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de Bisschop G, Ameur M, Ulryck N, Benattia F, Ponchon L, Sargueil B, Chamond N. HIV-1 gRNA, a biological substrate, uncovers the potency of DDX3X biochemical activity. Biochimie 2019; 164:83-94. [PMID: 30910425 DOI: 10.1016/j.biochi.2019.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/12/2019] [Indexed: 11/30/2022]
Abstract
DEAD-box helicases play central roles in the metabolism of many RNAs and ribonucleoproteins by assisting their synthesis, folding, function and even their degradation or disassembly. They have been implicated in various phenomena, and it is often difficult to rationalize their molecular roles from in vivo studies. Once purified in vitro, most of them only exhibit a marginal activity and poor specificity. The current model is that they gain specificity and activity through interaction of their intrinsically disordered domains with specific RNA or proteins. DDX3 is a DEAD-box cellular helicase that has been involved in several steps of the HIV viral cycle, including transcription, RNA export to the cytoplasm and translation. In this study, we investigated DDX3 biochemical properties in the context of a biological substrate. DDX3 was overexpressed, purified and its enzymatic activities as well as its RNA binding properties were characterized using both model substrates and a biological substrate, HIV-1 gRNA. Biochemical characterization of DDX3 in the context of a biological substrate identifies HIV-1 gRNA as a rare example of specific substrate and unravels the extent of DDX3 ATPase activity. Analysis of DDX3 binding capacity indicates an unexpected dissociation between its binding capacity and its biochemical activity. We further demonstrate that interaction of DDX3 with HIV-1 gRNA relies both on specific RNA determinants and on the disordered N- and C-terminal regions of the protein. These findings shed a new light regarding the potentiality of DDX3 biochemical activity supporting its multiple cellular functions.
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Affiliation(s)
| | - Mélissa Ameur
- CiTCOM, Université Paris Descartes, CNRS UMR 8038, Paris, France
| | - Nathalie Ulryck
- CiTCOM, Université Paris Descartes, CNRS UMR 8038, Paris, France
| | - Fatima Benattia
- CiTCOM, Université Paris Descartes, CNRS UMR 8038, Paris, France
| | - Luc Ponchon
- CiTCOM, Université Paris Descartes, CNRS UMR 8038, Paris, France
| | - Bruno Sargueil
- CiTCOM, Université Paris Descartes, CNRS UMR 8038, Paris, France.
| | - Nathalie Chamond
- CiTCOM, Université Paris Descartes, CNRS UMR 8038, Paris, France.
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2
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Abstract
DEAD-box helicases (DDXs) regulate RNA processing and metabolism by unwinding short double-stranded (ds) RNAs. Sharing a helicase core composed of two RecA-like domains (D1D2), DDXs function in an ATP-dependent, non-processive manner. As an attractive target for cancer and AIDS treatment, DDX3X and its orthologs are extensively studied, yielding a wealth of biochemical and biophysical data, including structures of apo-D1D2 and post-unwound D1D2:single-stranded RNA complex, and the structure of a D2:dsRNA complex that is thought to represent a pre-unwound state. However, the structure of a pre-unwound D1D2:dsRNA complex remains elusive, and thus, the mechanism of DDX action is not fully understood. Here, we describe the structure of a D1D2 core in complex with a 23-base pair dsRNA at pre-unwound state, revealing that two DDXs recognize a 2-turn dsRNA, each DDX mainly recognizes a single RNA strand, and conformational changes induced by ATP binding unwinds the RNA duplex in a cooperative manner.
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Affiliation(s)
- He Song
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Xinhua Ji
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, 21702, USA.
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3
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Zaremba M, Toliusis P, Grigaitis R, Manakova E, Silanskas A, Tamulaitiene G, Szczelkun MD, Siksnys V. DNA cleavage by CgII and NgoAVII requires interaction between N- and R-proteins and extensive nucleotide hydrolysis. Nucleic Acids Res 2014; 42:13887-96. [PMID: 25429977 PMCID: PMC4267653 DOI: 10.1093/nar/gku1236] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 10/31/2014] [Accepted: 11/10/2014] [Indexed: 01/07/2023] Open
Abstract
The stress-sensitive restriction-modification (RM) system CglI from Corynebacterium glutamicum and the homologous NgoAVII RM system from Neisseria gonorrhoeae FA1090 are composed of three genes: a DNA methyltransferase (M.CglI and M.NgoAVII), a putative restriction endonuclease (R.CglI and R.NgoAVII, or R-proteins) and a predicted DEAD-family helicase/ATPase (N.CglI and N.NgoAVII or N-proteins). Here we report a biochemical characterization of the R- and N-proteins. Size-exclusion chromatography and SAXS experiments reveal that the isolated R.CglI, R.NgoAVII and N.CglI proteins form homodimers, while N.NgoAVII is a monomer in solution. Moreover, the R.CglI and N.CglI proteins assemble in a complex with R2N2 stoichiometry. Next, we show that N-proteins have ATPase activity that is dependent on double-stranded DNA and is stimulated by the R-proteins. Functional ATPase activity and extensive ATP hydrolysis (∼170 ATP/s/monomer) are required for site-specific DNA cleavage by R-proteins. We show that ATP-dependent DNA cleavage by R-proteins occurs at fixed positions (6-7 nucleotides) downstream of the asymmetric recognition sequence 5'-GCCGC-3'. Despite similarities to both Type I and II restriction endonucleases, the CglI and NgoAVII enzymes may employ a unique catalytic mechanism for DNA cleavage.
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Affiliation(s)
- Mindaugas Zaremba
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Paulius Toliusis
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Rokas Grigaitis
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Elena Manakova
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Arunas Silanskas
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Giedre Tamulaitiene
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Virginijus Siksnys
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
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4
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Tuteja N, Tarique M, Banu MSA, Ahmad M, Tuteja R. Pisum sativum p68 DEAD-box protein is ATP-dependent RNA helicase and unique bipolar DNA helicase. Plant Mol Biol 2014; 85:639-51. [PMID: 24908423 DOI: 10.1007/s11103-014-0209-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 05/29/2014] [Indexed: 05/20/2023]
Abstract
DEAD-box helicases play essential role in DNA and RNA metabolism such as replication, repair, recombination, transcription, translation, ribosome biogenesis and splicing which regulate plant growth and development. The presence of helicases in the stress-induced ORFs identified by cDNA microarray indicates that helicases might be playing an important role in stabilizing growth in plants under stress. p68 DEAD-box helicase has been identified and characterized from animal systems but the properties and functions of plant p68 are poorly understood. In this study, the identification, purification and characterization of recombinant p68 from Pisum sativum (Psp68) is presented. Psp68 possesses all the characteristic motifs like DEAD-box ATP-binding and helicase C terminal motifs and is structurally similar to human p68 homologue. Psp68 exhibits ATPase activity in the presence of both DNA and RNA and it binds to DNA as well as RNA. It contains the characteristic RNA helicase activity. Interestingly Psp68 also shows the unique DNA helicase activity, which is bipolar in nature (unwinds DNA in both the 5'-3' and 3'-5' directions). The Km values of Psp68 for ATPase are 0.5126 and 0.9142 mM in the presence of DNA and RNA, respectively. The Km values of Psp68 are 1.6129 and 1.14 nM for DNA helicase and RNA helicase, respectively. The unique properties of Psp68 suggest that it could be a multifunctional protein involved in different aspect of DNA and RNA metabolism. This discovery should make an important contribution to better understanding of nucleic acids metabolism plants.
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Affiliation(s)
- Narendra Tuteja
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India,
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5
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Markov DA, Wojtas ID, Tessitore K, Henderson S, McAllister WT. Yeast DEAD box protein Mss116p is a transcription elongation factor that modulates the activity of mitochondrial RNA polymerase. Mol Cell Biol 2014; 34:2360-9. [PMID: 24732805 PMCID: PMC4054322 DOI: 10.1128/mcb.00160-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 02/20/2014] [Accepted: 04/01/2014] [Indexed: 01/08/2023] Open
Abstract
DEAD box proteins have been widely implicated in regulation of gene expression. Here, we show that the yeast Saccharomyces cerevisiae DEAD box protein Mss116p, previously known as a mitochondrial splicing factor, also acts as a transcription factor that modulates the activity of the single-subunit mitochondrial RNA polymerase encoded by RPO41. Binding of Mss116p stabilizes paused mitochondrial RNA polymerase elongation complexes in vitro and favors the posttranslocated state of the enzyme, resulting in a lower concentration of nucleotide substrate required to escape the pause; this mechanism of action is similar to that of elongation factors that enhance the processivity of multisubunit RNA polymerases. In a yeast strain in which the RNA splicing-related functions of Mss116p are dispensable, overexpression of RPO41 or MSS116 increases cell survival from colonies that were exposed to low temperature, suggesting a role for Mss116p in enhancing the efficiency of mitochondrial transcription under stress conditions.
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Affiliation(s)
- Dmitriy A Markov
- Department of Cell Biology, Rowan University, School of Osteopathic Medicine, Stratford, New Jersey, USA
| | - Ireneusz D Wojtas
- Department of Cell Biology, Rowan University, School of Osteopathic Medicine, Stratford, New Jersey, USA
| | - Kassandra Tessitore
- Summer Undergraduate Research Experience Program, Rowan University, School of Osteopathic Medicine, Stratford, New Jersey, USA
| | - Simmone Henderson
- Graduate School of Biomedical Sciences, Rowan University, School of Osteopathic Medicine, Stratford, New Jersey, USA
| | - William T McAllister
- Department of Cell Biology, Rowan University, School of Osteopathic Medicine, Stratford, New Jersey, USA
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Kwok J, Hui KPY, Lescar J, Kotaka M. Expression, purification, crystallization and preliminary X-ray analysis of full-length human RIG-I. Acta Crystallogr F Struct Biol Commun 2014; 70:248-51. [PMID: 24637767 PMCID: PMC3936451 DOI: 10.1107/s2053230x14000430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 01/08/2014] [Indexed: 11/10/2022] Open
Abstract
The human innate immune system can detect invasion by microbial pathogens through pattern-recognition receptors that recognize structurally conserved pathogen-associated molecular patterns. Retinoic acid-inducible gene I (RIG-I)-like helicases (RLHs) are one of the two major families of pattern-recognition receptors that can detect viral RNA. RIG-I, belonging to the RLH family, is capable of recognizing intracellular viral RNA from RNA viruses, including influenza virus and Ebola virus. Here, full-length human RIG-I (hRIG-I) was cloned in Escherichia coli and expressed in a recombinant form with a His-SUMO tag. The protein was purified and crystallized at 291 K using the hanging-drop vapour-diffusion method. X-ray diffraction data were collected to 2.85 Å resolution; the crystal belonged to space group F23, with unit-cell parameters a = b = c = 216.43 Å, α = β = γ = 90°.
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Affiliation(s)
- Jane Kwok
- Department of Physiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Kenrie P. Y. Hui
- Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
| | - Julien Lescar
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore 138673, Singapore
| | - Masayo Kotaka
- Department of Physiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
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Tuteja N, Sahoo RK, Garg B, Tuteja R. OsSUV3 dual helicase functions in salinity stress tolerance by maintaining photosynthesis and antioxidant machinery in rice (Oryza sativa L. cv. IR64). Plant J 2013; 76:115-27. [PMID: 23808500 DOI: 10.1111/tpj.12277] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 06/17/2013] [Accepted: 06/24/2013] [Indexed: 05/20/2023]
Abstract
To overcome the salinity-induced loss of crop yield, a salinity-tolerant trait is required. The SUV3 helicase is involved in the regulation of RNA surveillance and turnover in mitochondria, but the helicase activity of plant SUV3 and its role in abiotic stress tolerance have not been reported so far. Here we report that the Oryza sativa (rice) SUV3 protein exhibits DNA and RNA helicase, and ATPase activities. Furthermore, we report that SUV3 is induced in rice seedlings in response to high levels of salt. Its expression, driven by a constitutive cauliflower mosaic virus 35S promoter in IR64 transgenic rice plants, confers salinity tolerance. The T1 and T2 sense transgenic lines showed tolerance to high salinity and fully matured without any loss in yields. The T2 transgenic lines also showed tolerance to drought stress. These results suggest that the introduced trait is functional and stable in transgenic rice plants. The rice SUV3 sense transgenic lines showed lesser lipid peroxidation, electrolyte leakage and H2 O2 production, along with higher activities of antioxidant enzymes under salinity stress, as compared with wild type, vector control and antisense transgenic lines. These results suggest the existence of an efficient antioxidant defence system to cope with salinity-induced oxidative damage. Overall, this study reports that plant SUV3 exhibits DNA and RNA helicase and ATPase activities, and provides direct evidence of its function in imparting salinity stress tolerance without yield loss. The possible mechanism could be that OsSUV3 helicase functions in salinity stress tolerance by improving photosynthesis and antioxidant machinery in transgenic rice.
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Affiliation(s)
- Narendra Tuteja
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
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8
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Katibah GE, Lee HJ, Huizar JP, Vogan JM, Alber T, Collins K. tRNA binding, structure, and localization of the human interferon-induced protein IFIT5. Mol Cell 2013; 49:743-50. [PMID: 23317505 PMCID: PMC3615435 DOI: 10.1016/j.molcel.2012.12.015] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 12/19/2012] [Accepted: 12/20/2012] [Indexed: 10/27/2022]
Abstract
Interferon-induced proteins, including the largely uncharacterized interferon-induced tetratricopeptide repeat (IFIT) protein family, provide defenses against pathogens. Differing from expectations for tetratricopeptide repeat (TPR) proteins and from human IFIT1, IFIT2, and IFIT3, we show that human IFIT5 recognizes cellular RNA instead of protein partners. In vivo and in vitro, IFIT5 bound to endogenous 5'-phosphate-capped RNAs, including transfer RNAs. The crystal structure of IFIT5 revealed a convoluted intramolecular packing of eight TPRs as a fold that we name the TPR eddy. Additional, non-TPR structural elements contribute to an RNA binding cleft. Instead of general cytoplasmic distribution, IFIT5 concentrated in actin-rich protrusions from the apical cell surface colocalized with the RNA-binding retinoic acid-inducible gene-I (RIG-I). These findings establish compartmentalized cellular RNA binding activity as a mechanism for IFIT5 function and reveal the TPR eddy as a scaffold for RNA recognition.
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MESH Headings
- Actins/metabolism
- Amino Acid Substitution
- Animals
- Crystallography, X-Ray
- DEAD Box Protein 58
- DEAD-box RNA Helicases/chemistry
- DEAD-box RNA Helicases/isolation & purification
- DEAD-box RNA Helicases/metabolism
- HEK293 Cells
- Humans
- Mice
- Models, Molecular
- Mutagenesis, Site-Directed
- Neoplasm Proteins/chemistry
- Neoplasm Proteins/isolation & purification
- Neoplasm Proteins/metabolism
- Protein Binding
- Protein Interaction Mapping
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Protein Transport
- RNA, Transfer, Met/chemistry
- RNA, Transfer, Met/metabolism
- Receptors, Immunologic
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Affiliation(s)
- George E. Katibah
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Ho Jun Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - John P. Huizar
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Jacob M. Vogan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Tom Alber
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
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9
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Lee SY, Jung HY, Kim TO, Im DW, You KY, Back JM, Kim Y, Kim HJ, Shin W, Heo YS. Cloning, purification, crystallization and preliminary X-ray crystallographic analysis of the N-terminal domain of DEAD-box RNA helicase from Staphylococcus aureus strain Mu50. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1674-1676. [PMID: 21139222 PMCID: PMC2998381 DOI: 10.1107/s1744309110043149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Accepted: 10/22/2010] [Indexed: 05/30/2023]
Abstract
DEAD-box helicases are enzymes with an ATP-dependent RNA-unwinding function that are involved in a variety of cellular processes including RNA splicing, ribosome biogenesis and RNA degradation. In this study, the N-terminal domain of DEAD-box RNA helicase from Staphylococcus aureus strain Mu50 was overexpressed in Escherichia coli, purified and crystallized. Diffraction data were collected to 2.60 Å resolution using a synchrotron-radiation source. The crystal belonged to space group P1, with unit-cell parameters a=70.81, b=80.23, c=86.25 Å, α=69.54, β=66.54, γ=87.32°. The unit cell contained six molecules, with a corresponding VM of 2.91 Å3 Da(-1) and a solvent content of 56.1%.
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Affiliation(s)
- Soo Young Lee
- Department of Chemistry, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
- Department of Chemistry, Seoul National University, Seoul 151-742, Republic of Korea
| | - Ha Yun Jung
- Department of Chemistry, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Tae-O Kim
- Department of Chemistry, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Dong-Won Im
- Department of Chemistry, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Ki-Young You
- Department of Chemistry, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Jang-Mi Back
- Department of Chemistry, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Yangmee Kim
- Department of Bioscience and Biotechnology, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
| | - Hak Jun Kim
- Korea Polar Research Institute, Incheon 406-840, Republic of Korea
| | - Whanchul Shin
- Department of Chemistry, Seoul National University, Seoul 151-742, Republic of Korea
| | - Yong-Seok Heo
- Department of Chemistry, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul 143-701, Republic of Korea
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Kudlinzki D, Nagel C, Ficner R. Crystallization and preliminary X-ray diffraction analysis of the C-terminal domain of the human spliceosomal DExD/H-box protein hPrp22. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:956-958. [PMID: 19724143 PMCID: PMC2795611 DOI: 10.1107/s1744309109031844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Accepted: 08/12/2009] [Indexed: 05/28/2023]
Abstract
The Homo sapiens DExD/H-box protein hPrp22 is a crucial component of the eukaryotic pre-mRNA splicing machinery. Within the splicing cycle, it is involved in the ligation of exons and generation of the lariat and it additionally catalyzes the release of mature mRNA from the spliceosomal U5 snRNP. The yeast homologue of this protein, yPrp22, shows ATP-dependent RNA-helicase activity and is capable of unwinding RNA/RNA duplex molecules. A truncated construct coding for residues 950-1183 of human Prp22, comprising the structurally and functionally uncharacterized C-terminal domain, was cloned into an Escherichia coli expression vector. The protein was subsequently overproduced, purified and crystallized. The crystals obtained diffracted to 2.1 A resolution, belonged to the tetragonal space group P4(1)2(1)2 or P4(3)2(1)2, with unit-cell parameters a = b = 78.2, c = 88.4 A, and contained one molecule in the asymmetric unit.
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Affiliation(s)
- Denis Kudlinzki
- Institut für Mikrobiologie und Genetik, Abteilung Molekulare Strukturbiologie, Georg-August-Universität Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
| | - Christian Nagel
- Institut für Mikrobiologie und Genetik, Abteilung Molekulare Strukturbiologie, Georg-August-Universität Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
| | - Ralf Ficner
- Institut für Mikrobiologie und Genetik, Abteilung Molekulare Strukturbiologie, Georg-August-Universität Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
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11
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Moon H, Choe J. Crystallization and preliminary crystallographic studies of human RIG-I in complex with double-stranded RNA. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:648-50. [PMID: 19478455 PMCID: PMC2688434 DOI: 10.1107/s1744309109018405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2009] [Accepted: 05/15/2009] [Indexed: 12/24/2022]
Abstract
Retinoic acid inducible gene-I (RIG-I) is an essential component of the innate immune system that is responsible for the detection and elimination of invading viruses. RIG-I recognizes viral RNAs inside the cell and then initiates downstream signalling to activate the IRF-3 and NF-kappaB genes, which results in the production of type I interferons. RIG-I is composed of an N-terminal CARD domain for signalling and C-terminal helicase and repressor domains for RNA recognition. A RIG-I-RNA binding assay was performed to investigate the in vitro RIG-I-RNA binding properties. Selenomethionine-incorporated RIG-I was expressed using Escherichia coli and purified for crystallization. X-ray data were collected from RIG-I-dsRNA complex crystals to 2.8 A resolution using synchrotron radiation.
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Affiliation(s)
- Hyunjin Moon
- Department of Biological Science, University of Seoul, 90 Cheonnong-dong, Dongdaemun-gu, Seoul 130-743, Republic of Korea
| | - Jungwoo Choe
- Department of Biological Science, University of Seoul, 90 Cheonnong-dong, Dongdaemun-gu, Seoul 130-743, Republic of Korea
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12
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Abstract
S. cerevisiae ribosome biogenesis is a highly ordered and dynamic process that involves over 100 accessory proteins, including 18 DExD/H-box proteins that act at discrete steps in the pathway. Although often termed RNA helicases, the biochemical functions of individual DExD/H-box proteins appear to vary considerably. Four DExD/H-box proteins, Dbp3p, Dbp4p, Rok1p, and Rrp3p, involved in yeast ribosome assembly were expressed in E. coli, and all were found to be active RNA-dependent ATPases with k(cat) values ranging from 13 to 170 min(-1) and K(M)(ATP) values ranging from 0.24 to 2.3 mM. All four proteins are activated by single-stranded oligonucleotides, but they require different chain lengths for maximal ATPase activity, ranging from 10 to >40 residues. None of the four proteins shows significant specificity for yeast rRNA, compared to nonspecific control RNAs since these large RNAs contain multiple binding sites that appear to be catalytically similar. This systematic comparison of four members of the DExD/H-box family demonstrates a range of biochemical properties and lays the foundation for relating the activities of proteins to their biological functions.
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Affiliation(s)
- Ivelitza Garcia
- Department of Biochemistry Molecular Biology, and Cellular Biology, Northwestern University, 2205 Tech Drive, Hogan 2-100, Evanston, IL 60208
| | - Olke C. Uhlenbeck
- Department of Biochemistry Molecular Biology, and Cellular Biology, Northwestern University, 2205 Tech Drive, Hogan 2-100, Evanston, IL 60208
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13
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Nithianantham S, Shilton BH. Analysis of the isolated SecA DEAD motor suggests a mechanism for chemical-mechanical coupling. J Mol Biol 2008; 383:380-9. [PMID: 18761349 DOI: 10.1016/j.jmb.2008.08.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Revised: 08/07/2008] [Accepted: 08/11/2008] [Indexed: 11/18/2022]
Abstract
The preprotein cross-linking domain and C-terminal domains of Escherichia coli SecA were removed to create a minimal DEAD motor, SecA-DM. SecA-DM hydrolyzes ATP and has the same affinity for ADP as full-length SecA. The crystal structure of SecA-DM in complex with ADP was solved and shows the DEAD motor in a closed conformation. Comparison with the structure of the E. coli DEAD motor in an open conformation (Protein Data Bank ID 2FSI) indicates main-chain conformational changes in two critical sequences corresponding to Motif III and Motif V of the DEAD helicase family. The structures that the Motif III and Motif V sequences adopt in the DEAD motor open conformation are incompatible with the closed conformation. Therefore, when the DEAD motor makes the transition from open to closed, Motif III and Motif V are forced to change their conformations, which likely functions to regulate passage through the transition state for ATP hydrolysis. The transition state for ATP hydrolysis for the SecA DEAD motor was modeled based on the conformation of the Vasa helicase in complex with adenylyl imidodiphosphate and RNA (Protein Data Bank ID 2DB3). A mechanism for chemical-mechanical coupling emerges, where passage through the transition state for ATP hydrolysis is hindered by the conformational changes required in Motif III and Motif V, and may be promoted by binding interactions with the preprotein substrate and/or other translocase domains and subunits.
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Affiliation(s)
- Stanley Nithianantham
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada N6A 5C1
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Liu HH, Liu J, Fan SL, Song MZ, Han XL, Liu F, Shen FF. Molecular cloning and characterization of a salinity stress-induced gene encoding DEAD-box helicase from the halophyte Apocynum venetum. J Exp Bot 2008; 59:633-44. [PMID: 18272921 DOI: 10.1093/jxb/erm355] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The genes encoding DEAD-box helicases play a key role in various abiotic stresses, including temperature, light, oxygen, and salt stress. A salt-responsive gene, designated AvDH1, was isolated from the halophyte dogbane (Apocynum venetum) by using suppression subtractive hybridization and RACE (rapid amplification of cDNA ends) PCR. The deduced amino acid sequence has nine conserved helicase motifs of the DEAD-box protein family. The AvDH1 gene is present as a single copy in the dogbane genome. This gene is expressed in response to NaCl and not polyethlene glycol (PEG) nor abscisic acid, and its expression increases with time. The transcription of AvDH1 is also induced by low temperature (4 degrees C), but its accumulation first increases then decreases with time. The purified recombinant protein contains ATP-dependent DNA helicase activity, ATP-independent RNA helicase activity, and DNA- or RNA-dependent ATPase activity. The ATPase activity of AvDH1 is stimulated more by single-stranded DNA than by double-stranded DNA or RNA. These results suggested that AvDH1 belonging to the DEAD-box helicase family is induced by salinity, functions as a typical helicase to unwind DNA and RNA, and may play an important role in salinity tolerance.
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Affiliation(s)
- H H Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, Shandong 271018, PR China
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Salzman DW, Shubert-Coleman J, Furneaux H. P68 RNA helicase unwinds the human let-7 microRNA precursor duplex and is required for let-7-directed silencing of gene expression. J Biol Chem 2007; 282:32773-9. [PMID: 17724023 DOI: 10.1074/jbc.m705054200] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs are short, single-stranded RNAs that arise from a transient precursor duplex. We have identified a novel activity in HeLa cell extracts that can unwind the let-7 microRNA duplex. Using partially purified material, we have shown that microRNA helicase activity requires ATP and has a native molecular mass of approximately 68 kDa. Affinity purification of the unwinding activity revealed co-purification of P68 RNA helicase. Importantly, recombinant P68 RNA helicase was sufficient to unwind the let-7 duplex. Moreover, like its native homolog, P68 RNA helicase did not unwind an analogous small interfering RNA duplex. We further showed that knockdown of P68 inhibited let-7 microRNA function. From our data, we conclude that P68 RNA helicase is an essential component of the let-7 microRNA pathway, and in conjunction with other factors, it may play a role in the loading of let-7 microRNA into the silencing complex.
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Affiliation(s)
- David W Salzman
- Department of Molecular, Microbial, and Structural Biology, University of Connecticut Health Center, 236 Farmington Avenue, Farmington, CT 06030, USA
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Abstract
Human DDX3 (hDDX3) is a DEAD-box protein shown to possess RNA-unwinding and adenosine triphosphatase (ATPase) activities. The hDDX3 protein has been implicated in nuclear mRNA export, cell growth control, and cancer progression. In addition, a role of this protein in the replication of human immunodeficiency virus Type 1 and in the pathogenesis of hepatitis C virus has been recently proposed. Its enzymological properties, however, are largely unknown. In this work, we characterized its ATPase activity. We show that hDDX3 ATPase activity is stimulated by various ribo- and deoxynucleic acids. Comparative analysis with different nucleoside triphosphate analogs showed that the hDDX3 ATPase couples high catalytic efficiency to a rather relaxed substrate specificity, both in terms of base selection and sugar selection. In addition, its ability to recognize the L-stereoisomers of both 3' deoxy- and 2',3' dideoxy-ribose, points to a relaxed stereoselectivity. On the basis of these results, we hypothesize the presence of structural determinants on both the base and the sugar moieties, critical for nucleoside binding to the enzyme. Our results expand the knowledge about the DEAD-box RNA helicases in general and can be used for rational design of selective inhibitors of hDDX3, to be tested as potential antitumor and antiviral agents.
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Affiliation(s)
- Raffaella Franca
- DNA Enzymology and Molecular Virology Unit, Istituto di Genetica Molecolare IGM-CNR, via Abbiategrasso 207, 27100 Pavia, Italy
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Rodamilans B, Montoya G. Expression, purification, crystallization and preliminary X-ray diffraction analysis of the DDX3 RNA helicase domain. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:283-6. [PMID: 17401195 PMCID: PMC2330201 DOI: 10.1107/s1744309107006434] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2006] [Accepted: 02/06/2007] [Indexed: 11/10/2022]
Abstract
DDX3 is a human RNA helicase that is involved in RNA processing and important human diseases. This enzyme belongs to the DEAD-box protein family, the members of which are characterized by the presence of nine conserved motifs including the Asp-Glu-Ala-Asp motif that defines the family. DDX3 has two distinct domains: an ATP-binding domain in the central region of the protein and a helicase domain in the carboxy-terminal region. The helicase domain of DDX3 was cloned and overexpressed in Escherichia coli. Crystallization experiments yielded crystals that were suitable for X-ray diffraction analysis. The final crystallization conditions were a reservoir solution consisting of 2 M ammonium sulfate, 0.1 M imidazole pH 6.4 plus 5 mM spermine tetrahydrochloride and a protein solution containing 10 mM HEPES, 500 mM ammonium sulfate pH 8.0. The crystals of the helicase domain belong to the monoclinic space group P2(1), with unit-cell parameters a = 43.85, b = 60.72, c = 88.39 A, alpha = gamma = 90, beta = 101.02 degrees , and contained three molecules per asymmetric unit. These crystals diffracted to a resolution limit of 2.2 A using synchrotron radiation at the European Synchrotron Radiation Facility (ESRF) and the Swiss Light Source (SLS).
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Affiliation(s)
- Bernardo Rodamilans
- Structural Biology and Biocomputing Programme, Spanish National Cancer Centre (CNIO) Macromolecular Crystallography Group, c/Melchor Fdez Almagro 3, 28029 Madrid, Spain
| | - Guillermo Montoya
- Structural Biology and Biocomputing Programme, Spanish National Cancer Centre (CNIO) Macromolecular Crystallography Group, c/Melchor Fdez Almagro 3, 28029 Madrid, Spain
- Correspondence e-mail:
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Shukalyuk AI, Golovnina KA, Baiborodin SI, Gunbin KV, Blinov AG, Isaeva VV. vasa-related genes and their expression in stem cells of colonial parasitic rhizocephalan barnacle Polyascus polygenea (Arthropoda: Crustacea: Cirripedia: Rhizocephala). Cell Biol Int 2007; 31:97-108. [PMID: 17085060 DOI: 10.1016/j.cellbi.2006.09.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2005] [Revised: 08/03/2006] [Accepted: 09/14/2006] [Indexed: 11/18/2022]
Abstract
vasa (vas)-related genes are members of the DEAD-box protein family and are expressed in the germ cells of many Metazoa. We cloned vasa-related genes (PpVLG, CpVLG) and other DEAD-box family related genes (PpDRH1, PpDRH2, CpDRH, AtDRHr) from the colonial parasitic rhizocephalan barnacle Polyascus polygenea, the non-colonial Clistosaccus paguri (Crustacea: Cirripedia: Rhizocephala), and the parasitic isopodan Athelgis takanoshimensis (Crustacea: Isopoda). The colonial Polyascus polygenea, a parasite of the coastal crabs Hemigrapsus sanguineus and Hemigrapsus longitarsis was used as a model object for further detailed investigations. Phylogenetic analysis suggested that PpVLG and CpVLG are closely related to vasa-like genes of other Arthropoda. The rest of the studied genes form their own separate branch on the phylogenetic tree and have a common ancestry with the p68 and PL10 subfamilies. We suppose this group may be a new subfamily of the DEAD-box RNA helicases that is specific for parasitic Crustacea. We found PpVLG and PpDRH1 expression products in stem cells from stolons and buds of internae, during asexual reproduction of colonial P. polygenea, and in germ cells from sexually reproducing externae, including male spermatogenic cells and female oogenic cells.
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Affiliation(s)
- Andrey I Shukalyuk
- Institute of Marine Biology, Far Eastern Branch of Russian Academy of Sciences, Laboratory of Embryology, 17, Pal'chevskogo Street, Vladivostok 690041, Russia.
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Halls C, Mohr S, Del Campo M, Yang Q, Jankowsky E, Lambowitz AM. Involvement of DEAD-box proteins in group I and group II intron splicing. Biochemical characterization of Mss116p, ATP hydrolysis-dependent and -independent mechanisms, and general RNA chaperone activity. J Mol Biol 2006; 365:835-55. [PMID: 17081564 PMCID: PMC1832103 DOI: 10.1016/j.jmb.2006.09.083] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2006] [Revised: 09/22/2006] [Accepted: 09/27/2006] [Indexed: 12/14/2022]
Abstract
The RNA-catalyzed splicing of group I and group II introns is facilitated by proteins that stabilize the active RNA structure or act as RNA chaperones to disrupt stable inactive structures that are kinetic traps in RNA folding. In Neurospora crassa and Saccharomyces cerevisiae, the latter function is fulfilled by specific DEAD-box proteins, denoted CYT-19 and Mss116p, respectively. Previous studies showed that purified CYT-19 stimulates the in vitro splicing of structurally diverse group I and group II introns, and uses the energy of ATP binding or hydrolysis to resolve kinetic traps. Here, we purified Mss116p and show that it has RNA-dependent ATPase activity, unwinds RNA duplexes in a non-polar fashion, and promotes ATP-independent strand-annealing. Further, we show that Mss116p binds RNA non-specifically and promotes in vitro splicing of both group I and group II intron RNAs, as well as RNA cleavage by the aI5gamma-derived D135 ribozyme. However, Mss116p also has ATP hydrolysis-independent effects on some of these reactions, which are not shared by CYT-19 and may reflect differences in its RNA-binding properties. We also show that a non-mitochondrial DEAD-box protein, yeast Ded1p, can function almost as efficiently as CYT-19 and Mss116p in splicing the yeast aI5gamma group II intron and less efficiently in splicing the bI1 group II intron. Together, our results show that Mss116p, like CYT-19, can act broadly as an RNA chaperone to stimulate the splicing of diverse group I and group II introns, and that Ded1p also has an RNA chaperone activity that can be assayed by its effect on splicing mitochondrial introns. Nevertheless, these DEAD-box protein RNA chaperones are not completely interchangeable and appear to function in somewhat different ways, using biochemical activities that have likely been tuned by coevolution to function optimally on specific RNA substrates.
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Affiliation(s)
- Coralie Halls
- Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, and Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, Austin, Texas 78712
| | - Sabine Mohr
- Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, and Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, Austin, Texas 78712
| | - Mark Del Campo
- Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, and Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, Austin, Texas 78712
| | - Quansheng Yang
- Department of Biochemistry and Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106
| | - Eckhard Jankowsky
- Department of Biochemistry and Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH 44106
| | - Alan M. Lambowitz
- Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, and Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, Austin, Texas 78712
- *Corresponding author: Phone: 512-232-3418, Fax: 512-232-3420, e-mail:
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Abstract
The vasa gene is essential for germline formation in Drosophila. Vasa-related genes have been isolated from several organisms including nematode, frog and mammals. In order to gain insight into the early events in vertebrate germline development, zebrafish was chosen as a model. Two zebrafish vasa-related genes were isolated, pl10a and vlg. The pl10a gene was shown to be widely expressed during embryogenesis. The vlg gene and vasa belong to the same subfamily of RNA helicase encoding genes. Putative maternal vlg transcripts were detected shortly after fertilization and from the blastula stage onwards, expression was restricted to migratory cells most likely to be primordial germ cells.
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Affiliation(s)
- L C Olsen
- Department of Molecular Biology, University of Bergen, Norway.
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