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Rossmanith W, Giegé P, Hartmann RK. Discovery, structure, mechanisms, and evolution of protein-only RNase P enzymes. J Biol Chem 2024; 300:105731. [PMID: 38336295 PMCID: PMC10941002 DOI: 10.1016/j.jbc.2024.105731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
The endoribonuclease RNase P is responsible for tRNA 5' maturation in all domains of life. A unique feature of RNase P is the variety of enzyme architectures, ranging from dual- to multi-subunit ribonucleoprotein forms with catalytic RNA subunits to protein-only enzymes, the latter occurring as single- or multi-subunit forms or homo-oligomeric assemblies. The protein-only enzymes evolved twice: a eukaryal protein-only RNase P termed PRORP and a bacterial/archaeal variant termed homolog of Aquifex RNase P (HARP); the latter replaced the RNA-based enzyme in a small group of thermophilic bacteria but otherwise coexists with the ribonucleoprotein enzyme in a few other bacteria as well as in those archaea that also encode a HARP. Here we summarize the history of the discovery of protein-only RNase P enzymes and review the state of knowledge on structure and function of bacterial HARPs and eukaryal PRORPs, including human mitochondrial RNase P as a paradigm of multi-subunit PRORPs. We also describe the phylogenetic distribution and evolution of PRORPs, as well as possible reasons for the spread of PRORPs in the eukaryal tree and for the recruitment of two additional protein subunits to metazoan mitochondrial PRORP. We outline potential applications of PRORPs in plant biotechnology and address diseases associated with mutations in human mitochondrial RNase P genes. Finally, we consider possible causes underlying the displacement of the ancient RNA enzyme by a protein-only enzyme in a small group of bacteria.
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Affiliation(s)
- Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, Vienna, Austria.
| | - Philippe Giegé
- Institute for Plant Molecular Biology, IBMP-CNRS, University of Strasbourg, Strasbourg, France.
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany.
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2
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Bach S, Demper JC, Grünweller A, Becker S, Biedenkopf N, Hartmann RK. Erratum for Bach et al., "Regulation of VP30-Dependent Transcription by RNA Sequence and Structure in the Genomic Ebola Virus Promoter". J Virol 2023; 97:e0125623. [PMID: 37787531 PMCID: PMC10617568 DOI: 10.1128/jvi.01256-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023] Open
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3
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Wiegard JC, Damm K, Lechner M, Thölken C, Ngo S, Putzer H, Hartmann RK. Processing and decay of 6S-1 and 6S-2 RNAs in Bacillus subtilis. RNA 2023; 29:1481-1499. [PMID: 37369528 PMCID: PMC10578484 DOI: 10.1261/rna.079666.123] [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] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023]
Abstract
Noncoding 6S RNAs regulate transcription by binding to the active site of bacterial RNA polymerase holoenzymes. Processing and decay of 6S-1 and 6S-2 RNA were investigated in Bacillus subtilis by northern blot and RNA-seq analyses using different RNase knockout strains, as well as by in vitro processing assays. For both 6S RNA paralogs, we identified a key-but mechanistically different-role of RNase J1. RNase J1 catalyzes 5'-end maturation of 6S-1 RNA, yet relatively inefficient and possibly via the enzyme's "sliding endonuclease" activity. 5'-end maturation has no detectable effect on 6S-1 RNA function, but rather regulates its decay: The generated 5'-monophosphate on matured 6S-1 RNA propels endonucleolytic cleavage in its apical loop region. The major 6S-2 RNA degradation pathway is initiated by endonucleolytic cleavage in the 5'-central bubble to trigger 5'-to-3'-exoribonucleolytic degradation of the downstream fragment by RNase J1. The four 3'-exonucleases of B. subtilis-RNase R, PNPase, YhaM, and particularly RNase PH-are involved in 3'-end trimming of both 6S RNAs, degradation of 6S-1 RNA fragments, and decay of abortive transcripts (so-called product RNAs, ∼14 nt in length) synthesized on 6S-1 RNA during outgrowth from stationary phase. In the case of the growth-retarded RNase Y deletion strain, we were unable to infer a specific role of RNase Y in 6S RNA decay. Yet, a participation of RNase Y in 6S RNA decay still remains possible, as evidence for such a function may have been obscured by overlapping substrate specificities of RNase Y, RNase J1, and RNase J2.
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Affiliation(s)
- Jana Christin Wiegard
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
| | - Katrin Damm
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
| | - Marcus Lechner
- Philipps-Universität Marburg, Center for Synthetic Microbiology (SYNMIKRO), Bioinformatics Core Facility, D-35032 Marburg, Germany
| | - Clemens Thölken
- Philipps-Universität Marburg, Center for Synthetic Microbiology (SYNMIKRO), Bioinformatics Core Facility, D-35032 Marburg, Germany
| | - Saravuth Ngo
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Harald Putzer
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Roland K Hartmann
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
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Gößringer M, Wäber NB, Wiegard JC, Hartmann RK. Characterization of RNA-based and protein-only RNases P from bacteria encoding both enzyme types. RNA 2023; 29:376-391. [PMID: 36604113 PMCID: PMC9945441 DOI: 10.1261/rna.079459.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
A small group of bacteria encode two types of RNase P, the classical ribonucleoprotein (RNP) RNase P as well as the protein-only RNase P HARP (homolog of Aquifex RNase P). We characterized the dual RNase P activities of five bacteria that belong to three different phyla. All five bacterial species encode functional RNA (gene rnpB) and protein (gene rnpA) subunits of RNP RNase P, but only the HARP of the thermophile Thermodesulfatator indicus (phylum Thermodesulfobacteria) was found to have robust tRNA 5'-end maturation activity in vitro and in vivo in an Escherichia coli RNase P depletion strain. These findings suggest that both types of RNase P are able to contribute to the essential tRNA 5'-end maturation activity in T. indicus, thus resembling the predicted evolutionary transition state in the progenitor of the Aquificaceae before the loss of rnpA and rnpB genes in this family of bacteria. Remarkably, T. indicus RNase P RNA is transcribed with a P12 expansion segment that is posttranscriptionally excised in vivo, such that the major fraction of the RNA is fragmented and thereby truncated by ∼70 nt in the native T. indicus host as well as in the E. coli complementation strain. Replacing the native P12 element of T. indicus RNase P RNA with the short P12 helix of Thermotoga maritima RNase P RNA abolished fragmentation, but simultaneously impaired complementation efficiency in E. coli cells, suggesting that intracellular fragmentation and truncation of T. indicus RNase P RNA may be beneficial to RNA folding and/or enzymatic activity.
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Affiliation(s)
- Markus Gößringer
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
| | - Nadine B Wäber
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
| | - Jana C Wiegard
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
| | - Roland K Hartmann
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
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Bach S, Demper JC, Klemm P, Schlereth J, Lechner M, Schoen A, Kämper L, Weber F, Becker S, Biedenkopf N, Hartmann RK. Identification and characterization of short leader and trailer RNAs synthesized by the Ebola virus RNA polymerase. PLoS Pathog 2021; 17:e1010002. [PMID: 34699554 PMCID: PMC8547711 DOI: 10.1371/journal.ppat.1010002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 10/04/2021] [Indexed: 11/21/2022] Open
Abstract
Transcription of non-segmented negative sense (NNS) RNA viruses follows a stop-start mechanism and is thought to be initiated at the genome’s very 3’-end. The synthesis of short abortive leader transcripts (leaderRNAs) has been linked to transcription initiation for some NNS viruses. Here, we identified the synthesis of abortive leaderRNAs (as well as trailer RNAs) that are specifically initiated opposite to (anti)genome nt 2; leaderRNAs are predominantly terminated in the region of nt ~ 60–80. LeaderRNA synthesis requires hexamer phasing in the 3’-leader promoter. We determined a steady-state NP mRNA:leaderRNA ratio of ~10 to 30-fold at 48 h after Ebola virus (EBOV) infection, and this ratio was higher (70 to 190-fold) for minigenome-transfected cells. LeaderRNA initiation at nt 2 and the range of termination sites were not affected by structure and length variation between promoter elements 1 and 2, nor the presence or absence of VP30. Synthesis of leaderRNA is suppressed in the presence of VP30 and termination of leaderRNA is not mediated by cryptic gene end (GE) signals in the 3’-leader promoter. We further found different genomic 3’-end nucleotide requirements for transcription versus replication, suggesting that promoter recognition is different in the replication and transcription mode of the EBOV polymerase. We further provide evidence arguing against a potential role of EBOV leaderRNAs as effector molecules in innate immunity. Taken together, our findings are consistent with a model according to which leaderRNAs are abortive replicative RNAs whose synthesis is not linked to transcription initiation. Rather, replication and transcription complexes are proposed to independently initiate RNA synthesis at separate sites in the 3’-leader promoter, i.e., at the second nucleotide of the genome 3’-end and at the more internally positioned transcription start site preceding the first gene, respectively, as reported for Vesicular stomatitis virus. The RNA polymerase (RdRp) of Ebola virus (EBOV) initiates RNA synthesis at the 3’-leader promoter of its encapsidated, non-segmented negative sense (NNS) RNA genome, either at the penultimate 3’-end position of the genome in the replicative mode or more internally (position 56) at the transcription start site (TSS) in its transcription mode. Here we identified the synthesis of abortive replicative RNAs that are specifically initiated opposite to genome nt 2 (termed leaderRNAs) and predominantly terminated in the region of nt ~ 60–80 near the TSS. The functional role of abortive leaderRNA synthesis is still enigmatic; a role in interferon induction could be excluded. Our findings indirectly link leaderRNA termination to nucleoprotein (NP) availability for encapsidation of nascent replicative RNA or to NP removal from the template RNA. Our findings further argue against the model that leaderRNA synthesis is a prerequisite for each transcription initiation event at the TSS. Rather, our findings are in line with the existence of distinct replicase and transcriptase complexes of RdRp that interact differently with the 3’-leader promoter and intiate RNA synthesis independently at different sites (position 2 or 56 of the genome), mechanistically similar to another NNS virus, Vesicular stomatitis virus.
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Affiliation(s)
- Simone Bach
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Jana-Christin Demper
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Paul Klemm
- Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Marburg, Germany
| | - Julia Schlereth
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Marcus Lechner
- Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, Marburg, Germany
| | - Andreas Schoen
- Institut für Virologie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Lennart Kämper
- Institut für Virologie, Philipps-Universität Marburg, Marburg, Germany
| | - Friedemann Weber
- Institut für Virologie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Stephan Becker
- Institut für Virologie, Philipps-Universität Marburg, Marburg, Germany
| | - Nadine Biedenkopf
- Institut für Virologie, Philipps-Universität Marburg, Marburg, Germany
- * E-mail: (NB); (RKH)
| | - Roland K. Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
- * E-mail: (NB); (RKH)
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Marszalkowski M, Werner A, Feltens R, Helmecke D, Gößringer M, Westhof E, Hartmann RK. Comparative study on tertiary contacts and folding of RNase P RNAs from a psychrophilic, a mesophilic/radiation-resistant, and a thermophilic bacterium. RNA 2021; 27:1204-1219. [PMID: 34266994 PMCID: PMC8457005 DOI: 10.1261/rna.078735.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
In most bacterial type A RNase P RNAs (P RNAs), two major loop-helix tertiary contacts (L8-P4 and L18-P8) help to orient the two independently folding S- and C-domains for concerted recognition of precursor tRNA substrates. Here, we analyze the effects of mutations in these tertiary contacts in P RNAs from three different species: (i) the psychrophilic bacterium Pseudoalteromonas translucida (Ptr), (ii) the mesophilic radiation-resistant bacterium Deinococcus radiodurans (Dra), and (iii) the thermophilic bacterium Thermus thermophilus (Tth). We show by UV melting experiments that simultaneous disruption of these two interdomain contacts has a stabilizing effect on all three P RNAs. This can be inferred from reduced RNA unfolding at lower temperatures and a more concerted unfolding at higher temperatures. Thus, when the two domains tightly interact via the tertiary contacts, one domain facilitates structural transitions in the other. P RNA mutants with disrupted interdomain contacts showed severe kinetic defects that were most pronounced upon simultaneous disruption of the L8-P4 and L18-P8 contacts. At 37°C, the mildest effects were observed for the thermostable Tth RNA. A third interdomain contact, L9-P1, makes only a minor contribution to P RNA tertiary folding. Furthermore, D. radiodurans RNase P RNA forms an additional pseudoknot structure between the P9 and P12 of its S-domain. This interaction was found to be particularly crucial for RNase P holoenzyme activity at near-physiological Mg2+ concentrations (2 mM). We further analyzed an exceptionally stable folding trap of the G,C-rich Tth P RNA.
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Affiliation(s)
- Michal Marszalkowski
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
| | - Andreas Werner
- Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, Architecture et Réactivité de l'ARN, F-67084 Strasbourg, France
| | - Ralph Feltens
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
| | - Dominik Helmecke
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
| | - Markus Gößringer
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
| | - Eric Westhof
- Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, Architecture et Réactivité de l'ARN, F-67084 Strasbourg, France
| | - Roland K Hartmann
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, D-35037 Marburg, Germany
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Ganapathy S, Wiegard JC, Hartmann RK. Rapid preparation of 6S RNA-free B. subtilis σ A-RNA polymerase and σ A. J Microbiol Methods 2021; 190:106324. [PMID: 34506811 DOI: 10.1016/j.mimet.2021.106324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/08/2021] [Revised: 08/17/2021] [Accepted: 09/06/2021] [Indexed: 11/25/2022]
Abstract
The regulatory 6S-1 and 6S-2 RNAs of B. subtilis bind to the housekeeping RNA polymerase holoenzyme (σA-RNAP) with submicromolar affinity. We observed copurification of endogenous 6S RNAs from a published B. subtilis strain expressing a His-tagged RNAP. Such 6S RNA contaminations in σA-RNAP preparations reduce the fraction of enzymes that are accessible for binding to DNA promoters. In addition, this leads to background RNA synthesis by σA-RNAP utilizing copurified 6S RNA as template for the synthesis of short abortive transcripts termed product RNAs (pRNAs). To avoid this problem we constructed a B. subtilis strain expressing His-tagged RNAP but carrying deletions of the two 6S RNA genes. The His-tagged, 6S RNA-free σA-RNAP holoenzyme can be prepared with sufficient purity and activity by a single affinity step. We also report expression and separate purification of B. subtilis σA that can be added to the His-tagged RNAP to maximize the amount of holoenzyme and, by inference, in vitro transcription activity.
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Affiliation(s)
- Sweetha Ganapathy
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Jana Christin Wiegard
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Roland K Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany.
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Cataldo PG, Klemm P, Thüring M, Saavedra L, Hebert EM, Hartmann RK, Lechner M. Insights into 6S RNA in lactic acid bacteria (LAB). BMC Genom Data 2021; 22:29. [PMID: 34479493 PMCID: PMC8414754 DOI: 10.1186/s12863-021-00983-2] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/12/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND 6S RNA is a regulator of cellular transcription that tunes the metabolism of cells. This small non-coding RNA is found in nearly all bacteria and among the most abundant transcripts. Lactic acid bacteria (LAB) constitute a group of microorganisms with strong biotechnological relevance, often exploited as starter cultures for industrial products through fermentation. Some strains are used as probiotics while others represent potential pathogens. Occasional reports of 6S RNA within this group already indicate striking metabolic implications. A conceivable idea is that LAB with 6S RNA defects may metabolize nutrients faster, as inferred from studies of Echerichia coli. This may accelerate fermentation processes with the potential to reduce production costs. Similarly, elevated levels of secondary metabolites might be produced. Evidence for this possibility comes from preliminary findings regarding the production of surfactin in Bacillus subtilis, which has functions similar to those of bacteriocins. The prerequisite for its potential biotechnological utility is a general characterization of 6S RNA in LAB. RESULTS We provide a genomic annotation of 6S RNA throughout the Lactobacillales order. It laid the foundation for a bioinformatic characterization of common 6S RNA features. This covers secondary structures, synteny, phylogeny, and product RNA start sites. The canonical 6S RNA structure is formed by a central bulge flanked by helical arms and a template site for product RNA synthesis. 6S RNA exhibits strong syntenic conservation. It is usually flanked by the replication-associated recombination protein A and the universal stress protein A. A catabolite responsive element was identified in over a third of all 6S RNA genes. It is known to modulate gene expression based on the available carbon sources. The presence of antisense transcripts could not be verified as a general trait of LAB 6S RNAs. CONCLUSIONS Despite a large number of species and the heterogeneity of LAB, the stress regulator 6S RNA is well-conserved both from a structural as well as a syntenic perspective. This is the first approach to describe 6S RNAs and short 6S RNA-derived transcripts beyond a single species, spanning a large taxonomic group covering multiple families. It yields universal insights into this regulator and complements the findings derived from other bacterial model organisms.
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Affiliation(s)
- Pablo Gabriel Cataldo
- Centro de Referencia para Lactobacilos (CERELA-CONICET), Chacabuco 145, San Miguel de Tucumán, 4000, Argentina
| | - Paul Klemm
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, Marburg, 35032, Germany
| | - Marietta Thüring
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, Marburg, 35032, Germany
| | - Lucila Saavedra
- Centro de Referencia para Lactobacilos (CERELA-CONICET), Chacabuco 145, San Miguel de Tucumán, 4000, Argentina
| | - Elvira Maria Hebert
- Centro de Referencia para Lactobacilos (CERELA-CONICET), Chacabuco 145, San Miguel de Tucumán, 4000, Argentina
| | - Roland K Hartmann
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, Marburg, 35032, Germany
| | - Marcus Lechner
- Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, Marburg, 35032, Germany. .,Philipps-Universität Marburg, Center for Synthetic Microbiology (Synmikro), Hans-Meerwein-Straße 6, Marburg, 35043, Germany.
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9
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Feyh R, Waeber NB, Prinz S, Giammarinaro PI, Bange G, Hochberg G, Hartmann RK, Altegoer F. Structure and mechanistic features of the prokaryotic minimal RNase P. eLife 2021; 10:70160. [PMID: 34180399 PMCID: PMC8266387 DOI: 10.7554/elife.70160] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 05/07/2021] [Accepted: 06/25/2021] [Indexed: 12/17/2022] Open
Abstract
Endonucleolytic removal of 5'-leader sequences from tRNA precursor transcripts (pre-tRNAs) by ribonuclease P (RNase P) is essential for protein synthesis. Beyond RNA-based RNase P enzymes, protein-only versions of the enzyme exert this function in various eukarya (there termed PRORPs) and in some bacteria (Aquifex aeolicus and close relatives); both enzyme types belong to distinct subgroups of the PIN domain metallonuclease superfamily. Homologs of Aquifex RNase P (HARPs) are also expressed in some other bacteria and many archaea, where they coexist with RNA-based RNase P and do not represent the main RNase P activity. Here, we solved the structure of the bacterial HARP from Halorhodospira halophila by cryo-electron microscopy, revealing a novel screw-like dodecameric assembly. Biochemical experiments demonstrate that oligomerization is required for RNase P activity of HARPs. We propose that the tRNA substrate binds to an extended spike-helix (SH) domain that protrudes from the screw-like assembly to position the 5'-end in close proximity to the active site of the neighboring dimer. The structure suggests that eukaryotic PRORPs and prokaryotic HARPs recognize the same structural elements of pre-tRNAs (tRNA elbow region and cleavage site). Our analysis thus delivers the structural and mechanistic basis for pre-tRNA processing by the prokaryotic HARP system.
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Affiliation(s)
- Rebecca Feyh
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Nadine B Waeber
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Simone Prinz
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Pietro Ivan Giammarinaro
- Center for Synthetic Microbiology and Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gert Bange
- Center for Synthetic Microbiology and Department of Chemistry, Philipps-University Marburg, Marburg, Germany.,Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Georg Hochberg
- Center for Synthetic Microbiology and Department of Chemistry, Philipps-University Marburg, Marburg, Germany.,Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Florian Altegoer
- Center for Synthetic Microbiology and Department of Chemistry, Philipps-University Marburg, Marburg, Germany
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10
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Bach S, Demper JC, Grünweller A, Becker S, Biedenkopf N, Hartmann RK. Regulation of VP30-Dependent Transcription by RNA Sequence and Structure in the Genomic Ebola Virus Promoter. J Virol 2021; 95:JVI.02215-20. [PMID: 33268520 PMCID: PMC8092829 DOI: 10.1128/jvi.02215-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 11/22/2020] [Indexed: 01/16/2023] Open
Abstract
Viral transcription and replication of Ebola virus (EBOV) is balanced by transcription factor VP30, an RNA binding protein. An RNA hairpin at the transcription start site (TSS) of the first gene (NP hairpin) in the 3'-leader promoter is thought to mediate the VP30 dependency of transcription. Here, we investigated the constraints of VP30 dependency using a series of monocistronic minigenomes with sequence, structure and length deviations from the native NP hairpin. Hairpin stabilizations decreased while destabilizations increased transcription in the absence of VP30, but in all cases, transcription activity was higher in the presence versus absence of VP30. This also pertains to a mutant that is unable to form any RNA secondary structure at the TSS, demonstrating that the activity of VP30 is not simply determined by the capacity to form a hairpin structure at the TSS. Introduction of continuous 3'-UN5 hexamer phasing between promoter elements PE1 and PE2 by a single point mutation in the NP hairpin boosted VP30-independent transcription. Moreover, this point mutation, but also hairpin stabilizations, impaired the relative increase of replication in the absence of VP30. Our results suggest that the native NP hairpin is optimized for tight regulation by VP30 while avoiding an extent of hairpin stability that impairs viral transcription, as well as for enabling the switch from transcription to replication when VP30 is not part of the polymerase complex.IMPORTANCE A detailed understanding is lacking how the Ebola virus (EBOV) protein VP30 regulates activity of the viral polymerase complex. Here, we studied how RNA sequence, length and structure at the transcription start site (TSS) in the 3'-leader promoter influence the impact of VP30 on viral polymerase activity. We found that hairpin stabilizations tighten the VP30 dependency of transcription but reduce transcription efficiency and attenuate the switch to replication in the absence of VP30. Upon hairpin destabilization, VP30-independent transcription - already weakly detectable at the native promoter - increases, but never reaches the same extent as in the presence of VP30. We conclude that the native hairpin structure involving the TSS (i) establishes an optimal balance between efficient transcription and tight regulation by VP30, (ii) is linked to hexamer phasing in the promoter, and (iii) favors the switch to replication when VP30 is absent.
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Affiliation(s)
- Simone Bach
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Jana-Christin Demper
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Arnold Grünweller
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Stephan Becker
- Institut für Virologie, Philipps-Universität Marburg, Hans-Meerwein-Str. 2, 35043 Marburg
| | - Nadine Biedenkopf
- Institut für Virologie, Philipps-Universität Marburg, Hans-Meerwein-Str. 2, 35043 Marburg
| | - Roland K Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
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11
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Bach S, Demper JC, Biedenkopf N, Becker S, Hartmann RK. RNA secondary structure at the transcription start site influences EBOV transcription initiation and replication in a length- and stability-dependent manner. RNA Biol 2020; 18:523-536. [PMID: 32882148 DOI: 10.1080/15476286.2020.1818459] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Ebola virus (EBOV) RNA has the potential to form hairpin structures at the transcription start sequence (TSS) and reinitiation sites of internal genes, both on the genomic and antigenomic/mRNA level. Hairpin formation involving the TSS and the spacer sequence between promotor elements (PE) 1 and 2 was suggested to regulate viral transcription. Here, we provide evidence that such RNA structures form during RNA synthesis by the viral polymerase and affect its activity. This was analysed using monocistronic minigenomes carrying hairpin structure variants in the TSS-spacer region that differ in length and stability. Transcription and replication were measured via reporter activity and by qRT-PCR quantification of the distinct viral RNA species. We demonstrate that viral RNA synthesis is remarkably tolerant to spacer extensions of up to ~54 nt, but declines beyond this length limit (~25% residual activity for a 66-nt extension). Minor incremental stabilizations of hairpin structures in the TSS-spacer region and on the mRNA/antigenomic level were found to rapidly abolish viral polymerase activity, which may be exploited for antisense strategies to inhibit viral RNA synthesis. Finally, balanced viral transcription and replication can still occur when any RNA structure formation potential at the TSS is eliminated, provided that hexamer phasing in the promoter region is maintained. Altogether, the findings deepen and refine our insight into structure and length constraints within the EBOV transcription and replication promoter and suggest a remarkable flexibility of the viral polymerase in recognition of PE1 and PE2.
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Affiliation(s)
- Simone Bach
- Institut fuür Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Jana-Christin Demper
- Institut fuür Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Nadine Biedenkopf
- Institut fuü;r Virologie, Philipps-Universität Marburg, Marburg, Germany
| | - Stephan Becker
- Institut fuü;r Virologie, Philipps-Universität Marburg, Marburg, Germany
| | - Roland K Hartmann
- Institut fuür Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
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12
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Thüring M, Ganapathy S, Schlüter MAC, Lechner M, Hartmann RK. 6S-2 RNA deletion in the undomesticated B. subtilis strain NCIB 3610 causes a biofilm derepression phenotype. RNA Biol 2020; 18:79-92. [PMID: 32862759 DOI: 10.1080/15476286.2020.1795408] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Bacterial 6S RNA regulates transcription via binding to the active site of RNA polymerase holoenzymes. 6S RNA has been identified in the majority of bacteria, in most cases encoded by a single gene. Firmicutes including Bacillus subtilis encode two 6S RNA paralogs, 6S-1 and 6S-2 RNA. Hypothesizing that the regulatory role of 6S RNAs may be particularly important under natural, constantly changing environmental conditions, we constructed 6S RNA deletion mutants of the undomesticated B. subtilis wild-type strain NCIB 3610. We observed a strong phenotype for the ∆6S-2 RNA strain that showed increased biofilm formation on solid media and the ability to form surface-attached biofilms in liquid culture. This phenotype remained undetected in derived laboratory strains (168, PY79) that are defective in biofilm formation. Quantitative RT-PCR data revealed transcriptional upregulation of biofilm marker genes such as tasA, epsA and bslA in the ∆6S-2 RNA strain, particularly during transition from exponential to stationary growth phase. Salt stress, which blocks sporulation at a very early stage, was found to override the derepressed biofilm phenotype of the ∆6S-2 RNA strain. Furthermore, the ∆6S-2 RNA strain showed retarded swarming activity and earlier spore formation. Finally, the ∆6S-1&2 RNA double deletion strain showed a prolonged lag phase of growth under oxidative, high salt and alkaline stress conditions, suggesting that the interplay of both 6S RNAs in B. subtilis optimizes and fine-tunes transcriptomic adaptations, thereby contributing to the fitness of B. subtilis under the unsteady and temporarily harsh conditions encountered in natural habitats.
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Affiliation(s)
- Marietta Thüring
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg , Marburg, Germany
| | - Sweetha Ganapathy
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg , Marburg, Germany
| | - M Amri C Schlüter
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg , Marburg, Germany
| | - Marcus Lechner
- Center for Synthetic Microbiology, Bioinformatics Core Facility , Marburg, Germany
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg , Marburg, Germany
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13
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Bolz M, Thomas L, Scheffer U, Kalden E, Hartmann RK, Göbel MW. Front Cover: Redirection of miRNA‐Argonaute Complexes to Specific Target Sites by Synthetic Adaptor Molecules (C&B 7/2020). Chem Biodivers 2020. [DOI: 10.1002/cbdv.202000517] [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: 11/09/2022]
Affiliation(s)
- Mathias Bolz
- Institute of Organic Chemistry and Chemical BiologyGoethe University Frankfurt Max-von-Laue-Str. 7 DE-60438 Frankfurt Germany
| | - Laura Thomas
- Institute of Pharmaceutical ChemistryPhilipps University Marburg Marbacher Weg 6–10 DE-35032 Marburg Germany
| | - Ute Scheffer
- Institute of Organic Chemistry and Chemical BiologyGoethe University Frankfurt Max-von-Laue-Str. 7 DE-60438 Frankfurt Germany
| | - Elisabeth Kalden
- Institute of Organic Chemistry and Chemical BiologyGoethe University Frankfurt Max-von-Laue-Str. 7 DE-60438 Frankfurt Germany
| | - Roland K. Hartmann
- Institute of Pharmaceutical ChemistryPhilipps University Marburg Marbacher Weg 6–10 DE-35032 Marburg Germany
| | - Michael W. Göbel
- Institute of Organic Chemistry and Chemical BiologyGoethe University Frankfurt Max-von-Laue-Str. 7 DE-60438 Frankfurt Germany
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14
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Bolz M, Thomas L, Scheffer U, Kalden E, Hartmann RK, Göbel MW. Redirection of miRNA-Argonaute Complexes to Specific Target Sites by Synthetic Adaptor Molecules. Chem Biodivers 2020; 17:e2000272. [PMID: 32428353 DOI: 10.1002/cbdv.202000272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 04/07/2020] [Accepted: 05/19/2020] [Indexed: 12/28/2022]
Abstract
Dysregulation of miRNAs is connected with a multitude of diseases for which antagomirs and miRNA replacement are discussed as therapeutic options. Here, we suggest an alternative concept based on the redirection of RISCs to non-native target sites. Metabolically stable DNA-LNA mixmers are used to mediate the binding of RISCs to mRNAs without any direct base complementarity to the presented guide RNA strand. Physical redirection of a dye-labeled miRNA model and of specific miRNA-programmed RISC fractions present in HeLa extracts is demonstrated by pull-down experiments with biotinylated capture oligonucleotides.
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Affiliation(s)
- Mathias Bolz
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, DE-60438, Frankfurt, Germany
| | - Laura Thomas
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6-10, DE-35032, Marburg, Germany
| | - Ute Scheffer
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, DE-60438, Frankfurt, Germany
| | - Elisabeth Kalden
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, DE-60438, Frankfurt, Germany
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6-10, DE-35032, Marburg, Germany
| | - Michael W Göbel
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Str. 7, DE-60438, Frankfurt, Germany
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15
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Bach S, Biedenkopf N, Grünweller A, Becker S, Hartmann RK. Hexamer phasing governs transcription initiation in the 3'-leader of Ebola virus. RNA 2020; 26:439-453. [PMID: 31924730 PMCID: PMC7075260 DOI: 10.1261/rna.073718.119] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 10/22/2019] [Accepted: 01/08/2020] [Indexed: 05/05/2023]
Abstract
The genomic, bipartite replication promoter of Ebola virus (EBOV) consists of elements 1 (PE1) and 2 (PE2). PE1 (55 nt at the 3'-terminus) is separated from PE2 (harboring eight 3'-UN5 hexamers) by the transcription start sequence (TSS) of the first nucleoprotein (NP) gene plus a spacer sequence. Insertions or deletions in the spacer were reported to support genome replication if comprising 6 or 12, but not 1/2/3/5/9 nt. This gave rise to the formulation of the "rule of 6" for the EBOV replication promoter. Here, we studied the impact of such hexamer phasing on viral transcription using a series of replication-competent and -deficient monocistronic minigenomes, in which the spacer of the NP gene was mutated or replaced with that of internal EBOV genes and mutated variants thereof. Beyond reporter gene assays, we conducted qRT-PCR to determine the levels of mRNA, genomic and antigenomic RNA. We demonstrate that hexamer phasing is also essential for viral transcription, that UN5 hexamer periodicity extends into PE1 and that the spacer region can be expanded by 48 nt without losses of transcriptional activity. Making the UN5 hexamer phasing continuous between PE1 and PE2 enhanced the efficiency of transcription and replication. We show that the 2 nt preceding the TSS are essential for transcription. We further propose a role for UN5 hexamer phasing in positioning NP during initiation of RNA synthesis, or in dissociation/reassociation of NP from the template RNA strand while threading the RNA through the active site of the elongating polymerase during replication and transcription.
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Affiliation(s)
- Simone Bach
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35037 Marburg, Germany
| | - Nadine Biedenkopf
- Institut für Virologie, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Arnold Grünweller
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35037 Marburg, Germany
| | - Stephan Becker
- Institut für Virologie, Philipps-Universität Marburg, 35043 Marburg, Germany
| | - Roland K Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35037 Marburg, Germany
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16
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Müller C, Obermann W, Schulte FW, Lange-Grünweller K, Oestereich L, Elgner F, Glitscher M, Hildt E, Singh K, Wendel HG, Hartmann RK, Ziebuhr J, Grünweller A. Comparison of broad-spectrum antiviral activities of the synthetic rocaglate CR-31-B (-) and the eIF4A-inhibitor Silvestrol. Antiviral Res 2020; 175:104706. [PMID: 31931103 PMCID: PMC7114339 DOI: 10.1016/j.antiviral.2020.104706] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [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: 09/26/2019] [Revised: 01/04/2020] [Accepted: 01/08/2020] [Indexed: 12/22/2022]
Abstract
Rocaglates, a class of natural compounds isolated from plants of the genus Aglaia, are potent inhibitors of translation initiation. They are proposed to form stacking interactions with polypurine sequences in the 5′-untranslated region (UTR) of selected mRNAs, thereby clamping the RNA substrate onto eIF4A and causing inhibition of the translation initiation complex. Since virus replication relies on the host translation machinery, it is not surprising that the rocaglate Silvestrol has broad-spectrum antiviral activity. Unfortunately, synthesis of Silvestrol is sophisticated and time-consuming, thus hampering the prospects for further antiviral drug development. Here, we present the less complex structured synthetic rocaglate CR-31-B (−) as a novel compound with potent broad-spectrum antiviral activity in primary cells and in an ex vivo bronchial epithelial cell system. CR-31-B (−) inhibited the replication of corona-, Zika-, Lassa-, Crimean Congo hemorrhagic fever viruses and, to a lesser extent, hepatitis E virus (HEV) at non-cytotoxic low nanomolar concentrations. Since HEV has a polypurine-free 5′-UTR that folds into a stable hairpin structure, we hypothesized that RNA clamping by Silvestrol and its derivatives may also occur in a polypurine-independent but structure-dependent manner. Interestingly, the HEV 5′-UTR conferred sensitivity towards Silvestrol but not to CR-31-B (−). However, if an exposed polypurine stretch was introduced into the HEV 5′-UTR, CR-31-B (−) became an active inhibitor comparable to Silvestrol. Moreover, thermodynamic destabilization of the HEV 5′-UTR led to reduced translational inhibition by Silvestrol, suggesting differences between rocaglates in their mode of action, most probably by engaging Silvestrol's additional dioxane moiety. The synthetic rocaglate CR-31-B (−) has broad-spectrum antiviral activity comparable to that of Silvestrol. Both compounds show remarkably low cytotoxicity in primary cells. Silvestrol and CR-31-B (−) are highly efficient against HCoV-229E in a primary human bronchial epithelial cell system. Both compounds reduce LASV and CCHFV titers by about 3–4 logs in primary murine hepatocytes. Only Silvestrol with its characteristic dioxane moiety can clamp polypurine-free structured RNAs onto the eIF4A helicase.
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Affiliation(s)
- Christin Müller
- Institut für Medizinische Virologie, Justus-Liebig-Universität Gießen, Schubertstraße 81, 35392, Gießen, Germany; Deutsches Zentrum für Infektionsforschung (DZIF) at the Partner Site Gießen-Marburg-Langen, Germany
| | - Wiebke Obermann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Falk W Schulte
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Kerstin Lange-Grünweller
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Lisa Oestereich
- Bernhard-Nocht-Institut für Tropenmedizin, Abteilung Virologie, Hamburg, Germany; Deutsches Zentrum für Infektionsforschung (DZIF) at the Partner Site Hamburg, Germany
| | - Fabian Elgner
- Paul-Ehrlich-Institut, Bundesinstitut für Impfstoffe und Biomedizinische Arzneimittel, Abteilung Virologie, Paul-Ehrlich-Straße 51-59, 63225, Langen, Germany
| | - Mirco Glitscher
- Paul-Ehrlich-Institut, Bundesinstitut für Impfstoffe und Biomedizinische Arzneimittel, Abteilung Virologie, Paul-Ehrlich-Straße 51-59, 63225, Langen, Germany
| | - Eberhard Hildt
- Paul-Ehrlich-Institut, Bundesinstitut für Impfstoffe und Biomedizinische Arzneimittel, Abteilung Virologie, Paul-Ehrlich-Straße 51-59, 63225, Langen, Germany
| | - Kamini Singh
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10023, USA
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10023, USA
| | - Roland K Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - John Ziebuhr
- Institut für Medizinische Virologie, Justus-Liebig-Universität Gießen, Schubertstraße 81, 35392, Gießen, Germany; Deutsches Zentrum für Infektionsforschung (DZIF) at the Partner Site Gießen-Marburg-Langen, Germany
| | - Arnold Grünweller
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany.
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17
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Kronschnabl P, Grünweller A, Hartmann RK, Aigner A, Weirauch U. Inhibition of PIM2 in liver cancer decreases tumor cell proliferation in vitro and in vivo primarily through the modulation of cell cycle progression. Int J Oncol 2019; 56:448-459. [PMID: 31894300 PMCID: PMC6959465 DOI: 10.3892/ijo.2019.4936] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 02/07/2019] [Accepted: 06/21/2019] [Indexed: 01/05/2023] Open
Abstract
Liver cancer is the fourth leading cause of cancer-related mortality worldwide with limited therapeutic options. Thus, novel treatment strategies are urgently required. While the oncogenic kinase, proviral integration site for Moloney murine leukemia virus 2 (PIM2), has been shown to be overexpressed in liver cancer, little is known about the role of PIM2 in this tumor entity. In this study, we explored the functional relevance and therapeutic potential of PIM2 in liver cancer. Using PIM2-specific siRNAs, we examined the effects of PIM2 knockdown on proliferation (WST-1 assays and spheroid assays), 3D-colony formation and colony spread, apoptosis (flow cytometry and caspase 3/caspase 7 activity), as well as cell cycle progression (flow cytometry, RT-qPCR and western blot analysis) in the two liver cancer cell lines, HepG2 and Huh-7. In subcutaneous liver cancer xenografts, we assessed the effects of PIM2 knockdown on tumor growth via the systemic delivery of polyethylenimine (PEI)-complexed siRNA. The knockdown of PIM2 resulted in potent anti-proliferative effects in cells grown on plastic dishes, as well as in spheroids. This was due to G0/G1 cell cycle blockade and the subsequent downregulation of genes related to the S phase as well as the G2/M phase of the cell cycle, whereas the apoptotic rates remained unaltered. Furthermore, colony formation and colony spread were markedly inhibited by PIM2 knockdown. Notably, we found that HepG2 cells were more sensitive to PIM2 knockdown than the Huh-7 cells. In vivo, the therapeutic nanoparticle-mediated delivery of PIM2 siRNA led to profound anti-tumor effects in a liver cancer xenograft mouse model. On the whole, the findings of this study underscore the oncogenic role of PIM2 and emphasize the potential of targeted therapies based on the specific inhibition of PIM2 in liver cancer.
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Affiliation(s)
- Pia Kronschnabl
- Rudolf‑Boehm‑Institute for Pharmacology and Toxicology, Clinical Pharmacology, Faculty of Medicine, University of Leipzig, D‑04107 Leipzig, Germany
| | - Arnold Grünweller
- Institute of Pharmaceutical Chemistry, Philipps‑University Marburg, D‑35037 Marburg, Germany
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps‑University Marburg, D‑35037 Marburg, Germany
| | - Achim Aigner
- Rudolf‑Boehm‑Institute for Pharmacology and Toxicology, Clinical Pharmacology, Faculty of Medicine, University of Leipzig, D‑04107 Leipzig, Germany
| | - Ulrike Weirauch
- Rudolf‑Boehm‑Institute for Pharmacology and Toxicology, Clinical Pharmacology, Faculty of Medicine, University of Leipzig, D‑04107 Leipzig, Germany
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18
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Peter Ventura AM, Haeberlein S, Lange-Grünweller K, Grünweller A, Hartmann RK, Grevelding CG, Schlitzer M. Development of Biarylalkyl Carboxylic Acid Amides with Improved Anti-schistosomal Activity. ChemMedChem 2019; 14:1856-1862. [PMID: 31454168 PMCID: PMC7687077 DOI: 10.1002/cmdc.201900423] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 07/16/2019] [Revised: 08/09/2019] [Indexed: 12/14/2022]
Abstract
The parasitic disease schistosomiasis is the cause of more than 200 000 human deaths per year. Although the disease is treatable, there is one major shortcoming: praziquantel has been the only drug used to combat these parasites since 1977. The risk of the emergence of resistant schistosomes is known to be increasing, as a reduced sensitivity of these parasites toward praziquantel has been observed. We developed a new class of substances, which are derived from inhibitors of human aldose reductase, and which showed promising activity against Schistosoma mansoni couples in vitro. Further optimisation of the compounds led to an increase in anti‐schistosomal activity with observed phenotypes such as reduced egg production, vitality, and motility as well as tegumental damage and gut dilatation. Here, we performed structure–activity relationship studies on the carboxylic acid moiety of biarylalkyl carboxylic acids. Out of 82 carboxylic acid amides, we identified 10 compounds that are active against S. mansoni at 25 μm. The best five compounds showed an anti‐schistosomal activity up to 10 μm and induced severe phenotypes. Cytotoxicity tests in human cell lines showed that two derivatives had no cytotoxicity at 50 or 100 μm. These compounds are promising candidates for further optimisation toward the new anti‐schistosomal agents.
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Affiliation(s)
- Alejandra M Peter Ventura
- Department of Pharmaceutical Chemistry, Philipps Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Simone Haeberlein
- BFS, Institute of Parasitology, Justus-Liebig-Universität Gießen, Schubertstrasse 81, 35392, Gießen, Germany
| | - Kerstin Lange-Grünweller
- Department of Pharmaceutical Chemistry, Philipps Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Arnold Grünweller
- Department of Pharmaceutical Chemistry, Philipps Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Roland K Hartmann
- Department of Pharmaceutical Chemistry, Philipps Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Christoph G Grevelding
- BFS, Institute of Parasitology, Justus-Liebig-Universität Gießen, Schubertstrasse 81, 35392, Gießen, Germany
| | - Martin Schlitzer
- Department of Pharmaceutical Chemistry, Philipps Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
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19
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Schwarz TS, Wäber NB, Feyh R, Weidenbach K, Schmitz RA, Marchfelder A, Hartmann RK. Homologs of aquifex aeolicus protein-only RNase P are not the major RNase P activities in the archaea haloferax volcanii and methanosarcina mazei. IUBMB Life 2019; 71:1109-1116. [PMID: 31283101 DOI: 10.1002/iub.2122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 05/09/2019] [Revised: 06/07/2019] [Accepted: 06/09/2019] [Indexed: 01/20/2023]
Abstract
The mature 5'-ends of tRNAs are generated by RNase P in all domains of life. The ancient form of the enzyme is a ribonucleoprotein consisting of a catalytic RNA and one or more protein subunits. However, in the hyperthermophilic bacterium Aquifex aeolicus and close relatives, RNase P is a protein-only enzyme consisting of a single type of polypeptide (Aq_880, ~23 kDa). In many archaea, homologs of Aq_880 were identified (termed HARPs for Homologs of Aquifex RNase P) in addition to the RNA-based RNase P, raising the question about the functions of HARP and the classical RNase P in these archaea. Here we investigated HARPs from two euryarchaeotes, Haloferax volcanii and Methanosarcina mazei. Archaeal strains with HARP gene knockouts showed no growth phenotypes under standard conditions, temperature and salt stress (H. volcanii) or nitrogen deficiency (M. mazei). Recombinant H. volcanii and M. mazei HARPs were basically able to catalyse specific tRNA 5'-end maturation in vitro. Furthermore, M. mazei HARP was able to rescue growth of an Escherichia coli RNase P depletion strain with comparable efficiency as Aq_880, while H. volcanii HARP was unable to do so. In conclusion, both archaeal HARPs showed the capacity (in at least one functional assay) to act as RNases P. However, the ease to obtain knockouts of the singular HARP genes and the lack of growth phenotypes upon HARP gene deletion contrasts with the findings that the canonical RNase P RNA gene cannot be deleted in H. volcanii, and a knockdown of RNase P RNA in H. volcanii results in severe tRNA processing defects. We conclude that archaeal HARPs do not make a major contribution to global tRNA 5'-end maturation in archaea, but may well exert a specialised, yet unknown function in (t)RNA metabolism. © 2019 IUBMB Life, 2019 © 2019 IUBMB Life, 71(8):1109-1116, 2019.
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Affiliation(s)
| | - Nadine B Wäber
- Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
| | - Rebecca Feyh
- Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
| | - Katrin Weidenbach
- Institute of General Microbiology, Christian-Albrechts-Universität, Kiel, Germany
| | - Ruth A Schmitz
- Institute of General Microbiology, Christian-Albrechts-Universität, Kiel, Germany
| | | | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
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20
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Kellershohn J, Thomas L, Hahnel SR, Grünweller A, Hartmann RK, Hardt M, Vilcinskas A, Grevelding CG, Haeberlein S. Insects in anthelminthics research: Lady beetle-derived harmonine affects survival, reproduction and stem cell proliferation of Schistosoma mansoni. PLoS Negl Trop Dis 2019; 13:e0007240. [PMID: 30870428 PMCID: PMC6436750 DOI: 10.1371/journal.pntd.0007240] [Citation(s) in RCA: 12] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/27/2019] [Accepted: 02/13/2019] [Indexed: 02/07/2023] Open
Abstract
Natural products have moved into the spotlight as possible sources for new drugs in the treatment of helminth infections including schistosomiasis. Surprisingly, insect-derived compounds have largely been neglected so far in the search for novel anthelminthics, despite the generally recognized high potential of insect biotechnology for drug discovery. This motivated us to assess the antischistosomal capacity of harmonine, an antimicrobial alkaloid from the harlequin ladybird Harmonia axyridis that raised high interest in insect biotechnology in recent years. We observed remarkably pleiotropic effects of harmonine on physiological, cellular, and molecular processes in adult male and female Schistosoma mansoni at concentrations as low as 5 μM in vitro. This included tegumental damage, gut dilatation, dysplasia of gonads, a complete stop of egg production at 10 μM, and increased production of abnormally shaped eggs at 5 μM. Motility was reduced with an EC50 of 8.8 μM and lethal effects occurred at 10–20 μM within 3 days of culture. Enzyme inhibition assays revealed acetylcholinesterase (AChE) as one potential target of harmonine. To assess possible effects on stem cells, which represent attractive anthelminthic targets, we developed a novel in silico 3D reconstruction of gonads based on confocal laser scanning microscopy of worms after EdU incorporation to allow for quantification of proliferating stem cells per organ. Harmonine significantly reduced the number of proliferating stem cells in testes, ovaries, and also the number of proliferating parenchymal neoblasts. This was further supported by a downregulated expression of the stem cell markers nanos-1 and nanos-2 in harmonine-treated worms revealed by quantitative real-time PCR. Our data demonstrate a multifaceted antischistosomal activity of the lady beetle-derived compound harmonine, and suggest AChE and stem cell genes as possible targets. Harmonine is the first animal-derived alkaloid detected to have antischistosomal capacity. This study highlights the potential of exploiting insects as a source for the discovery of anthelminthics. Natural compounds represent one of the richest sources for the discovery of new active compounds against diseases such as cancer or infections, including helminth infections that cause the highest disease burden in tropical countries. Surprisingly, insects have been almost completely neglected with respect to anthelminthics discovery although they represent the most species-rich class of animals known on earth, producing a wide spectrum of compounds with biological activities. In insect biotechnology, the harlequin ladybird Harmonia axyridis raised high interest being a rich source of antimicrobial compounds such as the alkaloid harmonine. Harmonine is thought to act as a chemical weapon keeping otherwise detrimental microsporidia in the beetle under control. Testing the antiparasitic potential of harmonine against adult Schistosoma mansoni, one of the most harmful helminths worldwide, resulted in multifaceted negative effects. The compound damaged tissues essential for survival and reproduction of schistosomes (tegument, intestine, gonads) and also affected stem-cell proliferation. Furthermore, we obtained first evidence for acetylcholinesterase as one potential molecular target, which was partially inhibited by harmonine. This is the first time to proof a direct effect of a defined insect-derived compound on a helminth parasite, a finding that will encourage further studies to explore insects as sources of novel anthelminthics.
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Affiliation(s)
- Josina Kellershohn
- Institute of Parasitology, BFS, Justus Liebig University, Giessen, Germany
| | - Laura Thomas
- Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
| | - Steffen R. Hahnel
- Institute of Parasitology, BFS, Justus Liebig University, Giessen, Germany
| | - Arnold Grünweller
- Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
| | - Roland K. Hartmann
- Institute of Pharmaceutical Chemistry, Philipps University, Marburg, Germany
| | - Martin Hardt
- Biomedical Research Center Seltersberg—Imaging Unit, Justus Liebig University, Giessen, Germany
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus Liebig University, Giessen, Germany
| | | | - Simone Haeberlein
- Institute of Parasitology, BFS, Justus Liebig University, Giessen, Germany
- * E-mail:
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21
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Aldag J, Persson T, Hartmann RK. 2'-Fluoro-Pyrimidine-Modified RNA Aptamers Specific for Lipopolysaccharide Binding Protein (LBP). Int J Mol Sci 2018; 19:ijms19123883. [PMID: 30563044 PMCID: PMC6321028 DOI: 10.3390/ijms19123883] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 12/12/2022] Open
Abstract
Lipopolysaccaride binding protein (LBP), a glycosylated acute phase protein, plays an important role in the pathophysiology of sepsis. LBP binds with high affinity to the lipid part of bacterial lipopolysaccaride (LPS). Inhibition of the LPS-LBP interaction or blockage of LBP-mediated transfer of LPS monomers to CD14 may be therapeutical strategies to prevent septic shock. LBP is also of interest as a biomarker to identify septic patients at high risk for death, as LBP levels are elevated during early stages of severe sepsis. As a first step toward such potential applications, we isolated aptamers specific for murine LBP (mLBP) by in vitro selection from a library containing a 60-nucleotide randomized region. Modified RNA pools were transcribed in the presence of 2′-fluoro-modified pyrimidine nucleotides to stabilize transcripts against nuclease degradation. As verified for one aptamer experimentally, the selected aptamers adopt a “three-helix junction” architecture, presenting single-stranded 7-nt (5′-YGCTTCY) or 6-nt (5′-RTTTCY) consensus sequences in their core. The best binder (aptamer A011; Kd of 270 nM for binding to mLBP), characterized in more detail by structure probing and boundary analysis, was demonstrated to bind with high specificity to murine LBP.
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Affiliation(s)
- Jasmin Aldag
- Jasmin Aldag, EUROIMMUN AG, Seekamp 31, D-23560 Lübeck, Germany.
| | - Tina Persson
- Tina Persson, Passage2Pro AB, Östra Kristinelundsvägen 4B, SE-21748 Malmö, Sweden.
| | - Roland K Hartmann
- Roland K. Hartmann, Philipps-Universität Marburg, Institut für Pharmazeutische Chemie, Marbacher Weg 6, D-35037 Marburg, Germany.
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22
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Müller C, Schulte FW, Lange-Grünweller K, Obermann W, Madhugiri R, Pleschka S, Ziebuhr J, Hartmann RK, Grünweller A. Broad-spectrum antiviral activity of the eIF4A inhibitor silvestrol against corona- and picornaviruses. Antiviral Res 2017; 150:123-129. [PMID: 29258862 PMCID: PMC7113723 DOI: 10.1016/j.antiviral.2017.12.010] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [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: 10/05/2017] [Revised: 12/12/2017] [Accepted: 12/14/2017] [Indexed: 11/28/2022]
Abstract
Coronaviruses (CoV) and picornaviruses are plus-strand RNA viruses that use 5′ cap-dependent and cap-independent strategies, respectively, for viral mRNA translation initiation. Here, we analyzed the effects of the plant compound silvestrol, a specific inhibitor of the DEAD-box RNA helicase eIF4A, on viral translation using a dual luciferase assay and virus-infected primary cells. Silvestrol was recently shown to have potent antiviral activity in Ebola virus-infected human macrophages. We found that silvestrol is also a potent inhibitor of cap-dependent viral mRNA translation in CoV-infected human embryonic lung fibroblast (MRC-5) cells. EC50 values of 1.3 nM and 3 nM silvestrol were determined for MERS-CoV and HCoV-229E, respectively. For the highly pathogenic MERS-CoV, the potent antiviral activities of silvestrol were also confirmed using peripheral blood mononuclear cells (PBMCs) as a second type of human primary cells. Silvestrol strongly inhibits the expression of CoV structural and nonstructural proteins (N, nsp8) and the formation of viral replication/transcription complexes. Furthermore, potential antiviral effects against human rhinovirus (HRV) A1 and poliovirus type 1 (PV), representing different species in the genus Enterovirus (family Picornaviridae), were investigated. The two viruses employ an internal ribosomal entry site (IRES)-mediated translation initiation mechanism. For PV, which is known to require the activity of eIF4A, an EC50 value of 20 nM silvestrol was determined in MRC-5 cells. The higher EC50 value of 100 nM measured for HRV A1 indicates a less critical role of eIF4A activity in HRV A1 IRES-mediated translation initiation. Taken together, the data reveal a broad-spectrum antiviral activity of silvestrol in infected primary cells by inhibiting eIF4A-dependent viral mRNA translation. The eIF4A inhibitor silvestrol is a potent antiviral compound that inhibits the replication of coronaviruses. Silvestrol is also effective against picornaviruses with an eIF4A-dependent Type 1 IRES element. In primary cells silvestrol has potent antiviral activity and low toxicity. Targeting the host factor eIF4A is a promising broad-spectrum antiviral strategy.
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Affiliation(s)
- Christin Müller
- Institut für Medizinische Virologie, Justus-Liebig-Universität Gießen, Schubertstraße 81, 35392 Gießen, Germany; Deutsches Zentrum für Infektionsforschung (DZIF) at the partner site Gießen-Marburg-Langen, Germany
| | - Falk W Schulte
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Kerstin Lange-Grünweller
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Wiebke Obermann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Ramakanth Madhugiri
- Institut für Medizinische Virologie, Justus-Liebig-Universität Gießen, Schubertstraße 81, 35392 Gießen, Germany
| | - Stephan Pleschka
- Institut für Medizinische Virologie, Justus-Liebig-Universität Gießen, Schubertstraße 81, 35392 Gießen, Germany; Deutsches Zentrum für Infektionsforschung (DZIF) at the partner site Gießen-Marburg-Langen, Germany
| | - John Ziebuhr
- Institut für Medizinische Virologie, Justus-Liebig-Universität Gießen, Schubertstraße 81, 35392 Gießen, Germany; Deutsches Zentrum für Infektionsforschung (DZIF) at the partner site Gießen-Marburg-Langen, Germany
| | - Roland K Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Arnold Grünweller
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany.
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23
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Gößringer M, Lechner M, Brillante N, Weber C, Rossmanith W, Hartmann RK. Protein-only RNase P function in Escherichia coli: viability, processing defects and differences between PRORP isoenzymes. Nucleic Acids Res 2017; 45:7441-7454. [PMID: 28499021 PMCID: PMC5499578 DOI: 10.1093/nar/gkx405] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [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: 04/07/2017] [Accepted: 05/02/2017] [Indexed: 11/12/2022] Open
Abstract
The RNase P family comprises structurally diverse endoribonucleases ranging from complex ribonucleoproteins to single polypeptides. We show that the organellar (AtPRORP1) and the two nuclear (AtPRORP2,3) single-polypeptide RNase P isoenzymes from Arabidopsis thaliana confer viability to Escherichia coli cells with a lethal knockdown of its endogenous RNA-based RNase P. RNA-Seq revealed that AtPRORP1, compared with bacterial RNase P or AtPRORP3, cleaves several precursor tRNAs (pre-tRNAs) aberrantly in E. coli. Aberrant cleavage by AtPRORP1 was mainly observed for pre-tRNAs that can form short acceptor-stem extensions involving G:C base pairs, including tRNAAsp(GUC), tRNASer(CGA) and tRNAHis. However, both AtPRORP1 and 3 were defective in processing of E. coli pre-tRNASec carrying an acceptor stem expanded by three G:C base pairs. Instead, pre-tRNASec was degraded, suggesting that tRNASec is dispensable for E. coli under laboratory conditions. AtPRORP1, 2 and 3 are also essentially unable to process the primary transcript of 4.5S RNA, a hairpin-like non-tRNA substrate processed by E. coli RNase P, indicating that PRORP enzymes have a narrower, more tRNA-centric substrate spectrum than bacterial RNA-based RNase P enzymes. The cells' viability also suggests that the essential function of the signal recognition particle can be maintained with a 5΄-extended 4.5S RNA.
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Affiliation(s)
- Markus Gößringer
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Marcus Lechner
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Nadia Brillante
- Center for Anatomy & Cell Biology, Medical University of Vienna, Währinger Straße 13, 1090 Vienna, Austria
| | - Christoph Weber
- Center for Anatomy & Cell Biology, Medical University of Vienna, Währinger Straße 13, 1090 Vienna, Austria
| | - Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, Währinger Straße 13, 1090 Vienna, Austria
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35037 Marburg, Germany
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24
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Elkina D, Weber L, Lechner M, Burenina O, Weisert A, Kubareva E, Hartmann RK, Klug G. 6S RNA in Rhodobacter sphaeroides: 6S RNA and pRNA transcript levels peak in late exponential phase and gene deletion causes a high salt stress phenotype. RNA Biol 2017; 14:1627-1637. [PMID: 28692405 DOI: 10.1080/15476286.2017.1342933] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
The function of 6S RNA, a global regulator of transcription, was studied in the photosynthetic α-proteobacterium Rhodobacter sphaeroides. The cellular levels of R. sphaeroides 6S RNA peak toward the transition to stationary phase and strongly decrease during extended stationary phase. The synthesis of so-called product RNA transcripts (mainly 12-16-mers) on 6S RNA as template by RNA polymerase was found to be highest in late exponential phase. Product RNA ≥ 13-mers are expected to trigger the dissociation of 6S RNA:RNA polymerase complexes. A 6S RNA deletion in R. sphaeroides had no impact on growth under various metabolic and oxidative stress conditions (with the possible exception of tert-butyl hydroperoxide stress). However, the 6S RNA knockout resulted in a robust growth defect under high salt stress (0.25 M NaCl). Remarkably, the sspA gene encoding the putative salt stress-induced membrane protein SspA and located immediately downstream of the 6S RNA (ssrS) gene on the antisense strand was expressed at elevated levels in the ΔssrS strain when grown in the presence of 250 mM NaCl.
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Affiliation(s)
- Daria Elkina
- a Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology , M.V. Lomonosov Moscow State University , Leninskie Gory 1, Moscow , Russia
| | - Lennart Weber
- b Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-University-Gießen, Heinrich-Buff-Ring 26-32 , Gießen , Germany
| | - Marcus Lechner
- c Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6 , Marburg , Germany ; Skolkovo Institute for Science and Technology , Skoltech, Moscow
| | - Olga Burenina
- a Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology , M.V. Lomonosov Moscow State University , Leninskie Gory 1, Moscow , Russia
| | - Andrea Weisert
- b Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-University-Gießen, Heinrich-Buff-Ring 26-32 , Gießen , Germany
| | - Elena Kubareva
- a Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology , M.V. Lomonosov Moscow State University , Leninskie Gory 1, Moscow , Russia
| | - Roland K Hartmann
- c Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6 , Marburg , Germany ; Skolkovo Institute for Science and Technology , Skoltech, Moscow
| | - Gabriele Klug
- b Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-University-Gießen, Heinrich-Buff-Ring 26-32 , Gießen , Germany
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25
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Affiliation(s)
- Arnold Grünweller
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Roland K Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
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26
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Pelaz B, Alexiou C, Alvarez-Puebla RA, Alves F, Andrews AM, Ashraf S, Balogh LP, Ballerini L, Bestetti A, Brendel C, Bosi S, Carril M, Chan WCW, Chen C, Chen X, Chen X, Cheng Z, Cui D, Du J, Dullin C, Escudero A, Feliu N, Gao M, George M, Gogotsi Y, Grünweller A, Gu Z, Halas NJ, Hampp N, Hartmann RK, Hersam MC, Hunziker P, Jian J, Jiang X, Jungebluth P, Kadhiresan P, Kataoka K, Khademhosseini A, Kopeček J, Kotov NA, Krug HF, Lee DS, Lehr CM, Leong KW, Liang XJ, Ling Lim M, Liz-Marzán LM, Ma X, Macchiarini P, Meng H, Möhwald H, Mulvaney P, Nel AE, Nie S, Nordlander P, Okano T, Oliveira J, Park TH, Penner RM, Prato M, Puntes V, Rotello VM, Samarakoon A, Schaak RE, Shen Y, Sjöqvist S, Skirtach AG, Soliman MG, Stevens MM, Sung HW, Tang BZ, Tietze R, Udugama BN, VanEpps JS, Weil T, Weiss PS, Willner I, Wu Y, Yang L, Yue Z, Zhang Q, Zhang Q, Zhang XE, Zhao Y, Zhou X, Parak WJ. Diverse Applications of Nanomedicine. ACS Nano 2017; 11:2313-2381. [PMID: 28290206 PMCID: PMC5371978 DOI: 10.1021/acsnano.6b06040] [Citation(s) in RCA: 733] [Impact Index Per Article: 104.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Indexed: 04/14/2023]
Abstract
The design and use of materials in the nanoscale size range for addressing medical and health-related issues continues to receive increasing interest. Research in nanomedicine spans a multitude of areas, including drug delivery, vaccine development, antibacterial, diagnosis and imaging tools, wearable devices, implants, high-throughput screening platforms, etc. using biological, nonbiological, biomimetic, or hybrid materials. Many of these developments are starting to be translated into viable clinical products. Here, we provide an overview of recent developments in nanomedicine and highlight the current challenges and upcoming opportunities for the field and translation to the clinic.
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Affiliation(s)
- Beatriz Pelaz
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Christoph Alexiou
- ENT-Department, Section of Experimental Oncology & Nanomedicine
(SEON), Else Kröner-Fresenius-Stiftung-Professorship for Nanomedicine, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Ramon A. Alvarez-Puebla
- Department of Physical Chemistry, Universitat Rovira I Virgili, 43007 Tarragona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Frauke Alves
- Department of Haematology and Medical Oncology, Department of Diagnostic
and Interventional Radiology, University
Medical Center Göttingen, 37075 Göttingen Germany
- Department of Molecular Biology of Neuronal Signals, Max-Planck-Institute for Experimental Medicine, 37075 Göttingen, Germany
| | - Anne M. Andrews
- California NanoSystems Institute, Department of Chemistry
and Biochemistry and Department of Psychiatry and Semel Institute
for Neuroscience and Human Behavior, Division of NanoMedicine and Center
for the Environmental Impact of Nanotechnology, and Department of Materials Science
and Engineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Sumaira Ashraf
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Lajos P. Balogh
- AA Nanomedicine & Nanotechnology Consultants, North Andover, Massachusetts 01845, United States
| | - Laura Ballerini
- International School for Advanced Studies (SISSA/ISAS), 34136 Trieste, Italy
| | - Alessandra Bestetti
- School of Chemistry & Bio21 Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Cornelia Brendel
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Susanna Bosi
- Department of Chemical
and Pharmaceutical Sciences, University
of Trieste, 34127 Trieste, Italy
| | - Monica Carril
- CIC biomaGUNE, Paseo de Miramón 182, 20014, Donostia - San Sebastián, Spain
- Ikerbasque, Basque Foundation
for Science, 48013 Bilbao, Spain
| | - Warren C. W. Chan
- Institute of Biomaterials
and Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Chunying Chen
- CAS Center for Excellence in Nanoscience and CAS Key
Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of
China, Beijing 100190, China
| | - Xiaodong Chen
- School of Materials
Science and Engineering, Nanyang Technological
University, Singapore 639798
| | - Xiaoyuan Chen
- Laboratory of Molecular Imaging and Nanomedicine,
National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Zhen Cheng
- Molecular
Imaging Program at Stanford and Bio-X Program, Canary Center at Stanford
for Cancer Early Detection, Stanford University, Stanford, California 94305, United States
| | - Daxiang Cui
- Institute of Nano Biomedicine and Engineering, Department of Instrument
Science and Engineering, School of Electronic Information and Electronical
Engineering, National Center for Translational Medicine, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Jianzhong Du
- Department of Polymeric Materials, School of Materials
Science and Engineering, Tongji University, Shanghai, China
| | - Christian Dullin
- Department of Haematology and Medical Oncology, Department of Diagnostic
and Interventional Radiology, University
Medical Center Göttingen, 37075 Göttingen Germany
| | - Alberto Escudero
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
- Instituto
de Ciencia de Materiales de Sevilla. CSIC, Universidad de Sevilla, 41092 Seville, Spain
| | - Neus Feliu
- Department of Clinical Science, Intervention, and Technology (CLINTEC), Karolinska Institutet, 141 86 Stockholm, Sweden
| | - Mingyuan Gao
- Institute of Chemistry, Chinese
Academy of Sciences, 100190 Beijing, China
| | | | - Yury Gogotsi
- Department of Materials Science and Engineering and A.J. Drexel Nanomaterials
Institute, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Arnold Grünweller
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Zhongwei Gu
- College of Polymer Science and Engineering, Sichuan University, 610000 Chengdu, China
| | - Naomi J. Halas
- Departments of Physics and Astronomy, Rice
University, Houston, Texas 77005, United
States
| | - Norbert Hampp
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Roland K. Hartmann
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Mark C. Hersam
- Departments of Materials Science and Engineering, Chemistry,
and Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Patrick Hunziker
- University Hospital, 4056 Basel, Switzerland
- CLINAM,
European Foundation for Clinical Nanomedicine, 4058 Basel, Switzerland
| | - Ji Jian
- Department of Polymer Science and Engineering and Center for
Bionanoengineering and Department of Chemical and Biological Engineering, Zhejiang University, 310027 Hangzhou, China
| | - Xingyu Jiang
- CAS Center for Excellence in Nanoscience and CAS Key
Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of
China, Beijing 100190, China
| | - Philipp Jungebluth
- Thoraxklinik Heidelberg, Universitätsklinikum
Heidelberg, 69120 Heidelberg, Germany
| | - Pranav Kadhiresan
- Institute of Biomaterials
and Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada
| | | | | | - Jindřich Kopeček
- Biomedical Polymers Laboratory, University of Utah, Salt Lake City, Utah 84112, United States
| | - Nicholas A. Kotov
- Emergency Medicine, University of Michigan, Ann Arbor, Michigan 48019, United States
| | - Harald F. Krug
- EMPA, Federal Institute for Materials
Science and Technology, CH-9014 St. Gallen, Switzerland
| | - Dong Soo Lee
- Department of Molecular Medicine and Biopharmaceutical
Sciences and School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea
| | - Claus-Michael Lehr
- Department of Pharmacy, Saarland University, 66123 Saarbrücken, Germany
- HIPS - Helmhotz Institute for Pharmaceutical Research Saarland, Helmholtz-Center for Infection Research, 66123 Saarbrücken, Germany
| | - Kam W. Leong
- Department of Biomedical Engineering, Columbia University, New York City, New York 10027, United States
| | - Xing-Jie Liang
- CAS Center for Excellence in Nanoscience and CAS Key
Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of
China, Beijing 100190, China
- Laboratory of Controllable Nanopharmaceuticals, Chinese Academy of Sciences (CAS), 100190 Beijing, China
| | - Mei Ling Lim
- Department of Clinical Science, Intervention, and Technology (CLINTEC), Karolinska Institutet, 141 86 Stockholm, Sweden
| | - Luis M. Liz-Marzán
- CIC biomaGUNE, Paseo de Miramón 182, 20014, Donostia - San Sebastián, Spain
- Ikerbasque, Basque Foundation
for Science, 48013 Bilbao, Spain
- Biomedical Research Networking Center in Bioengineering Biomaterials and Nanomedicine, Ciber-BBN, 20014 Donostia - San Sebastián, Spain
| | - Xiaowei Ma
- Laboratory of Controllable Nanopharmaceuticals, Chinese Academy of Sciences (CAS), 100190 Beijing, China
| | - Paolo Macchiarini
- Laboratory of Bioengineering Regenerative Medicine (BioReM), Kazan Federal University, 420008 Kazan, Russia
| | - Huan Meng
- California NanoSystems Institute, Department of Chemistry
and Biochemistry and Department of Psychiatry and Semel Institute
for Neuroscience and Human Behavior, Division of NanoMedicine and Center
for the Environmental Impact of Nanotechnology, and Department of Materials Science
and Engineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Helmuth Möhwald
- Department of Interfaces, Max-Planck
Institute of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Paul Mulvaney
- School of Chemistry & Bio21 Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andre E. Nel
- California NanoSystems Institute, Department of Chemistry
and Biochemistry and Department of Psychiatry and Semel Institute
for Neuroscience and Human Behavior, Division of NanoMedicine and Center
for the Environmental Impact of Nanotechnology, and Department of Materials Science
and Engineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Shuming Nie
- Emory University, Atlanta, Georgia 30322, United States
| | - Peter Nordlander
- Departments of Physics and Astronomy, Rice
University, Houston, Texas 77005, United
States
| | - Teruo Okano
- Tokyo Women’s Medical University, Tokyo 162-8666, Japan
| | | | - Tai Hyun Park
- Department of Molecular Medicine and Biopharmaceutical
Sciences and School of Chemical and Biological Engineering, Seoul National University, Seoul, South Korea
- Advanced Institutes of Convergence Technology, Suwon, South Korea
| | - Reginald M. Penner
- Department of Chemistry, University of
California, Irvine, California 92697, United States
| | - Maurizio Prato
- Department of Chemical
and Pharmaceutical Sciences, University
of Trieste, 34127 Trieste, Italy
- CIC biomaGUNE, Paseo de Miramón 182, 20014, Donostia - San Sebastián, Spain
- Ikerbasque, Basque Foundation
for Science, 48013 Bilbao, Spain
| | - Victor Puntes
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
- Institut Català de Nanotecnologia, UAB, 08193 Barcelona, Spain
- Vall d’Hebron University Hospital
Institute of Research, 08035 Barcelona, Spain
| | - Vincent M. Rotello
- Department
of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Amila Samarakoon
- Institute of Biomaterials
and Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Raymond E. Schaak
- Department of Chemistry, The
Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Youqing Shen
- Department of Polymer Science and Engineering and Center for
Bionanoengineering and Department of Chemical and Biological Engineering, Zhejiang University, 310027 Hangzhou, China
| | - Sebastian Sjöqvist
- Department of Clinical Science, Intervention, and Technology (CLINTEC), Karolinska Institutet, 141 86 Stockholm, Sweden
| | - Andre G. Skirtach
- Department of Interfaces, Max-Planck
Institute of Colloids and Interfaces, 14476 Potsdam, Germany
- Department of Molecular Biotechnology, University of Ghent, B-9000 Ghent, Belgium
| | - Mahmoud G. Soliman
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Molly M. Stevens
- Department of Materials,
Department of Bioengineering, Institute for Biomedical Engineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Hsing-Wen Sung
- Department of Chemical Engineering and Institute of Biomedical
Engineering, National Tsing Hua University, Hsinchu City, Taiwan,
ROC 300
| | - Ben Zhong Tang
- Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Hong Kong, China
| | - Rainer Tietze
- ENT-Department, Section of Experimental Oncology & Nanomedicine
(SEON), Else Kröner-Fresenius-Stiftung-Professorship for Nanomedicine, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Buddhisha N. Udugama
- Institute of Biomaterials
and Biomedical Engineering, University of
Toronto, Toronto, Ontario M5S 3G9, Canada
| | - J. Scott VanEpps
- Emergency Medicine, University of Michigan, Ann Arbor, Michigan 48019, United States
| | - Tanja Weil
- Institut für
Organische Chemie, Universität Ulm, 89081 Ulm, Germany
- Max-Planck-Institute for Polymer Research, 55128 Mainz, Germany
| | - Paul S. Weiss
- California NanoSystems Institute, Department of Chemistry
and Biochemistry and Department of Psychiatry and Semel Institute
for Neuroscience and Human Behavior, Division of NanoMedicine and Center
for the Environmental Impact of Nanotechnology, and Department of Materials Science
and Engineering, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Itamar Willner
- Institute of Chemistry, The Center for
Nanoscience and Nanotechnology, The Hebrew
University of Jerusalem, Jerusalem 91904, Israel
| | - Yuzhou Wu
- Max-Planck-Institute for Polymer Research, 55128 Mainz, Germany
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, 430074 Wuhan, China
| | | | - Zhao Yue
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Qian Zhang
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
| | - Qiang Zhang
- School of Pharmaceutical Science, Peking University, 100191 Beijing, China
| | - Xian-En Zhang
- National Laboratory of Biomacromolecules,
CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing, 100101, China
| | - Yuliang Zhao
- CAS Center for Excellence in Nanoscience and CAS Key
Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of
China, Beijing 100190, China
| | - Xin Zhou
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Wolfgang J. Parak
- Fachbereich Physik, Fachbereich Medizin, Fachbereich Pharmazie, and Department of Chemistry, Philipps Universität Marburg, 35037 Marburg, Germany
- CIC biomaGUNE, Paseo de Miramón 182, 20014, Donostia - San Sebastián, Spain
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Biedenkopf N, Lange-Grünweller K, Schulte FW, Weißer A, Müller C, Becker D, Becker S, Hartmann RK, Grünweller A. The natural compound silvestrol is a potent inhibitor of Ebola virus replication. Antiviral Res 2016; 137:76-81. [PMID: 27864075 DOI: 10.1016/j.antiviral.2016.11.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 11/10/2016] [Accepted: 11/11/2016] [Indexed: 12/31/2022]
Abstract
The DEAD-box RNA helicase eIF4A, which is part of the heterotrimeric translation initiation complex in eukaryotes, is an important novel drug target in cancer research because its helicase activity is required to unwind extended and highly structured 5'-UTRs of several proto-oncogenes. Silvestrol, a natural compound isolated from the plant Aglaia foveolata, is a highly efficient, non-toxic and specific inhibitor of eIF4A. Importantly, 5'-capped viral mRNAs often contain structured 5'-UTRs as well, which may suggest a dependence on eIF4A for their translation by the host protein synthesis machinery. In view of the recent Ebola virus (EBOV) outbreak in West Africa, the identification of potent antiviral compounds is urgently required. Since Ebola mRNAs are 5'-capped and harbor RNA secondary structures in their extended 5'-UTRs, we initiated a BSL4 study to analyze silvestrol in EBOV-infected Huh-7 cells and in primary human macrophages for its antiviral activity. We observed that silvestrol inhibits EBOV infection at low nanomolar concentrations, as inferred from large reductions of viral titers. This correlated with an almost complete disappearance of EBOV proteins, comparable in effect to the translational shutdown of expression of the proto-oncoprotein PIM1, a cellular kinase known to be affected by silvestrol. Effective silvestrol concentrations were non-toxic in the tested cell systems. Thus, silvestrol appears to be a promising first-line drug for the treatment of acute EBOV and possibly other viral infections.
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Affiliation(s)
- Nadine Biedenkopf
- Institut für Virologie, Philipps-Universität Marburg, Hans-Meerwein-Str. 2, 35043, Marburg, Germany; Deutsches Zentrum für Infektionsforschung (DZIF) at the Partner Site Gießen-Marburg-Langen, Germany
| | - Kerstin Lange-Grünweller
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037, Marburg, Germany
| | - Falk W Schulte
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037, Marburg, Germany
| | - Aileen Weißer
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037, Marburg, Germany
| | - Christin Müller
- Institut für Medizinische Virologie, Justus-Liebig-Universität Gießen, Schubertstraße 81, 35392, Gießen, Germany; Deutsches Zentrum für Infektionsforschung (DZIF) at the Partner Site Gießen-Marburg-Langen, Germany
| | - Dirk Becker
- Institut für Virologie, Philipps-Universität Marburg, Hans-Meerwein-Str. 2, 35043, Marburg, Germany; Deutsches Zentrum für Infektionsforschung (DZIF) at the Partner Site Gießen-Marburg-Langen, Germany
| | - Stephan Becker
- Institut für Virologie, Philipps-Universität Marburg, Hans-Meerwein-Str. 2, 35043, Marburg, Germany; Deutsches Zentrum für Infektionsforschung (DZIF) at the Partner Site Gießen-Marburg-Langen, Germany
| | - Roland K Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037, Marburg, Germany
| | - Arnold Grünweller
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037, Marburg, Germany.
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Walczyk D, Willkomm DK, Hartmann RK. Bacterial type B RNase P: functional characterization of the L5.1-L15.1 tertiary contact and antisense inhibition. RNA 2016; 22:1699-1709. [PMID: 27604960 PMCID: PMC5066622 DOI: 10.1261/rna.057422.116] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/06/2016] [Indexed: 06/06/2023]
Abstract
Ribonuclease P is the ubiquitous endonuclease that generates the mature 5'-ends of precursor tRNAs. In bacteria, the enzyme is composed of a catalytic RNA (∼400 nucleotides) and a small essential protein subunit (∼13 kDa). Most bacterial RNase P RNAs (P RNAs) belong to the architectural type A; type B RNase P RNA is confined to the low-G+C Gram-positive bacteria. Here we demonstrate that the L5.1-L15.1 intradomain contact in the catalytic domain of the prototypic type B RNase P RNA of Bacillus subtilis is crucial for adopting a compact functional conformation: Disruption of the L5.1-L15.1 contact by antisense oligonucleotides or mutation reduced P RNA-alone and holoenzyme activity by one to two orders of magnitude in vitro, largely retarded gel mobility of the RNA and further affected the structure of regions P7/P8/P10.1, P15 and L15.2, and abolished the ability of B. subtilis P RNA to complement a P RNA-deficient Escherichia coli strain. We also provide mutational evidence that an L9-P1 tertiary contact, as found in some Mycoplasma type B RNAs, is not formed in canonical type B RNAs as represented by B. subtilis P RNA. We finally explored the P5.1 and P15 stem-loop structures as targets for LNA-modified antisense oligonucleotides. Oligonucleotides targeting P15, but not those directed against P5.1, were found to efficiently anneal to P RNA and to inhibit activity (IC50 of ∼2 nM) when incubated with preassembled B. subtilis RNase P holoenzymes.
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Affiliation(s)
- Dennis Walczyk
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, D-35037 Marburg, Germany
| | - Dagmar K Willkomm
- Klinik für Infektiologie und Mikrobiologie, Universitätsklinikum Schleswig-Holstein Campus Lübeck, D-23538 Lübeck, Germany
| | - Roland K Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, D-35037 Marburg, Germany
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Walczyk D, Gößringer M, Rossmanith W, Zatsepin TS, Oretskaya TS, Hartmann RK. Analysis of the Cleavage Mechanism by Protein-Only RNase P Using Precursor tRNA Substrates with Modifications at the Cleavage Site. J Mol Biol 2016; 428:4917-4928. [PMID: 27769719 DOI: 10.1016/j.jmb.2016.10.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 07/12/2016] [Revised: 09/28/2016] [Accepted: 10/16/2016] [Indexed: 12/23/2022]
Abstract
Ribonuclease P (RNase P) is the enzyme that endonucleolytically removes 5'-precursor sequences from tRNA transcripts in all domains of life. RNase P activities are either ribonucleoprotein (RNP) or protein-only RNase P (PRORP) enzymes, raising the question about the mechanistic strategies utilized by these architecturally different enzyme classes to catalyze the same type of reaction. Here, we analyzed the kinetics and cleavage-site selection by PRORP3 from Arabidopsis thaliana (AtPRORP3) using precursor tRNAs (pre-tRNAs) with individual modifications at the canonical cleavage site, with either Rp- or Sp-phosphorothioate, or 2'-deoxy, 2'-fluoro, 2'-amino, or 2'-O-methyl substitutions. We observed a small but robust rescue effect of Sp-phosphorothioate-modified pre-tRNA in the presence of thiophilic Cd2+ ions, consistent with metal-ion coordination to the (pro-)Sp-oxygen during catalysis. Sp-phosphorothioate, 2'-deoxy, 2'-amino, and 2'-O-methyl modification redirected the cleavage mainly to the next unmodified phosphodiester in the 5'-direction. Our findings are in line with the 2'-OH substituent at nucleotide -1 being involved in an H-bonding acceptor function. In contrast to bacterial RNase P, AtPRORP3 was found to be able to utilize the canonical and upstream cleavage site with similar efficiency (corresponding to reduced cleavage fidelity), and the two cleavage pathways appear less interdependent than in the bacterial RNA-based system.
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Affiliation(s)
- Dennis Walczyk
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, 35037 Marburg, Germany
| | - Markus Gößringer
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, 35037 Marburg, Germany
| | - Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Timofei S Zatsepin
- Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia; Skolkovo Institute of Science and Technology, 3 Nobel street, Innovation Center "Skolkovo", 143026 Skolkovo, Russia
| | - Tatiana S Oretskaya
- Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, 35037 Marburg, Germany.
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Abstract
The transcription factor VP30 of the non-segmented RNA negative strand Ebola virus balances viral transcription and replication. Here, we comprehensively studied RNA binding by VP30. Using a novel VP30:RNA electrophoretic mobility shift assay, we tested truncated variants of 2 potential natural RNA substrates of VP30 - the genomic Ebola viral 3'-leader region and its complementary antigenomic counterpart (each ∼155 nt in length) - and a series of other non-viral RNAs. Based on oligonucleotide interference, the major VP30 binding region on the genomic 3'-leader substrate was assigned to the internal expanded single-stranded region (∼ nt 125-80). Best binding to VP30 was obtained with ssRNAs of optimally ∼ 40 nt and mixed base composition; underrepresentation of purines or pyrimidines was tolerated, but homopolymeric sequences impaired binding. A stem-loop structure, particularly at the 3'-end or positioned internally, supports stable binding to VP30. In contrast, dsRNA or RNAs exposing large internal loops flanked by entirely helical arms on both sides are not bound. Introduction of a 5´-Cap(0) structure impaired VP30 binding. Also, ssDNAs bind substantially weaker than isosequential ssRNAs and heparin competes with RNA for binding to VP30, indicating that ribose 2'-hydroxyls and electrostatic contacts of the phosphate groups contribute to the formation of VP30:RNA complexes. Our results indicate a rather relaxed RNA binding specificity of filoviral VP30, which largely differs from that of the functionally related transcription factor of the Paramyxoviridae which binds to ssRNAs as short as 13 nt with a preference for oligo(A) sequences.
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Affiliation(s)
- Julia Schlereth
- a Institut für Pharmazeutische Chemie, Philipps-Universität Marburg , Marburg , Germany
| | - Arnold Grünweller
- a Institut für Pharmazeutische Chemie, Philipps-Universität Marburg , Marburg , Germany
| | - Nadine Biedenkopf
- b Institut für Virologie, Philipps-Universität Marburg , Marburg , Germany
| | - Stephan Becker
- b Institut für Virologie, Philipps-Universität Marburg , Marburg , Germany
| | - Roland K Hartmann
- a Institut für Pharmazeutische Chemie, Philipps-Universität Marburg , Marburg , Germany
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Mäder P, Blohm AS, Quack T, Lange-Grünweller K, Grünweller A, Hartmann RK, Grevelding CG, Schlitzer M. Biarylalkyl Carboxylic Acid Derivatives as Novel Antischistosomal Agents. ChemMedChem 2016; 11:1459-68. [PMID: 27159334 DOI: 10.1002/cmdc.201600127] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 03/02/2016] [Revised: 04/06/2016] [Indexed: 11/10/2022]
Abstract
Parasitic platyhelminths are responsible for serious infectious diseases, such as schistosomiasis, which affect humans as well as animals across vast regions of the world. The drug arsenal available for the treatment of these diseases is limited; for example, praziquantel is the only drug currently used to treat ≥240 million people each year infected with Schistosoma spp., and there is justified concern about the emergence of drug resistance. In this study, we screened biarylalkyl carboxylic acid derivatives for their antischistosomal activity against S. mansoni. These compounds showed significant influence on egg production, pairing stability, and vitality. Tegumental lesions or gut dilatation was also observed. Substitution of the terminal phenyl residue in the biaryl scaffold with a 3-hydroxy moiety and derivatization of the terminal carboxylic acid scaffold with carboxamides yielded compounds that displayed significant antischistosomal activity at concentrations as low as 10 μm with satisfying cytotoxicity values. The present study provides detailed insight into the structure-activity relationships of biarylalkyl carboxylic acid derivatives and thereby paves the way for a new drug-hit moiety for fighting schistosomiasis.
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Affiliation(s)
- Patrick Mäder
- Department of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Ariane S Blohm
- BFS, Institute for Parasitology, Justus-Liebig-Universität Gießen, Schubertstraße 81, 35392, Gießen, Germany
| | - Thomas Quack
- BFS, Institute for Parasitology, Justus-Liebig-Universität Gießen, Schubertstraße 81, 35392, Gießen, Germany
| | - Kerstin Lange-Grünweller
- Department of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Arnold Grünweller
- Department of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Roland K Hartmann
- Department of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Christoph G Grevelding
- BFS, Institute for Parasitology, Justus-Liebig-Universität Gießen, Schubertstraße 81, 35392, Gießen, Germany.
| | - Martin Schlitzer
- Department of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany.
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Hoch PG, Schlereth J, Lechner M, Hartmann RK. Bacillus subtilis 6S-2 RNA serves as a template for short transcripts in vivo. RNA 2016; 22:614-622. [PMID: 26873600 PMCID: PMC4793215 DOI: 10.1261/rna.055616.115] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 12/09/2015] [Accepted: 01/14/2016] [Indexed: 06/05/2023]
Abstract
The global transcriptional regulator 6S RNA is abundant in a broad range of bacteria. The RNA competes with DNA promoters for binding to the housekeeping RNA polymerase (RNAP) holoenzyme. When bound to RNAP, 6S RNA serves as a transcription template for RNAP in an RNA-dependent RNA polymerization reaction. The resulting short RNA transcripts (so-called product RNAs = pRNAs) can induce a stable structural rearrangement of 6S RNA when reaching a certain length. This rearrangement leads to the release of RNAP and thus the recovery of transcription at DNA promoters. While most bacteria express a single 6S RNA, some harbor a second 6S RNA homolog (termed 6S-2 RNA in Bacillus subtilis). Bacillus subtilis 6S-2 RNA was recently shown to exhibit essentially all hallmark features of a bona fide 6S RNA in vitro, but evidence for the synthesis of 6S-2 RNA-derived pRNAs in vivo has been lacking so far. This raised the question of whether the block of RNAP by 6S-2 RNA might be lifted by a mechanism other than pRNA synthesis. However, here we demonstrate that 6S-2 RNA is able to serve as a template for pRNA synthesis in vivo. We verify this finding by using three independent approaches including a novel primer extension assay. Thus, we demonstrate the first example of an organism that expresses two distinct 6S RNAs that both exhibit all mechanistic features defined for this type of regulatory RNA.
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Affiliation(s)
- Philipp G Hoch
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35037 Marburg, Germany
| | - Julia Schlereth
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35037 Marburg, Germany
| | - Marcus Lechner
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35037 Marburg, Germany
| | - Roland K Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35037 Marburg, Germany
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Brillante N, Gößringer M, Lindenhofer D, Toth U, Rossmanith W, Hartmann RK. Substrate recognition and cleavage-site selection by a single-subunit protein-only RNase P. Nucleic Acids Res 2016; 44:2323-36. [PMID: 26896801 PMCID: PMC4797305 DOI: 10.1093/nar/gkw080] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [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: 08/05/2015] [Accepted: 02/01/2016] [Indexed: 01/22/2023] Open
Abstract
RNase P is the enzyme that removes 5′ extensions from tRNA precursors. With its diversity of enzyme forms—either protein- or RNA-based, ranging from single polypeptides to multi-subunit ribonucleoproteins—the RNase P enzyme family represents a unique model system to compare the evolution of enzymatic mechanisms. Here we present a comprehensive study of substrate recognition and cleavage-site selection by the nuclear single-subunit proteinaceous RNase P PRORP3 from Arabidopsis thaliana. Compared to bacterial RNase P, the best-characterized RNA-based enzyme form, PRORP3 requires a larger part of intact tRNA structure, but little to no determinants at the cleavage site or interactions with the 5′ or 3′ extensions of the tRNA. The cleavage site depends on the combined dimensions of acceptor stem and T domain, but also requires the leader to be single-stranded. Overall, the single-subunit PRORP appears mechanistically more similar to the complex nuclear ribonucleoprotein enzymes than to the simpler bacterial RNase P. Mechanistic similarity or dissimilarity among different forms of RNase P thus apparently do not necessarily reflect molecular composition or evolutionary relationship.
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Affiliation(s)
- Nadia Brillante
- Center for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Markus Gößringer
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, 35037 Marburg, Germany
| | - Dominik Lindenhofer
- Center for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Ursula Toth
- Center for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Roland K Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, 35037 Marburg, Germany
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Grünweller A, Hartmann RK. Chemical modification of nucleic acids as a key technology for the development of RNA-based therapeutics. Pharmazie 2016; 71:8-16. [PMID: 26867347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
RNA-based effector molecules (nucleic acid effectors) are important tools in molecular medicine because they offer a strategy to address therapeutically interesting targets that are not "druggable" with classic small molecule inhibitors. However, for in vivo applications, RNA-based effectors require specific chemical modifications to improve their stability and pharmacokinetic properties, as well as to minimize toxic and unspecific off-target effects.
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Damm K, Bach S, Müller KMH, Klug G, Burenina OY, Kubareva EA, Grünweller A, Hartmann RK. Impact of RNA isolation protocols on RNA detection by Northern blotting. Methods Mol Biol 2015; 1296:29-38. [PMID: 25791588 DOI: 10.1007/978-1-4939-2547-6_4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We prepared total RNA from the Gram-positive soil bacterium Bacillus subtilis by different RNA extraction procedures to compare their suitability for Northern blot detection of tiny RNAs (~14-mers) or RNAs of intermediate size (100-200 nt) in terms of signal quality, intensity, and reproducibility. Our analysis included two hot phenol methods and two TRIzol extraction procedures. We found that signal intensity/detection sensitivity makes the key difference. Total RNAs prepared by the hot phenol method comprise the length spectrum from tRNAs to large ribosomal RNAs. Larger RNAs are less abundant in TRIzol preparations which instead enrich for RNAs of tRNA size and smaller. Thus, hot phenol methods are the choice for the detection of intermediate-sized and longer RNAs, whereas TRIzol extraction procedures are more suited for the detection of tiny RNAs.
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Affiliation(s)
- Katrin Damm
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037, Marburg, Germany
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Damm K, Bach S, Müller KMH, Klug G, Burenina OY, Kubareva EA, Grünweller A, Hartmann RK. Improved Northern blot detection of small RNAs using EDC crosslinking and DNA/LNA probes. Methods Mol Biol 2015; 1296:41-51. [PMID: 25791589 DOI: 10.1007/978-1-4939-2547-6_5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Successful detection of very small RNAs (tiny RNA, ~14 nt in length) by Northern blotting is dependent on improved Northern blot protocols that combine chemical crosslinking of RNA with 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) to positively charged membranes, the use of native polyacrylamide gels, and the development of highly sensitive and specific probes modified with locked nucleic acids (LNA). In this protocol, we show that Northern blot detection of tiny RNAs with 5'-digoxigenin-labeled DNA/LNA mixmer probes is a highly sensitive and specific method and, in our hands, more sensitive than using a corresponding DNA/LNA mixmer probe with a 5'-(32)P-end label.
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Affiliation(s)
- Katrin Damm
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35037, Marburg, Germany
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Abstract
6S RNA is a highly abundant small non-coding RNA widely spread among diverse bacterial groups. By competing with DNA promoters for binding to RNA polymerase (RNAP), the RNA regulates transcription on a global scale. RNAP produces small product RNAs derived from 6S RNA as template, which rearranges the 6S RNA structure leading to dissociation of 6S RNA:RNAP complexes. Although 6S RNA has been experimentally analysed in detail for some species, such as Escherichia coli and Bacillus subtilis, and was computationally predicted in many diverse bacteria, a complete and up-to-date overview of the distribution among all bacteria is missing. In this study we searched with new methods for 6S RNA genes in all currently available bacterial genomes. We ended up with a set of 1,750 6S RNA genes, of which 1,367 are novel and bona fide, distributed among 1,610 bacteria, and had a few tentative candidates among the remaining 510 assembled bacterial genomes accessible. We were able to confirm two tentative candidates by Northern blot analysis. We extended 6S RNA genes of the Flavobacteriia significantly in length compared to the present Rfam entry. We describe multiple homologs of 6S RNAs (including split 6S RNA genes) and performed a detailed synteny analysis.
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Affiliation(s)
- Stefanie Wehner
- a Department for Bioinformatics; Faculty of Mathematics and Computer Science ; Friedrich-Schiller-University of Jena , Jena , Germany
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Lechner M, Rossmanith W, Hartmann RK, Thölken C, Gutmann B, Giegé P, Gobert A. Distribution of Ribonucleoprotein and Protein-Only RNase P in Eukarya. Mol Biol Evol 2015; 32:3186-93. [PMID: 26341299 DOI: 10.1093/molbev/msv187] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
RNase P is the endonuclease that removes 5' leader sequences from tRNA precursors. In Eukarya, separate RNase P activities exist in the nucleus and mitochondria/plastids. Although all RNase P enzymes catalyze the same reaction, the different architectures found in Eukarya range from ribonucleoprotein (RNP) enzymes with a catalytic RNA and up to 10 protein subunits to single-subunit protein-only RNase P (PRORP) enzymes. Here, analysis of the phylogenetic distribution of RNP and PRORP enzymes in Eukarya revealed 1) a wealth of novel P RNAs in previously unexplored phylogenetic branches and 2) that PRORP enzymes are more widespread than previously appreciated, found in four of the five eukaryal supergroups, in the nuclei and/or organelles. Intriguingly, the occurrence of RNP RNase P and PRORP seems mutually exclusive in genetic compartments of modern Eukarya. Our comparative analysis provides a global picture of the evolution and diversification of RNase P throughout Eukarya.
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Affiliation(s)
- Marcus Lechner
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Walter Rossmanith
- Zentrum für Anatomie & Zellbiologie, Medizinische Universität Wien, Wien, Austria
| | - Roland K Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Clemens Thölken
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Bernard Gutmann
- Institut de Biologie Moléculaire des Plantes du CNRS, Strasbourg, France
| | - Philippe Giegé
- Institut de Biologie Moléculaire des Plantes du CNRS, Strasbourg, France
| | - Anthony Gobert
- Institut de Biologie Moléculaire des Plantes du CNRS, Strasbourg, France
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Köhler K, Duchardt-Ferner E, Lechner M, Damm K, Hoch PG, Salas M, Hartmann RK. Structural and mechanistic characterization of 6S RNA from the hyperthermophilic bacterium Aquifex aeolicus. Biochimie 2015; 117:72-86. [PMID: 25771336 DOI: 10.1016/j.biochi.2015.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [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: 12/01/2014] [Accepted: 03/03/2015] [Indexed: 01/26/2023]
Abstract
Bacterial 6S RNAs competitively inhibit binding of RNA polymerase (RNAP) holoenzymes to DNA promoters, thereby globally regulating transcription. RNAP uses 6S RNA itself as a template to synthesize short transcripts, termed pRNAs (product RNAs). Longer pRNAs (approx. ≥ 10 nt) rearrange the 6S RNA structure and thereby disrupt the 6S RNA:RNAP complex, which enables the enzyme to resume transcription at DNA promoters. We studied 6S RNA of the hyperthermophilic bacterium Aquifex aeolicus, representing the thermodynamically most stable 6S RNA known so far. Applying structure probing and NMR, we show that the RNA adopts the canonical rod-shaped 6S RNA architecture with little structure formation in the central bulge (CB) even at moderate temperatures (≤37 °C). 6S RNA:pRNA complex formation triggers an internal structure rearrangement of 6S RNA, i.e. formation of a so-called central bulge collapse (CBC) helix. The persistence of several characteristic NMR imino proton resonances upon pRNA annealing demonstrates that defined helical segments on both sides of the CB are retained in the pRNA-bound state, thus representing a basic framework of the RNA's architecture. RNA-seq analyses revealed pRNA synthesis from 6S RNA in A. aeolicus, identifying 9 to ∼17-mers as the major length species. A. aeolicus 6S RNA can also serve as a template for in vitro pRNA synthesis by RNAP from the mesophile Bacillus subtilis. Binding of a synthetic pRNA to A. aeolicus 6S RNA blocks formation of 6S RNA:RNAP complexes. Our findings indicate that A. aeolicus 6S RNA function in its hyperthermophilic host is mechanistically identical to that of other bacterial 6S RNAs. The use of artificial pRNA variants, designed to disrupt helix P2 from the 3'-CB instead of the 5'-CB but preventing formation of the CBC helix, indicated that the mechanism of pRNA-induced RNAP release has been evolutionarily optimized for transcriptional pRNA initiation in the 5'-CB.
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MESH Headings
- Bacteria/genetics
- Bacteria/metabolism
- Base Sequence
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA-Directed RNA Polymerases/metabolism
- Gene Expression Regulation, Bacterial
- Hot Temperature
- Magnetic Resonance Spectroscopy
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Binding
- RNA Stability
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Untranslated/chemistry
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- Sequence Analysis, RNA
- Substrate Specificity
- Transcription, Genetic
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Affiliation(s)
- Karen Köhler
- Philipps-Universität Marburg, Fachbereich Pharmazie, Institut für Pharmazeutische Chemie, Marbacher Weg 6, D-35037 Marburg, Germany.
| | - Elke Duchardt-Ferner
- Goethe-Universität Frankfurt am Main, Institut für Molekulare Biowissenschaften, Max-von-Laue-Straße 9, D-60438 Frankfurt am Main, Germany; Zentrum für biomagnetische Resonanzspektroskopie (BMRZ), Goethe-Universität Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.
| | - Marcus Lechner
- Philipps-Universität Marburg, Fachbereich Pharmazie, Institut für Pharmazeutische Chemie, Marbacher Weg 6, D-35037 Marburg, Germany.
| | - Katrin Damm
- Philipps-Universität Marburg, Fachbereich Pharmazie, Institut für Pharmazeutische Chemie, Marbacher Weg 6, D-35037 Marburg, Germany.
| | - Philipp G Hoch
- Philipps-Universität Marburg, Fachbereich Pharmazie, Institut für Pharmazeutische Chemie, Marbacher Weg 6, D-35037 Marburg, Germany.
| | - Margarita Salas
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.
| | - Roland K Hartmann
- Philipps-Universität Marburg, Fachbereich Pharmazie, Institut für Pharmazeutische Chemie, Marbacher Weg 6, D-35037 Marburg, Germany.
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Hoch PG, Burenina OY, Weber MHW, Elkina DA, Nesterchuk MV, Sergiev PV, Hartmann RK, Kubareva EA. Phenotypic characterization and complementation analysis of Bacillus subtilis 6S RNA single and double deletion mutants. Biochimie 2015; 117:87-99. [PMID: 25576829 DOI: 10.1016/j.biochi.2014.12.019] [Citation(s) in RCA: 15] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/22/2014] [Indexed: 10/24/2022]
Abstract
6S RNA, a global regulator of transcription in bacteria, binds to housekeeping RNA polymerase (RNAP) holoenzymes to competitively inhibit transcription from DNA promoters. Bacillus subtilis encodes two 6S RNA homologs whose differential functions are as yet unclear. We constructed derivative strains of B. subtilis PY79 lacking 6S-1 RNA (ΔbsrA), 6S-2 RNA (ΔbsrB) or both (ΔbsrAB) to study the physiological role of the two 6S RNAs. We observed two growth phenotypes of mutant strains: (i) accelerated decrease of optical density toward extended stationary phase and (ii) faster outgrowth from stationary phase under alkaline stress conditions (pH 9.8). The first phenotype was observed for bacteria lacking bsrA, and even more pronounced for ΔbsrAB bacteria, but not for those lacking bsrB. The magnitude of the second phenotype was relatively weak for ΔbsrB, moderate for ΔbsrA and again strongest for ΔbsrAB bacteria. Whereas ΔbsrAB bacteria complemented with bsrB or bsrA (strains ΔbsrAB + B and ΔbsrAB + A) mimicked the phenotypes of the ΔbsrA and ΔbsrB strains, respectively, complementation with the gene ssrS encoding Escherichia coli 6S RNA failed to cure the "low stationary optical density" phenotype of the double mutant, despite ssrS expression, in line with previous findings. Finally, proteomics (two-dimensional differential gel electrophoresis, 2D-DIGE) of B. subtilis 6S RNA deletion strains unveiled a set of proteins that were expressed at higher levels particularly during exponential growth and preferentially in mutant strains lacking 6S-2 RNA. Several of these proteins are involved in metabolism and stress responses.
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Affiliation(s)
- Philipp G Hoch
- Philipps-Universität Marburg, Fachbereich Pharmazie, Institut für Pharmazeutische Chemie, Marbacher Weg 6, D-35037 Marburg, Germany.
| | - Olga Y Burenina
- Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia.
| | - Michael H W Weber
- Philipps-Universität Marburg, Fachbereich Pharmazie, Institut für Pharmazeutische Chemie, Marbacher Weg 6, D-35037 Marburg, Germany.
| | - Daria A Elkina
- Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia.
| | - Mikhail V Nesterchuk
- Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia.
| | - Petr V Sergiev
- Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia.
| | - Roland K Hartmann
- Philipps-Universität Marburg, Fachbereich Pharmazie, Institut für Pharmazeutische Chemie, Marbacher Weg 6, D-35037 Marburg, Germany.
| | - Elena A Kubareva
- Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia.
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Lechner M, Hernandez-Rosales M, Doerr D, Wieseke N, Thévenin A, Stoye J, Hartmann RK, Prohaska SJ, Stadler PF. Orthology detection combining clustering and synteny for very large datasets. PLoS One 2014; 9:e105015. [PMID: 25137074 PMCID: PMC4138177 DOI: 10.1371/journal.pone.0105015] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 07/14/2014] [Indexed: 11/18/2022] Open
Abstract
The elucidation of orthology relationships is an important step both in gene function prediction as well as towards understanding patterns of sequence evolution. Orthology assignments are usually derived directly from sequence similarities for large data because more exact approaches exhibit too high computational costs. Here we present PoFF, an extension for the standalone tool Proteinortho, which enhances orthology detection by combining clustering, sequence similarity, and synteny. In the course of this work, FFAdj-MCS, a heuristic that assesses pairwise gene order using adjacencies (a similarity measure related to the breakpoint distance) was adapted to support multiple linear chromosomes and extended to detect duplicated regions. PoFF largely reduces the number of false positives and enables more fine-grained predictions than purely similarity-based approaches. The extension maintains the low memory requirements and the efficient concurrency options of its basis Proteinortho, making the software applicable to very large datasets.
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Affiliation(s)
- Marcus Lechner
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
- * E-mail:
| | - Maribel Hernandez-Rosales
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, Universität Leipzig, Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
- Departamento de Ciência da Computação, Instituto de Ciências Exatas, Universidade de Brasília, Brasília, Brasil
| | - Daniel Doerr
- Genome Informatics, Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Institute for Bioinformatics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Nicolas Wieseke
- Faculty of Mathematics and Computer Science University of Leipzig, Leipzig, Germany
| | - Annelyse Thévenin
- Genome Informatics, Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Institute for Bioinformatics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jens Stoye
- Genome Informatics, Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Institute for Bioinformatics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Roland K. Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Sonja J. Prohaska
- Computational EvoDevo Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science, Universität Leipzig, Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, Universität Leipzig, Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
- Center for non-coding RNA in Technology and Health, University of Copenhagen, Frederiksberg, Denmark
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
- RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology, Leipzig, Germany
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Weber C, Hartig A, Hartmann RK, Rossmanith W. Playing RNase P evolution: swapping the RNA catalyst for a protein reveals functional uniformity of highly divergent enzyme forms. PLoS Genet 2014; 10:e1004506. [PMID: 25101763 PMCID: PMC4125048 DOI: 10.1371/journal.pgen.1004506] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 05/27/2014] [Indexed: 11/22/2022] Open
Abstract
The RNase P family is a diverse group of endonucleases responsible for the removal of 5′ extensions from tRNA precursors. The diversity of enzyme forms finds its extremes in the eukaryal nucleus where RNA-based catalysis by complex ribonucleoproteins in some organisms contrasts with single-polypeptide enzymes in others. Such structural contrast suggests associated functional differences, and the complexity of the ribonucleoprotein was indeed proposed to broaden the enzyme's functionality beyond tRNA processing. To explore functional overlap and differences between most divergent forms of RNase P, we replaced the nuclear RNase P of Saccharomyces cerevisiae, a 10-subunit ribonucleoprotein, with Arabidopsis thaliana PRORP3, a single monomeric protein. Surprisingly, the RNase P-swapped yeast strains were viable, displayed essentially unimpaired growth under a wide variety of conditions, and, in a certain genetic background, their fitness even slightly exceeded that of the wild type. The molecular analysis of the RNase P-swapped strains showed a minor disturbance in tRNA metabolism, but did not point to any RNase P substrates or functions beyond that. Altogether, these results indicate the full functional exchangeability of the highly dissimilar enzymes. Our study thereby establishes the RNase P family, with its combination of structural diversity and functional uniformity, as an extreme case of convergent evolution. It moreover suggests that the apparently gratuitous complexity of some RNase P forms is the result of constructive neutral evolution rather than reflecting increased functional versatility. Many biocatalysts apparently evolved independently more than once, leading to structurally unrelated macromolecules catalyzing the same biochemical reaction. The RNase P enzyme family is an exceptional case of this phenomenon called convergent evolution. RNase P enzymes use not only unrelated, but chemically distinct macromolecules, either RNA or protein, to catalyze a specific step in the biogenesis of transfer RNAs, the ubiquitous adaptor molecules in protein synthesis. However, this fundamental difference in the identity of the actual catalyst, together with a broad variation in structural complexity of the diverse forms of RNase P, cast doubts on their functional equivalence. Here we compared two of the structurally most extreme variants of RNase P by replacing the yeast nuclear enzyme, a 10-subunit RNA-protein complex, with a single-protein from plants representing the apparently simplest form of RNase P. Surprisingly, the viability and fitness of these RNase P-swapped yeasts and their molecular analyses demonstrated the full functional exchangeability of the highly dissimilar enzymes. The RNase P family, with its combination of structural diversity and functional uniformity, thus not only truly represents an extraordinary case of convergent evolution, but also demonstrates that increased structural complexity does not necessarily entail broadened functionality, but may rather be the result of “neutral” evolutionary mechanisms.
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Affiliation(s)
- Christoph Weber
- Center for Anatomy & Cell Biology, Medical University of Vienna, Vienna, Austria
| | - Andreas Hartig
- Max F. Perutz Laboratories, Department of Biochemistry and Cell Biology, University of Vienna, Vienna, Austria
| | - Roland K. Hartmann
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, Vienna, Austria
- * E-mail:
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Lechner M, Nickel AI, Wehner S, Riege K, Wieseke N, Beckmann BM, Hartmann RK, Marz M. Genomewide comparison and novel ncRNAs of Aquificales. BMC Genomics 2014; 15:522. [PMID: 24965762 PMCID: PMC4227106 DOI: 10.1186/1471-2164-15-522] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 05/08/2014] [Indexed: 12/05/2022] Open
Abstract
Background The Aquificales are a diverse group of thermophilic bacteria that thrive in terrestrial and marine hydrothermal environments. They can be divided into the families Aquificaceae, Desulfurobacteriaceae and Hydrogenothermaceae. Although eleven fully sequenced and assembled genomes are available, only little is known about this taxonomic order in terms of RNA metabolism. Results In this work, we compare the available genomes, extend their protein annotation, identify regulatory sequences, annotate non-coding RNAs (ncRNAs) of known function, predict novel ncRNA candidates, show idiosyncrasies of the genetic decoding machinery, present two different types of transfer-messenger RNAs and variations of the CRISPR systems. Furthermore, we performed a phylogenetic analysis of the Aquificales based on entire genome sequences, and extended this by a classification among all bacteria using 16S rRNA sequences and a set of orthologous proteins. Combining several in silico features (e.g. conserved and stable secondary structures, GC-content, comparison based on multiple genome alignments) with an in vivo dRNA-seq transcriptome analysis of Aquifex aeolicus, we predict roughly 100 novel ncRNA candidates in this bacterium. Conclusions We have here re-analyzed the Aquificales, a group of bacteria thriving in extreme environments, sharing the feature of a small, compact genome with a reduced number of protein and ncRNA genes. We present several classical ncRNAs and riboswitch candidates. By combining in silico analysis with dRNA-seq data of A. aeolicus we predict nearly 100 novel ncRNA candidates.
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Affiliation(s)
| | | | | | | | | | | | - Roland K Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg, Germany.
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45
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Steuten B, Hoch PG, Damm K, Schneider S, Köhler K, Wagner R, Hartmann RK. Regulation of transcription by 6S RNAs: insights from the Escherichia coli and Bacillus subtilis model systems. RNA Biol 2014; 11:508-21. [PMID: 24786589 DOI: 10.4161/rna.28827] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Whereas, the majority of bacterial non-coding RNAs and functional RNA elements regulate post-transcriptional processes, either by interacting with other RNAs via base-pairing or through binding of small ligands (riboswitches), 6S RNAs affect transcription itself by binding to the housekeeping holoenzyme of RNA polymerase (RNAP). Remarkably, 6S RNAs serve as RNA templates for bacterial RNAP, giving rise to the de novo synthesis of short transcripts, termed pRNAs (product RNAs). Hence, 6S RNAs prompt the enzyme to act as an RNA-dependent RNA polymerase (RdRP). Synthesis of pRNAs exceeding a certain length limit (~13 nt) persistently rearrange the 6S RNA structure, which in turn, disrupts the 6S RNA:RNAP complex. This pRNA synthesis-mediated "reanimation" of sequestered RNAP molecules represents the conceivably fastest mechanism for resuming transcription in cells that enter a new exponential growth phase. The many different 6S RNAs found in a wide variety of bacteria do not share strong sequence homology but have in common a conserved rod-shaped structure with a large internal loop, termed the central bulge; this architecture mediates specific binding to the active site of RNAP. In this article, we summarize the overall state of knowledge as well as very recent findings on the structure, function, and physiological effects of 6S RNA examples from the two model organisms, Escherichia coli and Bacillus subtilis. Comparison of the presently known properties of 6S RNAs in the two organisms highlights common principles as well as diverse features.
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Affiliation(s)
- Benedikt Steuten
- Heinrich-Heine-Universität Düsseldorf; Institut für Physikalische Biologie Universitätsstr; Düsseldorf, Germany
| | | | - Katrin Damm
- Philipps-Universität Marburg; Marburg, Germany
| | - Sabine Schneider
- Heinrich-Heine-Universität Düsseldorf; Institut für Physikalische Biologie Universitätsstr; Düsseldorf, Germany
| | | | - Rolf Wagner
- Heinrich-Heine-Universität Düsseldorf; Institut für Physikalische Biologie Universitätsstr; Düsseldorf, Germany
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46
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Burenina OY, Hoch PG, Damm K, Salas M, Zatsepin TS, Lechner M, Oretskaya TS, Kubareva EA, Hartmann RK. Mechanistic comparison of Bacillus subtilis 6S-1 and 6S-2 RNAs--commonalities and differences. RNA 2014; 20:348-359. [PMID: 24464747 PMCID: PMC3923129 DOI: 10.1261/rna.042077.113] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [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: 08/20/2013] [Accepted: 11/22/2013] [Indexed: 06/03/2023]
Abstract
Bacterial 6S RNAs bind to the housekeeping RNA polymerase (σ(A)-RNAP in Bacillus subtilis) to regulate transcription in a growth phase-dependent manner. B. subtilis expresses two 6S RNAs, 6S-1 and 6S-2 RNA, with different expression profiles. We show in vitro that 6S-2 RNA shares hallmark features with 6S-1 RNA: Both (1) are able to serve as templates for pRNA transcription; (2) bind with comparable affinity to σ(A)-RNAP; (3) are able to specifically inhibit transcription from DNA promoters, and (4) can form stable 6S RNA:pRNA hybrid structures that (5) abolish binding to σ(A)-RNAP. However, pRNAs of equal length dissociate faster from 6S-2 than 6S-1 RNA, owing to the higher A,U-content of 6S-2 pRNAs. This could have two mechanistic implications: (1) Short 6S-2 pRNAs (<10 nt) dissociate faster instead of being elongated to longer pRNAs, which could make it more difficult for 6S-2 RNA-stalled RNAP molecules to escape from the sequestration; and (2) relative to 6S-1 RNA, 6S-2 pRNAs of equal length will dissociate more rapidly from 6S-2 RNA after RNAP release, which could affect pRNA turnover or the kinetics of 6S-2 RNA binding to a new RNAP molecule. As 6S-2 pRNAs have not yet been detected in vivo, we considered that cellular RNAP release from 6S-2 RNA might occur via 6S-1 RNA displacing 6S-2 RNA from the enzyme, either in the absence of pRNA transcription or upon synthesis of very short 6S-2 pRNAs (∼ 5-mers, which would escape detection by deep sequencing). However, binding competition experiments argued against these possibilities.
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Affiliation(s)
- Olga Y. Burenina
- Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Philipp G. Hoch
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35037 Marburg, Germany
| | - Katrin Damm
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35037 Marburg, Germany
| | - Margarita Salas
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Timofei S. Zatsepin
- Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Marcus Lechner
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35037 Marburg, Germany
| | - Tatiana S. Oretskaya
- Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Elena A. Kubareva
- Chemistry Department and A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Roland K. Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35037 Marburg, Germany
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47
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Thomas M, Lange-Grünweller K, Hartmann D, Golde L, Schlereth J, Streng D, Aigner A, Grünweller A, Hartmann RK. Analysis of transcriptional regulation of the human miR-17-92 cluster; evidence for involvement of Pim-1. Int J Mol Sci 2013; 14:12273-96. [PMID: 23749113 PMCID: PMC3709785 DOI: 10.3390/ijms140612273] [Citation(s) in RCA: 25] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 05/14/2013] [Accepted: 05/22/2013] [Indexed: 01/07/2023] Open
Abstract
The human polycistronic miRNA cluster miR-17-92 is frequently overexpressed in hematopoietic malignancies and cancers. Its transcription is in part controlled by an E2F-regulated host gene promoter. An intronic A/T-rich region directly upstream of the miRNA coding region also contributes to cluster expression. Our deletion analysis of the A/T-rich region revealed a strong dependence on c-Myc binding to the functional E3 site. Yet, constructs lacking the 5′-proximal ~1.3 kb or 3′-distal ~0.1 kb of the 1.5 kb A/T-rich region still retained residual specific promoter activity, suggesting multiple transcription start sites (TSS) in this region. Furthermore, the protooncogenic kinase, Pim-1, its phosphorylation target HP1γ and c-Myc colocalize to the E3 region, as inferred from chromatin immunoprecipitation. Analysis of pri-miR-17-92 expression levels in K562 and HeLa cells revealed that silencing of E2F3, c-Myc or Pim-1 negatively affects cluster expression, with a synergistic effect caused by c-Myc/Pim-1 double knockdown in HeLa cells. Thus, we show, for the first time, that the protooncogene Pim-1 is part of the network that regulates transcription of the human miR-17-92 cluster.
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Affiliation(s)
- Maren Thomas
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany; E-Mails: (M.T.); (K.L.-G.); (D.H.); (L.G.); (J.S.); (D.S.)
| | - Kerstin Lange-Grünweller
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany; E-Mails: (M.T.); (K.L.-G.); (D.H.); (L.G.); (J.S.); (D.S.)
| | - Dorothee Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany; E-Mails: (M.T.); (K.L.-G.); (D.H.); (L.G.); (J.S.); (D.S.)
| | - Lara Golde
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany; E-Mails: (M.T.); (K.L.-G.); (D.H.); (L.G.); (J.S.); (D.S.)
| | - Julia Schlereth
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany; E-Mails: (M.T.); (K.L.-G.); (D.H.); (L.G.); (J.S.); (D.S.)
| | - Dennis Streng
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany; E-Mails: (M.T.); (K.L.-G.); (D.H.); (L.G.); (J.S.); (D.S.)
| | - Achim Aigner
- Medizinische Fakultät, Rudolf-Boehm-Institut für Pharmakologie und Toxikologie, Klinische Pharmakologie, Universität Leipzig, 04107 Leipzig, Germany; E-Mail:
| | - Arnold Grünweller
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany; E-Mails: (M.T.); (K.L.-G.); (D.H.); (L.G.); (J.S.); (D.S.)
- Authors to whom correspondence should be addressed; E-Mails: (A.G.); (R.K.H.); Tel.: +49-6421-28-25553 (R.K.H.); Fax: +49-6421-28-25854 (R.K.H.)
| | - Roland K. Hartmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany; E-Mails: (M.T.); (K.L.-G.); (D.H.); (L.G.); (J.S.); (D.S.)
- Authors to whom correspondence should be addressed; E-Mails: (A.G.); (R.K.H.); Tel.: +49-6421-28-25553 (R.K.H.); Fax: +49-6421-28-25854 (R.K.H.)
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Weirauch U, Grünweller A, Cuellar L, Hartmann RK, Aigner A. U1 adaptors for the therapeutic knockdown of the oncogene pim-1 kinase in glioblastoma. Nucleic Acid Ther 2013; 23:264-72. [PMID: 23724780 DOI: 10.1089/nat.2012.0407] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
U1 small nuclear interference (U1i) has recently been described as a novel gene silencing mechanism. U1i employs short oligonucleotides, so-called U1 adaptors, for specific gene knockdown, expanding the field of current silencing strategies that are primarily based on RNA interference (RNAi) or antisense. Despite the potential of U1 adaptors as therapeutic agents, their in vivo application has not yet been studied. Here we explore U1i by analyzing U1 adaptor-mediated silencing of the oncogene Pim-1 in glioblastoma cells. We have generated Pim-1-specific U1 adaptors comprising DNA, locked nucleic acids (LNA), and 2'-O-Methyl RNA and demonstrate their ability to induce a Pim-1 knockdown, leading to antiproliferative and pro-apoptotic effects. For the therapeutic in vivo application of U1 adaptors, we establish their complexation with branched low molecular weight polyethylenimine (PEI). Upon injection of nanoscale PEI/adaptor complexes into subcutaneous glioblastoma xenografts in mice, we observed the knockdown of Pim-1 that resulted in the suppression of tumor growth. The absence of hepatotoxicity and immune stimulation also demonstrates the biocompatibility of PEI/adaptor complexes. We conclude that U1i represents an alternative to RNAi for the therapeutic silencing of pathologically upregulated genes and demonstrate the functional relevance of Pim-1 oncogene knockdown in glioblastoma. We furthermore introduce nanoscale PEI/adaptor complexes as efficient and safe for in vivo application, thus offering novel therapeutic approaches based on U1i-mediated gene knockdown.
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Affiliation(s)
- Ulrike Weirauch
- Rudolf-Boehm-Institute for Pharmacology and Toxicology, Clinical Pharmacology, University of Leipzig, Leipzig, Germany
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Kondo J, Dock-Bregeon AC, Willkomm DK, Hartmann RK, Westhof E. Structure of an A-form RNA duplex obtained by degradation of 6S RNA in a crystallization droplet. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:634-9. [PMID: 23722840 PMCID: PMC3668581 DOI: 10.1107/s1744309113013018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [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: 04/02/2013] [Accepted: 05/13/2013] [Indexed: 12/29/2022]
Abstract
In the course of a crystallographic study of a 132 nt variant of Aquifex aeolicus 6S RNA, a crystal structure of an A-form RNA duplex containing 12 base pairs was solved at a resolution of 2.6 Å. In fact, the RNA duplex is part of the 6S RNA and was obtained by accidental but precise degradation of the 6S RNA in a crystallization droplet. 6S RNA degradation was confirmed by microscopic observation of crystals and gel electrophoresis of crystallization droplets. The RNA oligomers obtained form regular A-form duplexes containing three GoU wobble-type base pairs, one of which engages in intermolecular contacts through a ribose-zipper motif at the crystal-packing interface.
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Affiliation(s)
- Jiro Kondo
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, Tokyo 102-8554, Japan.
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Weirauch U, Thomas M, Grünweller A, Hartmann RK, Aigner AM. Abstract 2187: RNAi- and U1 small nuclear interference (U1i)-mediated gene knockdown reveals the functional relevance of Pim-1 kinase in colon carcinoma and glioblastoma. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-2187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Pim-1 is a constitutively active serine/threonine kinase overexpressed in various tumors. Its role as proto-oncogene is based on several Pim-1 target proteins involved in pivotal cellular processes, and Pim-1 overexpression has been linked to poor prognosis.
RNAi-based knockdown approaches were used to inhibit Pim-1 in colon carcinoma cells. We demonstrate anti-proliferative, pro-apoptotic and overall antitumor effects of Pim-1 inhibition. The analysis of the molecular effects of Pim-1 inhibition reveals a complex regulatory network, with therapeutic Pim-1 repression leading to major changes in oncogenic signal transduction with regard to p21Cip1/WAF1, STAT3, JNK, c-Myc and survivin, and in the levels of apoptosis-related proteins Puma, Bax and Bcl-xL. Furthermore, Pim-1 knockdown sensitizes tumor cells towards 5-FU treatment, thereby antagonizing a 5-FU-triggered Pim-1 upregulation. This effect is mediated through decreased miR-15b levels, and our studies identify miR-15b and miR-33a to regulate Pim-1.
There is first evidence of Pim-1 overexpression also in glioblastoma, but the functional relevance is so far unknown. U1 small nuclear interference (U1i) has recently been described as novel gene silencing mechanism. It employs short oligonucleotides, so-called U1 adaptors, for specific gene knockdown. We generated Pim-1 specific U1 adaptors and demonstrate their ability to induce Pim-1 knockdown in GBM cells. U1 adaptor transfection leads to anti-proliferative and pro-apoptotic effects.
To explore therapeutic in vivo applications, we complexed siRNAs or U1 adaptors with a low molecular weight polyethylenimine (PEI) that mediates protection and cellular internalization. Treatment of tumor xenograft-bearing mice with PEI/siRNA or PEI/adaptor nanoparticles exhibits antitumor effects based on the knockdown of Pim-1, thus offering novel therapeutic strategies.
Conclusions: We demonstrate that Pim-1 plays a pivotal role in several tumor-relevant signalling pathways, and establish the functional relevance of Pim-1 in colon carcinoma and in glioblastoma. Our results also substantiate the RNAi-mediated Pim-1 knockdown based on polymeric PEI/siRNA nanoparticles as a promising therapeutic approach, and we show that U1i represents an alternative to RNAi for the therapeutic knockdown of pathologically upregulated genes.
Citation Format: Ulrike Weirauch, Maren Thomas, Arnold Grünweller, Roland K. Hartmann, Achim M. Aigner. RNAi- and U1 small nuclear interference (U1i)-mediated gene knockdown reveals the functional relevance of Pim-1 kinase in colon carcinoma and glioblastoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2187. doi:10.1158/1538-7445.AM2013-2187
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