1
|
Aupič J, Pokorná P, Ruthstein S, Magistrato A. Predicting Conformational Ensembles of Intrinsically Disordered Proteins: From Molecular Dynamics to Machine Learning. J Phys Chem Lett 2024; 15:8177-8186. [PMID: 39093570 DOI: 10.1021/acs.jpclett.4c01544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Intrinsically disordered proteins and regions (IDP/IDRs) are ubiquitous across all domains of life. Characterized by a lack of a stable tertiary structure, IDP/IDRs populate a diverse set of transiently formed structural states that can promiscuously adapt upon binding with specific interaction partners and/or certain alterations in environmental conditions. This malleability is foundational for their role as tunable interaction hubs in core cellular processes such as signaling, transcription, and translation. Tracing the conformational ensemble of an IDP/IDR and its perturbation in response to regulatory cues is thus paramount for illuminating its function. However, the conformational heterogeneity of IDP/IDRs poses several challenges. Here, we review experimental and computational methods devised to disentangle the conformational landscape of IDP/IDRs, highlighting recent computational advances that permit proteome-wide scans of IDP/IDRs conformations. We briefly evaluate selected computational methods using the disordered N-terminal of the human copper transporter 1 as a test case and outline further challenges in IDP/IDRs ensemble prediction.
Collapse
Affiliation(s)
- Jana Aupič
- CNR-IOM at International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
| | - Pavlína Pokorná
- CNR-IOM at International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
| | - Sharon Ruthstein
- Department of Chemistry, Faculty of Exact Sciences and the Institute for Nanotechnology and Advanced Materials (BINA), Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Alessandra Magistrato
- CNR-IOM at International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
| |
Collapse
|
2
|
Zambo B, Edelweiss E, Morlet B, Negroni L, Pajkos M, Dosztanyi Z, Ostergaard S, Trave G, Laporte J, Gogl G. Uncovering the BIN1-SH3 interactome underpinning centronuclear myopathy. eLife 2024; 13:RP95397. [PMID: 38995680 PMCID: PMC11245310 DOI: 10.7554/elife.95397] [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: 07/13/2024] Open
Abstract
Truncation of the protein-protein interaction SH3 domain of the membrane remodeling Bridging Integrator 1 (BIN1, Amphiphysin 2) protein leads to centronuclear myopathy. Here, we assessed the impact of a set of naturally observed, previously uncharacterized BIN1 SH3 domain variants using conventional in vitro and cell-based assays monitoring the BIN1 interaction with dynamin 2 (DNM2) and identified potentially harmful ones that can be also tentatively connected to neuromuscular disorders. However, SH3 domains are typically promiscuous and it is expected that other, so far unknown partners of BIN1 exist besides DNM2, that also participate in the development of centronuclear myopathy. In order to shed light on these other relevant interaction partners and to get a holistic picture of the pathomechanism behind BIN1 SH3 domain variants, we used affinity interactomics. We identified hundreds of new BIN1 interaction partners proteome-wide, among which many appear to participate in cell division, suggesting a critical role of BIN1 in the regulation of mitosis. Finally, we show that the identified BIN1 mutations indeed cause proteome-wide affinity perturbation, signifying the importance of employing unbiased affinity interactomic approaches.
Collapse
Affiliation(s)
- Boglarka Zambo
- Equipe Labellisee Ligue 2015, Departement de Biologie Structurale Integrative, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France
| | - Evelina Edelweiss
- Institut de Genetique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Bastien Morlet
- Institut de Genetique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Luc Negroni
- Institut de Genetique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Matyas Pajkos
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Zsuzsanna Dosztanyi
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Soren Ostergaard
- Novo Nordisk A/S, Global Research Technologies, Novo Nordisk Research Park, Maaloev, Denmark
| | - Gilles Trave
- Equipe Labellisee Ligue 2015, Departement de Biologie Structurale Integrative, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France
| | - Jocelyn Laporte
- Institut de Genetique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, Illkirch, France
| | - Gergo Gogl
- Equipe Labellisee Ligue 2015, Departement de Biologie Structurale Integrative, Institut de Genetique et de Biologie Moleculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Universite de Strasbourg, Illkirch, France
| |
Collapse
|
3
|
Ghosh D, Biswas A, Radhakrishna M. Advanced computational approaches to understand protein aggregation. BIOPHYSICS REVIEWS 2024; 5:021302. [PMID: 38681860 PMCID: PMC11045254 DOI: 10.1063/5.0180691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/18/2024] [Indexed: 05/01/2024]
Abstract
Protein aggregation is a widespread phenomenon implicated in debilitating diseases like Alzheimer's, Parkinson's, and cataracts, presenting complex hurdles for the field of molecular biology. In this review, we explore the evolving realm of computational methods and bioinformatics tools that have revolutionized our comprehension of protein aggregation. Beginning with a discussion of the multifaceted challenges associated with understanding this process and emphasizing the critical need for precise predictive tools, we highlight how computational techniques have become indispensable for understanding protein aggregation. We focus on molecular simulations, notably molecular dynamics (MD) simulations, spanning from atomistic to coarse-grained levels, which have emerged as pivotal tools in unraveling the complex dynamics governing protein aggregation in diseases such as cataracts, Alzheimer's, and Parkinson's. MD simulations provide microscopic insights into protein interactions and the subtleties of aggregation pathways, with advanced techniques like replica exchange molecular dynamics, Metadynamics (MetaD), and umbrella sampling enhancing our understanding by probing intricate energy landscapes and transition states. We delve into specific applications of MD simulations, elucidating the chaperone mechanism underlying cataract formation using Markov state modeling and the intricate pathways and interactions driving the toxic aggregate formation in Alzheimer's and Parkinson's disease. Transitioning we highlight how computational techniques, including bioinformatics, sequence analysis, structural data, machine learning algorithms, and artificial intelligence have become indispensable for predicting protein aggregation propensity and locating aggregation-prone regions within protein sequences. Throughout our exploration, we underscore the symbiotic relationship between computational approaches and empirical data, which has paved the way for potential therapeutic strategies against protein aggregation-related diseases. In conclusion, this review offers a comprehensive overview of advanced computational methodologies and bioinformatics tools that have catalyzed breakthroughs in unraveling the molecular basis of protein aggregation, with significant implications for clinical interventions, standing at the intersection of computational biology and experimental research.
Collapse
Affiliation(s)
- Deepshikha Ghosh
- Department of Biological Sciences and Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
| | - Anushka Biswas
- Department of Chemical Engineering, Indian Institute of Technology (IIT) Gandhinagar, Palaj, Gujarat 382355, India
| | | |
Collapse
|
4
|
Luige J, Armaos A, Tartaglia GG, Ørom UAV. Predicting nuclear G-quadruplex RNA-binding proteins with roles in transcription and phase separation. Nat Commun 2024; 15:2585. [PMID: 38519458 PMCID: PMC10959947 DOI: 10.1038/s41467-024-46731-9] [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: 04/06/2023] [Accepted: 03/08/2024] [Indexed: 03/25/2024] Open
Abstract
RNA-binding proteins are central for many biological processes and their characterization has demonstrated a broad range of functions as well as a wide spectrum of target structures. RNA G-quadruplexes are important regulatory elements occurring in both coding and non-coding transcripts, yet our knowledge of their structure-based interactions is at present limited. Here, using theoretical predictions and experimental approaches, we show that many chromatin-binding proteins bind to RNA G-quadruplexes, and we classify them based on their RNA G-quadruplex-binding potential. Combining experimental identification of nuclear RNA G-quadruplex-binding proteins with computational approaches, we build a prediction tool that assigns probability score for a nuclear protein to bind RNA G-quadruplexes. We show that predicted G-quadruplex RNA-binding proteins exhibit a high degree of protein disorder and hydrophilicity and suggest involvement in both transcription and phase-separation into membrane-less organelles. Finally, we present the G4-Folded/UNfolded Nuclear Interaction Explorer System (G4-FUNNIES) for estimating RNA G4-binding propensities at http://service.tartaglialab.com/new_submission/G4FUNNIES .
Collapse
Affiliation(s)
- Johanna Luige
- RNA Biology and Innovation, Institute of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Alexandros Armaos
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy
| | - Gian Gaetano Tartaglia
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy.
- Catalan Institution for Research and Advanced Studies ICREA Passeig Lluis Companys, 23 08010, Barcelona, Spain.
| | - Ulf Andersson Vang Ørom
- RNA Biology and Innovation, Institute of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
| |
Collapse
|
5
|
Luebbert L, Hoang C, Kumar M, Pachter L. Fast and scalable querying of eukaryotic linear motifs with gget elm. Bioinformatics 2024; 40:btae095. [PMID: 38377393 PMCID: PMC10927331 DOI: 10.1093/bioinformatics/btae095] [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: 11/28/2023] [Revised: 01/31/2024] [Accepted: 02/18/2024] [Indexed: 02/22/2024] Open
Abstract
MOTIVATION Eukaryotic linear motifs (ELMs), or Short Linear Motifs, are protein interaction modules that play an essential role in cellular processes and signaling networks and are often involved in diseases like cancer. The ELM database is a collection of manually curated motif knowledge from scientific papers. It has become a crucial resource for investigating motif biology and recognizing candidate ELMs in novel amino acid sequences. Users can search amino acid sequences or UniProt Accessions on the ELM resource web interface. However, as with many web services, there are limitations in the swift processing of large-scale queries through the ELM web interface or API calls, and, therefore, integration into protein function analysis pipelines is limited. RESULTS To allow swift, large-scale motif analyses on protein sequences using ELMs curated in the ELM database, we have extended the gget suite of Python and command line tools with a new module, gget elm, which does not rely on the ELM server for efficiently finding candidate ELMs in user-submitted amino acid sequences and UniProt Accessions. gget elm increases accessibility to the information stored in the ELM database and allows scalable searches for motif-mediated interaction sites in the amino acid sequences. AVAILABILITY AND IMPLEMENTATION The manual and source code are available at https://github.com/pachterlab/gget.
Collapse
Affiliation(s)
- Laura Luebbert
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - Chi Hoang
- California Institute of Technology, Pasadena, CA 91125, United States
| | - Manjeet Kumar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125, United States
| |
Collapse
|
6
|
Mickael M, Łazarczyk M, Kubick N, Gurba A, Kocki T, Horbańczuk JO, Atanasov AG, Sacharczuk M, Religa P. FEZF2 and AIRE1: An Evolutionary Trade-off in the Elimination of Auto-reactive T Cells in the Thymus. J Mol Evol 2024; 92:72-86. [PMID: 38285197 DOI: 10.1007/s00239-024-10157-0] [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: 09/05/2023] [Accepted: 01/15/2024] [Indexed: 01/30/2024]
Abstract
Autoimmune Regulator 1 (AIRE1) and Forebrain Embryonic Zinc Finger-Like Protein 2 (FEZF2) play pivotal roles in orchestrating the expression of tissue-restricted antigens (TRA) to facilitate the elimination of autoreactive T cells. AIRE1's presence in the gonads of various vertebrates has raised questions about its potential involvement in gene expression control for germline cell selection. Nevertheless, the evolutionary history of these genes has remained enigmatic, as has the rationale behind their apparent redundancy in vertebrates. Furthermore, the origin of the elimination process itself has remained elusive. To shed light on these mysteries, we conducted a comprehensive evolutionary analysis employing a range of tools, including multiple sequence alignment, phylogenetic tree construction, ancestral sequence reconstruction, and positive selection assessment. Our investigations revealed intriguing insights. AIRE1 homologs emerged during the divergence of T cells in higher vertebrates, signifying its role in this context. Conversely, FEZF2 exhibited multiple homologs spanning invertebrates, lampreys, and higher vertebrates. Ancestral sequence reconstruction demonstrated distinct origins for AIRE1 and FEZF2, underscoring that their roles in regulating TRA have evolved through disparate pathways. Furthermore, it became evident that both FEZF2 and AIRE1 govern a diverse repertoire of genes, encompassing ancient and more recently diverged targets. Notably, FEZF2 demonstrates expression in both vertebrate and invertebrate embryos and germlines, accentuating its widespread role. Intriguingly, FEZF2 harbors motifs associated with autophagy, such as DKFPHP, SYSELWKSSL, and SYSEL, a process integral to cell selection in invertebrates. Our findings suggest that FEZF2 initially emerged to regulate self-elimination in the gonads of invertebrates. As organisms evolved toward greater complexity, AIRE1 likely emerged to complement FEZF2's role, participating in the regulation of cell selection for elimination in both gonads and the thymus. This dynamic interplay between AIRE1 and FEZF2 underscores their multifaceted contributions to TRA expression regulation across diverse evolutionary contexts.
Collapse
Affiliation(s)
- Michel Mickael
- Department of Experimental Genomics, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Postępu 36A, 05-552, Jastrzebiec, Poland.
- Department of Immunology, PM Forskningscentreum, Väpnaregatan 22, 58649, Linköping, Sweden.
| | - Marzena Łazarczyk
- Department of Experimental Genomics, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Postępu 36A, 05-552, Jastrzebiec, Poland
| | - Norwin Kubick
- Department of Biology, Institute of Plant Science and Microbiology, University of Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Agata Gurba
- Department of Pharmacodynamics, Faculty of Pharmacy, Warsaw Medical University, L Banacha 1, 02-697, Warsaw, Poland
| | - Tomasz Kocki
- Department of Experimental and Clinical Pharmacology, Medical University of Lublin, Jaczewskiego 8B, 20090, Lublin, Poland
| | - Jarosław Olav Horbańczuk
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Postępu 36A, 05-552, Jastrzebiec, Poland
| | - Atanas G Atanasov
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Postępu 36A, 05-552, Jastrzebiec, Poland
- Ludwig Boltzmann Institute Digital Health and Patient Safety, Medical University of Vienna, Vienna, Austria
| | - Mariusz Sacharczuk
- Department of Experimental Genomics, Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Postępu 36A, 05-552, Jastrzebiec, Poland
- Department of Pharmacodynamics, Faculty of Pharmacy, Warsaw Medical University, L Banacha 1, 02-697, Warsaw, Poland
| | - Piotr Religa
- Department of Medicine, Karolinska Institute, 171 77, Solna, Sweden.
| |
Collapse
|
7
|
Rashmi R, Nandi C, Majumdar S. Bioinformatic analysis of THAP9 transposase homolog: conserved regions, novel motifs. Curr Res Struct Biol 2023; 7:100113. [PMID: 38292821 PMCID: PMC10824691 DOI: 10.1016/j.crstbi.2023.100113] [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: 09/01/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 02/01/2024] Open
Abstract
THAP9 is a transposable element-derived gene that encodes the THAP9 protein, which is homologous to the Drosophila P-element transposase (DmTNP) and can cut and paste DNA. However, the exact functional role of THAP9 is unknown. Here, we perform structure prediction, evolutionary analysis and extensive in silico characterization of THAP9, including predicting domains and putative post-translational modification sites. Comparison of the AlphaFold-predicted structure of THAP9 with the DmTNP CryoEM structure, provided insights about the C2CH motif and other DNA binding residues, RNase H-like catalytic domain and insertion domain of the THAP9 protein. We also predicted previously unreported mammalian-specific post-translational modification sites that may play a role in the subcellular localization of THAP9. Furthermore, we observed that there are distinct organism class-specific conservation patterns of key functional residues in certain THAP9 domains.
Collapse
Affiliation(s)
- Richa Rashmi
- Discipline of Biological Engineering, IIT Gandhinagar, Gandhinagar, Gujarat, India
| | - Chandan Nandi
- Discipline of Biological Engineering, IIT Gandhinagar, Gandhinagar, Gujarat, India
| | - Sharmistha Majumdar
- Discipline of Biological Engineering, IIT Gandhinagar, Gandhinagar, Gujarat, India
| |
Collapse
|
8
|
Kurgan L, Hu G, Wang K, Ghadermarzi S, Zhao B, Malhis N, Erdős G, Gsponer J, Uversky VN, Dosztányi Z. Tutorial: a guide for the selection of fast and accurate computational tools for the prediction of intrinsic disorder in proteins. Nat Protoc 2023; 18:3157-3172. [PMID: 37740110 DOI: 10.1038/s41596-023-00876-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/21/2023] [Indexed: 09/24/2023]
Abstract
Intrinsic disorder is instrumental for a wide range of protein functions, and its analysis, using computational predictions from primary structures, complements secondary and tertiary structure-based approaches. In this Tutorial, we provide an overview and comparison of 23 publicly available computational tools with complementary parameters useful for intrinsic disorder prediction, partly relying on results from the Critical Assessment of protein Intrinsic Disorder prediction experiment. We consider factors such as accuracy, runtime, availability and the need for functional insights. The selected tools are available as web servers and downloadable programs, offer state-of-the-art predictions and can be used in a high-throughput manner. We provide examples and instructions for the selected tools to illustrate practical aspects related to the submission, collection and interpretation of predictions, as well as the timing and their limitations. We highlight two predictors for intrinsically disordered proteins, flDPnn as accurate and fast and IUPred as very fast and moderately accurate, while suggesting ANCHOR2 and MoRFchibi as two of the best-performing predictors for intrinsically disordered region binding. We link these tools to additional resources, including databases of predictions and web servers that integrate multiple predictive methods. Altogether, this Tutorial provides a hands-on guide to comparatively evaluating multiple predictors, submitting and collecting their own predictions, and reading and interpreting results. It is suitable for experimentalists and computational biologists interested in accurately and conveniently identifying intrinsic disorder, facilitating the functional characterization of the rapidly growing collections of protein sequences.
Collapse
Affiliation(s)
- Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA.
| | - Gang Hu
- School of Statistics and Data Science, LPMC and KLMDASR, Nankai University, Tianjin, China
| | - Kui Wang
- School of Statistics and Data Science, LPMC and KLMDASR, Nankai University, Tianjin, China
| | - Sina Ghadermarzi
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Bi Zhao
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Nawar Malhis
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gábor Erdős
- MTA-ELTE Momentum Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Jörg Gsponer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
- Byrd Alzheimer's Center and Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Zsuzsanna Dosztányi
- MTA-ELTE Momentum Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary.
| |
Collapse
|
9
|
Idrees S, Paudel KR, Sadaf T, Hansbro PM. How different viruses perturb host cellular machinery via short linear motifs. EXCLI JOURNAL 2023; 22:1113-1128. [PMID: 38054205 PMCID: PMC10694346 DOI: 10.17179/excli2023-6328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/18/2023] [Indexed: 12/07/2023]
Abstract
The virus interacts with its hosts by developing protein-protein interactions. Most viruses employ protein interactions to imitate the host protein: A viral protein with the same amino acid sequence or structure as the host protein attaches to the host protein's binding partner and interferes with the host protein's pathways. Being opportunistic, viruses have evolved to manipulate host cellular mechanisms by mimicking short linear motifs. In this review, we shed light on the current understanding of mimicry via short linear motifs and focus on viral mimicry by genetically different viral subtypes by providing recent examples of mimicry evidence and how high-throughput methods can be a reliable source to study SLiM-mediated viral mimicry.
Collapse
Affiliation(s)
- Sobia Idrees
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
- Centre for Inflammation, Centenary Institute and the University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, New South Wales, Australia
| | - Keshav Raj Paudel
- Centre for Inflammation, Centenary Institute and the University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, New South Wales, Australia
| | - Tayyaba Sadaf
- Centre for Inflammation, Centenary Institute and the University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, New South Wales, Australia
| | - Philip M. Hansbro
- Centre for Inflammation, Centenary Institute and the University of Technology Sydney, School of Life Sciences, Faculty of Science, Sydney, New South Wales, Australia
| |
Collapse
|
10
|
Psakhye I, Kawasumi R, Abe T, Hirota K, Branzei D. PCNA recruits cohesin loader Scc2 to ensure sister chromatid cohesion. Nat Struct Mol Biol 2023; 30:1286-1294. [PMID: 37592094 PMCID: PMC10497406 DOI: 10.1038/s41594-023-01064-x] [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: 07/01/2022] [Accepted: 07/12/2023] [Indexed: 08/19/2023]
Abstract
Sister chromatid cohesion, established during replication by the ring-shaped multiprotein complex cohesin, is essential for faithful chromosome segregation. Replisome-associated proteins are required to generate cohesion by two independent pathways. One mediates conversion of cohesins bound to unreplicated DNA ahead of replication forks into cohesive entities behind them, while the second promotes cohesin de novo loading onto newly replicated DNA. The latter process depends on the cohesin loader Scc2 (NIPBL in vertebrates) and the alternative PCNA loader CTF18-RFC. However, the mechanism of de novo cohesin loading during replication is unknown. Here we show that PCNA physically recruits the yeast cohesin loader Scc2 via its C-terminal PCNA-interacting protein motif. Binding to PCNA is crucial, as the scc2-pip mutant deficient in Scc2-PCNA interaction is defective in cohesion when combined with replisome mutants of the cohesin conversion pathway. Importantly, the role of NIPBL recruitment to PCNA for cohesion generation is conserved in vertebrate cells.
Collapse
Affiliation(s)
- Ivan Psakhye
- IFOM ETS, the AIRC Institute of Molecular Oncology, Milan, Italy.
| | - Ryotaro Kawasumi
- IFOM ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji-shi, Japan
| | - Takuya Abe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji-shi, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Hachioji-shi, Japan
| | - Dana Branzei
- IFOM ETS, the AIRC Institute of Molecular Oncology, Milan, Italy.
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy.
| |
Collapse
|
11
|
Guzmán-Vega FJ, González-Álvarez AC, Peña-Guerra KA, Cardona-Londoño KJ, Arold ST. Leveraging AI Advances and Online Tools for Structure-Based Variant Analysis. Curr Protoc 2023; 3:e857. [PMID: 37540795 DOI: 10.1002/cpz1.857] [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: 08/06/2023]
Abstract
Understanding how a gene variant affects protein function is important in life science, as it helps explain traits or dysfunctions in organisms. In a clinical setting, this understanding makes it possible to improve and personalize patient care. Bioinformatic tools often only assign a pathogenicity score, rather than providing information about the molecular basis for phenotypes. Experimental testing can furnish this information, but this is slow and costly and requires expertise and equipment not available in a clinical setting. Conversely, mapping a gene variant onto the three-dimensional (3D) protein structure provides a fast molecular assessment free of charge. Before 2021, this type of analysis was severely limited by the availability of experimentally determined 3D protein structures. Advances in artificial intelligence algorithms now allow confident prediction of protein structural features from sequence alone. The aim of the protocols presented here is to enable non-experts to use databases and online tools to investigate the molecular effect of a genetic variant. The Basic Protocol relies only on the online resources AlphaFold, Protein Structure Database, and UniProt. Alternate Protocols document the usage of the Protein Data Bank, SWISS-MODEL, ColabFold, and PyMOL for structure-based variant analysis. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: 3D Mapping based on UniProt and AlphaFold Alternate Protocol 1: Using experimental models from the PDB Alternate Protocol 2: Using information from homology modeling with SWISS-MODEL Alternate Protocol 3: Predicting 3D structures with ColabFold Alternate Protocol 4: Structure visualization and analysis with PyMOL.
Collapse
Affiliation(s)
- Francisco J Guzmán-Vega
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, KAUST, Thuwal, Saudi Arabia
| | - Ana C González-Álvarez
- Bioengineering Program, Biological and Environmental Science and Engineering Division, KAUST, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, KAUST, Thuwal, Saudi Arabia
| | - Karla A Peña-Guerra
- Bioengineering Program, Biological and Environmental Science and Engineering Division, KAUST, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, KAUST, Thuwal, Saudi Arabia
| | - Kelly J Cardona-Londoño
- Bioengineering Program, Biological and Environmental Science and Engineering Division, KAUST, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, KAUST, Thuwal, Saudi Arabia
| | - Stefan T Arold
- Bioscience Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
- Bioengineering Program, Biological and Environmental Science and Engineering Division, KAUST, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, KAUST, Thuwal, Saudi Arabia
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université de Montpellier, Montpellier, France
| |
Collapse
|
12
|
Barbeito P, Martin-Morales R, Palencia-Campos A, Cerrolaza J, Rivas-Santos C, Gallego-Colastra L, Caparros-Martin JA, Martin-Bravo C, Martin-Hurtado A, Sánchez-Bellver L, Marfany G, Ruiz-Perez VL, Garcia-Gonzalo FR. EVC-EVC2 complex stability and ciliary targeting are regulated by modification with ubiquitin and SUMO. Front Cell Dev Biol 2023; 11:1190258. [PMID: 37576597 PMCID: PMC10413113 DOI: 10.3389/fcell.2023.1190258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/17/2023] [Indexed: 08/15/2023] Open
Abstract
Ellis van Creveld syndrome and Weyers acrofacial dysostosis are two rare genetic diseases affecting skeletal development. They are both ciliopathies, as they are due to malfunction of primary cilia, microtubule-based plasma membrane protrusions that function as cellular antennae and are required for Hedgehog signaling, a key pathway during skeletal morphogenesis. These ciliopathies are caused by mutations affecting the EVC-EVC2 complex, a transmembrane protein heterodimer that regulates Hedgehog signaling from inside primary cilia. Despite the importance of this complex, the mechanisms underlying its stability, targeting and function are poorly understood. To address this, we characterized the endogenous EVC protein interactome in control and Evc-null cells. This proteomic screen confirmed EVC's main known interactors (EVC2, IQCE, EFCAB7), while revealing new ones, including USP7, a deubiquitinating enzyme involved in Hedgehog signaling. We therefore looked at EVC-EVC2 complex ubiquitination. Such ubiquitination exists but is independent of USP7 (and of USP48, also involved in Hh signaling). We did find, however, that monoubiquitination of EVC-EVC2 cytosolic tails greatly reduces their protein levels. On the other hand, modification of EVC-EVC2 cytosolic tails with the small ubiquitin-related modifier SUMO3 has a different effect, enhancing complex accumulation at the EvC zone, immediately distal to the ciliary transition zone, possibly via increased binding to the EFCAB7-IQCE complex. Lastly, we find that EvC zone targeting of EVC-EVC2 depends on two separate EFCAB7-binding motifs within EVC2's Weyers-deleted peptide. Only one of these motifs had been characterized previously, so we have mapped the second herein. Altogether, our data shed light on EVC-EVC2 complex regulatory mechanisms, with implications for ciliopathies.
Collapse
Affiliation(s)
- Pablo Barbeito
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Instituto de Investigaciones Biomédicas “Alberto Sols” (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Instituto de Investigación del Hospital Universitario de La Paz (IdiPAZ), Madrid, Spain
| | - Raquel Martin-Morales
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Instituto de Investigaciones Biomédicas “Alberto Sols” (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Instituto de Investigación del Hospital Universitario de La Paz (IdiPAZ), Madrid, Spain
| | - Adrian Palencia-Campos
- Instituto de Investigaciones Biomédicas “Alberto Sols” (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Juan Cerrolaza
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Instituto de Investigaciones Biomédicas “Alberto Sols” (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain
| | - Celia Rivas-Santos
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Instituto de Investigaciones Biomédicas “Alberto Sols” (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain
| | - Leticia Gallego-Colastra
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Instituto de Investigaciones Biomédicas “Alberto Sols” (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain
| | - Jose Antonio Caparros-Martin
- Instituto de Investigaciones Biomédicas “Alberto Sols” (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Carolina Martin-Bravo
- Instituto de Investigaciones Biomédicas “Alberto Sols” (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain
| | - Ana Martin-Hurtado
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Instituto de Investigaciones Biomédicas “Alberto Sols” (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain
| | - Laura Sánchez-Bellver
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
| | - Gemma Marfany
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institut de Biomedicina—Institut de Recerca Sant Joan de Déu (IBUB-IRSJD), Universitat de Barcelona, Barcelona, Spain
- DBGen Ocular Genomics, Barcelona, Spain
| | - Victor L. Ruiz-Perez
- Instituto de Investigaciones Biomédicas “Alberto Sols” (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Francesc R. Garcia-Gonzalo
- Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM), Madrid, Spain
- Instituto de Investigaciones Biomédicas “Alberto Sols” (IIBM), Consejo Superior de Investigaciones Científicas (CSIC)-UAM, Madrid, Spain
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Instituto de Investigación del Hospital Universitario de La Paz (IdiPAZ), Madrid, Spain
| |
Collapse
|
13
|
Amani K, Shivnauth V, Castroverde CDM. CBP60-DB: An AlphaFold-predicted plant kingdom-wide database of the CALMODULIN-BINDING PROTEIN 60 protein family with a novel structural clustering algorithm. PLANT DIRECT 2023; 7:e509. [PMID: 37435612 PMCID: PMC10331130 DOI: 10.1002/pld3.509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 04/17/2023] [Accepted: 05/23/2023] [Indexed: 07/13/2023]
Abstract
Molecular genetic analyses in the model species Arabidopsis thaliana have demonstrated the major roles of different CALMODULIN-BINDING PROTEIN 60 (CBP60) proteins in growth, stress signaling, and immune responses. Prominently, CBP60g and SARD1 are paralogous CBP60 transcription factors that regulate numerous components of the immune system, such as cell surface and intracellular immune receptors, MAP kinases, WRKY transcription factors, and biosynthetic enzymes for immunity-activating metabolites salicylic acid (SA) and N-hydroxypipecolic acid (NHP). However, their function, regulation, and diversification in most species remain unclear. Here, we have created CBP60-DB (https://cbp60db.wlu.ca/), a structural and bioinformatic database that comprehensively characterized 1052 CBP60 gene homologs (encoding 2376 unique transcripts and 1996 unique proteins) across 62 phylogenetically diverse genomes in the plant kingdom. We have employed deep learning-predicted structural analyses using AlphaFold2 and then generated dedicated web pages for all plant CBP60 proteins. Importantly, we have generated a novel clustering visualization algorithm to interrogate kingdom-wide structural similarities for more efficient inference of conserved functions across various plant taxa. Because well-characterized CBP60 proteins in Arabidopsis are known to be transcription factors with putative calmodulin-binding domains, we have integrated external bioinformatic resources to analyze protein domains and motifs. Collectively, we present a plant kingdom-wide identification of this important protein family in a user-friendly AlphaFold-anchored database, representing a novel and significant resource for the broader plant biology community.
Collapse
Affiliation(s)
- Keaun Amani
- Department of BiologyWilfrid Laurier UniversityWaterlooOntarioCanada
| | - Vanessa Shivnauth
- Department of BiologyWilfrid Laurier UniversityWaterlooOntarioCanada
| | | |
Collapse
|
14
|
Abstract
There are over 100 computational predictors of intrinsic disorder. These methods predict amino acid-level propensities for disorder directly from protein sequences. The propensities can be used to annotate putative disordered residues and regions. This unit provides a practical and holistic introduction to the sequence-based intrinsic disorder prediction. We define intrinsic disorder, explain the format of computational prediction of disorder, and identify and describe several accurate predictors. We also introduce recently released databases of intrinsic disorder predictions and use an illustrative example to provide insights into how predictions should be interpreted and combined. Lastly, we summarize key experimental methods that can be used to validate computational predictions. © 2023 Wiley Periodicals LLC.
Collapse
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, Florida
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, Richmond, Virginia
| |
Collapse
|
15
|
Shui K, Wang C, Zhang X, Ma S, Li Q, Ning W, Zhang W, Chen M, Peng D, Hu H, Fang Z, Guo A, Gao G, Ye M, Zhang L, Xue Y. Small-sample learning reveals propionylation in determining global protein homeostasis. Nat Commun 2023; 14:2813. [PMID: 37198164 DOI: 10.1038/s41467-023-38414-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Proteostasis is fundamental for maintaining organismal health. However, the mechanisms underlying its dynamic regulation and how its disruptions lead to diseases are largely unclear. Here, we conduct in-depth propionylomic profiling in Drosophila, and develop a small-sample learning framework to prioritize the propionylation at lysine 17 of H2B (H2BK17pr) to be functionally important. Mutating H2BK17 which eliminates propionylation leads to elevated total protein level in vivo. Further analyses reveal that H2BK17pr modulates the expression of 14.7-16.3% of genes in the proteostasis network, and determines global protein level by regulating the expression of genes involved in the ubiquitin-proteasome system. In addition, H2BK17pr exhibits daily oscillation, mediating the influences of feeding/fasting cycles to drive rhythmic expression of proteasomal genes. Our study not only reveals a role of lysine propionylation in regulating proteostasis, but also implements a generally applicable method which can be extended to other issues with little prior knowledge.
Collapse
Affiliation(s)
- Ke Shui
- Key Laboratory of Molecular Biophysics of Ministry of Education, 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, 430074, Hubei, China
| | - Chenwei Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, 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, 430074, Hubei, China
| | - Xuedi Zhang
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, 201210, Shanghai, China
| | - Shanshan Ma
- Key Laboratory of Molecular Biophysics of Ministry of Education, 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, 430074, Hubei, China
| | - Qinyu Li
- Key Laboratory of Molecular Biophysics of Ministry of Education, 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, 430074, Hubei, China
| | - Wanshan Ning
- Key Laboratory of Molecular Biophysics of Ministry of Education, 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, 430074, Hubei, China
| | - Weizhi Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, 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, 430074, Hubei, China
| | - Miaomiao Chen
- Key Laboratory of Molecular Biophysics of Ministry of Education, 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, 430074, Hubei, China
| | - Di Peng
- Key Laboratory of Molecular Biophysics of Ministry of Education, 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, 430074, Hubei, China
| | - Hui Hu
- Key Laboratory of Molecular Biophysics of Ministry of Education, 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, 430074, Hubei, China
| | - Zheng Fang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
| | - Anyuan Guo
- Key Laboratory of Molecular Biophysics of Ministry of Education, 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, 430074, Hubei, China
| | - Guanjun Gao
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, 201210, Shanghai, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023, Dalian, China
| | - Luoying Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, 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, 430074, Hubei, China.
- Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan, 430022, Hubei, China.
| | - Yu Xue
- Key Laboratory of Molecular Biophysics of Ministry of Education, 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, 430074, Hubei, China.
- Nanjing University Institute of Artificial Intelligence Biomedicine, Nanjing, 210031, Jiangsu, China.
| |
Collapse
|
16
|
Pueyo JI, Salazar J, Grincho C, Berni J, Towler BP, Newbury SF. Purriato is a conserved small open reading frame gene that interacts with the CASA pathway to regulate muscle homeostasis and epithelial tissue growth in Drosophila. Front Cell Dev Biol 2023; 11:1117454. [PMID: 36968202 PMCID: PMC10036370 DOI: 10.3389/fcell.2023.1117454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/24/2023] [Indexed: 03/12/2023] Open
Abstract
Recent advances in proteogenomic techniques and bioinformatic pipelines have permitted the detection of thousands of translated small Open Reading Frames (smORFs), which contain less than 100 codons, in eukaryotic genomes. Hundreds of these actively translated smORFs display conserved sequence, structure and evolutionary signatures indicating that the translated peptides could fulfil important biological roles. Despite their abundance, only tens of smORF genes have been fully characterised; these act mainly as regulators of canonical proteins involved in essential cellular processes. Importantly, some of these smORFs display conserved functions with their mutations being associated with pathogenesis. Thus, investigating smORF roles in Drosophila will not only expand our understanding of their functions but it may have an impact in human health. Here we describe the function of a novel and essential Drosophila smORF gene named purriato (prto). prto belongs to an ancient gene family whose members have expanded throughout the Protostomia clade. prto encodes a transmembrane peptide which is localized in endo-lysosomes and perinuclear and plasma membranes. prto is dynamically expressed in mesodermal tissues and imaginal discs. Targeted prto knockdown (KD) in these organs results in changes in nuclear morphology and endo-lysosomal distributions correlating with the loss of sarcomeric homeostasis in muscles and reduction of mitosis in wing discs. Consequently, prto KD mutants display severe reduction of motility, and shorter wings. Finally, our genetic interaction experiments show that prto function is closely associated to the CASA pathway, a conserved mechanism involved in turnover of mis-folded proteins and linked to muscle dystrophies and neurodegenerative diseases. Thus, this study shows the relevance of smORFs in regulating important cellular functions and supports the systematic characterisation of this class of genes to understand their functions and evolution.
Collapse
Affiliation(s)
- Jose I. Pueyo
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Jorge Salazar
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Carolina Grincho
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Jimena Berni
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Benjamin P. Towler
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Sarah F. Newbury
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| |
Collapse
|
17
|
The TFIIS N-terminal domain (TND): a transcription assembly module at the interface of order and disorder. Biochem Soc Trans 2023; 51:125-135. [PMID: 36651856 PMCID: PMC9987994 DOI: 10.1042/bst20220342] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023]
Abstract
Interaction scaffolds that selectively recognize disordered protein strongly shape protein interactomes. An important scaffold of this type that contributes to transcription is the TFIIS N-terminal domain (TND). The TND is a five-helical bundle that has no known enzymatic activity, but instead selectively reads intrinsically disordered sequences of other proteins. Here, we review the structural and functional properties of TNDs and their cognate disordered ligands known as TND-interacting motifs (TIMs). TNDs or TIMs are found in prominent members of the transcription machinery, including TFIIS, super elongation complex, SWI/SNF, Mediator, IWS1, SPT6, PP1-PNUTS phosphatase, elongin, H3K36me3 readers, the transcription factor MYC, and others. We also review how the TND interactome contributes to the regulation of transcription. Because the TND is the most significantly enriched fold among transcription elongation regulators, TND- and TIM-driven interactions have widespread roles in the regulation of many transcriptional processes.
Collapse
|
18
|
Ikeda K, Maezawa Y, Yonezawa T, Shimizu Y, Tashiro T, Kanai S, Sugaya N, Masuda Y, Inoue N, Niimi T, Masuya K, Mizuguchi K, Furuya T, Osawa M. DLiP-PPI library: An integrated chemical database of small-to-medium-sized molecules targeting protein-protein interactions. Front Chem 2023; 10:1090643. [PMID: 36700083 PMCID: PMC9868583 DOI: 10.3389/fchem.2022.1090643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 12/09/2022] [Indexed: 01/11/2023] Open
Abstract
Protein-protein interactions (PPIs) are recognized as important targets in drug discovery. The characteristics of molecules that inhibit PPIs differ from those of small-molecule compounds. We developed a novel chemical library database system (DLiP) to design PPI inhibitors. A total of 32,647 PPI-related compounds are registered in the DLiP. It contains 15,214 newly synthesized compounds, with molecular weight ranging from 450 to 650, and 17,433 active and inactive compounds registered by extracting and integrating known compound data related to 105 PPI targets from public databases and published literature. Our analysis revealed that the compounds in this database contain unique chemical structures and have physicochemical properties suitable for binding to the protein-protein interface. In addition, advanced functions have been integrated with the web interface, which allows users to search for potential PPI inhibitor compounds based on types of protein-protein interfaces, filter results by drug-likeness indicators important for PPI targeting such as rule-of-4, and display known active and inactive compounds for each PPI target. The DLiP aids the search for new candidate molecules for PPI drug discovery and is available online (https://skb-insilico.com/dlip).
Collapse
Affiliation(s)
- Kazuyoshi Ikeda
- HPC—and AI-driven Drug Development Platform Division, Center for Computational Science, Yokohama, Kanagawa, Japan,Division of Physics for Life Functions, Keio University Faculty of Pharmacy, Tokyo, Japan,*Correspondence: Kazuyoshi Ikeda,
| | | | - Tomoki Yonezawa
- Division of Physics for Life Functions, Keio University Faculty of Pharmacy, Tokyo, Japan
| | - Yugo Shimizu
- Division of Physics for Life Functions, Keio University Faculty of Pharmacy, Tokyo, Japan
| | | | | | | | | | - Naoko Inoue
- PeptiDream Inc., Chiyoda-Ku, Kanagawa, Japan
| | | | | | - Kenji Mizuguchi
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan,Institute for Protein Research, Osaka University, Osaka, Japan
| | | | - Masanori Osawa
- Division of Physics for Life Functions, Keio University Faculty of Pharmacy, Tokyo, Japan
| |
Collapse
|
19
|
Welch N, Singh SS, Musich R, Mansuri MS, Bellar A, Mishra S, Chelluboyina AK, Sekar J, Attaway AH, Li L, Willard B, Hornberger TA, Dasarathy S. Shared and unique phosphoproteomics responses in skeletal muscle from exercise models and in hyperammonemic myotubes. iScience 2022; 25:105325. [PMID: 36345342 PMCID: PMC9636548 DOI: 10.1016/j.isci.2022.105325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 08/22/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Skeletal muscle generation of ammonia, an endogenous cytotoxin, is increased during exercise. Perturbations in ammonia metabolism consistently occur in chronic diseases, and may blunt beneficial skeletal muscle molecular responses and protein homeostasis with exercise. Phosphorylation of skeletal muscle proteins mediates cellular signaling responses to hyperammonemia and exercise. Comparative bioinformatics and machine learning-based analyses of published and experimentally derived phosphoproteomics data identified differentially expressed phosphoproteins that were unique and shared between hyperammonemic murine myotubes and skeletal muscle from exercise models. Enriched processes identified in both hyperammonemic myotubes and muscle from exercise models with selected experimental validation included protein kinase A (PKA), calcium signaling, mitogen-activated protein kinase (MAPK) signaling, and protein homeostasis. Our approach of feature extraction from comparative untargeted "omics" data allows for selection of preclinical models that recapitulate specific human exercise responses and potentially optimize functional capacity and skeletal muscle protein homeostasis with exercise in chronic diseases.
Collapse
Affiliation(s)
- Nicole Welch
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Shashi Shekhar Singh
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Ryan Musich
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | - M. Shahid Mansuri
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Annette Bellar
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Saurabh Mishra
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | | | - Jinendiran Sekar
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Amy H. Attaway
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Ling Li
- Proteomics Core, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Belinda Willard
- Proteomics Core, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Troy A. Hornberger
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Srinivasan Dasarathy
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, OH 44195, USA
| |
Collapse
|
20
|
Solís C, Thompson WC, Peña JR, McDermott-Roe C, Langa P, Warren CM, Chrzanowska M, Wolska BM, Solaro RJ, Pieter Detombe, Goldspink PH. Mechano-growth factor E-domain modulates cardiac contractile function through 14-3-3 protein interactomes. Front Physiol 2022; 13:1028345. [PMID: 36467694 PMCID: PMC9709209 DOI: 10.3389/fphys.2022.1028345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/31/2022] [Indexed: 11/18/2022] Open
Abstract
In the heart, alternative splicing of the igf-I gene produces two isoforms: IGF-IEa and IGF-IEc, (Mechano-growth factor, MGF). The sequence divergence between their E-domain regions suggests differential isoform function. To define the biological actions of MGF's E-domain, we performed in silico analysis of the unique C-terminal sequence and identified a phosphorylation consensus site residing within a putative 14-3-3 binding motif. To test the functional significance of Ser 18 phosphorylation, phospho-mimetic (S/E18) and phospho-null (S/A18) peptides were delivered to mice at different doses for 2 weeks. Cardiovascular function was measured using echocardiography and a pressure-volume catheter. At the lowest (2.25 mg/kg/day) and highest (9 mg/kg/day) doses, the peptides produced a depression in systolic and diastolic parameters. However, at 4.5 mg/kg/day the peptides produced opposing effects on cardiac function. Fractional shortening analysis also showed a similar trend, but with no significant change in cardiac geometry. Microarray analysis discovered 21 genes (FDR p < 0.01), that were expressed accordant with the opposing effects on contractile function at 4.5 mg/kg/day, with the nuclear receptor subfamily 4 group A member 2 (Nr4a2) identified as a potential target of peptide regulation. Testing the regulation of the Nr4a family, showed the E-domain peptides modulate Nr4a gene expression following membrane depolarization with KCl in vitro. To determine the potential role of 14-3-3 proteins, we examined 14-3-3 isoform expression and distribution. 14-3-3γ localized to the myofilaments in neonatal cardiac myocytes, the cardiac myocytes and myofilament extracts from the adult heart. Thermal shift analysis of recombinant 14-3-3γ protein showed the S/A18 peptide destabilized 14-3-3γ folding. Also, the S/A18 peptide significantly inhibited 14-3-3γ's ability to interact with myosin binding protein C (MYPC3) and phospholamban (PLN) in heart lysates from dobutamine injected mice. Conversely, the S/E18 peptide showed no effect on 14-3-3γ stability, did not inhibit 14-3-3γ's interaction with PLN but did inhibit the interaction with MYPC3. Replacing the glutamic acid with a phosphate group on Ser 18 (pSer18), significantly increased 14-3-3γ protein stability. We conclude that the state of Ser 18 phosphorylation within the 14-3-3 binding motif of MGF's E-domain, modulates protein-protein interactions within the 14-3-3γ interactome, which includes proteins involved in the regulation of contractile function.
Collapse
Affiliation(s)
- Christopher Solís
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL, United States
| | - Walter C. Thompson
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL, United States
| | - James R. Peña
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Christopher McDermott-Roe
- Department of Medicine, and Department of Genetics, Perelman School of Medicine, Cardiovascular Institute, University of Pennsylvania, Philadelphia, PA, United States
| | - Paulina Langa
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL, United States,Center for Cardiovascular Research, University of Illinois at Chicago, Chicago, IL, United States
| | - Chad M. Warren
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL, United States,Center for Cardiovascular Research, University of Illinois at Chicago, Chicago, IL, United States
| | - Magdalena Chrzanowska
- Blood Research Institute, Versiti, Department of Pharmacology and Toxicology, Cardiovascular Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Beata M. Wolska
- Center for Cardiovascular Research, University of Illinois at Chicago, Chicago, IL, United States,Department of Medicine, Division of Cardiology, University of Illinois at Chicago, Chicago, IL, United States
| | - R. John Solaro
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL, United States,Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Pieter Detombe
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL, United States,Phymedexp, Université de Montpellier, Inserm, CNRS, Montpellier, France
| | - Paul H. Goldspink
- Department of Physiology and Biophysics, University of Illinois Chicago, Chicago, IL, United States,Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States,*Correspondence: Paul H. Goldspink,
| |
Collapse
|
21
|
Pan-claudin family interactome analysis reveals shared and specific interactions. Cell Rep 2022; 41:111588. [DOI: 10.1016/j.celrep.2022.111588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 07/04/2022] [Accepted: 10/11/2022] [Indexed: 11/09/2022] Open
|
22
|
Ostendorp A, Ostendorp S, Zhou Y, Chaudron Z, Wolffram L, Rombi K, von Pein L, Falke S, Jeffries CM, Svergun DI, Betzel C, Morris RJ, Kragler F, Kehr J. Intrinsically disordered plant protein PARCL colocalizes with RNA in phase-separated condensates whose formation can be regulated by mutating the PLD. J Biol Chem 2022; 298:102631. [PMID: 36273579 PMCID: PMC9679465 DOI: 10.1016/j.jbc.2022.102631] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 11/21/2022] Open
Abstract
In higher plants, long-distance RNA transport via the phloem is crucial for communication between distant plant tissues to align development with stress responses and reproduction. Several recent studies suggest that specific RNAs are among the potential long-distance information transmitters. However, it is yet not well understood how these RNAs enter the phloem stream, how they are transported, and how they are released at their destination. It was proposed that phloem RNA-binding proteins facilitate RNA translocation. In the present study, we characterized two orthologs of the phloem-associated RNA chaperone-like (PARCL) protein from Arabidopsis thaliana and Brassica napus at functional and structural levels. Microscale thermophoresis showed that these phloem-abundant proteins can bind a broad spectrum of RNAs and show RNA chaperone activity in FRET-based in vitro assays. Our SAXS experiments revealed a high degree of disorder, typical for RNA-binding proteins. In agroinfiltrated tobacco plants, eYFP-PARCL proteins mainly accumulated in nuclei and nucleoli and formed cytosolic and nuclear condensates. We found that formation of these condensates was impaired by tyrosine-to-glutamate mutations in the predicted prion-like domain (PLD), while C-terminal serine-to-glutamate mutations did not affect condensation but reduced RNA binding and chaperone activity. Furthermore, our in vitro experiments confirmed phase separation of PARCL and colocalization of RNA with the condensates, while mutation as well as phosphorylation of the PLD reduced phase separation. Together, our results suggest that RNA binding and condensate formation of PARCL can be regulated independently by modification of the C-terminus and/or the PLD.
Collapse
Affiliation(s)
- Anna Ostendorp
- Universität Hamburg, Department of Biology, Institute of Plant Science and Microbiology, Hamburg, Germany,For correspondence: Anna Ostendorp
| | - Steffen Ostendorp
- Universität Hamburg, Department of Biology, Institute of Plant Science and Microbiology, Hamburg, Germany
| | - Yuan Zhou
- Max Planck Institute of Molecular Plant Physiology, Department II, Potsdam, Germany
| | - Zoé Chaudron
- Universität Hamburg, Department of Biology, Institute of Plant Science and Microbiology, Hamburg, Germany
| | - Lukas Wolffram
- Universität Hamburg, Department of Biology, Institute of Plant Science and Microbiology, Hamburg, Germany
| | - Khadija Rombi
- Universität Hamburg, Department of Biology, Institute of Plant Science and Microbiology, Hamburg, Germany
| | - Linn von Pein
- Universität Hamburg, Department of Biology, Institute of Plant Science and Microbiology, Hamburg, Germany
| | - Sven Falke
- Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Hamburg, Germany,Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Hamburg, Germany
| | - Cy M. Jeffries
- European Molecular Biology Laboratory (EMBL) Hamburg Site, c/o DESY, Hamburg, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL) Hamburg Site, c/o DESY, Hamburg, Germany
| | - Christian Betzel
- Laboratory for Structural Biology of Infection and Inflammation, c/o DESY, Hamburg, Germany,Universität Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Hamburg, Germany
| | - Richard J. Morris
- Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Friedrich Kragler
- Max Planck Institute of Molecular Plant Physiology, Department II, Potsdam, Germany
| | - Julia Kehr
- Universität Hamburg, Department of Biology, Institute of Plant Science and Microbiology, Hamburg, Germany
| |
Collapse
|
23
|
The Cancermuts software package for the prioritization of missense cancer variants: a case study of AMBRA1 in melanoma. Cell Death Dis 2022; 13:872. [PMID: 36243772 PMCID: PMC9569343 DOI: 10.1038/s41419-022-05318-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/27/2022] [Accepted: 10/03/2022] [Indexed: 11/07/2022]
Abstract
Cancer genomics and cancer mutation databases have made an available wealth of information about missense mutations found in cancer patient samples. Contextualizing by means of annotation and predicting the effect of amino acid change help identify which ones are more likely to have a pathogenic impact. Those can be validated by means of experimental approaches that assess the impact of protein mutations on the cellular functions or their tumorigenic potential. Here, we propose the integrative bioinformatic approach Cancermuts, implemented as a Python package. Cancermuts is able to gather known missense cancer mutations from databases such as cBioPortal and COSMIC, and annotate them with the pathogenicity score REVEL as well as information on their source. It is also able to add annotations about the protein context these mutations are found in, such as post-translational modification sites, structured/unstructured regions, presence of short linear motifs, and more. We applied Cancermuts to the intrinsically disordered protein AMBRA1, a key regulator of many cellular processes frequently deregulated in cancer. By these means, we classified mutations of AMBRA1 in melanoma, where AMBRA1 is highly mutated and displays a tumor-suppressive role. Next, based on REVEL score, position along the sequence, and their local context, we applied cellular and molecular approaches to validate the predicted pathogenicity of a subset of mutations in an in vitro melanoma model. By doing so, we have identified two AMBRA1 mutations which show enhanced tumorigenic potential and are worth further investigation, highlighting the usefulness of the tool. Cancermuts can be used on any protein targets starting from minimal information, and it is available at https://www.github.com/ELELAB/cancermuts as free software.
Collapse
|
24
|
Kastano K, Mier P, Dosztányi Z, Promponas VJ, Andrade-Navarro MA. Functional Tuning of Intrinsically Disordered Regions in Human Proteins by Composition Bias. Biomolecules 2022; 12:biom12101486. [PMID: 36291695 PMCID: PMC9599065 DOI: 10.3390/biom12101486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022] Open
Abstract
Intrinsically disordered regions (IDRs) in protein sequences are flexible, have low structural constraints and as a result have faster rates of evolution. This lack of evolutionary conservation greatly limits the use of sequence homology for the classification and functional assessment of IDRs, as opposed to globular domains. The study of IDRs requires other properties for their classification and functional prediction. While composition bias is not a necessary property of IDRs, compositionally biased regions (CBRs) have been noted as frequent part of IDRs. We hypothesized that to characterize IDRs, it could be helpful to study their overlap with particular types of CBRs. Here, we evaluate this overlap in the human proteome. A total of 2/3 of residues in IDRs overlap CBRs. Considering CBRs enriched in one type of amino acid, we can distinguish CBRs that tend to be fully included within long IDRs (R, H, N, D, P, G), from those that partially overlap shorter IDRs (S, E, K, T), and others that tend to overlap IDR terminals (Q, A). CBRs overlap more often IDRs in nuclear proteins and in proteins involved in liquid-liquid phase separation (LLPS). Study of protein interaction networks reveals the enrichment of CBRs in IDRs by tandem repetition of short linear motifs (rich in S or P), and the existence of E-rich polar regions that could support specific protein interactions with non-specific interactions. Our results open ways to pin down the function of IDRs from their partial compositional biases.
Collapse
Affiliation(s)
- Kristina Kastano
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Pablo Mier
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Zsuzsanna Dosztányi
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter stny 1/c, H-1117 Budapest, Hungary
| | - Vasilis J. Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, 1678 Nicosia, Cyprus
| | - Miguel A. Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
- Correspondence:
| |
Collapse
|
25
|
Noor F, Ashfaq UA, Asif M, Adeel MM, Alshammari A, Alharbi M. Comprehensive computational analysis reveals YXXΦ[I/L/M/F/V] motif and YXXΦ-like tetrapeptides across HFRS causing Hantaviruses and their association with viral pathogenesis and host immune regulation. Front Immunol 2022; 13:1031608. [PMID: 36275660 PMCID: PMC9584616 DOI: 10.3389/fimmu.2022.1031608] [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: 08/30/2022] [Accepted: 09/20/2022] [Indexed: 11/18/2022] Open
Abstract
Hemorrhagic fever with renal syndrome (HFRS) is an acute zoonotic disease transmitted through aerosolized excrement of rodents. The etiology of HFRS is complex due to the involvement of viral factors and host immune and genetic factors. The viral species that dominantly cause HFRS are Puumala virus (PUUV), Seoul virus (SEOV), Dobrava-Belgrade virus (DOBV), and Hantaan virus (HTNV). Despite continuous prevention and control measures, HFRS remains a significant public health problem worldwide. The nucleocapsid protein of PUUV, SEOV, DOBV, and HTNV is a multifunctional viral protein involved in various stages of the viral replication cycle. However, the exact role of nucleoproteins in viral pathogenesis is yet to be discovered. Targeting a universal host protein exploited by most viruses would be a game-changing strategy that offers broad-spectrum solutions and rapid epidemic control. The objective of this study is to understand the replication and pathogenesis of PUUV, SEOV, DOBV, and HTNV by targeting tyrosine-based motif (YXXΦ[I/L/M/F/V]) and YXXΦ-like tetrapeptides. In the light of the current study, in silico analysis uncovered many different YXXΦ[I/L/M/F/V] motifs and YXXΦ-like tetrapeptides within nucleoproteins of PUUV, SEOV, DOBV, and HTNV. Following that, the 3D structures of nucleoproteins were predicted using AlphaFold2 to map the location of YXXΦ[I/L/M/F/V] motif and YXXΦ-like tetrapeptides in a 3D environment. Further, in silico analysis and characterization of Post Translational Modifications (PTMs) revealed multiple PTMs sites within YXXΦ[I/L/M/F/V] motif and YXXΦ-like tetrapeptides, which contribute to virulence and host immune regulation. Our study proposed that the predicted YXXΦ[I/L/M/F/V] motif and YXXΦ-like tetrapeptides may confer specific functions such as virulence, host immune regulation, and pathogenesis to nucleoproteins of PUUV, SEOV, DOBV, and HTNV. However, in vivo and in vitro studies on YXXΦ[I/L/M/F/V] motif and YXXΦ-like tetrapeptides will assign new biological roles to these antiviral targets.
Collapse
Affiliation(s)
- Fatima Noor
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
- *Correspondence: Usman Ali Ashfaq,
| | - Muhammad Asif
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Muzammal Adeel
- Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, GA, United States
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
26
|
Sordaria macrospora Sterile Mutant pro34 Is Impaired in Respiratory Complex I Assembly. J Fungi (Basel) 2022; 8:jof8101015. [PMID: 36294581 PMCID: PMC9605262 DOI: 10.3390/jof8101015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 11/21/2022] Open
Abstract
The formation of fruiting bodies is a highly regulated process that requires the coordinated formation of different cell types. By analyzing developmental mutants, many developmental factors have already been identified. Yet, a complete understanding of fruiting body formation is still lacking. In this study, we analyzed developmental mutant pro34 of the filamentous ascomycete Sordaria macrospora. Genome sequencing revealed a deletion in the pro34 gene encoding a putative mitochondrial complex I assembly factor homologous to Neurospora crassa CIA84. We show that PRO34 is required for fast vegetative growth, fruiting body and ascospore formation. The pro34 transcript undergoes adenosine to inosine editing, a process correlated with sexual development in fruiting body-forming ascomycetes. Fluorescence microscopy and western blot analysis showed that PRO34 is a mitochondrial protein, and blue-native PAGE revealed that the pro34 mutant lacks mitochondrial complex I. Inhibitor experiments revealed that pro34 respires via complexes III and IV, but also shows induction of alternative oxidase, a shunt pathway to bypass complexes III and IV. We discuss the hypothesis that alternative oxidase is induced to prevent retrograde electron transport to complex I intermediates, thereby protecting from oxidative stress.
Collapse
|
27
|
Behrendt A, Golchin P, König F, Mulnaes D, Stalke A, Dröge C, Keitel V, Gohlke H. Vasor: Accurate prediction of variant effects for amino acid substitutions in multidrug resistance protein 3. Hepatol Commun 2022; 6:3098-3111. [PMID: 36111625 PMCID: PMC9592774 DOI: 10.1002/hep4.2088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 07/26/2022] [Accepted: 08/16/2022] [Indexed: 12/14/2022] Open
Abstract
The phosphatidylcholine floppase multidrug resistance protein 3 (MDR3) is an essential hepatobiliary transport protein. MDR3 dysfunction is associated with various liver diseases, ranging from severe progressive familial intrahepatic cholestasis to transient forms of intrahepatic cholestasis of pregnancy and familial gallstone disease. Single amino acid substitutions are often found as causative of dysfunction, but identifying the substitution effect in in vitro studies is time and cost intensive. We developed variant assessor of MDR3 (Vasor), a machine learning-based model to classify novel MDR3 missense variants into the categories benign or pathogenic. Vasor was trained on the largest data set to date that is specific for benign and pathogenic variants of MDR3 and uses general predictors, namely Evolutionary Models of Variant Effects (EVE), EVmutation, PolyPhen-2, I-Mutant2.0, MUpro, MAESTRO, and PON-P2 along with other variant properties, such as half-sphere exposure and posttranslational modification site, as input. Vasor consistently outperformed the integrated general predictors and the external prediction tool MutPred2, leading to the current best prediction performance for MDR3 single-site missense variants (on an external test set: F1-score, 0.90; Matthew's correlation coefficient, 0.80). Furthermore, Vasor predictions cover the entire sequence space of MDR3. Vasor is accessible as a webserver at https://cpclab.uni-duesseldorf.de/mdr3_predictor/ for users to rapidly obtain prediction results and a visualization of the substitution site within the MDR3 structure. The MDR3-specific prediction tool Vasor can provide reliable predictions of single-site amino acid substitutions, giving users a fast way to initially assess whether a variant is benign or pathogenic.
Collapse
Affiliation(s)
- Annika Behrendt
- Institute for Pharmaceutical and Medicinal ChemistryHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Pegah Golchin
- Department of Electrical Engineering and Information TechnologyTechnische Universität DarmstadtDarmstadtGermany
| | - Filip König
- Institute for Pharmaceutical and Medicinal ChemistryHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Daniel Mulnaes
- Institute for Pharmaceutical and Medicinal ChemistryHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Amelie Stalke
- Department of Human GeneticsHannover Medical SchoolHannoverGermany,Division of Kidney, Department of Pediatric Gastroenterology and Hepatology, Liver, and Metabolic DiseasesHannover Medical SchoolHannoverGermany
| | - Carola Dröge
- Department for Gastroenterology, Hepatology, and Infectious Diseases, Medical FacultyOtto von Guericke UniversityMagdeburgGermany,Department for Gastroenterology, Hepatology, and Infectious DiseasesUniversity Hospital, Medical FacultyHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Verena Keitel
- Department for Gastroenterology, Hepatology, and Infectious Diseases, Medical FacultyOtto von Guericke UniversityMagdeburgGermany,Department for Gastroenterology, Hepatology, and Infectious DiseasesUniversity Hospital, Medical FacultyHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal ChemistryHeinrich Heine University DüsseldorfDüsseldorfGermany,John‐von‐Neumann‐Institute for Computing, Jülich Supercomputing Center, Institute of Biological Information Processing (IBI‐7: Structural Biochemistry), and Institute of Bio‐ and Geosciences (IBG‐4: Bioinformatics)Forschungszentrum Jülich GmbHJülichGermany
| |
Collapse
|
28
|
Lee B, Jaberi-Lashkari N, Calo E. A unified view of low complexity regions (LCRs) across species. eLife 2022; 11:e77058. [PMID: 36098382 PMCID: PMC9470157 DOI: 10.7554/elife.77058] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Low complexity regions (LCRs) play a role in a variety of important biological processes, yet we lack a unified view of their sequences, features, relationships, and functions. Here, we use dotplots and dimensionality reduction to systematically define LCR type/copy relationships and create a map of LCR sequence space capable of integrating LCR features and functions. By defining LCR relationships across the proteome, we provide insight into how LCR type and copy number contribute to higher order assemblies, such as the importance of K-rich LCR copy number for assembly of the nucleolar protein RPA43 in vivo and in vitro. With LCR maps, we reveal the underlying structure of LCR sequence space, and relate differential occupancy in this space to the conservation and emergence of higher order assemblies, including the metazoan extracellular matrix and plant cell wall. Together, LCR relationships and maps uncover and identify scaffold-client relationships among E-rich LCR-containing proteins in the nucleolus, and revealed previously undescribed regions of LCR sequence space with signatures of higher order assemblies, including a teleost-specific T/H-rich sequence space. Thus, this unified view of LCRs enables discovery of how LCRs encode higher order assemblies of organisms.
Collapse
Affiliation(s)
- Byron Lee
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Nima Jaberi-Lashkari
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Eliezer Calo
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of TechnologyCambridgeUnited States
| |
Collapse
|
29
|
Kafkia E, Andres-Pons A, Ganter K, Seiler M, Smith TS, Andrejeva A, Jouhten P, Pereira F, Franco C, Kuroshchenkova A, Leone S, Sawarkar R, Boston R, Thaventhiran J, Zaugg JB, Lilley KS, Lancrin C, Beck M, Patil KR. Operation of a TCA cycle subnetwork in the mammalian nucleus. SCIENCE ADVANCES 2022; 8:eabq5206. [PMID: 36044572 PMCID: PMC9432838 DOI: 10.1126/sciadv.abq5206] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 07/14/2022] [Indexed: 05/23/2023]
Abstract
Nucleic acid and histone modifications critically depend on the tricarboxylic acid (TCA) cycle for substrates and cofactors. Although a few TCA cycle enzymes have been reported in the nucleus, the corresponding pathways are considered to operate in mitochondria. Here, we show that a part of the TCA cycle is operational also in the nucleus. Using 13C-tracer analysis, we identified activity of glutamine-to-fumarate, citrate-to-succinate, and glutamine-to-aspartate routes in the nuclei of HeLa cells. Proximity labeling mass spectrometry revealed a spatial vicinity of the involved enzymes with core nuclear proteins. We further show nuclear localization of aconitase 2 and 2-oxoglutarate dehydrogenase in mouse embryonic stem cells. Nuclear localization of the latter enzyme, which produces succinyl-CoA, changed from pluripotency to a differentiated state with accompanying changes in the nuclear protein succinylation. Together, our results demonstrate operation of an extended metabolic pathway in the nucleus, warranting a revision of the canonical view on metabolic compartmentalization.
Collapse
Affiliation(s)
- Eleni Kafkia
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Amparo Andres-Pons
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Kerstin Ganter
- European Molecular Biology Laboratory (EMBL), Rome, Italy
| | - Markus Seiler
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Tom S. Smith
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Anna Andrejeva
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Paula Jouhten
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- VTT Technical Research Center of Finland, Helsinki, Finland
| | - Filipa Pereira
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Catarina Franco
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Anna Kuroshchenkova
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Sergio Leone
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Ritwick Sawarkar
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Rebecca Boston
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - James Thaventhiran
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Judith B. Zaugg
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | | | - Martin Beck
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Kiran Raosaheb Patil
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| |
Collapse
|
30
|
Structural and Functional Characterization at the Molecular Level of the MATE Gene Family in Wheat in Silico. CONTRAST MEDIA & MOLECULAR IMAGING 2022. [DOI: 10.1155/2022/9289007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A series of multidrug extransporters known as the multidrug and potentially toxic extrusion (MATE) genes are found in all living things and are crucial for the removal of heavy metal ions, metalloids, exogenous xenobiotics, endogenous secondary metabolites, and other toxic substances from the cells. However, there has only been a small amount of them in silico analysis of the MATE family of genes in plant species. In the current study, the MATE gene family was characterized in silico where two families and seven subfamilies based on their evolutionary relationships were proposed. Plant breeders may use TraesCS1D02G030400, TraesCS4B02G244400, and TraesCS1A02G029900 genes for marker-assisted or transgenic breeding to develop novel cultivars since these genes have been hypothesized from protein-protein interaction study to play a critical role in the transport of toxic chemicals across cells. The exon number varies from 01 to 14. One exon has TraesCS1A02G188100, TraesCS5B02G562500, TraesCS6A02G256400, and TraesCS6D02G384300 genes, while 14 exons have only two genes that are TraesCS6A02G418800 and TraesCS6D02G407900. Biological stress (infestations of disease) affects the expression of most of the MATE genes, with the gene TraesCS5D02G355500 having the highest expression level in the wheat expression browser tool. Using the Grain interpretation search engine tool, it is found that the vast bulk of MATE genes are voiced throughout biotic environmental stresses caused by disease pests, with the genotype TraesCS5B02G326600.1 from family 1 exhibiting the greatest level of expression throughout Fusarium head blight infection by Fusarium graminearum after 4 days of infection. The researchers constructed 39 ternary plots, each with a distinct degree of expression under biotic and abiotic stress settings, and observed that 44% of the triplets have imbalanced outputs (extreme values) due to their higher tissue specificity and increased intensity.
Collapse
|
31
|
Day-Walsh PE, Keeble B, Pirabagar G, Fountain SJ, Kroon PA. Transcriptional and Post-Translational Regulation of Junctional Adhesion Molecule-B (JAM-B) in Leukocytes under Inflammatory Stimuli. Int J Mol Sci 2022; 23:ijms23158646. [PMID: 35955781 PMCID: PMC9369439 DOI: 10.3390/ijms23158646] [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: 06/13/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
Junctional adhesion molecules (JAMs; comprising JAM-A, -B and -C) act as receptors for viruses, mediate cell permeability, facilitate leukocyte migration during sterile and non-sterile inflammation and are important for the maintenance of epithelial barrier integrity. As such, they are implicated in the development of both communicable and non-communicable chronic diseases. Here, we investigated the expression and regulation of JAM-B in leukocytes under pathogen- and host-derived inflammatory stimuli using immunoassays, qPCR and pharmacological inhibitors of inflammatory signalling pathways. We show that JAM-B is expressed at both the mRNA and protein level in leukocytes. JAM-B protein is localised to the cytoplasm, Golgi apparatus and in the nucleus around ring-shaped structures. We also provide evidence that JAM-B nuclear localisation occurs via the classical importin-α/β pathway, which is likely mediated through JAM-B protein nuclear localisation signals (NLS) and export signals (NES). In addition, we provide evidence that under both pathogen- and host-derived inflammatory stimuli, JAM-B transcription is regulated via the NF-κB-dependent pathways, whereas at the post-translational level JAM-B is regulated by ubiquitin-proteosome pathways. Anaphase-promoting ubiquitin ligase complex (APC/C) and herpes simplex virus-associated ubiquitin-specific protease (HAUSP/USP) were identified as candidates for JAM-B ubiquitination and de-ubiquitination, respectively. The expression and regulation of JAM-B in leukocytes reported here is a novel observation and contrasts with previous reports. The data reported here suggest that JAM-B expression in leukocytes is under the control of common inflammatory pathways.
Collapse
Affiliation(s)
- Priscilla E. Day-Walsh
- Quadram Institute Bioscience, Food Innovation & Health Programme, Norwich Research Park, Rosalind Franklin Road, Norwich NR4 7UQ, UK; (P.E.D.-W.); (B.K.); (G.P.)
| | - Bryony Keeble
- Quadram Institute Bioscience, Food Innovation & Health Programme, Norwich Research Park, Rosalind Franklin Road, Norwich NR4 7UQ, UK; (P.E.D.-W.); (B.K.); (G.P.)
| | - Gothai Pirabagar
- Quadram Institute Bioscience, Food Innovation & Health Programme, Norwich Research Park, Rosalind Franklin Road, Norwich NR4 7UQ, UK; (P.E.D.-W.); (B.K.); (G.P.)
| | - Samuel J. Fountain
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK;
| | - Paul A. Kroon
- Quadram Institute Bioscience, Food Innovation & Health Programme, Norwich Research Park, Rosalind Franklin Road, Norwich NR4 7UQ, UK; (P.E.D.-W.); (B.K.); (G.P.)
- Correspondence:
| |
Collapse
|
32
|
Kakkanas A, Karamichali E, Koufogeorgou EI, Kotsakis SD, Georgopoulou U, Foka P. Targeting the YXXΦ Motifs of the SARS Coronaviruses 1 and 2 ORF3a Peptides by In Silico Analysis to Predict Novel Virus-Host Interactions. Biomolecules 2022; 12:1052. [PMID: 36008946 PMCID: PMC9405953 DOI: 10.3390/biom12081052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/21/2022] [Accepted: 07/25/2022] [Indexed: 02/08/2023] Open
Abstract
The emerging SARS-CoV and SARS-CoV-2 belong to the family of "common cold" RNA coronaviruses, and they are responsible for the 2003 epidemic and the current pandemic with over 6.3 M deaths worldwide. The ORF3a gene is conserved in both viruses and codes for the accessory protein ORF3a, with unclear functions, possibly related to viral virulence and pathogenesis. The tyrosine-based YXXΦ motif (Φ: bulky hydrophobic residue-L/I/M/V/F) was originally discovered to mediate clathrin-dependent endocytosis of membrane-spanning proteins. Many viruses employ the YXXΦ motif to achieve efficient receptor-guided internalisation in host cells, maintain the structural integrity of their capsids and enhance viral replication. Importantly, this motif has been recently identified on the ORF3a proteins of SARS-CoV and SARS-CoV-2. Given that the ORF3a aa sequence is not fully conserved between the two SARS viruses, we aimed to map in silico structural differences and putative sequence-driven alterations of regulatory elements within and adjacently to the YXXΦ motifs that could predict variations in ORF3a functions. Using robust bioinformatics tools, we investigated the presence of relevant post-translational modifications and the YXXΦ motif involvement in protein-protein interactions. Our study suggests that the predicted YXXΦ-related features may confer specific-yet to be discovered-functions to ORF3a proteins, significant to the new virus and related to enhanced propagation, host immune regulation and virulence.
Collapse
Affiliation(s)
- Athanassios Kakkanas
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115-21 Athens, Greece; (A.K.); (E.K.); (E.I.K.); (U.G.)
| | - Eirini Karamichali
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115-21 Athens, Greece; (A.K.); (E.K.); (E.I.K.); (U.G.)
| | - Efthymia Ioanna Koufogeorgou
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115-21 Athens, Greece; (A.K.); (E.K.); (E.I.K.); (U.G.)
| | - Stathis D. Kotsakis
- Laboratory of Bacteriology, Hellenic Pasteur Institute, 115-21 Athens, Greece;
| | - Urania Georgopoulou
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115-21 Athens, Greece; (A.K.); (E.K.); (E.I.K.); (U.G.)
| | - Pelagia Foka
- Laboratory of Molecular Virology, Hellenic Pasteur Institute, 115-21 Athens, Greece; (A.K.); (E.K.); (E.I.K.); (U.G.)
| |
Collapse
|
33
|
Basant A, Way M. The relative binding position of Nck and Grb2 adaptors impacts actin-based motility of Vaccinia virus. eLife 2022; 11:74655. [PMID: 35796545 PMCID: PMC9333988 DOI: 10.7554/elife.74655] [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: 10/12/2021] [Accepted: 07/06/2022] [Indexed: 11/19/2022] Open
Abstract
Phosphotyrosine (pTyr) motifs in unstructured polypeptides orchestrate important cellular processes by engaging SH2-containing adaptors to assemble complex signalling networks. The concept of phase separation has recently changed our appreciation of multivalent networks, however, the role of pTyr motif positioning in their function remains to be explored. We have now investigated this parameter in the operation of the signalling cascade driving actin-based motility and spread of Vaccinia virus. This network involves two pTyr motifs in the viral protein A36 that recruit the adaptors Nck and Grb2 upstream of N-WASP and Arp2/3 complex-mediated actin polymerisation. Manipulating the position of pTyr motifs in A36 and the unrelated p14 from Orthoreovirus, we find that only specific spatial arrangements of Nck and Grb2 binding sites result in robust N-WASP recruitment, Arp2/3 complex driven actin polymerisation and viral spread. This suggests that the relative position of pTyr adaptor binding sites is optimised for signal output. This finding may explain why the relative positions of pTyr motifs are frequently conserved in proteins from widely different species. It also has important implications for regulation of physiological networks, including those undergoing phase transitions.
Collapse
Affiliation(s)
- Angika Basant
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, London, United Kingdom
| | - Michael Way
- Cellular signalling and cytoskeletal function laboratory, The Francis Crick Institute, London, United Kingdom
| |
Collapse
|
34
|
Kogan GL, Mikhaleva EA, Olenkina OM, Ryazansky SS, Galzitskaya OV, Abramov YA, Leinsoo TA, Akulenko NV, Lavrov SA, Gvozdev VA. Extended disordered regions of ribosome-associated NAC proteins paralogs belong only to the germline in Drosophila melanogaster. Sci Rep 2022; 12:11191. [PMID: 35778515 PMCID: PMC9249742 DOI: 10.1038/s41598-022-15233-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/21/2022] [Indexed: 11/20/2022] Open
Abstract
The nascent polypeptide-associated complex (NAC) consisting of α- and β-subunits is an essential ribosome-associated protein conserved in eukaryotes. NAC is a ubiquitously expressed co-translational regulator of nascent protein folding and sorting providing for homeostasis of cellular proteins. Here we report on discovering the germline-specific NACαβ paralogs (gNACs), whose β-subunits, non-distinguishable by ordinary immunodetection, are encoded by five highly homologous gene copies, while the α-subunit is encoded by a single αNAC gene. The gNAC expression is detected in the primordial embryonic and adult gonads via immunostaining. The germline-specific α and β subunits differ from the ubiquitously expressed paralogs by the extended intrinsically disordered regions (IDRs) acquired at the N- and C-termini of the coding regions, predicted to be phosphorylated. The presence of distinct phosphorylated isoforms of gNAC-β subunits is confirmed by comparing of their profiles by 2D-isoeletrofocusing resolution before and after phosphatase treatment of testis ribosomes. We revealed that the predicted S/T sites of phosphorylation in the individual orthologous IDRs of gNAC-β sequences of Drosophila species are positionally conserved despite these disordered regions are drastically different. We propose the IDR-dependent molecular crowding and specific coordination of NAC and other proteostasis regulatory factors at the ribosomes of germinal cells. Our findings imply that there may be a functional crosstalk between the germinal and ubiquitous α- and β-subunits based on assessing their depletion effects on the fly viability and gonad development.
Collapse
Affiliation(s)
- Galina L Kogan
- NRC "Kurchatov Institute"-Institute of Molecular Genetics, 123182, Moscow, Russia
| | - Elena A Mikhaleva
- NRC "Kurchatov Institute"-Institute of Molecular Genetics, 123182, Moscow, Russia
| | - Oxana M Olenkina
- NRC "Kurchatov Institute"-Institute of Molecular Genetics, 123182, Moscow, Russia
| | - Sergei S Ryazansky
- NRC "Kurchatov Institute"-Institute of Molecular Genetics, 123182, Moscow, Russia
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290, Pushchino, Russia.,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290, Pushchino, Russia
| | - Yuri A Abramov
- NRC "Kurchatov Institute"-Institute of Molecular Genetics, 123182, Moscow, Russia
| | - Toomas A Leinsoo
- NRC "Kurchatov Institute"-Institute of Molecular Genetics, 123182, Moscow, Russia
| | - Natalia V Akulenko
- NRC "Kurchatov Institute"-Institute of Molecular Genetics, 123182, Moscow, Russia
| | - Sergey A Lavrov
- NRC "Kurchatov Institute"-Institute of Molecular Genetics, 123182, Moscow, Russia
| | - Vladimir A Gvozdev
- NRC "Kurchatov Institute"-Institute of Molecular Genetics, 123182, Moscow, Russia.
| |
Collapse
|
35
|
Ferla MP, Pagnamenta AT, Koukouflis L, Taylor JC, Marsden BD. Venus: Elucidating the Impact of Amino Acid Variants on Protein Function Beyond Structure Destabilisation. J Mol Biol 2022; 434:167567. [PMID: 35662467 PMCID: PMC9742853 DOI: 10.1016/j.jmb.2022.167567] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 03/11/2022] [Accepted: 03/22/2022] [Indexed: 12/15/2022]
Abstract
Exploring the functional effect of a non-synonymous coding variant at the protein level requires multiple pieces of information to be interpreted appropriately. This is particularly important when embarking on the study of a potentially pathogenic variant linked to a rare or monogenic disease. Whereas accurate protein stability predictions alone are generally informative, other effects, such as disruption of post-translational modifications or weakened ligand binding, may also contribute to the disease phenotype. Furthermore, consideration of nearby variants that are found in the healthy population may strengthen or refute a given mechanistic hypothesis. Whilst there are several bioinformatics tools available that score a genetic variant in terms of deleteriousness, there is no single tool that assembles multiple effects of a variant on the encoded protein, beyond structural stability, and presents them on the structure for inspection. Venus is a web application which, given a protein substitution, rapidly estimates the predicted effect on protein stability of the variant, flags if the variant affects a post-translational modification site, a predicted linear motif or known annotation, and determines the effect on protein stability of variants which affect nearby residues and have been identified in healthy populations. Venus is built upon Michelanglo and the results can be exported to it, allowing them to be annotated and shared with other researchers. Venus is freely accessible at https://venus.cmd.ox.ac.uk and its source code is openly available at https://github.com/CMD-Oxford/Michelanglo-and-Venus.
Collapse
Affiliation(s)
- Matteo P Ferla
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Oxford NIHR Biomedical Research Centre, Oxford, UK.
| | - Alistair T Pagnamenta
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Oxford NIHR Biomedical Research Centre, Oxford, UK. https://twitter.com/@alistairp2011
| | - Leonidas Koukouflis
- Centre for Medicines Discovery, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK
| | - Jenny C Taylor
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Oxford NIHR Biomedical Research Centre, Oxford, UK
| | - Brian D Marsden
- Centre for Medicines Discovery, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, UK; Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, UK. https://twitter.com/@bmarsden19
| |
Collapse
|
36
|
Wagner C, Hois V, Taschler U, Schupp M, Lass A. KIAA1363-A Multifunctional Enzyme in Xenobiotic Detoxification and Lipid Ester Hydrolysis. Metabolites 2022; 12:516. [PMID: 35736449 PMCID: PMC9229287 DOI: 10.3390/metabo12060516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 12/04/2022] Open
Abstract
KIAA1363, annotated as neutral cholesterol ester hydrolase 1 (NCEH1), is a member of the arylacetamide deacetylase (AADAC) protein family. The name-giving enzyme, AADAC, is known to hydrolyze amide and ester bonds of a number of xenobiotic substances, as well as clinical drugs and of endogenous lipid substrates such as diglycerides, respectively. Similarly, KIAA1363, annotated as the first AADAC-like protein, exhibits enzymatic activities for a diverse substrate range including the xenobiotic insecticide chlorpyrifos oxon and endogenous substrates, acetyl monoalkylglycerol ether, cholesterol ester, and retinyl ester. Two independent knockout mouse models have been generated and characterized. However, apart from reduced acetyl monoalkylglycerol ether and cholesterol ester hydrolase activity in specific tissues and cell types, no gross-phenotype has been reported. This raises the question of its physiological role and whether it functions as drug detoxifying enzyme and/or as hydrolase/lipase of endogenous substrates. This review delineates the current knowledge about the structure, function and of the physiological role of KIAA1363, as evident from the phenotypical changes inflicted by pharmacological inhibition or by silencing as well as knockout of KIAA1363 gene expression in cells, as well as mouse models, respectively.
Collapse
Affiliation(s)
- Carina Wagner
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria; (C.W.); (U.T.)
| | - Victoria Hois
- Division of Endocrinology and Diabetology, Medical University of Graz, 8036 Graz, Austria;
| | - Ulrike Taschler
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria; (C.W.); (U.T.)
| | - Michael Schupp
- Cardiovascular Metabolic Renal (CMR)—Research Center, Institute of Pharmacology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10115 Berlin, Germany;
| | - Achim Lass
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria; (C.W.); (U.T.)
- BioTechMed-Graz, 8010 Graz, Austria
- Field of Excellence BioHealth, 8010 Graz, Austria
| |
Collapse
|
37
|
Fabre B, Choteau SA, Duboé C, Pichereaux C, Montigny A, Korona D, Deery MJ, Camus M, Brun C, Burlet-Schiltz O, Russell S, Combier JP, Lilley KS, Plaza S. In Depth Exploration of the Alternative Proteome of Drosophila melanogaster. Front Cell Dev Biol 2022; 10:901351. [PMID: 35721519 PMCID: PMC9204603 DOI: 10.3389/fcell.2022.901351] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/25/2022] [Indexed: 12/13/2022] Open
Abstract
Recent studies have shown that hundreds of small proteins were occulted when protein-coding genes were annotated. These proteins, called alternative proteins, have failed to be annotated notably due to the short length of their open reading frame (less than 100 codons) or the enforced rule establishing that messenger RNAs (mRNAs) are monocistronic. Several alternative proteins were shown to be biologically active molecules and seem to be involved in a wide range of biological functions. However, genome-wide exploration of the alternative proteome is still limited to a few species. In the present article, we describe a deep peptidomics workflow which enabled the identification of 401 alternative proteins in Drosophila melanogaster. Subcellular localization, protein domains, and short linear motifs were predicted for 235 of the alternative proteins identified and point toward specific functions of these small proteins. Several alternative proteins had approximated abundances higher than their canonical counterparts, suggesting that these alternative proteins are actually the main products of their corresponding genes. Finally, we observed 14 alternative proteins with developmentally regulated expression patterns and 10 induced upon the heat-shock treatment of embryos, demonstrating stage or stress-specific production of alternative proteins.
Collapse
Affiliation(s)
- Bertrand Fabre
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, INP, CNRS, Auzeville-Tolosane, France,Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom,*Correspondence: Bertrand Fabre, ; Serge Plaza,
| | - Sebastien A. Choteau
- Aix-Marseille Université, INSERM, TAGC, Turing Centre for Living Systems, Marseille, France
| | - Carine Duboé
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, INP, CNRS, Auzeville-Tolosane, France
| | - Carole Pichereaux
- Fédération de Recherche (FR3450), Agrobiosciences, Interactions et Biodiversité (AIB), CNRS, Toulouse, France,Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France,Infrastructure Nationale de Protéomique, ProFI, FR 2048, Toulouse, France
| | - Audrey Montigny
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, INP, CNRS, Auzeville-Tolosane, France
| | - Dagmara Korona
- Cambridge Systems Biology Centre and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Michael J. Deery
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Mylène Camus
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France,Infrastructure Nationale de Protéomique, ProFI, FR 2048, Toulouse, France
| | - Christine Brun
- Aix-Marseille Université, INSERM, TAGC, Turing Centre for Living Systems, Marseille, France,CNRS, Marseille, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France,Infrastructure Nationale de Protéomique, ProFI, FR 2048, Toulouse, France
| | - Steven Russell
- Cambridge Systems Biology Centre and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Jean-Philippe Combier
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, INP, CNRS, Auzeville-Tolosane, France
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Serge Plaza
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, UPS, INP, CNRS, Auzeville-Tolosane, France,*Correspondence: Bertrand Fabre, ; Serge Plaza,
| |
Collapse
|
38
|
Elkhaligy H, Balbin CA, Siltberg-Liberles J. Comparative Analysis of Structural Features in SLiMs from Eukaryotes, Bacteria, and Viruses with Importance for Host-Pathogen Interactions. Pathogens 2022; 11:pathogens11050583. [PMID: 35631103 PMCID: PMC9147284 DOI: 10.3390/pathogens11050583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 11/19/2022] Open
Abstract
Protein-protein interactions drive functions in eukaryotes that can be described by short linear motifs (SLiMs). Conservation of SLiMs help illuminate functional SLiMs in eukaryotic protein families. However, the simplicity of eukaryotic SLiMs makes them appear by chance due to mutational processes not only in eukaryotes but also in pathogenic bacteria and viruses. Further, functional eukaryotic SLiMs are often found in disordered regions. Although proteomes from pathogenic bacteria and viruses have less disorder than eukaryotic proteomes, their proteins can successfully mimic eukaryotic SLiMs and disrupt host cellular function. Identifying important SLiMs in pathogens is difficult but essential for understanding potential host-pathogen interactions. We performed a comparative analysis of structural features for experimentally verified SLiMs from the Eukaryotic Linear Motif (ELM) database across viruses, bacteria, and eukaryotes. Our results revealed that many viral SLiMs and specific motifs found across viruses and eukaryotes, such as some glycosylation motifs, have less disorder. Analyzing the disorder and coil properties of equivalent SLiMs from pathogens and eukaryotes revealed that some motifs are more structured in pathogens than their eukaryotic counterparts and vice versa. These results support a varying mechanism of interaction between pathogens and their eukaryotic hosts for some of the same motifs.
Collapse
|
39
|
Tonello F, Massimino ML, Peggion C. Nucleolin: a cell portal for viruses, bacteria, and toxins. Cell Mol Life Sci 2022; 79:271. [PMID: 35503380 PMCID: PMC9064852 DOI: 10.1007/s00018-022-04300-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/08/2022] [Accepted: 04/10/2022] [Indexed: 12/18/2022]
Abstract
The main localization of nucleolin is the nucleolus, but this protein is present in multiple subcellular sites, and it is unconventionally secreted. On the cell surface, nucleolin acts as a receptor for various viruses, some bacteria, and some toxins. Aim of this review is to discuss the characteristics that make nucleolin able to act as receptor or co-receptor of so many and different pathogens. The important features that emerge are its multivalence, and its role as a bridge between the cell surface and the nucleus. Multiple domains, short linear motifs and post-translational modifications confer and modulate nucleolin ability to interact with nucleic acids, with proteins, but also with carbohydrates and lipids. This modular multivalence allows nucleolin to participate in different types of biomolecular condensates and to move to various subcellular locations, where it can act as a kind of molecular glue. It moves from the nucleus to the cell surface and can accompany particles in the reverse direction, from the cell surface into the nucleus, which is the destination of several pathogens to manipulate the cell in their favour.
Collapse
Affiliation(s)
- Fiorella Tonello
- CNR of Italy, Neuroscience Institute, viale G. Colombo 3, 35131, Padua, Italy.
| | | | - Caterina Peggion
- Department of Biomedical Sciences, University of Padua, Via Ugo Bassi, 58/B, 35131, Padua, Italy
| |
Collapse
|
40
|
Patterson LL, Velayutham TS, Byerly CD, Bui DC, Patel J, Veljkovic V, Paessler S, McBride JW. Ehrlichia SLiM Ligand Mimetic Activates Notch Signaling in Human Monocytes. mBio 2022; 13:e0007622. [PMID: 35357214 PMCID: PMC9040721 DOI: 10.1128/mbio.00076-22] [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: 01/11/2022] [Accepted: 03/14/2022] [Indexed: 12/15/2022] Open
Abstract
Ehrlichia chaffeensis evades innate host defenses by reprogramming the mononuclear phagocyte through mechanisms that involve the exploitation of multiple evolutionarily conserved cellular signaling pathways, including Notch. This immune evasion strategy is directed in part by tandem repeat protein (TRP) effectors. Specifically, the TRP120 effector activates and regulates Notch signaling through interactions with the Notch receptor and the negative regulator, F-Box and WD repeat domain-containing 7 (FBW7). However, the specific molecular interactions and motifs required for E. chaffeensis TRP120-Notch receptor interaction and activation have not been defined. To investigate the molecular basis of TRP120 Notch activation, we compared TRP120 with endogenous canonical/noncanonical Notch ligands and identified a short region of sequence homology within the tandem repeat (TR) domain. TRP120 was predicted to share biological function with Notch ligands, and a function-associated sequence in the TR domain was identified. To investigate TRP120-Notch receptor interactions, colocalization between TRP120 and endogenous Notch-1 was observed. Moreover, direct interactions between full-length TRP120, the TRP120 TR domain containing the putative Notch ligand sequence, and the Notch receptor LBR were demonstrated. To molecularly define the TRP120 Notch activation motif, peptide mapping was used to identify an 11-amino acid short linear motif (SLiM) located within the TRP120 TR that activated Notch signaling and downstream gene expression. Peptide mutants of the Notch SLiM or anti-Notch SLiM antibody reduced or eliminated Notch activation and NICD nuclear translocation. This investigation reveals a novel molecularly defined pathogen encoded Notch SLiM mimetic that activates Notch signaling consistent with endogenous ligands. IMPORTANCE E. chaffeensis infects and replicates in mononuclear phagocytes, but how it evades innate immune defenses of this indispensable primary innate immune cell is not well understood. This investigation revealed the molecular details of a ligand mimicry cellular reprogramming strategy that involved a short linear motif (SLiM), which enabled E. chaffeensis to exploit host cell signaling to establish and maintain infection. E. chaffeensis TRP120 is a moonlighting effector that has been associated with cellular activation and other functions, including ubiquitin ligase activity. Herein, we identified and demonstrated that a SLiM present within each tandem repeat of TRP120 activated Notch signaling. Notch is an evolutionarily conserved signaling pathway responsible for many cell functions, including cell fate, development, and innate immunity. This study is significant because it revealed the first molecularly defined pathogen encoded SLiM that appears to have evolved de novo to mimic endogenous Notch ligands. Understanding Notch activation during E. chaffeensis infection provides a model to study pathogen exploitation of signaling pathways and will be useful in developing molecularly targeted countermeasures for inhibiting infection by a multitude of disease-causing pathogens that exploit cell signaling through molecular mimicry.
Collapse
Affiliation(s)
- LaNisha L. Patterson
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | | | - Caitlan D. Byerly
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Duc Cuong Bui
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jignesh Patel
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | | | - Slobodan Paessler
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jere W. McBride
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
- Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
| |
Collapse
|
41
|
Kim SJ, Woo Y, Kim HJ, Goo BS, Nhung TTM, Lee SA, Suh BK, Mun DJ, Kim JH, Park SK. Retinoic acid-induced protein 14 controls dendritic spine dynamics associated with depressive-like behaviors. eLife 2022; 11:77755. [PMID: 35467532 PMCID: PMC9068211 DOI: 10.7554/elife.77755] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/24/2022] [Indexed: 11/24/2022] Open
Abstract
Dendritic spines are the central postsynaptic machinery that determines synaptic function. The F-actin within dendritic spines regulates their dynamic formation and elimination. Rai14 is an F-actin-regulating protein with a membrane-shaping function. Here, we identified the roles of Rai14 for the regulation of dendritic spine dynamics associated with stress-induced depressive-like behaviors. Rai14-deficient neurons exhibit reduced dendritic spine density in the Rai14+/- mouse brain, resulting in impaired functional synaptic activity. Rai14 was protected from degradation by complex formation with Tara, and accumulated in the dendritic spine neck, thereby enhancing spine maintenance. Concurrently, Rai14 deficiency in mice altered gene expression profile relevant to depressive conditions and increased depressive-like behaviors. Moreover, Rai14 expression was reduced in the prefrontal cortex of the mouse stress model, which was blocked by antidepressant treatment. Thus, we propose that Rai14-dependent regulation of dendritic spines may underlie the plastic changes of neuronal connections relevant to depressive-like behaviors.
Collapse
Affiliation(s)
- Soo Jeong Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Youngsik Woo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Hyun Jin Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Bon Seong Goo
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Truong Thi My Nhung
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Seol-Ae Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Bo Kyoung Suh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Dong Jin Mun
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Joung-Hun Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Sang Ki Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| |
Collapse
|
42
|
Chaurasia R, Marroquin AS, Vinetz JM, Matthias MA. Pathogenic Leptospira Evolved a Unique Gene Family Comprised of Ricin B-Like Lectin Domain-Containing Cytotoxins. Front Microbiol 2022; 13:859680. [PMID: 35422779 PMCID: PMC9002632 DOI: 10.3389/fmicb.2022.859680] [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: 01/21/2022] [Accepted: 02/08/2022] [Indexed: 12/29/2022] Open
Abstract
Leptospirosis is a globally important neglected zoonotic disease. Previous data suggest that a family of virulence-modifying (VM) proteins (PF07598) is a distinctive feature of group I pathogenic Leptospira that evolved as important virulence determinants. Here, we show that one such VM protein, LA3490 (also known as Q8F0K3), is expressed by Leptospira interrogans serovar Lai, as a secreted genotoxin that is potently cytotoxic to human cells. Structural homology searches using Phyre2 suggested that VM proteins are novel R-type lectins containing tandem N-terminal ricin B-chain-like β-trefoil domains. Recombinant LA3490 (rLA3490) and an N-terminal fragment, t3490, containing only the predicted ricin B domain, bound to the terminal galactose and N-acetyl-galactosamine residues, asialofetuin, and directly competed for asialofetuin-binding sites with recombinant ricin B chain. t3490 alone was sufficient for binding, both to immobilized asialofetuin and to the HeLa cell surface but was neither internalized nor cytotoxic. Treatment of HeLa cells with rLA3490 led to cytoskeleton disassembly, caspase-3 activation, and nuclear fragmentation, and was rapidly cytolethal. rLA3490 had DNase activity on mammalian and bacterial plasmid DNA. The combination of cell surface binding, internalization, nuclear translocation, and DNase functions indicate that LA3490 and other VM proteins evolved as novel forms of the bacterial AB domain-containing toxin paradigm.
Collapse
Affiliation(s)
- Reetika Chaurasia
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, United States
| | - Alan S Marroquin
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, United States
| | - Joseph M Vinetz
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, United States
| | - Michael A Matthias
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, United States
| |
Collapse
|
43
|
Short Linear Motifs (SLiMs) in “Core” RxLR Effectors of
Phytophthora parasitica
var.
nicotianae
: a Case of PpRxLR1 Effector. Microbiol Spectr 2022; 10:e0177421. [PMID: 35404090 PMCID: PMC9045269 DOI: 10.1128/spectrum.01774-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Oomycetes of the genus Phytophthora encompass several of the most successful plant pathogens described to date. The success of infection by Phytophthora species is attributed to the pathogens’ ability to secrete effector proteins that alter the host’s physiological processes. Structural analyses of effector proteins mainly from bacterial and viral pathogens have revealed the presence of intrinsically disordered regions that host short linear motifs (SLiMs). These motifs play important biological roles by facilitating protein-protein interactions as well as protein translocation. Nonetheless, SLiMs in Phytophthora species RxLR effectors have not been investigated previously and their roles remain unknown. Using a bioinformatics pipeline, we identified 333 candidate RxLR effectors in the strain INRA 310 of Phytophthora parasitica. Of these, 71 (21%) were also found to be present in 10 other genomes of P. parasitica, and hence, these were designated core RxLR effectors (CREs). Within the CRE sequences, the N terminus exhibited enrichment in intrinsically disordered regions compared to the C terminus, suggesting a potential role of disorder in effector translocation. Although the disorder content was reduced in the C-terminal regions, it is important to mention that most SLiMs were in this terminus. PpRxLR1 is one of the 71 CREs identified in this study, and its genes encode a 6-amino acid (aa)-long SLiM at the C terminus. We showed that PpRxLR1 interacts with several host proteins that are implicated in defense. Structural analysis of this effector using homology modeling revealed the presence of potential ligand-binding sites. Among key residues that were predicted to be crucial for ligand binding, L102 and Y106 were of interest since they form part of the 6-aa-long PpRxLR1 SLiM. In silico substitution of these two residues to alanine was predicted to have a significant effect on both the function and the structure of PpRxLR1 effector. Molecular docking simulations revealed possible interactions between PpRxLR1 effector and ubiquitin-associated proteins. The ubiquitin-like SLiM carried in this effector was shown to be a potential mediator of these interactions. Further studies are required to validate and elucidate the underlying molecular mechanism of action. IMPORTANCE The continuous gain and loss of RxLR effectors makes the control of Phytophthora spp. difficult. Therefore, in this study, we endeavored to identify RxLR effectors that are highly conserved among species, also known as “core” RxLR effectors (CREs). We reason that these highly conserved effectors target conserved proteins or processes; thus, they can be harnessed in breeding for durable resistance in plants. To further understand the mechanisms of action of CREs, structural dissection of these proteins is crucial. Intrinsically disordered regions (IDRs) that do not adopt a fixed, three-dimensional fold carry short linear motifs (SLiMs) that mediate biological functions of proteins. The presence and potential role of these SLiMs in CREs of Phytophthora spp. have been overlooked. To our knowledge, we have effectively identified CREs as well as SLiMs with the potential of promoting effector virulence. Together, this work has advanced our comprehension of Phytophthora RxLR effector function and may facilitate the development of innovative and effective control strategies.
Collapse
|
44
|
Ghadie MA, Xia Y. Are transient protein-protein interactions more dispensable? PLoS Comput Biol 2022; 18:e1010013. [PMID: 35404956 PMCID: PMC9000134 DOI: 10.1371/journal.pcbi.1010013] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 03/11/2022] [Indexed: 12/12/2022] Open
Abstract
Protein-protein interactions (PPIs) are key drivers of cell function and evolution. While it is widely assumed that most permanent PPIs are important for cellular function, it remains unclear whether transient PPIs are equally important. Here, we estimate and compare dispensable content among transient PPIs and permanent PPIs in human. Starting with a human reference interactome mapped by experiments, we construct a human structural interactome by building three-dimensional structural models for PPIs, and then distinguish transient PPIs from permanent PPIs using several structural and biophysical properties. We map common mutations from healthy individuals and disease-causing mutations onto the structural interactome, and perform structure-based calculations of the probabilities for common mutations (assumed to be neutral) and disease mutations (assumed to be mildly deleterious) to disrupt transient PPIs and permanent PPIs. Using Bayes' theorem we estimate that a similarly small fraction (<~20%) of both transient and permanent PPIs are completely dispensable, i.e., effectively neutral upon disruption. Hence, transient and permanent interactions are subject to similarly strong selective constraints in the human interactome.
Collapse
Affiliation(s)
| | - Yu Xia
- Department of Bioengineering, McGill University, Montreal, Canada
| |
Collapse
|
45
|
Hassan SS, Kodakandla V, Redwan EM, Lundstrom K, Pal Choudhury P, Abd El-Aziz TM, Takayama K, Kandimalla R, Lal A, Serrano-Aroca Á, Azad GK, Aljabali AA, Palù G, Chauhan G, Adadi P, Tambuwala M, Brufsky AM, Baetas-da-Cruz W, Barh D, Azevedo V, Bazan NG, Andrade BS, Santana Silva RJ, Uversky VN. An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. PeerJ 2022; 10:e13136. [PMID: 35341060 PMCID: PMC8944340 DOI: 10.7717/peerj.13136] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/27/2022] [Indexed: 01/12/2023] Open
Abstract
Open reading frame 8 (ORF8) shows one of the highest levels of variability among accessory proteins in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits the presentation of viral antigens by the major histocompatibility complex class I (MHC-I), which interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 in evading immunity and plays a role in SARS-CoV-2 replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents, which include Africa, Asia, Europe and South America. Based on various quantitative features, such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, nine possible T-ORF8 unique variants were defined. The question as to whether T-ORF8 variants function similarly to the wild type ORF8 is yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.
Collapse
Affiliation(s)
- Sk. Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, India
| | - Vaishnavi Kodakandla
- Department of Life sciences, Sophia College For Women, University of Mumbai, Mumbai, India
| | - Elrashdy M. Redwan
- Faculty of Science, Department of Biological Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | | | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic Rochester, Rochester, NY, United States
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigacion Traslacional San Alberto Magno, Universidad Catolica de Valencia San Vicente Martir, Valencia, Spain
| | | | - Alaa A.A. Aljabali
- Department of Pharmaceutics and Pharmaceutical, Yarmouk University, Irbid, Jordan
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, Mexico
| | - Parise Adadi
- Department of Food Science, University of Otago, University of Otago, Dunedin, New Zealand
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, UK
| | - Adam M. Brufsky
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and 46 Applied Biotechnology (IIOAB), Nonakuri, India
| | - Vasco Azevedo
- Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Nikolas G. Bazan
- Neuroscience Center of Excellence, School of Medicine, LSU Health New Orleans, New Orleans, LA, United States
| | - Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, Brazil
| | - Raner José Santana Silva
- Departamento de Ciencias Biologicas (DCB), Programa de Pos-Graduacao em Genetica e Biologia Molecular (PPGGBM), Universidade Estadual de Santa Cruz (UESC), Ilheus, Brazil
| | - Vladimir N. Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL, United States
| |
Collapse
|
46
|
Characterization of the pVHL Interactome in Human Testis Using High-Throughput Library Screening. Cancers (Basel) 2022; 14:cancers14041009. [PMID: 35205757 PMCID: PMC8869832 DOI: 10.3390/cancers14041009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/12/2022] [Accepted: 02/13/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The von Hippel–Lindau (pVHL) tumor suppressor is a protein that regulates the normal cell adaptation to low oxygen concentrations. When its function is altered by inherited or acquired mutation pVHL becomes causative of a familiar predisposition to develop different types of cancers. Besides this role, pVHL is also thought to have other relevant cell functions, and studies in mice demonstrated that this protein is crucial for correct testis development and sperm maturation. By scanning the testis-specific library, we identified 55 novel proteins that interact with the human pVHL, with many of them directly participating in metabolic pathways frequently altered in cancer. Furthermore, our results suggest that pVHL may be also important for correct gonad function in men. Abstract Functional impairment of the von Hippel–Lindau tumor suppressor (pVHL) is causative of a familiar increased risk of developing cancer. As an E3 substrate recognition particle, pVHL marks the hypoxia inducible factor 1α (HIF-1α) for degradation in normoxic conditions, thus acting as a key regulator of both acute and chronic cell adaptation to hypoxia. The male mice model carrying VHL gene conditional knockout presents significant abnormalities in testis development paired with defects in spermatogenesis and infertility, indicating that pVHL exerts testis-specific roles. Here we aimed to explore whether pVHL could have a similar role in humans by performing a testis-tissue library screening complemented with in-depth bioinformatics analysis. We identified 55 novel pVHL binding proteins directly involved in spermatogenesis, cell differentiation and reproductive metabolism. In addition, computational investigation of these new interactors identified multiple pVHL-specific binding motifs and demonstrated that somatic mutations described in human cancers reside in these binding regions. Collectively, these findings suggest that, in addition to its role in cancer formation, pVHL may also be pivotal in normal gonadal development in humans.
Collapse
|
47
|
Cibulka J, Bisaccia F, Radisavljević K, Gudino Carrillo RM, Köhler A. Assembly principle of a membrane-anchored nuclear pore basket scaffold. SCIENCE ADVANCES 2022; 8:eabl6863. [PMID: 35148185 PMCID: PMC8836807 DOI: 10.1126/sciadv.abl6863] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Nuclear pore complexes (NPCs) are membrane-embedded gatekeepers of traffic between the nucleus and cytoplasm. Key features of the NPC symmetric core have been elucidated, but little is known about the NPC basket, a prominent structure with numerous roles in gene expression. Studying the basket was hampered by its instability and connection to the inner nuclear membrane (INM). Here, we reveal the assembly principle of the yeast NPC basket by reconstituting a recombinant Nup60-Mlp1-Nup2 scaffold on a synthetic membrane. Nup60 serves as the basket's flexible suspension cable, harboring an array of short linear motifs (SLiMs). These bind multivalently to the INM, the coiled-coil protein Mlp1, the FG-nucleoporin Nup2, and the NPC core. We suggest that SLiMs, embedded in disordered regions, allow the basket to adapt its structure in response to bulky cargo and changes in gene expression. Our study opens avenues for the higher-order reconstitution of basket-anchored NPC assemblies on membranes.
Collapse
|
48
|
Bondarenko V, Wells MM, Chen Q, Tillman TS, Singewald K, Lawless MJ, Caporoso J, Brandon N, Coleman JA, Saxena S, Lindahl E, Xu Y, Tang P. Structures of highly flexible intracellular domain of human α7 nicotinic acetylcholine receptor. Nat Commun 2022; 13:793. [PMID: 35145092 PMCID: PMC8831596 DOI: 10.1038/s41467-022-28400-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/10/2022] [Indexed: 11/24/2022] Open
Abstract
The intracellular domain (ICD) of Cys-loop receptors mediates diverse functions. To date, no structure of a full-length ICD is available due to challenges stemming from its dynamic nature. Here, combining nuclear magnetic resonance (NMR) and electron spin resonance experiments with Rosetta computations, we determine full-length ICD structures of the human α7 nicotinic acetylcholine receptor in a resting state. We show that ~57% of the ICD residues are in highly flexible regions, primarily in a large loop (loop L) with the most mobile segment spanning ~50 Å from the central channel axis. Loop L is anchored onto the MA helix and virtually forms two smaller loops, thereby increasing its stability. Previously known motifs for cytoplasmic binding, regulation, and signaling are found in both the helices and disordered flexible regions, supporting the essential role of the ICD conformational plasticity in orchestrating a broad range of biological processes. The intracellular domain (ICD) of Cys-loop receptors mediates many of their functions, but no complete structure of a Cys-loop receptor ICD is available to date. Here, the authors combine NMR and ESR spectroscopy to determine the full-length ICD structures of the human α7 nicotinic acetylcholine receptor (α7nAChR).
Collapse
Affiliation(s)
- Vasyl Bondarenko
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Marta M Wells
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Qiang Chen
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Tommy S Tillman
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Kevin Singewald
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Matthew J Lawless
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Joel Caporoso
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Nicole Brandon
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Jonathan A Coleman
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden.,Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Solna, Sweden
| | - Yan Xu
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA.,Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, 15260, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15260, USA.,Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Pei Tang
- Depatment of Anesthesiology and Perioperative Medicine, University of Pittsburgh, Pittsburgh, PA, 15260, USA. .,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15260, USA. .,Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
| |
Collapse
|
49
|
Huskey ALW, Merner ND. An investigation into the role of inherited CEACAM gene family variants and colorectal cancer risk. BMC Res Notes 2022; 15:26. [PMID: 35115044 PMCID: PMC8815132 DOI: 10.1186/s13104-022-05907-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/11/2022] [Indexed: 01/03/2023] Open
Abstract
Objective This study was designed to determine if CEACAM mutations are associated with inherited risk of colorectal cancer. Recently, protein-truncating mutations in the CEACAM gene family were associated with inherited breast cancer risk. That discovery, along with aberrant expression of CEACAM genes in colorectal cancer tumors and that colorectal cancer and breast cancer share many risk factors, including genetics, inspired our team to search for inherited CEACAM mutations in colorectal cancer cases. Specifically utilizing The Cancer Genome Atlas (TCGA) blood-derived whole-exome sequencing data from the colorectal cancer cohort, rare protein-truncating variants and missense variants were investigated through single variant and aggregation analyses in European American and African American cases and compared to ethnic-matched controls. Results A total of 34 and 14 different CEACAM variants were identified in European American and African American colorectal cancer cases, respectively. Nine missense variants were individually associated with risk, two in African Americans and seven in European Americans. No identified protein-truncating variants were associated with CRC risk in either ethnicity. Gene family and gene-specific aggregation analyses did not yield any significant results. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-022-05907-6.
Collapse
Affiliation(s)
- Anna L W Huskey
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, 1130 Wire Road, Auburn, AL, 36849, USA.,Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, 3306 Walker Building, Auburn, AL, 36849, USA
| | - Nancy D Merner
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, 1130 Wire Road, Auburn, AL, 36849, USA.
| |
Collapse
|
50
|
Varga JK, Diffley K, Welker Leng KR, Fierke CA, Schueler-Furman O. Structure-based prediction of HDAC6 substrates validated by enzymatic assay reveals determinants of promiscuity and detects new potential substrates. Sci Rep 2022; 12:1788. [PMID: 35110592 PMCID: PMC8810773 DOI: 10.1038/s41598-022-05681-2] [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: 10/15/2021] [Accepted: 01/17/2022] [Indexed: 01/25/2023] Open
Abstract
Histone deacetylases play important biological roles well beyond the deacetylation of histone tails. In particular, HDAC6 is involved in multiple cellular processes such as apoptosis, cytoskeleton reorganization, and protein folding, affecting substrates such as ɑ-tubulin, Hsp90 and cortactin proteins. We have applied a biochemical enzymatic assay to measure the activity of HDAC6 on a set of candidate unlabeled peptides. These served for the calibration of a structure-based substrate prediction protocol, Rosetta FlexPepBind, previously used for the successful substrate prediction of HDAC8 and other enzymes. A proteome-wide screen of reported acetylation sites using our calibrated protocol together with the enzymatic assay provide new peptide substrates and avenues to novel potential functional regulatory roles of this promiscuous, multi-faceted enzyme. In particular, we propose novel regulatory roles of HDAC6 in tumorigenesis and cancer cell survival via the regulation of EGFR/Akt pathway activation. The calibration process and comparison of the results between HDAC6 and HDAC8 highlight structural differences that explain the established promiscuity of HDAC6.
Collapse
Affiliation(s)
- Julia K Varga
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University of Jerusalem, Faculty of Medicine, POB 12272, 9112102, Jerusalem, Israel
| | - Kelsey Diffley
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI, 48109, USA
| | - Katherine R Welker Leng
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI, 48109, USA
| | - Carol A Fierke
- Department of Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, MI, 48109, USA
- Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA, 02453, USA
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada (IMRIC), The Hebrew University of Jerusalem, Faculty of Medicine, POB 12272, 9112102, Jerusalem, Israel.
| |
Collapse
|