1
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Scheele R, Weber Y, Nintzel FEH, Herger M, Kaminski TS, Hollfelder F. Ultrahigh Throughput Evolution of Tryptophan Synthase in Droplets via an Aptamer Sensor. ACS Catal 2024; 14:6259-6271. [PMID: 38660603 PMCID: PMC11036396 DOI: 10.1021/acscatal.4c00230] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/29/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024]
Abstract
Tryptophan synthase catalyzes the synthesis of a wide array of noncanonical amino acids and is an attractive target for directed evolution. Droplet microfluidics offers an ultrahigh throughput approach to directed evolution (up to 107 experiments per day), enabling the search for biocatalysts in wider regions of sequence space with reagent consumption minimized to the picoliter volume (per library member). While the majority of screening campaigns in this format on record relied on an optically active reaction product, a new assay is needed for tryptophan synthase. Tryptophan is not fluorogenic in the visible light spectrum and thus falls outside the scope of conventional droplet microfluidic readouts, which are incompatible with UV light detection at high throughput. Here, we engineer a tryptophan DNA aptamer into a sensor to quantitatively report on tryptophan production in droplets. The utility of the sensor was validated by identifying five-fold improved tryptophan synthases from ∼100,000 protein variants. More generally, this work establishes the use of DNA-aptamer sensors with a fluorogenic read-out in widening the scope of droplet microfluidic evolution.
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Affiliation(s)
- Remkes
A. Scheele
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K.
| | - Yanik Weber
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K.
| | | | - Michael Herger
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K.
| | - Tomasz S. Kaminski
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K.
- Department
of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Florian Hollfelder
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K.
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2
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Weber Y, Böck D, Ivașcu A, Mathis N, Rothgangl T, Ioannidi EI, Blaudt AC, Tidecks L, Vadovics M, Muramatsu H, Reichmuth A, Marquart KF, Kissling L, Pardi N, Jinek M, Schwank G. Enhancing prime editor activity by directed protein evolution in yeast. Nat Commun 2024; 15:2092. [PMID: 38453904 PMCID: PMC10920827 DOI: 10.1038/s41467-024-46107-z] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/14/2024] [Indexed: 03/09/2024] Open
Abstract
Prime editing is a highly versatile genome editing technology that enables the introduction of base substitutions, insertions, and deletions. However, compared to traditional Cas9 nucleases prime editors (PEs) are less active. In this study we use OrthoRep, a yeast-based platform for directed protein evolution, to enhance the editing efficiency of PEs. After several rounds of evolution with increased selection pressure, we identify multiple mutations that have a positive effect on PE activity in yeast cells and in biochemical assays. Combining the two most effective mutations - the A259D amino acid substitution in nCas9 and the K445T substitution in M-MLV RT - results in the variant PE_Y18. Delivery of PE_Y18, encoded on DNA, mRNA or as a ribonucleoprotein complex into mammalian cell lines increases editing rates up to 3.5-fold compared to PEmax. In addition, PE_Y18 supports higher prime editing rates when delivered in vivo into the liver or brain. Our study demonstrates proof-of-concept for the application of OrthoRep to optimize genome editing tools in eukaryotic cells.
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Affiliation(s)
- Yanik Weber
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Desirée Böck
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Anastasia Ivașcu
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Nicolas Mathis
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Tanja Rothgangl
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Eleonora I Ioannidi
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Alex C Blaudt
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Lisa Tidecks
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Máté Vadovics
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hiromi Muramatsu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andreas Reichmuth
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Kim F Marquart
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Lucas Kissling
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Norbert Pardi
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Gerald Schwank
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland.
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3
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Rosenow F, Baier H, Bien C, Bösebeck F, Dümpelmann M, Hamer H, Kellinghaus C, Knake S, Schreiber M, Surges R, Staack A, Tergau F, von Podewils F, Weber Y, Wehner T, Winter Y, Zöllner J, Strzelczyk A, Willems L. P 67 Satisfaction with and reliability of in-hospital video-electroencephalography monitoring systems in epilepsy diagnosis among German epilepsy centers. Clin Neurophysiol 2022. [DOI: 10.1016/j.clinph.2022.01.098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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4
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Wijntjes C, Weber Y, Höger S, Hollert H, Schäffer A. Effects of algae and fungicides on the fate of a sulfonylurea herbicide in a water-sediment system. Chemosphere 2022; 290:133234. [PMID: 34902390 DOI: 10.1016/j.chemosphere.2021.133234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 10/04/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
The impact of pesticide mixtures on various soil parameters has been extensively studied, whereas research on effects in the aquatic environment is scarce. Furthermore, investigations on the consequences of chemical mixtures on the biodegradation kinetics of parent compounds remain deficient. Our research intended to evaluate potential effects by combined application of an agriculturally employed tank mixture to aquatic sediment systems under controlled laboratory conditions. The mixture contained two fungicides and one radiolabeled herbicide of which the route and rate of degradation was followed. One set of aquatic sediment vessels was incubated in the dark. A second set of vessels was controlled under identical conditions, except for being continuously irradiated to promote algal growth. In addition, the algal biomass in irradiated aquatic sediment was monitored to determine its effects and a potential role in the biodegradation of iodosulfuron-methyl-sodium. The study results showed that the herbicide, although hydro- and photolytically stable throughout the study, metabolized faster (DT50 1.1-1.2-fold and DT90 2.8-4.5-fold) when continuously irradiated in comparison to dark aquatic sediment. Both fungicides had a significant prolonging effect on the biodegradation rate of the herbicide. In the presence of fungicides, DT90 values increased 1.5-fold in the irradiated, and 2.5-fold in the dark systems. Additionally, algae may have influenced the metabolization of the herbicide in the irradiated systems, where shorter DT90 values were evaluated. Even so, the algal influence was concluded to be indirect.
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Affiliation(s)
- Christiaan Wijntjes
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany; Innovative Environmental Services (IES) Ltd, Benkenstrasse 260, 4108, Witterswil, Switzerland.
| | - Yanik Weber
- Innovative Environmental Services (IES) Ltd, Benkenstrasse 260, 4108, Witterswil, Switzerland
| | - Stefan Höger
- Innovative Environmental Services (IES) Ltd, Benkenstrasse 260, 4108, Witterswil, Switzerland
| | - Henner Hollert
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue-Strasse 13, 60438, Frankfurt Am Main, Germany
| | - Andreas Schäffer
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, 52074, Aachen, Germany
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5
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Scherer M, Milosevic L, Guggenberger R, Volker M, Naros G, Grimm F, Bucurenciu I, Steinhoff B, Weber Y, Lerche H, Weiss D, Rona S, Gharabaghi A. FV 25 Cortical α-activity identifies responders to anterior thalamic deep brain stimulation for epilepsy. Clin Neurophysiol 2019. [DOI: 10.1016/j.clinph.2019.04.634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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6
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Bauer S, Baier H, Baumgartner C, Bohlmann K, Fauser S, Graf W, Hillenbrand B, Hirsch M, Last C, Lerche H, Mayer T, Schulze-Bonhage A, Steinhoff B, Weber Y, Hartlep A, Rosenow F, Hamer H. Transcutaneous Vagus Nerve Stimulation (tVNS) for Treatment of Drug-Resistant Epilepsy: A Randomized, Double-Blind Clinical Trial (cMPsE02). Brain Stimul 2016; 9:356-363. [DOI: 10.1016/j.brs.2015.11.003] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 11/10/2015] [Accepted: 11/14/2015] [Indexed: 11/28/2022] Open
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7
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Bischof F, Weber Y. Fampridin: Gute Krankengymnastik reicht aus – Kontra. Akt Neurol 2015. [DOI: 10.1055/s-0035-1552711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- F. Bischof
- Abteilung Neurologie mit Schwerpunkt Vaskuläre Neurologie, Universität Tübingen
| | - Y. Weber
- Abteilung Neurologie mit Schwerpunkt Epileptologie, Hertie Institut für Klinische Hirnforschung, Universität Tübingen
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8
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Wolking S, Weber Y. Genetik der epileptischen Enzephalopathien. Akt Neurol 2015. [DOI: 10.1055/s-0035-1559619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- S. Wolking
- Neurologie mit Schwerpunkt Epileptologie, Hertie-Institut für klinische Hirnforschung, Universitätsklinikum Tübingen
| | - Y. Weber
- Neurologie mit Schwerpunkt Epileptologie, Hertie-Institut für klinische Hirnforschung, Universitätsklinikum Tübingen
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9
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Wolking S, Becker F, Rau S, Weber Y, Depondt C, Sisodiya S, Lerche H. P88. Identification of genome-based biomarkers for response to specific antiepileptic drugs in focal and idiopathic generalized epilepsies. Clin Neurophysiol 2015. [DOI: 10.1016/j.clinph.2015.04.238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Lauxmann S, Weber Y, Lerche H, Koch H. P97. The pathophysiology of sudden unexpected death in epilepsy (SUDEP). Clin Neurophysiol 2015. [DOI: 10.1016/j.clinph.2015.04.247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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Schubert J, Siekierska A, Esguerra C, Weber Y, Lerche H. V23. Mutations in STX1B encoding a presynaptic protein cause fever-associated epilepsy syndromes. Clin Neurophysiol 2015. [DOI: 10.1016/j.clinph.2015.04.101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Hallmann K, Zsurka G, Moskau-Hartmann S, Kirschner J, Korinthenberg R, Ruppert AK, Ozdemir O, Weber Y, Becker F, Lerche H, Elger CE, Thiele H, Nurnberg P, Sander T, Kunz WS. A homozygous splice-site mutation in CARS2 is associated with progressive myoclonic epilepsy. Neurology 2014; 83:2183-7. [DOI: 10.1212/wnl.0000000000001055] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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13
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Dihné M, Schmidt-Wilcke T, Focke N, Weber Y, Lerche H. Neues aus der Epileptologie. Akt Neurol 2012. [DOI: 10.1055/s-0032-1305247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- M. Dihné
- Abteilung Neurologie mit Schwerpunkt Epileptologie, Hertie Institut für Klinische Hirnforschung, Universität Tübingen
| | - T. Schmidt-Wilcke
- Abteilung Neurologie mit Schwerpunkt Epileptologie, Hertie Institut für Klinische Hirnforschung, Universität Tübingen
| | - N. Focke
- Abteilung Neurologie mit Schwerpunkt Epileptologie, Hertie Institut für Klinische Hirnforschung, Universität Tübingen
| | - Y. Weber
- Abteilung Neurologie mit Schwerpunkt Epileptologie, Hertie Institut für Klinische Hirnforschung, Universität Tübingen
| | - H. Lerche
- Abteilung Neurologie mit Schwerpunkt Epileptologie, Hertie Institut für Klinische Hirnforschung, Universität Tübingen
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14
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Lerche H, Vezzani A, Beck H, Blümcke I, Weber Y, Elger C. [New developments in epileptogenesis and therapeutic perspectives]. Nervenarzt 2011; 82:978-85. [PMID: 21789691 DOI: 10.1007/s00115-011-3260-4] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Epileptogenesis describes the mechanisms of how epilepsies are generated. We have chosen four areas in which significant progress has been achieved in understanding epileptogenesis. Those are (1) inflammatory processes which play an increasingly important role for the generation of temporal lobe epilepsy with hippocampal sclerosis (TLE with HS), (2) disturbances of intrinsic properties of neuronal compartments, in particular acquired defects of ion channels of which those in dendrites are described here for TLE with HS, (3) epigenetic effects, which affect for example the methylation of promoters and secondarily can change the expression of specific genes in TLE with HS, and finally (4) the epileptogenesis of idiopathic epilepsies which are caused by inborn genetic alterations affecting mainly ion channels. Apart from aspects of basic research, we will describe clinical consequences and therapeutic perspectives.
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Affiliation(s)
- H Lerche
- Abt. Neurologie mit Schwerpunkt Epileptologie, Hertie-Institut für klinische Hirnforschung, Universitätsklinikum Tübingen, Hoppe-Seyler-Str. 3, 72076 Tübingen, Deutschland.
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15
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Knauer C, Weber Y, Steinwald V, Knauer K, Ludolph AC, Huber R. Palataler Myoklonus nach ischämischem Thalamusinsult. Akt Neurol 2009. [DOI: 10.1055/s-0029-1238597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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16
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Weber Y, Swoboda RK, Ernst JF. Sec20p-interacting proteins (Tip20p, Ufe1p) in the retrograde secretory pathway of the fungal pathogen Candida albicans. Mol Genet Genomics 2002; 268:468-76. [PMID: 12471444 DOI: 10.1007/s00438-002-0777-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [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: 07/05/2002] [Accepted: 10/16/2002] [Indexed: 10/27/2022]
Abstract
Sec20p is an essential Type-II membrane protein of the human fungal pathogen Candida albicans, which is thought to be involved in mediating retrograde vesicle traffic from the Golgi to the endoplasmic reticulum (ER). Using an epitope-tagged Sec20p we obtained evidence for its localization in ER membranes, which is consistent with its proposed role in an ER-tSNARE complex. Two genes encoding potential interaction partners for Sec20p, Tip20p and Ufe1p, were identified in genomic sequences of C. albicans; these show 18% and 27% identity, respectively, to homologues in Saccharomyces cerevisiae. An interaction between the cytoplasmic domain of Sec20p and Tip20p was demonstrated by two-hybrid analysis; in addition, Tip20p was found to form homodimers. Interaction between Sec20p and Tip20p in vivo was verified by co-immunoprecipation experiments. CaUFE1, which encodes a potential ER-tSNARE, was able to complement a thermosensitive ufe1 mutation in S. cerevisiae, suggesting functional conservation between the two fungal proteins. Thus, although the sequences of some components of the ER-tSNARE complex have diverged considerably during evolution, it appears that they have retained similar functions in C. albicans and S. cerevisiae.
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Affiliation(s)
- Y Weber
- Institut für Mikrobiologie, Heinrich-Heine-Universität, Universitätsstrasse 1, Geb. 26.12, 40225 Düsseldorf, Germany
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17
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Weber Y, Santore UJ, Ernst JF, Swoboda RK. Divergence of eukaryotic secretory components: the Candida albicans homolog of the Saccharomyces cerevisiae ++Sec20 protein is N terminally truncated, and its levels determine antifungal drug resistance and growth. J Bacteriol 2001; 183:46-54. [PMID: 11114899 PMCID: PMC94848 DOI: 10.1128/jb.183.1.46-54.2001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sec20p is a component of the yeast Saccharomyces cerevisiae secretory pathway that does not have a close homolog in higher eukaryotic cells. To verify the function of Sec20p in other fungal species, we characterized the gene encoding a Sec20p homolog in the human fungal pathogen Candida albicans. The deduced protein has 27% identity with, but is missing about 100 N-terminal residues compared to S. cerevisiae Sec20p, which is part of the cytoplasmic tail interacting with the cytoplasmic protein Tip20p. Because a strain lacking both C. albicans SEC20 alleles could not be constructed, we placed SEC20 under transcriptional control of two regulatable promoters, MET3p and PCK1p. Repression of SEC20 expression in these strains prevented (MET3p-SEC20 allele) or retarded (PCK1p-SEC20 allele) growth and led to the appearance of extensive intracellular membranes, which frequently formed stacks. Reduced SEC20 expression in the PCK1p-SEC20 strain did not affect morphogenesis but led to a series of hypersensitivity phenotypes including supersensitivity to aminoglycoside antibiotics, to nystatin, to sodium dodecyl sulfate, and to cell wall inhibitors. These results demonstrate the occurrence and function of Sec20p in a fungal species other than S. cerevisiae, but the lack of the N-terminal domain and the apparent absence of a close TIP20 homolog in the C. albicans genome also indicate a considerable diversity in mechanisms of retrograde vesicle traffic in eukaryotes.
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Affiliation(s)
- Y Weber
- Institut für Mikrobiologie, Heinrich-Heine-Universität, D-40225 Düsseldorf, Germany
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18
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Jacobs S, Schilf C, Fliegert F, Koling S, Weber Y, Schürmann A, Joost HG. ADP-ribosylation factor (ARF)-like 4, 6, and 7 represent a subgroup of the ARF family characterization by rapid nucleotide exchange and a nuclear localization signal. FEBS Lett 1999; 456:384-8. [PMID: 10462049 DOI: 10.1016/s0014-5793(99)00759-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The novel ARF-like GTPase ARL7 is a close relative of ARL4 and ARL6 (71% and 59%) identical amino acids). A striking characteristic of these GTPases is their basic C-terminus which, when fused to the C-terminus of green fluorescent protein (GFP), targets the constructs to the nucleus of transfected COS-7 cells. Full length ARL4 was detected in both nuclear and extranuclear compartments, whereas a construct of ARL4 lacking its C-terminus was excluded from the nucleus. Nucleotide exchange rates of recombinant ARL4, ARL6 and ARL7 were similar and appeared considerably higher than those of other members of the ARF family (ARF1, ARP). It is concluded that ARL4, ARL6 and ARL7 form a subgroup within the ARF family with similar, possibly nuclear, function.
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Affiliation(s)
- S Jacobs
- Institut für Pharmakologie und Toxikologie, Medizinische Fakultät der RWTH Aachen, Germany
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19
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Leder S, Weber Y, Altafaj X, Estivill X, Joost HG, Becker W. Cloning and characterization of DYRK1B, a novel member of the DYRK family of protein kinases. Biochem Biophys Res Commun 1999; 254:474-9. [PMID: 9918863 DOI: 10.1006/bbrc.1998.9967] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The DYRK1A gene on human chromosome 21 encodes a protein kinase presumed to be involved in the pathogenesis of mental retardation in Down's syndrome. Here we describe a highly similar homolog, DYRK1B, which is, in contrast to DYRK1A, predominately expressed in muscle and testis. The human DYRK1B gene was mapped to chromosome 19 (19q12-13.11) by radiation hybrid analysis. The amino acid sequences of DYRK1A and DYRK1B are 84% identical in the N-terminus and the catalytic domain but show no extended sequence similarity in the C-terminal region. DYRK1B contains all motifs characteristic for the DYRK family of protein kinases. In addition, the sequence comprises a bipartite nuclear localization motif. A green fluorescent protein (GFP) fusion protein of DYRK1B was found mainly in the nucleus of transfected COS-7 cells. These data suggest that DYRK1B is a muscle- and testis-specific isoform of DYRK1A and is involved in the regulation of nuclear functions.
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Affiliation(s)
- S Leder
- Institut für Pharmakologie und Toxikologie, RWTH Aachen, Aachen, D-52057, Germany
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20
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Becker W, Weber Y, Wetzel K, Eirmbter K, Tejedor FJ, Joost HG. Sequence characteristics, subcellular localization, and substrate specificity of DYRK-related kinases, a novel family of dual specificity protein kinases. J Biol Chem 1998; 273:25893-902. [PMID: 9748265 DOI: 10.1074/jbc.273.40.25893] [Citation(s) in RCA: 227] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DYRK1 is a dual specificity protein kinase presumably involved in brain development. Here we show that the kinase belongs to a new family of protein kinases comprising at least seven mammalian isoforms (DYRK1A, DYRK1B, DYRK1C, DYRK2, DYRK3, DYRK4A, and DYRK4B), the yeast homolog Yak1p, and the Drosophila kinase minibrain (MNB). In rat tissues, DYRK1A is expressed ubiquitously, whereas transcripts for DYRK1B, DYRK2, DYRK3, and DYRK4 were detected predominantly in testes of adult but not prepuberal rats. By fluorescence microscopy and subcellular fractionation, a green fluorescent protein (GFP) fusion protein of DYRK1A was found to accumulate in the nucleus of transfected COS-7 and HEK293 cells, whereas GFP-DYRK2 was predominantly detected in the cytoplasm. DYRK1A exhibited a punctate pattern of GFP fluorescence inside the nucleus and was co-purified with the nuclear matrix. Analysis of GFP-DYRK1A deletion constructs showed that the nuclear localization of DYRK1A was mediated by its nuclear targeting signal (amino acids 105-139) but that its characteristic subnuclear distribution depended on additional N-terminal elements (amino acids 1-104). When expressed in Escherichia coli, DYRK1A, DYRK2, DYRK3, MNB, and Yak1p catalyzed their autophosphorylation on tyrosine residues. The kinases differed in their substrate specificity in that DYRK2 and DYRK3, but not DYRK1A and MNB, catalyzed phosphorylation of histone H2B. The heterogeneity of their subcellular localization and substrate specificity suggests that the kinases are involved in different cellular functions.
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Affiliation(s)
- W Becker
- Institut für Pharmakologie und Toxikologie, RWTH Aachen, D-52057 Aachen, Germany
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21
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Steinberger D, Weber Y, Korinthenberg R, Deuschl G, Benecke R, Martinius J, Müller U. High penetrance and pronounced variation in expressivity of GCH1 mutations in five families with dopa-responsive dystonia. Ann Neurol 1998; 43:634-9. [PMID: 9585358 DOI: 10.1002/ana.410430512] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We performed a clinical and molecular genetic analysis in members of five families with dopa-responsive dystonia. Four mutations were detected in the gene GCH1 that codes for GTP cyclohydrolase I. Two of these mutations, a delG309 in exon 1 and a C544T transition in exon 5, have not been described before. They result in inactivation of the enzyme by truncation. The remaining two mutations, both A to G transitions, a(-2)g in intron 1 and a(-2)g in intron 2, cause truncation by abnormal splicing. The genotype of family members was correlated to their clinical phenotype (obtained before molecular analysis). Clinical symptoms observed in the families included generalized and focal dystonia, abnormal gait, and subtle signs such as an abnormal writing test. High penetrance (0.8-1.0) was observed in four of five families if minor symptoms and signs were considered. A given mutation was more likely to cause symptoms in females than in males, thus confirming the well-established higher incidence of dopa-responsive dystonia in females than in males.
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Affiliation(s)
- D Steinberger
- Institut für Humangenetik, Justus-Liebig-Universität, Giessen, Germany
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Weber Y, Steinberger D, Deuschl G, Benecke R, Müller U. Two previously unrecognized splicing mutations of GCH1 in Dopa-responsive dystonia: exon skipping and one base insertion. Neurogenetics 1997; 1:125-7. [PMID: 10732814 DOI: 10.1007/s100480050018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We describe two previously unrecognized splice site mutations of GCH1 in Dopa responsive dystonia (DRD). Both mutations affect consensus splice acceptor (AG) sites. The first mutation is an A-->G transition at position -2 of intron 1 of GCH1. This mutation results in skipping of exon 2. Fusion of exons 1 and 3 causes a frame shift that generates a premature stop codon. The second mutation is an A-->G transition at position -2 of intron 2. The mutation generates a new splice acceptor site AG one base pair upstream of the wild-type splice site. This, together with a pyrimidine stretch upstream of the new splice site, renders this site functional and generates a transcript with the insertion of one base, i.e. the G of the wild-type splice site. This in turn causes a frame shift including the introduction of a premature stop codon. The two different mutations generate truncated GTP cyclohydrolase polypeptides.
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Affiliation(s)
- Y Weber
- Institut für Humangenetik, Justus-Liebig-Universität, Giessen, Germany
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