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Shang R, Kretov DA, Adamson SI, Treiber T, Treiber N, Vedanayagam J, Chuang J, Meister G, Cifuentes D, Lai E. Regulated dicing of pre-mir-144 via reshaping of its terminal loop. Nucleic Acids Res 2022; 50:7637-7654. [PMID: 35801921 PMCID: PMC9303283 DOI: 10.1093/nar/gkac568] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/10/2022] [Accepted: 06/18/2022] [Indexed: 11/17/2022] Open
Abstract
Although the route to generate microRNAs (miRNAs) is often depicted as a linear series of sequential and constitutive cleavages, we now appreciate multiple alternative pathways as well as diverse strategies to modulate their processing and function. Here, we identify an unusually profound regulatory role of conserved loop sequences in vertebrate pre-mir-144, which are essential for its cleavage by the Dicer RNase III enzyme in human and zebrafish models. Our data indicate that pre-mir-144 dicing is positively regulated via its terminal loop, and involves the ILF3 complex (NF90 and its partner NF45/ILF2). We provide further evidence that this regulatory switch involves reshaping of the pre-mir-144 apical loop into a structure that is appropriate for Dicer cleavage. In light of our recent findings that mir-144 promotes the nuclear biogenesis of its neighbor mir-451, these data extend the complex hierarchy of nuclear and cytoplasmic regulatory events that can control the maturation of clustered miRNAs.
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Affiliation(s)
- Renfu Shang
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA
| | - Dmitry A Kretov
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Scott I Adamson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Thomas Treiber
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Nora Treiber
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Jeffrey Vedanayagam
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Daniel Cifuentes
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Eric C Lai
- To whom correspondence should be addressed. Tel: +1 212 639 5578; Fax: +1 212 717 3604;
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2
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Gaza A, Fritz V, Malek L, Wormser L, Treiber N, Danner J, Kremer AE, Thasler WE, Siebler J, Meister G, Neurath MF, Hellerbrand C, Bosserhoff AK, Dietrich P. Identification of novel targets of miR-622 in hepatocellular carcinoma reveals common regulation of cooperating genes and outlines the oncogenic role of zinc finger CCHC-type containing 11. Neoplasia 2021; 23:502-514. [PMID: 33901943 PMCID: PMC8099721 DOI: 10.1016/j.neo.2021.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 12/26/2022] Open
Abstract
The poor prognosis of advanced hepatocellular carcinoma (HCC) is driven by diverse features including dysregulated microRNAs inducing drug resistance and stemness. Lin-28 homolog A (LIN28A) and its partner zinc finger CCHC-type containing 11 (ZCCHC11) cooperate in binding, oligouridylation and subsequent degradation of tumorsuppressive let-7 precursor microRNAs. Functionally, activation of LIN28A was recently shown to promote stemness and chemoresistance in HCC. However, the expression and regulation of LIN28A in HCC had been unclear. Moreover, the expression, regulation and function of ZCCHC11 in liver cancer remained elusive. In contrast to "one-microRNA-one-target" interactions, we identified common binding sites for miR-622 in both LIN28A and ZCCHC11, suggesting miR-622 to function as a superior pathway regulator. Applying comprehensive microRNA database screening, human hepatocytes and HCC cell lines, patient-derived tissue samples as well as "The Cancer Genome Atlas" (TCGA) patient cohorts, we demonstrated that loss of tumorsuppressive miR-622 mediates derepression and overexpression of LIN28A in HCC. Moreover, the cooperator of LIN28A, ZCCHC11, was newly identified as a prognostic and therapeutic target of miR-622 in liver cancer. Together, identification of novel miR-622 target genes revealed common regulation of cooperating genes and outlines the previously unknown oncogenic role of ZCCHC11 in liver cancer.
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Affiliation(s)
- Anne Gaza
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen, Germany
| | - Valerie Fritz
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Lara Malek
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Laura Wormser
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Nora Treiber
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, Germany
| | - Johannes Danner
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, Germany
| | - Andreas E Kremer
- Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen, Germany
| | - Wolfgang E Thasler
- Department of General and Visceral Surgery, Red Cross Hospital of Munich, Germany
| | - Jürgen Siebler
- Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, Germany
| | - Markus F Neurath
- Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen, Germany; Comprehensive Cancer Center (CCC) Erlangen-EMN, Erlangen, Germany
| | - Claus Hellerbrand
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center (CCC) Erlangen-EMN, Erlangen, Germany
| | - Anja K Bosserhoff
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center (CCC) Erlangen-EMN, Erlangen, Germany
| | - Peter Dietrich
- Institute of Biochemistry, Emil-Fischer-Zentrum, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Department of Medicine, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany; Deutsches Zentrum für Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and University Hospital Erlangen, Erlangen, Germany.
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3
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de Gregorio A, Huober J, Widschwendter P, Swerev T, Bauer E, Schochter F, Janni W, Koretz K, Lormes E, Treiber N, de Gregorio N. Auftreten eines fortgeschrittenen Ovarialkarzinoms unter laufender Therapie mit Pembrolizumab für ein metastasiertes Bindehautmelanom. Geburtshilfe Frauenheilkd 2019. [DOI: 10.1055/s-0039-1693897] [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: 10/26/2022] Open
Affiliation(s)
| | | | | | | | - E Bauer
- Universitätsfrauenklinik Ulm
| | | | - W Janni
- Universitätsfrauenklinik Ulm
| | - K Koretz
- Institut für Pathologie, Universitätsklinikum Ulm
| | - E Lormes
- Klinik für Dermatologie, Universitätsklinikum Ulm
| | - N Treiber
- Klinik für Dermatologie, Universitätsklinikum Ulm
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Schäfer P, Tüting C, Schönemann L, Kühn U, Treiber T, Treiber N, Ihling C, Graber A, Keller W, Meister G, Sinz A, Wahle E. Reconstitution of mammalian cleavage factor II involved in 3' processing of mRNA precursors. RNA 2018; 24:1721-1737. [PMID: 30139799 PMCID: PMC6239180 DOI: 10.1261/rna.068056.118] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 08/17/2018] [Indexed: 05/05/2023]
Abstract
Cleavage factor II (CF II) is a poorly characterized component of the multiprotein complex catalyzing 3' cleavage and polyadenylation of mammalian mRNA precursors. We have reconstituted CF II as a heterodimer of hPcf11 and hClp1. The heterodimer is active in partially reconstituted cleavage reactions, whereas hClp1 by itself is not. Pcf11 moderately stimulates the RNA 5' kinase activity of hClp1; the kinase activity is dispensable for RNA cleavage. CF II binds RNA with nanomolar affinity. Binding is mediated mostly by the two zinc fingers in the C-terminal region of hPcf11. RNA is bound without pronounced sequence-specificity, but extended G-rich sequences appear to be preferred. We discuss the possibility that CF II contributes to the recognition of cleavage/polyadenylation substrates through interaction with G-rich far-downstream sequence elements.
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Affiliation(s)
- Peter Schäfer
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Christian Tüting
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Lars Schönemann
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Uwe Kühn
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Thomas Treiber
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Nora Treiber
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Christian Ihling
- Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Anne Graber
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Walter Keller
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Gunter Meister
- Biochemistry Center Regensburg, Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Andrea Sinz
- Institute of Pharmacy, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
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6
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Ustianenko D, Chiu HS, Treiber T, Weyn-Vanhentenryck SM, Treiber N, Meister G, Sumazin P, Zhang C. LIN28 Selectively Modulates a Subclass of Let-7 MicroRNAs. Mol Cell 2018; 71:271-283.e5. [PMID: 30029005 PMCID: PMC6238216 DOI: 10.1016/j.molcel.2018.06.029] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [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: 10/03/2017] [Revised: 04/27/2018] [Accepted: 06/19/2018] [Indexed: 02/06/2023]
Abstract
LIN28 is a bipartite RNA-binding protein that post-transcriptionally inhibits the biogenesis of let-7 microRNAs to regulate development and influence disease states. However, the mechanisms of let-7 suppression remain poorly understood because LIN28 recognition depends on coordinated targeting by both the zinc knuckle domain (ZKD), which binds a GGAG-like element in the precursor, and the cold shock domain (CSD), whose binding sites have not been systematically characterized. By leveraging single-nucleotide-resolution mapping of LIN28 binding sites in vivo, we determined that the CSD recognizes a (U)GAU motif. This motif partitions the let-7 microRNAs into two subclasses, precursors with both CSD and ZKD binding sites (CSD+) and precursors with ZKD but no CSD binding sites (CSD-). LIN28 in vivo recognition-and subsequent 3' uridylation and degradation-of CSD+ precursors is more efficient, leading to their stronger suppression in LIN28-activated cells and cancers. Thus, CSD binding sites amplify the regulatory effects of LIN28.
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Affiliation(s)
- Dmytro Ustianenko
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Hua-Sheng Chiu
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Thomas Treiber
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Sebastien M Weyn-Vanhentenryck
- Department of Systems Biology, Columbia University, New York, NY 10032, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Nora Treiber
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Pavel Sumazin
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Chaolin Zhang
- Department of Systems Biology, Columbia University, New York, NY 10032, USA.
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7
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Basu A, Munir S, Mulaw M, Singh K, Herold B, Crisan D, Sindrilaru A, Treiber N, Wlaschek M, Huber-Lang M, Gebhard F, Scharffetter-Kochanek K. 1422 A novel S100A8/A9 induced fingerprint of mesenchymal stem cells is associated with enhanced wound healing. J Invest Dermatol 2018. [DOI: 10.1016/j.jid.2018.03.1440] [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: 10/17/2022]
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8
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Schöller E, Weichmann F, Treiber T, Ringle S, Treiber N, Flatley A, Feederle R, Bruckmann A, Meister G. Interactions, localization, and phosphorylation of the m 6A generating METTL3-METTL14-WTAP complex. RNA 2018; 24:499-512. [PMID: 29348140 PMCID: PMC5855951 DOI: 10.1261/rna.064063.117] [Citation(s) in RCA: 265] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/03/2018] [Indexed: 05/04/2023]
Abstract
N6-methyladenine (m6A) is found on many eukaryotic RNAs including mRNAs. m6A modification has been implicated in mRNA stability and turnover, localization, or translation efficiency. A heterodimeric enzyme complex composed of METTL3 and METTL14 generates m6A on mRNAs. METTL3/14 is found in the nucleus where it is localized to nuclear speckles and the splicing regulator WTAP is required for this distinct nuclear localization pattern. Although recent crystal structures revealed how the catalytic MT-A70 domains of METTL3 and METTL14 interact with each other, a more global architecture including WTAP and RNA interactions has not been reported so far. Here, we used recombinant proteins and mapped binding surfaces within the METTL3/14-WTAP complex. Furthermore, we identify nuclear localization signals and identify phosphorylation sites on the endogenous proteins. Using an in vitro methylation assay, we confirm that monomeric METTL3 is soluble and inactive while the catalytic center of METTL14 is degenerated and thus also inactive. In addition, we show that the C-terminal RGG repeats of METTL14 are required for METTL3/14 activity by contributing to RNA substrate binding. Our biochemical work identifies characteristic features of METTL3/14-WTAP and reveals novel insight into the overall architecture of this important enzyme complex.
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Affiliation(s)
- Eva Schöller
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Franziska Weichmann
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Thomas Treiber
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Sam Ringle
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Nora Treiber
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Andrew Flatley
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute for Diabetes and Obesity, Monoclonal Antibody Core Facility and Research Group, 85764 Neuherberg, Germany
| | - Regina Feederle
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute for Diabetes and Obesity, Monoclonal Antibody Core Facility and Research Group, 85764 Neuherberg, Germany
| | - Astrid Bruckmann
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
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9
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Abstract
MicroRNA (miRNA) biogenesis is regulated intricately at multiple levels. In addition to transcriptional control of pri-miRNA loci, sequence as well as structural features of the pri-miRNA-stem loop determine its processing efficiency by the endonucleases Drosha and Dicer. On the one hand, general features are necessary to allow a hairpin to be recognized by the processing machinery; on the other hand, specific sequence motifs of individual miRNA precursors can be read by RNA binding proteins (RBPs) that regulate processing, leading to increased or decreased levels of functional miRNAs. In a pulldown experiment using the pri-miRNA hairpin as immobilized bait, cognate RBPs can be isolated and analyzed by immunoblotting or mass spectrometry, allowing for the discovery or analysis of protein regulators of miRNA biogenesis.
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Affiliation(s)
- Thomas Treiber
- Laboratory for RNA Biology, Biochemistry Center Regensburg (BZR), University of Regensburg, Regensburg, Germany
| | - Nora Treiber
- Laboratory for RNA Biology, Biochemistry Center Regensburg (BZR), University of Regensburg, Regensburg, Germany
| | - Gunter Meister
- Laboratory for RNA Biology, Biochemistry Center Regensburg (BZR), University of Regensburg, Regensburg, Germany.
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10
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Treiber T, Treiber N, Plessmann U, Harlander S, Daiß JL, Eichner N, Lehmann G, Schall K, Urlaub H, Meister G. A Compendium of RNA-Binding Proteins that Regulate MicroRNA Biogenesis. Mol Cell 2017; 66:270-284.e13. [PMID: 28431233 DOI: 10.1016/j.molcel.2017.03.014] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 12/22/2016] [Accepted: 03/20/2017] [Indexed: 12/19/2022]
Abstract
During microRNA (miRNA) biogenesis, two endonucleolytic reactions convert stem-loop-structured precursors into mature miRNAs. These processing steps can be posttranscriptionally regulated by RNA-binding proteins (RBPs). Here, we have used a proteomics-based pull-down approach to map and characterize the interactome of a multitude of pre-miRNAs. We identify ∼180 RBPs that interact specifically with distinct pre-miRNAs. For functional validation, we combined RNAi and CRISPR/Cas-mediated knockout experiments to analyze RBP-dependent changes in miRNA levels. Indeed, a large number of the investigated candidates, including splicing factors and other mRNA processing proteins, have effects on miRNA processing. As an example, we show that TRIM71/LIN41 is a potent regulator of miR-29a processing and its inactivation directly affects miR-29a targets. We provide an extended database of RBPs that interact with pre-miRNAs in extracts of different cell types, highlighting a widespread layer of co- and posttranscriptional regulation of miRNA biogenesis.
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Affiliation(s)
- Thomas Treiber
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Nora Treiber
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Uwe Plessmann
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute of Biophysical Chemistry, 37077 Göttingen, Germany
| | - Simone Harlander
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Julia-Lisa Daiß
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Norbert Eichner
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Gerhard Lehmann
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Kevin Schall
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max-Planck-Institute of Biophysical Chemistry, 37077 Göttingen, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany.
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11
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Crisan D, Gülke J, Janetzko C, Kastler S, Treiber N, Scharffetter-Kochanek K, Schneider LA. Digit preserving surgery of subungual melanoma: a case series using vacuum assisted closure and full-thickness skin grafting. J Eur Acad Dermatol Venereol 2017; 31:e537-e538. [PMID: 28609554 DOI: 10.1111/jdv.14400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- D Crisan
- Department of Dermatology & Allergology, University of Ulm Albert Einstein Allee 23, D89081 Ulm, Germany
| | - J Gülke
- Section of Hand and Plastic Surgery, University of Ulm Albert Einstein Allee 23, D89081 Ulm, Germany
| | - C Janetzko
- Department of Dermatology & Allergology, University of Ulm Albert Einstein Allee 23, D89081 Ulm, Germany
| | - S Kastler
- Department of Dermatology & Allergology, University of Ulm Albert Einstein Allee 23, D89081 Ulm, Germany
| | - N Treiber
- Department of Dermatology & Allergology, University of Ulm Albert Einstein Allee 23, D89081 Ulm, Germany
| | - K Scharffetter-Kochanek
- Department of Dermatology & Allergology, University of Ulm Albert Einstein Allee 23, D89081 Ulm, Germany
| | - L A Schneider
- Department of Dermatology and Dermatosurgery, Helios Hospital Rottweil, Krankenhausstr. 30, D78628, Rottweil, Germany
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Crisan D, Scharffetter-Kochanek K, Dummer R, Treiber N, Sindrilaru A, Kastler S, Schneider LA. Beware when the hair turns dark again: clinical presentation and management of melanoma in situ in a giant congenital naevus on the scalp. J Eur Acad Dermatol Venereol 2016; 31:e226-e228. [PMID: 27878885 DOI: 10.1111/jdv.14055] [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: 12/01/2022]
Affiliation(s)
- D Crisan
- Klinik für Dermatologie und Allergologie, Universitätsklinikum Ulm, Albert Einstein Allee 23, 89081, Ulm, Germany
| | - K Scharffetter-Kochanek
- Klinik für Dermatologie und Allergologie, Universitätsklinikum Ulm, Albert Einstein Allee 23, 89081, Ulm, Germany
| | - R Dummer
- Dermatologische Klinik, Universitätsspital Zürich, Rämistraße 100, Ch8006, Zürich, Schweiz
| | - N Treiber
- Klinik für Dermatologie und Allergologie, Universitätsklinikum Ulm, Albert Einstein Allee 23, 89081, Ulm, Germany
| | - A Sindrilaru
- Klinik für Dermatologie und Allergologie, Universitätsklinikum Ulm, Albert Einstein Allee 23, 89081, Ulm, Germany
| | - S Kastler
- Klinik für Dermatologie und Allergologie, Universitätsklinikum Ulm, Albert Einstein Allee 23, 89081, Ulm, Germany
| | - L A Schneider
- Klinik für Dermatologie und Allergologie, Universitätsklinikum Ulm, Albert Einstein Allee 23, 89081, Ulm, Germany.,Helios Klinikum Rottweil, Klinik für Dermatologie und Dermatochirurgie, Krankenhausstr. 30, D-78628, Rottweil, Germany
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Jakob L, Treiber T, Treiber N, Gust A, Kramm K, Hansen K, Stotz M, Wankerl L, Herzog F, Hannus S, Grohmann D, Meister G. Structural and functional insights into the fly microRNA biogenesis factor Loquacious. RNA 2016; 22:383-396. [PMID: 26769856 PMCID: PMC4748816 DOI: 10.1261/rna.055426.115] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 12/02/2015] [Indexed: 06/05/2023]
Abstract
In the microRNA (miRNA) pathway, Dicer processes precursors to mature miRNAs. For efficient processing, double-stranded RNA-binding proteins support Dicer proteins. In flies, Loquacious (Loqs) interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. Here, we have solved the structure of the third double-stranded RNA-binding domain (dsRBD) of Loqs and define specific structural elements that interact with dmDcr1. In addition, we show that the linker preceding dsRBD3 contributes significantly to dmDcr1 binding. Furthermore, our structural work demonstrates that the third dsRBD of Loqs forms homodimers. Mutations in the dimerization interface abrogate dmDcr1 interaction. Loqs, however, binds to dmDcr1 as a monomer using the identified dimerization surface, which suggests that Loqs might form dimers under conditions where dmDcr1 is absent or not accessible. Since critical sequence elements are conserved, we suggest that dimerization might be a general feature of dsRBD proteins in gene silencing.
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Affiliation(s)
- Leonhard Jakob
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Thomas Treiber
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Nora Treiber
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Alexander Gust
- Department of Microbiology and Archaea Centre, Laboratory of Single-Molecule Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Kevin Kramm
- Department of Microbiology and Archaea Centre, Laboratory of Single-Molecule Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Kerrin Hansen
- Intana Bioscience GmbH, 82152 Planegg, Martinsried, Germany
| | - Mathias Stotz
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Ludwig Wankerl
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Franz Herzog
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University, 81377 München, Germany
| | - Stefan Hannus
- Intana Bioscience GmbH, 82152 Planegg, Martinsried, Germany
| | - Dina Grohmann
- Department of Microbiology and Archaea Centre, Laboratory of Single-Molecule Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Gunter Meister
- Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
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Schneider LA, Weiss T, Kastler S, Barth T, Crisan D, Psotta Schachtner C, Treiber N, Bottke D, Mayer-Steinacker R. Interdisziplinäre onkologische Versorgung eines Patienten mit Angiosarkom des Nasensattels und mechanischer Herzklappe. Akt Dermatol 2015. [DOI: 10.1055/s-0035-1558605] [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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15
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Schneider LA, Eigentler T, Crisan D, Neckermann V, Kampilafkos P, Sindrilaru A, Scharffetter-Kochanek K, Treiber N. Erkennungshäufigkeit und Zeitraster bei der Erkennung von Melanomen durch den Patienten selbst und was bedeutet das für den Chirurgen? Akt Dermatol 2015. [DOI: 10.1055/s-0035-1558619] [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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16
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Scheurmann J, Treiber N, Weber C, Renkl AC, Frenzel D, Trenz-Buback F, Ruess A, Schulz G, Scharffetter-Kochanek K, Weiss JM. Mice with heterozygous deficiency of manganese superoxide dismutase (SOD2) have a skin immune system with features of "inflamm-aging". Arch Dermatol Res 2013; 306:143-55. [PMID: 23856836 DOI: 10.1007/s00403-013-1389-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 06/24/2013] [Accepted: 06/28/2013] [Indexed: 01/10/2023]
Abstract
Dendritic cells (DC) are central in regulating skin immunity. Immunosenescence is associated with a chronic inflammatory state. Little is known about the contribution of DC to "inflamm-aging". When determining langerhans cell (LC) numbers, we found a 60 % reduction of LC in aged epidermis. Reactive oxygen species(ROS) are linked with aging. The mitochondrial manganese superoxide dismutase (SOD2) is in the first line of antioxidant defense. We investigated the function of DC from SOD2 heterozygous mice (SOD2+/-) and found that at 4 months of age LC numbers are not altered, but activated LC have impaired expression of MHC-II and CD44. Immature SOD2+/- DC produced increased proinflammatory IL-6 and chemokines CXCL1 and CXCL2. Upon challenge SOD2+/- DC accumulated ROS. When activating SOD2+/- DC by LPS they less efficiently upregulated MHC-II, CD86 and CD44. Surprisingly, in vivo contact hypersensitivity (CHS) was enhanced in SOD2+/- mice although SOD2+/- DC were less potent in stimulating wt T cells. However, SOD2+/- T cells showed increased proliferation, even when stimulated with SOD2+/- DC, possibly explaining the increased CHS. Our findings suggest that SOD2 is a molecular candidate in the regulation of "inflamm-aging" conveying both immunosuppressive and proinflammatory signals through alteration of DC and T cell functions.
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Affiliation(s)
- J Scheurmann
- Department of Dermatology and Allergology, University of Ulm, Albert-Einstein-Allee 23, 89081, Ulm, Germany
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17
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Treiber T, Treiber N, Meister G. Regulation of microRNA biogenesis and function. Thromb Haemost 2012; 107:605-10. [PMID: 22318703 DOI: 10.1160/th11-12-0836] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 01/11/2012] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are considered as key regulators of literally all cellular pathways. Therefore, miRNA biosynthesis and their individual cellular functions must be tightly regulated as well. MiRNAs are transcribed as primary transcripts, which are processed to mature miRNAs in two consecutive maturation steps. Finally, the mature miRNA is incorporated into a miRNA-protein complex, where it directly interacts with a member of the Argonaute (Ago) protein family. The miRNA guides such protein complexes to partial complementary target sites, which are typically located in the 3' untranslated region (UTR) of mRNAs leading to inhibition of gene expression. MiRNA activity and abundance is regulated on various levels ranging from transcription and processing to target site binding and miRNA stability. Recent advances in our understanding of how miRNA activity is regulated in mammalian cells are summarised and discussed in this review article.
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Affiliation(s)
- T Treiber
- Gunter Meister, Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
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18
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Richters L, Lange N, Renner R, Treiber N, Ghanem A, Tiemann K, Scharffetter-Kochanek K, Bloch W, Brixius K. Exercise-induced adaptations of cardiac redox homeostasis and remodeling in heterozygous SOD2-knockout mice. J Appl Physiol (1985) 2011; 111:1431-40. [DOI: 10.1152/japplphysiol.01392.2010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A reduced expression of the manganese-dependent superoxide dismutase (SOD2) is characterized by increased cardiac oxidative stress. Oxidative stress has also been described in situations of physical exercise. We investigated the influence of physical exercise (EX; treadmill 1 h/day at 15 m/min, 5 days/wk, at an angle of 5° for a duration of 8 wk) on cardiac function [heart frequency (HF), echocardiography, morphometry], oxidative stress [reactive oxygen species (ROS)], and antioxidative defence capacity (peroxiredoxin 1–6) in male SOD2-knockout (SOD2_EX) and wild-type mice (WT_EX) compared with untrained age-matched animals (WT_CON; SOD2_CON). In SOD2_CON, heart weight, cardiomyocyte diameter, and cardiac ROS were significantly larger and peroxiredoxin isoforms 4–6 lower than in WT_CON. The vessel-to-cardiomyocyte ratio, cardiac VEGF-concentration, and cardiac function were similar in SOD2_CON and WT_CON. Both groups tolerated the exercise protocol well. In WT, exercise significantly increased vessel-to-cardiomyocyte ratio and ROS-generation and downregulated peroxiredoxin isoforms 4–6 and VEGF generation. The vessel-to-cardiomyocyte ratio, cardiac VEGF concentration, and cardiac ROS were not altered in SOD2_EX compared with SOD2_CON, but a significant upregulation of cardiac peroxiredoxin 1 and 4 was observed. Similar to the result observed in WT_EX, peroxiredoxin 3 was upregulated in SOD2_EX. Chronic exercise shifted the (mal)adaptive hypertrophic into a compensated dilated cardiac phenotype in SOD2_EX. In conclusion, downregulation of SOD2 induces a maladaptive cardiac hypertrophy. In this situation, physical exercise results in a further deterioration of cardiac remodeling despite an upregulation of the antioxidative defense system.
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Affiliation(s)
- L. Richters
- Department of Molecular and Cellular Sport Medicine, Institute of Cardiology and Sport Medicine, German Sport University Cologne, Cologne
- Department of Obstetrics and Gynecology, University Hospital of Cologne, Cologne, Germany
| | - N. Lange
- Department of Molecular and Cellular Sport Medicine, Institute of Cardiology and Sport Medicine, German Sport University Cologne, Cologne
- Department of Obstetrics and Gynecology, University Hospital of Cologne, Cologne, Germany
| | - R. Renner
- Department of Molecular and Cellular Sport Medicine, Institute of Cardiology and Sport Medicine, German Sport University Cologne, Cologne
| | - N. Treiber
- Department of Dermatology and Allergology, University of Ulm, Ulm
| | - A. Ghanem
- Clinic and Policlinic II, University of Bonn, Bonn
| | - K. Tiemann
- University Hospital of Muenster, Department of Cardiology and Angiology, Muenster; and
| | | | - W. Bloch
- Department of Molecular and Cellular Sport Medicine, Institute of Cardiology and Sport Medicine, German Sport University Cologne, Cologne
| | - K. Brixius
- Department of Molecular and Cellular Sport Medicine, Institute of Cardiology and Sport Medicine, German Sport University Cologne, Cologne
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Treiber N, Treiber T, Zocher G, Grosschedl R. Structure of an Ebf1:DNA complex reveals unusual DNA recognition and structural homology with Rel proteins. Genes Dev 2010; 24:2270-5. [PMID: 20876732 DOI: 10.1101/gad.1976610] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Early B-cell factor 1 (Ebf1) is a key transcriptional determinant of B-lymphocyte differentiation whose DNA-binding domain has no sequence similarity to other transcription factor families. Here we report the crystal structure of an Ebf1 dimer bound to its palindromic recognition site. The DNA-binding domain adopts a pseudoimmunoglobulin-like fold with novel topology, but is structurally similar to the Rel homology domains of NFAT and NF-κB. Ebf1 contacts the DNA with two loop-based modules and a unique Zn coordination motif whereby each Ebf1 monomer interacts with both palindromic half-sites. This unusual mode of DNA recognition generates an extended contact area that may be crucial for the function of Ebf1 in chromatin.
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Affiliation(s)
- Nora Treiber
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology, 79108 Freiburg, Germany
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20
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Schmidt F, Treiber N, Zocher G, Bjelic S, Steinmetz MO, Kalbacher H, Stehle T, Dodt G. Insights into peroxisome function from the structure of PEX3 in complex with a soluble fragment of PEX19. J Biol Chem 2010; 285:25410-7. [PMID: 20554521 PMCID: PMC2919104 DOI: 10.1074/jbc.m110.138503] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [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: 04/27/2010] [Revised: 05/17/2010] [Indexed: 11/06/2022] Open
Abstract
The human peroxins PEX3 and PEX19 play a central role in peroxisomal membrane biogenesis. The membrane-anchored PEX3 serves as the receptor for cytosolic PEX19, which in turn recognizes newly synthesized peroxisomal membrane proteins. After delivering these proteins to the peroxisomal membrane, PEX19 is recycled to the cytosol. The molecular mechanisms underlying these processes are not well understood. Here, we report the crystal structure of the cytosolic domain of PEX3 in complex with a PEX19-derived peptide. PEX3 adopts a novel fold that is best described as a large helical bundle. A hydrophobic groove at the membrane-distal end of PEX3 engages the PEX19 peptide with nanomolar affinity. Mutagenesis experiments identify phenylalanine 29 in PEX19 as critical for this interaction. Because key PEX3 residues involved in complex formation are highly conserved across species, the observed binding mechanism is of general biological relevance.
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Affiliation(s)
- Friederike Schmidt
- From the Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Nora Treiber
- the Institute for Organic Chemistry and Biochemistry, University of Freiburg, 79106 Freiburg, Germany
| | - Georg Zocher
- From the Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Sasa Bjelic
- the Laboratory of Biomolecular Research, Structural Biology, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland, and
| | - Michel O. Steinmetz
- the Laboratory of Biomolecular Research, Structural Biology, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland, and
| | - Hubert Kalbacher
- From the Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Thilo Stehle
- From the Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
- the Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Gabriele Dodt
- From the Interfaculty Institute for Biochemistry, University of Tübingen, 72076 Tübingen, Germany
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21
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Treiber N, Reinert DJ, Carpusca I, Aktories K, Schulz GE. Structure and mode of action of a mosquitocidal holotoxin. J Mol Biol 2008; 381:150-9. [PMID: 18586267 DOI: 10.1016/j.jmb.2008.05.067] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2008] [Revised: 05/23/2008] [Accepted: 05/28/2008] [Indexed: 10/22/2022]
Abstract
The crystal structure of the full mosquitocidal toxin from Bacillus sphaericus (MTX(holo)) has been determined at 2.5 A resolution by the molecular replacement method. The resulting structure revealed essentially the complete chain consisting of four ricin B-type domains curling around the catalytic domain in a hedgehog-like assembly. As the structure was virtually identical in three different crystal packings, it is probably not affected by packing contacts. The structure of MTX(holo) explains earlier autoinhibition data. An analysis of published complexes comprising ricin B-type lectin domains and sugar molecules shows that the general construction principle applies to all four lectin domains of MTX(holo), indicating 12 putative sugar-binding sites. These sites are sequence-related to those of the cytotoxin pierisin from cabbage butterfly, which are known to bind glycolipids. It seems therefore likely that MTX(holo) also binds glycolipids. The seven contact interfaces between the five domains are predominantly polar and not stronger than common crystal contacts so that in an appropriate environment, the multidomain structure would likely uncurl into a string of single domains. The structure of the isolated catalytic domain plus an extended linker was established earlier in three crystal packings, two of which showed a peculiar association around a 7-fold axis. The catalytic domain of the reported MTX(holo) closely resembles all three published structures, except one with an appreciable deviation of the 40 N-terminal residues. A comparison of all structures suggests a possible scenario for the translocation of the toxin into the cytosol.
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Affiliation(s)
- Nora Treiber
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany
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22
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Treiber N, Schulz GE. Structure of 2,6-dihydroxypyridine 3-hydroxylase from a nicotine-degrading pathway. J Mol Biol 2008; 379:94-104. [PMID: 18440023 DOI: 10.1016/j.jmb.2008.03.032] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Revised: 03/17/2008] [Accepted: 03/18/2008] [Indexed: 11/25/2022]
Abstract
The enzyme 2,6-dihydroxypyridine-3-hydroxylase catalyzes the sixth step of the nicotine degradation pathway in Arthrobacter nicotinovorans. The enzyme was produced in Escherichia coli, purified and crystallized. The crystal structure was solved at 2.6 A resolution, revealing a significant structural relationship with the family of FAD-dependent aromatic hydroxylases, but essentially no sequence homology. The structure was aligned with those of the established family members, showing that the FAD molecules are bound at virtually identical locations. The reported enzyme is a dimer like most other family members, but its dimerization contact differs from the others. The binding position of NAD(P)H to this enzyme family is not clear. Since the reported enzyme accepts only NADH for flavin reduction in contrast to the other established members using NADPH, we searched through the structural alignment and found an indication for the position of the 2'-phosphate of NADPH that is in general agreement with mutational studies on a related enzyme, but contradicts a crystal soaking experiment. Using a bound glycerol molecule and the known substrate positions of three related enzymes as a guide, the substrate 2,6-dihydroxypyridine was placed into the active center. The access to the binding site is discussed. The new active center geometry introduces constraints that render some reaction scenarios more likely than others. It suggests that flavin is reduced at its out-position and then drawn into its in-position, where it binds molecular oxygen. The geometry is consistent with the proposal that peroxy-flavin is protonated by the solvent to yield the electrophilic hydroperoxy-flavin. The substrate is activated by two buried histidines but there is no appropriate base to store the surplus proton of the hydroxylated carbon atom. The implications of this problem are discussed.
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Affiliation(s)
- Nora Treiber
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstr. 21, 79104 Freiburg im Breisgau, Germany
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Abstract
The analysis of natural contact interfaces between protein subunits and between proteins has disclosed some general rules governing their association. We have applied these rules to produce a number of novel assemblies, demonstrating that a given protein can be engineered to form contacts at various points of its surface. Symmetry plays an important role because it defines the multiplicity of a designed contact and therefore the number of required mutations. Some of the proteins needed only a single side-chain alteration in order to associate to a higher-order complex. The mobility of the buried side chains has to be taken into account. Four assemblies have been structurally elucidated. Comparisons between the designed contacts and the results will provide useful guidelines for the development of future architectures.
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Affiliation(s)
- Dirk Grueninger
- Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany
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Bartlett R, Treiber N. Clinical Significance of Mixed Bacterial Cultures of Urine. J Urol 1985. [DOI: 10.1016/s0022-5347(17)48940-3] [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: 10/19/2022]
Affiliation(s)
- R.C. Bartlett
- Division of Microbiology, Department of Pathology, Hartford Hospital, Hartford, Connecticut
| | - N. Treiber
- Division of Microbiology, Department of Pathology, Hartford Hospital, Hartford, Connecticut
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Abstract
The frequency with which isolation of more than one bacterial species from urine signifies treatable mixed infection versus contamination or colonization is not known. The authors studied 247 patients yielding mixed urine cultures. Specimens were collected by clean catch (CC) from 88 and from closed drainage systems (CDS) from 159. A second specimen was collected within 48 hours, and the results of the two cultures were compared. The percentages in which the initial mixed culture was found to represent probable, possible, and improbable treatable mixed infection were as follows: for CC specimens, 11%, 20%, and 67%, and for CDS specimens, 3%, 21%, and 77%. The authors have found that empiric antibiotic therapy and reporting of mixed cultures based on culture morphology without complete identification or antibiotic susceptibilities (except for certain colony types suggesting potentially multi-drug resistant strains) with request for resubmission represents a cost-effective solution to the mixed culture problem in the diagnosis and treatment of urinary tract infection.
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