the proliferative, asexual stages and transmissible, sexual gametocyte stages of P...
January 17, 2022: Molecular & Cellular Proteomics: MCP
https://read.qxmd.com/read/34264677/comprehensive-analysis-of-lysine-lactylation-in-rice-oryza-sativa-grains
#18
JOURNAL ARTICLE
Xiaoxi Meng, Jonathan M Baine, Tingcai Yan, Shu Wang
Protein lysine lactylation is a new post-translational modification (PTM) prevalently found in fungi and mammalian cells that directly stimulates gene transcription and regulates the glycolytic flux. However, lysine lactylation sites and regulations remain largely unexplored, especially in cereal crops. Herein, we report the first global lactylome profile in rice, which effectively identified 638 lysine lactylation sites across 342 proteins in rice grains. Functional annotations demonstrated that lysine lactylation was enriched in proteins associated with central carbon metabolism and protein biosynthesis...
July 15, 2021: Journal of Agricultural and Food Chemistry
https://read.qxmd.com/read/34123170/examining-histone-modification-crosstalk-using-immobilized-libraries-established-from-ligation-ready-nucleosomes
#19
JOURNAL ARTICLE
Diego Aparicio Pelaz, Zhadyra Yerkesh, Sören Kirchgäßner, Henriette Mahler, Vladlena Kharchenko, Dulat Azhibek, Mariusz Jaremko, Henning D Mootz, Łukasz Jaremko, Dirk Schwarzer, Wolfgang Fischle
Chromatin signaling relies on a plethora of posttranslational modifications (PTM) of the histone proteins which package the long DNA molecules of our cells in reoccurring units of nucleosomes. Determining the biological function and molecular working mechanisms of different patterns of histone PTMs requires access to various chromatin substrates of defined modification status. Traditionally, these are achieved by individual reconstitution of single nucleosomes or arrays of nucleosomes in conjunction with modified histones produced by means of chemical biology...
August 20, 2020: Chemical Science
https://read.qxmd.com/read/33979327/molecular-dynamics-shows-complex-interplay-and-long-range-effects-of-post-translational-modifications-in-yeast-protein-interactions
#20
JOURNAL ARTICLE
Nikolina ŠoŠtarić, Vera van Noort
Post-translational modifications (PTMs) play a vital, yet often overlooked role in the living cells through modulation of protein properties, such as localization and affinity towards their interactors, thereby enabling quick adaptation to changing environmental conditions. We have previously benchmarked a computational framework for the prediction of PTMs' effects on the stability of protein-protein interactions, which has molecular dynamics simulations followed by free energy calculations at its core. In the present work, we apply this framework to publicly available data on Saccharomyces cerevisiae protein structures and PTM sites, identified in both normal and stress conditions...
May 12, 2021: PLoS Computational Biology
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