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Klein T, Funke F, Rossbach O, Lehmann G, Vockenhuber M, Medenbach J, Suess B, Meister G, Babinger P. Investigating the Prevalence of RNA-Binding Metabolic Enzymes in E. coli. Int J Mol Sci 2023; 24:11536. [PMID: 37511294 PMCID: PMC10380284 DOI: 10.3390/ijms241411536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/07/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
An open research field in cellular regulation is the assumed crosstalk between RNAs, metabolic enzymes, and metabolites, also known as the REM hypothesis. High-throughput assays have produced extensive interactome data with metabolic enzymes frequently found as hits, but only a few examples have been biochemically validated, with deficits especially in prokaryotes. Therefore, we rationally selected nineteen Escherichia coli enzymes from such datasets and examined their ability to bind RNAs using two complementary methods, iCLIP and SELEX. Found interactions were validated by EMSA and other methods. For most of the candidates, we observed no RNA binding (12/19) or a rather unspecific binding (5/19). Two of the candidates, namely glutamate-5-kinase (ProB) and quinone oxidoreductase (QorA), displayed specific and previously unknown binding to distinct RNAs. We concentrated on the interaction of QorA to the mRNA of yffO, a grounded prophage gene, which could be validated by EMSA and MST. Because the physiological function of both partners is not known, the biological relevance of this interaction remains elusive. Furthermore, we found novel RNA targets for the MS2 phage coat protein that served us as control. Our results indicate that RNA binding of metabolic enzymes in procaryotes is less frequent than suggested by the results of high-throughput studies, but does occur.
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Affiliation(s)
- Thomas Klein
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Franziska Funke
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Oliver Rossbach
- Institute of Biochemistry, Faculty of Biology and Chemistry, University of Giessen, D-35392 Giessen, Germany
| | - Gerhard Lehmann
- Institute of Biochemistry, Genetics and Microbiology, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Michael Vockenhuber
- Centre for Synthetic Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Jan Medenbach
- Institute of Biochemistry, Genetics and Microbiology, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Beatrix Suess
- Centre for Synthetic Biology, Technical University of Darmstadt, D-64287 Darmstadt, Germany
| | - Gunter Meister
- Institute of Biochemistry, Genetics and Microbiology, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
| | - Patrick Babinger
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, D-93040 Regensburg, Germany
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Hirner H, Günes C, Bischof J, Wolff S, Grothey A, Kühl M, Oswald F, Wegwitz F, Bösl MR, Trauzold A, Henne-Bruns D, Peifer C, Leithäuser F, Deppert W, Knippschild U. Impaired CK1 delta activity attenuates SV40-induced cellular transformation in vitro and mouse mammary carcinogenesis in vivo. PLoS One 2012; 7:e29709. [PMID: 22235331 PMCID: PMC3250488 DOI: 10.1371/journal.pone.0029709] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2011] [Accepted: 12/01/2011] [Indexed: 02/05/2023] Open
Abstract
Simian virus 40 (SV40) is a powerful tool to study cellular transformation in vitro, as well as tumor development and progression in vivo. Various cellular kinases, among them members of the CK1 family, play an important role in modulating the transforming activity of SV40, including the transforming activity of T-Ag, the major transforming protein of SV40, itself. Here we characterized the effects of mutant CK1δ variants with impaired kinase activity on SV40-induced cell transformation in vitro, and on SV40-induced mammary carcinogenesis in vivo in a transgenic/bi-transgenic mouse model. CK1δ mutants exhibited a reduced kinase activity compared to wtCK1δ in in vitro kinase assays. Molecular modeling studies suggested that mutation N172D, located within the substrate binding region, is mainly responsible for impaired mutCK1δ activity. When stably over-expressed in maximal transformed SV-52 cells, CK1δ mutants induced reversion to a minimal transformed phenotype by dominant-negative interference with endogenous wtCK1δ. To characterize the effects of CK1δ on SV40-induced mammary carcinogenesis, we generated transgenic mice expressing mutant CK1δ under the control of the whey acidic protein (WAP) gene promoter, and crossed them with SV40 transgenic WAP-T-antigen (WAP-T) mice. Both WAP-T mice as well as WAP-mutCK1δ/WAP-T bi-transgenic mice developed breast cancer. However, tumor incidence was lower and life span was significantly longer in WAP-mutCK1δ/WAP-T bi-transgenic animals. The reduced CK1δ activity did not affect early lesion formation during tumorigenesis, suggesting that impaired CK1δ activity reduces the probability for outgrowth of in situ carcinomas to invasive carcinomas. The different tumorigenic potential of SV40 in WAP-T and WAP-mutCK1δ/WAP-T tumors was also reflected by a significantly different expression of various genes known to be involved in tumor progression, specifically of those involved in wnt-signaling and DNA repair. Our data show that inactivating mutations in CK1δ impair SV40-induced cellular transformation in vitro and mouse mammary carcinogenesis in vivo.
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MESH Headings
- Animals
- Antigens, Viral, Tumor/immunology
- Casein Kinase Idelta/chemistry
- Casein Kinase Idelta/genetics
- Casein Kinase Idelta/metabolism
- Cell Line
- Cell Line, Tumor
- Cell Transformation, Viral/genetics
- Disease Progression
- Female
- Gene Expression Regulation
- Male
- Mammary Glands, Animal/metabolism
- Mammary Glands, Animal/pathology
- Mammary Glands, Animal/virology
- Mammary Neoplasms, Experimental/enzymology
- Mammary Neoplasms, Experimental/genetics
- Mammary Neoplasms, Experimental/pathology
- Mammary Neoplasms, Experimental/virology
- Mice
- Mice, Inbred BALB C
- Mice, Transgenic
- Milk Proteins/genetics
- Models, Molecular
- Mutation
- Phenotype
- Phosphorylation
- Promoter Regions, Genetic/genetics
- Protein Structure, Tertiary
- Simian virus 40/immunology
- Simian virus 40/physiology
- Survival Analysis
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Affiliation(s)
- Heidrun Hirner
- Department of General-, Visceral- and Transplantation Surgery, University of Ulm, Ulm, Germany
| | - Cagatay Günes
- Institute of Molecular Medicine and Max-Planck-Research Group on Stem Cell Aging, University of Ulm, Ulm, Germany
| | - Joachim Bischof
- Department of General-, Visceral- and Transplantation Surgery, University of Ulm, Ulm, Germany
| | - Sonja Wolff
- Department of General-, Visceral- and Transplantation Surgery, University of Ulm, Ulm, Germany
| | - Arnhild Grothey
- Department of General-, Visceral- and Transplantation Surgery, University of Ulm, Ulm, Germany
| | - Marion Kühl
- Department of Tumor Virology, Heinrich-Pette-Institute, Leibniz-Center for Experimental Virology, Hamburg, Germany
| | - Franz Oswald
- Department of Internal Medicine I, University of Ulm, Ulm, Germany
| | - Florian Wegwitz
- Department of Tumor Virology, Heinrich-Pette-Institute, Leibniz-Center for Experimental Virology, Hamburg, Germany
| | - Michael R. Bösl
- Max Planck Institute of Neurobiology Transgenic Mouse Models, Max Planck Institute, Martinsried, Germany
| | - Anna Trauzold
- Division of Molecular Oncology, Institute for Experimental Cancer Research, CCCNorth, UK S-H, Kiel, Germany
| | - Doris Henne-Bruns
- Department of General-, Visceral- and Transplantation Surgery, University of Ulm, Ulm, Germany
| | | | | | - Wolfgang Deppert
- Department of Tumor Virology, Heinrich-Pette-Institute, Leibniz-Center for Experimental Virology, Hamburg, Germany
| | - Uwe Knippschild
- Department of General-, Visceral- and Transplantation Surgery, University of Ulm, Ulm, Germany
- * E-mail:
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Schiltz E, Burger S, Grafmüller R, Deppert WR, Haehnel W, Wagner E. Primary structure of maize chloroplast adenylate kinase. EUROPEAN JOURNAL OF BIOCHEMISTRY 1994; 222:949-54. [PMID: 8026505 DOI: 10.1111/j.1432-1033.1994.tb18944.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
This paper describes the sequence of adenylate kinase (Mg-ATP+AMP<-->Mg-ADP+ADP) from maize chloroplasts. This light-inducible enzyme is important for efficient CO2 fixation in the C4 cycle, by removing and recycling AMP produced in the reversible pyruvate phosphate dikinase reaction. The complete sequence was determined by analyzing peptides from cleavages with trypsin, AspN protease and CNBr and subcleavage of a major CNBr peptide with chymotrypsin. N-terminal Edman degradation and carboxypeptidase digestion established the terminal residues. Electrospray mass spectrometry confirmed the final sequence of 222 residues (M(r) = 24867) including one cysteine and one tryptophan. The sequence shows this enzyme to be a long-variant-type adenylate kinase, the nearest relatives being adenylate kinases from Enterobacteriaceae. Alignment of the sequence with the adenylate kinase from Escherichia coli reveals 44% identical residues. Since the E. coli structure has been published recently at 0.19-nm resolution with the inhibitor adenosine(5')pentaphospho(5')adenosine (Ap5A) [Müller, C. W. & Schulz, G. E. (1992) J. Mol. Biol. 224, 159-177], catalytically essential residues could be compared and were found to be mostly conserved. Surprisingly, in the nucleotide-binding Gly-rich loop Gly-Xaa-Pro-Gly-Xaa-Gly-Lys the middle Gly is replaced by Ala. This is, however, compensated by an Ile-->Val exchange in the nearest spatial neighborhood. A Thr-->Ala exchange explains the unusual tolerance of the enzyme for pyrimidine nucleotides in the acceptor site.
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Affiliation(s)
- E Schiltz
- Institut für Organische Chemie und Biochemie, Universität Freiburg i. Br., Germany
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