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Li H, Tan Y, Basu D, Corbett K, Zhang D. Unveiling the multifaceted domain polymorphism of the Menshen antiphage system. Nucleic Acids Res 2025; 53:gkaf357. [PMID: 40347139 PMCID: PMC12065111 DOI: 10.1093/nar/gkaf357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/14/2025] [Accepted: 04/17/2025] [Indexed: 05/12/2025] Open
Abstract
Recent advances have significantly enriched our understanding of complex bacteria-phage interactions. To date, over one hundred bacterial antiphage systems have been identified, yet the mechanisms of many, including the recently discovered Menshen system, remain elusive. We employed comparative genomics and protein bioinformatics for a systematic investigation of the Menshen system, focusing on its organization, structure, function, and evolution. By delineating six primary domain determinants and predicting their functions, we propose that the three components (NsnA-B-C) of Menshen likely act as sensor, transducer, and effector modules, respectively. Notably, we unveil remarkable polymorphism in domain composition within both NsnA and NsnC. NsnA proteins universally share ParB-DUF262 and DNA-binding ParBDB domains, and often include additional DNA-binding modules at their N-termini. NsnC effectors exhibit diverse inactive PIN (inPIN)-like domains for target recognition in their N-termini, and multiple nuclease domains for toxicity in their C-termini. We demonstrate that this multifaceted polymorphism results from the independent integration of various sensor domains into NsnA, alongside constant shuffling and diversification of the inPIN and effector domains in NsnC. These findings not only elucidate the functional diversity and inter-subunit interactions of the Menshen system, but also underscore its exceptional capacity for adaptability and versatility in the ongoing arms race between bacteria and phages.
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Affiliation(s)
- Huan Li
- Department of Biology, College of Arts and Sciences, Saint Louis University, Saint Louis, MO 63103, United States
| | - Yongjun Tan
- Department of Biology, College of Arts and Sciences, Saint Louis University, Saint Louis, MO 63103, United States
| | - Dwaipayan Basu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, United States
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, United States
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, United States
| | - Dapeng Zhang
- Department of Biology, College of Arts and Sciences, Saint Louis University, Saint Louis, MO 63103, United States
- Program of Bioinformatics and Computational Biology, School of Science and Engineering, Saint Louis University, Saint Louis, MO 63103, United States
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2
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Taniguchi N, Watanuki K, Nakato D, Takenouchi T, Kosaki K, Koga H. PURA-related neurodevelopmental disorders: a systematic review on genotype-phenotype correlations. J Med Genet 2025; 62:191-198. [PMID: 39824548 DOI: 10.1136/jmg-2024-110379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Accepted: 12/22/2024] [Indexed: 01/20/2025]
Abstract
INTRODUCTION Genotype-phenotype correlations in PURA-related neurodevelopmental disorders (PURA-NDDs) remain unclear. This systematic review aimed to clarify these correlations. METHODS Searches of PubMed and Embase were conducted on 8 August 2024 to identify studies that had investigated genetically diagnosed PURA-NDDs (5q31.3 deletion syndrome and PURA syndrome). All types and languages of studies were included. Study quality was assessed using a 20-item criterion checklist. Genetic and clinical data were extracted from each article and genotype-phenotype correlations were explored. RESULTS Our analysis included 46 studies encompassing 230 patients with PURA-NDDs (5q31.3 deletion syndrome 18 (8%) and PURA syndrome 212 (92%)). Patients with 5q31.3 deletion syndrome exhibited more congenital defects (50% vs 12%, p<0.0001), respiratory difficulties (94% vs 63%, p=0.013) and walking disability (94% vs 55%, p=0.0026) than patients with PURA syndrome. In PURA syndrome, protein-truncating (nonsense or frameshift) variants were associated with more speech deficits (93% vs 80%, p=0.014) than non-protein-truncating (missense or in-frame) variants. PURA variant location had no effect on congenital defect occurrence or neurodevelopmental outcome. Overall, respiratory difficulties, walking disability and speech deficits were more commonly observed in the following order: 5q31.3 deletion (94%, 94% and 100%, respectively), multiple PUR-repeat deletions (68%, 60% and 95%, respectively), single PUR-repeat deletion or alteration (61%, 53% and 85%, respectively), and deletion or alteration located outside PUR repeats (38%, 33% and 43%, respectively). CONCLUSION The clinical severity of PURA-NDDs appears to be associated with the deletion/alteration size including PUR repeats rather than the location of PURA variants.
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Affiliation(s)
| | - Keisuke Watanuki
- Department of Pediatrics, NHO Beppu Medical Center, Beppu, Oita, Japan
| | - Daisuke Nakato
- Center for Medical Genetics, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| | - Toshiki Takenouchi
- Department of Pediatrics, Keio University Hospital, Shinjuku, Tokyo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| | - Hiroshi Koga
- Department of Pediatrics, NHO Beppu Medical Center, Beppu, Oita, Japan
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3
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Aggarwal T, Kondabagil K. Proteome-scale structural prediction of the giant Marseillevirus reveals conserved folds and putative homologs of the hypothetical proteins. Arch Virol 2024; 169:222. [PMID: 39414627 DOI: 10.1007/s00705-024-06155-8] [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: 06/10/2024] [Accepted: 09/02/2024] [Indexed: 10/18/2024]
Abstract
A significant proportion of the highly divergent and novel proteins of giant viruses are termed "hypothetical" due to the absence of detectable homologous sequences in the existing databases. The quality of genome and proteome annotations often relies on the identification of signature sequences and motifs in order to assign putative functions to the gene products. These annotations serve as the first set of information for researchers to develop workable hypotheses for further experimental research. The structure-function relationship of proteins suggests that proteins with similar functions may also exhibit similar folding patterns. Here, we report the first proteome-wide structure prediction of the giant Marseillevirus. We use AlphaFold-predicted structures and their comparative analysis with the experimental structures in the PDB database to preliminarily annotate the viral proteins. Our work highlights the conservation of structural folds in proteins with highly divergent sequences and reveals potentially paralogous relationships among them. We also provide evidence for gene duplication and fusion as contributing factors to giant viral genome expansion and evolution. With the easily accessible AlphaFold and other advanced bioinformatics tools for high-confidence de novo structure prediction, we propose a combined sequence and predicted-structure-based proteome annotation approach for the initial characterization of novel and complex organisms or viruses.
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Affiliation(s)
- Tanvi Aggarwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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4
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Enustun E, Armbruster EG, Lee J, Zhang S, Yee BA, Malukhina K, Gu Y, Deep A, Naritomi J, Liang Q, Aigner S, Adler B, Cress B, Doudna J, Chaikeeratisak V, Cleveland D, Ghassemian M, Bintu B, Yeo G, Pogliano J, Corbett K. A phage nucleus-associated RNA-binding protein is required for jumbo phage infection. Nucleic Acids Res 2024; 52:4440-4455. [PMID: 38554115 PMCID: PMC11077065 DOI: 10.1093/nar/gkae216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 04/01/2024] Open
Abstract
Large-genome bacteriophages (jumbo phages) of the proposed family Chimalliviridae assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and DNA-targeting CRISPR-Cas nucleases. While the nuclear shell provides broad protection against host nucleases, it necessitates transport of mRNA out of the nucleus-like compartment for translation by host ribosomes, and transport of specific proteins into the nucleus-like compartment to support DNA replication and mRNA transcription. Here, we identify a conserved phage nuclear shell-associated protein that we term Chimallin C (ChmC), which adopts a nucleic acid-binding fold, binds RNA with high affinity in vitro, and binds phage mRNAs in infected cells. ChmC also forms phase-separated condensates with RNA in vitro. Targeted knockdown of ChmC using mRNA-targeting dCas13d results in accumulation of phage-encoded mRNAs in the phage nucleus, reduces phage protein production, and compromises virion assembly. Taken together, our data show that the conserved ChmC protein plays crucial roles in the viral life cycle, potentially by facilitating phage mRNA translocation through the nuclear shell to promote protein production and virion development.
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Affiliation(s)
- Eray Enustun
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Emily G Armbruster
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Jina Lee
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Sitao Zhang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Brian A Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Kseniya Malukhina
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Yajie Gu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Amar Deep
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Jack T Naritomi
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Qishan Liang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Benjamin A Adler
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Brady F Cress
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Vorrapon Chaikeeratisak
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Don W Cleveland
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - Majid Ghassemian
- Biomolecular and Proteomics Mass Spectrometry Facility, University of California San Diego, La Jolla, CA 92093, USA
| | - Bogdan Bintu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - Joe Pogliano
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Kevin D Corbett
- Department of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
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5
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Proske M, Janowski R, Bacher S, Kang HS, Monecke T, Koehler T, Hutten S, Tretter J, Crois A, Molitor L, Varela-Rial A, Fino R, Donati E, De Fabritiis G, Dormann D, Sattler M, Niessing D. PURA syndrome-causing mutations impair PUR-domain integrity and affect P-body association. eLife 2024; 13:RP93561. [PMID: 38655849 PMCID: PMC11042805 DOI: 10.7554/elife.93561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024] Open
Abstract
Mutations in the human PURA gene cause the neurodevelopmental PURA syndrome. In contrast to several other monogenetic disorders, almost all reported mutations in this nucleic acid-binding protein result in the full disease penetrance. In this study, we observed that patient mutations across PURA impair its previously reported co-localization with processing bodies. These mutations either destroyed the folding integrity, RNA binding, or dimerization of PURA. We also solved the crystal structures of the N- and C-terminal PUR domains of human PURA and combined them with molecular dynamics simulations and nuclear magnetic resonance measurements. The observed unusually high dynamics and structural promiscuity of PURA indicated that this protein is particularly susceptible to mutations impairing its structural integrity. It offers an explanation why even conservative mutations across PURA result in the full penetrance of symptoms in patients with PURA syndrome.
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Affiliation(s)
- Marcel Proske
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz MunichNeuherbergGermany
- Institute of Pharmaceutical Biotechnology, Ulm UniversityUlmGermany
| | - Robert Janowski
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz MunichNeuherbergGermany
| | - Sabrina Bacher
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz MunichNeuherbergGermany
| | - Hyun-Seo Kang
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz MunichNeuherbergGermany
- Chemistry Department, Biomolecular NMR and Center for Integrated Protein Science Munich, Technical University of MunichMainzGermany
| | - Thomas Monecke
- Institute of Pharmaceutical Biotechnology, Ulm UniversityUlmGermany
| | - Tony Koehler
- Institute of Pharmaceutical Biotechnology, Ulm UniversityUlmGermany
| | - Saskia Hutten
- Biocenter, Institute of Molecular Physiology, Johannes Gutenberg-Universität (JGU)MainzGermany
| | - Jana Tretter
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz MunichNeuherbergGermany
| | - Anna Crois
- Institute of Pharmaceutical Biotechnology, Ulm UniversityUlmGermany
| | - Lena Molitor
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz MunichNeuherbergGermany
| | | | | | | | | | - Dorothee Dormann
- Biocenter, Institute of Molecular Physiology, Johannes Gutenberg-Universität (JGU)MainzGermany
- Institute of Molecular Biology (IMB)MainzGermany
| | - Michael Sattler
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz MunichNeuherbergGermany
- Chemistry Department, Biomolecular NMR and Center for Integrated Protein Science Munich, Technical University of MunichMainzGermany
| | - Dierk Niessing
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz MunichNeuherbergGermany
- Institute of Pharmaceutical Biotechnology, Ulm UniversityUlmGermany
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6
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Enustun E, Armbruster EG, Lee J, Zhang S, Yee BA, Gu Y, Deep A, Naritomi JT, Liang Q, Aigner S, Adler BA, Cress BF, Doudna JA, Chaikeeratisak V, Cleveland DW, Ghassemian M, Yeo GW, Pogliano J, Corbett KD. A phage nucleus-associated RNA-binding protein is required for jumbo phage infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.559000. [PMID: 37790334 PMCID: PMC10542519 DOI: 10.1101/2023.09.22.559000] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Large-genome bacteriophages (jumbo phages) of the Chimalliviridae family assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and CRISPR/Cas nucleases. While the nuclear shell provides broad protection against host nucleases, it necessitates transport of mRNA out of the nucleus-like compartment for translation by host ribosomes, and transport of specific proteins into the nucleus-like compartment to support DNA replication and mRNA transcription. Here we identify a conserved phage nuclear shell-associated protein that we term Chimallin C (ChmC), which adopts a nucleic acid-binding fold, binds RNA with high affinity in vitro, and binds phage mRNAs in infected cells. ChmC also forms phase-separated condensates with RNA in vitro. Targeted knockdown of ChmC using mRNA-targeting dCas13d halts infections at an early stage. Taken together, our data suggest that the conserved ChmC protein acts as a chaperone for phage mRNAs, potentially stabilizing these mRNAs and driving their translocation through the nuclear shell to promote translation and infection progression.
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Affiliation(s)
- Eray Enustun
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Emily G. Armbruster
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Jina Lee
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Sitao Zhang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Brian A. Yee
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yajie Gu
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Amar Deep
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jack T. Naritomi
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Qishan Liang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Benjamin A. Adler
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Brady F. Cress
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Jennifer A. Doudna
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Don W. Cleveland
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - Majid Ghassemian
- Biomolecular and Proteomics Mass Spectrometry Facility, University of California San Diego, La Jolla, CA, USA
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - Joe Pogliano
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
| | - Kevin D. Corbett
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
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7
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Foote AT, Kelm RJ. Aromatic Residues Dictate the Transcriptional Repressor and Single-Stranded DNA Binding Activities of Purine-Rich Element Binding Protein B. Biochemistry 2023; 62:2597-2610. [PMID: 37556352 DOI: 10.1021/acs.biochem.3c00204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
Purine-rich element binding protein B (Purβ) is a single-stranded DNA (ssDNA) and RNA-binding protein that functions as a transcriptional repressor of genes encoding certain muscle-restricted contractile proteins in the setting of cellular stress or tissue injury. A prior report from our laboratory implicated specific basic amino acid residues in the physical and functional interaction of Purβ with the smooth muscle-α actin gene (Acta2) promoter. Independent structural analysis of fruit fly Purα uncovered a role for several aromatic residues in the binding of this related protein to ssDNA. Herein, we examine the functional importance of a comparable set of hydrophobic residues that are positionally conserved in the repeat I (Y59), II (F155), and III (F256) domains of murine Purβ. Site-directed Y/F to alanine substitutions were engineered, and the resultant Purβ point mutants were tested in various biochemical and cell-based assays. None of the mutations affected the cellular expression, structural stability, or dimerization capacity of Purβ. However, the Y59A and F155A mutants demonstrated weaker Acta2 repressor activity in transfected fibroblasts and reduced binding affinity for the purine-rich strand of an Acta2 cis-regulatory element in vitro. Mutation of Y59 and F155 also altered the multisite binding properties of Purβ for ssDNA and diminished the interaction of Purβ with Y-box binding protein 1, a co-repressor of Acta2. Collectively, these findings suggest that some of the same aromatic residues, which govern the specific and high-affinity binding of Purβ to ssDNA, also mediate certain heterotypic protein interactions underlying the Acta2 repressor function of Purβ.
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Affiliation(s)
- Andrea T Foote
- Department of Medicine, University of Vermont, Larner College of Medicine, Burlington, Vermont 05405, United States
| | - Robert J Kelm
- Department of Medicine, University of Vermont, Larner College of Medicine, Burlington, Vermont 05405, United States
- Department of Biochemistry, University of Vermont, Larner College of Medicine, Burlington, Vermont 05405, United States
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8
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Molitor L, Klostermann M, Bacher S, Merl-Pham J, Spranger N, Burczyk S, Ketteler C, Rusha E, Tews D, Pertek A, Proske M, Busch A, Reschke S, Feederle R, Hauck S, Blum H, Drukker M, Fischer-Posovszky P, König J, Zarnack K, Niessing D. Depletion of the RNA-binding protein PURA triggers changes in posttranscriptional gene regulation and loss of P-bodies. Nucleic Acids Res 2023; 51:1297-1316. [PMID: 36651277 PMCID: PMC9943675 DOI: 10.1093/nar/gkac1237] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 01/19/2023] Open
Abstract
The RNA-binding protein PURA has been implicated in the rare, monogenetic, neurodevelopmental disorder PURA Syndrome. PURA binds both DNA and RNA and has been associated with various cellular functions. Only little is known about its main cellular roles and the molecular pathways affected upon PURA depletion. Here, we show that PURA is predominantly located in the cytoplasm, where it binds to thousands of mRNAs. Many of these transcripts change abundance in response to PURA depletion. The encoded proteins suggest a role for PURA in immune responses, mitochondrial function, autophagy and processing (P)-body activity. Intriguingly, reduced PURA levels decrease the expression of the integral P-body components LSM14A and DDX6 and strongly affect P-body formation in human cells. Furthermore, PURA knockdown results in stabilization of P-body-enriched transcripts, whereas other mRNAs are not affected. Hence, reduced PURA levels, as reported in patients with PURA Syndrome, influence the formation and composition of this phase-separated RNA processing machinery. Our study proposes PURA Syndrome as a new model to study the tight connection between P-body-associated RNA regulation and neurodevelopmental disorders.
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Affiliation(s)
- Lena Molitor
- Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Melina Klostermann
- Buchmann Institute for Molecular Life Sciences (BMLS) and Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt a.M., Germany
| | - Sabrina Bacher
- Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Juliane Merl-Pham
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Nadine Spranger
- Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Sandra Burczyk
- Institute of Pharmaceutical Biotechnology, Ulm University, 89081 Ulm, Germany
| | - Carolin Ketteler
- Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Ejona Rusha
- Induced Pluripotent Stem Cell Core Facility, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Daniel Tews
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, 89070 Ulm, Germany
| | - Anna Pertek
- Induced Pluripotent Stem Cell Core Facility, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Marcel Proske
- Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Pharmaceutical Biotechnology, Ulm University, 89081 Ulm, Germany
| | - Anke Busch
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Sarah Reschke
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Regina Feederle
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Stefanie M Hauck
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Micha Drukker
- Institute of Stem Cell Research, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, 2333 CC Leiden, The Netherlands
| | - Pamela Fischer-Posovszky
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, 89070 Ulm, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) and Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt a.M., Germany
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute of Pharmaceutical Biotechnology, Ulm University, 89081 Ulm, Germany
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9
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Dai W, Sun Y, Fan Y, Gao Y, Zhan Y, Wang L, Xiao B, Qiu W, Gu X, Sun K, Yu Y, Xu N. A 25 Mainland Chinese cohort of patients with PURA-related neurodevelopmental disorders: clinical delineation and genotype-phenotype correlations. Eur J Hum Genet 2023; 31:112-121. [PMID: 36376392 PMCID: PMC9822978 DOI: 10.1038/s41431-022-01217-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/23/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022] Open
Abstract
PURA-related neurodevelopmental disorders (PURA-NDDs) include 5q31.3 microdeletion syndrome and PURA syndrome. PURA has been proposed as a candidate gene responsible for 5q31.3 microdeletion syndrome. Phenotype comparisons between patients with PURA mutations and 5q31.3 microdeletions encompassing more than PURA gene are lacking. A total of 25 previously undescribed Mainland China patients were evaluated. Clinical data were obtained from medical record review and standardized medical history questionnaire. Clinical profile and genetic spectrum of the patients with PURA syndrome and genotype-phenotype correlations between PURA mutations group and 5q31.3 microdeletions group were analyzed. Our identified seventeen de nove PURA variants were novel, and two recurrent frameshift variants, c.697_699del (p.F233del) and c.159dup (p.L54Afs*147) were detected in the four independent pedigrees. One patient with 5q31.3 microdeletion further supported the shortest overlapping region only contains PURA and IGIP gene. Developmental delay/intellectual disability, neonatal hypotonia, neonatal feeding difficulties, hypersomnolence and dysmorphic features were prominent clinical features in PURA syndrome. There was no significant difference between two groups in incidence of neonatal problems, developmental delay and common medical comorbidities. We observed a higher frequency of abnormal brain MRI and specific facial dysmorphism in 5q31.3 microdeletion group. This is the first work describing a largest cohort of Mainland China patients broaden the clinical and molecular spectrum of PURA-NDDs. Our findings not only demonstrated that PURA haploinsufficiency was a major contributor to the important phenotypes of 5q31.3 microdeletion, but also implied that additional genes still played a role in the 5q31.3 microdeletion.
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Affiliation(s)
- Weiqian Dai
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yu Sun
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yanjie Fan
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yan Gao
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yongkun Zhan
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute for Pediatric Research, Shanghai, China
| | - Lili Wang
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute for Pediatric Research, Shanghai, China
| | - Bing Xiao
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute for Pediatric Research, Shanghai, China
| | - Wenjuan Qiu
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute for Pediatric Research, Shanghai, China
| | - Xuefan Gu
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute for Pediatric Research, Shanghai, China
| | - Kun Sun
- Center of Clinical Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Institute for Pediatric Research, Shanghai, China.
| | - Na Xu
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Institute for Pediatric Research, Shanghai, China.
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10
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Hypotonic Infant with PURA Syndrome-related Channelopathy Successfully Treated with Pyridostigmine. Neuromuscul Disord 2022; 32:166-169. [DOI: 10.1016/j.nmd.2022.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 10/31/2021] [Accepted: 01/12/2022] [Indexed: 11/21/2022]
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11
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Li H, Tan Y, Zhang D. Genomic discovery and structural dissection of a novel type of polymorphic toxin system in gram-positive bacteria. Comput Struct Biotechnol J 2022; 20:4517-4531. [PMID: 36051883 PMCID: PMC9424270 DOI: 10.1016/j.csbj.2022.08.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/15/2022] [Accepted: 08/15/2022] [Indexed: 11/26/2022] Open
Abstract
Bacteria have developed several molecular conflict systems to facilitate kin recognition and non-kin competition to gain advantages in the acquisition of growth niches and of limited resources. One such example is a large class of so-called polymorphic toxin systems (PTSs), which comprise a variety of the toxin proteins secreted via T2SS, T5SS, T6SS, T7SS and many others. These systems are highly divergent in terms of sequence/structure, domain architecture, toxin-immunity association, and organization of the toxin loci, which makes it difficult to identify and characterize novel systems using traditional experimental and bioinformatic strategies. In recent years, we have been developing and utilizing unique genome-mining strategies and pipelines, based on the organizational principles of both domain architectures and genomic loci of PTSs, for an effective and comprehensive discovery of novel PTSs, dissection of their components, and prediction of their structures and functions. In this study, we present our systematic discovery of a new type of PTS (S8-PTS) in several gram-positive bacteria. We show that the S8-PTS contains three components: a peptidase of the S8 family (subtilases), a polymorphic toxin, and an immunity protein. We delineated the typical organization of these polymorphic toxins, in which a N-terminal signal peptide is followed by a potential receptor binding domain, BetaH, and one of 16 toxin domains. We classified each toxin domain by the distinct superfamily to which it belongs, identifying nine BECR ribonucleases, one Restriction Endonuclease, one HNH nuclease, two novel toxin domains homologous to the VOC enzymes, one toxin domain with the Frataxin-like fold, and several other unique toxin families such as Ntox33 and HicA. Accordingly, we identified 20 immunity families and classified them into different classes of folds. Further, we show that the S8-PTS-associated peptidases are analogous to many other processing peptidases found in T5SS, T7SS, T9SS, and many proprotein-processing peptidases, indicating that they function to release the toxin domains during secretion. The S8-PTSs are mostly found in animal and plant-associated bacteria, including many pathogens. We propose S8-PTSs will facilitate the competition of these bacteria with other microbes or contribute to the pathogen-host interactions.
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Affiliation(s)
- Huan Li
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63103, USA
| | - Yongjun Tan
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63103, USA
| | - Dapeng Zhang
- Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63103, USA
- Program of Bioinformatics and Computational Biology, College of Arts & Sciences, Saint Louis University, MO 63103, USA
- Corresponding author at: Department of Biology, College of Arts & Sciences, Saint Louis University, Saint Louis, MO 63103, USA.
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12
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Molitor L, Bacher S, Burczyk S, Niessing D. The Molecular Function of PURA and Its Implications in Neurological Diseases. Front Genet 2021; 12:638217. [PMID: 33777106 PMCID: PMC7990775 DOI: 10.3389/fgene.2021.638217] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/09/2021] [Indexed: 12/19/2022] Open
Abstract
In recent years, genome-wide analyses of patients have resulted in the identification of a number of neurodevelopmental disorders. Several of them are caused by mutations in genes that encode for RNA-binding proteins. One of these genes is PURA, for which in 2014 mutations have been shown to cause the neurodevelopmental disorder PURA syndrome. Besides intellectual disability (ID), patients develop a variety of symptoms, including hypotonia, metabolic abnormalities as well as epileptic seizures. This review aims to provide a comprehensive assessment of research of the last 30 years on PURA and its recently discovered involvement in neuropathological abnormalities. Being a DNA- and RNA-binding protein, PURA has been implicated in transcriptional control as well as in cytoplasmic RNA localization. Molecular interactions are described and rated according to their validation state as physiological targets. This information will be put into perspective with available structural and biophysical insights on PURA’s molecular functions. Two different knock-out mouse models have been reported with partially contradicting observations. They are compared and put into context with cell biological observations and patient-derived information. In addition to PURA syndrome, the PURA protein has been found in pathological, RNA-containing foci of patients with the RNA-repeat expansion diseases such as fragile X-associated tremor ataxia syndrome (FXTAS) and amyotrophic lateral sclerosis (ALS)/fronto-temporal dementia (FTD) spectrum disorder. We discuss the potential role of PURA in these neurodegenerative disorders and existing evidence that PURA might act as a neuroprotective factor. In summary, this review aims at informing researchers as well as clinicians on our current knowledge of PURA’s molecular and cellular functions as well as its implications in very different neuronal disorders.
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Affiliation(s)
- Lena Molitor
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Sabrina Bacher
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Sandra Burczyk
- Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany
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13
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Mishra S, Girisha KM, Shukla A. Expanding the phenotype of PURA-related neurodevelopmental disorder: a close differential diagnosis of infantile hypotonia with psychomotor retardation and characteristic facies. Clin Dysmorphol 2021; 30:1-5. [PMID: 33229923 PMCID: PMC9944571 DOI: 10.1097/mcd.0000000000000360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Purine-rich element-binding protein A (PURA) encodes Pur-alpha, a transcriptional activator protein is crucial for normal brain development. Pathogenic variants in PURA are known to cause mental retardation, autosomal dominant 31, characterized by psychomotor delay, absent or poor speech, hypotonia, feeding difficulties, seizures or 'seizure-like' movements, and dysmorphism. PURA-related neurodevelopmental disorder (PURA-related NDD) result either from heterozygous pathogenic sequence variants in PURA or microdeletions spanning PURA. Singleton whole-exome sequencing (WES) was performed for the proband after a clinical diagnosis of infantile hypotonia with psychomotor retardation and characteristic facies (IHPRF) was made. The pathogenic variant was validated by Sanger sequencing in the proband and parents. Comparison of PURA-related NDD and IHPRF was carried out. WES identified a novel, de-novo stop-gain variant c.178G>T in PURA. In addition to typical phenotype, subject also had hypersensitivity to various stimuli which was not reported in PURA-related NDD. Significant phenotypic overlap was observed in subjects with PURA-related NDD and IHPRF especially with IHPRF2, caused by biallelic pathogenic variants in UNC80. This study expands the phenotypic and mutational spectrum of PURA-related NDD. We propose PURA-related NDD to be considered as a close differential diagnosis of IHPRF.
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Affiliation(s)
- Shivani Mishra
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
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14
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Cinquina V, Ciaccio C, Venturini M, Masson R, Ritelli M, Colombi M. Expanding the PURA syndrome phenotype: A child with the recurrent PURA p.(Phe233del) pathogenic variant showing similarities with cutis laxa. Mol Genet Genomic Med 2021; 9:e1562. [PMID: 33275834 PMCID: PMC7963414 DOI: 10.1002/mgg3.1562] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/18/2020] [Accepted: 11/09/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND PURA syndrome is rare autosomal dominant condition characterized by moderate to severe neurodevelopmental delay with absence of speech in nearly all patients and lack of independent ambulation in many. Early-onset problems include excessive hiccups, hypotonia, hypersomnolence, hypothermia, feeding difficulties, recurrent apneas, epileptic seizures, and abnormal nonepileptic movements. Other less common manifestations comprise congenital heart defects, urogenital malformations, and various skeletal, ophthalmological, gastrointestinal, and endocrine anomalies. Up to now, 78 individuals with PURA syndrome and 64 different pathogenic variants have been reported, but no clear-cut genotype-phenotype correlations have emerged so far. Herein, we report the clinical and molecular characterization of a 3-year-old girl with severe hypotonia, global developmental delay, and soft, loose skin, who came to our attention with a suspicion of cutis laxa (CL), which denotes another condition with variable neurodevelopmental problems. METHODS Amplicon-based whole exome sequencing was performed, and an in-house pipeline was used to conduct filtering and prioritization of variants. New prediction algorithms for indels were used to validate the pathogenicity of the PURA variant, and results were confirmed with the Sanger method. Finally, we collected clinical and mutational data of all PURA syndrome patients reported yet and compared the clinical features with those of our patient. RESULTS Clinical evaluation and biochemical investigations excluded CL and prompted to perform whole exome sequencing, which confirmed the absence of pathogenic variants in all CL-related genes and revealed the known PURA c.697_699del, p.(Phe233del) variant, identified hitherto in seven additional children with PURA syndrome. CONCLUSIONS Our data expand the phenotypic spectrum of PURA syndrome by showing that it can be regarded as a differential diagnosis for cutis laxa in early infancy. Our patient and literature review emphasize that a wide clinical variability exists not only between individuals with different PURA variants, but also among patients with the same causal mutation.
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Affiliation(s)
- Valeria Cinquina
- Division of Biology and GeneticsDepartment of Molecular and Translational MedicineUniversity of BresciaBresciaItaly
| | - Claudia Ciaccio
- Developmental Neurology UnitFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
| | - Marina Venturini
- Division of DermatologyDepartment of Clinical and Experimental SciencesSpedali Civili University Hospital BresciaBresciaItaly
| | - Riccardo Masson
- Developmental Neurology UnitFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
| | - Marco Ritelli
- Division of Biology and GeneticsDepartment of Molecular and Translational MedicineUniversity of BresciaBresciaItaly
| | - Marina Colombi
- Division of Biology and GeneticsDepartment of Molecular and Translational MedicineUniversity of BresciaBresciaItaly
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15
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Janowski R, Niessing D. The large family of PC4-like domains - similar folds and functions throughout all kingdoms of life. RNA Biol 2020; 17:1228-1238. [PMID: 32476604 PMCID: PMC7549692 DOI: 10.1080/15476286.2020.1761639] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RNA- and DNA-binding domains are essential building blocks for specific regulation of gene expression. While a number of canonical nucleic acid binding domains share sequence and structural conservation, others are less obviously linked by evolutionary traits. In this review, we describe a protein fold of about 150 aa in length, bearing a conserved β-β-β-β-α-linker-β-β-β-β-α topology and similar nucleic acid binding properties but no apparent sequence conservation. The same overall fold can also be achieved by dimerization of two proteins, each bearing a β-β-β-β-α topology. These proteins include but are not limited to the transcription factors PC4 and P24 from humans and plants, respectively, the human RNA-transport factor Pur-α (also termed PURA), as well as the ssDNA-binding SP_0782 protein from Streptococcus pneumonia and the bacteriophage coat proteins PP7 and MS2. Besides their common overall topology, these proteins share common nucleic acids binding surfaces and thus functional similarity. We conclude that these PC4-like domains include proteins from all kingdoms of life and are much more abundant than previously known.
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Affiliation(s)
- Robert Janowski
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health , Neuherberg, Germany
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health , Neuherberg, Germany.,Institute of Pharmaceutical Biotechnology, Ulm University , Ulm, Germany
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16
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Wortman MJ, Dagdanova AV, Clark AM, Godfrey EW, Pascal SM, Johnson EM, Daniel DC. A synthetic Pur-based peptide binds and alters G-quadruplex secondary structure present in the expanded RNA repeat of C9orf72 ALS/FTD. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118674. [PMID: 32035967 DOI: 10.1016/j.bbamcr.2020.118674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/20/2019] [Accepted: 02/02/2020] [Indexed: 12/26/2022]
Abstract
Increased Pur-alpha (Pura) protein levels in animal models alleviate certain cellular symptoms of the disease spectrum amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD). Pura is a member of the Pur family of evolutionarily conserved guanine-rich polynucleotide binding proteins containing a repeated signature PUR domain of 60-80 amino acids. Here we have employed a synthetic peptide, TZIP, similar to a Pur domain, but with sequence alterations based on a consensus of evolutionarily conserved Pur family binding domains and having an added transporter sequence. A major familial form of ALS/FTD, C9orf72 (C9), is due to a hexanucleotide repeat expansion (HRE) of (GGGGCC), a Pur binding element. We show by circular dichroism that RNA oligonucleotides containing this purine-rich sequence consist largely of parallel G-quadruplexes. TZIP peptide binds this repeat sequence in both DNA and RNA. It binds the RNA element, including the G-quadruplexes, with a high degree of specificity versus a random oligonucleotide. In addition, TZIP binds both linear and G-quadruplex repeat RNA to form higher order G-quadruplex secondary structures. This change in conformational form by Pur-based peptide represents a new mechanism for regulating G quadruplex secondary structure within the C9 repeat. TZIP modulation of C9 RNA structural configuration may alter interaction of the complex with other proteins. This Pur-based mechanism provides new targets for therapy, and it may help to explain Pura alleviation of certain cellular pathological aspects of ALS/FTD.
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Affiliation(s)
- Margaret J Wortman
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Ayuna V Dagdanova
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Andrea M Clark
- Old Dominion University, Department of Chemistry and Biochemistry, Norfolk, VA 23529, USA
| | - Earl W Godfrey
- School of Health Professions, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Steven M Pascal
- Old Dominion University, Department of Chemistry and Biochemistry, Norfolk, VA 23529, USA
| | - Edward M Johnson
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Dianne C Daniel
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA.
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17
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Jutras BL, Savage CR, Arnold WK, Lethbridge KG, Carroll DW, Tilly K, Bestor A, Zhu H, Seshu J, Zückert WR, Stewart PE, Rosa PA, Brissette CA, Stevenson B. The Lyme disease spirochete's BpuR DNA/RNA-binding protein is differentially expressed during the mammal-tick infectious cycle, which affects translation of the SodA superoxide dismutase. Mol Microbiol 2019; 112:973-991. [PMID: 31240776 PMCID: PMC6736767 DOI: 10.1111/mmi.14336] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2019] [Indexed: 12/24/2022]
Abstract
When the Lyme disease spirochete, Borrelia burgdorferi, transfers from a feeding tick into a human or other vertebrate host, the bacterium produces vertebrate‐specific proteins and represses factors needed for arthropod colonization. Previous studies determined that the B. burgdorferi BpuR protein binds to its own mRNA and autoregulates its translation, and also serves as co‐repressor of erp transcription. Here, we demonstrate that B. burgdorferi controls transcription of bpuR, expressing high levels of bpuR during tick colonization but significantly less during mammalian infection. The master regulator of chromosomal replication, DnaA, was found to bind specifically to a DNA sequence that overlaps the bpuR promoter. Cultured B. burgdorferi that were genetically manipulated to produce elevated levels of BpuR exhibited altered levels of several proteins, although BpuR did not impact mRNA levels. Among these was the SodA superoxide dismutase, which is essential for mammalian infection. BpuR bound to sodA mRNA in live B. burgdorferi, and a specific BpuR‐binding site was mapped 5′ of the sodA open reading frame. Recognition of posttranscriptional regulation of protein levels by BpuR adds another layer to our understanding of the B. burgdorferi regulome, and provides further evidence that bacterial protein levels do not always correlate directly with mRNA levels.
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Affiliation(s)
- Brandon L Jutras
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Christina R Savage
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, USA
| | - William K Arnold
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Kathryn G Lethbridge
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Dustin W Carroll
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Kit Tilly
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Aaron Bestor
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Janakiram Seshu
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Wolfram R Zückert
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Philip E Stewart
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Patricia A Rosa
- Laboratory of Bacteriology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Catherine A Brissette
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, USA
| | - Brian Stevenson
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, Lexington, KY, USA.,Department of Entomology, University of Kentucky, Lexington, KY, USA
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18
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Ferris LA, Kelm RJ. Structural and functional analysis of single-nucleotide polymorphic variants of purine-rich element-binding protein B. J Cell Biochem 2018; 120:5835-5851. [PMID: 30387171 DOI: 10.1002/jcb.27869] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 09/20/2018] [Indexed: 12/14/2022]
Abstract
Purine-rich element-binding protein B (Purβ) inhibits myofibroblast differentiation by repressing the expression of the smooth muscle α-actin gene (Acta2). Several reports have identified the structural domains in Purβ that enable its characteristic interaction with purine-rich single-stranded DNA (ssDNA) sequences in the Acta2 promoter. However, little is known about the physical and functional effects of single-nucleotide polymorphisms that alter individual amino acid residues in Purβ. This study evaluated seven rare single amino acid variants of human PURB engineered into the homologous mouse Purβ protein. Mapping the location of variant residues on a homology model of the Purβ homodimer suggested that most of the altered residues are remote from the predicted ssDNA-binding regions of the protein. The repressor activity of each Purβ variant was assessed in transfected fibroblasts and smooth muscle cells via Acta2 promoter-reporter assays. A Q64* nonsense variant was completely inactive while missense variants exhibited repressor activity that ranged from ~1.5-fold greater to ~2-fold less than wild-type Purβ. Lower activity variants P223L and R297Q were expressed in bacteria and purified to homogeneity. Each variant was physically indistinguishable from wild-type Purβ in terms of quaternary structure and thermostability. Results of DNA and protein-binding assays indicated that the P223L and R297Q variants retained high affinity and specificity for purine-rich ssDNA sequences but differed in their interaction with other Acta2 regulatory proteins. These findings suggest that the presence of certain variant residues affects the Acta2 repressor activity of Purβ by altering its interaction with other transcription factors but not with ssDNA.
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Affiliation(s)
- Lauren A Ferris
- Department of Biochemistry, University of Vermont, Robert Larner, M. D. College of Medicine, Burlington, Vermont
| | - Robert J Kelm
- Department of Biochemistry, University of Vermont, Robert Larner, M. D. College of Medicine, Burlington, Vermont
- Department of Medicine, Division of Cardiovascular Medicine, University of Vermont, Robert Larner, M. D. College qof Medicine, Burlington, Vermont
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19
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Reich NO, Dang E, Kurnik M, Pathuri S, Woodcock CB. The highly specific, cell cycle-regulated methyltransferase from Caulobacter crescentus relies on a novel DNA recognition mechanism. J Biol Chem 2018; 293:19038-19046. [PMID: 30323065 DOI: 10.1074/jbc.ra118.005212] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 10/09/2018] [Indexed: 12/15/2022] Open
Abstract
Two DNA methyltransferases, Dam and β-class cell cycle-regulated DNA methyltransferase (CcrM), are key mediators of bacterial epigenetics. CcrM from the bacterium Caulobacter crescentus (CcrM C. crescentus, methylates adenine at 5'-GANTC-3') displays 105-107-fold sequence discrimination against noncognate sequences. However, the underlying recognition mechanism is unclear. Here, CcrM C. crescentus activity was either improved or mildly attenuated with substrates having one to three mismatched bp within or adjacent to the recognition site, but only if the strand undergoing methylation is left unchanged. By comparison, single-mismatched substrates resulted in up to 106-fold losses of activity with α (Dam) and γ-class (M.HhaI) DNA methyltransferases. We found that CcrM C. crescentus has a greatly expanded DNA-interaction surface, covering six nucleotides on the 5' side and eight nucleotides on the 3' side of its recognition site. Such a large interface may contribute to the enzyme's high sequence fidelity. CcrM C. crescentus displayed the same sequence discrimination with single-stranded substrates, and a surprisingly large (>107-fold) discrimination against ssRNA was largely due to the presence of two or more riboses within the cognate (DNA) site but not outside the site. Results from C-terminal truncations and point mutants supported our hypothesis that the recently identified C-terminal, 80-residue segment is essential for dsDNA recognition but is not required for single-stranded substrates. CcrM orthologs from Agrobacterium tumefaciens and Brucella abortus share some of these newly discovered features of the C. crescentus enzyme, suggesting that the recognition mechanism is conserved. In summary, CcrM C. crescentus uses a previously unknown DNA recognition mechanism.
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Affiliation(s)
- Norbert O Reich
- From the Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Eric Dang
- From the Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Martin Kurnik
- From the Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Sarath Pathuri
- From the Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Clayton B Woodcock
- From the Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
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20
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Healy MD, Hospenthal MK, Hall RJ, Chandra M, Chilton M, Tillu V, Chen KE, Celligoi DJ, McDonald FJ, Cullen PJ, Lott JS, Collins BM, Ghai R. Structural insights into the architecture and membrane interactions of the conserved COMMD proteins. eLife 2018; 7:e35898. [PMID: 30067224 PMCID: PMC6089597 DOI: 10.7554/elife.35898] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/31/2018] [Indexed: 12/31/2022] Open
Abstract
The COMMD proteins are a conserved family of proteins with central roles in intracellular membrane trafficking and transcription. They form oligomeric complexes with each other and act as components of a larger assembly called the CCC complex, which is localized to endosomal compartments and mediates the transport of several transmembrane cargos. How these complexes are formed however is completely unknown. Here, we have systematically characterised the interactions between human COMMD proteins, and determined structures of COMMD proteins using X-ray crystallography and X-ray scattering to provide insights into the underlying mechanisms of homo- and heteromeric assembly. All COMMD proteins possess an α-helical N-terminal domain, and a highly conserved C-terminal domain that forms a tightly interlocked dimeric structure responsible for COMMD-COMMD interactions. The COMM domains also bind directly to components of CCC and mediate non-specific membrane association. Overall these studies show that COMMD proteins function as obligatory dimers with conserved domain architectures.
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Affiliation(s)
- Michael D Healy
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | | | - Ryan J Hall
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | - Mintu Chandra
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | - Molly Chilton
- School of Biochemistry, Biomedical Sciences BuildingUniversity of BristolBristolUnited Kingdom
| | - Vikas Tillu
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | - Kai-En Chen
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | - Dion J Celligoi
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
| | | | - Peter J Cullen
- School of Biochemistry, Biomedical Sciences BuildingUniversity of BristolBristolUnited Kingdom
| | - J Shaun Lott
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
| | - Brett M Collins
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
| | - Rajesh Ghai
- Institute for Molecular BioscienceThe University of QueenslandSt. LuciaAustralia
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21
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Qiao Y, Bagheri H, Tang F, Badduke C, Martell S, Lewis SME, Robinson W, Connolly MB, Arbour L, Rajcan-Separovic E. Exome sequencing identified a de novo mutation of PURA gene in a patient with familial Xp22.31 microduplication. Eur J Med Genet 2018; 62:103-108. [PMID: 29908350 DOI: 10.1016/j.ejmg.2018.06.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 06/08/2018] [Accepted: 06/10/2018] [Indexed: 11/28/2022]
Abstract
The clinical significance of Xp22.31 microduplication is controversial as it is reported in subjects with developmental delay (DD), their unaffected relatives and unrelated controls. We performed multifaceted studies in a family of a boy with hypotonia, dysmorphic features and DD who carried a 600 Kb Xp22.31 microduplication (7515787-8123310bp, hg19) containing two genes, VCX and PNPLA4. The duplication was transmitted from his cognitively normal maternal grandfather. We found no evidence of the duplication causing the proband's DD and congenital anomalies based on unaltered expression of PNPLA4 in the proband and his mother in comparison to controls and preferential activation of the paternal chromosome X with Xp22.31 duplication in proband's mother. However, a de novo, previously reported deleterious, missense mutation in Pur-alpha gene (PURA) (5q31.2), with a role in neuronal differentiation was detected in the proband by exome sequencing. We propose that the variability in the phenotype in carriers of Xp22.31 microduplication can be due to a second and more deleterious genetic mutation in more severely affected carriers. Widespread use of whole genome next generation sequencing in families with Xp22.31 CNV could help identify such cases.
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Affiliation(s)
- Ying Qiao
- Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada; BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Hani Bagheri
- Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada
| | - Flamingo Tang
- Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada
| | | | - Sally Martell
- Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada
| | - Suzanne M E Lewis
- BC Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Medical Genetics, UBC, Vancouver, BC, Canada
| | - Wendy Robinson
- Department of Medical Genetics, UBC, Vancouver, BC, Canada
| | - Mary B Connolly
- Division of Pediatric Neurology, Department of Pediatrics, UBC and BC Children's Hospital, Vancouver, BC, Canada
| | - Laura Arbour
- Department of Medical Genetics, University of Victoria, Victoria, BC, Canada.
| | - Evica Rajcan-Separovic
- Department of Pathology and Laboratory Medicine, UBC, Vancouver, BC, Canada; BC Children's Hospital Research Institute, Vancouver, BC, Canada.
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22
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Reijnders MRF, Janowski R, Alvi M, Self JE, van Essen TJ, Vreeburg M, Rouhl RPW, Stevens SJC, Stegmann APA, Schieving J, Pfundt R, van Dijk K, Smeets E, Stumpel CTRM, Bok LA, Cobben JM, Engelen M, Mansour S, Whiteford M, Chandler KE, Douzgou S, Cooper NS, Tan EC, Foo R, Lai AHM, Rankin J, Green A, Lönnqvist T, Isohanni P, Williams S, Ruhoy I, Carvalho KS, Dowling JJ, Lev DL, Sterbova K, Lassuthova P, Neupauerová J, Waugh JL, Keros S, Clayton-Smith J, Smithson SF, Brunner HG, van Hoeckel C, Anderson M, Clowes VE, Siu VM, DDD study T, Selber P, Leventer RJ, Nellaker C, Niessing D, Hunt D, Baralle D. PURA syndrome: clinical delineation and genotype-phenotype study in 32 individuals with review of published literature. J Med Genet 2018; 55:104-113. [PMID: 29097605 PMCID: PMC5800346 DOI: 10.1136/jmedgenet-2017-104946] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 08/29/2017] [Accepted: 09/13/2017] [Indexed: 01/09/2023]
Abstract
BACKGROUND De novo mutations in PURA have recently been described to cause PURA syndrome, a neurodevelopmental disorder characterised by severe intellectual disability (ID), epilepsy, feeding difficulties and neonatal hypotonia. OBJECTIVES To delineate the clinical spectrum of PURA syndrome and study genotype-phenotype correlations. METHODS Diagnostic or research-based exome or Sanger sequencing was performed in individuals with ID. We systematically collected clinical and mutation data on newly ascertained PURA syndrome individuals, evaluated data of previously reported individuals and performed a computational analysis of photographs. We classified mutations based on predicted effect using 3D in silico models of crystal structures of Drosophila-derived Pur-alpha homologues. Finally, we explored genotype-phenotype correlations by analysis of both recurrent mutations as well as mutation classes. RESULTS We report mutations in PURA (purine-rich element binding protein A) in 32 individuals, the largest cohort described so far. Evaluation of clinical data, including 22 previously published cases, revealed that all have moderate to severe ID and neonatal-onset symptoms, including hypotonia (96%), respiratory problems (57%), feeding difficulties (77%), exaggerated startle response (44%), hypersomnolence (66%) and hypothermia (35%). Epilepsy (54%) and gastrointestinal (69%), ophthalmological (51%) and endocrine problems (42%) were observed frequently. Computational analysis of facial photographs showed subtle facial dysmorphism. No strong genotype-phenotype correlation was identified by subgrouping mutations into functional classes. CONCLUSION We delineate the clinical spectrum of PURA syndrome with the identification of 32 additional individuals. The identification of one individual through targeted Sanger sequencing points towards the clinical recognisability of the syndrome. Genotype-phenotype analysis showed no significant correlation between mutation classes and disease severity.
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Affiliation(s)
- Margot R F Reijnders
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Robert Janowski
- Institute of Structural Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Mohsan Alvi
- Visual Geometry Group, Department of Engineering Science, University of Oxford, Oxford, UK
| | - Jay E Self
- Department of Ophthalmology, Southampton General Hospital, Southampton, UK
- Department of Clinical and Experimental Sciences, School of Medicine, University of Southampton, Southampton, UK
| | - Ton J van Essen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Maaike Vreeburg
- Department of Clinical Genetics and School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Rob P W Rouhl
- Department of Neurology, Maastricht University Medical Center, Maastricht, The Netherlands
- School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
- Academic Center for Epileptology, Kempenhaeghe/MUMC, Maastricht, The Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics and School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics and School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jolanda Schieving
- Department of Pediatric Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Katinke van Dijk
- Department of Pediatrics, Rijnstate Hospital, Arnhem, The Netherlands
| | - Eric Smeets
- Department of Clinical Genetics and School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Connie T R M Stumpel
- Department of Clinical Genetics and School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Levinus A Bok
- Department of Pediatrics, Máxima Medisch Centrum, Veldhoven, The Netherlands
| | - Jan Maarten Cobben
- Department of Pediatric Neurology, Academic Medical Center, Amsterdam, The Netherlands
| | - Marc Engelen
- Department of Neurology and Pediatric Neurology, Emma Children’s Hospital/Academic Medical Center, Amsterdam, The Netherlands
| | - Sahar Mansour
- SW Thames Regional Genetics Service, St. George’s University NHS Foundation Trust, London, UK
| | - Margo Whiteford
- Department of Clinical Genetics, Laboratory Medicine Building, Queen Elizabeth University Hospital, Glasgow, UK
| | - Kate E Chandler
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Sofia Douzgou
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
| | - Nicola S Cooper
- West Midlands Regional Clinical Genetics Service, Birmingham Women’s NHS Foundation Trust, Birmingham, UK
| | - Ene-Choo Tan
- KK Research Laboratory, KK Women’s and Children’s Hospital, Singapore
| | - Roger Foo
- National University Health Systems, Cardiovascular Research Institute, Singapore, Singapore
- Genome Institute of Singapore, Singapore, Singapore
| | - Angeline H M Lai
- Departmentof Paediatrics, Genetics Service, KK Women’s and Children’s Hospital, Singapore
| | - Julia Rankin
- Department of Clinical Genetics, Royal Devon and Exeter NHS Trust, Exeter, UK
| | - Andrew Green
- Department of Clinical Genetics, School of Medicine and Medical Science, Our Lady’s Hospital, University College Dublin, Dublin, Ireland
| | - Tuula Lönnqvist
- Department of Child Neurology, Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Pirjo Isohanni
- Department of Child Neurology, Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Programs Unit, Molecular Neurology, Biomedicum-Helsinki, University of Helsinki, Helsinki, Finland
| | - Shelley Williams
- Department of Pediatric Neurology, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, USA
| | - Ilene Ruhoy
- Division of Pediatric Neurology, Seattle Children’s Hospital/University of Washington, Seattle, Washington, USA
| | - Karen S Carvalho
- Department of Pediatrics, Section of Neurology, St. Christopher’s Hospital for Children, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - James J Dowling
- Division of Neurology and Program for Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Dorit L Lev
- The Rina Mor Institute of Medical Genetics, Holon, Israel
| | - Katalin Sterbova
- Department of Pediatric Neurology, Second Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Petra Lassuthova
- Department of Pediatric Neurology, Second Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Jana Neupauerová
- Department of Pediatric Neurology, Second Faculty of Medicine, Charles University in Prague and University Hospital Motol, Prague, Czech Republic
| | - Jeff L Waugh
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Sotirios Keros
- Sanford Children’s Hospital, University of South Dakota, Sioux Falls, South Dakota, USA
| | - Jill Clayton-Smith
- Faculty of Medical and Human Sciences, Institute of Evolution, Systems and Genomics, University of Manchester, Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Sarah F Smithson
- Department of Clinical Genetics, University Hospitals Bristol, Bristol, UK
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Clinical Genetics and School for Oncology and Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | | | | | - Virginia E Clowes
- North West Thames Regional Genetics Service, London North West Healthcare NHS Trust, London, UK
| | - Victoria Mok Siu
- Division of Medical Genetics, Department of Pediatrics, Schulich School of Medicine, University of Western Ontario, London, Ontario, Canada
| | - The DDD study
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Paulo Selber
- Department of Orthopaedics, Royal Children’s Hospital, Melbourne, Victoria, Australia
| | - Richard J Leventer
- Department of Neurology, University of Melbourne Department of Paediatrics, The Royal Children’s Hospital, Murdoch Children’s Research Institute, Melbourne, Victoria, Australia
| | - Christoffer Nellaker
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Nuffield Department of Obstetrics and Gynaecology, John Radcliffe Hospital Women’s Centre, University of Oxford, Oxford, UK
- Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Oxford, UK
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
- Department of Cell Biology, Biomedical Center of the Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - David Hunt
- Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Diana Baralle
- Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
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23
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Uversky VN. The roles of intrinsic disorder-based liquid-liquid phase transitions in the "Dr. Jekyll-Mr. Hyde" behavior of proteins involved in amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Autophagy 2017; 13:2115-2162. [PMID: 28980860 DOI: 10.1080/15548627.2017.1384889] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pathological developments leading to amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are associated with misbehavior of several key proteins, such as SOD1 (superoxide dismutase 1), TARDBP/TDP-43, FUS, C9orf72, and dipeptide repeat proteins generated as a result of the translation of the intronic hexanucleotide expansions in the C9orf72 gene, PFN1 (profilin 1), GLE1 (GLE1, RNA export mediator), PURA (purine rich element binding protein A), FLCN (folliculin), RBM45 (RNA binding motif protein 45), SS18L1/CREST, HNRNPA1 (heterogeneous nuclear ribonucleoprotein A1), HNRNPA2B1 (heterogeneous nuclear ribonucleoprotein A2/B1), ATXN2 (ataxin 2), MAPT (microtubule associated protein tau), and TIA1 (TIA1 cytotoxic granule associated RNA binding protein). Although these proteins are structurally and functionally different and have rather different pathological functions, they all possess some levels of intrinsic disorder and are either directly engaged in or are at least related to the physiological liquid-liquid phase transitions (LLPTs) leading to the formation of various proteinaceous membrane-less organelles (PMLOs), both normal and pathological. This review describes the normal and pathological functions of these ALS- and FTLD-related proteins, describes their major structural properties, glances at their intrinsic disorder status, and analyzes the involvement of these proteins in the formation of normal and pathological PMLOs, with the ultimate goal of better understanding the roles of LLPTs and intrinsic disorder in the "Dr. Jekyll-Mr. Hyde" behavior of those proteins.
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Affiliation(s)
- Vladimir N Uversky
- a Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute , Morsani College of Medicine , University of South Florida , Tampa , FL , USA.,b Institute for Biological Instrumentation of the Russian Academy of Sciences , Pushchino, Moscow region , Russia
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24
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Daniel DC, Johnson EM. PURA, the gene encoding Pur-alpha, member of an ancient nucleic acid-binding protein family with mammalian neurological functions. Gene 2017; 643:133-143. [PMID: 29221753 DOI: 10.1016/j.gene.2017.12.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 12/04/2017] [Accepted: 12/04/2017] [Indexed: 12/20/2022]
Abstract
The PURA gene encodes Pur-alpha, a 322 amino acid protein with repeated nucleic acid binding domains that are highly conserved from bacteria through humans. PUR genes with a single copy of this domain have been detected so far in spirochetes and bacteroides. Lower eukaryotes possess one copy of the PUR gene, whereas chordates possess 1 to 4 PUR family members. Human PUR genes encode Pur-alpha (Pura), Pur-beta (Purb) and two forms of Pur-gamma (Purg). Pur-alpha is a protein that binds specific DNA and RNA sequence elements. Human PURA, located at chromosome band 5q31, is under complex control of three promoters. The entire protein coding sequence of PURA is contiguous within a single exon. Several studies have found that overexpression or microinjection of Pura inhibits anchorage-independent growth of oncogenically transformed cells and blocks proliferation at either G1-S or G2-M checkpoints. Effects on the cell cycle may be mediated by interaction of Pura with cellular proteins including Cyclin/Cdk complexes and the Rb tumor suppressor protein. PURA knockout mice die shortly after birth with effects on brain and hematopoietic development. In humans environmentally induced heterozygous deletions of PURA have been implicated in forms of myelodysplastic syndrome and progression to acute myelogenous leukemia. Pura plays a role in AIDS through association with the HIV-1 protein, Tat. In the brain Tat and Pura association in glial cells activates transcription and replication of JC polyomavirus, the agent causing the demyelination disease, progressive multifocal leukoencephalopathy. Tat and Pura also act to stimulate replication of the HIV-1 RNA genome. In neurons Pura accompanies mRNA transcripts to sites of translation in dendrites. Microdeletions in the PURA locus have been implicated in several neurological disorders. De novo PURA mutations have been related to a spectrum of phenotypes indicating a potential PURA syndrome. The nucleic acid, G-rich Pura binding element is amplified as expanded polynucleotide repeats in several brain diseases including fragile X syndrome and a familial form of amyotrophic lateral sclerosis/fronto-temporal dementia. Throughout evolution the Pura protein plays a critical role in survival, based on conservation of its nucleic acid binding properties. These Pura properties have been adapted in higher organisms to the as yet unfathomable development of the human brain.
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Affiliation(s)
- Dianne C Daniel
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Edward M Johnson
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA.
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25
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Banerjee A, Vest KE, Pavlath GK, Corbett AH. Nuclear poly(A) binding protein 1 (PABPN1) and Matrin3 interact in muscle cells and regulate RNA processing. Nucleic Acids Res 2017; 45:10706-10725. [PMID: 28977530 PMCID: PMC5737383 DOI: 10.1093/nar/gkx786] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/27/2017] [Indexed: 01/01/2023] Open
Abstract
The polyadenylate binding protein 1 (PABPN1) is a ubiquitously expressed RNA binding protein vital for multiple steps in RNA metabolism. Although PABPN1 plays a critical role in the regulation of RNA processing, mutation of the gene encoding this ubiquitously expressed RNA binding protein causes a specific form of muscular dystrophy termed oculopharyngeal muscular dystrophy (OPMD). Despite the tissue-specific pathology that occurs in this disease, only recently have studies of PABPN1 begun to explore the role of this protein in skeletal muscle. We have used co-immunoprecipitation and mass spectrometry to identify proteins that interact with PABPN1 in mouse skeletal muscles. Among the interacting proteins we identified Matrin 3 (MATR3) as a novel protein interactor of PABPN1. The MATR3 gene is mutated in a form of distal myopathy and amyotrophic lateral sclerosis (ALS). We demonstrate, that like PABPN1, MATR3 is critical for myogenesis. Furthermore, MATR3 controls critical aspects of RNA processing including alternative polyadenylation and intron retention. We provide evidence that MATR3 also binds and regulates the levels of long non-coding RNA (lncRNA) Neat1 and together with PABPN1 is required for normal paraspeckle function. We demonstrate that PABPN1 and MATR3 are required for paraspeckles, as well as for adenosine to inosine (A to I) RNA editing of Ctn RNA in muscle cells. We provide a functional link between PABPN1 and MATR3 through regulation of a common lncRNA target with downstream impact on paraspeckle morphology and function. We extend our analysis to a mouse model of OPMD and demonstrate altered paraspeckle morphology in the presence of endogenous levels of alanine-expanded PABPN1. In this study, we report protein-binding partners of PABPN1, which could provide insight into novel functions of PABPN1 in skeletal muscle and identify proteins that could be sequestered with alanine-expanded PABPN1 in the nuclear aggregates found in OPMD.
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Affiliation(s)
- Ayan Banerjee
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Katherine E Vest
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Grace K Pavlath
- Department of Pharmacology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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26
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Okamoto N, Nakao H, Niihori T, Aoki Y. Patient with a novel purine-rich element binding protein A mutation. Congenit Anom (Kyoto) 2017; 57:201-204. [PMID: 28164378 DOI: 10.1111/cga.12214] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 01/17/2017] [Accepted: 01/30/2017] [Indexed: 12/30/2022]
Abstract
There have been several reports on 5q31.3 microdeletion syndrome. The overlapping deleted region includes purine-rich element binding protein A (PURA), which encodes transcriptional activator protein Pur-α. Patients with PURA mutations show moderate to severe neurodevelopmental delay and learning disability. Neonatal hypotonia, respiratory insufficiency, feeding difficulties, and seizures are often seen. Dysmorphic features including myopathic faces are helpful as clinical signs of the diagnosis. We report a patient with a novel PURA mutation detected by whole-exome sequencing. We suggest that PURA abnormality is a recognizable syndrome.
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Affiliation(s)
- Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - Hideto Nakao
- Department of Neonatology, Hyogo Prefectural Kobe Children's Hospital Perinatal Center, Kobe, Japan
| | - Tetsuya Niihori
- Department of Medical Genetics, Tohoku University School of Medicine, Sendai, Japan
| | - Yoko Aoki
- Department of Medical Genetics, Tohoku University School of Medicine, Sendai, Japan
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27
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Kelm RJ, Lamba GS, Levis JE, Holmes CE. Characterization of purine-rich element binding protein B as a novel biomarker in acute myelogenous leukemia prognostication. J Cell Biochem 2017; 119:2073-2083. [PMID: 28834593 DOI: 10.1002/jcb.26369] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 08/22/2017] [Indexed: 12/17/2022]
Abstract
Acute myelogenous leukemia (AML) is an aggressive hematologic cancer characterized by infiltration of proliferative, clonal, abnormally differentiated cells of myeloid lineage in the bone marrow and blood. Malignant cells in AML often exhibit chromosomal and other genetic or epigenetic abnormalities that are useful in prognostic risk assessment. In this study, the relative expression and novel single-stranded DNA (ssDNA) binding function of purine-rich element binding proteins A and B (Purα and Purβ) were systematically evaluated in established leukemia cell lines and in lineage committed myeloid cells isolated from patients diagnosed with a hematologic malignancy. Western blotting revealed that Purα and Purβ are markedly elevated in CD33+ /CD66b+ cells from AML patients compared to healthy subjects and to patients with other types of myeloid cell disorders. Results of in silico database analysis of PURA and PURB mRNA expression during hematopoiesis in conjunction with the quantitative immunoassay of the ssDNA-binding activities of Purα and Purβ in transformed leukocyte cell lines pointed to Purβ as the more distinguishing biomarker of myeloid cell differentiation status. Purβ ssDNA-binding activity was significantly increased in myeloid cells from AML patients but not from individuals with other myeloid-related diseases. The highest levels of Purβ activity were detected in myeloid cells from primary AML patients and from AML patients displaying other risk factors forecasting a poor prognosis. Collectively, these findings suggest that the enhanced ssDNA-binding activity of Purβ in transformed myeloid cells may serve as a unique and measurable phenotypic trait for improving prognostic risk stratification in AML.
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Affiliation(s)
- Robert J Kelm
- Division of Cardiovascular Medicine, Department of Medicine, University of Vermont, Robert Larner, M. D. College of Medicine, Burlington, Vermont
| | - Gurpreet S Lamba
- Division of Hematology/Oncology, Department of Medicine, University of Vermont, Robert Larner, M. D. College of Medicine, Burlington, Vermont
| | - Jamie E Levis
- Translational Research Laboratory, University of Vermont Cancer Center, Burlington, Vermont
| | - Chris E Holmes
- Division of Hematology/Oncology, Department of Medicine, University of Vermont, Robert Larner, M. D. College of Medicine, Burlington, Vermont
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28
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Woodcock CB, Yakubov AB, Reich NO. Caulobacter crescentus Cell Cycle-Regulated DNA Methyltransferase Uses a Novel Mechanism for Substrate Recognition. Biochemistry 2017; 56:3913-3922. [PMID: 28661661 DOI: 10.1021/acs.biochem.7b00378] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Caulobacter crescentus relies on DNA methylation by the cell cycle-regulated methyltransferase (CcrM) in addition to key transcription factors to control the cell cycle and direct cellular differentiation. CcrM is shown here to efficiently methylate its cognate recognition site 5'-GANTC-3' in single-stranded and hemimethylated double-stranded DNA. We report the Km, kcat, kmethylation, and Kd for single-stranded and hemimethylated substrates, revealing discrimination of 107-fold for noncognate sequences. The enzyme also shows a similar discrimination against single-stranded RNA. Two independent assays clearly show that CcrM is highly processive with single-stranded and hemimethylated DNA. Collectively, the data provide evidence that CcrM and other DNA-modifying enzymes may use a new mechanism to recognize DNA in a key epigenetic process.
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Affiliation(s)
- Clayton B Woodcock
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
| | - Aziz B Yakubov
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
| | - Norbert O Reich
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
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Tanaka AJ, Bai R, Cho MT, Anyane-Yeboa K, Ahimaz P, Wilson AL, Kendall F, Hay B, Moss T, Nardini M, Bauer M, Retterer K, Juusola J, Chung WK. De novo mutations in PURA are associated with hypotonia and developmental delay. Cold Spring Harb Mol Case Stud 2016; 1:a000356. [PMID: 27148565 PMCID: PMC4850890 DOI: 10.1101/mcs.a000356] [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] [Indexed: 12/30/2022] Open
Abstract
PURA is the leading candidate gene responsible for the developmental phenotype in the 5q31.3 microdeletion syndrome. De novo mutations in PURA were recently reported in 15 individuals with developmental features similar to the 5q31.3 microdeletion syndrome. Here we describe six unrelated children who were identified by clinical whole-exome sequencing (WES) to have novel de novo variants in PURA with a similar phenotype of hypotonia and developmental delay and frequently associated with seizures. The protein Purα (encoded by PURA) is involved in neuronal proliferation, dendrite maturation, and the transport of mRNA to translation sites during neuronal development. Mutations in PURA may alter normal brain development and impair neuronal function, leading to developmental delay and the seizures observed in patients with mutations in PURA.
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Affiliation(s)
- Akemi J Tanaka
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10029, USA
| | - Renkui Bai
- GeneDx, Gaithersburg, Maryland 20877, USA
| | | | - Kwame Anyane-Yeboa
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10029, USA
| | - Priyanka Ahimaz
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10029, USA
| | - Ashley L Wilson
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10029, USA
| | - Fran Kendall
- VMP Genetics, Roswell, Georgia 30076, USA;; Department of Kinesiology, University of Georgia, Athens, Georgia 30605, USA
| | - Beverly Hay
- Division of Genetics, UMass Memorial Medical Center, Worcester, Massachusetts 01655, USA
| | - Timothy Moss
- Center for Personalized Genetic Healthcare, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Monica Nardini
- Center for Personalized Genetic Healthcare, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Mislen Bauer
- Department of Genetics, Miami Children's Hospital, Miami, Florida 33155, USA
| | | | | | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, New York 10029, USA;; Department of Medicine, Columbia University Medical Center, New York, New York 10032, USA
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Rumora AE, Ferris LA, Wheeler TR, Kelm RJ. Electrostatic and Hydrophobic Interactions Mediate Single-Stranded DNA Recognition and Acta2 Repression by Purine-Rich Element-Binding Protein B. Biochemistry 2016; 55:2794-805. [PMID: 27064749 DOI: 10.1021/acs.biochem.6b00006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Myofibroblast differentiation is characterized by an increased level of expression of cytoskeletal smooth muscle α-actin. In human and murine fibroblasts, the gene encoding smooth muscle α-actin (Acta2) is tightly regulated by a network of transcription factors that either activate or repress the 5' promoter-enhancer in response to environmental cues signaling tissue repair and remodeling. Purine-rich element-binding protein B (Purβ) suppresses the expression of Acta2 by cooperatively interacting with the sense strand of a 5' polypurine sequence containing an inverted MCAT cis element required for gene activation. In this study, we evaluated the chemical basis of nucleoprotein complex formation between the Purβ repressor and the purine-rich strand of the MCAT element in the mouse Acta2 promoter. Quantitative single-stranded DNA (ssDNA) binding assays conducted in the presence of increasing concentrations of monovalent salt or anionic detergent suggested that the assembly of a high-affinity nucleoprotein complex is driven by a combination of electrostatic and hydrophobic interactions. Consistent with the results of pH titration analysis, site-directed mutagenesis revealed several basic amino acid residues in the intermolecular (R267) and intramolecular (K82 and R159) subdomains that are essential for Purβ transcriptional repressor function in Acta2 promoter-reporter assays. In keeping with their diminished Acta2 repressor activity in fibroblasts, purified Purβ variants containing an R267A mutation exhibited reduced binding affinity for purine-rich ssDNA. Moreover, certain double and triple-point mutants were also defective in binding to the Acta2 corepressor protein, Y-box-binding protein 1. Collectively, these findings establish the repertoire of noncovalent interactions that account for the unique structural and functional properties of Purβ.
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Affiliation(s)
- Amy E Rumora
- Department of Biochemistry, ‡Department of Medicine, and §Cardiovascular Research Institute of Vermont, University of Vermont College of Medicine , Burlington, Vermont 05405, United States
| | - Lauren A Ferris
- Department of Biochemistry, ‡Department of Medicine, and §Cardiovascular Research Institute of Vermont, University of Vermont College of Medicine , Burlington, Vermont 05405, United States
| | - Tamar R Wheeler
- Department of Biochemistry, ‡Department of Medicine, and §Cardiovascular Research Institute of Vermont, University of Vermont College of Medicine , Burlington, Vermont 05405, United States
| | - Robert J Kelm
- Department of Biochemistry, ‡Department of Medicine, and §Cardiovascular Research Institute of Vermont, University of Vermont College of Medicine , Burlington, Vermont 05405, United States
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Weber J, Bao H, Hartlmüller C, Wang Z, Windhager A, Janowski R, Madl T, Jin P, Niessing D. Structural basis of nucleic-acid recognition and double-strand unwinding by the essential neuronal protein Pur-alpha. eLife 2016; 5:e11297. [PMID: 26744780 PMCID: PMC4764581 DOI: 10.7554/elife.11297] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/07/2016] [Indexed: 01/01/2023] Open
Abstract
The neuronal DNA-/RNA-binding protein Pur-alpha is a transcription regulator and core factor for mRNA localization. Pur-alpha-deficient mice die after birth with pleiotropic neuronal defects. Here, we report the crystal structure of the DNA-/RNA-binding domain of Pur-alpha in complex with ssDNA. It reveals base-specific recognition and offers a molecular explanation for the effect of point mutations in the 5q31.3 microdeletion syndrome. Consistent with the crystal structure, biochemical and NMR data indicate that Pur-alpha binds DNA and RNA in the same way, suggesting binding modes for tri- and hexanucleotide-repeat RNAs in two neurodegenerative RNAopathies. Additionally, structure-based in vitro experiments resolved the molecular mechanism of Pur-alpha's unwindase activity. Complementing in vivo analyses in Drosophila demonstrated the importance of a highly conserved phenylalanine for Pur-alpha's unwinding and neuroprotective function. By uncovering the molecular mechanisms of nucleic-acid binding, this study contributes to understanding the cellular role of Pur-alpha and its implications in neurodegenerative diseases.
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Affiliation(s)
- Janine Weber
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Han Bao
- Department of Human Genetics, Emory University, Atlanta, United States
| | - Christoph Hartlmüller
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Munich, Germany
| | - Zhiqin Wang
- Department of Human Genetics, Emory University, Atlanta, United States
| | - Almut Windhager
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Robert Janowski
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Tobias Madl
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Munich, Germany
- Institute of Molecular Biology & Biochemistry, Center of Molecular Medicine, Medical University of Graz, Graz, Austria
- Omics Center Graz, BioTechMed Graz, Graz, Austria
| | - Peng Jin
- Department of Human Genetics, Emory University, Atlanta, United States
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department Cell Biology, Biomedical Center of the Ludwig-Maximilians-University München, Planegg-Martinsried, Germany
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32
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Pur-alpha functionally interacts with FUS carrying ALS-associated mutations. Cell Death Dis 2015; 6:e1943. [PMID: 26492376 PMCID: PMC4632316 DOI: 10.1038/cddis.2015.295] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 08/24/2015] [Indexed: 02/08/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder due to motor neuron loss. Fused in sarcoma (FUS) protein carrying ALS-associated mutations localizes to stress granules and causes their coalescence into larger aggregates. Here we show that Pur-alpha physically interacts with mutated FUS in an RNA-dependent manner. Pur-alpha colocalizes with FUS carrying mutations in stress granules of motoneuronal cells differentiated from induced pluripotent stem cells and that are derived from ALS patients. We observe that both Pur-alpha and mutated FUS upregulate phosphorylation of the translation initiation factor eukaryotic translation initiation factor 2 alpha and consistently inhibit global protein synthesis. In vivo expression of Pur-alpha in different Drosophila tissues significatively exacerbates the neurodegeneration caused by mutated FUS. Conversely, the downregulation of Pur-alpha in neurons expressing mutated FUS significatively improves fly climbing activity. All these findings suggest that Pur-alpha, through the control of mRNA translation, might be involved in the pathogenesis of ALS associated with the mutation of FUS, and that an alteration of protein synthesis may be directly implicated in the disease. Finally, in vivo RNAi-mediated ablation of Pur-alpha produced locomotion defects in Drosophila, indicating a pivotal role for this protein in the motoneuronal function.
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33
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Cheng H, Liao Y, Schaeffer RD, Grishin NV. Manual classification strategies in the ECOD database. Proteins 2015; 83:1238-51. [PMID: 25917548 DOI: 10.1002/prot.24818] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 03/30/2015] [Accepted: 04/19/2015] [Indexed: 12/28/2022]
Abstract
ECOD (Evolutionary Classification Of protein Domains) is a comprehensive and up-to-date protein structure classification database. The majority of new structures released from the PDB (Protein Data Bank) each week already have close homologs in the ECOD hierarchy and thus can be reliably partitioned into domains and classified by software without manual intervention. However, those proteins that lack confidently detectable homologs require careful analysis by experts. Although many bioinformatics resources rely on expert curation to some degree, specific examples of how this curation occurs and in what cases it is necessary are not always described. Here, we illustrate the manual classification strategy in ECOD by example, focusing on two major issues in protein classification: domain partitioning and the relationship between homology and similarity scores. Most examples show recently released and manually classified PDB structures. We discuss multi-domain proteins, discordance between sequence and structural similarities, difficulties with assessing homology with scores, and integral membrane proteins homologous to soluble proteins. By timely assimilation of newly available structures into its hierarchy, ECOD strives to provide a most accurate and updated view of the protein structure world as a result of combined computational and expert-driven analysis.
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Affiliation(s)
- Hua Cheng
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, 75390
| | - Yuxing Liao
- Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390
| | - R Dustin Schaeffer
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, 75390
| | - Nick V Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, 75390.,Department of Biophysics and Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, 75390
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Lalani SR, Zhang J, Schaaf CP, Brown CW, Magoulas P, Tsai ACH, El-Gharbawy A, Wierenga KJ, Bartholomew D, Fong CT, Barbaro-Dieber T, Kukolich MK, Burrage LC, Austin E, Keller K, Pastore M, Fernandez F, Lotze T, Wilfong A, Purcarin G, Zhu W, Craigen WJ, McGuire M, Jain M, Cooney E, Azamian M, Bainbridge MN, Muzny DM, Boerwinkle E, Person RE, Niu Z, Eng CM, Lupski JR, Gibbs RA, Beaudet AL, Yang Y, Wang MC, Xia F. Mutations in PURA cause profound neonatal hypotonia, seizures, and encephalopathy in 5q31.3 microdeletion syndrome. Am J Hum Genet 2014; 95:579-83. [PMID: 25439098 DOI: 10.1016/j.ajhg.2014.09.014] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 09/22/2014] [Indexed: 11/30/2022] Open
Abstract
5q31.3 microdeletion syndrome is characterized by neonatal hypotonia, encephalopathy with or without epilepsy, and severe developmental delay, and the minimal critical deletion interval harbors three genes. We describe 11 individuals with clinical features of 5q31.3 microdeletion syndrome and de novo mutations in PURA, encoding transcriptional activator protein Pur-α, within the critical region. These data implicate causative PURA mutations responsible for the severe neurological phenotypes observed in this syndrome.
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Affiliation(s)
- Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Jing Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Chester W Brown
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Pilar Magoulas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anne Chun-Hui Tsai
- Department of Molecular and Medical Genetics, Oregon Health and Sciences University, Portland, OR 97239, USA
| | - Areeg El-Gharbawy
- Department of Pediatrics and Division of Medical Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Klaas J Wierenga
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Dennis Bartholomew
- Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Chin-To Fong
- Clinic of Inherited Metabolic Disease, University of Rochester Medical Center, Rochester, NY 14642, USA
| | | | - Mary K Kukolich
- Clinical Genetics, Cook Children's Hospital, Fort Worth, TX 76102, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Elise Austin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kory Keller
- Department of Molecular and Medical Genetics, Oregon Health and Sciences University, Portland, OR 97239, USA
| | - Matthew Pastore
- Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Fabio Fernandez
- Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Timothy Lotze
- Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Angus Wilfong
- Department of Neurology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gabriela Purcarin
- Department of Neurology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Wenmiao Zhu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - William J Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marianne McGuire
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mahim Jain
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Erin Cooney
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mahshid Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew N Bainbridge
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Whole Genome Laboratory, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Human Genetics Center, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Richard E Person
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Whole Genome Laboratory, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhiyv Niu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Whole Genome Laboratory, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Whole Genome Laboratory, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Texas Children's Hospital, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Whole Genome Laboratory, Baylor College of Medicine, Houston, TX 77030, USA
| | - Meng C Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Whole Genome Laboratory, Baylor College of Medicine, Houston, TX 77030, USA.
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Theme 9 in vitro experimental models. Amyotroph Lateral Scler Frontotemporal Degener 2014; 15 Suppl 1:161-78. [PMID: 25382839 DOI: 10.3109/21678421.2014.960186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Hunt D, Leventer RJ, Simons C, Taft R, Swoboda KJ, Gawne-Cain M, Magee AC, Turnpenny PD, Baralle D. Whole exome sequencing in family trios reveals de novo mutations in PURA as a cause of severe neurodevelopmental delay and learning disability. J Med Genet 2014; 51:806-13. [PMID: 25342064 PMCID: PMC4251168 DOI: 10.1136/jmedgenet-2014-102798] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background De novo mutations are emerging as an important cause of neurocognitive impairment, and whole exome sequencing of case-parent trios is a powerful way of detecting them. Here, we report the findings in four such trios. Methods The Deciphering Developmental Disorders study is using whole exome sequencing in family trios to investigate children with severe, sporadic, undiagnosed developmental delay. Three of our patients were ascertained from the first 1133 children to have been investigated through this large-scale study. Case 4 was a phenotypically isolated case recruited into an undiagnosed rare disorders sequencing study. Results Protein-altering de novo mutations in PURA were identified in four subjects. They include two different frameshifts, one inframe deletion and one missense mutation. PURA encodes Pur-α, a highly conserved multifunctional protein that has an important role in normal postnatal brain development in animal models. The associated human phenotype of de novo heterozygous mutations in this gene is variable, but moderate to severe neurodevelopmental delay and learning disability are common to all. Neonatal hypotonia, early feeding difficulties and seizures, or ‘seizure-like’ movements, were also common. Additionally, it is suspected that anterior pituitary dysregulation may be within the spectrum of this disorder. Psychomotor developmental outcomes appear variable between patients, and we propose a possible genotype–phenotype correlation, with disruption of Pur repeat III resulting in a more severe phenotype. Conclusions These findings provide definitive evidence for the role of PURA in causing a variable syndrome of neurodevelopmental delay, learning disability, neonatal hypotonia, feeding difficulties, abnormal movements and epilepsy in humans, and help clarify the role of PURA in the previously described 5q31.3 microdeletion phenotype.
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Affiliation(s)
- David Hunt
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Richard J Leventer
- The Royal Children's Hospital Department of Neurology, University of Melbourne Department of Paediatrics and the Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
| | - Cas Simons
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia
| | - Ryan Taft
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, Australia Departments of Integrated Systems Biology and of Pediatrics, School of Medicine and Health Sciences, George Washington University, USA Illumina, Inc., San Diego, California, USA
| | - Kathryn J Swoboda
- Pediatric Motor Disorders Research Program, Department of Neurology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Mary Gawne-Cain
- Department of Radiology, Southampton General Hospital, Southampton, UK
| | | | - Alex C Magee
- Genetic Medicine, Belfast City Hospital, Belfast, Northern Ireland
| | - Peter D Turnpenny
- Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital (Heavitree), Exeter, UK
| | - Diana Baralle
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, Hampshire, UK
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Heym RG, Zimmermann D, Edelmann FT, Israel L, Ökten Z, Kovar DR, Niessing D. In vitro reconstitution of an mRNA-transport complex reveals mechanisms of assembly and motor activation. ACTA ACUST UNITED AC 2014; 203:971-84. [PMID: 24368805 PMCID: PMC3871432 DOI: 10.1083/jcb.201302095] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The budding yeast SHE mRNA-transport complex dimerizes to activate processive RNA transport, irrespective of the presence of RNA cargo, and multimerizes upon binding RNAs with multiple localization elements. The assembly and composition of ribonucleic acid (RNA)–transporting particles for asymmetric messenger RNA (mRNA) localization is not well understood. During mitosis of budding yeast, the Swi5p-dependent HO expression (SHE) complex transports a set of mRNAs into the daughter cell. We recombinantly reconstituted the core SHE complex and assessed its properties. The cytoplasmic precomplex contains only one motor and is unable to support continuous transport. However, a defined interaction with a second, RNA-bound precomplex after its nuclear export dimerizes the motor and activates processive RNA transport. The run length observed in vitro is compatible with long-distance transport in vivo. Surprisingly, SHE complexes that either contain or lack RNA cargo show similar motility properties, demonstrating that the RNA-binding protein and not its cargo activates motility. We further show that SHE complexes have a defined size but multimerize into variable particles upon binding of RNAs with multiple localization elements. Based on these findings, we provide an estimate of number, size, and composition of such multimeric SHE particles in the cell.
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Affiliation(s)
- Roland G Heym
- Institute of Structural Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, 85764 Neuherberg, Germany
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Dickey TH, Altschuler SE, Wuttke DS. Single-stranded DNA-binding proteins: multiple domains for multiple functions. Structure 2014; 21:1074-84. [PMID: 23823326 DOI: 10.1016/j.str.2013.05.013] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 05/15/2013] [Accepted: 05/20/2013] [Indexed: 10/26/2022]
Abstract
The recognition of single-stranded DNA (ssDNA) is integral to myriad cellular functions. In eukaryotes, ssDNA is present stably at the ends of chromosomes and at some promoter elements. Furthermore, it is formed transiently by several cellular processes including telomere synthesis, transcription, and DNA replication, recombination, and repair. To coordinate these diverse activities, a variety of proteins have evolved to bind ssDNA in a manner specific to their function. Here, we review the recognition of ssDNA through the analysis of high-resolution structures of proteins in complex with ssDNA. This functionally diverse set of proteins arises from a limited set of structural motifs that can be modified and arranged to achieve distinct activities, including a range of ligand specificities. We also investigate the ways in which these domains interact in the context of large multidomain proteins/complexes. These comparisons reveal the structural features that define the range of functions exhibited by these proteins.
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Affiliation(s)
- Thayne H Dickey
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
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Velvarska H, Niessing D. Structural insights into the globular tails of the human type v myosins Myo5a, Myo5b, And Myo5c. PLoS One 2013; 8:e82065. [PMID: 24339992 PMCID: PMC3858360 DOI: 10.1371/journal.pone.0082065] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 10/21/2013] [Indexed: 01/11/2023] Open
Abstract
Vertebrate type V myosins (MyoV) Myo5a, Myo5b, and Myo5c mediate transport of several different cargoes. All MyoV paralogs bind to cargo complexes mainly by their C-terminal globular domains. In absence of cargo, the globular domain of Myo5a inhibits its motor domain. Here, we report low-resolution SAXS models for the globular domains from human Myo5a, Myo5b, and Myo5c, which suggest very similar overall shapes of all three paralogs. We determined the crystal structures of globular domains from Myo5a and Myo5b, and provide a homology model for human Myo5c. When we docked the Myo5a crystal structure into a previously published electron microscopy density of the autoinhibited full-length Myo5a, only one domain orientation resulted in a good fit. This structural arrangement suggests the participation of additional region of the globular domain in autoinhibition. Quantification of the interaction of the Myo5a globular domain with its motor complex revealed a tight binding with dissociation half-life in the order of minutes, suggesting a rather slow transition between the active and inactive states.
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Affiliation(s)
- Hana Velvarska
- Institute of Structural Biology; Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University, München, Germany
| | - Dierk Niessing
- Institute of Structural Biology; Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University, München, Germany
- * E-mail:
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Acquisition of an Archaea-like ribonuclease H domain by plant L1 retrotransposons supports modular evolution. Proc Natl Acad Sci U S A 2013; 110:20140-5. [PMID: 24277848 DOI: 10.1073/pnas.1310958110] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although a variety of non-LTR retrotransposons of the L1 superfamily have been found in plant genomes over recent decades, their diversity, distribution, and evolution have yet to be analyzed in depth. Here, we perform comprehensive comparative and evolutionary analyses of L1 retrotransposons from 29 genomes of land plants covering a wide range of taxa. We identify numerous L1 elements in these genomes and detect a striking diversity of their domain composition. We show that all known land plant L1 retrotransposons can be grouped into five major families based on their phylogenetic relationships and domain composition. Moreover, we trace the putative evolution timeline that created the current variants and reveal that evolutionary events included losses and acquisitions of diverse putative RNA-binding domains and the acquisition of an Archaea-like ribonuclease H (RNH) domain. We also show that the latter RNH domain is autonomously active in vitro and speculate that retrotransposons may play a role in the horizontal transfer of RNH between plants, Archaea, and bacteria. The acquisition of an Archaea-like RNH domain by plant L1 retrotransposons negates the hypothesis that RNH domains in non-LTR retrotransposons have a single origin and provides evidence that acquisition happened at least twice. Together, our data indicate that the evolution of the investigated retrotransposons can be mainly characterized by repeated events of domain rearrangements and identify modular evolution as a major trend in the evolution of plant L1 retrotransposons.
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Jutras BL, Jones GS, Verma A, Brown NA, Antonicello AD, Chenail AM, Stevenson B. Posttranscriptional self-regulation by the Lyme disease bacterium's BpuR DNA/RNA-binding protein. J Bacteriol 2013; 195:4915-23. [PMID: 23974034 PMCID: PMC3807498 DOI: 10.1128/jb.00819-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 08/21/2013] [Indexed: 01/21/2023] Open
Abstract
Bacteria require explicit control over their proteomes in order to compete and survive in dynamic environments. The Lyme disease spirochete Borrelia burgdorferi undergoes substantial protein profile changes during its cycling between vector ticks and vertebrate hosts. In an effort to understand regulation of these transitions, we recently isolated and functionally characterized the borrelial nucleic acid-binding protein BpuR, a PUR domain-containing protein. We now report that this regulatory protein governs its own synthesis through direct interactions with bpuR mRNA. In vitro and in vivo techniques indicate that BpuR binds with high affinity and specificity to the 5' region of its message, thereby inhibiting translation. This negative feedback could permit the bacteria to fine-tune cellular BpuR concentrations. These data add to the understanding of this newly described class of prokaryotic DNA- and RNA-binding regulatory proteins.
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Affiliation(s)
| | - Grant S. Jones
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | | | - Nicholas A. Brown
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Alyssa D. Antonicello
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Alicia M. Chenail
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Brian Stevenson
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, USA
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Production of pure and functional RNA for in vitro reconstitution experiments. Methods 2013; 65:333-41. [PMID: 24021718 DOI: 10.1016/j.ymeth.2013.08.034] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/30/2013] [Accepted: 08/31/2013] [Indexed: 11/22/2022] Open
Abstract
Reconstitution of protein complexes has been a valuable tool to test molecular functions and to interpret in vivo observations. In recent years, a large number of RNA-protein complexes has been identified to regulate gene expression and to be important for a range of cellular functions. In contrast to protein complexes, in vitro analyses of RNA-protein complexes are hampered by the fact that recombinant expression and purification of RNA molecules is more difficult and less well established than for proteins. Here we review the current state of technology available for in vitro experiments with RNAs. We outline the possibilities to produce and purify large amounts of homogenous RNA and to perform the required quality controls. RNA-specific problems such as degradation, 5' and 3' end heterogeneity, co-existence of different folding states, and prerequisites for reconstituting RNAs with recombinantly expressed proteins are discussed. Additionally a number of techniques for the characterization of direct and indirect RNA-protein interactions are explained.
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Jutras BL, Chenail AM, Carroll DW, Miller MC, Zhu H, Bowman A, Stevenson B. Bpur, the Lyme disease spirochete's PUR domain protein: identification as a transcriptional modulator and characterization of nucleic acid interactions. J Biol Chem 2013; 288:26220-26234. [PMID: 23846702 PMCID: PMC3764826 DOI: 10.1074/jbc.m113.491357] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The PUR domain is a nucleic acid-binding motif found in critical regulatory proteins of higher eukaryotes and in certain species of bacteria. During investigations into mechanisms by which the Lyme disease spirochete controls synthesis of its Erp surface proteins, it was discovered that the borrelial PUR domain protein, Bpur, binds with high affinity to double-stranded DNA adjacent to the erp transcriptional promoter. Bpur was found to enhance the effects of the erp repressor protein, BpaB. Bpur also bound single-stranded DNA and RNA, with relative affinities RNA > double-stranded DNA > single-stranded DNA. Rational site-directed mutagenesis of Bpur identified amino acid residues and domains critical for interactions with nucleic acids, and it revealed that the PUR domain has a distinct mechanism of interaction with each type of nucleic acid ligand. These data shed light on both gene regulation in the Lyme spirochete and functional mechanisms of the widely distributed PUR domain.
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Affiliation(s)
- Brandon L Jutras
- From the Department of Microbiology, Immunology, and Molecular Genetics and
| | - Alicia M Chenail
- From the Department of Microbiology, Immunology, and Molecular Genetics and
| | - Dustin W Carroll
- the Graduate Center for Toxicology, University of Kentucky College of Medicine, Lexington, Kentucky 40536
| | - M Clarke Miller
- the James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202, and
| | - Haining Zhu
- the Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, Kentucky 40536
| | - Amy Bowman
- From the Department of Microbiology, Immunology, and Molecular Genetics and
| | - Brian Stevenson
- From the Department of Microbiology, Immunology, and Molecular Genetics and.
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Rumora AE, Wang SX, Ferris LA, Everse SJ, Kelm RJ. Structural basis of multisite single-stranded DNA recognition and ACTA2 repression by purine-rich element binding protein B (Purβ). Biochemistry 2013; 52:4439-50. [PMID: 23724822 DOI: 10.1021/bi400283r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A hallmark of dysfunctional fibroblast to myofibroblast differentiation associated with fibrotic disorders is persistent expression of ACTA2, the gene encoding the cyto-contractile protein smooth muscle α-actin. In this study, a PURB-specific gene knockdown approach was used in conjunction with biochemical analyses of protein subdomain structure and function to reveal the mechanism by which purine-rich element binding protein B (Purβ) restricts ACTA2 expression in mouse embryo fibroblasts (MEFs). Consistent with the hypothesized role of Purβ as a suppressor of myofibroblast differentiation, stable short hairpin RNA-mediated knockdown of Purβ in cultured MEFs promoted changes in cell morphology, actin isoform expression, and cell migration indicative of conversion to a myofibroblast-like phenotype. Promoter-reporter assays in transfected Purβ knockdown MEFs confirmed that these changes were attributable, in part, to derepression of ACTA2 transcription. To map the domains in Purβ responsible for ACTA2 repression, several recombinant truncation mutants were generated and analyzed based on hypothetical, computationally derived models of the tertiary and quaternary structure of Purβ. Discrete subdomains mediating sequence- and strand-specific cis-element binding, protein-protein interaction, and inhibition of a composite ACTA2 enhancer were identified using a combination of biochemical, biophysical, and cell-based assays. Our results indicate that the Purβ homodimer possesses three separate but unequal single-stranded DNA-binding modules formed by subdomain-specific inter- and intramolecular interactions. This structural arrangement suggests that the cooperative assembly of the dimeric Purβ repressor on the sense strand of the ACTA2 enhancer is dictated by the association of each subdomain with distinct purine-rich binding sites within the enhancer.
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Affiliation(s)
- Amy E Rumora
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, Vermont 05405, USA
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Sahoo GC, Yousuf Ansari M, Dikhit MR, Kannan M, Rana S, Das P. Structure prediction of gBP21 protein ofL. donovaniand its molecular interaction. J Biomol Struct Dyn 2013; 32:709-29. [DOI: 10.1080/07391102.2013.789400] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Baculovirus VP1054 is an acquired cellular PURα, a nucleic acid-binding protein specific for GGN repeats. J Virol 2013; 87:8465-80. [PMID: 23720732 DOI: 10.1128/jvi.00068-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Baculovirus VP1054 protein is a structural component of both of the virion types budded virus (BV) and occlusion-derived virus (ODV), but its exact role in virion morphogenesis is poorly defined. In this paper, we reveal sequence and functional similarity between the baculovirus protein VP1054 and the cellular purine-rich element binding protein PUR-alpha (PURα). The data strongly suggest that gene transfer has occurred from a host to an ancestral baculovirus. Deletion of the Autographa californica multiple nucleopolyhedrovirus (AcMNPV) vp1054 gene completely prevented viral cell-to-cell spread. Electron microscopy data showed that assembly of progeny nucleocapsids is dramatically reduced in the absence of VP1054. More precisely, VP1054 is required for proper viral DNA encapsidation, as deduced from the formation of numerous electron-lucent capsid-like tubules. Complementary searching identified the presence of genetic elements composed of repeated GGN trinucleotide motifs in baculovirus genomes, the target sequence for PURα proteins. Interestingly, these GGN-rich sequences are disproportionally distributed in baculoviral genomes and mostly occurred in proximity to the gene for the major occlusion body protein polyhedrin. We further demonstrate that the VP1054 protein specifically recognizes these GGN-rich islands, which at the same time encode crucial proline-rich domains in p78/83, an essential gene adjacent to the polyhedrin gene in the AcMNPV genome. While some viruses, like human immunodeficiency virus type 1 (HIV-1) and human JC virus (JCV), utilize host PURα protein, baculoviruses encode the PURα-like protein VP1054, which is crucial for viral progeny production.
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Bhattacharjee A, Oeemig JS, Kolodziejczyk R, Meri T, Kajander T, Lehtinen MJ, Iwaï H, Jokiranta TS, Goldman A. Structural basis for complement evasion by Lyme disease pathogen Borrelia burgdorferi. J Biol Chem 2013; 288:18685-95. [PMID: 23658013 DOI: 10.1074/jbc.m113.459040] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Borrelia burgdorferi spirochetes that cause Lyme borreliosis survive for a long time in human serum because they successfully evade the complement system, an important arm of innate immunity. The outer surface protein E (OspE) of B. burgdorferi is needed for this because it recruits complement regulator factor H (FH) onto the bacterial surface to evade complement-mediated cell lysis. To understand this process at the molecular level, we used a structural approach. First, we solved the solution structure of OspE by NMR, revealing a fold that has not been seen before in proteins involved in complement regulation. Next, we solved the x-ray structure of the complex between OspE and the FH C-terminal domains 19 and 20 (FH19-20) at 2.83 Å resolution. The structure shows that OspE binds FH19-20 in a way similar to, but not identical with, that used by endothelial cells to bind FH via glycosaminoglycans. The observed interaction of OspE with FH19-20 allows the full function of FH in down-regulation of complement activation on the bacteria. This reveals the molecular basis for how B. burgdorferi evades innate immunity and suggests how OspE could be used as a potential vaccine antigen.
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Affiliation(s)
- Arnab Bhattacharjee
- Haartman Institute, Department of Bacteriology and Immunology, and Research Programs Unit, Immunobiology, University of Helsinki, FIN-00014 Helsinki, Finland
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Johnson EM, Daniel DC, Gordon J. The pur protein family: genetic and structural features in development and disease. J Cell Physiol 2013; 228:930-7. [PMID: 23018800 PMCID: PMC3747735 DOI: 10.1002/jcp.24237] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 09/21/2012] [Indexed: 12/19/2022]
Abstract
The Pur proteins are an ancient family of sequence-specific single-stranded nucleic acid-binding proteins. They bind a G-rich element in either single- or double-stranded nucleic acids and are capable of displacing the complementary C-rich strand. Recently several reports have described Pur family member knockouts, mutations, and disease aberrations. Together with a recent crystal structure of Purα, these data reveal conserved structural features of these proteins that have been adapted to serve functions unique to higher eukaryotes. In humans Pur proteins are critical for myeloid cell development, muscle development, and brain development, including trafficking of mRNA to neuronal dendrites. Pur family members have been implicated in diseases as diverse as cancer, premature aging, and fragile-X mental retardation syndrome.
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Affiliation(s)
- Edward M Johnson
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507-1696, USA.
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Rossi P, Barbieri CM, Aramini JM, Bini E, Lee HW, Janjua H, Xiao R, Acton TB, Montelione GT. Structures of apo- and ssDNA-bound YdbC from Lactococcus lactis uncover the function of protein domain family DUF2128 and expand the single-stranded DNA-binding domain proteome. Nucleic Acids Res 2013; 41:2756-68. [PMID: 23303792 PMCID: PMC3575825 DOI: 10.1093/nar/gks1348] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Single-stranded DNA (ssDNA) binding proteins are important in basal metabolic pathways for gene transcription, recombination, DNA repair and replication in all domains of life. Their main cellular role is to stabilize melted duplex DNA and protect genomic DNA from degradation. We have uncovered the molecular function of protein domain family domain of unknown function DUF2128 (PF09901) as a novel ssDNA binding domain. This bacterial domain strongly associates into a dimer and presents a highly positively charged surface that is consistent with its function in non-specific ssDNA binding. Lactococcus lactis YdbC is a representative of DUF2128. The solution NMR structures of the 20 kDa apo-YdbC dimer and YdbC:dT19G1 complex were determined. The ssDNA-binding energetics to YdbC were characterized by isothermal titration calorimetry. YdbC shows comparable nanomolar affinities for pyrimidine and mixed oligonucleotides, and the affinity is sufficiently strong to disrupt duplex DNA. In addition, YdbC binds with lower affinity to ssRNA, making it a versatile nucleic acid-binding domain. The DUF2128 family is related to the eukaryotic nuclear protein positive cofactor 4 (PC4) family and to the PUR family both by fold similarity and molecular function.
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Affiliation(s)
- Paolo Rossi
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, and the Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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Aumiller V, Graebsch A, Kremmer E, Niessing D, Förstemann K. Drosophila Pur-α binds to trinucleotide-repeat containing cellular RNAs and translocates to the early oocyte. RNA Biol 2012; 9:633-43. [PMID: 22614836 DOI: 10.4161/rna.19760] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Pur-α was identified as a DNA-binding protein with high affinity for the single-stranded PUR-motif (GGN)n. Bound to DNA, Pur-α can both activate and repress transcription. In addition, Pur-α binds to RNA and may participate in nuclear RNA export as well as transport of cytoplasmic neuronal mRNP granules. The heritable trinucleotide-repeat expansion disease Fragile X associated Tremor and Ataxia Syndrome (FXTAS) leads to interaction of Pur-α with mutant, abnormally long r(CGG)n stretches, which appears to titrate the protein away from its physiologic mRNA targets into nuclear RNA-protein aggregates. We examined the function of Drosophila Pur-α and demonstrate that the protein accumulates in the growing oocyte early in oogenesis. Co-purifying proteins reveal that Pur-α is part of transported mRNP complexes, analogous to its reported role in nerve cells. We analyzed the subcellular localization of mutant GFP-Pur-α fusion proteins where either nucleic acid binding or dimerization, or both, were prevented. We propose that association with mRNAs occurs in the nucleus and is required for nuclear export of the complex. Furthermore, efficient translocation into the oocyte also requires RNA binding as well as dimerization. RNA binding assays demonstrate that recombinant Drosophila Pur-α can bind r(CGG) 4 with higher affinity than previously thought. Related sequences, such as r(CAG) 4 and the consensus sequence of the opa-repeat r(CAG) 3CAA, can also associate with Pur-α in vitro and in vivo. The mRNA target spectrum of Pur-α may therefore be larger than previously anticipated.
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Affiliation(s)
- Verena Aumiller
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, München, Germany
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