Research progress in protein posttranslational modification site prediction

2018 ◽  
Vol 18 (4) ◽  
pp. 220-229 ◽  
Author(s):  
Wenying He ◽  
Leyi Wei ◽  
Quan Zou
Keyword(s):  
Posttranslational Modifications ◽  
Cell Biology ◽  
Research Progress ◽  
Future Research ◽  
Cellular Processes ◽  
Machine Learning Methods ◽  
Bioinformatics Tools ◽  
Glycosylation Sites ◽  
Almost All ◽  
And Function

AbstractPosttranslational modifications (PTMs) play an important role in regulating protein folding, activity and function and are involved in almost all cellular processes. Identification of PTMs of proteins is the basis for elucidating the mechanisms of cell biology and disease treatments. Compared with the laboriousness of equivalent experimental work, PTM prediction using various machine-learning methods can provide accurate, simple and rapid research solutions and generate valuable information for further laboratory studies. In this review, we manually curate most of the bioinformatics tools published since 2008. We also summarize the approaches for predicting ubiquitination sites and glycosylation sites. Moreover, we discuss the challenges of current PTM bioinformatics tools and look forward to future research possibilities.

scholarly journals N-linked glycosylation enzymes in the diatom Thalassiosira oceanica exhibit a diel cycle in transcript abundance and favor for NXT-type sites

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Joerg Behnke ◽  
Alejandro M. Cohen ◽  
Julie LaRoche
Keyword(s):  
Cell Biology ◽  
Biochemical Characterization ◽  
Solid Phase ◽  
Transcript Abundance ◽  
Growth Conditions ◽  
Iron Starvation ◽  
Glycosylation Sites ◽  
Glycosylation Pathway ◽  
And Function

AbstractN-linked glycosylation is a posttranslational modification affecting protein folding and function. The N-linked glycosylation pathway in algae is poorly characterized, and further knowledge is needed to understand the cell biology of algae and the evolution of N-linked glycosylation. This study investigated the N-linked glycosylation pathway in Thalassiosira oceanica, an open ocean diatom adapted to survive at growth-limiting iron concentrations. Here we identified and annotated the genes coding for the essential enzymes involved in the N-linked glycosylation pathway of T. oceanica. Transcript levels for genes coding for calreticulin, oligosaccharyltransferase (OST), N-acetylglucosaminyltransferase (GnT1), and UDP-glucose glucosyltransferase (UGGT) under high- and low-iron growth conditions revealed diel transcription patterns with a significant decrease of calreticulin and OST transcripts under iron-limitation. Solid-phase extraction of N-linked glycosylated peptides (SPEG) revealed 118 N-linked glycosylated peptides from cells grown in high- and low-iron growth conditions. The identified peptides had 81% NXT-type motifs, with X being any amino acids except proline. The presence of N-linked glycosylation sites in the iron starvation-induced protein 1a (ISIP1a) confirmed its predicted topology, contributing to the biochemical characterization of ISIP1 proteins. Analysis of extensive oceanic gene databases showed a global distribution of calreticulin, OST, and UGGT, reinforcing the importance of glycosylation in microalgae.

scholarly journals Knockout of the Golgi stacking proteins GRASP55 and GRASP65 impairs Golgi structure and function

2017 ◽  
Vol 28 (21) ◽  
pp. 2833-2842 ◽  
Author(s):  
Michael E. Bekier ◽  
Leibin Wang ◽  
Jie Li ◽  
Haoran Huang ◽  
Danming Tang ◽  
...  
Keyword(s):  
Posttranslational Modifications ◽  
Protein Trafficking ◽  
Critical Role ◽  
Hek293 Cells ◽  
Double Knockout ◽  
Knock Out ◽  
Golgi Stack ◽  
Cellular Processes ◽  
Golgi Structure ◽  
And Function

Golgi reassembly stacking protein of 65 kDa (GRASP65) and Golgi reassembly stacking protein of 55 kDa (GRASP55) were originally identified as Golgi stacking proteins; however, subsequent GRASP knockdown experiments yielded inconsistent results with respect to the Golgi structure, indicating a limitation of RNAi-based depletion. In this study, we have applied the recently developed clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology to knock out GRASP55 and GRASP65, individually or in combination, in HeLa and HEK293 cells. We show that double knockout of GRASP proteins disperses the Golgi stack into single cisternae and tubulovesicular structures, accelerates protein trafficking, and impairs accurate glycosylation of proteins and lipids. These results demonstrate a critical role for GRASPs in maintaining the stacked structure of the Golgi, which is required for accurate posttranslational modifications in the Golgi. Additionally, the GRASP knockout cell lines developed in this study will be useful tools for studying the role of GRASP proteins in other important cellular processes.

scholarly journals MiREDiBase, a manually curated database of validated and putative editing events in microRNAs

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Gioacchino P. Marceca ◽  
Rosario Distefano ◽  
Luisa Tomasello ◽  
Alessandro Lagana ◽  
Francesco Russo ◽  
...  
Keyword(s):  
Rna Editing ◽  
Cell Biology ◽  
Enrichment Analysis ◽  
Minimum Free Energy ◽  
Binding Ability ◽  
Cellular Processes ◽  
Non Coding Rnas ◽  
Target Binding ◽  
And Function ◽  
Mirna Editing

AbstractMicroRNAs (miRNAs) are regulatory small non-coding RNAs that function as translational repressors. MiRNAs are involved in most cellular processes, and their expression and function are presided by several factors. Amongst, miRNA editing is an epitranscriptional modification that alters the original nucleotide sequence of selected miRNAs, possibly influencing their biogenesis and target-binding ability. A-to-I and C-to-U RNA editing are recognized as the canonical types, with the A-to-I type being the predominant one. Albeit some bioinformatics resources have been implemented to collect RNA editing data, it still lacks a comprehensive resource explicitly dedicated to miRNA editing. Here, we present MiREDiBase, a manually curated catalog of editing events in miRNAs. The current version includes 3,059 unique validated and putative editing sites from 626 pre-miRNAs in humans and three primates. Editing events in mature human miRNAs are supplied with miRNA-target predictions and enrichment analysis, while minimum free energy structures are inferred for edited pre-miRNAs. MiREDiBase represents a valuable tool for cell biology and biomedical research and will be continuously updated and expanded at https://ncrnaome.osumc.edu/miredibase.

scholarly journals Posttranslational modifications in proteins: resources, tools and prediction methods

Database ◽  
2021 ◽  
Author(s):  
Shahin Ramazi ◽  
Javad Zahiri
Keyword(s):  
Computational Methods ◽  
Posttranslational Modifications ◽  
Side Chain ◽  
Amino Acid Side Chain ◽  
Cellular Processes ◽  
Online Databases ◽  
Different Types ◽  
Protein Functions ◽  
And Function ◽  
Molecular Regulatory Mechanisms

Abstract Posttranslational modifications (PTMs) refer to amino acid side chain modification in some proteins after their biosynthesis. There are more than 400 different types of PTMs affecting many aspects of protein functions. Such modifications happen as crucial molecular regulatory mechanisms to regulate diverse cellular processes. These processes have a significant impact on the structure and function of proteins. Disruption in PTMs can lead to the dysfunction of vital biological processes and hence to various diseases. High-throughput experimental methods for discovery of PTMs are very laborious and time-consuming. Therefore, there is an urgent need for computational methods and powerful tools to predict PTMs. There are vast amounts of PTMs data, which are publicly accessible through many online databases. In this survey, we comprehensively reviewed the major online databases and related tools. The current challenges of computational methods were reviewed in detail as well.

scholarly journals Proximity interactome of LC3B in normal growth conditions

2021 ◽  
Author(s):  
Marie Nollet ◽  
Alexander Agrotis ◽  
Fanourios Michailidis ◽  
Arran David Dokal ◽  
Vinothini Rajeeve ◽  
...  
Keyword(s):  
Cell Biology ◽  
Normal Growth ◽  
Growth Conditions ◽  
Biological Functions ◽  
Normal Medium ◽  
Outer Membranes ◽  
Cellular Processes ◽  
Proteomic Approach ◽  
And Function

LC3 (Light Chain 3) is a key player of autophagy, a major stress-responsive proteolysis pathway promoting cellular homeostasis. It coordinates the formation and maturation of autophagosomes and recruits cargo to be further degraded upon autophagosome-lysosome fusion. To orchestrate its functions, LC3 binds to multiple proteins from the autophagosomes inner and outer membranes, but the full extent of these interactions is not known. Moreover, LC3 has been increasingly reported in other cellular locations than the autophagosome, with cellular outcome not fully understood and not all related to autophagy. Furthermore, novel functions of LC3 as well as autophagy can occur in cells growing in a normal medium thus in non-stressed conditions. A better knowledge of the molecule in proximity to LC3 in normal growth conditions will improve the understanding of LC3 function in autophagy and in other cell biology function. Using an APEX2 based proteomic approach, we have detected 407 proteins in proximity to the well-characterised LC3B isoform in non-stress conditions. These include known and novel LC3B proximity proteins, associated with various cell localisation and biological functions. Sixty-nine of these proteins contain a putative LIR (LC3 Interacting Region) including 41 not reported associated to autophagy. Several APEX2 hits were validated by co-immunoprecipitation and co-immunofluorescence. This study uncovers the LC3B global interactome and reveals novel LC3B interactors, irrespective of LC3B localisation and function. This knowledge could be exploited to better understand the role of LC3B in autophagy and non-autophagy cellular processes.

scholarly journals Microtubule Regulation and Function during Virus Infection

2017 ◽  
Vol 91 (16) ◽  
Author(s):  
Mojgan H. Naghavi ◽  
Derek Walsh
Keyword(s):  
Posttranslational Modifications ◽  
Intracellular Transport ◽  
Spatial Organization ◽  
Virus Particles ◽  
Cellular Processes ◽  
Wide Range ◽  
Associated Proteins ◽  
And Function ◽  
Induced Changes ◽  
Growth Pause

ABSTRACT Microtubules (MTs) form a rapidly adaptable network of filaments that radiate throughout the cell. These dynamic arrays facilitate a wide range of cellular processes, including the capture, transport, and spatial organization of cargos and organelles, as well as changes in cell shape, polarity, and motility. Nucleating from MT-organizing centers, including but by no means limited to the centrosome, MTs undergo rapid transitions through phases of growth, pause, and catastrophe, continuously exploring and adapting to the intracellular environment. Subsets of MTs can become stabilized in response to environmental cues, acquiring distinguishing posttranslational modifications and performing discrete functions as specialized tracks for cargo trafficking. The dynamic behavior and organization of the MT array is regulated by MT-associated proteins (MAPs), which include a subset of highly specialized plus-end-tracking proteins (+TIPs) that respond to signaling cues to alter MT behavior. As pathogenic cargos, viruses require MTs to transport to and from their intracellular sites of replication. While interactions with and functions for MT motor proteins are well characterized and extensively reviewed for many viruses, this review focuses on MT filaments themselves. Changes in the spatial organization and dynamics of the MT array, mediated by virus- or host-induced changes to MT regulatory proteins, not only play a central role in the intracellular transport of virus particles but also regulate a wider range of processes critical to the outcome of infection.

scholarly journals FADD in Cancer: Mechanisms of Altered Expression and Function, and Clinical Implications

Cancers ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 1462 ◽  
Author(s):  
José L Marín-Rubio ◽  
Laura Vela-Martín ◽  
José Fernández-Piqueras ◽  
María Villa-Morales
Keyword(s):  
Posttranslational Modifications ◽  
Cell Cycle Control ◽  
Regulation Of Gene Expression ◽  
Death Receptor ◽  
Clinical Implications ◽  
Altered Expression ◽  
Cellular Processes ◽  
Potential Biomarker ◽  
And Function ◽  
And Control

FADD was initially described as an adaptor molecule for death receptor-mediated apoptosis, but subsequently it has been implicated in nonapoptotic cellular processes such as proliferation and cell cycle control. During the last decade, FADD has been shown to play a pivotal role in most of the signalosome complexes, such as the necroptosome and the inflammasome. Interestingly, various mechanisms involved in regulating FADD functions have been identified, essentially posttranslational modifications and secretion. All these aspects have been thoroughly addressed in previous reviews. However, FADD implication in cancer is complex, due to pleiotropic effects. It has been reported either as anti- or protumorigenic, depending on the cell type. Regulation of FADD expression in cancer is a complex issue since both overexpression and downregulation have been reported, but the mechanisms underlying such alterations have not been fully unveiled. Posttranslational modifications also constitute a relevant mechanism controlling FADD levels and functions in tumor cells. In this review, we aim to provide detailed, updated information on alterations leading to changes in FADD expression and function in cancer. The participation of FADD in various biological processes is recapitulated, with a mention of interesting novel functions recently proposed for FADD, such as regulation of gene expression and control of metabolic pathways. Finally, we gather all the available evidence regarding the clinical implications of FADD alterations in cancer, especially as it has been proposed as a potential biomarker with prognostic value.

scholarly journals MiREDiBase: a manually curated database of validated and putative editing events in microRNAs

2020 ◽  
Author(s):  
Gioacchino P. Marceca ◽  
Rosario Distefano ◽  
Luisa Tomasello ◽  
Alessandro Lagana ◽  
Francesco Russo ◽  
...  
Keyword(s):  
Rna Editing ◽  
Cell Biology ◽  
Enrichment Analysis ◽  
Minimum Free Energy ◽  
Binding Ability ◽  
Cellular Processes ◽  
Non Coding Rnas ◽  
Target Binding ◽  
And Function ◽  
Mirna Editing

AbstractMicroRNAs (miRNAs) are regulatory small non-coding RNAs that function as translational repressors. MiRNAs are involved in most cellular processes, and their expression and function are presided by several factors. Amongst, miRNA editing is an epitranscriptional modification that alters the original nucleotide sequence of selected miRNAs, possibly influencing their biogenesis and target-binding ability. A-to-I and C-to-U RNA editing are recognized as the canonical types, with the A-to-I type being the predominant one. Albeit some bioinformatics resources have been implemented to collect RNA editing data, it still lacks a comprehensive resource explicitly dedicated to miRNA editing. Here, we present MiREDiBase, a manually curated catalog of editing events in miRNAs. The current version includes 3,059 unique validated and putative editing sites from 626 pre-miRNAs in humans and three primates. Editing events in mature human miRNAs are supplied with miRNA-target predictions and enrichment analysis, while minimum free energy structures are inferred for edited pre-miRNAs. MiREDiBase represents a valuable tool for cell biology and biomedical research and will be continuously updated and expanded at https://ncrnaome.osumc.edu/miredibase.

scholarly journals Cdc48: A Swiss Army Knife of Cell Biology

2013 ◽  
Vol 2013 ◽  
pp. 1-12 ◽  
Author(s):  
Guem Hee Baek ◽  
Haili Cheng ◽  
Vitnary Choe ◽  
Xin Bao ◽  
Jia Shao ◽  
...  
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Atpase Activity ◽  
Cell Biology ◽  
Protein Complexes ◽  
Biological Functions ◽  
Cellular Processes ◽  
Broad Array ◽  
And Function ◽  
Regulatory Functions ◽  
Lateral Sclerosis

Cdc48 (also called VCP and p97) is an abundant protein that plays essential regulatory functions in a broad array of cellular processes. Working with various cofactors, Cdc48 utilizes its ATPase activity to promote the assembly and disassembly of protein complexes. Here, we review key biological functions and regulation of Cdc48 in ubiquitin-related events. Given the broad employment of Cdc48 in cell biology and its intimate ties to human diseases (e.g., amyotrophic lateral sclerosis), studies of Cdc48 will bring significant insights into the mechanism and function of ubiquitin in health and diseases.

scholarly journals Milestones in Bacillus subtilis sporulation research

2021 ◽  
Vol 8 (1) ◽  
pp. 1-16
Author(s):  
Eammon P. Riley ◽  
Corinna Schwarz ◽  
Alan I. Derman ◽  
Javier Lopez-Garrido
Keyword(s):  
Gene Expression ◽  
Bacillus Subtilis ◽  
Cell Biology ◽  
Chromosome Translocation ◽  
Future Research ◽  
Specific Gene ◽  
Rapid Progress ◽  
Specific Gene Expression ◽  
General Aspects ◽  
And Function

Endospore formation has been a rich field of research for more than a century, and has benefited from the powerful genetic tools available in Bacillus subtilis. In this review, we highlight foundational discoveries that shaped the sporulation field, from its origins to the present day, tracing a chronology that spans more than one hundred eighty years. We detail how cell-specific gene expression has been harnessed to investigate the existence and function of intercellular proteinaceous channels in sporulating cells, and we illustrate the rapid progress in our understanding of the cell biology of sporulation in recent years using the process of chromosome translocation as a storyline. Finally, we sketch general aspects of sporulation that remain largely unexplored, and that we envision will be fruitful areas of future research.

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