151
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Plasticity of an ultrafast interaction between nucleoporins and nuclear transport receptors. Cell 2015; 163:734-45. [PMID: 26456112 PMCID: PMC4622936 DOI: 10.1016/j.cell.2015.09.047] [Citation(s) in RCA: 213] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/17/2015] [Accepted: 09/23/2015] [Indexed: 11/23/2022]
Abstract
The mechanisms by which intrinsically disordered proteins engage in rapid and highly selective binding is a subject of considerable interest and represents a central paradigm to nuclear pore complex (NPC) function, where nuclear transport receptors (NTRs) move through the NPC by binding disordered phenylalanine-glycine-rich nucleoporins (FG-Nups). Combining single-molecule fluorescence, molecular simulations, and nuclear magnetic resonance, we show that a rapidly fluctuating FG-Nup populates an ensemble of conformations that are prone to bind NTRs with near diffusion-limited on rates, as shown by stopped-flow kinetic measurements. This is achieved using multiple, minimalistic, low-affinity binding motifs that are in rapid exchange when engaging with the NTR, allowing the FG-Nup to maintain an unexpectedly high plasticity in its bound state. We propose that these exceptional physical characteristics enable a rapid and specific transport mechanism in the physiological context, a notion supported by single molecule in-cell assays on intact NPCs. Integrative structural biology reveals the basis of rapid nuclear transport Transient binding of disordered nucleoporins leaves their plasticity unaffected Multiple minimalistic low-affinity binding motifs create a polyvalent complex A highly reactive and dynamic surface permits an ultrafast binding mechanism
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152
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Tompa P, Schad E, Tantos A, Kalmar L. Intrinsically disordered proteins: emerging interaction specialists. Curr Opin Struct Biol 2015; 35:49-59. [PMID: 26402567 DOI: 10.1016/j.sbi.2015.08.009] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/23/2015] [Accepted: 08/28/2015] [Indexed: 12/22/2022]
Abstract
Intrinsically disordered proteins or regions of proteins (IDPs/IDRs) most often function through protein-protein interactions, when they permanently or transiently bind partner molecules with diverse functional consequences. There is a rapid advance in our understanding of the ensuing functional modes, obtained from describing atomic details of individual complexes, proteome-wide studies of interactomes and characterizing loosely assembled hydrogels and tightly packed amyloids. Here we briefly survey the most important recent methodological developments and structural-functional observations, with the aim of increasing the general appreciation of IDPs/IDRs as 'interaction specialists'.
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Affiliation(s)
- Peter Tompa
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium; Vrije Universiteit Brussel, Brussels, Belgium; Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary.
| | - Eva Schad
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Agnes Tantos
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Lajos Kalmar
- Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
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153
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Mackowiak SD, Zauber H, Bielow C, Thiel D, Kutz K, Calviello L, Mastrobuoni G, Rajewsky N, Kempa S, Selbach M, Obermayer B. Extensive identification and analysis of conserved small ORFs in animals. Genome Biol 2015; 16:179. [PMID: 26364619 PMCID: PMC4568590 DOI: 10.1186/s13059-015-0742-x] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/05/2015] [Indexed: 02/06/2023] Open
Abstract
Background There is increasing evidence that transcripts or transcript regions annotated as non-coding can harbor functional short open reading frames (sORFs). Loss-of-function experiments have identified essential developmental or physiological roles for a few of the encoded peptides (micropeptides), but genome-wide experimental or computational identification of functional sORFs remains challenging. Results Here, we expand our previously developed method and present results of an integrated computational pipeline for the identification of conserved sORFs in human, mouse, zebrafish, fruit fly, and the nematode C. elegans. Isolating specific conservation signatures indicative of purifying selection on amino acid (rather than nucleotide) sequence, we identify about 2,000 novel small ORFs located in the untranslated regions of canonical mRNAs or on transcripts annotated as non-coding. Predicted sORFs show stronger conservation signatures than those identified in previous studies and are sometimes conserved over large evolutionary distances. The encoded peptides have little homology to known proteins and are enriched in disordered regions and short linear interaction motifs. Published ribosome profiling data indicate translation of more than 100 novel sORFs, and mass spectrometry data provide evidence for more than 70 novel candidates. Conclusions Taken together, we identify hundreds of previously unknown conserved sORFs in major model organisms. Our computational analyses and integration with experimental data show that these sORFs are expressed, often translated, and sometimes widely conserved, in some cases even between vertebrates and invertebrates. We thus provide an integrated resource of putatively functional micropeptides for functional validation in vivo. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0742-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sebastian D Mackowiak
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Henrik Zauber
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Chris Bielow
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany. .,Berlin Institute of Health, Kapelle-Ufer 2, 10117, Berlin, Germany.
| | - Denise Thiel
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Kamila Kutz
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Lorenzo Calviello
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Guido Mastrobuoni
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Nikolaus Rajewsky
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Stefan Kempa
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Matthias Selbach
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
| | - Benedikt Obermayer
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
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154
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Krejci A, Hupp TR, Lexa M, Vojtesek B, Muller P. Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets. Bioinformatics 2015; 32:9-16. [PMID: 26342231 PMCID: PMC4681989 DOI: 10.1093/bioinformatics/btv522] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 08/27/2015] [Indexed: 12/30/2022] Open
Abstract
Motivation: Proteins often recognize their interaction partners on the basis of short linear motifs located in disordered regions on proteins’ surface. Experimental techniques that study such motifs use short peptides to mimic the structural properties of interacting proteins. Continued development of these methods allows for large-scale screening, resulting in vast amounts of peptide sequences, potentially containing information on multiple protein-protein interactions. Processing of such datasets is a complex but essential task for large-scale studies investigating protein-protein interactions. Results: The software tool presented in this article is able to rapidly identify multiple clusters of sequences carrying shared specificity motifs in massive datasets from various sources and generate multiple sequence alignments of identified clusters. The method was applied on a previously published smaller dataset containing distinct classes of ligands for SH3 domains, as well as on a new, an order of magnitude larger dataset containing epitopes for several monoclonal antibodies. The software successfully identified clusters of sequences mimicking epitopes of antibody targets, as well as secondary clusters revealing that the antibodies accept some deviations from original epitope sequences. Another test indicates that processing of even much larger datasets is computationally feasible. Availability and implementation: Hammock is published under GNU GPL v. 3 license and is freely available as a standalone program (from http://www.recamo.cz/en/software/hammock-cluster-peptides/) or as a tool for the Galaxy toolbox (from https://toolshed.g2.bx.psu.edu/view/hammock/hammock). The source code can be downloaded from https://github.com/hammock-dev/hammock/releases. Contact:muller@mou.cz Supplementaryinformation:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Adam Krejci
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 65653, Brno, Czech Republic
| | - Ted R Hupp
- University of Edinburgh, Institute of Genetics and Molecular Medicine, Cancer Research Centre, Edinburgh EH4 2XR, UK and
| | - Matej Lexa
- Faculty of Informatics, Masaryk University, Botanicka 68a, 60200 Brno, Czech Republic
| | - Borivoj Vojtesek
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 65653, Brno, Czech Republic
| | - Petr Muller
- RECAMO, Masaryk Memorial Cancer Institute, Zluty kopec 7, 65653, Brno, Czech Republic
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155
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Kohoutová L, Kourová H, Nagy SK, Volc J, Halada P, Mészáros T, Meskiene I, Bögre L, Binarová P. The Arabidopsis mitogen-activated protein kinase 6 is associated with γ-tubulin on microtubules, phosphorylates EB1c and maintains spindle orientation under nitrosative stress. THE NEW PHYTOLOGIST 2015; 207:1061-74. [PMID: 26061286 DOI: 10.1111/nph.13501] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 05/05/2015] [Indexed: 05/07/2023]
Abstract
Stress-activated plant mitogen-activated protein (MAP) kinase pathways play roles in growth adaptation to the environment by modulating cell division through cytoskeletal regulation, but the mechanisms are poorly understood. We performed protein interaction and phosphorylation experiments with cytoskeletal proteins, mass spectrometric identification of MPK6 complexes and immunofluorescence analyses of the microtubular cytoskeleton of mitotic cells using wild-type, mpk6-2 mutant and plants overexpressing the MAP kinase-inactivating phosphatase, AP2C3. We showed that MPK6 interacted with γ-tubulin and co-sedimented with plant microtubules polymerized in vitro. It was the active form of MAP kinase that was enriched with microtubules and followed similar dynamics to γ-tubulin, moving from poles to midzone during the anaphase-to-telophase transition. We found a novel substrate for MPK6, the microtubule plus end protein, EB1c. The mpk6-2 mutant was sensitive to 3-nitro-l-tyrosine (NO2 -Tyr) treatment with respect to mitotic abnormalities, and root cells overexpressing AP2C3 showed defects in chromosome segregation and spindle orientation. Our data suggest that the active form of MAP kinase interacts with γ-tubulin on specific subsets of mitotic microtubules during late mitosis. MPK6 phosphorylates EB1c, but not EB1a, and has a role in maintaining regular planes of cell division under stress conditions.
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Affiliation(s)
- Lucie Kohoutová
- Institute of Microbiology AS CR, v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Hana Kourová
- Institute of Microbiology AS CR, v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Szilvia K Nagy
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Tűzoltó u. 37-47, H-1094, Budapest, Hungary
| | - Jindřich Volc
- Institute of Microbiology AS CR, v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Petr Halada
- Institute of Microbiology AS CR, v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Tamás Mészáros
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Tűzoltó u. 37-47, H-1094, Budapest, Hungary
- Technical Analytical Research Group of HAS, Szent Gellért tér 4, H-1111, Budapest, Hungary
| | - Irute Meskiene
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- Institute of Biotechnology, University of Vilnius, Vilnius, Lithuania
| | - László Bögre
- School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
| | - Pavla Binarová
- Institute of Microbiology AS CR, v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
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156
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Lees JG, Ranea JA, Orengo CA. Identifying and characterising key alternative splicing events in Drosophila development. BMC Genomics 2015; 16:608. [PMID: 26275604 PMCID: PMC4537583 DOI: 10.1186/s12864-015-1674-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/29/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND In complex Metazoans a given gene frequently codes for multiple protein isoforms, through processes such as alternative splicing. Large scale functional annotation of these isoforms is a key challenge for functional genomics. This annotation gap is increasing with the large numbers of multi transcript genes being identified by technologies such as RNASeq. Furthermore attempts to characterise the functions of splicing in an organism are complicated by the difficulty in distinguishing functional isoforms from those produced by splicing errors or transcription noise. Tools to help prioritise candidate isoforms for testing are largely absent. RESULTS In this study we implement a Time-course Switch (TS) score for ranking isoforms by their likelihood of producing additional functions based on their developmental expression profiles, as reported by modENCODE. The TS score allows us to better investigate functional roles of different isoforms expressed in multi transcript genes. From this analysis, we find that isoforms with high TS scores have sequence feature changes consistent with more deterministic splicing and functional changes and tend to gain domains or whole exons which could carry additional functions. Furthermore these functions appear to be particularly important for essential regulatory roles, establishing functional isoform switching as key for regulatory processes. Based on the TS score we develop a Transcript Annotations Pipeline for Alternative Splicing (TAPAS) that identifies functional neighbourhoods of potentially interesting isoforms. CONCLUSIONS We have identified a subset of protein isoforms which appear to have high functional significance, particularly in regulation. This has been made possible through the development of novel methods that make use of transcript expression profiles. The methods and analyses we present here represent important first steps in the development of tools to address the near complete lack of isoform specific function annotation. In turn the tools allow us to better characterise the regulatory functions of alternative splicing in more detail.
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Affiliation(s)
- Jonathan G Lees
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, UK.
| | - Juan A Ranea
- Department of Molecular Biology and Biochemistry-CIBER de Enfermedades Raras, University of Malaga, Malaga, 29071, Spain.
| | - Christine A Orengo
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, UK.
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157
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Kpetemey M, Dasgupta S, Rajendiran S, Das S, Gibbs LD, Shetty P, Gryczynski Z, Vishwanatha JK. MIEN1, a novel interactor of Annexin A2, promotes tumor cell migration by enhancing AnxA2 cell surface expression. Mol Cancer 2015; 14:156. [PMID: 26272794 PMCID: PMC4536591 DOI: 10.1186/s12943-015-0428-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 08/05/2015] [Indexed: 12/14/2022] Open
Abstract
Background Migration and invasion enhancer 1 (MIEN1) is a novel gene found to be abundantly expressed in breast tumor tissues and functions as a critical regulator of tumor cell migration and invasion to promote systemic metastases. Previous studies have identified post-translational modifications by isoprenylation at the C-terminal tail of MIEN1 to favor its translocation to the inner leaflet of plasma membrane and its function as a membrane-bound adapter molecule. However, the exact molecular events at the membrane interface activating the MIEN1-driven tumor cell motility are vaguely understood. Methods MIEN1 was first studied using in-silico analysis on available RNA sequencing data of human breast tissues and its expression was ascertained in breast cells. We performed several assays including co-immunoprecipitation, wound healing, western blotting and immunofluorescence to decipher the molecular events involved in MIEN1-mediated tumor cell migration. Results Clinically, MIEN1 is predominantly overexpressed in Her-2 and luminal B subtypes of breast tumors, and its increased expression correlates with poor disease free survival. Molecular studies identified a phosphorylation-dependent activation signal in the immunoreceptor tyrosine based activation motif (ITAM) of MIEN1 and the phosphorylation-deficient MIEN1-mutants (Y39F/50 F) to regulate filopodia generation, migration and invasion. We found that ITAM-phosphorylation of MIEN1 is significantly impaired in isoprenylation-deficient MIEN1 mutants indicating that prenylation of MIEN1 and membrane association is required for cross-phosphorylation of tyrosine residues. Furthermore, we identified MIEN1 as a novel interactor of Annexin A2 (AnxA2), a Ca2+ -dependent phospholipid binding protein, which serves as an extracellular proteolytic center regulating plasmin generation. Fluorescence resonance energy transfer (FRET) confirmed that MIEN1 physically interacts with AnxA2 and functional studies revealed that they mutually cooperate to accentuate tumor cell motility. Interestingly, our study identified that ectopic overexpression of MIEN1 significantly enhances Tyr23-phosphorylation on AnxA2, thereby stimulating cell surface translocation of AnxA2 and catalyzing the activation of its proteolytic activity. Conclusion Our data show that the presence and interaction of both MIEN1 and AnxA2 in breast tumors are crucial drivers of cell motility. Our study has now deciphered a novel regulatory network governing the vicious process of breast tumor cell invasion-metastasis, and findings suggest MIEN1-AnxA2 as prospective targets to counter the deadly disease. Electronic supplementary material The online version of this article (doi:10.1186/s12943-015-0428-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marilyne Kpetemey
- Department of Molecular and Medical Genetics and Institute for Cancer Research, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA. .,Institute for Cancer Research, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA.
| | - Subhamoy Dasgupta
- Department of Molecular and Medical Genetics and Institute for Cancer Research, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA. .,Institute for Cancer Research, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA.
| | - Smrithi Rajendiran
- Department of Molecular and Medical Genetics and Institute for Cancer Research, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA. .,Institute for Cancer Research, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA.
| | - Susobhan Das
- Department of Molecular and Medical Genetics and Institute for Cancer Research, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA. .,Institute for Cancer Research, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA.
| | - Lee D Gibbs
- Department of Molecular and Medical Genetics and Institute for Cancer Research, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA. .,Institute for Cancer Research, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA.
| | - Praveenkumar Shetty
- Department of Molecular and Medical Genetics and Institute for Cancer Research, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA. .,Institute for Cancer Research, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA.
| | - Zygmunt Gryczynski
- Department of Molecular and Medical Genetics and Institute for Cancer Research, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA. .,Institute for Cancer Research, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA.
| | - Jamboor K Vishwanatha
- Department of Molecular and Medical Genetics and Institute for Cancer Research, University of North Texas Health Science Center, 3500 Camp Bowie Blvd., Fort Worth, TX, 76107, USA. .,Institute for Cancer Research, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA. .,Texas Center for Health Disparities, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA.
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158
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Song T, Bu X, Gu H. Combining intrinsic disorder prediction and augmented training of hidden Markov models improves discriminative motif discovery. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.06.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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159
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Kanchan K, Fuxreiter M, Fésüs L. Physiological, pathological, and structural implications of non-enzymatic protein-protein interactions of the multifunctional human transglutaminase 2. Cell Mol Life Sci 2015; 72:3009-35. [PMID: 25943306 PMCID: PMC11113818 DOI: 10.1007/s00018-015-1909-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 04/10/2015] [Accepted: 04/13/2015] [Indexed: 12/26/2022]
Abstract
Transglutaminase 2 (TG2) is a ubiquitously expressed member of an enzyme family catalyzing Ca(2+)-dependent transamidation of proteins. It is a multifunctional protein having several well-defined enzymatic (GTP binding and hydrolysis, protein disulfide isomerase, and protein kinase activities) and non-enzymatic (multiple interactions in protein scaffolds) functions. Unlike its enzymatic interactions, the significance of TG2's non-enzymatic regulation of its activities has recently gained importance. In this review, we summarize all the partners that directly interact with TG2 in a non-enzymatic manner and analyze how these interactions could modulate the crosslinking activity and cellular functions of TG2 in different cell compartments. We have found that TG2 mostly acts as a scaffold to bridge various proteins, leading to different functional outcomes. We have also studied how specific structural features, such as intrinsically disordered regions and embedded short linear motifs contribute to multifunctionality of TG2. Conformational diversity of intrinsically disordered regions enables them to interact with multiple partners, which can result in different biological outcomes. Indeed, ID regions in TG2 were identified in functionally relevant locations, indicating that they could facilitate conformational transitions towards the catalytically competent form. We reason that these structural features contribute to modulating the physiological and pathological functions of TG2 and could provide a new direction for detecting unique regulatory partners. Additionally, we have assembled all known anti-TG2 antibodies and have discussed their significance as a toolbox for identifying and confirming novel TG2 regulatory functions.
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Affiliation(s)
- Kajal Kanchan
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, 4010 Hungary
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Mónika Fuxreiter
- MTA-DE Momentum Laboratory of Protein Dynamics, University of Debrecen, Debrecen, Hungary
| | - László Fésüs
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, 4010 Hungary
- MTA-DE Apoptosis, Genomics and Stem Cell Research Group of the Hungarian Academy of Sciences, Debrecen, Hungary
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160
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Computational and statistical methods for high-throughput analysis of post-translational modifications of proteins. J Proteomics 2015. [PMID: 26216596 DOI: 10.1016/j.jprot.2015.07.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The investigation of post-translational modifications (PTMs) represents one of the main research focuses for the study of protein function and cell signaling. Mass spectrometry instrumentation with increasing sensitivity improved protocols for PTM enrichment and recently established pipelines for high-throughput experiments allow large-scale identification and quantification of several PTM types. This review addresses the concurrently emerging challenges for the computational analysis of the resulting data and presents PTM-centered approaches for spectra identification, statistical analysis, multivariate analysis and data interpretation. We furthermore discuss the potential of future developments that will help to gain deep insight into the PTM-ome and its biological role in cells. This article is part of a Special Issue entitled: Computational Proteomics.
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161
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Song T, Gu H. Discovering short linear protein motif based on selective training of profile hidden Markov models. J Theor Biol 2015; 377:75-84. [PMID: 25791288 DOI: 10.1016/j.jtbi.2015.03.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 03/06/2015] [Accepted: 03/07/2015] [Indexed: 11/20/2022]
Abstract
Short linear motifs (SLiMs) in proteins are relatively conservative sequence patterns within disordered regions of proteins, typically 3-10 amino acids in length. They play an important role in mediating protein-protein interactions. Discovering SLiMs by computational methods has attracted more and more attention, most of which were based on regular expressions and profiles. In this paper, a de novo motif discovery method was proposed based on profile hidden Markov models (HMMs), which can not only provide the emission probabilities of amino acids in the defined positions of SLiMs, but also model the undefined positions. We adopted the ordered region masking and the relative local conservation (RLC) masking to improve the signal to noise ratio of the query sequences while applying evolutionary weighting to make the important sequences in evolutionary process get more attention by the selective training of profile HMMs. The experimental results show that our method and the profile-based method returned different subsets within a SLiMs dataset, and the performance of the two approaches are equivalent on a more realistic discovery dataset. Profile HMM-based motif discovery methods complement the existing methods and provide another way for SLiMs analysis.
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Affiliation(s)
- Tao Song
- Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian, Liaoning 116024, China
| | - Hong Gu
- Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian, Liaoning 116024, China.
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162
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Meng F, Badierah RA, Almehdar HA, Redwan EM, Kurgan L, Uversky VN. Unstructural biology of the dengue virus proteins. FEBS J 2015; 282:3368-94. [DOI: 10.1111/febs.13349] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2015] [Revised: 06/01/2015] [Accepted: 06/15/2015] [Indexed: 01/02/2023]
Affiliation(s)
- Fanchi Meng
- Department of Electrical and Computer Engineering; University of Alberta; Edmonton Alberta Canada
| | - Reaid A. Badierah
- Biological Department; Faculty of Science; King Abdulaziz University; Jeddah Saudi Arabia
| | - Hussein A. Almehdar
- Biological Department; Faculty of Science; King Abdulaziz University; Jeddah Saudi Arabia
| | - Elrashdy M. Redwan
- Biological Department; Faculty of Science; King Abdulaziz University; Jeddah Saudi Arabia
- Therapeutic and Protective Proteins Laboratory; Protein Research Department; Genetic Engineering and Biotechnology Research Institute; City for Scientific Research and Technology Applications; New Borg El-Arab Alexandria Egypt
| | - Lukasz Kurgan
- Department of Electrical and Computer Engineering; University of Alberta; Edmonton Alberta Canada
| | - Vladimir N. Uversky
- Biological Department; Faculty of Science; King Abdulaziz University; Jeddah Saudi Arabia
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute; Morsani College of Medicine; University of South Florida; Tampa FL USA
- Laboratory of Structural Dynamics, Stability and Folding of Proteins; Institute of Cytology; Russian Academy of Sciences; St Petersburg Russia
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163
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Teilum K, Olsen JG, Kragelund BB. Globular and disordered-the non-identical twins in protein-protein interactions. Front Mol Biosci 2015. [PMID: 26217672 PMCID: PMC4496568 DOI: 10.3389/fmolb.2015.00040] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In biology proteins from different structural classes interact across and within classes in ways that are optimized to achieve balanced functional outputs. The interactions between intrinsically disordered proteins (IDPs) and other proteins rely on changes in flexibility and this is seen as a strong determinant for their function. This has fostered the notion that IDP's bind with low affinity but high specificity. Here we have analyzed available detailed thermodynamic data for protein-protein interactions to put to the test if the thermodynamic profiles of IDP interactions differ from those of other protein-protein interactions. We find that ordered proteins and the disordered ones act as non-identical twins operating by similar principles but where the disordered proteins complexes are on average less stable by 2.5 kcal mol(-1).
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Affiliation(s)
- Kaare Teilum
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Johan G Olsen
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen Copenhagen, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen Copenhagen, Denmark
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164
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A Dynein Light Chain 1 Binding Motif in Rabies Virus Polymerase L Protein Plays a Role in Microtubule Reorganization and Viral Primary Transcription. J Virol 2015; 89:9591-600. [PMID: 26157129 DOI: 10.1128/jvi.01298-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/04/2015] [Indexed: 02/06/2023] Open
Abstract
UNLABELLED Rabies virus (RABV) polymerase L together with phosphoprotein P forms the PL polymerase complex that is essential for replication and transcription. However, its exact mechanism of action, interactions with cellular factors, and intracellular distribution are yet to be understood. Here by imaging a fluorescently tagged polymerase (mCherry-RABV-L), we show that L accumulates at acetylated and reorganized microtubules (MT). In silico analysis revealed a dynein light chain 1 (DLC1) binding motif in L that could mediate MT binding through dynein motors. As DLC1 binding by polymerase cofactor P is known, we compared the impact of the DLC1-binding motifs in P and L. Viruses with mutations in the respective motifs revealed that both motifs are required for efficient primary transcription, indicating that DLC1 acts as a transcription enhancer by binding to both P and L. Notably, also the levels of cellular DLC1 protein were regulated by both motifs, suggesting regulation of the DLC1 gene expression by both P and L. Finally, disruption of the motif in L resulted in a cell-type-specific loss of MT localization, demonstrating that DLC1 is involved in L-mediated cytoskeleton reorganization. Overall, we conclude that DLC1 acts as a transcription factor that stimulates primary RABV transcription by binding to both P and L. We further conclude that L influences MT organization and posttranslational modification, suggesting a model in which MT manipulation by L contributes to efficient intracellular transport of virus components and thus may serve as an important step in virus replication. IMPORTANCE Regulation of rabies virus polymerase complex by viral and cellular factors thus far has not been fully understood. Although cellular dynein light chain 1 (DLC1) has been reported to increase primary transcription by binding to polymerase cofactor phosphoprotein P, the detailed mechanism is unknown, and it is also not known whether the large enzymatic polymerase subunit L is involved. By fluorescence microscopy analysis of fluorescence-tagged rabies virus L, in silico identification of a potential DLC1 binding site in L, and characterization of recombinant rabies virus mutants, we show that a DLC1 binding motif in L is involved in cytoskeleton localization and reorganization, primary transcription regulation by DLC1, and regulation of cellular DLC1 gene expression. By providing evidence for a direct contribution of a DLC1 binding motif in L, our data significantly increase the understanding of rabies virus polymerase regulation and host manipulation by the virus as well.
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165
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Bordat A, Houvenaghel MC, German-Retana S. Gibson assembly: an easy way to clone potyviral full-length infectious cDNA clones expressing an ectopic VPg. Virol J 2015; 12:89. [PMID: 26070311 PMCID: PMC4475333 DOI: 10.1186/s12985-015-0315-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 05/29/2015] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Approaches to simplify and accelerate the construction of full-length infectious cDNA clones for plant potyviruses have been described, based on cloning strategies involving in vitro ligation or homologous recombination in yeast. In the present study, we developed a faster and more efficient in vitro recombination system using Gibson assembly (GA), to engineer a Lettuce mosaic virus (LMV) infectious clone expressing an ectopic mcherry-tagged VPg (Viral protein genome-linked) for in planta subcellular localization of the viral protein in an infection context. METHODS Three overlapping long distance PCR fragments were amplified and assembled in a single-step process based on in vitro recombination (Gibson assembly). The resulting 17.5 kbp recombinant plasmids (LMVmchVPg_Ec) were inoculated by biolistic on lettuce plants and then propagated mechanically on Nicotiana benthamiana. Confocal microscopy was used to analyze the subcellular localization of the ectopically expressed mcherry-VPg fusion protein. RESULTS The Gibson assembly allowed the cloning of the expected plasmids without any deletion. All the inoculated plants displayed symptoms characteristic of LMV infection. The majority of the mcherry fluorescent signal observed using confocal microscopy was located in the nucleus and nucleolus as expected for a potyviral VPg. CONCLUSIONS This is the first report of the use of the Gibson assembly method to construct full-length infectious cDNA clones of a potyvirus genome. This is also the first description of the ectopic expression of a tagged version of a potyviral VPg without affecting the viability of the recombinant potyvirus.
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Affiliation(s)
- Amandine Bordat
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon, France.
- Université de Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon, France.
| | - Marie-Christine Houvenaghel
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon, France.
- Université de Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon, France.
| | - Sylvie German-Retana
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon, France.
- Université de Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, CS 20032, 33882, Villenave d'Ornon, France.
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166
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Wong A, Gehring C, Irving HR. Conserved Functional Motifs and Homology Modeling to Predict Hidden Moonlighting Functional Sites. Front Bioeng Biotechnol 2015; 3:82. [PMID: 26106597 PMCID: PMC4460814 DOI: 10.3389/fbioe.2015.00082] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/18/2015] [Indexed: 12/11/2022] Open
Abstract
Moonlighting functional centers within proteins can provide them with hitherto unrecognized functions. Here, we review how hidden moonlighting functional centers, which we define as binding sites that have catalytic activity or regulate protein function in a novel manner, can be identified using targeted bioinformatic searches. Functional motifs used in such searches include amino acid residues that are conserved across species and many of which have been assigned functional roles based on experimental evidence. Molecules that were identified in this manner seeking cyclic mononucleotide cyclases in plants are used as examples. The strength of this computational approach is enhanced when good homology models can be developed to test the functionality of the predicted centers in silico, which, in turn, increases confidence in the ability of the identified candidates to perform the predicted functions. Computational characterization of moonlighting functional centers is not diagnostic for catalysis but serves as a rapid screening method, and highlights testable targets from a potentially large pool of candidates for subsequent in vitro and in vivo experiments required to confirm the functionality of the predicted moonlighting centers.
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Affiliation(s)
- Aloysius Wong
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology , Thuwal , Saudi Arabia
| | - Chris Gehring
- Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology , Thuwal , Saudi Arabia
| | - Helen R Irving
- Monash Institute of Pharmaceutical Sciences, Monash University , Melbourne, VIC , Australia
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167
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Stokes C, Treinin M, Papke RL. Looking below the surface of nicotinic acetylcholine receptors. Trends Pharmacol Sci 2015; 36:514-23. [PMID: 26067101 DOI: 10.1016/j.tips.2015.05.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/13/2015] [Accepted: 05/14/2015] [Indexed: 01/10/2023]
Abstract
The amino acid sequences of nicotinic acetylcholine receptors (nAChRs) from diverse species can be compared across extracellular, transmembrane, and intracellular domains. The intracellular domains are most divergent among subtypes, yet relatively consistent among species. The diversity indicates that each nAChR subtype has a unique language for communication with its host cell. The conservation across species also suggests that the intracellular domains have defining functional roles for each subtype. Secondary structure prediction indicates two relatively conserved alpha helices within the intracellular domains of all nAChRs. Among all subtypes, the intracellular domain of α7 nAChR is one of the most well conserved, and α7 nAChRs have effects in non-neuronal cells independent of generating ion currents, making it likely that the α7 intracellular domain directly mediates signal transduction. There are potential phosphorylation and protein-binding sites in the α7 intracellular domain, which are conserved and may be the basis for α7-mediated signal transduction.
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Affiliation(s)
- Clare Stokes
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610, USA
| | - Millet Treinin
- Department of Medical Neurobiology, Hadassah Medical School, Hebrew University, Jerusalem 91120, Israel
| | - Roger L Papke
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610, USA.
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168
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Xu W, Meng Y, Surana P, Fuerst G, Nettleton D, Wise RP. The knottin-like Blufensin family regulates genes involved in nuclear import and the secretory pathway in barley-powdery mildew interactions. FRONTIERS IN PLANT SCIENCE 2015; 6:409. [PMID: 26089830 PMCID: PMC4454880 DOI: 10.3389/fpls.2015.00409] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 05/21/2015] [Indexed: 05/24/2023]
Abstract
Plants have evolved complex regulatory mechanisms to control a multi-layered defense response to microbial attack. Both temporal and spatial gene expression are tightly regulated in response to pathogen ingress, modulating both positive and negative control of defense. BLUFENSINs, small knottin-like peptides in barley, wheat, and rice, are highly induced by attack from fungal pathogens, in particular, the obligate biotrophic fungus, Blumeria graminis f. sp. hordei (Bgh), causal agent of barley powdery mildew. Previous research indicated that Blufensin1 (Bln1) functions as a negative regulator of basal defense mechanisms. In the current report, we show that BLN1 and BLN2 can both be secreted to the apoplast and Barley stripe mosaic virus (BSMV)-mediated overexpression of Bln2 increases susceptibility of barley to Bgh. Bimolecular fluorescence complementation (BiFC) assays signify that BLN1 and BLN2 can interact with each other, and with calmodulin. We then used BSMV-induced gene silencing to knock down Bln1, followed by Barley1 GeneChip transcriptome analysis, to identify additional host genes influenced by Bln1. Analysis of differential expression revealed a gene set enriched for those encoding proteins annotated to nuclear import and the secretory pathway, particularly Importin α1-b and Sec61 γ subunits. Further functional analysis of these two affected genes showed that when silenced, they also reduced susceptibility to Bgh. Taken together, we postulate that Bln1 is co-opted by Bgh to facilitate transport of disease-related host proteins or effectors, influencing the establishment of Bgh compatibility on its barley host.
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Affiliation(s)
- Weihui Xu
- Department of Plant Pathology and Microbiology, Center for Plant Responses to Environmental Stresses, Iowa State UniversityAmes, IA, USA
| | - Yan Meng
- Department of Plant Pathology and Microbiology, Center for Plant Responses to Environmental Stresses, Iowa State UniversityAmes, IA, USA
| | - Priyanka Surana
- Department of Plant Pathology and Microbiology, Center for Plant Responses to Environmental Stresses, Iowa State UniversityAmes, IA, USA
- Bioinformatics and Computational Biology Graduate Program, Iowa State UniversityAmes, IA, USA
| | - Greg Fuerst
- Department of Plant Pathology and Microbiology, Center for Plant Responses to Environmental Stresses, Iowa State UniversityAmes, IA, USA
- Corn Insects and Crop Genetics Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Iowa State UniversityAmes, IA, USA
| | - Dan Nettleton
- Department of Statistics, Iowa State UniversityAmes, IA, USA
| | - Roger P. Wise
- Department of Plant Pathology and Microbiology, Center for Plant Responses to Environmental Stresses, Iowa State UniversityAmes, IA, USA
- Corn Insects and Crop Genetics Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Iowa State UniversityAmes, IA, USA
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169
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Bianchin A, Bell A, Chubb AJ, Doolan N, Leneghan D, Stavropoulos I, Shields DC, Mooney C. Design and evaluation of antimalarial peptides derived from prediction of short linear motifs in proteins related to erythrocyte invasion. PLoS One 2015; 10:e0127383. [PMID: 26039561 PMCID: PMC4454681 DOI: 10.1371/journal.pone.0127383] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 04/15/2015] [Indexed: 11/19/2022] Open
Abstract
The purpose of this study was to investigate the blood stage of the malaria causing parasite, Plasmodium falciparum, to predict potential protein interactions between the parasite merozoite and the host erythrocyte and design peptides that could interrupt these predicted interactions. We screened the P. falciparum and human proteomes for computationally predicted short linear motifs (SLiMs) in cytoplasmic portions of transmembrane proteins that could play roles in the invasion of the erythrocyte by the merozoite, an essential step in malarial pathogenesis. We tested thirteen peptides predicted to contain SLiMs, twelve of them palmitoylated to enhance membrane targeting, and found three that blocked parasite growth in culture by inhibiting the initiation of new infections in erythrocytes. Scrambled peptides for two of the most promising peptides suggested that their activity may be reflective of amino acid properties, in particular, positive charge. However, one peptide showed effects which were stronger than those of scrambled peptides. This was derived from human red blood cell glycophorin-B. We concluded that proteome-wide computational screening of the intracellular regions of both host and pathogen adhesion proteins provides potential lead peptides for the development of anti-malarial compounds.
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Affiliation(s)
- Alessandra Bianchin
- Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, Ireland
| | - Angus Bell
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, Ireland
| | - Anthony J. Chubb
- Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Nathalie Doolan
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Darren Leneghan
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, Ireland
| | - Ilias Stavropoulos
- Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Denis C. Shields
- Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Catherine Mooney
- Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland
- Complex and Adaptive Systems Laboratory, University College Dublin, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
- * E-mail:
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170
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Abolnik C. Genomic and single nucleotide polymorphism analysis of infectious bronchitis coronavirus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2015; 32:416-24. [PMID: 25843648 PMCID: PMC7106318 DOI: 10.1016/j.meegid.2015.03.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/13/2015] [Accepted: 03/26/2015] [Indexed: 01/03/2023]
Abstract
Infectious bronchitis virus (IBV) is a Gammacoronavirus that causes a highly contagious respiratory disease in chickens. A QX-like strain was analysed by high-throughput Illumina sequencing and genetic variation across the entire viral genome was explored at the sub-consensus level by single nucleotide polymorphism (SNP) analysis. Thirteen open reading frames (ORFs) in the order 5'-UTR-1a-1ab-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3'UTR were predicted. The relative frequencies of missense: silent SNPs were calculated to obtain a comparative measure of variability in specific genes. The most variable ORFs in descending order were E, 3b, 5'UTR, N, 1a, S, 1ab, M, 4c, 5a, 6b. The E and 3b protein products play key roles in coronavirus virulence, and RNA folding demonstrated that the mutations in the 5'UTR did not alter the predicted secondary structure. The frequency of SNPs in the Spike (S) protein ORF of 0.67% was below the genomic average of 0.76%. Only three SNPS were identified in the S1 subunit, none of which were located in hypervariable region (HVR) 1 or HVR2. The S2 subunit was considerably more variable containing 87% of the polymorphisms detected across the entire S protein. The S2 subunit also contained a previously unreported multi-A insertion site and a stretch of four consecutive mutated amino acids, which mapped to the stalk region of the spike protein. Template-based protein structure modelling produced the first theoretical model of the IBV spike monomer. Given the lack of diversity observed at the sub-consensus level, the tenet that the HVRs in the S1 subunit are very tolerant of amino acid changes produced by genetic drift is questioned.
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Affiliation(s)
- Celia Abolnik
- Poultry Section, Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa.
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171
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Convergent evolution and mimicry of protein linear motifs in host–pathogen interactions. Curr Opin Struct Biol 2015; 32:91-101. [DOI: 10.1016/j.sbi.2015.03.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 03/09/2015] [Accepted: 03/15/2015] [Indexed: 12/21/2022]
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172
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Lalle M, Camerini S, Cecchetti S, Finelli R, Sferra G, Müller J, Ricci G, Pozio E. The FAD-dependent glycerol-3-phosphate dehydrogenase of Giardia duodenalis: an unconventional enzyme that interacts with the g14-3-3 and it is a target of the antitumoral compound NBDHEX. Front Microbiol 2015; 6:544. [PMID: 26082764 PMCID: PMC4450592 DOI: 10.3389/fmicb.2015.00544] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 05/17/2015] [Indexed: 12/18/2022] Open
Abstract
The flagellated protozoan Giardia duodenalis is a worldwide parasite causing giardiasis, an acute and chronic diarrheal disease. Metabolism in G. duodenalis has a limited complexity thus making metabolic enzymes ideal targets for drug development. However, only few metabolic pathways (i.e., carbohydrates) have been described so far. Recently, the parasite homolog of the mitochondrial-like glycerol-3-phosphate dehydrogenase (gG3PD) has been identified among the interactors of the g14-3-3 protein. G3PD is involved in glycolysis, electron transport, glycerophospholipids metabolism, and hyperosmotic stress response, and is emerging as promising target in tumor treatment. In this work, we demonstrate that gG3PD is a functional flavoenzyme able to convert glycerol-3-phosphate into dihydroxyacetone phosphate and that its activity and the intracellular glycerol level increase during encystation. Taking advantage of co-immunoprecipitation assays and deletion mutants, we provide evidence that gG3PD and g14-3-3 interact at the trophozoite stage, the intracellular localization of gG3PD is stage dependent and it partially co-localizes with mitosomes during cyst development. Finally, we demonstrate that the gG3PD activity is affected by the antitumoral compound 6-(7-nitro-2,1,3-benzoxadiazol-4-ylthio)hexanol, that results more effective in vitro at killing G. duodenalis trophozoites than the reference drug metronidazole. Overall, our results highlight the involvement of gG3PD in processes crucial for the parasite survival thus proposing this enzyme as target for novel antigiardial interventions.
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Affiliation(s)
- Marco Lalle
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità Rome, Italy
| | - Serena Camerini
- Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità Rome, Italy
| | - Serena Cecchetti
- Department of Cell Biology and Neurosciences, Istituto Superiore di Sanità Rome, Italy
| | - Renata Finelli
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità Rome, Italy
| | - Gabriella Sferra
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità Rome, Italy
| | - Joachim Müller
- Institute of Parasitology, Vetsuisse Faculty, University of Bern Bern, Switzerland
| | - Giorgio Ricci
- Department of Sciences and Chemical Technologies, University of Rome "Tor Vergata" Rome, Italy
| | - Edoardo Pozio
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità Rome, Italy
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173
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Tay AP, Pang CNI, Twine NA, Hart-Smith G, Harkness L, Kassem M, Wilkins MR. Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data. J Proteome Res 2015; 14:3541-54. [PMID: 25961807 DOI: 10.1021/pr5011394] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Human proteome analysis now requires an understanding of protein isoforms. We recently published the PG Nexus pipeline, which facilitates high confidence validation of exons and splice junctions by integrating genomics and proteomics data. Here we comprehensively explore how RNA-seq transcriptomics data, and proteomic analysis of the same sample, can identify protein isoforms. RNA-seq data from human mesenchymal (hMSC) stem cells were analyzed with our new TranscriptCoder tool to generate a database of protein isoform sequences. MS/MS data from matching hMSC samples were then matched against the TranscriptCoder-derived database, along with Ensembl and the neXtProt database. Querying the TranscriptCoder-derived or Ensembl database could unambiguously identify ∼450 protein isoforms, with isoform-specific proteotypic peptides, including candidate hMSC-specific isoforms for the genes DPYSL2 and FXR1. Where isoform-specific peptides did not exist, groups of nonisoform-specific proteotypic peptides could specifically identify many isoforms. In both the above cases, isoforms will be detectable with targeted MS/MS assays. Unfortunately, our analysis also revealed that some isoforms will be difficult to identify unambiguously as they do not have peptides that are sufficiently distinguishing. We covisualize mRNA isoforms and peptides in a genome browser to illustrate the above situations. Mass spectrometry data is available via ProteomeXchange (PXD001449).
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Affiliation(s)
- Aidan P Tay
- Systems Biology Initiative, The University of New South Wales , Sydney, New South Wales 2052, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia
| | - Chi Nam Ignatius Pang
- Systems Biology Initiative, The University of New South Wales , Sydney, New South Wales 2052, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia
| | - Natalie A Twine
- Systems Biology Initiative, The University of New South Wales , Sydney, New South Wales 2052, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia
| | - Gene Hart-Smith
- Systems Biology Initiative, The University of New South Wales , Sydney, New South Wales 2052, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia
| | - Linda Harkness
- Endocrine Research Laboratory (KMEB), Department of Endocrinology and Metabolism, Odense University Hospital & University of Southern Denmark , Odense 5230, Denmark
| | - Moustapha Kassem
- Endocrine Research Laboratory (KMEB), Department of Endocrinology and Metabolism, Odense University Hospital & University of Southern Denmark , Odense 5230, Denmark
| | - Marc R Wilkins
- Systems Biology Initiative, The University of New South Wales , Sydney, New South Wales 2052, Australia.,School of Biotechnology and Biomolecular Sciences, The University of New South Wales , Sydney, New South Wales 2052, Australia
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174
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Varadi M, Guharoy M, Zsolyomi F, Tompa P. DisCons: a novel tool to quantify and classify evolutionary conservation of intrinsic protein disorder. BMC Bioinformatics 2015; 16:153. [PMID: 25968230 PMCID: PMC4427981 DOI: 10.1186/s12859-015-0592-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 04/23/2015] [Indexed: 12/03/2022] Open
Abstract
Background Analyzing the amino acid sequence of an intrinsically disordered protein (IDP) in an evolutionary context can yield novel insights on the functional role of disordered regions and sequence element(s). However, in the case of many IDPs, the lack of evolutionary conservation of the primary sequence can hamper the study of functionality, because the conservation of their disorder profile and ensuing function(s) may not appear in a traditional analysis of the evolutionary history of the protein. Results Here we present DisCons (Disorder Conservation), a novel pipelined tool that combines the quantification of sequence- and disorder conservation to classify disordered residue positions. According to this scheme, the most interesting categories (for functional purposes) are constrained disordered residues and flexible disordered residues. The former residues show conservation of both the sequence and the property of disorder and are associated mainly with specific binding functionalities (e.g., short, linear motifs, SLiMs), whereas the latter class correspond to segments where disorder as a feature is important for function as opposed to the identity of the underlying sequence (e.g., entropic chains and linkers). DisCons therefore helps with elucidating the function(s) arising from the disordered state by analyzing individual proteins as well as large-scale proteomics datasets. Conclusions DisCons is an openly accessible sequence analysis tool that identifies and highlights structurally disordered segments of proteins where the conformational flexibility is conserved across homologs, and therefore potentially functional. The tool is freely available both as a web application and as stand-alone source code hosted at http://pedb.vib.be/discons.
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Affiliation(s)
- Mihaly Varadi
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium. .,Vrije Universiteit Brussel, Brussels, Belgium.
| | - Mainak Guharoy
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium. .,Vrije Universiteit Brussel, Brussels, Belgium.
| | | | - Peter Tompa
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium. .,Vrije Universiteit Brussel, Brussels, Belgium. .,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.
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175
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Varadi M, Guharoy M, Zsolyomi F, Tompa P. DisCons: a novel tool to quantify and classify evolutionary conservation of intrinsic protein disorder. BMC Bioinformatics 2015. [PMID: 25968230 DOI: 10.1186/s12859‐015‐0592‐2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Analyzing the amino acid sequence of an intrinsically disordered protein (IDP) in an evolutionary context can yield novel insights on the functional role of disordered regions and sequence element(s). However, in the case of many IDPs, the lack of evolutionary conservation of the primary sequence can hamper the study of functionality, because the conservation of their disorder profile and ensuing function(s) may not appear in a traditional analysis of the evolutionary history of the protein. RESULTS Here we present DisCons (Disorder Conservation), a novel pipelined tool that combines the quantification of sequence- and disorder conservation to classify disordered residue positions. According to this scheme, the most interesting categories (for functional purposes) are constrained disordered residues and flexible disordered residues. The former residues show conservation of both the sequence and the property of disorder and are associated mainly with specific binding functionalities (e.g., short, linear motifs, SLiMs), whereas the latter class correspond to segments where disorder as a feature is important for function as opposed to the identity of the underlying sequence (e.g., entropic chains and linkers). DisCons therefore helps with elucidating the function(s) arising from the disordered state by analyzing individual proteins as well as large-scale proteomics datasets. CONCLUSIONS DisCons is an openly accessible sequence analysis tool that identifies and highlights structurally disordered segments of proteins where the conformational flexibility is conserved across homologs, and therefore potentially functional. The tool is freely available both as a web application and as stand-alone source code hosted at http://pedb.vib.be/discons .
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Affiliation(s)
- Mihaly Varadi
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium. .,Vrije Universiteit Brussel, Brussels, Belgium.
| | - Mainak Guharoy
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium. .,Vrije Universiteit Brussel, Brussels, Belgium.
| | | | - Peter Tompa
- VIB Structural Biology Research Center (SBRC), Brussels, Belgium. .,Vrije Universiteit Brussel, Brussels, Belgium. .,Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.
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176
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Abstract
RBFOX2 (RNA-binding protein, Fox-1 homologue 2)/RBM9 (RNA-binding-motif protein 9)/RTA (repressor of tamoxifen action)/HNRBP2 (hexaribonucleotide-binding protein 2) encodes an RNA-binding protein involved in tissue specific alternative splicing regulation and steroid receptors transcriptional activity. Its ability to regulate specific splicing profiles depending on context has been related to different expression levels of the RBFOX2 protein itself and that of other splicing regulatory proteins involved in the shared modulation of specific genes splicing. However, this cannot be the sole explanation as to why RBFOX2 plays a widespread role in numerous cellular mechanisms from development to cell survival dependent on cell/tissue type. RBFOX2 isoforms with altered protein domains exist. In the present article, we describe the main RBFOX2 protein domains, their importance in the context of splicing and transcriptional regulation and we propose that RBFOX2 isoform distribution may play a fundamental role in RBFOX2-specific cellular effects.
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177
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Petsalaki E, Helbig AO, Gopal A, Pasculescu A, Roth FP, Pawson T. SELPHI: correlation-based identification of kinase-associated networks from global phospho-proteomics data sets. Nucleic Acids Res 2015; 43:W276-82. [PMID: 25948583 PMCID: PMC4489257 DOI: 10.1093/nar/gkv459] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 04/27/2015] [Indexed: 12/13/2022] Open
Abstract
While phospho-proteomics studies have shed light on the dynamics of cellular signaling, they mainly describe global effects and rarely explore mechanistic details, such as kinase/substrate relationships. Tools and databases, such as NetworKIN and PhosphoSitePlus, provide valuable regulatory details on signaling networks but rely on prior knowledge. They therefore provide limited information on less studied kinases and fewer unexpected relationships given that better studied signaling events can mask condition- or cell-specific ‘network wiring’. SELPHI is a web-based tool providing in-depth analysis of phospho-proteomics data that is intuitive and accessible to non-bioinformatics experts. It uses correlation analysis of phospho-sites to extract kinase/phosphatase and phospho-peptide associations, and highlights the potential flow of signaling in the system under study. We illustrate SELPHI via analysis of phospho-proteomics data acquired in the presence of erlotinib—a tyrosine kinase inhibitor (TKI)—in cancer cells expressing TKI-resistant and -sensitive variants of the Epidermal Growth Factor Receptor. In this data set, SELPHI revealed information overlooked by the reporting study, including the known role of MET and EPHA2 kinases in conferring resistance to erlotinib in TKI sensitive strains. SELPHI can significantly enhance the analysis of phospho-proteomics data contributing to improved understanding of sample-specific signaling networks. SELPHI is freely available via http://llama.mshri.on.ca/SELPHI.
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Affiliation(s)
- Evangelia Petsalaki
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X8, Canada
| | - Andreas O Helbig
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X8, Canada Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, Ontario, M5G 1X5, Canada
| | - Anjali Gopal
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X8, Canada
| | - Adrian Pasculescu
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X8, Canada
| | - Frederick P Roth
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X8, Canada Donnelly Centre and Departments of Molecular Genetics and Computer Science, University of Toronto, Toronto, Ontario, M5G 1X8, Canada Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, 02215, USA Canadian Institute for Advanced Research, Toronto, Ontario, M5G 1Z8, Canada
| | - Tony Pawson
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X8, Canada
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178
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Chen TS, Petrey D, Garzon JI, Honig B. Predicting peptide-mediated interactions on a genome-wide scale. PLoS Comput Biol 2015; 11:e1004248. [PMID: 25938916 PMCID: PMC4418708 DOI: 10.1371/journal.pcbi.1004248] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 03/18/2015] [Indexed: 12/20/2022] Open
Abstract
We describe a method to predict protein-protein interactions (PPIs) formed between structured domains and short peptide motifs. We take an integrative approach based on consensus patterns of known motifs in databases, structures of domain-motif complexes from the PDB and various sources of non-structural evidence. We combine this set of clues using a Bayesian classifier that reports the likelihood of an interaction and obtain significantly improved prediction performance when compared to individual sources of evidence and to previously reported algorithms. Our Bayesian approach was integrated into PrePPI, a structure-based PPI prediction method that, so far, has been limited to interactions formed between two structured domains. Around 80,000 new domain-motif mediated interactions were predicted, thus enhancing PrePPI’s coverage of the human protein interactome. Complexes formed between a structured domain on one protein and an unstructured peptide on another are ubiquitous. However, they are often quite difficult to detect experimentally. The development of computational approaches to predict domain-motif interactions is therefore an important goal. We report a method to predict domain-motif interactions using a Bayesian approach to integrate evidence from a variety of sources, including three-dimensional structural and non-structural information. The method was applied to the entire human proteome and showed significant improvement over existing methods. The method was incorporated into PrePPI, a computational pipeline for the prediction of protein-protein interactions that relies heavily on structural information. Approximately 80,000 new interactions were detected. The new PrePPI database provides easy access to about 400,000 human protein-protein interactions and should thus constitute a valuable resource in a variety of biological applications including the characterization of molecular interaction networks and, more generally, in the study of interactions mediated by proteins in families that may not be extensively studied experimentally.
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Affiliation(s)
- T. Scott Chen
- Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America
| | - Donald Petrey
- Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America
| | - Jose Ignacio Garzon
- Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America
| | - Barry Honig
- Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
- Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, United States of America
- * E-mail:
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179
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Healy AR, Houston DR, Remnant L, Huart AS, Brychtova V, Maslon MM, Meers O, Muller P, Krejci A, Blackburn EA, Vojtesek B, Hernychova L, Walkinshaw MD, Westwood NJ, Hupp TR. Discovery of a novel ligand that modulates the protein-protein interactions of the AAA+ superfamily oncoprotein reptin. Chem Sci 2015; 6:3109-3116. [PMID: 28706685 PMCID: PMC5490336 DOI: 10.1039/c4sc03885a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/20/2015] [Indexed: 12/31/2022] Open
Abstract
Developing approaches to discover protein-protein interactions (PPIs) remains a fundamental challenge. A chemical biology platform is applied here to identify novel PPIs for the AAA+ superfamily oncoprotein reptin. An in silico screen coupled with chemical optimization provided Liddean, a nucleotide-mimetic which modulates reptin's oligomerization status, protein-binding activity and global conformation. Combinatorial peptide phage library screening of Liddean-bound reptin with next generation sequencing identified interaction motifs including a novel reptin docking site on the p53 tumor suppressor protein. Proximity ligation assays demonstrated that endogenous reptin forms a predominantly cytoplasmic complex with its paralog pontin in cancer cells and Liddean promotes a shift of this complex to the nucleus. An emerging view of PPIs in higher eukaryotes is that they occur through a striking diversity of linear peptide motifs. The discovery of a compound that alters reptin's protein interaction landscape potentially leads to novel avenues for therapeutic development.
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Affiliation(s)
- Alan R Healy
- School of Chemistry & Biomedical Sciences Research Complex , University of St Andrews & EaStCHEM , North Haugh, St Andrews , KY16 9ST , UK .
| | - Douglas R Houston
- Centre for Chemical Biology , University of Edinburgh , EH9 3JG , UK .
| | - Lucy Remnant
- Edinburgh Cancer Research Centre , Cell Signalling Unit , University of Edinburgh , EH4 2XR , UK .
| | - Anne-Sophie Huart
- Edinburgh Cancer Research Centre , Cell Signalling Unit , University of Edinburgh , EH4 2XR , UK .
| | - Veronika Brychtova
- RECAMO , Masaryk Memorial Cancer Institute , 656 53 Brno , Czech Republic
| | - Magda M Maslon
- Edinburgh Cancer Research Centre , Cell Signalling Unit , University of Edinburgh , EH4 2XR , UK .
| | - Olivia Meers
- Edinburgh Cancer Research Centre , Cell Signalling Unit , University of Edinburgh , EH4 2XR , UK .
| | - Petr Muller
- RECAMO , Masaryk Memorial Cancer Institute , 656 53 Brno , Czech Republic
| | - Adam Krejci
- RECAMO , Masaryk Memorial Cancer Institute , 656 53 Brno , Czech Republic
| | | | - Borek Vojtesek
- RECAMO , Masaryk Memorial Cancer Institute , 656 53 Brno , Czech Republic
| | - Lenka Hernychova
- RECAMO , Masaryk Memorial Cancer Institute , 656 53 Brno , Czech Republic
| | | | - Nicholas J Westwood
- School of Chemistry & Biomedical Sciences Research Complex , University of St Andrews & EaStCHEM , North Haugh, St Andrews , KY16 9ST , UK .
| | - Ted R Hupp
- Edinburgh Cancer Research Centre , Cell Signalling Unit , University of Edinburgh , EH4 2XR , UK .
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180
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Subramaniam G, Campsteijn C, Thompson EM. Co-expressed Cyclin D variants cooperate to regulate proliferation of germline nuclei in a syncytium. Cell Cycle 2015; 14:2129-41. [PMID: 25928155 DOI: 10.1080/15384101.2015.1041690] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
The role of the G1-phase Cyclin D-CDK 4/6 regulatory module in linking germline stem cell (GSC) proliferation to nutrition is evolutionarily variable. In invertebrate Drosophila and C. elegans GSC models, G1 is nearly absent and Cyclin E is expressed throughout the cell cycle, whereas vertebrate spermatogonial stem cells have a distinct G1 and Cyclin D1 plays an important role in GSC renewal. In the invertebrate, chordate, Oikopleura, where germline nuclei proliferate asynchronously in a syncytium, we show a distinct G1-phase in which 2 Cyclin D variants are co-expressed. Cyclin Dd, present in both somatic endocycling cells and the germline, localized to germline nuclei during G1 before declining at G1/S. Cyclin Db, restricted to the germline, remained cytoplasmic, co-localizing in foci with the Cyclin-dependent Kinase Inhibitor, CKIa. These foci showed a preferential spatial distribution adjacent to syncytial germline nuclei at G1/S. During nutrient-restricted growth arrest, upregulated CKIa accumulated in arrested somatic endoreduplicative nuclei but did not do so in germline nuclei. In the latter context, Cyclin Dd levels gradually decreased. In contrast, the Cyclin Dbβ splice variant, lacking the Rb-interaction domain and phosphodegron, was specifically upregulated and the number of cytoplasmic foci containing this variant increased. This upregulation was dependent on stress response MAPK p38 signaling. We conclude that under favorable conditions, Cyclin Dbβ-CDK6 sequesters CKIa in the cytoplasm to cooperate with Cyclin Dd-CDK6 in promoting germline nuclear proliferation. Under nutrient-restriction, this sequestration function is enhanced to permit continued, though reduced, cycling of the germline during somatic growth arrest.
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Key Words
- CAK, CDK Activating Kinase
- CDK, Cyclin-Dependent Kinase
- CKI, CDK inhibitor
- CREB, CRE Binding protein
- CRM, Chromosome Region Maintenance
- ERK, Extracellular signal-regulated kinases
- G-phase, Gap phase
- GA, Growth Arrest
- GFP, Green Fluorescent Protein
- GSC, Germline Stem Cell
- IdU, 5-Iodo-2′-deoxyuridine.
- M-phase, Mitotic phase
- MAPK p38
- MAPK, Mitogen Activated Protein Kinase
- MSK, Mitogen and Stress activating Kinase
- NLS, Nuclear Localization Sequence
- PCNA, Proliferating cell nuclear antigen
- Rb, Retinoblastoma protein
- S-phase, DNA Synthesis phase
- SCF complex, Skp, Cullin, F-box containing complex
- TOR signaling
- TOR:Target Of Rapamycin
- cyclin D splice variants
- cyclin-dependent kinase inhibitor
- cytoplasmic sequestration
- growth arrest
- niche
- stem cell
- syncytium
- urochordate
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Affiliation(s)
- Gunasekaran Subramaniam
- a Sars International Center for Marine Molecular Biology; University of Bergen ; Bergen , Norway
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181
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CD2v Interacts with Adaptor Protein AP-1 during African Swine Fever Infection. PLoS One 2015; 10:e0123714. [PMID: 25915900 PMCID: PMC4411086 DOI: 10.1371/journal.pone.0123714] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 03/06/2015] [Indexed: 11/19/2022] Open
Abstract
African swine fever virus (ASFV) CD2v protein is believed to be involved in virulence enhancement, viral hemadsorption, and pathogenesis, although the molecular mechanisms of the function of this viral protein are still not fully understood. Here we describe that CD2v localized around viral factories during ASFV infection, suggesting a role in the generation and/or dynamics of these viral structures and hence in disturbing cellular traffic. We show that CD2v targeted the regulatory trans-Golgi network (TGN) protein complex AP-1, a key element in cellular traffic. This interaction was disrupted by brefeldin A even though the location of CD2v around the viral factory remained unchanged. CD2v-AP-1 binding was independent of CD2v glycosylation and occurred on the carboxy-terminal part of CD2v, where a canonical di-Leu motif previously reported to mediate AP-1 binding in eukaryotic cells, was identified. This motif was shown to be functionally interchangeable with the di-Leu motif present in HIV-Nef protein in an AP-1 binding assay. However, we demonstrated that it was not involved either in CD2v cellular distribution or in CD2v-AP-1 binding. Taken together, these findings shed light on CD2v function during ASFV infection by identifying AP-1 as a cellular factor targeted by CD2v and hence elucidate the cellular pathways used by the virus to enhance infectivity.
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182
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Baëza M, Viala S, Heim M, Dard A, Hudry B, Duffraisse M, Rogulja-Ortmann A, Brun C, Merabet S. Inhibitory activities of short linear motifs underlie Hox interactome specificity in vivo. eLife 2015; 4. [PMID: 25869471 PMCID: PMC4392834 DOI: 10.7554/elife.06034] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/16/2015] [Indexed: 12/30/2022] Open
Abstract
Hox proteins are well-established developmental regulators that coordinate cell fate and morphogenesis throughout embryogenesis. In contrast, our knowledge of their specific molecular modes of action is limited to the interaction with few cofactors. Here, we show that Hox proteins are able to interact with a wide range of transcription factors in the live Drosophila embryo. In this context, specificity relies on a versatile usage of conserved short linear motifs (SLiMs), which, surprisingly, often restrains the interaction potential of Hox proteins. This novel buffering activity of SLiMs was observed in different tissues and found in Hox proteins from cnidarian to mouse species. Although these interactions remain to be analysed in the context of endogenous Hox regulatory activities, our observations challenge the traditional role assigned to SLiMs and provide an alternative concept to explain how Hox interactome specificity could be achieved during the embryonic development. DOI:http://dx.doi.org/10.7554/eLife.06034.001 In all animals, it is important that cells are correctly organised into tissues and organs. This organisation starts in the embryo, and cells are instructed to perform different roles depending on their position within the body. A family of proteins called the Hox proteins coordinates the organisation of the cells in the animal embryo by binding to and controlling the expression of specific genes. To properly control their target genes, Hox proteins need to interact with other proteins called transcription factors that can also bind to the genes. However, only a few of these transcription factors have been identified so far, and it is not clear how Hox proteins are able to interact with them. Here, Baëza, Viala, Heim et al. identified several more transcription factors that can bind to the Hox proteins in fruit fly embryos. The experiments show that Hox proteins are able to bind to many transcription factors that are very different from each other. Baëza, Viala, Heim et al. also show that two short sections within the Hox proteins known as short linear motifs are important for controlling these interactions. A fly Hox protein that was missing these motifs was able to interact with new transcription factors. This inhibitory role was found in Hox proteins from mice and sea anemones, suggesting that these motifs may play the same role in all animals. Baëza, Viala, Heim et al.'s findings challenge the traditional view of the role of the short linear motifs in interactions between proteins. Also, the findings provide an alternative explanation for how the Hox proteins are only able to interact with particular transcription factors in animal embryos. The next step will be to find out whether the inhibitory role of short linear motifs could more generally apply to many other protein families. DOI:http://dx.doi.org/10.7554/eLife.06034.002
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Affiliation(s)
- Manon Baëza
- Institut de génomique fonctionnelle de Lyon, Centre National de Recherche Scientifique, Lyon, France
| | - Séverine Viala
- Institut de génomique fonctionnelle de Lyon, Centre National de Recherche Scientifique, Lyon, France
| | - Marjorie Heim
- Institut de génomique fonctionnelle de Lyon, Centre National de Recherche Scientifique, Lyon, France
| | - Amélie Dard
- Institut de génomique fonctionnelle de Lyon, Centre National de Recherche Scientifique, Lyon, France
| | - Bruno Hudry
- MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
| | - Marilyne Duffraisse
- Institut de génomique fonctionnelle de Lyon, Centre National de Recherche Scientifique, Lyon, France
| | | | - Christine Brun
- Technological Advances for Genomics and clinics, Institut national de la santé et de la recherche médicale, University Aix-Marseille, Parc Scientifique de Luminy, Marseille, France
| | - Samir Merabet
- Institut de génomique fonctionnelle de Lyon, Centre National de Recherche Scientifique, Lyon, France
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183
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A modular toolkit to inhibit proline-rich motif-mediated protein-protein interactions. Proc Natl Acad Sci U S A 2015; 112:5011-6. [PMID: 25848013 DOI: 10.1073/pnas.1422054112] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Small-molecule competitors of protein-protein interactions are urgently needed for functional analysis of large-scale genomics and proteomics data. Particularly abundant, yet so far undruggable, targets include domains specialized in recognizing proline-rich segments, including Src-homology 3 (SH3), WW, GYF, and Drosophila enabled (Ena)/vasodilator-stimulated phosphoprotein (VASP) homology 1 (EVH1) domains. Here, we present a modular strategy to obtain an extendable toolkit of chemical fragments (ProMs) designed to replace pairs of conserved prolines in recognition motifs. As proof-of-principle, we developed a small, selective, peptidomimetic inhibitor of Ena/VASP EVH1 domain interactions. Highly invasive MDA MB 231 breast-cancer cells treated with this ligand showed displacement of VASP from focal adhesions, as well as from the front of lamellipodia, and strongly reduced cell invasion. General applicability of our strategy is illustrated by the design of an ErbB4-derived ligand containing two ProM-1 fragments, targeting the yes-associated protein 1 (YAP1)-WW domain with a fivefold higher affinity.
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184
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Hsieh LS, Su WM, Han GS, Carman GM. Phosphorylation regulates the ubiquitin-independent degradation of yeast Pah1 phosphatidate phosphatase by the 20S proteasome. J Biol Chem 2015; 290:11467-78. [PMID: 25809482 DOI: 10.1074/jbc.m115.648659] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Indexed: 01/08/2023] Open
Abstract
Saccharomyces cerevisiae Pah1 phosphatidate phosphatase, which catalyzes the conversion of phosphatidate to diacylglycerol for triacylglycerol synthesis and simultaneously controls phosphatidate levels for phospholipid synthesis, is subject to the proteasome-mediated degradation in the stationary phase of growth. In this study, we examined the mechanism for its degradation using purified Pah1 and isolated proteasomes. Pah1 expressed in S. cerevisiae or Escherichia coli was not degraded by the 26S proteasome, but by its catalytic 20S core particle, indicating that its degradation is ubiquitin-independent. The degradation of Pah1 by the 20S proteasome was dependent on time and proteasome concentration at the pH optimum of 7.0. The 20S proteasomal degradation was conserved for human lipin 1 phosphatidate phosphatase. The degradation analysis using Pah1 truncations and its fusion with GFP indicated that proteolysis initiates at the N- and C-terminal unfolded regions. The folded region of Pah1, in particular the haloacid dehalogenase-like domain containing the DIDGT catalytic sequence, was resistant to the proteasomal degradation. The structural change of Pah1, as reflected by electrophoretic mobility shift, occurs through its phosphorylation by Pho85-Pho80, and the phosphorylation sites are located within its N- and C-terminal unfolded regions. Phosphorylation of Pah1 by Pho85-Pho80 inhibited its degradation, extending its half-life by ∼2-fold. The dephosphorylation of endogenously phosphorylated Pah1 by the Nem1-Spo7 protein phosphatase, which is highly specific for the sites phosphorylated by Pho85-Pho80, stimulated the 20S proteasomal degradation and reduced its half-life by 2.6-fold. These results indicate that the proteolysis of Pah1 by the 20S proteasome is controlled by its phosphorylation state.
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Affiliation(s)
- Lu-Sheng Hsieh
- From the Department of Food Science, Rutgers Center for Lipid Research, and New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901
| | - Wen-Min Su
- From the Department of Food Science, Rutgers Center for Lipid Research, and New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901
| | - Gil-Soo Han
- From the Department of Food Science, Rutgers Center for Lipid Research, and New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901
| | - George M Carman
- From the Department of Food Science, Rutgers Center for Lipid Research, and New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901
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185
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Wuertenberger S, Groemping Y. A single PXXP motif in the C-terminal region of srGAP3 mediates binding to multiple SH3 domains. FEBS Lett 2015; 589:1156-63. [PMID: 25819436 DOI: 10.1016/j.febslet.2015.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 03/18/2015] [Accepted: 03/18/2015] [Indexed: 11/17/2022]
Abstract
The Slit-Robo GTPase-activating protein 3 (srGAP3) has been implicated in different critical aspects of neuronal development. These findings have mainly been based on the characterisation of the three conserved globular N-terminal domains, while the function of the C-terminal region (CTR) is still unknown. We show that this predicted unstructured region acts as an adaptor by binding to the endocytic proteins Amphiphysin, Endophilin-A2, Endophilin-A1, as well as the Ras signalling protein Grb2. All these interactions depend on a single proline-rich motif in the CTR and the Src-homology 3 domains of the binding partners. Via these interactions srGAP3 could link receptor signalling events to the endocytic machinery.
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Affiliation(s)
- Silvia Wuertenberger
- Max Planck Institute for Developmental Biology, Department of Protein Evolution, Spemannstr. 35, D-72076 Tübingen, Germany
| | - Yvonne Groemping
- Max Planck Institute for Developmental Biology, Department of Protein Evolution, Spemannstr. 35, D-72076 Tübingen, Germany.
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186
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Petrov P, Syrjänen R, Smith J, Gutowska MW, Uchida T, Vainio O, Burt DW. Characterization of the avian Trojan gene family reveals contrasting evolutionary constraints. PLoS One 2015; 10:e0121672. [PMID: 25803627 PMCID: PMC4372362 DOI: 10.1371/journal.pone.0121672] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 02/03/2015] [Indexed: 12/12/2022] Open
Abstract
"Trojan" is a leukocyte-specific, cell surface protein originally identified in the chicken. Its molecular function has been hypothesized to be related to anti-apoptosis and the proliferation of immune cells. The Trojan gene has been localized onto the Z sex chromosome. The adjacent two genes also show significant homology to Trojan, suggesting the existence of a novel gene/protein family. Here, we characterize this Trojan family, identify homologues in other species and predict evolutionary constraints on these genes. The two Trojan-related proteins in chicken were predicted as a receptor-type tyrosine phosphatase and a transmembrane protein, bearing a cytoplasmic immuno-receptor tyrosine-based activation motif. We identified the Trojan gene family in ten other bird species and found related genes in three reptiles and a fish species. The phylogenetic analysis of the homologues revealed a gradual diversification among the family members. Evolutionary analyzes of the avian genes predicted that the extracellular regions of the proteins have been subjected to positive selection. Such selection was possibly a response to evolving interacting partners or to pathogen challenges. We also observed an almost complete lack of intracellular positively selected sites, suggesting a conserved signaling mechanism of the molecules. Therefore, the contrasting patterns of selection likely correlate with the interaction and signaling potential of the molecules.
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Affiliation(s)
- Petar Petrov
- Institute of Diagnostics, Department of Medical Microbiology and Immunology, University of Oulu, Oulu, Finland
- Nordlab Oulu, Oulu University Hospital, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Riikka Syrjänen
- Institute of Diagnostics, Department of Medical Microbiology and Immunology, University of Oulu, Oulu, Finland
- Nordlab Oulu, Oulu University Hospital, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Jacqueline Smith
- Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Roslin, United Kingdom
| | - Maria Weronika Gutowska
- Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Roslin, United Kingdom
| | - Tatsuya Uchida
- Institute of Diagnostics, Department of Medical Microbiology and Immunology, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Olli Vainio
- Institute of Diagnostics, Department of Medical Microbiology and Immunology, University of Oulu, Oulu, Finland
- Nordlab Oulu, Oulu University Hospital, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - David W Burt
- Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Roslin, United Kingdom
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187
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Abstract
Although members of the L1 (LINE-1) clade of non-LTR retrotransposons can be deleterious, the L1 clade has remained active in most mammals for ∼100 million years and generated almost 40% of the human genome. The details of L1-host interaction are largely unknown, however. Here we report that L1 activity requires phosphorylation of the protein encoded by the L1 ORF1 (ORF1p). Critical phospho-acceptor residues (two serines and two threonines) reside in four conserved proline-directed protein kinase (PDPK) target sites. The PDPK family includes mitogen-activated protein kinases and cyclin-dependent kinases. Mutation of any PDPK phospho-acceptor inhibits L1 retrotransposition. The phosphomimetic aspartic acid can restore activity at the two serine sites, but not at either threonine site, where it is strongly inhibitory. ORF1p also contains conserved PDPK docking sites, which promote specific interaction of PDPKs with their targets. As expected, mutations in these sites also inhibit L1 activity. PDPK mutations in ORF1p that inactivate L1 have no significant effect on the ability of ORF1p to anneal RNA in vitro, an important biochemical property of the protein. We show that phosphorylated PDPK sites in ORF1p are required for an interaction with the peptidyl prolyl isomerase 1 (Pin1), a critical component of PDPK-mediated regulation. Pin1 acts via isomerization of proline side chains at phosphorylated PDPK motifs, thereby affecting substrate conformation and activity. Our demonstration that L1 activity is dependent on and integrated with cellular phosphorylation regulatory cascades significantly increases our understanding of interactions between L1 and its host.
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188
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Palopoli N, Lythgow KT, Edwards RJ. QSLiMFinder: improved short linear motif prediction using specific query protein data. Bioinformatics 2015; 31:2284-93. [PMID: 25792551 PMCID: PMC4495300 DOI: 10.1093/bioinformatics/btv155] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 03/16/2015] [Indexed: 12/16/2022] Open
Abstract
Motivation: The sensitivity of de novo short linear motif (SLiM) prediction is limited by the number of patterns (the motif space) being assessed for enrichment. QSLiMFinder uses specific query protein information to restrict the motif space and thereby increase the sensitivity and specificity of predictions. Results: QSLiMFinder was extensively benchmarked using known SLiM-containing proteins and simulated protein interaction datasets of real human proteins. Exploiting prior knowledge of a query protein likely to be involved in a SLiM-mediated interaction increased the proportion of true positives correctly returned and reduced the proportion of datasets returning a false positive prediction. The biggest improvement was seen if a short region of the query protein flanking the interaction site was known. Availability and implementation: All the tools and data used in this study, including QSLiMFinder and the SLiMBench benchmarking software, are freely available under a GNU license as part of SLiMSuite, at: http://bioware.soton.ac.uk. Contact:richard.edwards@unsw.edu.au Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nicolas Palopoli
- Centre for Biological Sciences, University of Southampton, Southampton, UK
| | - Kieren T Lythgow
- Centre for Biological Sciences, University of Southampton, Southampton, UK, Public Health England, London, UK
| | - Richard J Edwards
- Centre for Biological Sciences, University of Southampton, Southampton, UK, Institute for Life Sciences, University of Southampton, Southampton, UK and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
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189
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Sarkar D, Jana T, Saha S. LMPID: a manually curated database of linear motifs mediating protein-protein interactions. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav014. [PMID: 25776024 PMCID: PMC4360622 DOI: 10.1093/database/bav014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Linear motifs (LMs), used by a subset of all protein-protein interactions (PPIs), bind to globular receptors or domains and play an important role in signaling networks. LMPID (Linear Motif mediated Protein Interaction Database) is a manually curated database which provides comprehensive experimentally validated information about the LMs mediating PPIs from all organisms on a single platform. About 2200 entries have been compiled by detailed manual curation of PubMed abstracts, of which about 1000 LM entries were being annotated for the first time, as compared with the Eukaryotic LM resource. The users can submit their query through a user-friendly search page and browse the data in the alphabetical order of the bait gene names and according to the domains interacting with the LM. LMPID is freely accessible at http://bicresources.jcbose. ac.in/ssaha4/lmpid and contains 1750 unique LM instances found within 1181 baits interacting with 552 prey proteins. In summary, LMPID is an attempt to enrich the existing repertoire of resources available for studying the LMs implicated in PPIs and may help in understanding the patterns of LMs binding to a specific domain and develop prediction model to identify novel LMs specific to a domain and further able to predict inhibitors/modulators of PPI of interest.
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Affiliation(s)
| | - Tanmoy Jana
- Bioinformatics Centre, Bose Institute, Kolkata, India
| | - Sudipto Saha
- Bioinformatics Centre, Bose Institute, Kolkata, India
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190
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Henriet S, Sumic S, Doufoundou-Guilengui C, Jensen MF, Grandmougin C, Fal K, Thompson E, Volff JN, Chourrout D. Embryonic expression of endogenous retroviral RNAs in somatic tissues adjacent to the Oikopleura germline. Nucleic Acids Res 2015; 43:3701-11. [PMID: 25779047 PMCID: PMC4402516 DOI: 10.1093/nar/gkv169] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 02/20/2015] [Indexed: 11/19/2022] Open
Abstract
Selective pressure to maintain small genome size implies control of transposable elements, and most old classes of retrotransposons are indeed absent from the very compact genome of the tunicate Oikopleura dioica. Nonetheless, two families of retrotransposons are present, including the Tor elements. The gene organization within Tor elements is similar to that of LTR retrotransposons and retroviruses. In addition to gag and pol, many Tor elements carry a third gene encoding viral envelope-like proteins (Env) that may mediate infection. We show that the Tor family contains distinct classes of elements. In some classes, env mRNA is transcribed from the 5′LTR as in retroviruses. In others, env is transcribed from an additional promoter located downstream of the 5′LTR. Tor Env proteins are membrane-associated glycoproteins which exhibit some features of viral membrane fusion proteins. Whereas some elements are expressed in the adult testis, many others are specifically expressed in embryonic somatic cells adjacent to primordial germ cells. Such embryonic expression depends on determinants present in the Tor elements and not on their surrounding genomic environment. Our study shows that unusual modes of transcription and expression close to the germline may contribute to the proliferation of Tor elements.
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Affiliation(s)
- Simon Henriet
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Norway
| | - Sara Sumic
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Norway
| | | | - Marit Flo Jensen
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Norway
| | - Camille Grandmougin
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Norway
| | - Kateryna Fal
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Norway
| | - Eric Thompson
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Norway Department of Biology, University of Bergen, Bergen, N-5020, Norway
| | - Jean-Nicolas Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon - CNRS UMR 5242 - INRA USC 1370, Lyon, 69364 Lyon cedex 07, France
| | - Daniel Chourrout
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, N-5008, Norway
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191
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The plant Polycomb repressive complex 1 (PRC1) existed in the ancestor of seed plants and has a complex duplication history. BMC Evol Biol 2015; 15:44. [PMID: 25881027 PMCID: PMC4397884 DOI: 10.1186/s12862-015-0319-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 02/24/2015] [Indexed: 12/31/2022] Open
Abstract
Background Polycomb repressive complex 1 (PRC1) is an essential protein complex for plant development. It catalyzes ubiquitination of histone H2A that is an important part of the transcription repression machinery. Absence of PRC1 subunits in Arabidopsis thaliana plants causes severe developmental defects. Many aspects of the plant PRC1 are elusive, including its origin and phylogenetic distribution. Results We established the evolutionary history of the plant PRC1 subunits (LHP1, Ring1a-b, Bmi1a-c, EMF1, and VRN1), enabled by sensitive phylogenetic methods and newly sequenced plant genomes from previously unsampled taxonomic groups. We showed that all PRC1 core subunits exist in gymnosperms, earlier than previously thought, and that VRN1 is a recent addition, found exclusively in eudicots. The retention of individual subunits in chlorophytes, mosses, lycophytes and monilophytes indicates that they can moonlight as part of other complexes or processes. Moreover, we showed that most PRC1 subunits underwent a complex, duplication-rich history that differs significantly between Brassicaceae and other eudicots. Conclusions PRC1 existed in the last common ancestor of seed plants where it likely played an important regulatory role, aiding their radiation. The presence of LHP1, Ring1 and Bmi1 in mosses, lycophytes and monilophytes also suggests the presence of a primitive yet functional PRC1. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0319-z) contains supplementary material, which is available to authorized users.
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192
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Madeira F, Tinti M, Murugesan G, Berrett E, Stafford M, Toth R, Cole C, MacKintosh C, Barton GJ. 14-3-3-Pred: improved methods to predict 14-3-3-binding phosphopeptides. Bioinformatics 2015; 31:2276-83. [PMID: 25735772 PMCID: PMC4495292 DOI: 10.1093/bioinformatics/btv133] [Citation(s) in RCA: 149] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 02/25/2015] [Indexed: 01/19/2023] Open
Abstract
MOTIVATION The 14-3-3 family of phosphoprotein-binding proteins regulates many cellular processes by docking onto pairs of phosphorylated Ser and Thr residues in a constellation of intracellular targets. Therefore, there is a pressing need to develop new prediction methods that use an updated set of 14-3-3-binding motifs for the identification of new 14-3-3 targets and to prioritize the downstream analysis of >2000 potential interactors identified in high-throughput experiments. RESULTS Here, a comprehensive set of 14-3-3-binding targets from the literature was used to develop 14-3-3-binding phosphosite predictors. Position-specific scoring matrix, support vector machines (SVM) and artificial neural network (ANN) classification methods were trained to discriminate experimentally determined 14-3-3-binding motifs from non-binding phosphopeptides. ANN, position-specific scoring matrix and SVM methods showed best performance for a motif window spanning from -6 to +4 around the binding phosphosite, achieving Matthews correlation coefficient of up to 0.60. Blind prediction showed that all three methods outperform two popular 14-3-3-binding site predictors, Scansite and ELM. The new methods were used for prediction of 14-3-3-binding phosphosites in the human proteome. Experimental analysis of high-scoring predictions in the FAM122A and FAM122B proteins confirms the predictions and suggests the new 14-3-3-predictors will be generally useful. AVAILABILITY AND IMPLEMENTATION A standalone prediction web server is available at http://www.compbio.dundee.ac.uk/1433pred. Human candidate 14-3-3-binding phosphosites were integrated in ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome database.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Geoffrey J Barton
- Division of Computational Biology, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
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193
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Jun SE, Cho KH, Hwang JY, Abdel-Fattah W, Hammermeister A, Schaffrath R, Bowman JL, Kim GT. Comparative analysis of the conserved functions of Arabidopsis DRL1 and yeast KTI12. Mol Cells 2015; 38:243-50. [PMID: 25518926 PMCID: PMC4363724 DOI: 10.14348/molcells.2015.2297] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/03/2014] [Accepted: 12/03/2014] [Indexed: 12/18/2022] Open
Abstract
Patterning of the polar axis during the early leaf developmental stage is established by cell-to-cell communication between the shoot apical meristem (SAM) and the leaf primordia. In a previous study, we showed that the DRL1 gene, which encodes a homolog of the Elongator-associated protein KTI12 of yeast, acts as a positive regulator of adaxial leaf patterning and shoot meristem activity. To determine the evolutionally conserved functions of DRL1, we performed a comparison of the deduced amino acid sequence of DRL1 and its yeast homolog, KTI12, and found that while overall homology was low, well-conserved domains were presented. DRL1 contained two conserved plant-specific domains. Expression of the DRL1 gene in a yeast KTI12-deficient yeast mutant suppressed the growth retardation phenotype, but did not rescue the caffeine sensitivity, indicating that the role of Arabidopsis Elongator-associated protein is partially conserved with yeast KTI12, but may have changed between yeast and plants in response to caffeine during the course of evolution. In addition, elevated expression of DRL1 gene triggered zymocin sensitivity, while overexpression of KTI12 maintained zymocin resistance, indicating that the function of Arabidopsis DRL1 may not overlap with yeast KTI12 with regards to toxin sensitivity. In this study, expression analysis showed that class-I KNOX genes were downregulated in the shoot apex, and that YAB and KAN were upregulated in leaves of the Arabidopsis drl1-101 mutant. Our results provide insight into the communication network between the SAM and leaf primordia required for the establishment of leaf polarity by mediating histone acetylation or through other mechanisms.
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Affiliation(s)
- Sang Eun Jun
- Department of Molecular Biotechnology, Dong-A University, Busan 604-714,
Korea
| | - Kiu-Hyung Cho
- Department of Molecular Biotechnology, Dong-A University, Busan 604-714,
Korea
| | - Ji-Young Hwang
- Department of Molecular Biotechnology, Dong-A University, Busan 604-714,
Korea
| | - Wael Abdel-Fattah
- Institut für Biologie, FG Mikrobiologie, Universität Kassel,
Germany
| | | | - Raffael Schaffrath
- Department of Genetics, University of Leicester,
UK
- Institut für Biologie, FG Mikrobiologie, Universität Kassel,
Germany
| | - John L. Bowman
- School of Biological Sciences, Monash University, Melbourne,
Australia
| | - Gyung-Tae Kim
- Department of Molecular Biotechnology, Dong-A University, Busan 604-714,
Korea
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194
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Irimia M, Weatheritt RJ, Ellis JD, Parikshak NN, Gonatopoulos-Pournatzis T, Babor M, Quesnel-Vallières M, Tapial J, Raj B, O'Hanlon D, Barrios-Rodiles M, Sternberg MJE, Cordes SP, Roth FP, Wrana JL, Geschwind DH, Blencowe BJ. A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell 2015; 159:1511-23. [PMID: 25525873 DOI: 10.1016/j.cell.2014.11.035] [Citation(s) in RCA: 422] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/20/2014] [Accepted: 11/18/2014] [Indexed: 12/16/2022]
Abstract
Alternative splicing (AS) generates vast transcriptomic and proteomic complexity. However, which of the myriad of detected AS events provide important biological functions is not well understood. Here, we define the largest program of functionally coordinated, neural-regulated AS described to date in mammals. Relative to all other types of AS within this program, 3-15 nucleotide "microexons" display the most striking evolutionary conservation and switch-like regulation. These microexons modulate the function of interaction domains of proteins involved in neurogenesis. Most neural microexons are regulated by the neuronal-specific splicing factor nSR100/SRRM4, through its binding to adjacent intronic enhancer motifs. Neural microexons are frequently misregulated in the brains of individuals with autism spectrum disorder, and this misregulation is associated with reduced levels of nSR100. The results thus reveal a highly conserved program of dynamic microexon regulation associated with the remodeling of protein-interaction networks during neurogenesis, the misregulation of which is linked to autism.
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Affiliation(s)
- Manuel Irimia
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 88 Dr. Aiguader, Barcelona 08003, Spain.
| | - Robert J Weatheritt
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jonathan D Ellis
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Neelroop N Parikshak
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | | | - Mariana Babor
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | | | - Javier Tapial
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 88 Dr. Aiguader, Barcelona 08003, Spain
| | - Bushra Raj
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Dave O'Hanlon
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Miriam Barrios-Rodiles
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Michael J E Sternberg
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Sabine P Cordes
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Frederick P Roth
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Department of Computer Science, University of Toronto, 10 King's College Road, Toronto, ON M5S 3G4, Canada; Canadian Institute For Advanced Research, 180 Dundas Street West, Toronto, ON M5G 1Z8, Canada
| | - Jeffrey L Wrana
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Daniel H Geschwind
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
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195
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Dodson EJ, Fishbain-Yoskovitz V, Rotem-Bamberger S, Schueler-Furman O. Versatile communication strategies among tandem WW domain repeats. Exp Biol Med (Maywood) 2015; 240:351-60. [PMID: 25710931 PMCID: PMC4436281 DOI: 10.1177/1535370214566558] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Interactions mediated by short linear motifs in proteins play major roles in regulation of cellular homeostasis since their transient nature allows for easy modulation. We are still far from a full understanding and appreciation of the complex regulation patterns that can be, and are, achieved by this type of interaction. The fact that many linear-motif-binding domains occur in tandem repeats in proteins indicates that their mutual communication is used extensively to obtain complex integration of information toward regulatory decisions. This review is an attempt to overview, and classify, different ways by which two and more tandem repeats cooperate in binding to their targets, in the well-characterized family of WW domains and their corresponding polyproline ligands.
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Affiliation(s)
- Emma Joy Dodson
- Department of Microbiology and Molecular Genetics, Institute of Biomedical Research Israel-Canada IMRIC, Faculty of Medicine, Ein Kerem Campus, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Vered Fishbain-Yoskovitz
- Department of Microbiology and Molecular Genetics, Institute of Biomedical Research Israel-Canada IMRIC, Faculty of Medicine, Ein Kerem Campus, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Shahar Rotem-Bamberger
- Department of Microbiology and Molecular Genetics, Institute of Biomedical Research Israel-Canada IMRIC, Faculty of Medicine, Ein Kerem Campus, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute of Biomedical Research Israel-Canada IMRIC, Faculty of Medicine, Ein Kerem Campus, The Hebrew University of Jerusalem, 91120 Jerusalem, Israel
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196
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Binding properties of SUMO-interacting motifs (SIMs) in yeast. J Mol Model 2015; 21:50. [PMID: 25690366 DOI: 10.1007/s00894-015-2597-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/26/2015] [Indexed: 11/27/2022]
Abstract
Small ubiquitin-like modifier (SUMO) conjugation and interaction play an essential role in many cellular processes. A large number of yeast proteins is known to interact non-covalently with SUMO via short SUMO-interacting motifs (SIMs), but the structural details of this interaction are yet poorly characterized. In the present work, sequence analysis of a large dataset of 148 yeast SIMs revealed the existence of a hydrophobic core binding motif and a preference for acidic residues either within or adjacent to the core motif. Thus the sequence properties of yeast SIMs are highly similar to those described for human. Molecular dynamics simulations were performed to investigate the binding preferences for four representative SIM peptides differing in the number and distribution of acidic residues. Furthermore, the relative stability of two previously observed alternative binding orientations (parallel, antiparallel) was assessed. For all SIMs investigated, the antiparallel binding mode remained stable in the simulations and the SIMs were tightly bound via their hydrophobic core residues supplemented by polar interactions of the acidic residues. In contrary, the stability of the parallel binding mode is more dependent on the sequence features of the SIM motif like the number and position of acidic residues or the presence of additional adjacent interaction motifs. This information should be helpful to enhance the prediction of SIMs and their binding properties in different organisms to facilitate the reconstruction of the SUMO interactome.
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197
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Dacheux D, Roger B, Bosc C, Landrein N, Roche E, Chansel L, Trian T, Andrieux A, Papaxanthos-Roche A, Marthan R, Robinson DR, Bonhivers M. Human FAM154A (SAXO1) is a microtubule-stabilizing protein specific to cilia and related structures. J Cell Sci 2015; 128:1294-307. [PMID: 25673876 DOI: 10.1242/jcs.155143] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Cilia and flagella are microtubule-based organelles present at the surface of most cells, ranging from protozoa to vertebrates, in which these structures are implicated in processes from morphogenesis to cell motility. In vertebrate neurons, microtubule-associated MAP6 proteins stabilize cold-resistant microtubules through their Mn and Mc modules, and play a role in synaptic plasticity. Although centrioles, cilia and flagella have cold-stable microtubules, MAP6 proteins have not been identified in these organelles, suggesting that additional proteins support this role in these structures. Here, we characterize human FAM154A (hereafter referred to as hSAXO1) as the first human member of a widely conserved family of MAP6-related proteins specific to centrioles and cilium microtubules. Our data demonstrate that hSAXO1 binds specifically to centriole and cilium microtubules. We identify, in vivo and in vitro, hSAXO1 Mn modules as responsible for microtubule binding and stabilization as well as being necessary for ciliary localization. Finally, overexpression and knockdown studies show that hSAXO1 modulates axoneme length. Taken together, our findings suggest a fine regulation of hSAXO1 localization and important roles in cilium biogenesis and function.
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Affiliation(s)
- Denis Dacheux
- University Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France Institut Polytechnique de Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France
| | - Benoit Roger
- University Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France
| | - Christophe Bosc
- INSERM, Centre de Recherche U836, F-38000, Grenoble, France University Grenoble Alpes, Grenoble Institut des Neurosciences, F-38000, Grenoble, France
| | - Nicolas Landrein
- University Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France
| | - Emmanuel Roche
- University Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France
| | - Lucie Chansel
- CHU de Bordeaux, Centre Aliénor d'Aquitaine, Laboratoire de Biologie de la Reproduction, F-33000 Bordeaux, France
| | - Thomas Trian
- University Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, F-33000 Bordeaux, France INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, F-33000 Bordeaux, France
| | - Annie Andrieux
- INSERM, Centre de Recherche U836, F-38000, Grenoble, France University Grenoble Alpes, Grenoble Institut des Neurosciences, F-38000, Grenoble, France CEA, Institut de Recherches en Technologies et Sciences pour le Vivant, GPC, F-38000 Grenoble, France
| | - Aline Papaxanthos-Roche
- CHU de Bordeaux, Centre Aliénor d'Aquitaine, Laboratoire de Biologie de la Reproduction, F-33000 Bordeaux, France
| | - Roger Marthan
- University Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, F-33000 Bordeaux, France INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, F-33000 Bordeaux, France
| | - Derrick R Robinson
- University Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France
| | - Mélanie Bonhivers
- University Bordeaux, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France CNRS, Microbiologie Fondamentale et Pathogénicité, UMR 5234, F-33000 Bordeaux, France
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198
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Di Fiore B, Davey NE, Hagting A, Izawa D, Mansfeld J, Gibson TJ, Pines J. The ABBA motif binds APC/C activators and is shared by APC/C substrates and regulators. Dev Cell 2015; 32:358-372. [PMID: 25669885 PMCID: PMC4713905 DOI: 10.1016/j.devcel.2015.01.003] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 09/03/2014] [Accepted: 01/05/2015] [Indexed: 11/30/2022]
Abstract
The anaphase-promoting complex or cyclosome (APC/C) is the ubiquitin ligase that regulates mitosis by targeting specific proteins for degradation at specific times under the control of the spindle assembly checkpoint (SAC). How the APC/C recognizes its different substrates is a key problem in the control of cell division. Here, we have identified the ABBA motif in cyclin A, BUBR1, BUB1, and Acm1, and we show that it binds to the APC/C coactivator CDC20. The ABBA motif in cyclin A is required for its proper degradation in prometaphase through competing with BUBR1 for the same site on CDC20. Moreover, the ABBA motifs in BUBR1 and BUB1 are necessary for the SAC to work at full strength and to recruit CDC20 to kinetochores. Thus, we have identified a conserved motif integral to the proper control of mitosis that connects APC/C substrate recognition with the SAC.
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Affiliation(s)
- Barbara Di Fiore
- The Gurdon Institute and Department of Zoology, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Norman E. Davey
- Department of Physiology and Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Baden-Württemberg 69117, Germany
| | - Anja Hagting
- The Gurdon Institute and Department of Zoology, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Daisuke Izawa
- The Gurdon Institute and Department of Zoology, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Jörg Mansfeld
- Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Toby J. Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Baden-Württemberg 69117, Germany
| | - Jonathon Pines
- The Gurdon Institute and Department of Zoology, University of Cambridge, Cambridge, CB2 1QN, UK
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199
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Insect inhibitor-of-apoptosis (IAP) proteins are negatively regulated by signal-induced N-terminal degrons absent within viral IAP proteins. J Virol 2015; 89:4481-93. [PMID: 25653450 DOI: 10.1128/jvi.03659-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
UNLABELLED Inhibitor-of-apoptosis (IAP) proteins are key regulators of the innate antiviral response by virtue of their capacity to respond to signals affecting cell survival. In insects, wherein the host IAP provides a primary restriction to apoptosis, diverse viruses trigger rapid IAP depletion that initiates caspase-mediated apoptosis, thereby limiting virus multiplication. We report here that the N-terminal leader of two insect IAPs, Spodoptera frugiperda SfIAP and Drosophila melanogaster DIAP1, contain distinct instability motifs that regulate IAP turnover and apoptotic consequences. Functioning as a protein degron, the cellular IAP leader dramatically shortened the life span of a long-lived viral IAP (Op-IAP3) when fused to its N terminus. The SfIAP degron contains mitogen-activated kinase (MAPK)-like regulatory sites, responsible for MAPK inhibitor-sensitive phosphorylation of SfIAP. Hyperphosphorylation correlated with increased SfIAP turnover independent of the E3 ubiquitin-ligase activity of the SfIAP RING, which also regulated IAP stability. Together, our findings suggest that the SfIAP phospho-degron responds rapidly to a signal-activated kinase cascade, which regulates SfIAP levels and thus apoptosis. The N-terminal leader of dipteran DIAP1 also conferred virus-induced IAP depletion by a caspase-independent mechanism. DIAP1 instability mapped to previously unrecognized motifs that are not found in lepidopteran IAPs. Thus, the leaders of cellular IAPs from diverse insects carry unique signal-responsive degrons that control IAP turnover. Rapid response pathways that trigger IAP degradation and initiate apoptosis independent of canonical prodeath gene (Reaper-Grim-Hid) expression may provide important innate immune advantages. Furthermore, the elimination of these response motifs within viral IAPs, including those of baculoviruses, explains their unusual stability and their potent antiapoptotic activity. IMPORTANCE Apoptosis is an effective means by which a host controls virus infection. In insects, inhibitor-of-apoptosis (IAP) proteins act as regulatory sentinels by responding to cellular signals that determine the fate of infected cells. We discovered that lepidopteran (moth and butterfly) IAPs, which are degraded upon baculovirus infection, are controlled by a conserved phosphorylation-sensitive degron within the IAP N-terminal leader. The degron likely responds to virus-induced kinase-specific signals for degradation through SKP1/Cullin/F-box complex-mediated ubiquitination. Such signal-induced destruction of cellular IAPs is distinct from degradation caused by well-known IAP antagonists, which act to expel IAP-bound caspases. The major implication of this study is that insects have multiple signal-responsive mechanisms by which the sentinel IAPs are actively degraded to initiate host apoptosis. Such diversity of pathways likely provides insects with rapid and efficient strategies for pathogen control. Furthermore, the absence of analogous degrons in virus-encoded IAPs explains their relative stability and antiapoptotic potency.
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200
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Spinazzola JM, Smith TC, Liu M, Luna EJ, Barton ER. Gamma-sarcoglycan is required for the response of archvillin to mechanical stimulation in skeletal muscle. Hum Mol Genet 2015; 24:2470-81. [PMID: 25605665 DOI: 10.1093/hmg/ddv008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 01/13/2015] [Indexed: 01/23/2023] Open
Abstract
Loss of gamma-sarcoglycan (γ-SG) induces muscle degeneration and signaling defects in response to mechanical load, and its absence is common to both Duchenne and limb girdle muscular dystrophies. Growing evidence suggests that aberrant signaling contributes to the disease pathology; however, the mechanisms of γ-SG-mediated mechanical signaling are poorly understood. To uncover γ-SG signaling pathway components, we performed yeast two-hybrid screens and identified the muscle-specific protein archvillin as a γ-SG and dystrophin interacting protein. Archvillin protein and message levels were significantly upregulated at the sarcolemma of murine γ-SG-null (gsg(-/-)) muscle but delocalized in dystrophin-deficient mdx muscle. Similar elevation of archvillin protein was observed in human quadriceps muscle lacking γ-SG. Reintroduction of γ-SG in gsg(-/-) muscle by rAAV injection restored archvillin levels to that of control C57 muscle. In situ eccentric contraction of tibialis anterior (TA) muscles from C57 mice caused ERK1/2 phosphorylation, nuclear activation of P-ERK1/2 and stimulus-dependent archvillin association with P-ERK1/2. In contrast, TA muscles from gsg(-/-) and mdx mice exhibited heightened P-ERK1/2 and increased nuclear P-ERK1/2 localization following eccentric contractions, but the archvillin-P-ERK1/2 association was completely ablated. These results position archvillin as a mechanically sensitive component of the dystrophin complex and demonstrate that signaling defects caused by loss of γ-SG occur both at the sarcolemma and in the nucleus.
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Affiliation(s)
- Janelle M Spinazzola
- Department of Anatomy and Cell Biology, School of Dental Medicine, Pennsylvania Muscle Institute, and
| | - Tara C Smith
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Min Liu
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA and
| | - Elizabeth J Luna
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Elisabeth R Barton
- Department of Anatomy and Cell Biology, School of Dental Medicine, Pennsylvania Muscle Institute, and
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