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Bickel D, Vranken W. Effects of Phosphorylation on Protein Backbone Dynamics and Conformational Preferences. J Chem Theory Comput 2024; 20:4998-5011. [PMID: 38830621 PMCID: PMC11210476 DOI: 10.1021/acs.jctc.4c00206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/22/2024] [Accepted: 05/22/2024] [Indexed: 06/05/2024]
Abstract
Phosphorylations are the most common and extensively studied post-translational modification (PTM) of proteins in eukaryotes. They constitute a major regulatory mechanism, modulating protein function, protein-protein interactions, as well as subcellular localization. Phosphorylation sites are preferably located in intrinsically disordered regions and have been shown to trigger structural rearrangements and order-to-disorder transitions. They can therefore have a significant effect on protein backbone dynamics or conformation, but only sparse experimental data are available. To obtain a more general description of how and when phosphorylations have a significant effect on protein behavior, molecular dynamics (MD) currently provides the only suitable framework to study these effects at a large scale in atomistic detail. This study develops a systematic MD simulation framework to explore the influence of phosphorylations on the local backbone dynamics and conformational propensities of proteins. Through a series of glycine-backbone peptides, we studied the effects of amino acid residues including the three most common phosphorylations (Ser, Thr, and Tyr), on local backbone dynamics and conformational propensities. We further extended our study to investigate the interactions of all such residues between position i to positions i + 1, i + 2, i + 3, and i + 4 in such peptides. The final data set comprises structural ensembles for 3393 sequences with more than 1 μs of sampling for each ensemble. To validate the relevance of the results, the structural and conformational properties extracted from the MD simulations are compared to NMR data from the Biological Magnetic Resonance Data Bank. The systematic nature of this study enables the projection of the gained knowledge onto any phosphorylation site in the proteome and provides a general framework for the study of further PTMs. The full data set is publicly available, as a training and reference set.
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Affiliation(s)
- David Bickel
- Interuniversity
Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
- Structural
Biology Brussels, Vrije Universiteit Brussels, 1050 Brussels, Belgium
| | - Wim Vranken
- Interuniversity
Institute of Bioinformatics in Brussels, 1050 Brussels, Belgium
- Structural
Biology Brussels, Vrije Universiteit Brussels, 1050 Brussels, Belgium
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2
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Koyama T, Iso N, Norizoe Y, Sakaue T, Yoshimura SH. Charge block-driven liquid-liquid phase separation - mechanism and biological roles. J Cell Sci 2024; 137:jcs261394. [PMID: 38855848 DOI: 10.1242/jcs.261394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024] Open
Abstract
Liquid-liquid phase separation (LLPS) has increasingly been found to play pivotal roles in a number of intracellular events and reactions, and has introduced a new paradigm in cell biology to explain protein-protein and enzyme-ligand interactions beyond conventional molecular and biochemical theories. LLPS is driven by the cumulative effects of weak and promiscuous interactions, including electrostatic, hydrophobic and cation-π interactions, among polypeptides containing intrinsically disordered regions (IDRs) and describes the macroscopic behaviours of IDR-containing proteins in an intracellular milieu. Recent studies have revealed that interactions between 'charge blocks' - clusters of like charges along the polypeptide chain - strongly induce LLPS and play fundamental roles in its spatiotemporal regulation. Introducing a new parameter, termed 'charge blockiness', into physicochemical models of disordered polypeptides has yielded a better understanding of how the intrinsic amino acid sequence of a polypeptide determines the spatiotemporal occurrence of LLPS within a cell. Charge blockiness might also explain why some post-translational modifications segregate within IDRs and how they regulate LLPS. In this Review, we summarise recent progress towards understanding the mechanism and biological roles of charge block-driven LLPS and discuss how this new characteristic parameter of polypeptides offers new possibilities in the fields of structural biology and cell biology.
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Affiliation(s)
- Tetsu Koyama
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Naoki Iso
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Yuki Norizoe
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Takahiro Sakaue
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Shige H Yoshimura
- Graduate School of Biostudies , Kyoto University, Yoshida-konoe, Sakyo-ku, Kyoto, 606-8501, Japan
- Center for Living Systems Information Science (CeLiSIS) , Kyoto University, Yoshida-Konoe-Cho, Sakyo-ku, Kyoto, 606-8501, Japan
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3
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McKnight SL. Protein domains of low sequence complexity-dark matter of the proteome. Genes Dev 2024; 38:205-212. [PMID: 38503517 PMCID: PMC11065162 DOI: 10.1101/gad.351465.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
This perspective begins with a speculative consideration of the properties of the earliest proteins to appear during evolution. What did these primitive proteins look like, and how were they of benefit to early forms of life? I proceed to hypothesize that primitive proteins have been preserved through evolution and now serve diverse functions important to the dynamics of cell morphology and biological regulation. The primitive nature of these modern proteins is easy to spot. They are composed of a limited subset of the 20 amino acids used by traditionally evolved proteins and thus are of low sequence complexity. This chemical simplicity limits protein domains of low sequence complexity to forming only a crude and labile type of protein structure currently hidden from the computational powers of machine learning. I conclude by hypothesizing that this structural weakness represents the underlying virtue of proteins that, at least for the moment, constitute the dark matter of the proteome.
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Affiliation(s)
- Steven L McKnight
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390-9152, USA
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4
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Gupta MN, Uversky VN. Protein structure-function continuum model: Emerging nexuses between specificity, evolution, and structure. Protein Sci 2024; 33:e4968. [PMID: 38532700 DOI: 10.1002/pro.4968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/18/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
The rationale for replacing the old binary of structure-function with the trinity of structure, disorder, and function has gained considerable ground in recent years. A continuum model based on the expanded form of the existing paradigm can now subsume importance of both conformational flexibility and intrinsic disorder in protein function. The disorder is actually critical for understanding the protein-protein interactions in many regulatory processes, formation of membrane-less organelles, and our revised notions of specificity as amply illustrated by moonlighting proteins. While its importance in formation of amyloids and function of prions is often discussed, the roles of intrinsic disorder in infectious diseases and protein function under extreme conditions are also becoming clear. This review is an attempt to discuss how our current understanding of protein function, specificity, and evolution fit better with the continuum model. This integration of structure and disorder under a single model may bring greater clarity in our continuing quest for understanding proteins and molecular mechanisms of their functionality.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, New Delhi, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
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5
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Zhu Z, Li S, Yin X, Sun K, Song J, Ren W, Gao L, Zhi K. Review: Protein O-GlcNAcylation regulates DNA damage response: A novel target for cancer therapy. Int J Biol Macromol 2024; 264:130351. [PMID: 38403231 DOI: 10.1016/j.ijbiomac.2024.130351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 02/02/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024]
Abstract
The DNA damage response (DDR) safeguards the stable genetic information inheritance by orchestrating a complex protein network in response to DNA damage. However, this mechanism can often hamper the effectiveness of radiotherapy and DNA-damaging chemotherapy in destroying tumor cells, causing cancer resistance. Inhibiting DDR can significantly improve tumor cell sensitivity to radiotherapy and DNA-damaging chemotherapy. Thus, DDR can be a potential target for cancer treatment. Post-translational modifications (PTMs) of DDR-associated proteins profoundly affect their activity and function by covalently attaching new functional groups. O-GlcNAcylation (O-linked-N-acetylglucosaminylation) is an emerging PTM associated with adding and removing O-linked N-acetylglucosamine to serine and threonine residues of proteins. It acts as a dual sensor for nutrients and stress in the cell and is sensitive to DNA damage. However, the explanation behind the specific role of O-GlcNAcylation in the DDR remains remains to be elucidated. To illustrate the complex relationship between O-GlcNAcylation and DDR, this review systematically describes the role of O-GlcNAcylation in DNA repair, cell cycle, and chromatin. We also discuss the defects of current strategies for targeting O-GlcNAcylation-regulated DDR in cancer therapy and suggest potential directions to address them.
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Affiliation(s)
- Zhuang Zhu
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Shaoming Li
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Xiaopeng Yin
- Department of Oral and Maxillofacial Surgery, Central Laboratory of Jinan Stamotological Hospital, Jinan Key Laboratory of Oral Tissue Regeneration, Jinan 250001, Shandong Province, China
| | - Kai Sun
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China
| | - Jianzhong Song
- Department of Oral and Maxilloafacial Surgery, People's Hospital of Rizhao, Rizhao, Shandong, China
| | - Wenhao Ren
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| | - Ling Gao
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Key Lab of Oral Clinical Medicine, the Affiliated Hospital of Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
| | - Keqian Zhi
- Department of Oral and Maxillofacial Reconstruction, the Affiliated Hospital of Qingdao University, Qingdao 266555, China; School of Stomatology, Qingdao University, Qingdao 266003, China; Key Lab of Oral Clinical Medicine, the Affiliated Hospital of Qingdao University, Qingdao 266003, China; Department of Oral and Maxillofacial Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266555, China.
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6
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da Silva ANR, Pereira GRC, Bonet LFS, Outeiro TF, De Mesquita JF. In silico analysis of alpha-synuclein protein variants and posttranslational modifications related to Parkinson's disease. J Cell Biochem 2024; 125:e30523. [PMID: 38239037 DOI: 10.1002/jcb.30523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/11/2023] [Accepted: 12/29/2023] [Indexed: 03/12/2024]
Abstract
Parkinson's disease (PD) is among the most prevalent neurodegenerative disorders, affecting over 10 million people worldwide. The protein encoded by the SNCA gene, alpha-synuclein (ASYN), is the major component of Lewy body (LB) aggregates, a histopathological hallmark of PD. Mutations and posttranslational modifications (PTMs) in ASYN are known to influence protein aggregation and LB formation, possibly playing a crucial role in PD pathogenesis. In this work, we applied computational methods to characterize the effects of missense mutations and PTMs on the structure and function of ASYN. Missense mutations in ASYN were compiled from the literature/databases and underwent a comprehensive predictive analysis. Phosphorylation and SUMOylation sites of ASYN were retrieved from databases and predicted by algorithms. ConSurf was used to estimate the evolutionary conservation of ASYN amino acids. Molecular dynamics (MD) simulations of ASYN wild-type and variants A30G, A30P, A53T, and G51D were performed using the GROMACS package. Seventy-seven missense mutations in ASYN were compiled. Although most mutations were not predicted to affect ASYN stability, aggregation propensity, amyloid formation, and chaperone binding, the analyzed mutations received relatively high rates of deleterious predictions and predominantly occurred at evolutionarily conserved sites within the protein. Moreover, our predictive analyses suggested that the following mutations may be possibly harmful to ASYN and, consequently, potential targets for future investigation: K6N, T22I, K34E, G36R, G36S, V37F, L38P, G41D, and K102E. The MD analyses pointed to remarkable flexibility and essential dynamics alterations at nearly all domains of the studied variants, which could lead to impaired contact between NAC and the C-terminal domain triggering protein aggregation. These alterations may have functional implications for ASYN and provide important insight into the molecular mechanism of PD, supporting the design of future biomedical research and improvements in existing therapies for the disease.
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Affiliation(s)
- Aloma N R da Silva
- Bioinformatics and Computational Biology Laboratory, Department of Genetics and Molecular Biology, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriel R C Pereira
- Bioinformatics and Computational Biology Laboratory, Department of Genetics and Molecular Biology, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luiz Felippe Sarmento Bonet
- Bioinformatics and Computational Biology Laboratory, Department of Genetics and Molecular Biology, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tiago Fleming Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Max Planck Institute for Experimental Medicine, Göttingen, Germany
| | - Joelma F De Mesquita
- Bioinformatics and Computational Biology Laboratory, Department of Genetics and Molecular Biology, Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Rio de Janeiro, Brazil
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7
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Peng Z, Schussheim B, Chatterjee P. PTM-Mamba: A PTM-Aware Protein Language Model with Bidirectional Gated Mamba Blocks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.581983. [PMID: 38464112 PMCID: PMC10925343 DOI: 10.1101/2024.02.28.581983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Proteins serve as the workhorses of living organisms, orchestrating a wide array of vital functions. Post-translational modifications (PTMs) of their amino acids greatly influence the structural and functional diversity of different protein types and uphold proteostasis, allowing cells to swiftly respond to environmental changes and intricately regulate complex biological processes. To this point, efforts to model the complex features of proteins have involved the training of large and expressive protein language models (pLMs) such as ESM-2 and ProtT5, which accurately encode structural, functional, and physicochemical properties of input protein sequences. However, the over 200 million sequences that these pLMs were trained on merely scratch the surface of proteomic diversity, as they neither input nor account for the effects of PTMs. In this work, we fill this major gap in protein sequence modeling by introducing PTM tokens into the pLM training regime. We then leverage recent advancements in structured state space models (SSMs), specifically Mamba, which utilizes efficient hardware-aware primitives to overcome the quadratic time complexities of Transformers. After adding a comprehensive set of PTM tokens to the model vocabulary, we train bidirectional Mamba blocks whose outputs are fused with state-of-the-art ESM-2 embeddings via a novel gating mechanism. We demonstrate that our resultant PTM-aware pLM, PTM-Mamba , improves upon ESM-2's performance on various PTM-specific tasks. PTM-Mamba is the first and only pLM that can uniquely input and represent both wild-type and PTM sequences, motivating downstream modeling and design applications specific to post-translationally modified proteins. To facilitate PTM-aware protein language modeling applications, we have made our model available at: https://huggingface.co/ChatterjeeLab/PTM-Mamba .
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8
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Gupta MN, Uversky VN. Biological importance of arginine: A comprehensive review of the roles in structure, disorder, and functionality of peptides and proteins. Int J Biol Macromol 2024; 257:128646. [PMID: 38061507 DOI: 10.1016/j.ijbiomac.2023.128646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/02/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024]
Abstract
Arginine shows Jekyll and Hyde behavior in several respects. It participates in protein folding via ionic and H-bonds and cation-pi interactions; the charge and hydrophobicity of its side chain make it a disorder-promoting amino acid. Its methylation in histones; RNA binding proteins; chaperones regulates several cellular processes. The arginine-centric modifications are important in oncogenesis and as biomarkers in several cardiovascular diseases. The cross-links involving arginine in collagen and cornea are involved in pathogenesis of tissues but have also been useful in tissue engineering and wound-dressing materials. Arginine is a part of active site of several enzymes such as GTPases, peroxidases, and sulfotransferases. Its metabolic importance is obvious as it is involved in production of urea, NO, ornithine and citrulline. It can form unusual functional structures such as molecular tweezers in vitro and sprockets which engage DNA chains as part of histones in vivo. It has been used in design of cell-penetrating peptides as drugs. Arginine has been used as an excipient in both solid and injectable drug formulations; its role in suppressing opalescence due to liquid-liquid phase separation is particularly very promising. It has been known as a suppressor of protein aggregation during protein refolding. It has proved its usefulness in protein bioseparation processes like ion-exchange, hydrophobic and affinity chromatographies. Arginine is an amino acid, whose importance in biological sciences and biotechnology continues to grow in diverse ways.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi 110016, India
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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9
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Ramazi S, Tabatabaei SAH, Khalili E, Nia AG, Motarjem K. Analysis and review of techniques and tools based on machine learning and deep learning for prediction of lysine malonylation sites in protein sequences. Database (Oxford) 2024; 2024:baad094. [PMID: 38245002 PMCID: PMC10799748 DOI: 10.1093/database/baad094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/30/2023] [Accepted: 12/20/2023] [Indexed: 01/22/2024]
Abstract
The post-translational modifications occur as crucial molecular regulatory mechanisms utilized to regulate diverse cellular processes. Malonylation of proteins, a reversible post-translational modification of lysine/k residues, is linked to a variety of biological functions, such as cellular regulation and pathogenesis. This modification plays a crucial role in metabolic pathways, mitochondrial functions, fatty acid oxidation and other life processes. However, accurately identifying malonylation sites is crucial to understand the molecular mechanism of malonylation, and the experimental identification can be a challenging and costly task. Recently, approaches based on machine learning (ML) have been suggested to address this issue. It has been demonstrated that these procedures improve accuracy while lowering costs and time constraints. However, these approaches also have specific shortcomings, including inappropriate feature extraction out of protein sequences, high-dimensional features and inefficient underlying classifiers. As a result, there is an urgent need for effective predictors and calculation methods. In this study, we provide a comprehensive analysis and review of existing prediction models, tools and benchmark datasets for predicting malonylation sites in protein sequences followed by a comparison study. The review consists of the specifications of benchmark datasets, explanation of features and encoding methods, descriptions of the predictions approaches and their embedding ML or deep learning models and the description and comparison of the existing tools in this domain. To evaluate and compare the prediction capability of the tools, a new bunch of data has been extracted based on the most updated database and the tools have been assessed based on the extracted data. Finally, a hybrid architecture consisting of several classifiers including classical ML models and a deep learning model has been proposed to ensemble the prediction results. This approach demonstrates the better performance in comparison with all prediction tools included in this study (the source codes of the models presented in this manuscript are available in https://github.com/Malonylation). Database URL: https://github.com/A-Golshan/Malonylation.
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Affiliation(s)
| | - Seyed Amir Hossein Tabatabaei
- Department of Computer Science, Faculty of Mathematical Sciences, University of Guilan, Namjoo St. Postal, Rasht 41938-33697, Iran
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Jalal AleAhmad, Tehran 14117-13116, Iran
| | - Elham Khalili
- Department of Plant Sciences, Faculty of Science, Tarbiat Modares University, Jalal AleAhmad, Tehran 14117-13116, Iran
| | - Amirhossein Golshan Nia
- Department of Mathematics and Computer Science, Amirkabir University of Technology, No. 350, Hafez Ave, Tehran 15916-34311, Iran
| | - Kiomars Motarjem
- Department of Statistics, Faculty of Mathematical Sciences, Tarbiat Modares University, Jalal AleAhmad, Tehran 14117-13116, Iran
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Basu S, Zhao B, Biró B, Faraggi E, Gsponer J, Hu G, Kloczkowski A, Malhis N, Mirdita M, Söding J, Steinegger M, Wang D, Wang K, Xu D, Zhang J, Kurgan L. DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options. Nucleic Acids Res 2024; 52:D426-D433. [PMID: 37933852 PMCID: PMC10767971 DOI: 10.1093/nar/gkad985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 11/08/2023] Open
Abstract
The DescribePROT database of amino acid-level descriptors of protein structures and functions was substantially expanded since its release in 2020. This expansion includes substantial increase in the size, scope, and quality of the underlying data, the addition of experimental structural information, the inclusion of new data download options, and an upgraded graphical interface. DescribePROT currently covers 19 structural and functional descriptors for proteins in 273 reference proteomes generated by 11 accurate and complementary predictive tools. Users can search our resource in multiple ways, interact with the data using the graphical interface, and download data at various scales including individual proteins, entire proteomes, and whole database. The annotations in DescribePROT are useful for a broad spectrum of studies that include investigations of protein structure and function, development and validation of predictive tools, and to support efforts in understanding molecular underpinnings of diseases and development of therapeutics. DescribePROT can be freely accessed at http://biomine.cs.vcu.edu/servers/DESCRIBEPROT/.
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Affiliation(s)
- Sushmita Basu
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Bi Zhao
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Bálint Biró
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA
- Department of Animal Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Eshel Faraggi
- Physics Department, Indiana University, Indianapolis, IN, USA
| | - Jörg Gsponer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gang Hu
- School of Statistics and Data Science, LPMC and KLMDASR, Nankai University, Tianjin, P.R. China
| | - Andrzej Kloczkowski
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, USA
| | - Nawar Malhis
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Milot Mirdita
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Johannes Söding
- Quantitative and Computational Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Martin Steinegger
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
- Institute of Molecular Biology & Genetics, Seoul National University, Seoul, Republic of Korea
- Artificial Intelligence Institute, Seoul National University, Seoul, South Korea
| | - Duolin Wang
- Department of Electrical Engineer and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, USA
| | - Kui Wang
- School of Statistics and Data Science, LPMC and KLMDASR, Nankai University, Tianjin, P.R. China
| | - Dong Xu
- Department of Electrical Engineer and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, USA
| | - Jian Zhang
- School of Computer and Information Technology, Xinyang Normal University, Xinyang, P.R. China
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA
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11
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Poretsky E, Andorf CM, Sen TZ. PhosBoost: Improved phosphorylation prediction recall using gradient boosting and protein language models. PLANT DIRECT 2023; 7:e554. [PMID: 38124705 PMCID: PMC10732782 DOI: 10.1002/pld3.554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 12/23/2023]
Abstract
Protein phosphorylation is a dynamic and reversible post-translational modification that regulates a variety of essential biological processes. The regulatory role of phosphorylation in cellular signaling pathways, protein-protein interactions, and enzymatic activities has motivated extensive research efforts to understand its functional implications. Experimental protein phosphorylation data in plants remains limited to a few species, necessitating a scalable and accurate prediction method. Here, we present PhosBoost, a machine-learning approach that leverages protein language models and gradient-boosting trees to predict protein phosphorylation from experimentally derived data. Trained on data obtained from a comprehensive plant phosphorylation database, qPTMplants, we compared the performance of PhosBoost to existing protein phosphorylation prediction methods, PhosphoLingo and DeepPhos. For serine and threonine prediction, PhosBoost achieved higher recall than PhosphoLingo and DeepPhos (.78, .56, and .14, respectively) while maintaining a competitive area under the precision-recall curve (.54, .56, and .42, respectively). PhosphoLingo and DeepPhos failed to predict any tyrosine phosphorylation sites, while PhosBoost achieved a recall score of .6. Despite the precision-recall tradeoff, PhosBoost offers improved performance when recall is prioritized while consistently providing more confident probability scores. A sequence-based pairwise alignment step improved prediction results for all classifiers by effectively increasing the number of inferred positive phosphosites. We provide evidence to show that PhosBoost models are transferable across species and scalable for genome-wide protein phosphorylation predictions. PhosBoost is freely and publicly available on GitHub.
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Affiliation(s)
- Elly Poretsky
- Agricultural Research Service, Crop Improvement and Genetics Research UnitU.S. Department of AgricultureAlbanyCAUnited States
| | - Carson M. Andorf
- Agricultural Research Service, Corn Insects and Crop Genetics ResearchU.S. Department of AgricultureAmesIAUnited States
- Department of Computer ScienceIowa State UniversityAmesIAUnited States
| | - Taner Z. Sen
- Agricultural Research Service, Crop Improvement and Genetics Research UnitU.S. Department of AgricultureAlbanyCAUnited States
- Department of BioengineeringUniversity of CaliforniaBerkeleyCAUnited States
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12
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Esmaili F, Pourmirzaei M, Ramazi S, Shojaeilangari S, Yavari E. A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1266-1285. [PMID: 37863385 PMCID: PMC11082408 DOI: 10.1016/j.gpb.2023.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 01/16/2023] [Accepted: 03/23/2023] [Indexed: 10/22/2023]
Abstract
Post-translational modifications (PTMs) have key roles in extending the functional diversity of proteins and, as a result, regulating diverse cellular processes in prokaryotic and eukaryotic organisms. Phosphorylation modification is a vital PTM that occurs in most proteins and plays a significant role in many biological processes. Disorders in the phosphorylation process lead to multiple diseases, including neurological disorders and cancers. The purpose of this review is to organize this body of knowledge associated with phosphorylation site (p-site) prediction to facilitate future research in this field. At first, we comprehensively review all related databases and introduce all steps regarding dataset creation, data preprocessing, and method evaluation in p-site prediction. Next, we investigate p-site prediction methods, which are divided into two computational groups: algorithmic and machine learning (ML). Additionally, it is shown that there are basically two main approaches for p-site prediction by ML: conventional and end-to-end deep learning methods, both of which are given an overview. Moreover, this review introduces the most important feature extraction techniques, which have mostly been used in p-site prediction. Finally, we create three test sets from new proteins related to the released version of the database of protein post-translational modifications (dbPTM) in 2022 based on general and human species. Evaluating online p-site prediction tools on newly added proteins introduced in the dbPTM 2022 release, distinct from those in the dbPTM 2019 release, reveals their limitations. In other words, the actual performance of these online p-site prediction tools on unseen proteins is notably lower than the results reported in their respective research papers.
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Affiliation(s)
- Farzaneh Esmaili
- Department of Information Technology, Tarbiat Modares University, Tehran 14115-111, Iran
| | - Mahdi Pourmirzaei
- Department of Information Technology, Tarbiat Modares University, Tehran 14115-111, Iran
| | - Shahin Ramazi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-111, Iran.
| | - Seyedehsamaneh Shojaeilangari
- Biomedical Engineering Group, Department of Electrical Engineering and Information Technology, Iranian Research Organization for Science and Technology (IROST), Tehran 33535-111, Iran
| | - Elham Yavari
- Department of Information Technology, Tarbiat Modares University, Tehran 14115-111, Iran
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13
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Uversky VN. Functional unfoldomics: Roles of intrinsic disorder in protein (multi)functionality. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:179-210. [PMID: 38220424 DOI: 10.1016/bs.apcsb.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Intrinsically disordered proteins (IDPs), which are functional proteins without stable tertiary structure, and hybrid proteins containing ordered domains and intrinsically disordered regions (IDRs) constitute prominent parts of all proteomes collectively known as unfoldomes. IDPs/IDRs exist as highly dynamic structural ensembles of rapidly interconverting conformations and are characterized by the exceptional structural heterogeneity, where their different parts are (dis)ordered to different degree, and their overall structure represents a complex mosaic of foldons, inducible foldons, inducible morphing foldons, non-foldons, semifoldons, and even unfoldons. Despite their lack of unique 3D structures, IDPs/IDRs play crucial roles in the control of various biological processes and the regulation of different cellular pathways and are commonly involved in recognition and signaling, indicating that the disorder-based functional repertoire is complementary to the functions of ordered proteins. Furthermore, IDPs/IDRs are frequently multifunctional, and this multifunctionality is defined by their structural flexibility and heterogeneity. Intrinsic disorder phenomenon is at the roots of the structure-function continuum model, where the structure continuum is defined by the presence of differently (dis)ordered regions, and the function continuum arises from the ability of all these differently (dis)ordered parts to have different functions. In their everyday life, IDPs/IDRs utilize a broad spectrum of interaction mechanisms thereby acting as interaction specialists. They are crucial for the biogenesis of numerous proteinaceous membrane-less organelles driven by the liquid-liquid phase separation. This review introduces functional unfoldomics by representing some aspects of the intrinsic disorder-based functionality.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.
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14
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Yoshida Y, Nishiyama A, Suameitria Dewi DNS, Yamazaki T, Yokoyama A, Kobayashi D, Kondo H, Ozeki Y, Matsumoto S. Limited proteolysis of mycobacterial DNA-binding protein 1 with an extended, lysine-rich, intrinsically disordered region to unveil posttranslational modifications. Biochem Biophys Res Commun 2023; 681:111-119. [PMID: 37774568 DOI: 10.1016/j.bbrc.2023.09.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/13/2023] [Accepted: 09/13/2023] [Indexed: 10/01/2023]
Abstract
The basic, intrinsically disordered regions of eukaryotic histones and their bacterial counterparts are presumed to act as signaling hubs to regulate the compaction of chromosomes or nucleoids and various DNA processes such as gene expression, recombination, and DNA replication. Posttranslational modifications (PTMs) on these regions are pivotal in regulating chromosomal or nucleoid compaction and DNA processes. However, the low sequence complexity and the presence of short lysine-rich repeats in the regions have hindered the accurate determination of types and locations of PTMs using conventional proteomic procedures. We described a limited proteolysis protocol using trypsin to analyze PTMs on mycobacterial DNA-binding protein 1 (MDP1), a nucleoid-associated protein in mycobacterial species that possesses an extended, lysine-rich, intrinsically disordered region in its C-terminal domain. This limited proteolysis approach successfully revealed significant methylation on many lysine residues in the C-terminal domain of MDP1 purified from Mycobacterium tuberculosis, which was lacking in the corresponding region of recombinant MDP1 expressed in Escherichia coli.
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Affiliation(s)
- Yutaka Yoshida
- Department of Bacteriology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan.
| | - Akihito Nishiyama
- Department of Bacteriology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
| | - Desak Nyoman Surya Suameitria Dewi
- Department of Bacteriology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
| | - Tomoya Yamazaki
- Department of Bacteriology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
| | - Akira Yokoyama
- Department of Bacteriology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
| | - Daiki Kobayashi
- Omics Unit, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
| | - Hitoshi Kondo
- Department of Bacteriology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
| | - Yuriko Ozeki
- Department of Bacteriology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
| | - Sohkichi Matsumoto
- Department of Bacteriology, Niigata University Graduate School of Medical and Dental Sciences, 1-757 Asahimachi-Dori, Chuo-Ku, Niigata, 951-8510, Japan
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15
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Kaufmann C, Wutz A. IndiSPENsable for X Chromosome Inactivation and Gene Silencing. EPIGENOMES 2023; 7:28. [PMID: 37987303 PMCID: PMC10660550 DOI: 10.3390/epigenomes7040028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
For about 30 years, SPEN has been the subject of research in many different fields due to its variety of functions and its conservation throughout a wide spectrum of species, like worms, arthropods, and vertebrates. To date, 216 orthologues have been documented. SPEN had been studied for its role in gene regulation in the context of cell signaling, including the NOTCH or nuclear hormone receptor signaling pathways. More recently, SPEN has been identified as a major regulator of initiation of chromosome-wide gene silencing during X chromosome inactivation (XCI) in mammals, where its function remains to be fully understood. Dependent on the biological context, SPEN functions via mechanisms which include different domains. While some domains of SPEN are highly conserved in sequence and secondary structure, species-to-species differences exist that might lead to mechanistic differences. Initiation of XCI appears to be different between humans and mice, which raises additional questions about the extent of generalization of SPEN's function in XCI. In this review, we dissect the mechanism of SPEN in XCI. We discuss its subregions and domains, focusing on its role as a major regulator. We further highlight species-related research, specifically of mouse and human SPEN, with the aim to reveal and clarify potential species-to-species differences in SPEN's function.
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Affiliation(s)
| | - Anton Wutz
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology ETH Hönggerberg, 8093 Zurich, Switzerland;
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16
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Manyilov VD, Ilyinsky NS, Nesterov SV, Saqr BMGA, Dayhoff GW, Zinovev EV, Matrenok SS, Fonin AV, Kuznetsova IM, Turoverov KK, Ivanovich V, Uversky VN. Chaotic aging: intrinsically disordered proteins in aging-related processes. Cell Mol Life Sci 2023; 80:269. [PMID: 37634152 PMCID: PMC11073068 DOI: 10.1007/s00018-023-04897-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 07/03/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023]
Abstract
The development of aging is associated with the disruption of key cellular processes manifested as well-established hallmarks of aging. Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) have no stable tertiary structure that provide them a power to be configurable hubs in signaling cascades and regulate many processes, potentially including those related to aging. There is a need to clarify the roles of IDPs/IDRs in aging. The dataset of 1702 aging-related proteins was collected from established aging databases and experimental studies. There is a noticeable presence of IDPs/IDRs, accounting for about 36% of the aging-related dataset, which is however less than the disorder content of the whole human proteome (about 40%). A Gene Ontology analysis of the used here aging proteome reveals an abundance of IDPs/IDRs in one-third of aging-associated processes, especially in genome regulation. Signaling pathways associated with aging also contain IDPs/IDRs on different hierarchical levels, revealing the importance of "structure-function continuum" in aging. Protein-protein interaction network analysis showed that IDPs present in different clusters associated with different aging hallmarks. Protein cluster with IDPs enrichment has simultaneously high liquid-liquid phase separation (LLPS) probability, "nuclear" localization and DNA-associated functions, related to aging hallmarks: genomic instability, telomere attrition, epigenetic alterations, and stem cells exhaustion. Intrinsic disorder, LLPS, and aggregation propensity should be considered as features that could be markers of pathogenic proteins. Overall, our analyses indicate that IDPs/IDRs play significant roles in aging-associated processes, particularly in the regulation of DNA functioning. IDP aggregation, which can lead to loss of function and toxicity, could be critically harmful to the cell. A structure-based analysis of aging and the identification of proteins that are particularly susceptible to disturbances can enhance our understanding of the molecular mechanisms of aging and open up new avenues for slowing it down.
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Affiliation(s)
- Vladimir D Manyilov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, Dolgoprudny, 141700, Russia
| | - Nikolay S Ilyinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, Dolgoprudny, 141700, Russia.
| | - Semen V Nesterov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, Dolgoprudny, 141700, Russia
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, 194064, Russia
| | - Baraa M G A Saqr
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, Dolgoprudny, 141700, Russia
| | - Guy W Dayhoff
- Department of Chemistry, University of South Florida, Tampa, FL, USA
| | - Egor V Zinovev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, Dolgoprudny, 141700, Russia
| | - Simon S Matrenok
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, Dolgoprudny, 141700, Russia
| | - Alexander V Fonin
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, 194064, Russia
| | - Irina M Kuznetsova
- Institute of Cytology, Russian Academy of Sciences, Saint Petersburg, 194064, Russia
| | | | - Valentin Ivanovich
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, Dolgoprudny, 141700, Russia
| | - Vladimir N Uversky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy Pereulok, 9, Dolgoprudny, 141700, Russia.
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL, 33612, USA.
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17
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Taylor Gonzalez DJ, Djulbegovic M, Antonietti M, Cordova M, Dayhoff GW, Mattes R, Galor A, Uversky VN, Karp CL. Intrinsic Disorder in the Human Tear Proteome. Invest Ophthalmol Vis Sci 2023; 64:14. [PMID: 37561450 PMCID: PMC10424804 DOI: 10.1167/iovs.64.11.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/30/2023] [Indexed: 08/11/2023] Open
Abstract
Purpose We aimed to characterize the proteome of human tears and assess for the presence of intrinsically disordered proteins (IDPs). IDPs, despite lacking a rigid three-dimensional structure, maintain biological functionality and could shed light on the molecular interactions within tears. Methods We analyzed a dataset of 1475 proteins identified in the tear film of three healthy subjects. We employed several computational tools, including the Compositional Profiler, Rapid Intrinsic Disorder Analysis Online, Search Tool for the Retrieval of Interacting Genes, and Database of Disordered Protein Predictors to evaluate the intrinsic disorder, protein interactions, and functional characterization of the disordered regions within this proteome. Results Our analysis showed a notable inclination toward intrinsic disorder. Two out of 10 order-promoting residues and five out of 10 disorder-promoting residues were found enriched. Using the Predictor of Natural Disordered Regions (PONDR) VSL2 output, 95% of these proteins were classified as highly or moderately disordered. We revealed an extensive protein-protein interaction network with significant interaction enrichment. The most disordered proteins exhibited higher disorder binding sites and diverse posttranslational modifications compared to the most ordered ones. Conclusions To the best of our knowledge, our study is the first comprehensive analysis of intrinsic disorder in the human tear film proteome, and it revealed an abundance of IDPs and their role in protein function and interaction networks. These findings suggest that variations in the intrinsic disorder of a tear film could be impacted by systemic and ocular conditions, offering promising avenues for disease biomarker identification and drug target development. Further research is needed to understand the implications of these findings in human health and disease.
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Affiliation(s)
| | - Mak Djulbegovic
- Bascom Palmer Eye Institute, University of Miami, Miami, Florida, United States
| | - Michael Antonietti
- Bascom Palmer Eye Institute, University of Miami, Miami, Florida, United States
| | - Matthew Cordova
- Bascom Palmer Eye Institute, University of Miami, Miami, Florida, United States
| | - Guy W. Dayhoff
- Department of Chemistry, University of South Florida, Tampa, Florida, United States
| | - Robby Mattes
- Bascom Palmer Eye Institute, University of Miami, Miami, Florida, United States
| | - Anat Galor
- Bascom Palmer Eye Institute, University of Miami, Miami, Florida, United States
- Ophthalmology, Miami Veterans Affairs Medical Center, Miami, Florida, United States
- Research Services, Miami Veterans Affairs Medical Center, Miami, Florida, United States
| | - Vladimir N. Uversky
- Molecular Medicine and USF Health Byrd Alzheimer's Center and Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, United States
| | - Carol L. Karp
- Bascom Palmer Eye Institute, University of Miami, Miami, Florida, United States
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18
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Záhonová K, Low RS, Warren CJ, Cantoni D, Herman EK, Yiangou L, Ribeiro CA, Phanprasert Y, Brown IR, Rueckert S, Baker NL, Tachezy J, Betts EL, Gentekaki E, van der Giezen M, Clark CG, Jackson AP, Dacks JB, Tsaousis AD. Evolutionary analysis of cellular reduction and anaerobicity in the hyper-prevalent gut microbe Blastocystis. Curr Biol 2023:S0960-9822(23)00620-6. [PMID: 37267944 DOI: 10.1016/j.cub.2023.05.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 03/22/2023] [Accepted: 05/11/2023] [Indexed: 06/04/2023]
Abstract
Blastocystis is the most prevalent microbial eukaryote in the human and animal gut, yet its role as commensal or parasite is still under debate. Blastocystis has clearly undergone evolutionary adaptation to the gut environment and possesses minimal cellular compartmentalization, reduced anaerobic mitochondria, no flagella, and no reported peroxisomes. To address this poorly understood evolutionary transition, we have taken a multi-disciplinary approach to characterize Proteromonas lacertae, the closest canonical stramenopile relative of Blastocystis. Genomic data reveal an abundance of unique genes in P. lacertae but also reductive evolution of the genomic complement in Blastocystis. Comparative genomic analysis sheds light on flagellar evolution, including 37 new candidate components implicated with mastigonemes, the stramenopile morphological hallmark. The P. lacertae membrane-trafficking system (MTS) complement is only slightly more canonical than that of Blastocystis, but notably, we identified that both organisms encode the complete enigmatic endocytic TSET complex, a first for the entire stramenopile lineage. Investigation also details the modulation of mitochondrial composition and metabolism in both P. lacertae and Blastocystis. Unexpectedly, we identify in P. lacertae the most reduced peroxisome-derived organelle reported to date, which leads us to speculate on a mechanism of constraint guiding the dynamics of peroxisome-mitochondrion reductive evolution on the path to anaerobiosis. Overall, these analyses provide a launching point to investigate organellar evolution and reveal in detail the evolutionary path that Blastocystis has taken from a canonical flagellated protist to the hyper-divergent and hyper-prevalent animal and human gut microbe.
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Affiliation(s)
- Kristína Záhonová
- Division of Infectious Diseases, Department of Medicine, University of Alberta, 1-124 Clinical Sciences Building, 11350-83 Avenue, Edmonton T6G 2G3, Canada; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, České Budějovice (Budweis) 370 05, Czech Republic; Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, Vestec 252 50, Czech Republic; Life Science Research Centre, Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, Ostrava 710 00, Czech Republic
| | - Ross S Low
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Christopher J Warren
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Diego Cantoni
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Emily K Herman
- Division of Infectious Diseases, Department of Medicine, University of Alberta, 1-124 Clinical Sciences Building, 11350-83 Avenue, Edmonton T6G 2G3, Canada; Department of Agricultural, Food, and Nutritional Science, Faculty of Agricultural, Life, and Environmental Sciences, University of Alberta, 2-31 General Services Building, Edmonton, AB T6G 2H1, Canada
| | - Lyto Yiangou
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Cláudia A Ribeiro
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Yasinee Phanprasert
- Division of Infectious Diseases, Department of Medicine, University of Alberta, 1-124 Clinical Sciences Building, 11350-83 Avenue, Edmonton T6G 2G3, Canada; School of Science, Mae Fah Luang Universit, 333 Moo 1, T. Tasud, Muang District, Chiang Rai 57100, Thailand
| | - Ian R Brown
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Sonja Rueckert
- School of Applied Sciences, Sighthill Campus, Room 3.B.36, Edinburgh EH11 4BN, Scotland; Faculty of Biology, AG Eukaryotische Mikrobiologie, Universitätsstrasse 5, S05 R04 H83, Essen 45141, Germany
| | - Nicola L Baker
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, Vestec 252 50, Czech Republic
| | - Emma L Betts
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK; School of Applied Sciences, Sighthill Campus, Room 3.B.36, Edinburgh EH11 4BN, Scotland
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang Universit, 333 Moo 1, T. Tasud, Muang District, Chiang Rai 57100, Thailand; Gut Microbiome Research Group, Mae Fah Luang University, 333 Moo 1, T. Tasud, Muang District, Chiang Rai 57100, Thailand
| | - Mark van der Giezen
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger Richard Johnsens Gate 4, 4021 Stavanger, Norway; Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - C Graham Clark
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Andrew P Jackson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine, University of Alberta, 1-124 Clinical Sciences Building, 11350-83 Avenue, Edmonton T6G 2G3, Canada; Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, České Budějovice (Budweis) 370 05, Czech Republic; Centre for Life's Origin and Evolution, Division of Biosciences, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK.
| | - Anastasios D Tsaousis
- Laboratory of Molecular & Evolutionary Parasitology, RAPID Group, School of Biosciences, University of Kent, Giles Lane, Stacey Building, Canterbury, Kent CT2 7NJ, UK.
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19
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An JP, Zhang XW, Li HL, Wang DR, You CX, Han Y. The E3 ubiquitin ligases SINA1 and SINA2 integrate with the protein kinase CIPK20 to regulate the stability of RGL2a, a positive regulator of anthocyanin biosynthesis. THE NEW PHYTOLOGIST 2023. [PMID: 37235698 DOI: 10.1111/nph.18997] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023]
Abstract
Although DELLA protein destabilization mediated by post-translational modifications is essential for gibberellin (GA) signal transduction and GA-regulated anthocyanin biosynthesis, the related mechanisms remain largely unknown. In this study, we report the ubiquitination and phosphorylation of an apple DELLA protein MdRGL2a in response to GA signaling and its regulatory role in anthocyanin biosynthesis. MdRGL2a could interact with MdWRKY75 to enhance the MdWRKY75-activated transcription of anthocyanin activator MdMYB1 and interfere with the interaction between anthocyanin repressor MdMYB308 and MdbHLH3 or MdbHLH33, thereby promoting anthocyanin accumulation. A protein kinase MdCIPK20 was found to phosphorylate and protect MdRGL2a from degradation, and it was essential for MdRGL2a-promoting anthocyanin accumulation. However, MdRGL2a and MdCIPK20 were ubiquitinated and degraded by E3 ubiquitin ligases MdSINA1 and MdSINA2, respectively, both of which were activated in the presence of GA. Our results display the integration of SINA1/2 with CIPK20 to dynamically regulate GA signaling and will be helpful toward understanding the mechanism of GA signal transduction and GA-inhibited anthocyanin biosynthesis. The discovery of extensive interactions between DELLA and SINA and CIPK proteins in apple will provide reference for the study of ubiquitination and phosphorylation of DELLA proteins in other species.
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Affiliation(s)
- Jian-Ping An
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Xiao-Wei Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Hong-Liang Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Da-Ru Wang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Chun-Xiang You
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Yuepeng Han
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Hubei Hongshan Laboratory, The Innovative Academy of Seed Design of Chinese Academy of Sciences, Wuhan, 430074, China
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20
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Heng J, Hu Y, Pérez-Hernández G, Inoue A, Zhao J, Ma X, Sun X, Kawakami K, Ikuta T, Ding J, Yang Y, Zhang L, Peng S, Niu X, Li H, Guixà-González R, Jin C, Hildebrand PW, Chen C, Kobilka BK. Function and dynamics of the intrinsically disordered carboxyl terminus of β2 adrenergic receptor. Nat Commun 2023; 14:2005. [PMID: 37037825 PMCID: PMC10085991 DOI: 10.1038/s41467-023-37233-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 03/07/2023] [Indexed: 04/12/2023] Open
Abstract
Advances in structural biology have provided important mechanistic insights into signaling by the transmembrane core of G-protein coupled receptors (GPCRs); however, much less is known about intrinsically disordered regions such as the carboxyl terminus (CT), which is highly flexible and not visible in GPCR structures. The β2 adrenergic receptor's (β2AR) 71 amino acid CT is a substrate for GPCR kinases and binds β-arrestins to regulate signaling. Here we show that the β2AR CT directly inhibits basal and agonist-stimulated signaling in cell lines lacking β-arrestins. Combining single-molecule fluorescence resonance energy transfer (FRET), NMR spectroscopy, and molecular dynamics simulations, we reveal that the negatively charged β2AR-CT serves as an autoinhibitory factor via interacting with the positively charged cytoplasmic surface of the receptor to limit access to G-proteins. The stability of this interaction is influenced by agonists and allosteric modulators, emphasizing that the CT plays important role in allosterically regulating GPCR activation.
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Affiliation(s)
- Jie Heng
- School of Medicine, Tsinghua University, Beijing, 100084, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yunfei Hu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Science, Wuhan, 430071, China
| | - Guillermo Pérez-Hernández
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Charitéplatz 1, 10117, Berlin, Germany
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, 980-8578, Japan
| | - Jiawei Zhao
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiuyan Ma
- School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Xiaoou Sun
- School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Kouki Kawakami
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, 980-8578, Japan
| | - Tatsuya Ikuta
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, 980-8578, Japan
| | - Jienv Ding
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- College of Life Sciences, Peking University, Beijing, 100871, China
| | - Yujie Yang
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Lujia Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Sijia Peng
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaogang Niu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Hongwei Li
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Ramon Guixà-González
- Condensed Matter Theory Group, Paul Scherrer Institute, CH-5232, Villigen, PSI, Switzerland
| | - Changwen Jin
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Peter W Hildebrand
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Charitéplatz 1, 10117, Berlin, Germany
- Institute of Medical Physics and Biophysics, University Leipzig, 04107, Leipzig, Germany
- Berlin Institute of Health, 10178, Berlin, Germany
| | - Chunlai Chen
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.
- Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
- School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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21
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Sharma E, Bhatnagar A, Bhaskar A, Majee SM, Kieffer M, Kepinski S, Khurana P, Khurana JP. Stress-induced F-Box protein-coding gene OsFBX257 modulates drought stress adaptations and ABA responses in rice. PLANT, CELL & ENVIRONMENT 2023; 46:1207-1231. [PMID: 36404527 DOI: 10.1111/pce.14496] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 10/15/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
F-box (FB) proteins that form part of SKP1-CUL1-F-box (SCF) type of E3 ubiquitin ligases are important components of plant growth and development. Here we characterized OsFBX257, a rice FB protein-coding gene that is differentially expressed under drought conditions and other abiotic stresses. Population genomics analysis suggest that OsFBX257 shows high allelic diversity in aus accessions and has been under positive selection in some japonica, aromatic and indica cultivars. Interestingly, allelic variation at OsFBX257 in aus cultivar Nagina22 is associated with an alternatively spliced transcript. Conserved among land plants, OsFBX257 is a component of the SCF complex, can form homomers and interact molecularly with the 14-3-3 rice proteins GF14b and GF14c. OsFBX257 is co-expressed in a network involving protein kinases and phosphatases. We show that OsFBX257 can bind the kinases OsCDPK1 and OsSAPK2, and that its phosphorylation can be reversed by phosphatase OsPP2C08. OsFBX257 expression level modulates root architecture and drought stress tolerance in rice. OsFBX257 knockdown (OsFBX257KD ) lines show reduced total root length and depth, crown root number, panicle size and survival under stress. In contrast, its overexpression (OsFBX257OE ) increases root depth, leaf and grain length, number of panicles, and grain yield in rice. OsFBX257 is a promising breeding target for alleviating drought stress-induced damage in rice.
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Affiliation(s)
- Eshan Sharma
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Akanksha Bhatnagar
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Avantika Bhaskar
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Susmita M Majee
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Martin Kieffer
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Stefan Kepinski
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Global Food and Environment Institute, University of Leeds, Leeds, UK
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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22
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Ding WJ, Li XH, Tang CM, Yang XC, Sun Y, Song YP, Ling MY, Yan R, Gao HQ, Zhang WH, Yu N, Feng JC, Zhang Z, Xing YQ. Quantification and Proteomic Characterization of β-Hydroxybutyrylation Modification in the Hearts of AMPKα2 Knockout Mice. Mol Cell Proteomics 2023; 22:100494. [PMID: 36621768 PMCID: PMC9941199 DOI: 10.1016/j.mcpro.2023.100494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 01/07/2023] Open
Abstract
AMP-activated protein kinase alpha 2 (AMPKα2) regulates energy metabolism, protein synthesis, and glucolipid metabolism myocardial cells. Ketone bodies produced by fatty acid β-oxidation, especially β-hydroxybutyrate, are fatty energy-supplying substances for the heart, brain, and other organs during fasting and long-term exercise. They also regulate metabolic signaling for multiple cellular functions. Lysine β-hydroxybutyrylation (Kbhb) is a β-hydroxybutyrate-mediated protein posttranslational modification. Histone Kbhb has been identified in yeast, mouse, and human cells. However, whether AMPK regulates protein Kbhb is yet unclear. Hence, the present study explored the changes in proteomics and Kbhb modification omics in the hearts of AMPKα2 knockout mice using a comprehensive quantitative proteomic analysis. Based on mass spectrometry (LC-MS/MS) analysis, the number of 1181 Kbhb modified sites in 455 proteins were quantified between AMPKα2 knockout mice and wildtype mice; 244 Kbhb sites in 142 proteins decreased or increased after AMPKα2 knockout (fold change >1.5 or <1/1.5, p < 0.05). The regulation of Kbhb sites in 26 key enzymes of fatty acid degradation and tricarboxylic acid cycle was noted in AMPKα2 knockout mouse cardiomyocytes. These findings, for the first time, identified proteomic features and Kbhb modification of cardiomyocytes after AMPKα2 knockout, suggesting that AMPKα2 regulates energy metabolism by modifying protein Kbhb.
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Affiliation(s)
- Wen-Jing Ding
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, China; Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital of Shandong University, Jinan, China
| | - Xue-Hui Li
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, China; Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital of Shandong University, Jinan, China
| | - Cong-Min Tang
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, China; Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital of Shandong University, Jinan, China
| | - Xue-Chun Yang
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, China; Institute of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, China
| | - Yan Sun
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Yi-Ping Song
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, China; Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital of Shandong University, Jinan, China
| | - Ming-Ying Ling
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, China; Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital of Shandong University, Jinan, China; Institute of Basic Medical Sciences, Qilu Hospital of Shandong University, Jinan, China
| | - Rong Yan
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, China
| | - Hai-Qing Gao
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, China; Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital of Shandong University, Jinan, China
| | - Wen-Hua Zhang
- Division of Bacterial Anti-tumor Drugs, Shandong Precision Medicine Engineering Laboratory, Shandong Xinchuang Biotechnology Co., LTD, Jinan, Shandong, China
| | - Na Yu
- Division of Bacterial Anti-tumor Drugs, Shandong Precision Medicine Engineering Laboratory, Shandong Xinchuang Biotechnology Co., LTD, Jinan, Shandong, China
| | - Jun-Chao Feng
- Division of Bacterial Anti-tumor Drugs, Shandong Precision Medicine Engineering Laboratory, Shandong Xinchuang Biotechnology Co., LTD, Jinan, Shandong, China
| | - Zhen Zhang
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, China; Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital of Shandong University, Jinan, China.
| | - Yan-Qiu Xing
- Department of Geriatric Medicine, Qilu Hospital of Shandong University, Jinan, China; Key Laboratory of Cardiovascular Proteomics of Shandong Province, Qilu Hospital of Shandong University, Jinan, China.
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23
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Anand PP, Shibu Vardhanan Y. Molecular cloning, expression, mRNA secondary structure and immunological characterization of mussel foot proteins (Mfps) (Mollusca: Bivalvia). J Biomol Struct Dyn 2023; 41:12242-12266. [PMID: 36688334 DOI: 10.1080/07391102.2023.2166996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 01/01/2023] [Indexed: 01/24/2023]
Abstract
The macroscale production of mussel foot proteins (Mfps) in the expression system has not succeeded to date. The principal reasons for this are low levels of expression and yield of Mfps, lack of post-translational modifications (PTMs), and immunological toxic effects on the host system. Identification of post-translational modification sites, suitable expression hosts, and immunological responses through an experimental approach is very costly and time-consuming. However, in the present study, in silico post-translation modification, antigenicity, allergenicity, and the immunological reaction of all available Mfps were characterized. Furthermore, all Mfps were codon optimized in three different expression systems to determine the best expression host. Finally, we performed the in-silico cloning of all codon-optimized Mfps in a suitable host (E. coli K12, pET28a(+) vector) and analyzed the secondary structure of mRNA and its structural stability. Among the 78 Mfps, six fps are considered potential allergenic proteins, six fps are considered non-allergenic proteins, and all other fps are probably allergenic. High antigenicity was observed in bacterial cells as compared to yeast and tumor cells. Nevertheless, the predicted expression of Mfps in a bacterial host is higher than in other expression hosts. Important to note that all Mfps showed significant immunological activity in the human system, and we concluded that these antigenic, allergenic, and immunological properties are directly correlated with their amino acid composition. The study's major goal is to provide a comprehensive understanding of Mfps and aid in the future genetic engineering and expression of Mfps and its diverse applications in different fields.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- P P Anand
- Biochemistry & Toxicology Division, Department of Zoology, University of Calicut, Thenhipalam, Kerala, India
| | - Y Shibu Vardhanan
- Biochemistry & Toxicology Division, Department of Zoology, University of Calicut, Thenhipalam, Kerala, India
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24
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Biological soft matter: intrinsically disordered proteins in liquid-liquid phase separation and biomolecular condensates. Essays Biochem 2022; 66:831-847. [PMID: 36350034 DOI: 10.1042/ebc20220052] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/10/2022]
Abstract
The facts that many proteins with crucial biological functions do not have unique structures and that many biological processes are compartmentalized into the liquid-like biomolecular condensates, which are formed via liquid-liquid phase separation (LLPS) and are not surrounded by the membrane, are revolutionizing the modern biology. These phenomena are interlinked, as the presence of intrinsic disorder represents an important requirement for a protein to undergo LLPS that drives biogenesis of numerous membrane-less organelles (MLOs). Therefore, one can consider these phenomena as crucial constituents of a new IDP-LLPS-MLO field. Furthermore, intrinsically disordered proteins (IDPs), LLPS, and MLOs represent a clear link between molecular and cellular biology and soft matter and condensed soft matter physics. Both IDP and LLPS/MLO fields are undergoing explosive development and generate the ever-increasing mountain of crucial data. These new data provide answers to so many long-standing questions that it is difficult to imagine that in the very recent past, protein scientists and cellular biologists operated without taking these revolutionary concepts into account. The goal of this essay is not to deliver a comprehensive review of the IDP-LLPS-MLO field but to provide a brief and rather subjective outline of some of the recent developments in these exciting fields.
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25
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Post-Translational Modification of ZEB Family Members in Cancer Progression. Int J Mol Sci 2022; 23:ijms232315127. [PMID: 36499447 PMCID: PMC9737314 DOI: 10.3390/ijms232315127] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
Post-translational modification (PTM), the essential regulatory mechanisms of proteins, play essential roles in physiological and pathological processes. In addition, PTM functions in tumour development and progression. Zinc finger E-box binding homeobox (ZEB) family homeodomain transcription factors, such as ZEB1 and ZEB2, play a pivotal role in tumour progression and metastasis by induction epithelial-mesenchymal transition (EMT), with activation of stem cell traits, immune evasion and epigenetic reprogramming. However, the relationship between ZEB family members' post-translational modification (PTM) and tumourigenesis remains largely unknown. Therefore, we focussed on the PTM of ZEBs and potential therapeutic approaches in cancer progression. This review provides an overview of the diverse functions of ZEBs in cancer and the mechanisms and therapeutic implications that target ZEB family members' PTMs.
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26
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Irfan M, Iqbal T, Hashmi S, Ghani U, Bhatti A. Insilico prediction and functional analysis of nonsynonymous SNPs in human CTLA4 gene. Sci Rep 2022; 12:20441. [PMID: 36443461 PMCID: PMC9705290 DOI: 10.1038/s41598-022-24699-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
The CTLA4 receptor is an immune checkpoint involved in the downregulation of T cells. Polymorphisms in this gene have been found to be associated with different diseases like rheumatoid arthritis, autosomal dominant immune dysregulation syndrome, juvenile idiopathic arthritis and autoimmune Addison's disease. Therefore, the identification of polymorphisms that have an effect on the structure and function of CTLA4 gene is important. Here we identified the most damaging missense or non-synonymous SNPs (nsSNPs) that might be crucial for the structure and function of CTLA4 using different bioinformatics tools. These in silico tools included SIFT, PROVEAN, PhD-SNP, PolyPhen-2 followed by MutPred2, I-Mutant 2.0 and ConSurf. The protein structures were predicted using Phyre2 and I-TASSER, while the gene-gene interactions were predicted by GeneMANIA and STRING. Our study identified three damaging missense SNPs rs1553657429, rs1559591863 and rs778534474 in coding region of CTLA4 gene. Among these SNPs the rs1553657429 showed a loss of potential phosphorylation site and was found to be highly conserved. The prediction of gene-gene interaction showed the interaction of CTlA4 with other genes and its importance in different pathways. This investigation of damaging nsSNPs can be considered in future while studying CTLA4 related diseases and can be of great importance in precision medicine.
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Affiliation(s)
- Muhammad Irfan
- grid.412117.00000 0001 2234 2376Healthcare Biotechnology, National University of Science and Technology, Islamabad H-12, 44000 Pakistan
| | - Talha Iqbal
- grid.412117.00000 0001 2234 2376Healthcare Biotechnology, National University of Science and Technology, Islamabad H-12, 44000 Pakistan
| | - Sakina Hashmi
- grid.412117.00000 0001 2234 2376Healthcare Biotechnology, National University of Science and Technology, Islamabad H-12, 44000 Pakistan
| | - Uzma Ghani
- grid.412117.00000 0001 2234 2376Healthcare Biotechnology, National University of Science and Technology, Islamabad H-12, 44000 Pakistan
| | - Attya Bhatti
- grid.412117.00000 0001 2234 2376Healthcare Biotechnology, National University of Science and Technology, Islamabad H-12, 44000 Pakistan
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27
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Usher ET, Showalter SA. Biophysical insights into glucose-dependent transcriptional regulation by PDX1. J Biol Chem 2022; 298:102623. [PMID: 36272648 PMCID: PMC9691942 DOI: 10.1016/j.jbc.2022.102623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/22/2022] Open
Abstract
The pancreatic and duodenal homeobox 1 (PDX1) is a central regulator of glucose-dependent transcription of insulin in pancreatic β cells. PDX1 transcription factor activity is integral to the development and sustained health of the pancreas; accordingly, deciphering the complex network of cellular cues that lead to PDX1 activation or inactivation is an important step toward understanding the etiopathologies of pancreatic diseases and the development of novel therapeutics. Despite nearly 3 decades of research into PDX1 control of Insulin expression, the molecular mechanisms that dictate the function of PDX1 in response to glucose are still elusive. The transcriptional activation functions of PDX1 are regulated, in part, by its two intrinsically disordered regions, which pose a barrier to its structural and biophysical characterization. Indeed, many studies of PDX1 interactions, clinical mutations, and posttranslational modifications lack molecular level detail. Emerging methods for the quantitative study of intrinsically disordered regions and refined models for transactivation now enable us to validate and interrogate the biochemical and biophysical features of PDX1 that dictate its function. The goal of this review is to summarize existing PDX1 studies and, further, to generate a comprehensive resource for future studies of transcriptional control via PDX1.
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Affiliation(s)
- Emery T Usher
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Scott A Showalter
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA.
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28
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Djulbegovic MB, Taylor DJ, Uversky VN, Galor A, Shields CL, Karp CL. Intrinsic Disorder in BAP1 and Its Association with Uveal Melanoma. Genes (Basel) 2022; 13:1703. [PMID: 36292588 PMCID: PMC9601668 DOI: 10.3390/genes13101703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Specific subvariants of uveal melanoma (UM) are associated with increased rates of metastasis compared to other subvariants. BRCA1 (BReast CAncer gene 1)-associated protein-1 (BAP1) is encoded by a gene that has been linked to aggressive behavior in UM. Methods: We evaluated BAP1 for the presence of intrinsically disordered protein regions (IDPRs) and its protein−protein interactions (PPI). We evaluated specific sequence-based features of the BAP1 protein using a set of bioinformatic databases, predictors, and algorithms. Results: We show that BAP1’s structure contains extensive IDPRs as it is highly enriched in proline residues (the most disordered amino acid; p-value < 0.05), the average percent of predicted disordered residues (PPDR) was 57.34%, and contains 9 disorder-based binding sites (ie. molecular recognition features (MoRFs)). BAP1’s intrinsic disorder allows it to engage in a complex PPI network with at least 49 partners (p-value < 1.0 × 10−16). Conclusion: These findings show that BAP1 contains IDPRs and an intricate PPI network. Mutations in UM that are associated with the BAP1 gene may alter the function of the IDPRs embedded into its structure. These findings develop the understanding of UM and may provide a target for potential novel therapies to treat this aggressive neoplasm.
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Affiliation(s)
| | - David J. Taylor
- Bascom Palmer Eye Institute, University of Miami, Miami, FL 33136, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33613, USA
| | - Anat Galor
- Bascom Palmer Eye Institute, University of Miami, Miami, FL 33136, USA
- Ophthalmology, Miami Veterans Affairs Medical Center, Miami, FL 33136, USA
- Research Services, Miami Veterans Affairs Medical Center, Miami, FL 33136, USA
| | - Carol L. Shields
- Ocular Oncology Service, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Carol L. Karp
- Bascom Palmer Eye Institute, University of Miami, Miami, FL 33136, USA
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29
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Romero-Ramirez A, Casas-Sánchez A, Autheman D, Duffy CW, Brandt C, Clare S, Harcourt K, André MR, de Almeida Castilho Neto KJG, Teixeira MMG, Machado RZ, Coombes J, Flynn RJ, Wright GJ, Jackson AP. Vivaxin genes encode highly immunogenic, non-variant antigens on the Trypanosoma vivax cell-surface. PLoS Negl Trop Dis 2022; 16:e0010791. [PMID: 36129968 PMCID: PMC9529106 DOI: 10.1371/journal.pntd.0010791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 10/03/2022] [Accepted: 09/06/2022] [Indexed: 12/02/2022] Open
Abstract
Trypanosoma vivax is a unicellular hemoparasite, and a principal cause of animal African trypanosomiasis (AAT), a vector-borne and potentially fatal livestock disease across sub-Saharan Africa. Previously, we identified diverse T. vivax-specific genes that were predicted to encode cell surface proteins. Here, we examine the immune responses of naturally and experimentally infected hosts to these unique parasite antigens, to identify immunogens that could become vaccine candidates. Immunoprofiling of host serum shows that one particular family (Fam34) elicits a consistent IgG antibody response. This gene family, which we now call Vivaxin, encodes at least 124 transmembrane glycoproteins that display quite distinct expression profiles and patterns of genetic variation. We focused on one gene (viv-β8) that encodes one particularly immunogenic vivaxin protein and which is highly expressed during infections but displays minimal polymorphism across the parasite population. Vaccination of mice with VIVβ8 adjuvanted with Quil-A elicits a strong, balanced immune response and delays parasite proliferation in some animals but, ultimately, it does not prevent disease. Although VIVβ8 is localized across the cell body and flagellar membrane, live immunostaining indicates that VIVβ8 is largely inaccessible to antibody in vivo. However, our phylogenetic analysis shows that vivaxin includes other antigens shown recently to induce immunity against T. vivax. Thus, the introduction of vivaxin represents an important advance in our understanding of the T. vivax cell surface. Besides being a source of proven and promising vaccine antigens, the gene family is clearly an important component of the parasite glycocalyx, with potential to influence host-parasite interactions. Animal African trypanosomiasis (AAT) is an important livestock disease throughout sub-Saharan Africa and beyond. AAT is caused by Trypanosoma vivax, among other species, a unicellular parasite that is spread by biting tsetse flies and multiplies in the bloodstream and other tissues, leading to often fatal neurological conditions if untreated. Although concerted drug treatment and vector eradication programmes have succeeded in controlling Human African trypanosomiasis, AAT continues to adversely affect animal health and impede efficient food production and economic development in many less-developed countries. In this study, we attempted to identify parasite surface proteins that stimulated the strongest immune responses in naturally infected animals, as the basis for a vaccine. We describe the discovery of a new, species-specific protein family in T. vivax, which we call vivaxin. We show that one vivaxin protein (VIVβ8) is surface expressed and retards parasite proliferation when used to immunize mice, but does not prevent infection. Nevertheless, we also reveal that vivaxin includes another protein previously shown to induce protective immunity (IFX/VIVβ1). Besides its great potential for novel approaches to AAT control, the vivaxin family is revealed as a significant component of the T. vivax cell surface and may have important, species-specific roles in host interactions.
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Affiliation(s)
- Alessandra Romero-Ramirez
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Aitor Casas-Sánchez
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Delphine Autheman
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Craig W. Duffy
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Cordelia Brandt
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Simon Clare
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Katherine Harcourt
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Marcos Rogério André
- Department of Pathology, Reproduction and One Health, Faculty of Agrarian and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, Sao Paulo, Brazil
| | - Kayo José Garcia de Almeida Castilho Neto
- Department of Pathology, Reproduction and One Health, Faculty of Agrarian and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, Sao Paulo, Brazil
| | - Marta M. G. Teixeira
- Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Sao Paulo, Brazil
| | - Rosangela Zacharias Machado
- Department of Pathology, Reproduction and One Health, Faculty of Agrarian and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, Sao Paulo, Brazil
| | - Janine Coombes
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- School of Pharmacy and Life Sciences, The Robert Gordon University, Aberdeen, United Kingdom
| | - Robin J. Flynn
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Waterford Institute of Technology, Waterford, Ireland
| | - Gavin J. Wright
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, United Kingdom
| | - Andrew P. Jackson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- * E-mail:
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30
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DeGiosio RA, Grubisha MJ, MacDonald ML, McKinney BC, Camacho CJ, Sweet RA. More than a marker: potential pathogenic functions of MAP2. Front Mol Neurosci 2022; 15:974890. [PMID: 36187353 PMCID: PMC9525131 DOI: 10.3389/fnmol.2022.974890] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/29/2022] [Indexed: 12/27/2022] Open
Abstract
Microtubule-associated protein 2 (MAP2) is the predominant cytoskeletal regulator within neuronal dendrites, abundant and specific enough to serve as a robust somatodendritic marker. It influences microtubule dynamics and microtubule/actin interactions to control neurite outgrowth and synaptic functions, similarly to the closely related MAP Tau. Though pathology of Tau has been well appreciated in the context of neurodegenerative disorders, the consequences of pathologically dysregulated MAP2 have been little explored, despite alterations in its immunoreactivity, expression, splicing and/or stability being observed in a variety of neurodegenerative and neuropsychiatric disorders including Huntington’s disease, prion disease, schizophrenia, autism, major depression and bipolar disorder. Here we review the understood structure and functions of MAP2, including in neurite outgrowth, synaptic plasticity, and regulation of protein folding/transport. We also describe known and potential mechanisms by which MAP2 can be regulated via post-translational modification. Then, we assess existing evidence of its dysregulation in various brain disorders, including from immunohistochemical and (phospho) proteomic data. We propose pathways by which MAP2 pathology could contribute to endophenotypes which characterize these disorders, giving rise to the concept of a “MAP2opathy”—a series of disorders characterized by alterations in MAP2 function.
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Affiliation(s)
- Rebecca A. DeGiosio
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, United States
| | - Melanie J. Grubisha
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, United States
| | - Matthew L. MacDonald
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, United States
| | - Brandon C. McKinney
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, United States
| | - Carlos J. Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Robert A. Sweet
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, United States
- *Correspondence: Robert A. Sweet
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31
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Deepak Shyl ES, Malgija B, Iniyan AM, Vincent SGP. Mutation in
MCL1
predicted loop to helix structural transition stabilizes
MCL1–Bax
binding interaction favoring cancer cell survival. Proteins 2022; 90:1699-1713. [DOI: 10.1002/prot.26347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/14/2022] [Accepted: 03/27/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Eby‐nesar Stella‐glory Deepak Shyl
- International Centre for Nanobiotechnology (ICN), Centre for Marine Science and Technology (CMST) Manonmaniam Sundaranar University Kanyakumari Tamil Nadu India
| | - Beutline Malgija
- Computational Science Laboratory, MCC‐MRF Innovation Park Madras Christian College Chennai Tamil Nadu India
| | - Appadurai Muthamil Iniyan
- International Centre for Nanobiotechnology (ICN), Centre for Marine Science and Technology (CMST) Manonmaniam Sundaranar University Kanyakumari Tamil Nadu India
- York Bioscience Private Limited Ambattur Industrial Estate Chennai Tamil Nadu India
| | - Samuel Gnana Prakash Vincent
- International Centre for Nanobiotechnology (ICN), Centre for Marine Science and Technology (CMST) Manonmaniam Sundaranar University Kanyakumari Tamil Nadu India
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32
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Akter M, Khan SF, Sajib AA, Rima FS. A comprehensive in silico analysis of the deleterious nonsynonymous SNPs of human FOXP2 protein. PLoS One 2022; 17:e0272625. [PMID: 35944036 PMCID: PMC9362936 DOI: 10.1371/journal.pone.0272625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/11/2022] [Indexed: 11/19/2022] Open
Abstract
FOXP2 encodes the forkhead transcription factor that plays a significant role in language development. Single nucleotide polymorphisms in FOXP2 have been linked to speech- language disorder, autism, cancer and schizophrenia. So, scrutinizing the functional SNPs to better understand their association in disease is an uphill task. The purpose of the current study was to identify the missense SNPs which have detrimental structural and functional effects on the FOXP2 protein. Multiple computational tools were employed to investigate the deleterious role of non-synonymous SNPs. Five variants as Y531H, L558P, R536G and R553C were found to be associated with diseases and located at the forkhead domain of the FOXP2 protein. Molecular docking analysis of FOXP2 DNA binding domain with its most common target sequence 5’-CAAATT-3’ predicted that R553C and L558P mutant variants destabilize protein structure by changing protein-DNA interface interactions and disruption of hydrogen bonds that may reduce the specificity and affinity of the binding. Further experimental investigations may need to verify whether this kind of structural and functional variations dysregulate protein activities and induce formation of disease.
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Affiliation(s)
- Mahmuda Akter
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, Bangladesh
| | - Sumaiya Farah Khan
- Department of Genetic Engineering and Biotechnology, Jagannath University, Dhaka, Bangladesh
| | - Abu Ashfaqur Sajib
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Fahmida Sultana Rima
- Department of Biochemistry and Biotechnology, University of Barishal, Barishal, Bangladesh
- * E-mail:
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33
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Redwan EM, Aljadawi AA, Uversky VN. Hepatitis C Virus Infection and Intrinsic Disorder in the Signaling Pathways Induced by Toll-Like Receptors. BIOLOGY 2022; 11:1091. [PMID: 36101469 PMCID: PMC9312352 DOI: 10.3390/biology11071091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/07/2022] [Accepted: 07/19/2022] [Indexed: 11/23/2022]
Abstract
In this study, we examined the interplay between protein intrinsic disorder, hepatitis C virus (HCV) infection, and signaling pathways induced by Toll-like receptors (TLRs). To this end, 10 HCV proteins, 10 human TLRs, and 41 proteins from the TLR-induced downstream pathways were considered from the prevalence of intrinsic disorder. Mapping of the intrinsic disorder to the HCV-TLR interactome and to the TLR-based pathways of human innate immune response to the HCV infection demonstrates that substantial levels of intrinsic disorder are characteristic for proteins involved in the regulation and execution of these innate immunity pathways and in HCV-TLR interaction. Disordered regions, being commonly enriched in sites of various posttranslational modifications, may play important functional roles by promoting protein-protein interactions and support the binding of the analyzed proteins to other partners such as nucleic acids. It seems that this system represents an important illustration of the role of intrinsic disorder in virus-host warfare.
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Affiliation(s)
- Elrashdy M. Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (E.M.R.); (A.A.A.)
- Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, New Borg EL-Arab, Alexandria 21934, Egypt
| | - Abdullah A. Aljadawi
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (E.M.R.); (A.A.A.)
| | - Vladimir N. Uversky
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia; (E.M.R.); (A.A.A.)
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
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34
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Ahmad HI, Ijaz N, Afzal G, Asif AR, ur Rehman A, Rahman A, Ahmed I, Yousaf M, Elokil A, Muhammad SA, Albogami SM, Alotaibi SS. Computational Insights into the Structural and Functional Impacts of nsSNPs of Bone Morphogenetic Proteins. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4013729. [PMID: 35832847 PMCID: PMC9273450 DOI: 10.1155/2022/4013729] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 06/15/2022] [Indexed: 12/12/2022]
Abstract
BMPs (bone morphogenetic proteins) are multipurpose (transforming growth factor)TGF-superfamily released cytokines. These glycoproteins, acting as disulfide-linked homo- or heterodimers, are highly potent regulators of bone and cartilage production and repair, cell proliferation throughout embryonic development, and bone homeostasis in the adults. Due to the fact that genetic variation might influence structural functions, this study is aimed to determine the pathogenic effect of nonsynonymous single-nucleotide polymorphisms (nsSNPs) in BMP genes. The implications of these variations, investigated using computational analysis and molecular models of the mature TGF-β domain, revealed the impact of modifications on the function of BMP protein. The three-dimensional (3D) structure analysis was performed on the nsSNP Y316S, V386G, E387G, C389G, and C391G nsSNP in the TGF-β domain of chicken BMP2 and H344P, S347P, V357A nsSNP in the TGF-β domain of chicken BMP4 protein that was anticipated to be harmful and of high risk. The ability of the proteins to perform variety of tasks interact with other molecules depends on their tertiary structural composition. The current analysis revealed the four most damaging variants (Y316S, V386G, E387G, C389G, and C391G), highly conserved and functional and are located in the TGF-beta domain of BMP2 and BMP4. The amino acid substitutions E387G, C389G, and C391G are discovered in the binding region. It was observed that the mutations in the TGF-beta domain caused significant changes in its structural organization including the substrate binding sites. Current findings will assist future research focused on the role of these variants in BMP function loss and their role in skeletal disorders, and this will possibly help to develop practical strategies for treating bone-related conditions.
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Affiliation(s)
- Hafiz Ishfaq Ahmad
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Nabeel Ijaz
- Department of Clinical Science, Faculty of Veterinary Sciences, Bahauddin Zakariya University Multan, Pakistan
| | - Gulnaz Afzal
- Department of Zoology, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Akhtar Rasool Asif
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan, China
- University of Veterinary and Animal Sciences, Lahore, Sub-Campus Jhang, Pakistan
| | - Aziz ur Rehman
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Huazhong Agricultural University, Wuhan, China
- University of Veterinary and Animal Sciences, Lahore, Sub-Campus Jhang, Pakistan
| | - Abdur Rahman
- University of Veterinary and Animal Sciences, Lahore, Sub-Campus Jhang, Pakistan
- Department of Animal Nutrition, Afyon Kocatepe University, Turkey
| | - Irfan Ahmed
- Department of Animal Nutrition, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Pakistan
| | - Muhammad Yousaf
- Department of Animal Nutrition, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Pakistan
| | - Abdelmotaleb Elokil
- Department of Animal Production, Faculty of Agriculture, Benha University, Moshtohor 13736, Egypt
| | - Sayyed Aun Muhammad
- University of Veterinary and Animal Sciences, Lahore, Sub-Campus Jhang, Pakistan
| | - Sarah M. Albogami
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Saqer S. Alotaibi
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
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35
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Zhou X, Sumrow L, Tashiro K, Sutherland L, Liu D, Qin T, Kato M, Liszczak G, McKnight SL. Mutations linked to neurological disease enhance self-association of low-complexity protein sequences. Science 2022; 377:eabn5582. [PMID: 35771920 PMCID: PMC9610444 DOI: 10.1126/science.abn5582] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protein domains of low sequence complexity do not fold into stable, three-dimensional structures. Nevertheless, proteins with these sequences assist in many aspects of cell organization, including assembly of nuclear and cytoplasmic structures not surrounded by membranes. The dynamic nature of these cellular assemblies is caused by the ability of low-complexity domains (LCDs) to transiently self-associate through labile, cross-β structures. Mechanistic studies useful for the study of LCD self-association have evolved over the past decade in the form of simple assays of phase separation. Here, we have used such assays to demonstrate that the interactions responsible for LCD self-association can be dictated by labile protein structures poised close to equilibrium between the folded and unfolded states. Furthermore, missense mutations causing Charcot-Marie-Tooth disease, frontotemporal dementia, and Alzheimer's disease manifest their pathophysiology in vitro and in cultured cell systems by enhancing the stability of otherwise labile molecular structures formed upon LCD self-association.
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36
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Intrinsically disordered proteins and proteins with intrinsically disordered regions in neurodegenerative diseases. Biophys Rev 2022; 14:679-707. [DOI: 10.1007/s12551-022-00968-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 05/28/2022] [Indexed: 12/14/2022] Open
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37
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Theater in the Self-Cleaning Cell: Intrinsically Disordered Proteins or Protein Regions Acting with Membranes in Autophagy. MEMBRANES 2022; 12:membranes12050457. [PMID: 35629783 PMCID: PMC9143426 DOI: 10.3390/membranes12050457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 12/30/2022]
Abstract
Intrinsically disordered proteins and protein regions (IDPs/IDPRs) are mainly involved in signaling pathways, where fast regulation, temporal interactions, promiscuous interactions, and assemblies of structurally diverse components including membranes are essential. The autophagy pathway builds, de novo, a membrane organelle, the autophagosome, using carefully orchestrated interactions between proteins and lipid bilayers. Here, we discuss molecular mechanisms related to the protein disorder-based interactions of the autophagy machinery with membranes. We describe not only membrane binding phenomenon, but also examples of membrane remodeling processes including membrane tethering, bending, curvature sensing, and/or fragmentation of membrane organelles such as the endoplasmic reticulum, which is an important membrane source as well as cargo for autophagy. Summary of the current state of knowledge presented here will hopefully inspire new studies. A profound understanding of the autophagic protein–membrane interface is essential for advancements in therapeutic interventions against major human diseases, in which autophagy is involved including neurodegeneration, cancer as well as cardiovascular, metabolic, infectious, musculoskeletal, and other disorders.
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38
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Monahan RC, van den Beukel MD, Borggreven NV, Fronczek R, Huizinga TWJ, Kloppenburg M, Steup-Beekman GM, Trouw LA. Autoantibodies against specific post-translationally modified proteins are present in patients with lupus and associate with major neuropsychiatric manifestations. RMD Open 2022; 8:rmdopen-2021-002079. [PMID: 35450955 PMCID: PMC9024229 DOI: 10.1136/rmdopen-2021-002079] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/27/2022] [Indexed: 11/08/2022] Open
Abstract
Background Although autoantibodies are an important hallmark of systemic lupus erythematosus (SLE), most are not specific for SLE or any of its clinical manifestations. Autoantibodies against post-translationally modified (PTM) proteins have been studied extensively in rheumatoid arthritis and associate with disease progression. While PTMs have also been detected in patients with SLE, studies on anti-PTM antibodies remain scarce. We studied the presence of anti-PTM antibodies in SLE and neuropsychiatric SLE (NPSLE), a manifestation that lacks serological markers. Methods IgG antibody responses against six PTMs (malondialdehyde–acetaldehyde adducts (MAA), advanced glycation end-products (AGE), carbamylation (CarP), citrullination, acetylation and nitration) were tested using ELISA in sera of 349 patients with SLE (mean age 44±13 years; 87% female) and compared with 108 healthy controls. Levels and positivity were correlated with clinical features and SLE manifestations. Results Anti-MAA, anti-AGE and anti-CarP antibodies were more prevalent in SLE compared with controls (MAA: 29% vs 3%, AGE: 18% vs 4%, CarP: 14% vs 5%, all p≤0.0001). Anti-MAA and anti-AGE antibodies correlated with clinical manifestations and serological inflammatory markers. Patients with major NPSLE showed higher positivity of anti-MAA (39% vs 24%, p=0.01) and anti-CarP antibodies (20% vs 11%, p=0.04) than patients without major NPSLE. In addition, anti-PTM antibody levels correlated with brain volumes, an objective measure of nervous system involvement. Conclusions In our NPSLE cohort, a subset of patients with SLE have anti-PTM antibodies against MAA, AGE and CarP modified proteins. Interestingly, anti-MAA and anti-CarP were more prevalent in NPSLE, a manifestation for which no biomarkers exist.
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Affiliation(s)
- Rory C Monahan
- Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Rolf Fronczek
- Neurology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom W J Huizinga
- Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Margreet Kloppenburg
- Rheumatology, Leiden University Medical Center, Leiden, The Netherlands.,Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Gerda M Steup-Beekman
- Rheumatology, Leiden University Medical Center, Leiden, The Netherlands.,Rheumatology, Haaglanden Medical Center, The Hague, The Netherlands
| | - Leendert A Trouw
- Immunology, Leiden University Medical Center, Leiden, The Netherlands
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39
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Antifeeva IA, Fonin AV, Fefilova AS, Stepanenko OV, Povarova OI, Silonov SA, Kuznetsova IM, Uversky VN, Turoverov KK. Liquid-liquid phase separation as an organizing principle of intracellular space: overview of the evolution of the cell compartmentalization concept. Cell Mol Life Sci 2022; 79:251. [PMID: 35445278 PMCID: PMC11073196 DOI: 10.1007/s00018-022-04276-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/24/2022] [Accepted: 03/27/2022] [Indexed: 12/14/2022]
Abstract
At the turn of the twenty-first century, fundamental changes took place in the understanding of the structure and function of proteins and then in the appreciation of the intracellular space organization. A rather mechanistic model of the organization of living matter, where the function of proteins is determined by their rigid globular structure, and the intracellular processes occur in rigidly determined compartments, was replaced by an idea that highly dynamic and multifunctional "soft matter" lies at the heart of all living things. According this "new view", the most important role in the spatio-temporal organization of the intracellular space is played by liquid-liquid phase transitions of biopolymers. These self-organizing cellular compartments are open dynamic systems existing at the edge of chaos. They are characterized by the exceptional structural and compositional dynamics, and their multicomponent nature and polyfunctionality provide means for the finely tuned regulation of various intracellular processes. Changes in the external conditions can cause a disruption of the biogenesis of these cellular bodies leading to the irreversible aggregation of their constituent proteins, followed by the transition to a gel-like state and the emergence of amyloid fibrils. This work represents a historical overview of changes in our understanding of the intracellular space compartmentalization. It also reflects methodological breakthroughs that led to a change in paradigms in this area of science and discusses modern ideas about the organization of the intracellular space. It is emphasized here that the membrane-less organelles have to combine a certain resistance to the changes in their environment and, at the same time, show high sensitivity to the external signals, which ensures the normal functioning of the cell.
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Affiliation(s)
- Iuliia A Antifeeva
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Alexander V Fonin
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Anna S Fefilova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Olga I Povarova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Sergey A Silonov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL, 33612, USA.
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Av., 4, St. Petersburg, 194064, Russia.
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40
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England WE, Wang J, Chen S, Baldi P, Flynn RA, Spitale RC. An atlas of posttranslational modifications on RNA binding proteins. Nucleic Acids Res 2022; 50:4329-4339. [PMID: 35438783 PMCID: PMC9071496 DOI: 10.1093/nar/gkac243] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/24/2022] [Accepted: 04/15/2022] [Indexed: 12/13/2022] Open
Abstract
RNA structure and function are intimately tied to RNA binding protein recognition and regulation. Posttranslational modifications are chemical modifications which can control protein biology. The role of PTMs in the regulation RBPs is not well understood, in part due to a lacking analysis of PTM deposition on RBPs. Herein, we present an analysis of posttranslational modifications (PTMs) on RNA binding proteins (RBPs; a PTM RBP Atlas). We curate published datasets and primary literature to understand the landscape of PTMs and use protein-protein interaction data to understand and potentially provide a framework for understanding which enzymes are controlling PTM deposition and removal on the RBP landscape. Intersection of our data with The Cancer Genome Atlas also provides researchers understanding of mutations that would alter PTM deposition. Additional characterization of the RNA-protein interface provided from in-cell UV crosslinking experiments provides a framework for hypotheses about which PTMs could be regulating RNA binding and thus RBP function. Finally, we provide an online database for our data that is easy to use for the community. It is our hope our efforts will provide researchers will an invaluable tool to test the function of PTMs controlling RBP function and thus RNA biology.
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Affiliation(s)
- Whitney E England
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, CA, USA
| | - Jingtian Wang
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, CA, USA
| | - Siwei Chen
- School of Information and Computer Sciences, University of California, Irvine. Irvine, CA, USA
| | - Pierre Baldi
- School of Information and Computer Sciences, University of California, Irvine. Irvine, CA, USA
| | - Ryan A Flynn
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine. Irvine, CA, USA.,Department of Developmental and Cellular Biology, University of California, Irvine. Irvine, CA, USA.,Department of Chemistry, University of California, Irvine. Irvine, CA, USA
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41
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Aisenberg WH, McCray BA, Sullivan JM, Diehl E, DeVine LR, Alevy J, Bagnell AM, Carr P, Donohue JK, Goretzki B, Cole RN, Hellmich UA, Sumner CJ. Multiubiquitination of TRPV4 reduces channel activity independent of surface localization. J Biol Chem 2022; 298:101826. [PMID: 35300980 PMCID: PMC9010760 DOI: 10.1016/j.jbc.2022.101826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 02/19/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Ubiquitin (Ub)-mediated regulation of plasmalemmal ion channel activity canonically occurs via stimulation of endocytosis. Whether ubiquitination can modulate channel activity by alternative mechanisms remains unknown. Here, we show that the transient receptor potential vanilloid 4 (TRPV4) cation channel is multiubiquitinated within its cytosolic N-terminal and C-terminal intrinsically disordered regions (IDRs). Mutagenizing select lysine residues to block ubiquitination of the N-terminal but not C-terminal IDR resulted in a marked elevation of TRPV4-mediated intracellular calcium influx, without increasing cell surface expression levels. Conversely, enhancing TRPV4 ubiquitination via expression of an E3 Ub ligase reduced TRPV4 channel activity but did not decrease plasma membrane abundance. These results demonstrate Ub-dependent regulation of TRPV4 channel function independent of effects on plasma membrane localization. Consistent with ubiquitination playing a key negative modulatory role of the channel, gain-of-function neuropathy-causing mutations in the TRPV4 gene led to reduced channel ubiquitination in both cellular and Drosophila models of TRPV4 neuropathy, whereas increasing mutant TRPV4 ubiquitination partially suppressed channel overactivity. Together, these data reveal a novel mechanism via which ubiquitination of an intracellular flexible IDR domain modulates ion channel function independently of endocytic trafficking and identify a contributory role for this pathway in the dysregulation of TRPV4 channel activity by neuropathy-causing mutations.
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Affiliation(s)
- William H Aisenberg
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Brett A McCray
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jeremy M Sullivan
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Erika Diehl
- Department of Chemistry, Biochemistry Section, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Lauren R DeVine
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jonathan Alevy
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Anna M Bagnell
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Patrice Carr
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jack K Donohue
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Benedikt Goretzki
- Institute of Organic Chemistry and Macromolecular Chemistry, Cluster of Excellence 'Balance of the Microverse', Friedrich-Schiller-Universität, Jena, Germany; Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität, Frankfurt am Main, Germany
| | - Robert N Cole
- Institute of Organic Chemistry and Macromolecular Chemistry, Cluster of Excellence 'Balance of the Microverse', Friedrich-Schiller-Universität, Jena, Germany
| | - Ute A Hellmich
- Institute of Organic Chemistry and Macromolecular Chemistry, Cluster of Excellence 'Balance of the Microverse', Friedrich-Schiller-Universität, Jena, Germany; Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-Universität, Frankfurt am Main, Germany
| | - Charlotte J Sumner
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
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Fareed MM, Ullah S, Aziz S, Johnsen TA, Shityakov S. In-silico analysis of non-synonymous single nucleotide polymorphisms in human β-defensin type 1 gene reveals their impact on protein-ligand binding sites. Comput Biol Chem 2022; 98:107669. [DOI: 10.1016/j.compbiolchem.2022.107669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/18/2022] [Accepted: 03/19/2022] [Indexed: 01/11/2023]
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Bondos SE, Dunker AK, Uversky VN. Intrinsically disordered proteins play diverse roles in cell signaling. Cell Commun Signal 2022; 20:20. [PMID: 35177069 PMCID: PMC8851865 DOI: 10.1186/s12964-022-00821-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/11/2021] [Indexed: 11/29/2022] Open
Abstract
Abstract Signaling pathways allow cells to detect and respond to a wide variety of chemical (e.g. Ca2+ or chemokine proteins) and physical stimuli (e.g., sheer stress, light). Together, these pathways form an extensive communication network that regulates basic cell activities and coordinates the function of multiple cells or tissues. The process of cell signaling imposes many demands on the proteins that comprise these pathways, including the abilities to form active and inactive states, and to engage in multiple protein interactions. Furthermore, successful signaling often requires amplifying the signal, regulating or tuning the response to the signal, combining information sourced from multiple pathways, all while ensuring fidelity of the process. This sensitivity, adaptability, and tunability are possible, in part, due to the inclusion of intrinsically disordered regions in many proteins involved in cell signaling. The goal of this collection is to highlight the many roles of intrinsic disorder in cell signaling. Following an overview of resources that can be used to study intrinsically disordered proteins, this review highlights the critical role of intrinsically disordered proteins for signaling in widely diverse organisms (animals, plants, bacteria, fungi), in every category of cell signaling pathway (autocrine, juxtacrine, intracrine, paracrine, and endocrine) and at each stage (ligand, receptor, transducer, effector, terminator) in the cell signaling process. Thus, a cell signaling pathway cannot be fully described without understanding how intrinsically disordered protein regions contribute to its function. The ubiquitous presence of intrinsic disorder in different stages of diverse cell signaling pathways suggest that more mechanisms by which disorder modulates intra- and inter-cell signals remain to be discovered. Graphical abstract ![]()
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Affiliation(s)
- Sarah E Bondos
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX, 77843, USA.
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.,Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, Russia, 142290
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Tarapara B, Shah F. An in-silico analysis to identify structural, functional and regulatory role of SNPs in hMRE11. J Biomol Struct Dyn 2022; 41:2160-2174. [PMID: 35048780 DOI: 10.1080/07391102.2022.2028678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Meiotic recombination 11 (MRE11) is a component of the tri-molecular MRE11-RAD50-NBS1 (MRN) complex, which functions as an exonuclease and endonuclease which is involved in identifying, signalling, protecting and repairing double-strand breaks in DNA (DSBs). Ataxia-telangiectasia-like disorder (ATLD) 1 and Nijmegen breakage syndrome (NBS)-like disorder are MRE11 associated diseases. In the present study, we used an integrated computational approach to identify the most deleterious SNPs and their structural and functional impact on human MRE11. Five of the 68 observed non-synonymous SNP (nsSNPs; I162T, S273C, W210C, D311Y and R364L) should be worked on due to their strong possible pathogenicity and the risk of changing protein properties. All the nsSNPs were highly conserved and decrease the protein stability located in the MRE11 nuclease and MRE11 DNA binding presumed domain. R364L and I162T were predicted to be involved in post-translational modification (PTM) sites. Furthermore, we also analysed the regulatory effect of noncoding SNPs on MRE11 gene regulation in which 6 SNPs were found to affect gene regulation. All six noncoding SNPs predicted chromatin interactive site whereas only one SNP was noted its association with miRNA binding site which disrupts 5 miRNA conserved site. These findings help future studies to get more insights into the role of these variants in the alteration of the MRE11 function. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bhoomi Tarapara
- Department of Cancer Biology, Stem Cell Biology Lab, The Gujarat Cancer and Research Institute, Ahmedabad, India
| | - Franky Shah
- Department of Cancer Biology, Stem Cell Biology Lab, The Gujarat Cancer and Research Institute, Ahmedabad, India
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Wang C, Tan X, Tang D, Gou Y, Han C, Ning W, Lin S, Zhang W, Chen M, Peng D, Xue Y. GPS-Uber: a hybrid-learning framework for prediction of general and E3-specific lysine ubiquitination sites. Brief Bioinform 2022; 23:6509047. [PMID: 35037020 DOI: 10.1093/bib/bbab574] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 12/11/2021] [Accepted: 12/14/2021] [Indexed: 12/13/2022] Open
Abstract
As an important post-translational modification, lysine ubiquitination participates in numerous biological processes and is involved in human diseases, whereas the site specificity of ubiquitination is mainly decided by ubiquitin-protein ligases (E3s). Although numerous ubiquitination predictors have been developed, computational prediction of E3-specific ubiquitination sites is still a great challenge. Here, we carefully reviewed the existing tools for the prediction of general ubiquitination sites. Also, we developed a tool named GPS-Uber for the prediction of general and E3-specific ubiquitination sites. From the literature, we manually collected 1311 experimentally identified site-specific E3-substrate relations, which were classified into different clusters based on corresponding E3s at different levels. To predict general ubiquitination sites, we integrated 10 types of sequence and structure features, as well as three types of algorithms including penalized logistic regression, deep neural network and convolutional neural network. Compared with other existing tools, the general model in GPS-Uber exhibited a highly competitive accuracy, with an area under curve values of 0.7649. Then, transfer learning was adopted for each E3 cluster to construct E3-specific models, and in total 112 individual E3-specific predictors were implemented. Using GPS-Uber, we conducted a systematic prediction of human cancer-associated ubiquitination events, which could be helpful for further experimental consideration. GPS-Uber will be regularly updated, and its online service is free for academic research at http://gpsuber.biocuckoo.cn/.
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Affiliation(s)
- Chenwei Wang
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiaodan Tan
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Dachao Tang
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yujie Gou
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Cheng Han
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Wanshan Ning
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shaofeng Lin
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Weizhi Zhang
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Miaomiao Chen
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Di Peng
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yu Xue
- Department of Bioinformatics and Systems Biology, MOE Key Laboratory of Molecular Biophysics, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
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Maugars G, Mauvois X, Martin P, Aroua S, Rousseau K, Dufour S. New Insights Into the Evolution of Corticotropin-Releasing Hormone Family With a Special Focus on Teleosts. Front Endocrinol (Lausanne) 2022; 13:937218. [PMID: 35937826 PMCID: PMC9353778 DOI: 10.3389/fendo.2022.937218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 06/09/2022] [Indexed: 11/30/2022] Open
Abstract
Corticotropin-releasing hormone (CRH) was discovered for its role as a brain neurohormone controlling the corticotropic axis in vertebrates. An additional crh gene, crh2, paralog of crh (crh1), and likely resulting from the second round (2R) of vertebrate whole genome duplication (WGD), was identified in a holocephalan chondrichthyan, in basal mammals, various sauropsids and a non-teleost actinopterygian holostean. It was suggested that crh2 has been recurrently lost in some vertebrate groups including teleosts. We further investigated the fate of crh1 and crh2 in vertebrates with a special focus on teleosts. Phylogenetic and synteny analyses showed the presence of duplicated crh1 paralogs, crh1a and crh1b, in most teleosts, resulting from the teleost-specific WGD (3R). Crh1b is conserved in all teleosts studied, while crh1a has been lost independently in some species. Additional crh1 paralogs are present in carps and salmonids, resulting from specific WGD in these lineages. We identified crh2 gene in additional vertebrate groups such as chondrichthyan elasmobranchs, sarcopterygians including dipnoans and amphibians, and basal actinoperygians, Polypteridae and Chondrostei. We also revealed the presence of crh2 in teleosts, including elopomorphs, osteoglossomorphs, clupeiforms, and ostariophysians, while it would have been lost in Euteleostei along with some other groups. To get some insights on the functional evolution of the crh paralogs, we compared their primary and 3D structure, and by qPCR their tissue distribution, in two representative species, the European eel, which possesses three crh paralogs (crh1a, crh1b, crh2), and the Atlantic salmon, which possesses four crh paralogs of the crh1-type. All peptides conserved the structural characteristics of human CRH. Eel crh1b and both salmon crh1b genes were mainly expressed in the brain, supporting the major role of crh1b paralogs in controlling the corticotropic axis in teleosts. In contrast, crh1a paralogs were mainly expressed in peripheral tissues such as muscle and heart, in eel and salmon, reflecting a striking subfunctionalization between crh1a and b paralogs. Eel crh2 was weakly expressed in the brain and peripheral tissues. These results revisit the repertoire of crh in teleosts and highlight functional divergences that may have contributed to the differential conservation of various crh paralogs in teleosts.
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Affiliation(s)
- Gersende Maugars
- Muséum National d’Histoire Naturelle, Unité Mixte de Recherche Biologie des Organismes et Ecosystèmes Aquatiques (UMR BOREA), Biology of Aquatic Organisms and Ecosystems, Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Sorbonne Université, Paris, France
- Université Le Havre Normandie - Stress Environnementaux et Biosurveillance des milieux aquatiques UMR-I 02SEBIO -FR CNRS 3730 SCALE, Le Havre, France
- *Correspondence: Gersende Maugars,
| | - Xavier Mauvois
- Muséum National d’Histoire Naturelle, Unité Mixte de Recherche Biologie des Organismes et Ecosystèmes Aquatiques (UMR BOREA), Biology of Aquatic Organisms and Ecosystems, Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Sorbonne Université, Paris, France
| | - Patrick Martin
- Conservatoire National du Saumon Sauvage (CNSS), Chanteuges, France
| | - Salima Aroua
- Université Le Havre Normandie - Stress Environnementaux et Biosurveillance des milieux aquatiques UMR-I 02SEBIO -FR CNRS 3730 SCALE, Le Havre, France
| | - Karine Rousseau
- Muséum National d’Histoire Naturelle, Unité Mixte de Recherche Biologie des Organismes et Ecosystèmes Aquatiques (UMR BOREA), Biology of Aquatic Organisms and Ecosystems, Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Sorbonne Université, Paris, France
| | - Sylvie Dufour
- Muséum National d’Histoire Naturelle, Unité Mixte de Recherche Biologie des Organismes et Ecosystèmes Aquatiques (UMR BOREA), Biology of Aquatic Organisms and Ecosystems, Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Sorbonne Université, Paris, France
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Hassan SS, Lundstrom K, Serrano-Aroca Á, Adadi P, Aljabali AAA, Redwan EM, Lal A, Kandimalla R, El-Aziz TMA, Pal Choudhury P, Azad GK, Sherchan SP, Chauhan G, Tambuwala M, Takayama K, Barh D, Palu G, Basu P, Uversky VN. Emergence of unique SARS-CoV-2 ORF10 variants and their impact on protein structure and function. Int J Biol Macromol 2022; 194:128-143. [PMID: 34863825 PMCID: PMC8635690 DOI: 10.1016/j.ijbiomac.2021.11.151] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 02/07/2023]
Abstract
The devastating impact of the ongoing coronavirus disease 2019 (COVID-19) on public health, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has made targeting the COVID-19 pandemic a top priority in medical research and pharmaceutical development. Surveillance of SARS-CoV-2 mutations is essential for the comprehension of SARS-CoV-2 variant diversity and their impact on virulence and pathogenicity. The SARS-CoV-2 open reading frame 10 (ORF10) protein interacts with multiple human proteins CUL2, ELOB, ELOC, MAP7D1, PPT1, RBX1, THTPA, TIMM8B, and ZYG11B expressed in lung tissue. Mutations and co-occurring mutations in the emerging SARS-CoV-2 ORF10 variants are expected to impact the severity of the virus and its associated consequences. In this article, we highlight 128 single mutations and 35 co-occurring mutations in the unique SARS-CoV-2 ORF10 variants. The possible predicted effects of these mutations and co-occurring mutations on the secondary structure of ORF10 variants and host protein interactomes are presented. The findings highlight the possible effects of mutations and co-occurring mutations on the emerging 140 ORF10 unique variants from secondary structure and intrinsic protein disorder perspectives.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur 721140, West Bengal, India.
| | | | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigacion Traslacional San Alberto Magno, Universidad Catolica de Valencia San Vicente Martir, c/Guillem de Castro, 94, 46001 Valencia, Valencia, Spain.
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand
| | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University, Faculty of Pharmacy, Irbid 566, Jordan.
| | - Elrashdy M Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, New Borg EL-Arab 21934, Alexandria, Egypt.
| | - Amos Lal
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, Telangana, India; Department of Biocemistry, Kakatiya Medical College, Warangal, Telangana, India
| | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229-3900, USA; Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt.
| | - Pabitra Pal Choudhury
- Indian Statistical Institute, Applied Statistics Unit, 203 B T Road, Kolkata 700108, India.
| | | | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA, 70112, USA.
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, 64849 Monterrey, Nuevo Leon, Mexico.
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK.
| | - Kazuo Takayama
- Center for iPS Cell Research and Application, Kyoto University, Kyoto 6068507, Japan.
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur 721172, West Bengal, India; Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil.
| | - Giorgio Palu
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy.
| | - Pallab Basu
- School of Physics, University of the Witwatersrand, Johannesburg, Braamfontein 2000, 721140, South Africa.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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Alghamdi M, Alamry SA, Bahlas SM, Uversky VN, Redwan EM. Circulating extracellular vesicles and rheumatoid arthritis: a proteomic analysis. Cell Mol Life Sci 2021; 79:25. [PMID: 34971426 PMCID: PMC11072894 DOI: 10.1007/s00018-021-04020-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 12/14/2022]
Abstract
Circulating extracellular vesicles (EVs) are membrane-bound nanoparticles secreted by most cells for intracellular communication and transportation of biomolecules. EVs carry proteins, lipids, nucleic acids, and receptors that are involved in human physiology and pathology. EV cargo is variable and highly related to the type and state of the cellular origin. Three subtypes of EVs have been identified: exosomes, microvesicles, and apoptotic bodies. Exosomes are the smallest and the most well-studied class of EVs that regulate different biological processes and participate in several diseases, such as cancers and autoimmune diseases. Proteomic analysis of exosomes succeeded in profiling numerous types of proteins involved in disease development and prognosis. In rheumatoid arthritis (RA), exosomes revealed a potential function in joint inflammation. These EVs possess a unique function, as they can transfer specific autoantigens and mediators between distant cells. Current proteomic data demonstrated that exosomes could provide beneficial effects against autoimmunity and exert an immunosuppressive action, particularly in RA. Based on these observations, effective therapeutic strategies have been developed for arthritis and other inflammatory disorders.
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Affiliation(s)
- Mohammed Alghamdi
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia
- Laboratory Department, University Medical Services Center, King Abdulaziz University, P.O. Box 80200, Jeddah, 21589, Saudi Arabia
| | - Sultan Abdulmughni Alamry
- Immunology Diagnostic Laboratory Department, King Abdulaziz University Hospital, P.O Box 80215, Jeddah, 21589, Saudi Arabia
| | - Sami M Bahlas
- Department of Internal Medicine, Faculty of Medicine, King Abdulaziz University, P.O. Box 80215, Jeddah, 21589, Saudi Arabia
| | - Vladimir N Uversky
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Elrashdy M Redwan
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah, 21589, Saudi Arabia.
- Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, New Borg EL-Arab, 21934, Alexandria, Egypt.
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Kumari M, Pradhan UK, Joshi R, Punia A, Shankar R, Kumar R. In-depth assembly of organ and development dissected Picrorhiza kurroa proteome map using mass spectrometry. BMC PLANT BIOLOGY 2021; 21:604. [PMID: 34937558 PMCID: PMC8693493 DOI: 10.1186/s12870-021-03394-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Picrorhiza kurroa Royle ex Benth. being a rich source of phytochemicals, is a promising high altitude medicinal herb of Himalaya. The medicinal potential is attributed to picrosides i.e. iridoid glycosides, which synthesized in organ-specific manner through highly complex pathways. Here, we present a large-scale proteome reference map of P. kurroa, consisting of four morphologically differentiated organs and two developmental stages. RESULTS We were able to identify 5186 protein accessions (FDR < 1%) providing a deep coverage of protein abundance array, spanning around six orders of magnitude. Most of the identified proteins are associated with metabolic processes, response to abiotic stimuli and cellular processes. Organ specific sub-proteomes highlights organ specialized functions that would offer insights to explore tissue profile for specific protein classes. With reference to P. kurroa development, vegetative phase is enriched with growth related processes, however generative phase harvests more energy in secondary metabolic pathways. Furthermore, stress-responsive proteins, RNA binding proteins (RBPs) and post-translational modifications (PTMs), particularly phosphorylation and ADP-ribosylation play an important role in P. kurroa adaptation to alpine environment. The proteins involved in the synthesis of secondary metabolites are well represented in P. kurroa proteome. The phytochemical analysis revealed that marker compounds were highly accumulated in rhizome and overall, during the late stage of development. CONCLUSIONS This report represents first extensive proteomic description of organ and developmental dissected P. kurroa, providing a platform for future studies related to stress tolerance and medical applications.
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Affiliation(s)
- Manglesh Kumari
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Upendra Kumar Pradhan
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Studio of Computational Biology & Bioinformatics (Biotech Division), The Himalayan Centre for High-throughput Computational Biology (HiCHiCoB, A BIC Supported by DBT, India), CSIR-IHBT, Palampur, HP, 176061, India
- Present address: ICAR-Indian Agricultural Statistics Research Institute, Library Avenue, Pusa, New Delhi, Delhi, 110012, India
| | - Robin Joshi
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ashwani Punia
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ravi Shankar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Studio of Computational Biology & Bioinformatics (Biotech Division), The Himalayan Centre for High-throughput Computational Biology (HiCHiCoB, A BIC Supported by DBT, India), CSIR-IHBT, Palampur, HP, 176061, India
| | - Rajiv Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, 176061, HP, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Khan SM, Faisal ARM, Nila TA, Binti NN, Hosen MI, Shekhar HU. A computational in silico approach to predict high-risk coding and non-coding SNPs of human PLCG1 gene. PLoS One 2021; 16:e0260054. [PMID: 34793541 PMCID: PMC8601573 DOI: 10.1371/journal.pone.0260054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 10/31/2021] [Indexed: 11/28/2022] Open
Abstract
PLCG1 gene is responsible for many T-cell lymphoma subtypes, including peripheral T-cell lymphoma (PTCL), angioimmunoblastic T-cell lymphoma (AITL), cutaneous T-cell lymphoma (CTCL), adult T-cell leukemia/lymphoma along with other diseases. Missense mutations of this gene have already been found in patients of CTCL and AITL. The non-synonymous single nucleotide polymorphisms (nsSNPs) can alter the protein structure as well as its functions. In this study, probable deleterious and disease-related nsSNPs in PLCG1 were identified using SIFT, PROVEAN, PolyPhen-2, PhD-SNP, Pmut, and SNPS&GO tools. Further, their effect on protein stability was checked along with conservation and solvent accessibility analysis by I-mutant 2.0, MUpro, Consurf, and Netsurf 2.0 server. Some SNPs were finalized for structural analysis with PyMol and BIOVIA discovery studio visualizer. Out of the 16 nsSNPs which were found to be deleterious, ten nsSNPs had an effect on protein stability, and six mutations (L411P, R355C, G493D, R1158H, A401V and L455F) were predicted to be highly conserved. Among the six highly conserved mutations, four nsSNPs (R355C, A401V, L411P and L455F) were part of the catalytic domain. L411P, L455F and G493D made significant structural change in the protein structure. Two mutations-Y210C and R1158H had post-translational modification. In the 5' and 3' untranslated region, three SNPs, rs139043247, rs543804707, and rs62621919 showed possible miRNA target sites and DNA binding sites. This in silico analysis has provided a structured dataset of PLCG1 gene for further in vivo researches. With the limitation of computational study, it can still prove to be an asset for the identification and treatment of multiple diseases associated with the target gene.
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Affiliation(s)
- Safayat Mahmud Khan
- Department of Biochemistry and Molecular Biology, Clinical Biochemistry and Translational Medicine Laboratory, University of Dhaka, Dhaka, Bangladesh
| | - Ar-Rafi Md. Faisal
- Department of Biochemistry and Molecular Biology, Clinical Biochemistry and Translational Medicine Laboratory, University of Dhaka, Dhaka, Bangladesh
| | - Tasnin Akter Nila
- Department of Biochemistry and Molecular Biology, Clinical Biochemistry and Translational Medicine Laboratory, University of Dhaka, Dhaka, Bangladesh
| | - Nabila Nawar Binti
- Department of Biochemistry and Molecular Biology, Clinical Biochemistry and Translational Medicine Laboratory, University of Dhaka, Dhaka, Bangladesh
| | - Md. Ismail Hosen
- Department of Biochemistry and Molecular Biology, Clinical Biochemistry and Translational Medicine Laboratory, University of Dhaka, Dhaka, Bangladesh
| | - Hossain Uddin Shekhar
- Department of Biochemistry and Molecular Biology, Clinical Biochemistry and Translational Medicine Laboratory, University of Dhaka, Dhaka, Bangladesh
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