1
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Lühmann KL, Seemann S, Martinek N, Ostendorp S, Kehr J. The glycine-rich domain of GRP7 plays a crucial role in binding long RNAs and facilitating phase separation. Sci Rep 2024; 14:16018. [PMID: 38992080 PMCID: PMC11239674 DOI: 10.1038/s41598-024-66955-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 07/05/2024] [Indexed: 07/13/2024] Open
Abstract
Microscale thermophoresis (MST) is a well-established method to quantify protein-RNA interactions. In this study, we employed MST to analyze the RNA binding properties of glycine-rich RNA binding protein 7 (GRP7), which is known to have multiple biological functions related to its ability to bind different types of RNA. However, the exact mechanism of GRP7's RNA binding is not fully understood. While the RNA-recognition motif of GRP7 is known to be involved in RNA binding, the glycine-rich region (known as arginine-glycine-glycine-domain or RGG-domain) also influences this interaction. To investigate to which extend the RGG-domain of GRP7 is involved in RNA binding, mutation studies on putative RNA interacting or modulating sites were performed. In addition to MST experiments, we examined liquid-liquid phase separation of GRP7 and its mutants, both with and without RNA. Furthermore, we systemically investigated factors that might affect RNA binding selectivity of GRP7 by testing RNAs of different sizes, structures, and modifications. Consequently, our study revealed that GRP7 exhibits a high affinity for a variety of RNAs, indicating a lack of pronounced selectivity. Moreover, we established that the RGG-domain plays a crucial role in binding longer RNAs and promoting phase separation.
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Affiliation(s)
- Kim Lara Lühmann
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Silja Seemann
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Nina Martinek
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Steffen Ostendorp
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany
| | - Julia Kehr
- Department of Biology, Molecular Plant Genetics, Institute of Plant Science and Microbiology, Universität Hamburg, Hamburg, Germany.
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2
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The BCC7 Protein Contributes to the Toxoplasma Basal Pole by Interfacing between the MyoC Motor and the IMC Membrane Network. Int J Mol Sci 2022; 23:ijms23115995. [PMID: 35682673 PMCID: PMC9181098 DOI: 10.3390/ijms23115995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/18/2022] [Accepted: 05/24/2022] [Indexed: 11/30/2022] Open
Abstract
T. gondii is a eukaryotic parasite that has evolved a stage called tachyzoite which multiplies in host cells by producing two daughter cells internally. These nascent tachyzoites bud off their mother and repeat the division process until the expanding progenies escape to settle and multiply in other host cells. Over these intra- and extra-cellular phases, the tachyzoite maintains an essential apicobasal polarity that emerges through a unique bidirectional budding process of the elongating cells. This process requires the assembly of several molecular complexes that, at the nascent pole, encompass structural and myosin motor elements. To characterize a recently identified basal pole marker named BCC7 with respect to the posterior myosin J and myosin C motors, we used conventional biochemistry as well as advanced proteomic and in silico analysis in conjunction with live and super resolution microscopy of transgenic fluorescent tachyzoites. We document that BCC7 forms a ribbed ring below which myosin C motor entities distribute regularly. In addition, we identified—among 13 BCC7 putative partners—two novel and five known members of the inner membrane complex (IMC) family which ends at the apical side of the ring. Therefore, BCC7 could assist the stabilization of the IMC plaques and contribute to the parasite biomechanical properties.
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3
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Phase Separation of Intrinsically Disordered Nucleolar Proteins Relate to Localization and Function. Int J Mol Sci 2021; 22:ijms222313095. [PMID: 34884901 PMCID: PMC8657925 DOI: 10.3390/ijms222313095] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/11/2021] [Accepted: 11/28/2021] [Indexed: 01/10/2023] Open
Abstract
The process of phase separation allows for the establishment and formation of subcompartmentalized structures, thus enabling cells to perform simultaneous processes with precise organization and low energy requirements. Chemical modifications of proteins, RNA, and lipids alter the molecular environment facilitating enzymatic reactions at higher concentrations in particular regions of the cell. In this review, we discuss the nucleolus as an example of the establishment, dynamics, and maintenance of a membraneless organelle with a high level of organization.
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4
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Cissé OH, Ma L, Dekker JP, Khil PP, Youn JH, Brenchley JM, Blair R, Pahar B, Chabé M, Van Rompay KKA, Keesler R, Sukura A, Hirsch V, Kutty G, Liu Y, Peng L, Chen J, Song J, Weissenbacher-Lang C, Xu J, Upham NS, Stajich JE, Cuomo CA, Cushion MT, Kovacs JA. Genomic insights into the host specific adaptation of the Pneumocystis genus. Commun Biol 2021; 4:305. [PMID: 33686174 PMCID: PMC7940399 DOI: 10.1038/s42003-021-01799-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/04/2021] [Indexed: 11/21/2022] Open
Abstract
Pneumocystis jirovecii, the fungal agent of human Pneumocystis pneumonia, is closely related to macaque Pneumocystis. Little is known about other Pneumocystis species in distantly related mammals, none of which are capable of establishing infection in humans. The molecular basis of host specificity in Pneumocystis remains unknown as experiments are limited due to an inability to culture any species in vitro. To explore Pneumocystis evolutionary adaptations, we have sequenced the genomes of species infecting macaques, rabbits, dogs and rats and compared them to available genomes of species infecting humans, mice and rats. Complete whole genome sequence data enables analysis and robust phylogeny, identification of important genetic features of the host adaptation, and estimation of speciation timing relative to the rise of their mammalian hosts. Our data reveals insights into the evolution of P. jirovecii, the sole member of the genus able to infect humans. Cissé, Ma et al. utilize genomic data from Pneumocystis species infecting macaques, rabbit, dogs and rats to investigate the molecular basis of host specificity in Pneumocystis. Their analyses provide insight to the specific adaptations enabling the infection of humans by P. jirovecii.
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Affiliation(s)
- Ousmane H Cissé
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA.
| | - Liang Ma
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA.
| | - John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA.,Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Pavel P Khil
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD, USA.,Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Jung-Ho Youn
- Department of Laboratory Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | | | - Robert Blair
- Tulane National Primate Research Center, Tulane University, New Orleans, LA, USA
| | - Bapi Pahar
- Tulane National Primate Research Center, Tulane University, New Orleans, LA, USA
| | - Magali Chabé
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 9017-CIIL-Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Koen K A Van Rompay
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Rebekah Keesler
- California National Primate Research Center, University of California, Davis, CA, USA
| | - Antti Sukura
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Vanessa Hirsch
- Laboratory of Molecular Microbiology, NIAID, NIH, Bethesda, MD, USA
| | - Geetha Kutty
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Yueqin Liu
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Li Peng
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Chen
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jun Song
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Jie Xu
- Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Nathan S Upham
- Arizona State University, School of Life Sciences, Tempe, ARI, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology and Institute for Integrative Genome Biology, University of California, Riverside, Riverside-California, Riverside, CA, USA
| | - Christina A Cuomo
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Melanie T Cushion
- Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Joseph A Kovacs
- Critical Care Medicine Department, NIH Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA.
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5
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Nallapareddy V, Bogam S, Devarakonda H, Paliwal S, Bandyopadhyay D. DeepCys: Structure-based multiple cysteine function prediction method trained on deep neural network: Case study on domains of unknown functions belonging to COX2 domains. Proteins 2021; 89:745-761. [PMID: 33580578 DOI: 10.1002/prot.26056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/31/2021] [Indexed: 12/29/2022]
Abstract
Cysteine (Cys) is the most reactive amino acid participating in a wide range of biological functions. In-silico predictions complement the experiments to meet the need of functional characterization. Multiple Cys function prediction algorithm is scarce, in contrast to specific function prediction algorithms. Here we present a deep neural network-based multiple Cys function prediction, available on web-server (DeepCys) (https://deepcys.herokuapp.com/). DeepCys model was trained and tested on two independent datasets curated from protein crystal structures. This prediction method requires three inputs, namely, PDB identifier (ID), chain ID and residue ID for a given Cys and outputs the probabilities of four cysteine functions, namely, disulphide, metal-binding, thioether and sulphenylation and predicts the most probable Cys function. The algorithm exploits the local and global protein properties, like, sequence and secondary structure motifs, buried fractions, microenvironments and protein/enzyme class. DeepCys outperformed most of the multiple and specific Cys function algorithms. This method can predict maximum number of cysteine functions. Moreover, for the first time, explicitly predicts thioether function. This tool was used to elucidate the cysteine functions on domains of unknown functions belonging to cytochrome C oxidase subunit-II like transmembrane domains. Apart from the web-server, a standalone program is also available on GitHub (https://github.com/vam-sin/deepcys).
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Affiliation(s)
- Vamsi Nallapareddy
- Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, Telangana, India
| | - Shubham Bogam
- Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, Telangana, India
| | - Himaja Devarakonda
- Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, Telangana, India
| | - Shubham Paliwal
- Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, Telangana, India
| | - Debashree Bandyopadhyay
- Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, Telangana, India
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6
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Guillen-Chable F, Rodríguez Corona U, Pereira-Santana A, Bayona A, Rodríguez-Zapata LC, Aquino C, Šebestová L, Vitale N, Hozak P, Castano E. Fibrillarin Ribonuclease Activity is Dependent on the GAR Domain and Modulated by Phospholipids. Cells 2020; 9:cells9051143. [PMID: 32384686 PMCID: PMC7290794 DOI: 10.3390/cells9051143] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 12/16/2022] Open
Abstract
Fibrillarin is a highly conserved nucleolar methyltransferase responsible for ribosomal RNA methylation across evolution from Archaea to humans. It has been reported that fibrillarin is involved in the methylation of histone H2A in nucleoli and other processes, including viral progression, cellular stress, nuclear shape, and cell cycle progression. We show that fibrillarin has an additional activity as a ribonuclease. The activity is affected by phosphoinositides and phosphatidic acid and insensitive to ribonuclease inhibitors. Furthermore, the presence of phosphatidic acid releases the fibrillarin-U3 snoRNA complex. We show that the ribonuclease activity localizes to the GAR (glycine/arginine-rich) domain conserved in a small group of RNA interacting proteins. The introduction of the GAR domain occurred in evolution in the transition from archaea to eukaryotic cells. The interaction of this domain with phospholipids may allow a phase separation of this protein in nucleoli.
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Affiliation(s)
- Francisco Guillen-Chable
- Biochemistry and Molecular Plant Biology Department, Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida C.P. 97200, Yucatán, Mexico; (F.G.-C.); (U.R.C.); (A.B.); (C.A.)
| | - Ulises Rodríguez Corona
- Biochemistry and Molecular Plant Biology Department, Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida C.P. 97200, Yucatán, Mexico; (F.G.-C.); (U.R.C.); (A.B.); (C.A.)
| | - Alejandro Pereira-Santana
- Industrial Biotechnology Department, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Camino Arenero 1227, el Bajio, Zapopan C.P. 45019, Jalisco, Mexico;
- Dirección de Cátedras, Consejo Nacional de Ciencia y Tecnología, Av. Insurgentes Sur 1582, Alcaldia Benito Juarez C.P. 03940, Ciudad de Mexico, Mexico
| | - Andrea Bayona
- Biochemistry and Molecular Plant Biology Department, Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida C.P. 97200, Yucatán, Mexico; (F.G.-C.); (U.R.C.); (A.B.); (C.A.)
| | - Luis Carlos Rodríguez-Zapata
- Biotechnology Department, Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida C.P. 97200, Yucatan, Mexico;
| | - Cecilia Aquino
- Biochemistry and Molecular Plant Biology Department, Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida C.P. 97200, Yucatán, Mexico; (F.G.-C.); (U.R.C.); (A.B.); (C.A.)
| | - Lenka Šebestová
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the CAS, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic; (L.Š.); (P.H.)
- Faculty of Science, Charles University, Albertov 6, 128 00 Prague, Czech Republic
| | - Nicolas Vitale
- Institute of Celullar and Integrative Neuroscience (INCI), UPR-3212 The French National Centre for Scientific Research & University of Strasbourg, 67000 Strasbourg, France;
| | - Pavel Hozak
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the CAS, v.v.i., Videnska 1083, 142 20 Prague, Czech Republic; (L.Š.); (P.H.)
| | - Enrique Castano
- Biochemistry and Molecular Plant Biology Department, Centro de Investigación Científica de Yucatán, A.C. Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida C.P. 97200, Yucatán, Mexico; (F.G.-C.); (U.R.C.); (A.B.); (C.A.)
- Correspondence:
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7
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Altincekic N, Löhr F, Meier-Credo J, Langer JD, Hengesbach M, Richter C, Schwalbe H. Site-Specific Detection of Arginine Methylation in Highly Repetitive Protein Motifs of Low Sequence Complexity by NMR. J Am Chem Soc 2020; 142:7647-7654. [PMID: 32233470 DOI: 10.1021/jacs.0c02308] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Post-translational modifications of proteins are widespread in eukaryotes. To elucidate the functional role of these modifications, detection methods need to be developed that provide information at atomic resolution. Here, we report on the development of a novel Arg-specific NMR experiment that detects the methylation status and symmetry of each arginine side chain even in highly repetitive RGG amino acid sequence motifs found in numerous proteins within intrinsically disordered regions. The experiment relies on the excellent resolution of the backbone H,N correlation spectra even in these low complexity sequences. It requires 13C, 15N labeled samples.
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Affiliation(s)
- Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60438, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60438, Germany
| | - Frank Löhr
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60438, Germany.,Institute of Biophysical Chemistry, Goethe University Frankfurt am Main, Frankfurt 60438, Germany
| | - Jakob Meier-Credo
- Max Planck Institute of Biophysics, Frankfurt am Main, 60438, Germany
| | - Julian D Langer
- Max Planck Institute of Biophysics, Frankfurt am Main, 60438, Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60438, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60438, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60438, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60438, Germany
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8
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Lin MM, Gala K, Lobby J, Moazamian A, Kress TL. The RS/RGG Domain of the SR‐like Protein Npl3 is Required for Efficient RNA Splicing in Yeast. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.459.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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9
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Chai N, Gitler AD. Yeast screen for modifiers of C9orf72 poly(glycine-arginine) dipeptide repeat toxicity. FEMS Yeast Res 2019. [PMID: 29528392 DOI: 10.1093/femsyr/foy024] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A hexanucleotide repeat expansion in the C9orf72 gene has been identified as the most common cause of amyotrophic lateral sclerosis and frontotemporal dementia. The expanded hexanucleotide repeat is translated by an unconventional mechanism to produce five species of dipeptide repeat (DPR) proteins, glycine-proline (GP), glycine-alanine (GA), glycine-arginine (GR), proline-alanine (PA) and proline-arginine (PR). Of these, the arginine-rich ones, PR and GR, are highly toxic in a variety of model systems, ranging from human cells, to Drosophila, to even the budding yeast, Saccharomyces cerevisiae. We recently performed a genetic screen in yeast for modifiers of PR toxicity and identified suppressors and enhancers, many of which function in nucleocytoplasmic transport. Whether or not GR toxicity involves similar mechanisms to PR is unresolved. Therefore, we performed a genetic screen in yeast to identify modifiers of GR toxicity and compared the results of the GR screen to results from our previous PR screen. Surprisingly, there was only a small degree of overlap between the two screens, suggesting potential for distinct toxicity mechanisms between PR and GR.
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Affiliation(s)
- Noori Chai
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, M322 Alway Building, Stanford, CA 94305, USA.,Neurosciences Graduate Program, Stanford University School of Medicine, 1215 Welch Road, Modular B, Stanford, CA 94305, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, M322 Alway Building, Stanford, CA 94305, USA
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10
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Smith DL, Götze M, Bartolec TK, Hart-Smith G, Wilkins MR. Characterization of the Interaction between Arginine Methyltransferase Hmt1 and Its Substrate Npl3: Use of Multiple Cross-Linkers, Mass Spectrometric Approaches, and Software Platforms. Anal Chem 2018; 90:9101-9108. [PMID: 30004689 DOI: 10.1021/acs.analchem.8b01525] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This study investigated the enzyme-substrate interaction between Saccharomyces cerevisiae arginine methyltransferase Hmt1p and nucleolar protein Npl3p, using chemical cross linking/mass spectrometry (XL/MS). We show that XL/MS can capture transient interprotein interactions that occur during the process of methylation, involving a disordered region in Npl3p with tandem SRGG repeats, and we confirm that Hmt1p and Npl3p exist as homomultimers. Additionally, the study investigated the interdependencies between variables of an XL/MS experiment that lead to the identification of identical or different cross-linked peptides. We report that there are substantial benefits, in terms of biologically relevant cross-links identified, that result from the use of two mass-spectrometry-cleavable cross-linkers [disuccinimido sulfoxide (DSSO) and disuccinimido dibutyric urea (DSBU)], two fragmentation approaches [collision-induced dissociation and electron-transfer dissociation (CID+ETD)] and stepped high-energy collision dissociation (HCD)], and two programs (MeroX and XlinkX). We also show that there are specific combinations of XL/MS methods that are more successful than others for the two proteins investigated here; these are explored in detail in the text. Data are available via ProteomeXchange with identifier PXD008348.
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Affiliation(s)
- Daniela-Lee Smith
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences , University of New South Wales , Sydney , New South Wales 2052 , Australia
| | - Michael Götze
- Institute of Biochemistry , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3 , D-06120 Halle (Saale) , Germany
| | - Tara K Bartolec
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences , University of New South Wales , Sydney , New South Wales 2052 , Australia
| | - Gene Hart-Smith
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences , University of New South Wales , Sydney , New South Wales 2052 , Australia
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences , University of New South Wales , Sydney , New South Wales 2052 , Australia
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11
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Benhalevy D, Gupta SK, Danan CH, Ghosal S, Sun HW, Kazemier HG, Paeschke K, Hafner M, Juranek SA. The Human CCHC-type Zinc Finger Nucleic Acid-Binding Protein Binds G-Rich Elements in Target mRNA Coding Sequences and Promotes Translation. Cell Rep 2017; 18:2979-2990. [PMID: 28329689 DOI: 10.1016/j.celrep.2017.02.080] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 07/18/2016] [Accepted: 02/27/2017] [Indexed: 12/16/2022] Open
Abstract
The CCHC-type zinc finger nucleic acid-binding protein (CNBP/ZNF9) is conserved in eukaryotes and is essential for embryonic development in mammals. It has been implicated in transcriptional, as well as post-transcriptional, gene regulation; however, its nucleic acid ligands and molecular function remain elusive. Here, we use multiple systems-wide approaches to identify CNBP targets and function. We used photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) to identify 8,420 CNBP binding sites on 4,178 mRNAs. CNBP preferentially bound G-rich elements in the target mRNA coding sequences, most of which were previously found to form G-quadruplex and other stable structures in vitro. Functional analyses, including RNA sequencing, ribosome profiling, and quantitative mass spectrometry, revealed that CNBP binding did not influence target mRNA abundance but rather increased their translational efficiency. Considering that CNBP binding prevented G-quadruplex structure formation in vitro, we hypothesize that CNBP is supporting translation by resolving stable structures on mRNAs.
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Affiliation(s)
- Daniel Benhalevy
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Sanjay K Gupta
- Department of Biochemistry, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Charles H Danan
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Suman Ghosal
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA
| | - Hong-Wei Sun
- Biostatistics and Datamining Section, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hinke G Kazemier
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV Groningen, the Netherlands
| | - Katrin Paeschke
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV Groningen, the Netherlands
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD 20892, USA.
| | - Stefan A Juranek
- Department of Biochemistry, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany; European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV Groningen, the Netherlands.
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12
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Ariyachet C, Beißel C, Li X, Lorrey S, Mackenzie O, Martin PM, O'Brien K, Pholcharee T, Sim S, Krebber H, McBride AE. Post-translational modification directs nuclear and hyphal tip localization of Candida albicans mRNA-binding protein Slr1. Mol Microbiol 2017; 104:499-519. [PMID: 28187496 PMCID: PMC5405739 DOI: 10.1111/mmi.13643] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2017] [Indexed: 12/21/2022]
Abstract
The morphological transition of the opportunistic fungal pathogen Candida albicans from budding to hyphal growth has been implicated in its ability to cause disease in animal models. Absence of SR‐like RNA‐binding protein Slr1 slows hyphal formation and decreases virulence in a systemic candidiasis model, suggesting a role for post‐transcriptional regulation in these processes. SR (serine–arginine)‐rich proteins influence multiple steps in mRNA metabolism and their localization and function are frequently controlled by modification. We now demonstrate that Slr1 binds to polyadenylated RNA and that its intracellular localization is modulated by phosphorylation and methylation. Wildtype Slr1‐GFP is predominantly nuclear, but also co‐fractionates with translating ribosomes. The non‐phosphorylatable slr1‐6SA‐GFP protein, in which six serines in SR/RS clusters are substituted with alanines, primarily localizes to the cytoplasm in budding cells. Intriguingly, hyphal cells display a slr1‐6SA‐GFP focus at the tip near the Spitzenkörper, a vesicular structure involved in molecular trafficking to the tip. The presence of slr1‐6SA‐GFP hyphal tip foci is reduced in the absence of the mRNA‐transport protein She3, suggesting that unphosphorylated Slr1 associates with mRNA–protein complexes transported to the tip. The impact of SLR1 deletion on hyphal formation and function thus may be partially due to a role in hyphal mRNA transport.
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Affiliation(s)
| | - Christian Beißel
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften, Georg-August Universität Göttingen, Göttingen, Germany
| | - Xiang Li
- Biology Department, Bowdoin College, Brunswick, ME, 04011, USA
| | - Selena Lorrey
- Biology Department, Bowdoin College, Brunswick, ME, 04011, USA
| | | | | | | | | | - Sue Sim
- Biology Department, Bowdoin College, Brunswick, ME, 04011, USA
| | - Heike Krebber
- Abteilung für Molekulare Genetik, Institut für Mikrobiologie und Genetik, Göttinger Zentrum für Molekulare Biowissenschaften, Georg-August Universität Göttingen, Göttingen, Germany
| | - Anne E McBride
- Biology Department, Bowdoin College, Brunswick, ME, 04011, USA
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Chang KY, Lin TP, Shih LY, Wang CK. Analysis and prediction of the critical regions of antimicrobial peptides based on conditional random fields. PLoS One 2015; 10:e0119490. [PMID: 25803302 PMCID: PMC4372350 DOI: 10.1371/journal.pone.0119490] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 01/14/2015] [Indexed: 11/27/2022] Open
Abstract
Antimicrobial peptides (AMPs) are potent drug candidates against microbes such as bacteria, fungi, parasites, and viruses. The size of AMPs ranges from less than ten to hundreds of amino acids. Often only a few amino acids or the critical regions of antimicrobial proteins matter the functionality. Accurately predicting the AMP critical regions could benefit the experimental designs. However, no extensive analyses have been done specifically on the AMP critical regions and computational modeling on them is either non-existent or settled to other problems. With a focus on the AMP critical regions, we thus develop a computational model AMPcore by introducing a state-of-the-art machine learning method, conditional random fields. We generate a comprehensive dataset of 798 AMPs cores and a low similarity dataset of 510 representative AMP cores. AMPcore could reach a maximal accuracy of 90% and 0.79 Matthew’s correlation coefficient on the comprehensive dataset and a maximal accuracy of 83% and 0.66 MCC on the low similarity dataset. Our analyses of AMP cores follow what we know about AMPs: High in glycine and lysine, but low in aspartic acid, glutamic acid, and methionine; the abundance of α-helical structures; the dominance of positive net charges; the peculiarity of amphipathicity. Two amphipathic sequence motifs within the AMP cores, an amphipathic α-helix and an amphipathic π-helix, are revealed. In addition, a short sequence motif at the N-terminal boundary of AMP cores is reported for the first time: arginine at the P(-1) coupling with glycine at the P1 of AMP cores occurs the most, which might link to microbial cell adhesion.
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Affiliation(s)
- Kuan Y. Chang
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan
- * E-mail:
| | - Tung-pei Lin
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan
| | - Ling-Yi Shih
- Department of Computer Science and Engineering, National Taiwan Ocean University, Keelung, Taiwan
| | - Chien-Kuo Wang
- Department of Biotechnology, Asia University, Taichung, Taiwan
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14
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Low JKK, Wilkins MR. Protein arginine methylation in Saccharomyces cerevisiae. FEBS J 2012; 279:4423-43. [PMID: 23094907 DOI: 10.1111/febs.12039] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/10/2012] [Accepted: 10/19/2012] [Indexed: 11/27/2022]
Abstract
Recent research has implicated arginine methylation as a major regulator of cellular processes, including transcription, translation, nucleocytoplasmic transport, signalling, DNA repair, RNA processing and splicing. Arginine methylation is evolutionarily conserved, and it is now thought that it may rival other post-translational modifications such as phosphorylation in terms of its occurrence in the proteome. In addition, multiple recent examples demonstrate an exciting new theme: the interplay between methylation and other post-translational modifications such as phosphorylation. In this review, we summarize our current understanding of arginine methylation and the recent advances made, with a focus on the lower eukaryote Saccharomyces cerevisiae. We cover the types of methylated proteins, their responsible methyltransferases, where and how the effects of arginine methylation are seen in the cell, and, finally, discuss the conservation of the biological function of methylarginines between S. cerevisiae and mammals.
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Affiliation(s)
- Jason K K Low
- Systems Biology Laboratory, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, Australia
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15
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Birzele F, Fauti T, Stahl H, Lenter MC, Simon E, Knebel D, Weith A, Hildebrandt T, Mennerich D. Next-generation insights into regulatory T cells: expression profiling and FoxP3 occupancy in Human. Nucleic Acids Res 2011; 39:7946-60. [PMID: 21729870 PMCID: PMC3185410 DOI: 10.1093/nar/gkr444] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 04/27/2011] [Accepted: 05/13/2011] [Indexed: 01/14/2023] Open
Abstract
Regulatory T-cells (Treg) play an essential role in the negative regulation of immune answers by developing an attenuated cytokine response that allows suppressing proliferation and effector function of T-cells (CD4(+) Th). The transcription factor FoxP3 is responsible for the regulation of many genes involved in the Treg gene signature. Its ablation leads to severe immune deficiencies in human and mice. Recent developments in sequencing technologies have revolutionized the possibilities to gain insights into transcription factor binding by ChiP-seq and into transcriptome analysis by mRNA-seq. We combine FoxP3 ChiP-seq and mRNA-seq in order to understand the transcriptional differences between primary human CD4(+) T helper and regulatory T-cells, as well as to study the role of FoxP3 in generating those differences. We show, that mRNA-seq allows analyzing the transcriptomal landscape of T-cells including the expression of specific splice variants at much greater depth than previous approaches, whereas 50% of transcriptional regulation events have not been described before by using diverse array technologies. We discovered splicing patterns like the expression of a kinase-dead isoform of IRAK1 upon T-cell activation. The immunoproteasome is up-regulated in both Treg and CD4(+) Th cells upon activation, whereas the 'standard' proteasome is up-regulated in Tregs only upon activation.
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Affiliation(s)
- Fabian Birzele
- Department of Pulmonary Research, Group Genomics, Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorferstraße 67, 88397 Biberach an der Riß, Germany and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, CT 06877-0368, USA
| | - Tanja Fauti
- Department of Pulmonary Research, Group Genomics, Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorferstraße 67, 88397 Biberach an der Riß, Germany and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, CT 06877-0368, USA
| | - Heiko Stahl
- Department of Pulmonary Research, Group Genomics, Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorferstraße 67, 88397 Biberach an der Riß, Germany and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, CT 06877-0368, USA
| | - Martin C. Lenter
- Department of Pulmonary Research, Group Genomics, Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorferstraße 67, 88397 Biberach an der Riß, Germany and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, CT 06877-0368, USA
| | - Eric Simon
- Department of Pulmonary Research, Group Genomics, Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorferstraße 67, 88397 Biberach an der Riß, Germany and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, CT 06877-0368, USA
| | - Dagmar Knebel
- Department of Pulmonary Research, Group Genomics, Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorferstraße 67, 88397 Biberach an der Riß, Germany and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, CT 06877-0368, USA
| | - Andreas Weith
- Department of Pulmonary Research, Group Genomics, Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorferstraße 67, 88397 Biberach an der Riß, Germany and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, CT 06877-0368, USA
| | - Tobias Hildebrandt
- Department of Pulmonary Research, Group Genomics, Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorferstraße 67, 88397 Biberach an der Riß, Germany and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, CT 06877-0368, USA
| | - Detlev Mennerich
- Department of Pulmonary Research, Group Genomics, Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorferstraße 67, 88397 Biberach an der Riß, Germany and Department of Immunology and Inflammation, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, CT 06877-0368, USA
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Abstract
The cell nucleus is an intricate organelle that coordinates multiple activities that are associated with DNA replication and gene expression. In all eukaryotes, it stores the genetic information and the machineries that control the production of mature and export-competent messenger ribonucleoproteins (mRNPs), a multistep process that is regulated in a spatial and temporal manner. Recent studies suggest that post-translational modifications play a part in coordinating the co-transcriptional assembly, remodelling and export of mRNP complexes through nuclear pores, adding a new level of regulation to the process of gene expression.
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CHEN X, ZENG QC, LU XP, YU DQ, LI WZ. Characterization and Expression Analysis of Four Glycine-Rich RNA-Binding Proteins Involved in Osmotic Response in Tobacco (Nicotiana tabacum cv. Xanthi). ACTA ACUST UNITED AC 2010. [DOI: 10.1016/s1671-2927(09)60254-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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