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Manalastas-Cantos K, Adoni KR, Pfeifer M, Märtens B, Grünewald K, Thalassinos K, Topf M. Modeling Flexible Protein Structure With AlphaFold2 and Crosslinking Mass Spectrometry. Mol Cell Proteomics 2024; 23:100724. [PMID: 38266916 PMCID: PMC10884514 DOI: 10.1016/j.mcpro.2024.100724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/26/2024] Open
Abstract
We propose a pipeline that combines AlphaFold2 (AF2) and crosslinking mass spectrometry (XL-MS) to model the structure of proteins with multiple conformations. The pipeline consists of two main steps: ensemble generation using AF2 and conformer selection using XL-MS data. For conformer selection, we developed two scores-the monolink probability score (MP) and the crosslink probability score (XLP)-both of which are based on residue depth from the protein surface. We benchmarked MP and XLP on a large dataset of decoy protein structures and showed that our scores outperform previously developed scores. We then tested our methodology on three proteins having an open and closed conformation in the Protein Data Bank: Complement component 3 (C3), luciferase, and glutamine-binding periplasmic protein, first generating ensembles using AF2, which were then screened for the open and closed conformations using experimental XL-MS data. In five out of six cases, the most accurate model within the AF2 ensembles-or a conformation within 1 Å of this model-was identified using crosslinks, as assessed through the XLP score. In the remaining case, only the monolinks (assessed through the MP score) successfully identified the open conformation of glutamine-binding periplasmic protein, and these results were further improved by including the "occupancy" of the monolinks. This serves as a compelling proof-of-concept for the effectiveness of monolinks. In contrast, the AF2 assessment score was only able to identify the most accurate conformation in two out of six cases. Our results highlight the complementarity of AF2 with experimental methods like XL-MS, with the MP and XLP scores providing reliable metrics to assess the quality of the predicted models. The MP and XLP scoring functions mentioned above are available at https://gitlab.com/topf-lab/xlms-tools.
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Affiliation(s)
- Karen Manalastas-Cantos
- Center for Data and Computing in Natural Sciences, Universität Hamburg, Hamburg, Germany; Department of Integrative Virology, Leibniz-Institut für Virologie (LIV), Centre for Structural Systems Biology (CSSB), Hamburg, Germany
| | - Kish R Adoni
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK; Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Matthias Pfeifer
- Department of Integrative Virology, Leibniz-Institut für Virologie (LIV), Centre for Structural Systems Biology (CSSB), Hamburg, Germany; Universitätsklinikum Hamburg Eppendorf (UKE), Hamburg, Germany
| | - Birgit Märtens
- Department of Integrative Virology, Leibniz-Institut für Virologie (LIV), Centre for Structural Systems Biology (CSSB), Hamburg, Germany; Universitätsklinikum Hamburg Eppendorf (UKE), Hamburg, Germany
| | - Kay Grünewald
- Department of Integrative Virology, Leibniz-Institut für Virologie (LIV), Centre for Structural Systems Biology (CSSB), Hamburg, Germany; Department of Chemistry, Universität Hamburg, Hamburg, Germany
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK; Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Maya Topf
- Department of Integrative Virology, Leibniz-Institut für Virologie (LIV), Centre for Structural Systems Biology (CSSB), Hamburg, Germany; Universitätsklinikum Hamburg Eppendorf (UKE), Hamburg, Germany.
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Kaiser M, Wurm JP, Märtens B, Bläsi U, Pogoryelov D, Wöhnert J. Crystal structure of the translation recovery factor Trf from Sulfolobus solfataricus. FEBS Open Bio 2019; 10:221-228. [PMID: 31804766 PMCID: PMC6996347 DOI: 10.1002/2211-5463.12772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 09/13/2019] [Revised: 11/25/2019] [Accepted: 12/03/2019] [Indexed: 11/08/2022] Open
Abstract
During translation initiation, the heterotrimeric archaeal translation initiation factor 2 (aIF2) recruits the initiator tRNAi to the small ribosomal subunit. In the stationary growth phase and/or during nutrient stress, Sulfolobus solfataricus aIF2 has a second function: It protects leaderless mRNAs against degradation by binding to their 5'-ends. The S. solfataricus protein Sso2509 is a translation recovery factor (Trf) that interacts with aIF2 and is responsible for the release of aIF2 from bound mRNAs, thereby enabling translation re-initiation. It is a member of the domain of unknown function 35 (DUF35) protein family and is conserved in Sulfolobales as well as in other archaea. Here, we present the X-ray structure of S. solfataricus Trf solved to a resolution of 1.65 Å. Trf is composed of an N-terminal rubredoxin-like domain containing a bound zinc ion and a C-terminal oligosaccharide/oligonucleotide binding fold domain. The Trf structure reveals putative mRNA binding sites in both domains. Surprisingly, the Trf protein is structurally but not sequentially very similar to proteins linked to acyl-CoA utilization-for example, the Sso2064 protein from S. solfataricus-as well as to scaffold proteins found in the acetoacetyl-CoA thiolase/high-mobility group-CoA synthase complex of the archaeon Methanothermococcus thermolithotrophicus and in a steroid side-chain-cleaving aldolase complex from the bacterium Thermomonospora curvata. This suggests that members of the DUF35 protein family are able to act as scaffolding and binding proteins in a wide variety of biological processes.
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Affiliation(s)
- Marco Kaiser
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Germany
| | - Jan Philip Wurm
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Germany
| | - Birgit Märtens
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Austria
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Austria
| | | | - Jens Wöhnert
- Institute of Molecular Biosciences and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Germany
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Bassani F, Romagnoli A, Cacciamani T, Amici A, Benelli D, Londei P, Märtens B, Bläsi U, La Teana A. Modification of translation factor aIF5A from Sulfolobus solfataricus. Extremophiles 2018; 22:769-780. [PMID: 30047030 PMCID: PMC6105217 DOI: 10.1007/s00792-018-1037-4] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/24/2018] [Indexed: 01/30/2023]
Abstract
Eukaryotic eIF5A and its bacterial orthologue EF-P are translation elongation factors whose task is to rescue ribosomes from stalling during the synthesis of proteins bearing particular sequences such as polyproline stretches. Both proteins are characterized by unique post-translational modifications, hypusination and lysinylation, respectively, which are essential for their function. An orthologue is present in all Archaea but its function is poorly understood. Here, we show that aIF5A of the crenarchaeum Sulfolobus solfataricus is hypusinated and forms a stable complex with deoxyhypusine synthase, the first enzyme of the hypusination pathway. The recombinant enzyme is able to modify its substrate in vitro resulting in deoxyhypusinated aIF5A. Moreover, with the aim to identify the enzyme involved in the second modification step, i.e. hypusination, a set of proteins interacting with aIF5A was identified.
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Affiliation(s)
- F Bassani
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - A Romagnoli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - T Cacciamani
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy.,New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - A Amici
- Department of Clinical Sciences, Section of Biochemistry, Polytechnic University of Marche, Via Ranieri 67, 60131, Ancona, Italy
| | - D Benelli
- Department of Cellular Biotechnologies and Haematology, Sapienza University of Rome, Via Regina Elena 324, 00161, Rome, Italy
| | - P Londei
- Department of Cellular Biotechnologies and Haematology, Sapienza University of Rome, Via Regina Elena 324, 00161, Rome, Italy
| | - B Märtens
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030, Vienna, Austria
| | - U Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030, Vienna, Austria
| | - A La Teana
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy.
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Märtens B, Sharma K, Urlaub H, Bläsi U. The SmAP2 RNA binding motif in the 3'UTR affects mRNA stability in the crenarchaeum Sulfolobus solfataricus. Nucleic Acids Res 2017; 45:8957-8967. [PMID: 28911098 PMCID: PMC5587771 DOI: 10.1093/nar/gkx581] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/28/2017] [Indexed: 01/02/2023] Open
Abstract
Sm and Sm-like proteins represent an evolutionarily conserved family with key roles in RNA metabolism in Pro- and Eukaryotes. In this study, a collection of 53 mRNAs that co-purified with Sulfolobus solfataricus (Sso) SmAP2 were surveyed for a specific RNA binding motif (RBM). SmAP2 was shown to bind with high affinity to the deduced consensus RNA binding motif (SmAP2-cRBM) in vitro. Residues in SmAP2 interacting with the SmAP2-cRBM were mapped by UV-induced crosslinking in combination with mass-spectrometry, and verified by mutational analyses. The RNA-binding site on SmAP2 includes a modified uracil binding pocket containing a unique threonine (T40) located on the L3 face and a second residue, K25, located in the pore. To study the function of the SmAP2-RBM in vivo, three authentic RBMs were inserted in the 3′UTR of a lacS reporter gene. The presence of the SmAP2-RBM in the reporter-constructs resulted in decreased LacS activity and reduced steady state levels of lacS mRNA. Moreover, the presence of the SmAP2-cRBM in and the replacement of the lacS 3′UTR with that of Sso2194 encompassing a SmAP2-RBM apparently impacted on the stability of the chimeric transcripts. These results are discussed in light of the function(s) of eukaryotic Lsm proteins in RNA turnover.
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Affiliation(s)
- Birgit Märtens
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Kundan Sharma
- Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert Koch Strasse 40, 37075 Göttingen, Germany.,Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert Koch Strasse 40, 37075 Göttingen, Germany.,Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
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Märtens B, Hou L, Amman F, Wolfinger MT, Evguenieva-Hackenberg E, Bläsi U. The SmAP1/2 proteins of the crenarchaeon Sulfolobus solfataricus interact with the exosome and stimulate A-rich tailing of transcripts. Nucleic Acids Res 2017; 45:7938-7949. [PMID: 28520934 PMCID: PMC5570065 DOI: 10.1093/nar/gkx437] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 06/27/2016] [Accepted: 05/03/2017] [Indexed: 01/26/2023] Open
Abstract
The conserved Sm and Sm-like proteins are involved in different aspects of RNA metabolism. Here, we explored the interactome of SmAP1 and SmAP2 of the crenarchaeon Sulfolobus solfataricus (Sso) to shed light on their physiological function(s). Both, SmAP1 and SmAP2 co-purified with several proteins involved in RNA-processing/modification, translation and protein turnover as well as with components of the exosome involved in 3΄ to 5΄ degradation of RNA. In follow-up studies a direct interaction with the poly(A) binding and accessory exosomal subunit DnaG was demonstrated. Moreover, elevated levels of both SmAPs resulted in increased abundance of the soluble exosome fraction, suggesting that they affect the subcellular localization of the exosome in the cell. The increased solubility of the exosome was accompanied by augmented levels of RNAs with A-rich tails that were further characterized using RNASeq. Hence, the observation that the Sso SmAPs impact on the activity of the exosome revealed a hitherto unrecognized function of SmAPs in archaea.
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Affiliation(s)
- Birgit Märtens
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Linlin Hou
- Institute of Microbiology and Molecular Biology, Justus Liebig University Gießen, Heinrich-Buff-Ring 26-32, 35392 Gießen, Germany
| | - Fabian Amman
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17/3, 1090 Vienna, Austria
| | - Michael T Wolfinger
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17/3, 1090 Vienna, Austria.,Center for Anatomy and Cell Biology, Medical University of Vienna, Währingerstraße 13, 1090 Vienna, Austria
| | - Elena Evguenieva-Hackenberg
- Institute of Microbiology and Molecular Biology, Justus Liebig University Gießen, Heinrich-Buff-Ring 26-32, 35392 Gießen, Germany
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
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Arkhipova V, Stolboushkina E, Kravchenko O, Kljashtorny V, Gabdulkhakov A, Garber M, Nikonov S, Märtens B, Bläsi U, Nikonov O. Binding of the 5'-Triphosphate End of mRNA to the γ-Subunit of Translation Initiation Factor 2 of the Crenarchaeon Sulfolobus solfataricus. J Mol Biol 2015; 427:3086-95. [PMID: 26244522 DOI: 10.1016/j.jmb.2015.07.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 06/30/2015] [Accepted: 07/27/2015] [Indexed: 11/24/2022]
Abstract
The heterotrimeric archaeal IF2 orthologue of eukaryotic translation initiation factor 2 consists of the α-subunit, β-subunit and γ-subunit. Previous studies showed that the γ-subunit of aIF2, besides its central role in Met-tRNAi binding, has an additional function: it binds to the 5'-triphosphorylated end of mRNA and protects its 5'-part from degradation. Competition studies with nucleotides and mRNA, as well as structural and kinetic analyses of aIF2γ mutants, strongly implicate the canonical GTP/GDP-binding pocket in binding to the 5'-triphosphate end of mRNAs. The biological implication of these findings is being discussed.
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Affiliation(s)
- Valentina Arkhipova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russian Federation
| | - Elena Stolboushkina
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russian Federation
| | - Olesya Kravchenko
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russian Federation
| | - Vladislav Kljashtorny
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russian Federation
| | - Azat Gabdulkhakov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russian Federation
| | - Maria Garber
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russian Federation
| | - Stanislav Nikonov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russian Federation
| | - Birgit Märtens
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9/4, A-1030 Vienna, Austria
| | - Udo Bläsi
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9/4, A-1030 Vienna, Austria
| | - Oleg Nikonov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russian Federation.
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Märtens B, Manoharadas S, Hasenöhrl D, Zeichen L, Bläsi U. Back to translation: removal of aIF2 from the 5'-end of mRNAs by translation recovery factor in the crenarchaeon Sulfolobus solfataricus. Nucleic Acids Res 2014; 42:2505-11. [PMID: 24271401 PMCID: PMC3936769 DOI: 10.1093/nar/gkt1169] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [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: 07/01/2013] [Revised: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 11/13/2022] Open
Abstract
The translation initiation factor aIF2 of the crenarchaeon Sulfolobus solfataricus (Sso) recruits initiator tRNA to the ribosome and stabilizes mRNAs by binding via the γ-subunit to their 5'-triphosphate end. It has been hypothesized that the latter occurs predominantly during unfavorable growth conditions, and that aIF2 or aIF2-γ is released on relief of nutrient stress to enable in particular anew translation of leaderless mRNAs. As leaderless mRNAs are prevalent in Sso and aIF2-γ bound to the 5'-end of a leaderless RNA inhibited ribosome binding in vitro, we aimed at elucidating the mechanism underlying aIF2/aIF2-γ recycling from mRNAs. We have identified a protein termed Trf (translation recovery factor) that co-purified with trimeric aIF2 during outgrowth of cells from prolonged stationary phase. Subsequent in vitro studies revealed that Trf triggers the release of trimeric aIF2 from RNA, and that Trf directly interacts with the aIF2-γ subunit. The importance of Trf is further underscored by an impaired protein synthesis during outgrowth from stationary phase in a Sso trf deletion mutant.
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Affiliation(s)
- Birgit Märtens
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Salim Manoharadas
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - David Hasenöhrl
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Lukas Zeichen
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohrgasse 9, 1030 Vienna, Austria
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Märtens B, Amman F, Manoharadas S, Zeichen L, Orell A, Albers SV, Hofacker I, Bläsi U. Alterations of the transcriptome of Sulfolobus acidocaldarius by exoribonuclease aCPSF2. PLoS One 2013; 8:e76569. [PMID: 24116119 PMCID: PMC3792030 DOI: 10.1371/journal.pone.0076569] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [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: 04/24/2013] [Accepted: 08/24/2013] [Indexed: 11/24/2022] Open
Abstract
Recent studies identified a 5´ to 3´ exoribonuclease termed Sso-RNase J in the crenarchaeon Sulfolobus solfataricus (Sso), which has been reclassified to the aCPSF2 (archaeal cleavage and polyadenylation specificity factor 2) group of β-CASP proteins. In this study, the Sso-aCPSF2 orthologue of Sulfolobus acidocaldarius (Saci-aCPSF2) was functionally characterized. Like Sso-aCPSF2, Saci-aCPSF2 degrades RNA with 5´ to 3´ directionality in vitro. To address the biological significance of Saci-aCPSF2, a deletion mutant was constructed, and the influence of Saci-aCPSF2 on the transcriptome profile was assessed employing high throughput RNA sequencing. This analysis revealed 560 genes with differential transcript abundance, suggesting a considerable role of this enzyme in RNA metabolism. In addition, bioinformatic analyses revealed several transcripts that are preferentially degraded at the 5´ end. This was exemplarily verified for two transcripts by Northern-blot analyses, showing for the first time that aCPSF2 proteins play a role in 5' to 3' directional mRNA decay in the crenarchaeal clade of Archaea.
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Affiliation(s)
- Birgit Märtens
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, Center of Molecular Biology, University of Vienna, Vienna, Austria
| | - Fabian Amman
- Institute for Theoretical Chemistry, University Vienna, Vienna, Austria
- Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Salim Manoharadas
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, Center of Molecular Biology, University of Vienna, Vienna, Austria
| | - Lukas Zeichen
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, Center of Molecular Biology, University of Vienna, Vienna, Austria
| | - Alvaro Orell
- Molecular Biology of Archaea, Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Max-Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Ivo Hofacker
- Institute for Theoretical Chemistry, University Vienna, Vienna, Austria
| | - Udo Bläsi
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, Center of Molecular Biology, University of Vienna, Vienna, Austria
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Karcher A, Büttner K, Märtens B, Jansen RP, Hopfner KP. X-ray structure of RLI, an essential twin cassette ABC ATPase involved in ribosome biogenesis and HIV capsid assembly. Structure 2005; 13:649-59. [PMID: 15837203 DOI: 10.1016/j.str.2005.02.008] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2004] [Revised: 02/01/2005] [Accepted: 02/01/2005] [Indexed: 11/28/2022]
Abstract
The ABC ATPase RNase-L inhibitor (RLI) emerges as a key enzyme in ribosome biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. To help reveal the structural mechanism of RLI, we determined the Mg2+-ADP bound crystal structure of the twin cassette ATPase of P. furiosus RLI at 1.9 A resolution and analyzed functional motifs in yeast in vivo. RLI shows similarities but also differences to known ABC enzyme structures. Twin nucleotide binding domains (NBD1 and NBD2) are arranged to form two composite active sites in their interface cleft, indicating they undergo the ATP-driven clamp-like motion of the NBDs of ABC transporters. An unusual "hinge" domain along the NBD1:NBD2 interface provides a frame for association and possibly ATP-driven conformational changes of the NBDs. Our results establish a first structural basis for ABC domain heterodimers and suggest that RLI may act as mechanochemical enzyme in ribosome and HIV capsid biogenesis.
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Affiliation(s)
- Annette Karcher
- Gene Center, Department of Chemistry and Biochemistry, University of Munich, Feodor-Lynen-Strasse 25, D-81377 Munich, Germany
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Affiliation(s)
- B. Märtens
- 1Martin-Luther-Universität, Institut für Zoologie, Domplatz 4, 06099 Halle (Saale), Germany
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