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  1. Article ; Online: Cryo-EM for Structure Determination of Mitochondrial Ribosome Samples.

    Hillen, Hauke S

    Methods in molecular biology (Clifton, N.J.)

    2023  Volume 2661, Page(s) 89–100

    Abstract: Single-particle cryoelectron microscopy (cryo-EM) allows structure determination of large macromolecular complexes from conformationally and compositionally heterogeneous mixtures of particles. This technique has been used to reveal the architecture of ... ...

    Abstract Single-particle cryoelectron microscopy (cryo-EM) allows structure determination of large macromolecular complexes from conformationally and compositionally heterogeneous mixtures of particles. This technique has been used to reveal the architecture of the mitochondrial ribosome and to visualize transient states that occur during the translation cycle or during mitoribosome biogenesis. Here, we outline an exemplary workflow for the analysis of single-particle cryo-EM data of human mitoribosome samples. In addition, we provide an example dataset which can be used for training purposes alongside the protocol.
    MeSH term(s) Humans ; Mitochondrial Ribosomes ; Cryoelectron Microscopy/methods ; Macromolecular Substances/chemistry ; Single Molecule Imaging ; Image Processing, Computer-Assisted/methods
    Chemical Substances Macromolecular Substances
    Language English
    Publishing date 2023-05-11
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3171-3_6
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  2. Article ; Online: Structure and function of SARS-CoV-2 polymerase.

    Hillen, Hauke S

    Current opinion in virology

    2021  Volume 48, Page(s) 82–90

    Abstract: Coronaviruses use an RNA-dependent RNA polymerase (RdRp) to replicate and express their genome. The RdRp associates with additional non-structural proteins (nsps) to form a replication-transcription complex (RTC) that carries out RNA synthesis, capping ... ...

    Abstract Coronaviruses use an RNA-dependent RNA polymerase (RdRp) to replicate and express their genome. The RdRp associates with additional non-structural proteins (nsps) to form a replication-transcription complex (RTC) that carries out RNA synthesis, capping and proofreading. However, the structure of the RdRp long remained elusive, thus limiting our understanding of coronavirus genome expression and replication. Recently, the cryo-electron microscopy structure of SARS-CoV-1 RdRp was reported. Driven by the ongoing COVID-19 pandemic, structural data on the SARS-CoV-2 polymerase and associated factors has since emerged at an unprecedented pace, with more than twenty structures released to date. This review provides an overview of the currently available coronavirus RdRp structures and outlines how they have, together with functional studies, led to a molecular understanding of the viral polymerase, its interactions with accessory factors and the mechanisms by which promising antivirals may inhibit coronavirus replication.
    MeSH term(s) Coronavirus RNA-Dependent RNA Polymerase/chemistry ; Coronavirus RNA-Dependent RNA Polymerase/metabolism ; Protein Binding ; Protein Conformation ; RNA, Viral/metabolism ; SARS-CoV-2/enzymology
    Chemical Substances RNA, Viral ; Coronavirus RNA-Dependent RNA Polymerase (EC 2.7.7.48)
    Language English
    Publishing date 2021-04-06
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 2611378-8
    ISSN 1879-6265 ; 1879-6257
    ISSN (online) 1879-6265
    ISSN 1879-6257
    DOI 10.1016/j.coviro.2021.03.010
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  3. Article: Structural and mechanistic basis of RNA processing by protein-only ribonuclease P enzymes.

    Bhatta, Arjun / Hillen, Hauke S

    Trends in biochemical sciences

    2022  Volume 47, Issue 11, Page(s) 965–977

    Abstract: Ribonuclease P (RNase P) enzymes are responsible for the 5' processing of tRNA precursors. In addition to the well-characterised ribozyme-based RNase P enzymes, an evolutionarily distinct group of protein-only RNase Ps exists. These proteinaceous RNase ... ...

    Abstract Ribonuclease P (RNase P) enzymes are responsible for the 5' processing of tRNA precursors. In addition to the well-characterised ribozyme-based RNase P enzymes, an evolutionarily distinct group of protein-only RNase Ps exists. These proteinaceous RNase Ps (PRORPs) can be found in all three domains of life and can be divided into two structurally different types: eukaryotic and prokaryotic. Recent structural studies on members of both families reveal a surprising diversity of molecular architectures, but also highlight conceptual and mechanistic similarities. Here, we provide a comparison between the different types of PRORP enzymes and review how the combination of structural, biochemical, and biophysical studies has led to a molecular picture of protein-mediated tRNA processing.
    MeSH term(s) Arabidopsis/genetics ; Humans ; RNA Processing, Post-Transcriptional ; RNA, Catalytic/metabolism ; RNA, Transfer/metabolism ; Ribonuclease P/chemistry ; Ribonuclease P/genetics ; Ribonuclease P/metabolism
    Chemical Substances RNA, Catalytic ; RNA, Transfer (9014-25-9) ; Ribonuclease P (EC 3.1.26.5)
    Language English
    Publishing date 2022-06-18
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 194216-5
    ISSN 1362-4326 ; 0968-0004 ; 0376-5067
    ISSN (online) 1362-4326
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2022.05.006
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  4. Article: Structural and mechanistic basis of RNA processing by protein-only ribonuclease P enzymes

    Bhatta, Arjun / Hillen, Hauke S.

    Trends in biochemical sciences. 2022,

    2022  

    Abstract: Ribonuclease P (RNase P) enzymes are responsible for the 5′ processing of tRNA precursors. In addition to the well-characterised ribozyme-based RNase P enzymes, an evolutionarily distinct group of protein-only RNase Ps exists. These proteinaceous RNase ... ...

    Abstract Ribonuclease P (RNase P) enzymes are responsible for the 5′ processing of tRNA precursors. In addition to the well-characterised ribozyme-based RNase P enzymes, an evolutionarily distinct group of protein-only RNase Ps exists. These proteinaceous RNase Ps (PRORPs) can be found in all three domains of life and can be divided into two structurally different types: eukaryotic and prokaryotic. Recent structural studies on members of both families reveal a surprising diversity of molecular architectures, but also highlight conceptual and mechanistic similarities. Here, we provide a comparison between the different types of PRORP enzymes and review how the combination of structural, biochemical, and biophysical studies has led to a molecular picture of protein-mediated tRNA processing.
    Keywords RNA precursors ; architecture ; ribonucleases
    Language English
    Publishing place Elsevier Ltd
    Document type Article
    Note Pre-press version
    ZDB-ID 194220-7
    ISSN 0968-0004 ; 0376-5067
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2022.05.006
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  5. Article ; Online: Structure of the multi-subunit chloroplast RNA polymerase.

    do Prado, Paula F V / Ahrens, Frederik M / Liebers, Monique / Ditz, Noah / Braun, Hans-Peter / Pfannschmidt, Thomas / Hillen, Hauke S

    Molecular cell

    2024  Volume 84, Issue 5, Page(s) 910–925.e5

    Abstract: Chloroplasts contain a dedicated genome that encodes subunits of the photosynthesis machinery. Transcription of photosynthesis genes is predominantly carried out by a plastid-encoded RNA polymerase (PEP), a nearly 1 MDa complex composed of core subunits ... ...

    Abstract Chloroplasts contain a dedicated genome that encodes subunits of the photosynthesis machinery. Transcription of photosynthesis genes is predominantly carried out by a plastid-encoded RNA polymerase (PEP), a nearly 1 MDa complex composed of core subunits with homology to eubacterial RNA polymerases (RNAPs) and at least 12 additional chloroplast-specific PEP-associated proteins (PAPs). However, the architecture of this complex and the functions of the PAPs remain unknown. Here, we report the cryo-EM structure of a 19-subunit PEP complex from Sinapis alba (white mustard). The structure reveals that the PEP core resembles prokaryotic and nuclear RNAPs but contains chloroplast-specific features that mediate interactions with the PAPs. The PAPs are unrelated to known transcription factors and arrange around the core in a unique fashion. Their structures suggest potential functions during transcription in the chemical environment of chloroplasts. These results reveal structural insights into chloroplast transcription and provide a framework for understanding photosynthesis gene expression.
    MeSH term(s) RNA, Chloroplast/metabolism ; DNA-Directed RNA Polymerases/genetics ; DNA-Directed RNA Polymerases/metabolism ; Chloroplasts/genetics ; Chloroplasts/metabolism ; Plastids/genetics ; Plastids/metabolism ; Gene Expression Regulation, Plant ; Transcription, Genetic
    Chemical Substances RNA, Chloroplast ; DNA-Directed RNA Polymerases (EC 2.7.7.6)
    Language English
    Publishing date 2024-02-29
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1415236-8
    ISSN 1097-4164 ; 1097-2765
    ISSN (online) 1097-4164
    ISSN 1097-2765
    DOI 10.1016/j.molcel.2024.02.003
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    Zs.A 5055: Show issues Location:
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  6. Article ; Online: Hierarchical folding of the catalytic core during mitochondrial ribosome biogenesis.

    Lavdovskaia, Elena / Hillen, Hauke S / Richter-Dennerlein, Ricarda

    Trends in cell biology

    2021  Volume 32, Issue 3, Page(s) 182–185

    Abstract: Final maturation steps during ribosome biogenesis require the assistance of assembly and quality control factors to ensure the folding of rRNA and proteins into a functional translation machinery. Here we integrate several recent structural snapshots of ... ...

    Abstract Final maturation steps during ribosome biogenesis require the assistance of assembly and quality control factors to ensure the folding of rRNA and proteins into a functional translation machinery. Here we integrate several recent structural snapshots of native large ribosomal subunit intermediates into the complex pathway of mitochondrial ribosome assembly.
    MeSH term(s) Catalytic Domain ; Humans ; Mitochondrial Ribosomes/chemistry ; Mitochondrial Ribosomes/metabolism ; Organelle Biogenesis ; RNA, Ribosomal/metabolism ; Ribosomal Proteins/analysis ; Ribosomal Proteins/genetics ; Ribosomal Proteins/metabolism ; Ribosomes/metabolism
    Chemical Substances RNA, Ribosomal ; Ribosomal Proteins
    Language English
    Publishing date 2021-10-08
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 30122-x
    ISSN 1879-3088 ; 0962-8924
    ISSN (online) 1879-3088
    ISSN 0962-8924
    DOI 10.1016/j.tcb.2021.09.004
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    Zs.MG 25: Show issues
    Zs.MO 113: Show issues
    Zs.A 3410: Show issues Location:
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  7. Article ; Online: Structural basis of RNA processing by human mitochondrial RNase P.

    Bhatta, Arjun / Dienemann, Christian / Cramer, Patrick / Hillen, Hauke S

    Nature structural & molecular biology

    2021  Volume 28, Issue 9, Page(s) 713–723

    Abstract: Human mitochondrial transcripts contain messenger and ribosomal RNAs flanked by transfer RNAs (tRNAs), which are excised by mitochondrial RNase (mtRNase) P and Z to liberate all RNA species. In contrast to nuclear or bacterial RNase P, mtRNase P is not a ...

    Abstract Human mitochondrial transcripts contain messenger and ribosomal RNAs flanked by transfer RNAs (tRNAs), which are excised by mitochondrial RNase (mtRNase) P and Z to liberate all RNA species. In contrast to nuclear or bacterial RNase P, mtRNase P is not a ribozyme but comprises three protein subunits that carry out RNA cleavage and methylation by unknown mechanisms. Here, we present the cryo-EM structure of human mtRNase P bound to precursor tRNA, which reveals a unique mechanism of substrate recognition and processing. Subunits TRMT10C and SDR5C1 form a subcomplex that binds conserved mitochondrial tRNA elements, including the anticodon loop, and positions the tRNA for methylation. The endonuclease PRORP is recruited and activated through interactions with its PPR and nuclease domains to ensure precise pre-tRNA cleavage. The structure provides the molecular basis for the first step of RNA processing in human mitochondria.
    MeSH term(s) 3-Hydroxyacyl CoA Dehydrogenases/chemistry ; 3-Hydroxyacyl CoA Dehydrogenases/metabolism ; Anticodon/chemistry ; Arabidopsis Proteins/chemistry ; Arabidopsis Proteins/metabolism ; Archaeal Proteins/chemistry ; Archaeal Proteins/metabolism ; Cryoelectron Microscopy ; Humans ; Methylation ; Methyltransferases/chemistry ; Methyltransferases/genetics ; Methyltransferases/metabolism ; Mitochondria/enzymology ; Models, Molecular ; Mutation, Missense ; Nucleic Acid Conformation ; Protein Binding ; Protein Conformation ; Protein Interaction Mapping ; RNA Precursors/metabolism ; RNA Processing, Post-Transcriptional ; RNA, Fungal/metabolism ; Recombinant Proteins/chemistry ; Recombinant Proteins/metabolism ; Ribonuclease P/chemistry ; Ribonuclease P/metabolism ; Species Specificity ; Structure-Activity Relationship ; Substrate Specificity
    Chemical Substances Anticodon ; Arabidopsis Proteins ; Archaeal Proteins ; RNA Precursors ; RNA, Fungal ; Recombinant Proteins ; 3-Hydroxyacyl CoA Dehydrogenases (EC 1.1.1.-) ; HSD17B10 protein, human (EC 1.1.1.35) ; Methyltransferases (EC 2.1.1.-) ; TRMT10c protein, human (EC 2.1.1.-) ; PRORP protein, human (EC 3.1.26.5) ; PRORP1 protein, Arabidopsis (EC 3.1.26.5) ; Ribonuclease P (EC 3.1.26.5)
    Language English
    Publishing date 2021-09-06
    Publishing country United States
    Document type Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2126708-X
    ISSN 1545-9985 ; 1545-9993
    ISSN (online) 1545-9985
    ISSN 1545-9993
    DOI 10.1038/s41594-021-00637-y
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  8. Article: [No title information]

    Cramer, Patrick / Kokic, Goran / Dienemann, Christian / Höbartner, Claudia / Hillen, Hauke S

    Biospektrum : Zeitschrift der Gesellschaft fur Biologishe Chemie (GBCH) und der Vereinigung fur Allgemeine und Angewandte Mikrobiologie (VAAM)

    2021  Volume 27, Issue 1, Page(s) 49–53

    Abstract: Coronaviruses use an RNA-dependent RNA polymerase to replicate and transcribe their RNA genome. The structure of the SARS-CoV-2 polymerase was determined by cryo-electron microscopy within a short time in spring 2020. The structure explains how the viral ...

    Title translation Coronavirus-Replikation: Mechanismus und Inhibition durch Remdesivir.
    Abstract Coronaviruses use an RNA-dependent RNA polymerase to replicate and transcribe their RNA genome. The structure of the SARS-CoV-2 polymerase was determined by cryo-electron microscopy within a short time in spring 2020. The structure explains how the viral enzyme synthesizes RNA and how it replicates the exceptionally large genome in a processive manner. The most recent structure-function studies further reveal the mechanism of polymerase inhibition by remdesivir, an approved drug for the treatment of COVID-19.
    Language German
    Publishing date 2021-02-12
    Publishing country Germany
    Document type English Abstract ; Journal Article ; Review
    ZDB-ID 2203536-9
    ISSN 1868-6249 ; 0947-0867
    ISSN (online) 1868-6249
    ISSN 0947-0867
    DOI 10.1007/s12268-021-1516-6
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  9. Article ; Online: Structural basis of mitochondrial transcription.

    Hillen, Hauke S / Temiakov, Dmitry / Cramer, Patrick

    Nature structural & molecular biology

    2018  Volume 25, Issue 9, Page(s) 754–765

    Abstract: The mitochondrial genome is transcribed by a single-subunit DNA-dependent RNA polymerase (mtRNAP) and its auxiliary factors. Structural studies have elucidated how mtRNAP cooperates with its dedicated transcription factors to direct RNA synthesis: ... ...

    Abstract The mitochondrial genome is transcribed by a single-subunit DNA-dependent RNA polymerase (mtRNAP) and its auxiliary factors. Structural studies have elucidated how mtRNAP cooperates with its dedicated transcription factors to direct RNA synthesis: initiation factors TFAM and TFB2M assist in promoter-DNA binding and opening by mtRNAP while the elongation factor TEFM increases polymerase processivity to the levels required for synthesis of long polycistronic mtRNA transcripts. Here, we review the emerging body of structural and functional studies of human mitochondrial transcription, provide a molecular movie that can be used for teaching purposes and discuss the open questions to guide future directions of investigation.
    MeSH term(s) Evolution, Molecular ; Humans ; Mitochondria/enzymology ; Mitochondria/metabolism ; Mitochondrial Proteins/chemistry ; Mitochondrial Proteins/genetics ; Protein Conformation ; Terminator Regions, Genetic ; Transcription, Genetic ; Transcriptional Elongation Factors/metabolism
    Chemical Substances Mitochondrial Proteins ; Transcriptional Elongation Factors
    Language English
    Publishing date 2018-09-06
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2126708-X
    ISSN 1545-9985 ; 1545-9993
    ISSN (online) 1545-9985
    ISSN 1545-9993
    DOI 10.1038/s41594-018-0122-9
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  10. Article ; Online: Structure of replicating SARS-CoV-2 polymerase.

    Hillen, Hauke S / Kokic, Goran / Farnung, Lucas / Dienemann, Christian / Tegunov, Dimitry / Cramer, Patrick

    Nature

    2020  Volume 584, Issue 7819, Page(s) 154–156

    Abstract: The new coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses an RNA-dependent RNA polymerase (RdRp) for the replication of its genome and the transcription of its ... ...

    Abstract The new coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses an RNA-dependent RNA polymerase (RdRp) for the replication of its genome and the transcription of its genes
    MeSH term(s) Adenosine Monophosphate/analogs & derivatives ; Adenosine Monophosphate/pharmacology ; Alanine/analogs & derivatives ; Alanine/pharmacology ; Betacoronavirus/drug effects ; Betacoronavirus/enzymology ; Betacoronavirus/genetics ; Betacoronavirus/ultrastructure ; Coronavirus RNA-Dependent RNA Polymerase ; Cryoelectron Microscopy ; Models, Molecular ; Protein Conformation ; RNA, Viral/biosynthesis ; RNA, Viral/chemistry ; RNA, Viral/metabolism ; RNA-Dependent RNA Polymerase/chemistry ; RNA-Dependent RNA Polymerase/genetics ; RNA-Dependent RNA Polymerase/metabolism ; RNA-Dependent RNA Polymerase/ultrastructure ; SARS-CoV-2 ; Viral Nonstructural Proteins/chemistry ; Viral Nonstructural Proteins/genetics ; Viral Nonstructural Proteins/metabolism ; Viral Nonstructural Proteins/ultrastructure
    Chemical Substances RNA, Viral ; Viral Nonstructural Proteins ; remdesivir (3QKI37EEHE) ; Adenosine Monophosphate (415SHH325A) ; Coronavirus RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; NSP12 protein, SARS-CoV-2 (EC 2.7.7.48) ; RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; Alanine (OF5P57N2ZX)
    Keywords covid19
    Language English
    Publishing date 2020-05-21
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-020-2368-8
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    Zs.MO 244: Show issues

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