1
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Powell BM, Davis JH. Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN. Nat Methods 2024:10.1038/s41592-024-02210-z. [PMID: 38459385 DOI: 10.1038/s41592-024-02210-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 02/13/2024] [Indexed: 03/10/2024]
Abstract
Cryo-electron tomography (cryo-ET) enables observation of macromolecular complexes in their native, spatially contextualized cellular environment. Cryo-ET processing software to visualize such complexes at nanometer resolution via iterative alignment and averaging are well developed but rely upon assumptions of structural homogeneity among the complexes of interest. Recently developed tools allow for some assessment of structural diversity but have limited capacity to represent highly heterogeneous structures, including those undergoing continuous conformational changes. Here we extend the highly expressive cryoDRGN (Deep Reconstructing Generative Networks) deep learning architecture, originally created for single-particle cryo-electron microscopy analysis, to cryo-ET. Our new tool, tomoDRGN, learns a continuous low-dimensional representation of structural heterogeneity in cryo-ET datasets while also learning to reconstruct heterogeneous structural ensembles supported by the underlying data. Using simulated and experimental data, we describe and benchmark architectural choices within tomoDRGN that are uniquely necessitated and enabled by cryo-ET. We additionally illustrate tomoDRGN's efficacy in analyzing diverse datasets, using it to reveal high-level organization of human immunodeficiency virus (HIV) capsid complexes assembled in virus-like particles and to resolve extensive structural heterogeneity among ribosomes imaged in situ.
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Affiliation(s)
- Barrett M Powell
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Joseph H Davis
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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2
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Zhang T, Vďačný P. Deciphering phylogenetic relationships of and delimiting species boundaries within the controversial ciliate genus Conchophthirus using an integrative morpho-evo approach. Mol Phylogenet Evol 2024; 190:107931. [PMID: 37742881 DOI: 10.1016/j.ympev.2023.107931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 09/26/2023]
Abstract
The phylum Ciliophora (ciliates) comprises about 2600 symbiotic and over 5500 free-living species. The inclusion of symbiotic ciliates in phylogenetic analyses often challenges traditional classification frameworks due to their morphological adaptions to the symbiotic lifestyle. Conchophthirus is such a controversial obligate endocommensal genus whose affinities to other symbiotic and free-living scuticociliates are still poorly understood. Using uni- and multivariate morphometrics as well as 2D-based molecular and phylogenetic analyses, we attempted to test for the monophyly of Conchophthirus, study the boundaries of Conchophthirus species isolated from various bivalves at mesoscale, and reveal the phylogenetic relationships of Conchophthirus to other scuticociliates. Multidimensional analyses of morphometric and cell geometric data generated the same homogenous clusters, as did phylogenetic analyses based on 144 new sequences of two mitochondrial and five nuclear molecular markers. Conchophthirus is not closely related to 'core' scuticociliates represented by the orders Pleuronematida and Philasterida, as assumed in the past using morphological data. Nuclear and mitochondrial markers consistently showed the free-living Dexiotricha and the mouthless endosymbiotic Haptophrya to be the nearest relatives of Conchophthirus. These three highly morphologically and ecologically dissimilar genera represent an orphan clade from the early radiation of scuticociliates in molecular phylogenies.
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Affiliation(s)
- Tengyue Zhang
- Department of Zoology, Comenius University in Bratislava, 842 15 Bratislava, Slovak Republic; Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China
| | - Peter Vďačný
- Department of Zoology, Comenius University in Bratislava, 842 15 Bratislava, Slovak Republic.
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3
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Lei L, Burton ZF. The 3 31 Nucleotide Minihelix tRNA Evolution Theorem and the Origin of Life. Life (Basel) 2023; 13:2224. [PMID: 38004364 PMCID: PMC10672568 DOI: 10.3390/life13112224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/08/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
There are no theorems (proven theories) in the biological sciences. We propose that the 3 31 nt minihelix tRNA evolution theorem be universally accepted as one. The 3 31 nt minihelix theorem completely describes the evolution of type I and type II tRNAs from ordered precursors (RNA repeats and inverted repeats). Despite the diversification of tRNAome sequences, statistical tests overwhelmingly support the theorem. Furthermore, the theorem relates the dominant pathway for the origin of life on Earth, specifically, how tRNAomes and the genetic code may have coevolved. Alternate models for tRNA evolution (i.e., 2 minihelix, convergent and accretion models) are falsified. In the context of the pre-life world, tRNA was a molecule that, via mutation, could modify anticodon sequences and teach itself to code. Based on the tRNA sequence, we relate the clearest history to date of the chemical evolution of life. From analysis of tRNA evolution, ribozyme-mediated RNA ligation was a primary driving force in the evolution of complexity during the pre-life-to-life transition. TRNA formed the core for the evolution of living systems on Earth.
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Affiliation(s)
- Lei Lei
- School of Biological Sciences, University of New England, Biddeford, ME 04005, USA;
| | - Zachary Frome Burton
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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4
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Mesentsev Y, Surkova A, Kamyshatskaya O, Nassonova E, Smirnov A. Re-isolation and revaluation of boundaries of Thecamoeba terricola Greeff, 1886 (Amoebozoa, Discosea, Thecamoebida), with description of Thecamoeba vicaria n. sp. Eur J Protistol 2023; 91:126030. [PMID: 37922856 DOI: 10.1016/j.ejop.2023.126030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/15/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
We studied a large species of Thecamoeba found in a glass dish with soaked moss and obtained 18s rRNA gene sequence of this organism. Morphologically, the strain was most similar to T. terricola sensu Page, but had significant differences in cell size and nuclear morphology. A more complete similarity was found with the original description of "Amoeba terricola" by Greeff, as well as with Penard's descriptions and slides. The analysis of literature data shows that the strain described by Page in 1977 as a re-isolated T. terricola differs from the original description of this species provided by Greeff in 1866 and data by Penard published in 1902 and 1913. Based on our observations as well as on Greeff's and Penard's data, we reassessed the species boundaries of T. terricola and established T. vicaria n. sp. for the organism described by Page in 1977. The species T. terricola was defined according to its original description. The observations of amoebae on agar have shown that T. terricola cells can form the "standing amoeba" stage, previously described only for Sappinia pedata. This and some other "behaviour" features of T. terricola may be associated with living conditions in terrestrial habitats.
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Affiliation(s)
- Yelisei Mesentsev
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya nab., 199034 St. Petersburg, Russia.
| | - Alina Surkova
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya nab., 199034 St. Petersburg, Russia
| | - Oksana Kamyshatskaya
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya nab., 199034 St. Petersburg, Russia; Laboratory of Cytology of Unicellular Organisms, Institute of Cytology RAS, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia
| | - Elena Nassonova
- Laboratory of Cytology of Unicellular Organisms, Institute of Cytology RAS, 4 Tikhoretsky ave., 194064 St. Petersburg, Russia
| | - Alexey Smirnov
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, 7/9 Universitetskaya nab., 199034 St. Petersburg, Russia
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5
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Rivas M, Fox GE. Ancestry of RNA/RNA interaction regions within segmented ribosomes. RNA (NEW YORK, N.Y.) 2023; 29:1388-1399. [PMID: 37263782 PMCID: PMC10573304 DOI: 10.1261/rna.079654.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/14/2023] [Indexed: 06/03/2023]
Abstract
The ribosome is the universally conserved ribozyme that translates DNA coded instructions into proteins with the assistance of other RNA molecules, including transfer and messenger RNAs. Of particular interest is the segmentation phenomena, which is found in trypanosomatids and other protists. In these organisms, the large subunit ribosomal RNA is assembled from multiple smaller RNAs. This phenomenon posits several challenges to the folding and stabilization of such ribosomes to retain functionality and efficiency. In earlier studies, RNA/protein interactions were suggested to fully compensate for the fragmentation. Recently, several conserved RNA/RNA interaction regions were described in the cryo-EM structures of segmented ribosomes from trypanosomatids. These regions also seemed to aid in the folding and stabilization of such ribosomes, even before the ribosomal proteins start their association. In the present study, the existence of conserved RNA/RNA interaction regions shared between trypanosomatid and Euglena gracilis segmented ribosomes was confirmed, despite differences in segmentation patterns. Analysis of the crystallographic structures of unsegmented ribosomes from other Eukaryotes, Bacteria, and Archaea allowed us to estimate the relative age of highly conserved RNA/RNA interaction regions. These results strongly suggest that common interaction regions likely date far back into the ribosomes of the last common ancestor. Results also revealed that single hydrogen bonds are overwhelmingly facilitated by the 2'OH, a distinctive RNA feature. This supports the notion that RNA predates DNA and places some constraints on alternative nucleic acids proposals.
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Affiliation(s)
- Mario Rivas
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA
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6
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Lai LB, Gopalan V, Jansson MD, Chen Q, Zhang X, Wolfram-Schauerte M, Höfer K. Making nucleic acid structures and schematics. Trends Biochem Sci 2023; 48:655-658. [PMID: 37451237 DOI: 10.1016/j.tibs.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 05/05/2023] [Indexed: 07/18/2023]
Affiliation(s)
- Lien B Lai
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
| | - Martin D Jansson
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.
| | - Qi Chen
- Molecular Medicine Program, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA.
| | - Xudong Zhang
- Molecular Medicine Program, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA.
| | | | - Katharina Höfer
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany; SYNMIKRO, Center for Synthetic Microbiology, 35043 Marburg, Germany.
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7
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Bose N, Moore SD. Variable Region Sequences Influence 16S rRNA Performance. Microbiol Spectr 2023; 11:e0125223. [PMID: 37212673 PMCID: PMC10269663 DOI: 10.1128/spectrum.01252-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/03/2023] [Indexed: 05/23/2023] Open
Abstract
16S rRNA gene sequences are commonly analyzed for taxonomic and phylogenetic studies because they contain variable regions that can help distinguish different genera. However, intra-genus distinction using variable region homology is often impossible due to the high overall sequence identities among closely related species, even though some residues may be conserved within respective species. Using a computational method that included the allelic diversity within individual genomes, we discovered that certain Escherichia and Shigella species can be distinguished by a multi-allelic 16S rRNA variable region single nucleotide polymorphism (SNP). To evaluate the performance of 16S rRNAs with altered variable regions, we developed an in vivo system that measures the acceptance and distribution of variant 16S rRNAs into a large pool of natural versions supporting normal translation and growth. We found that 16S rRNAs containing evolutionarily disparate variable regions were underpopulated both in ribosomes and in active translation pools, even for an SNP. Overall, this study revealed that variable region sequences can substantially influence the performance of 16S rRNAs and that this biological constraint can be leveraged to justify refining taxonomic assignments of variable region sequence data. IMPORTANCE This study reevaluates the notion that 16S rRNA gene variable region sequences are uninformative for intra-genus classification and that single nucleotide variations within them have no consequence to strains that bear them. We demonstrated that the performance of 16S rRNAs in Escherichia coli can be negatively impacted by sequence changes in variable regions, even for single nucleotide changes that are native to closely related Escherichia and Shigella species; thus, biological performance is likely constraining the evolution of variable regions in bacteria. Further, the native nucleotide variations we tested occur in all strains of their respective species and across their multiple 16S rRNA gene copies, suggesting that these species evolved beyond what would be discerned from a consensus sequence comparison. Therefore, this work also reveals that the multiple 16S rRNA gene alleles found in most bacteria can provide more informative phylogenetic and taxonomic detail than a single reference allele.
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Affiliation(s)
- Nikhil Bose
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Sean D. Moore
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
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8
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Powell BM, Davis JH. Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.31.542975. [PMID: 37398315 PMCID: PMC10312494 DOI: 10.1101/2023.05.31.542975] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Cryo-electron tomography (cryo-ET) allows one to observe macromolecular complexes in their native, spatially contextualized environment. Tools to visualize such complexes at nanometer resolution via iterative alignment and averaging are well-developed but rely on assumptions of structural homogeneity among the complexes under consideration. Recently developed downstream analysis tools allow for some assessment of macromolecular diversity but have limited capacity to represent highly heterogeneous macromolecules, including those undergoing continuous conformational changes. Here, we extend the highly expressive cryoDRGN deep learning architecture, originally created for cryo-electron microscopy single particle analysis, to sub-tomograms. Our new tool, tomoDRGN, learns a continuous low-dimensional representation of structural heterogeneity in cryo-ET datasets while also learning to reconstruct a large, heterogeneous ensemble of structures supported by the underlying data. Using simulated and experimental data, we describe and benchmark architectural choices within tomoDRGN that are uniquely necessitated and enabled by cryo-ET data. We additionally illustrate tomoDRGN's efficacy in analyzing an exemplar dataset, using it to reveal extensive structural heterogeneity among ribosomes imaged in situ.
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Affiliation(s)
- Barrett M. Powell
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Joseph H. Davis
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
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9
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Rivas M, Fox GE. How to build a protoribosome: structural insights from the first protoribosome constructs that have proven to be catalytically active. RNA (NEW YORK, N.Y.) 2023; 29:263-272. [PMID: 36604112 PMCID: PMC9945445 DOI: 10.1261/rna.079417.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 12/11/2022] [Indexed: 05/05/2023]
Abstract
The modern ribosome catalyzes all coded protein synthesis in extant organisms. It is likely that its core structure is a direct descendant from the ribosome present in the last common ancestor (LCA). Hence, its earliest origins likely predate the LCA and therefore date further back in time. Of special interest is the pseudosymmetrical region (SymR) that lies deep within the large subunit (LSU) where the peptidyl transfer reaction takes place. It was previously proposed that two RNA oligomers, representing the P- and A-regions of extant ribosomes dimerized to create a pore-like structure, which hosted the necessary properties that facilitate peptide bond formation. However, recent experimental studies show that this may not be the case. Instead, several RNA constructs derived exclusively from the P-region were shown to form a homodimer capable of peptide bond synthesis. Of special interest will be the origin issues because the homodimer would have allowed a pre-LCA ribosome that was significantly smaller than previously proposed. For the A-region, the immediate issue will likely be its origin and whether it enhances ribosome performance. Here, we reanalyze the RNA/RNA interaction regions that most likely lead to SymR formation in light of these recent findings. Further, it has been suggested that the ability of these RNA constructs to dimerize and enhance peptide bond formation is sequence-dependent. We have analyzed the implications of sequence variations as parts of functional and nonfunctional constructs.
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Affiliation(s)
- Mario Rivas
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA
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10
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Zhang T, Rurik I, Vďačný P. A holistic approach to inventory the diversity of mobilid ciliates (Protista: Ciliophora: Peritrichia). ORG DIVERS EVOL 2023. [DOI: 10.1007/s13127-022-00601-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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11
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Obert T, Zhang T, Rurik I, Vďačný P. First molecular evidence of hybridization in endosymbiotic ciliates (Protista, Ciliophora). Front Microbiol 2022; 13:1067315. [PMID: 36569075 PMCID: PMC9772525 DOI: 10.3389/fmicb.2022.1067315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
Hybridization is an important evolutionary process that can fuel diversification via formation of hybrid species or can lead to fusion of previously separated lineages by forming highly diverse species complexes. We provide here the first molecular evidence of hybridization in wild populations of ciliates, a highly diverse group of free-living and symbiotic eukaryotic microbes. The impact of hybridization was studied on the model of Plagiotoma, an obligate endosymbiont of the digestive tube of earthworms, using split decomposition analyses and species networks, 2D modeling of the nuclear rRNA molecules and compensatory base change analyses as well as multidimensional morphometrics. Gene flow slowed down and eventually hampered the diversification of Lumbricus-dwelling plagiotomids, which collapsed into a single highly variable biological entity, the P. lumbrici complex. Disruption of the species boundaries was suggested also by the continuum of morphological variability in the phenotypic space. On the other hand, hybridization conspicuously increased diversity in the nuclear rDNA cistron and somewhat weakened the host structural specificity of the P. lumbrici complex, whose members colonize a variety of phylogenetically closely related anecic and epigeic earthworms. By contrast, another recorded species, P. aporrectodeae sp. n., showed no signs of introgression, no variability in the rDNA cistron, and very high host specificity. These contrasting eco-evolutionary patterns indicate that hybridization might decrease the alpha-diversity by dissolving species boundaries, weaken the structural host specificity by broadening ecological amplitudes, and increase the nuclear rDNA variability by overcoming concerted evolution within the P. lumbrici species complex.
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12
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Stenamoeba aeronauta n. sp., a new case of sibling species in the order Thecamoebida (Amoebozoa, Discosea). Eur J Protistol 2022; 86:125941. [DOI: 10.1016/j.ejop.2022.125941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/02/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022]
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13
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Biesiada M, Hu MY, Williams LD, Purzycka KJ, Petrov AS. rRNA expansion segment 7 in eukaryotes: from Signature Fold to tentacles. Nucleic Acids Res 2022; 50:10717-10732. [PMID: 36200812 PMCID: PMC9561286 DOI: 10.1093/nar/gkac844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 09/13/2022] [Accepted: 09/22/2022] [Indexed: 11/14/2022] Open
Abstract
The ribosomal core is universally conserved across the tree of life. However, eukaryotic ribosomes contain diverse rRNA expansion segments (ESs) on their surfaces. Sites of ES insertions are predicted from sites of insertion of micro-ESs in archaea. Expansion segment 7 (ES7) is one of the most diverse regions of the ribosome, emanating from a short stem loop and ranging to over 750 nucleotides in mammals. We present secondary and full-atom 3D structures of ES7 from species spanning eukaryotic diversity. Our results are based on experimental 3D structures, the accretion model of ribosomal evolution, phylogenetic relationships, multiple sequence alignments, RNA folding algorithms and 3D modeling by RNAComposer. ES7 contains a distinct motif, the 'ES7 Signature Fold', which is generally invariant in 2D topology and 3D structure in all eukaryotic ribosomes. We establish a model in which ES7 developed over evolution through a series of elementary and recursive growth events. The data are sufficient to support an atomic-level accretion path for rRNA growth. The non-monophyletic distribution of some ES7 features across the phylogeny suggests acquisition via convergent processes. And finally, illustrating the power of our approach, we constructed the 2D and 3D structure of the entire LSU rRNA of Mus musculus.
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Affiliation(s)
- Marcin Biesiada
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Michael Y Hu
- Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Loren Dean Williams
- Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Katarzyna J Purzycka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Anton S Petrov
- Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
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14
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Strassler SE, Bowles IE, Dey D, Jackman JE, Conn GL. Tied up in knots: Untangling substrate recognition by the SPOUT methyltransferases. J Biol Chem 2022; 298:102393. [PMID: 35988649 PMCID: PMC9508554 DOI: 10.1016/j.jbc.2022.102393] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 10/25/2022] Open
Abstract
The SpoU-TrmD (SPOUT) methyltransferase superfamily was designated when structural similarity was identified between the transfer RNA-modifying enzymes TrmH (SpoU) and TrmD. SPOUT methyltransferases are found in all domains of life and predominantly modify transfer RNA or ribosomal RNA substrates, though one instance of an enzyme with a protein substrate has been reported. Modifications placed by SPOUT methyltransferases play diverse roles in regulating cellular processes such as ensuring translational fidelity, altering RNA stability, and conferring bacterial resistance to antibiotics. This large collection of S-adenosyl-L-methionine-dependent methyltransferases is defined by a unique α/β fold with a deep trefoil knot in their catalytic (SPOUT) domain. Herein, we describe current knowledge of SPOUT enzyme structure, domain architecture, and key elements of catalytic function, including S-adenosyl-L-methionine co-substrate binding, beginning with a new sequence alignment that divides the SPOUT methyltransferase superfamily into four major clades. Finally, a major focus of this review will be on our growing understanding of how these diverse enzymes accomplish the molecular feat of specific substrate recognition and modification, as highlighted by recent advances in our knowledge of protein-RNA complex structures and the discovery of the dependence of one SPOUT methyltransferase on metal ion binding for catalysis. Considering the broad biological roles of RNA modifications, developing a deeper understanding of the process of substrate recognition by the SPOUT enzymes will be critical for defining many facets of fundamental RNA biology with implications for human disease.
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Affiliation(s)
- Sarah E Strassler
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA; Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, Georgia, USA
| | - Isobel E Bowles
- Department of Chemistry and Biochemistry, Center for RNA Biology and Ohio State Biochemistry Program, Columbus, Ohio, USA
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jane E Jackman
- Department of Chemistry and Biochemistry, Center for RNA Biology and Ohio State Biochemistry Program, Columbus, Ohio, USA.
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA; Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, Georgia, USA.
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15
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Demongeot J, Seligmann H. Evolution of small and large ribosomal RNAs from accretion of tRNA subelements. Biosystems 2022; 222:104796. [DOI: 10.1016/j.biosystems.2022.104796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/02/2022]
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16
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Bhutada P, Favre S, Jaafar M, Hafner J, Liesinger L, Unterweger S, Bischof K, Darnhofer B, Siva Sankar D, Rechberger G, Abou Merhi R, Lebaron S, Birner-Gruenberger R, Kressler D, Henras AK, Pertschy B. Rbp95 binds to 25S rRNA helix H95 and cooperates with the Npa1 complex during early pre-60S particle maturation. Nucleic Acids Res 2022; 50:10053-10077. [PMID: 36018804 PMCID: PMC9508819 DOI: 10.1093/nar/gkac724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 08/05/2022] [Accepted: 08/12/2022] [Indexed: 11/21/2022] Open
Abstract
Eukaryotic ribosome synthesis involves more than 200 assembly factors, which promote ribosomal RNA (rRNA) processing, modification and folding, and assembly of ribosomal proteins. The formation and maturation of the earliest pre-60S particles requires structural remodeling by the Npa1 complex, but is otherwise still poorly understood. Here, we introduce Rbp95 (Ycr016w), a constituent of early pre-60S particles, as a novel ribosome assembly factor. We show that Rbp95 is both genetically and physically linked to most Npa1 complex members and to ribosomal protein Rpl3. We demonstrate that Rbp95 is an RNA-binding protein containing two independent RNA-interacting domains. In vivo, Rbp95 associates with helix H95 in the 3′ region of the 25S rRNA, in close proximity to the binding sites of Npa1 and Rpl3. Additionally, Rbp95 interacts with several snoRNAs. The absence of Rbp95 results in alterations in the protein composition of early pre-60S particles. Moreover, combined mutation of Rbp95 and Npa1 complex members leads to a delay in the maturation of early pre-60S particles. We propose that Rbp95 acts together with the Npa1 complex during early pre-60S maturation, potentially by promoting pre-rRNA folding events within pre-60S particles.
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Affiliation(s)
- Priya Bhutada
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Sébastien Favre
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Mariam Jaafar
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France.,Genomic Stability and Biotherapy (GSBT) Laboratory, Faculty of Sciences, Rafik Hariri Campus, Lebanese University, Beirut, Lebanon
| | - Jutta Hafner
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Laura Liesinger
- BioTechMed-Graz, Graz, Austria.,Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria
| | - Stefan Unterweger
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Karin Bischof
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria
| | - Barbara Darnhofer
- BioTechMed-Graz, Graz, Austria.,Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria
| | - Devanarayanan Siva Sankar
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Gerald Rechberger
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Raghida Abou Merhi
- Genomic Stability and Biotherapy (GSBT) Laboratory, Faculty of Sciences, Rafik Hariri Campus, Lebanese University, Beirut, Lebanon
| | - Simon Lebaron
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Ruth Birner-Gruenberger
- BioTechMed-Graz, Graz, Austria.,Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria.,Institute of Chemical Technologies and Analytics, Technische Universität Wien, Getreidemarkt 9/E164, 1060 Vienna, Austria
| | - Dieter Kressler
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Anthony K Henras
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Brigitte Pertschy
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010 Graz, Austria.,BioTechMed-Graz, Graz, Austria
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17
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Kumar J, Lackey L, Waldern JM, Dey A, Mustoe AM, Weeks KM, Mathews DH, Laederach A. Quantitative prediction of variant effects on alternative splicing in MAPT using endogenous pre-messenger RNA structure probing. eLife 2022; 11:73888. [PMID: 35695373 PMCID: PMC9236610 DOI: 10.7554/elife.73888] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 06/12/2022] [Indexed: 11/29/2022] Open
Abstract
Splicing is highly regulated and is modulated by numerous factors. Quantitative predictions for how a mutation will affect precursor mRNA (pre-mRNA) structure and downstream function are particularly challenging. Here, we use a novel chemical probing strategy to visualize endogenous precursor and mature MAPT mRNA structures in cells. We used these data to estimate Boltzmann suboptimal structural ensembles, which were then analyzed to predict consequences of mutations on pre-mRNA structure. Further analysis of recent cryo-EM structures of the spliceosome at different stages of the splicing cycle revealed that the footprint of the Bact complex with pre-mRNA best predicted alternative splicing outcomes for exon 10 inclusion of the alternatively spliced MAPT gene, achieving 74% accuracy. We further developed a β-regression weighting framework that incorporates splice site strength, RNA structure, and exonic/intronic splicing regulatory elements capable of predicting, with 90% accuracy, the effects of 47 known and 6 newly discovered mutations on inclusion of exon 10 of MAPT. This combined experimental and computational framework represents a path forward for accurate prediction of splicing-related disease-causing variants.
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Affiliation(s)
- Jayashree Kumar
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Lela Lackey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Department of Genetics and Biochemistry, Center for Human Genetics, Clemson University, Greenwood, United States
| | - Justin M Waldern
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Abhishek Dey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Anthony M Mustoe
- Verna and Marrs McClean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center (THINC), and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, United States
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - David H Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, Rochester, United States
| | - Alain Laederach
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, United States
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18
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Zhang M, Hwang IT, Li K, Bai J, Chen JF, Weissman T, Zou JY, Lu Z. Classification and clustering of RNA crosslink-ligation data reveal complex structures and homodimers. Genome Res 2022; 32:968-985. [PMID: 35332099 PMCID: PMC9104705 DOI: 10.1101/gr.275979.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 01/11/2022] [Indexed: 12/04/2022]
Abstract
The recent development and application of methods based on the general principle of "crosslinking and proximity ligation" (crosslink-ligation) are revolutionizing RNA structure studies in living cells. However, extracting structure information from such data presents unique challenges. Here, we introduce a set of computational tools for the systematic analysis of data from a wide variety of crosslink-ligation methods, specifically focusing on read mapping, alignment classification, and clustering. We design a new strategy to map short reads with irregular gaps at high sensitivity and specificity. Analysis of previously published data reveals distinct properties and bias caused by the crosslinking reactions. We perform rigorous and exhaustive classification of alignments and discover eight types of arrangements that provide distinct information on RNA structures and interactions. To deconvolve the dense and intertwined gapped alignments, we develop a network/graph-based tool Crosslinked RNA Secondary Structure Analysis using Network Techniques (CRSSANT), which enables clustering of gapped alignments and discovery of new alternative and dynamic conformations. We discover that multiple crosslinking and ligation events can occur on the same RNA, generating multisegment alignments to report complex high-level RNA structures and multi-RNA interactions. We find that alignments with overlapped segments are produced from potential homodimers and develop a new method for their de novo identification. Analysis of overlapping alignments revealed potential new homodimers in cellular noncoding RNAs and RNA virus genomes in the Picornaviridae family. Together, this suite of computational tools enables rapid and efficient analysis of RNA structure and interaction data in living cells.
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Affiliation(s)
- Minjie Zhang
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Irena T Hwang
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA
| | - Kongpan Li
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Jianhui Bai
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Jian-Fu Chen
- Center for Craniofacial Molecular Biology, University of Southern California (USC), Los Angeles, California 90033, USA
| | - Tsachy Weissman
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA
| | - James Y Zou
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA
- Department of Biomedical Data Science and Chan-Zuckerberg Biohub, Stanford University, Palo Alto, California 94305, USA
| | - Zhipeng Lu
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089, USA
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19
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Abstract
Recent events have pushed RNA research into the spotlight. Continued discoveries of RNA with unexpected diverse functions in healthy and diseased cells, such as the role of RNA as both the source and countermeasure to a severe acute respiratory syndrome coronavirus 2 infection, are igniting a new passion for understanding this functionally and structurally versatile molecule. Although RNA structure is key to function, many foundational characteristics of RNA structure are misunderstood, and the default state of RNA is often thought of and depicted as a single floppy strand. The purpose of this perspective is to help adjust mental models, equipping the community to better use the fundamental aspects of RNA structural information in new mechanistic models, enhance experimental design to test these models, and refine data interpretation. We discuss six core observations focused on the inherent nature of RNA structure and how to incorporate these characteristics to better understand RNA structure. We also offer some ideas for future efforts to make validated RNA structural information available and readily used by all researchers.
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Affiliation(s)
- Quentin Vicens
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO 80045
- RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045
| | - Jeffrey S. Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, School of Medicine, Aurora, CO 80045
- RNA BioScience Initiative, University of Colorado Denver School of Medicine, Aurora, CO 80045
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20
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Rataj M, Zhang T, Vd’ačný P. Nuclear and Mitochondrial SSU rRNA Genes Reveal Hidden Diversity of Haptophrya Endosymbionts in Freshwater Planarians and Challenge Their Traditional Classification in Astomatia. Front Microbiol 2022; 13:830951. [PMID: 35495648 PMCID: PMC9048206 DOI: 10.3389/fmicb.2022.830951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
Like many other aquatic animals, freshwater planarians have also become partners of symbiotic ciliates from the class Oligohymenophorea. In the present study, we explored the hidden diversity and addressed the questionable systematic position of mouthless obligatory gut endosymbionts of freshwater planarians, using the nuclear and mitochondrial SSU rRNA genes. Although all isolated ciliates morphologically corresponded to a single species, molecular analyses suggested the existence of three genetically distinct entities: Haptophrya planariarum, Haptophrya dugesiarum nov. spec., and Haptophrya schmidtearum nov. spec. The two former species share the same planarian host, which indicates a speciation model involving one duplication event without host switching. Such a diversification pattern was recognized also in astome ciliates inhabiting megascolecid and glossoscolecid earthworms. The present multi-gene phylogenies along with the secondary structure of the mitochondrial 16S rRNA molecule, however, challenge the traditional classification of Haptophrya within the subclass Astomatia. Haptophrya very likely evolved from an orphan scuticociliate lineage by the loss of oral apparatus and by the transformation of the thigmotactic field into an adhesive sucker. Since astomy evolved multiple times independently within the Oligohymenophorea, the loss of cell mouth cannot be used as a sole argument for the assignment of Haptophrya to the Astomatia anymore.
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21
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Bailey AD, Talkish J, Ding H, Igel H, Duran A, Mantripragada S, Paten B, Ares M. Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling. eLife 2022; 11:e76562. [PMID: 35384842 PMCID: PMC9045821 DOI: 10.7554/elife.76562] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/05/2022] [Indexed: 12/02/2022] Open
Abstract
Nucleotides in RNA and DNA are chemically modified by numerous enzymes that alter their function. Eukaryotic ribosomal RNA (rRNA) is modified at more than 100 locations, particularly at highly conserved and functionally important nucleotides. During ribosome biogenesis, modifications are added at various stages of assembly. The existence of differently modified classes of ribosomes in normal cells is unknown because no method exists to simultaneously evaluate the modification status at all sites within a single rRNA molecule. Using a combination of yeast genetics and nanopore direct RNA sequencing, we developed a reliable method to track the modification status of single rRNA molecules at 37 sites in 18 S rRNA and 73 sites in 25 S rRNA. We use our method to characterize patterns of modification heterogeneity and identify concerted modification of nucleotides found near functional centers of the ribosome. Distinct, undermodified subpopulations of rRNAs accumulate upon loss of Dbp3 or Prp43 RNA helicases, suggesting overlapping roles in ribosome biogenesis. Modification profiles are surprisingly resistant to change in response to many genetic and acute environmental conditions that affect translation, ribosome biogenesis, and pre-mRNA splicing. The ability to capture single-molecule RNA modification profiles provides new insights into the roles of nucleotide modifications in RNA function.
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Affiliation(s)
- Andrew D Bailey
- Department of Biomolecular Engineering and Santa Cruz Genomics Institute, University of California, Santa CruzSanta CruzUnited States
| | - Jason Talkish
- RNA Center and Department of Molecular, Cell & Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | - Hongxu Ding
- Department of Biomolecular Engineering and Santa Cruz Genomics Institute, University of California, Santa CruzSanta CruzUnited States
- Department of Pharmacy Practice & Science, College of Pharmacy, University of ArizonaTucsonUnited States
| | - Haller Igel
- RNA Center and Department of Molecular, Cell & Developmental Biology, University of California, Santa CruzSanta CruzUnited States
| | | | | | - Benedict Paten
- Department of Biomolecular Engineering and Santa Cruz Genomics Institute, University of California, Santa CruzSanta CruzUnited States
| | - Manuel Ares
- RNA Center and Department of Molecular, Cell & Developmental Biology, University of California, Santa CruzSanta CruzUnited States
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22
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Jüttner M, Ferreira-Cerca S. Looking through the lens of the ribosome biogenesis evolutionary history: possible implications for archaeal phylogeny and eukaryogenesis. Mol Biol Evol 2022; 39:6547259. [PMID: 35275997 PMCID: PMC8997704 DOI: 10.1093/molbev/msac054] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Our understanding of microbial diversity and its evolutionary relationships has increased substantially over the last decade. Such an understanding has been greatly fueled by culture-independent metagenomics analyses. However, the outcome of some of these studies and their biological and evolutionary implications, such as the origin of the eukaryotic lineage from the recently discovered archaeal Asgard superphylum, is debated. The sequences of the ribosomal constituents are amongst the most used phylogenetic markers. However, the functional consequences underlying the analysed sequence diversity and their putative evolutionary implications are essentially not taken into consideration. Here, we propose to exploit additional functional hallmarks of ribosome biogenesis to help disentangle competing evolutionary hypotheses. Using selected examples, such as the multiple origins of halophily in archaea or the evolutionary relationship between the Asgard archaea and Eukaryotes, we illustrate and discuss how function-aware phylogenetic framework can contribute to refining our understanding of archaeal phylogeny and the origin of eukaryotic cells.
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Affiliation(s)
- Michael Jüttner
- Regensburg Center for Biochemistry, Biochemistry III - Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Sébastien Ferreira-Cerca
- Regensburg Center for Biochemistry, Biochemistry III - Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
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23
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Rivas M, Fox GE. Nonstandard RNA/RNA interactions likely enhance folding and stability of segmented ribosomes. RNA (NEW YORK, N.Y.) 2022; 28:340-352. [PMID: 34876487 PMCID: PMC8848935 DOI: 10.1261/rna.079006.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 11/26/2021] [Indexed: 05/21/2023]
Abstract
The ribosome is the molecular factory that catalyzes all coded protein synthesis in extant organisms. Eukaryotic ribosomes are typically assembled out of four rRNAs; namely, 5S, 5.8S, 18S, and 28S. However, the 28S rRNA of some trypanosomatid organisms has been found to be segmented into six independent rRNAs of different sizes. The two largest segments have multiple sites where they jointly form stems comprised of standard base pairs that can hold them together. However, such regions of interaction are not observed among the four smaller RNAs. Early reports suggested that trypanosomatid segmented ribosome assembly was essentially achieved thanks to their association with rProteins. However, examination of cryo-EM ribosomal structures from Trypanosoma brucei, Leishmania donovani, and Trypanosoma cruzi reveals several long-range nonstandard RNA/RNA interactions. Most of these interactions are clusters of individual hydrogen bonds and so are not readily predictable. However, taken as a whole, they represent significant stabilizing energy that likely facilitates rRNA assembly and the overall stability of the segmented ribosomes. In the context of origin of life studies, the current results provide a better understanding of the true nature of RNA sequence space and what might be possible without an RNA replicase.
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Affiliation(s)
- Mario Rivas
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA
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24
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Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells. Nat Commun 2022; 13:911. [PMID: 35177610 PMCID: PMC8854666 DOI: 10.1038/s41467-022-28602-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 01/19/2022] [Indexed: 02/06/2023] Open
Abstract
Three-dimensional (3D) structures dictate the functions of RNA molecules in a wide variety of biological processes. However, direct determination of RNA 3D structures in vivo is difficult due to their large sizes, conformational heterogeneity, and dynamics. Here we present a method, Spatial 2′-Hydroxyl Acylation Reversible Crosslinking (SHARC), which uses chemical crosslinkers of defined lengths to measure distances between nucleotides in cellular RNA. Integrating crosslinking, exonuclease (exo) trimming, proximity ligation, and high throughput sequencing, SHARC enables transcriptome-wide tertiary structure contact maps at high accuracy and precision, revealing heterogeneous RNA structures and interactions. SHARC data provide constraints that improves Rosetta-based RNA 3D structure modeling at near-nanometer resolution. Integrating SHARC-exo with other crosslinking-based methods, we discover compact folding of the 7SK RNA, a critical regulator of transcriptional elongation. These results establish a strategy for measuring RNA 3D distances and alternative conformations in their native cellular context. Determination of RNA 3D structures in vivo is a challenging problem. Here, the authors describe a chemical crosslinking method (SHARC) that they use in combination with RNA sequencing to measure distances between nucleotides in RNA 3D structures.
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25
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Fractional 2'-O-methylation in the ribosomal RNA of Dictyostelium discoideum supports ribosome heterogeneity in Amoebozoa. Sci Rep 2022; 12:1952. [PMID: 35121764 PMCID: PMC8817022 DOI: 10.1038/s41598-022-05447-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/07/2022] [Indexed: 12/02/2022] Open
Abstract
A hallmark of ribosomal RNA (rRNA) are 2′-O-methyl groups that are introduced sequence specifically by box C/D small nucleolar RNAs (snoRNAs) in ribonucleoprotein particles. Most data on this chemical modification and its impact on RNA folding and stability are derived from organisms of the Opisthokonta supergroup. Using bioinformatics and RNA-seq data, we identify 30 novel box C/D snoRNAs in Dictyostelium discoideum, many of which are differentially expressed during the multicellular development of the amoeba. By applying RiboMeth-seq, we find 49 positions in the 17S and 26S rRNA 2′-O-methylated. Several of these nucleotides are substoichiometrically modified, with one displaying dynamic modification levels during development. Using homology-based models for the D. discoideum rRNA secondary structures, we localize many modified nucleotides in the vicinity of the ribosomal A, P and E sites. For most modified positions, a guiding box C/D snoRNA could be identified, allowing to determine idiosyncratic features of the snoRNA/rRNA interactions in the amoeba. Our data from D. discoideum represents the first evidence for ribosome heterogeneity in the Amoebozoa supergroup, allowing to suggest that it is a common feature of all eukaryotes.
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26
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Salaikumaran MR, Badiger VP, Burra VLSP. 16S rRNA Methyltransferases as Novel Drug Targets Against Tuberculosis. Protein J 2022; 41:97-130. [PMID: 35112243 DOI: 10.1007/s10930-021-10029-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2021] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB) is an airborne infectious disease caused by Mycobacterium tuberculosis (M.tb) whose natural history traces back to 70,000 years. TB remains a major global health burden. Methylation is a type of post-replication, post-transcriptional and post-translational epi-genetic modification involved in transcription, translation, replication, tissue specific expression, embryonic development, genomic imprinting, genome stability and chromatin structure, protein protein interactions and signal transduction indicating its indispensable role in survival of a pathogen like M.tb. The pathogens use this epigenetic mechanism to develop resistance against certain drug molecules and survive the lethality. Drug resistance has become a major challenge to tackle and also a major concern raised by WHO. Methyltransferases are enzymes that catalyze the methylation of various substrates. None of the current TB targets belong to methyltransferases which provides therapeutic opportunities to develop novel drugs through studying methyltransferases as potential novel targets against TB. Targeting 16S rRNA methyltransferases serves two purposes simultaneously: a) translation inhibition and b) simultaneous elimination of the ability to methylate its substrates hence stopping the emergence of drug resistance strains. There are ~ 40 different rRNA methyltransferases and 13 different 16S rRNA specific methyltransferases which are unexplored and provide a huge opportunity for treatment of TB.
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Affiliation(s)
- M R Salaikumaran
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed To Be) University, Vaddeswaram, Andhra Pradesh, 522 502, India
| | - Veena P Badiger
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed To Be) University, Vaddeswaram, Andhra Pradesh, 522 502, India
| | - V L S Prasad Burra
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed To Be) University, Vaddeswaram, Andhra Pradesh, 522 502, India.
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27
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Molecular signature characters complement taxonomic diagnoses: a bioinformatic approach exemplified by ciliated protists (Ciliophora, Oligotrichea). Mol Phylogenet Evol 2022; 170:107433. [DOI: 10.1016/j.ympev.2022.107433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/13/2022] [Accepted: 01/20/2022] [Indexed: 11/21/2022]
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28
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Abstract
Eukaryotic ribosome biogenesis involves the synthesis of ribosomal RNA (rRNA) and its stepwise folding into the unique structure present in mature ribosomes. rRNA folding starts already co-transcriptionally in the nucleolus and continues when pre-ribosomal particles further maturate in the nucleolus and upon their transit to the nucleoplasm and cytoplasm. While the approximate order of folding of rRNA subdomains is known, especially from cryo-EM structures of pre-ribosomal particles, the actual mechanisms of rRNA folding are less well understood. Both small nucleolar RNAs (snoRNAs) and proteins have been implicated in rRNA folding. snoRNAs hybridize to precursor rRNAs (pre-rRNAs) and thereby prevent premature folding of the respective rRNA elements. Ribosomal proteins (r-proteins) and ribosome assembly factors might have a similar function by binding to rRNA elements and preventing their premature folding. Besides that, a small group of ribosome assembly factors are thought to play a more active role in rRNA folding. In particular, multiple RNA helicases participate in individual ribosome assembly steps, where they are believed to coordinate RNA folding/unfolding events or the release of proteins from the rRNA. In this review, we summarize the current knowledge on mechanisms of RNA folding and on the specific function of the individual RNA helicases involved. As the yeast Saccharomyces cerevisiae is the organism in which ribosome biogenesis and the role of RNA helicases in this process is best studied, we focused our review on insights from this model organism, but also make comparisons to other organisms where applicable.
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Affiliation(s)
- Valentin Mitterer
- Biochemistry Center, Heidelberg University, Im Neuenheimer Feld 328, Heidelberg, Germany.,BioTechMed-Graz, Graz, Austria
| | - Brigitte Pertschy
- BioTechMed-Graz, Graz, Austria.,Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, Graz, Austria
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29
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Tirumalai MR, Rivas M, Tran Q, Fox GE. The Peptidyl Transferase Center: a Window to the Past. Microbiol Mol Biol Rev 2021; 85:e0010421. [PMID: 34756086 PMCID: PMC8579967 DOI: 10.1128/mmbr.00104-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In his 2001 article, "Translation: in retrospect and prospect," the late Carl Woese made a prescient observation that there was a need for the then-current view of translation to be "reformulated to become an all-embracing perspective about which 21st century Biology can develop" (RNA 7:1055-1067, 2001, https://doi.org/10.1017/s1355838201010615). The quest to decipher the origins of life and the road to the genetic code are both inextricably linked with the history of the ribosome. After over 60 years of research, significant progress in our understanding of how ribosomes work has been made. Particularly attractive is a model in which the ribosome may facilitate an ∼180° rotation of the CCA end of the tRNA from the A-site to the P-site while the acceptor stem of the tRNA would then undergo a translation from the A-site to the P-site. However, the central question of how the ribosome originated remains unresolved. Along the path from a primitive RNA world or an RNA-peptide world to a proto-ribosome world, the advent of the peptidyl transferase activity would have been a seminal event. This functionality is now housed within a local region of the large-subunit (LSU) rRNA, namely, the peptidyl transferase center (PTC). The PTC is responsible for peptide bond formation during protein synthesis and is usually considered to be the oldest part of the modern ribosome. What is frequently overlooked is that by examining the origins of the PTC itself, one is likely going back even further in time. In this regard, it has been proposed that the modern PTC originated from the association of two smaller RNAs that were once independent and now comprise a pseudosymmetric region in the modern PTC. Could such an association have survived? Recent studies have shown that the extant PTC is largely depleted of ribosomal protein interactions. It is other elements like metallic ion coordination and nonstandard base/base interactions that would have had to stabilize the association of RNAs. Here, we present a detailed review of the literature focused on the nature of the extant PTC and its proposed ancestor, the proto-ribosome.
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Affiliation(s)
- Madhan R. Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Mario Rivas
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Quyen Tran
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
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30
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Pöll G, Pilsl M, Griesenbeck J, Tschochner H, Milkereit P. Analysis of subunit folding contribution of three yeast large ribosomal subunit proteins required for stabilisation and processing of intermediate nuclear rRNA precursors. PLoS One 2021; 16:e0252497. [PMID: 34813592 PMCID: PMC8610266 DOI: 10.1371/journal.pone.0252497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/17/2021] [Indexed: 11/19/2022] Open
Abstract
In yeast and human cells many of the ribosomal proteins (r-proteins) are required for the stabilisation and productive processing of rRNA precursors. Functional coupling of r-protein assembly with the stabilisation and maturation of subunit precursors potentially promotes the production of ribosomes with defined composition. To further decipher mechanisms of such an intrinsic quality control pathway we analysed here the contribution of three yeast large ribosomal subunit r-proteins rpL2 (uL2), rpL25 (uL23) and rpL34 (eL34) for intermediate nuclear subunit folding steps. Structure models obtained from single particle cryo-electron microscopy analyses provided evidence for specific and hierarchic effects on the stable positioning and remodelling of large ribosomal subunit domains. Based on these structural and previous biochemical data we discuss possible mechanisms of r-protein dependent hierarchic domain arrangement and the resulting impact on the stability of misassembled subunits.
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Affiliation(s)
- Gisela Pöll
- Chair of Biochemistry III, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Michael Pilsl
- Structural Biochemistry Unit, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
| | - Joachim Griesenbeck
- Chair of Biochemistry III, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
- * E-mail: (JG); (HT); (PM)
| | - Herbert Tschochner
- Chair of Biochemistry III, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
- * E-mail: (JG); (HT); (PM)
| | - Philipp Milkereit
- Chair of Biochemistry III, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany
- * E-mail: (JG); (HT); (PM)
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31
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Sun X, Cheng J. Phylogenetic Signal Dissection of Heterogeneous 28S and 16S rRNA Genes in Spinicaudata (Branchiopoda, Diplostraca). Genes (Basel) 2021; 12:1705. [PMID: 34828311 PMCID: PMC8625258 DOI: 10.3390/genes12111705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 12/05/2022] Open
Abstract
It is still a challenge to reconstruct the deep phylogenetic relationships within spinicaudatans, and there are several different competing hypotheses regarding the interrelationships among Eocyzicidae, Cyzicidae s. s., Leptestheriidae, and Limnadiidae of the Suborder Spinicaudata. In order to explore the source of the inconsistencies, we focus on the sequence variation and the structure model of two rRNA genes based on extensive taxa sampling. The comparative sequence analysis revealed heterogeneity across species and the existence of conserved motifs in all spinicaudatan species. The level of intraspecific heterogeneity differed among species, which suggested that some species might have undergone a relaxed concerted evolution with respect to the 28S rRNA gene. The Bayesian analyses were performed on nuclear (28S rRNA, EF1α) and mitochondrial (16S rRNA, COI) genes. Further, we investigated compositional heterogeneity between lineages and assessed the potential for phylogenetic noise compared to signal in the combined data set. Reducing the non-phylogenetic signals and application of optimal rRNA model recovered a topology congruent with inference from the transcriptome data, whereby Limnadiidae was placed as a sister group to Leptestheriidae + Eocyzicidae with high support (topology I). Tests of alternative hypotheses provided implicit support for four competing topologies, and topology I was the best.
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Affiliation(s)
| | - Jinhui Cheng
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, No. 39, Beijing Eastroad, Nanjing 210008, China;
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32
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Aquino GRR, Hackert P, Krogh N, Pan KT, Jaafar M, Henras AK, Nielsen H, Urlaub H, Bohnsack KE, Bohnsack MT. The RNA helicase Dbp7 promotes domain V/VI compaction and stabilization of inter-domain interactions during early 60S assembly. Nat Commun 2021; 12:6152. [PMID: 34686661 PMCID: PMC8536713 DOI: 10.1038/s41467-021-26208-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 09/22/2021] [Indexed: 02/07/2023] Open
Abstract
Early pre-60S ribosomal particles are poorly characterized, highly dynamic complexes that undergo extensive rRNA folding and compaction concomitant with assembly of ribosomal proteins and exchange of assembly factors. Pre-60S particles contain numerous RNA helicases, which are likely regulators of accurate and efficient formation of appropriate rRNA structures. Here we reveal binding of the RNA helicase Dbp7 to domain V/VI of early pre-60S particles in yeast and show that in the absence of this protein, dissociation of the Npa1 scaffolding complex, release of the snR190 folding chaperone, recruitment of the A3 cluster factors and binding of the ribosomal protein uL3 are impaired. uL3 is critical for formation of the peptidyltransferase center (PTC) and is responsible for stabilizing interactions between the 5′ and 3′ ends of the 25S, an essential pre-requisite for subsequent pre-60S maturation events. Highlighting the importance of pre-ribosome remodeling by Dbp7, our data suggest that in the absence of Dbp7 or its catalytic activity, early pre-ribosomal particles are targeted for degradation. Early steps of large 60S ribosomal subunit biogenesis are not well understood. Here, the authors combine biochemical experiments with protein-RNA crosslinking and mass spectrometry to show that the RNA helicase Dbp7 is key player during early 60S ribosomal assembly. Dbp7 regulates a series of events driving compaction of domain V/VI in early pre60S ribosomal particles.
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Affiliation(s)
- Gerald Ryan R Aquino
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200N, Copenhagen, Denmark
| | - Kuan-Ting Pan
- Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry, 37077, Göttingen, Germany.,Hematology/Oncology, Department of Medicine II, Johann Wolfgang Goethe University, 60590, Frankfurt am Main, Germany.,Frankfurt Cancer Institute, Goethe University, 60596, Frankfurt am Main, Germany
| | - Mariam Jaafar
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062, Toulouse, France
| | - Anthony K Henras
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062, Toulouse, France
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200N, Copenhagen, Denmark.,Genomics Group, Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Henning Urlaub
- Max Planck Institute for Biophysical Chemistry, Bioanalytical Mass Spectrometry, 37077, Göttingen, Germany.,Institute for Clinical Chemistry, University Medical Center Göttingen, 37075, Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073, Göttingen, Germany. .,Göttingen Centre for Molecular Biosciences, Georg-August-University, Justus-von-Liebig Weg 11, 37077, Göttingen, Germany.
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33
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Penev PI, Fakhretaha-Aval S, Patel VJ, Cannone JJ, Gutell RR, Petrov AS, Williams LD, Glass JB. Supersized Ribosomal RNA Expansion Segments in Asgard Archaea. Genome Biol Evol 2021; 12:1694-1710. [PMID: 32785681 PMCID: PMC7594248 DOI: 10.1093/gbe/evaa170] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2020] [Indexed: 12/11/2022] Open
Abstract
The ribosome’s common core, comprised of ribosomal RNA (rRNA) and universal ribosomal proteins, connects all life back to a common ancestor and serves as a window to relationships among organisms. The rRNA of the common core is similar to rRNA of extant bacteria. In eukaryotes, the rRNA of the common core is decorated by expansion segments (ESs) that vastly increase its size. Supersized ESs have not been observed previously in Archaea, and the origin of eukaryotic ESs remains enigmatic. We discovered that the large ribosomal subunit (LSU) rRNA of two Asgard phyla, Lokiarchaeota and Heimdallarchaeota, considered to be the closest modern archaeal cell lineages to Eukarya, bridge the gap in size between prokaryotic and eukaryotic LSU rRNAs. The elongated LSU rRNAs in Lokiarchaeota and Heimdallarchaeota stem from two supersized ESs, called ES9 and ES39. We applied chemical footprinting experiments to study the structure of Lokiarchaeota ES39. Furthermore, we used covariation and sequence analysis to study the evolution of Asgard ES39s and ES9s. By defining the common eukaryotic ES39 signature fold, we found that Asgard ES39s have more and longer helices than eukaryotic ES39s. Although Asgard ES39s have sequences and structures distinct from eukaryotic ES39s, we found overall conservation of a three-way junction across the Asgard species that matches eukaryotic ES39 topology, a result consistent with the accretion model of ribosomal evolution.
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Affiliation(s)
- Petar I Penev
- Georgia Institute of Technology, NASA Center for the Origin of Life, Atlanta, Georgia.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Sara Fakhretaha-Aval
- Georgia Institute of Technology, NASA Center for the Origin of Life, Atlanta, Georgia.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - Vaishnavi J Patel
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas
| | - Jamie J Cannone
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas
| | - Robin R Gutell
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas
| | - Anton S Petrov
- Georgia Institute of Technology, NASA Center for the Origin of Life, Atlanta, Georgia.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - Loren Dean Williams
- Georgia Institute of Technology, NASA Center for the Origin of Life, Atlanta, Georgia.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia
| | - Jennifer B Glass
- Georgia Institute of Technology, NASA Center for the Origin of Life, Atlanta, Georgia.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.,School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia
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34
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Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA. Proc Natl Acad Sci U S A 2021; 118:2020837118. [PMID: 33658370 DOI: 10.1073/pnas.2020837118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Both the small and large subunits of the ribosome, the molecular machine that synthesizes proteins, are complexes of ribosomal RNAs (rRNAs) and a number of proteins. In bacteria, the small subunit has a single 16S rRNA whose folding is the first step in its assembly. The central domain of the 16S rRNA folds independently, driven either by Mg2+ ions or by interaction with ribosomal proteins. To provide a quantitative description of ion-induced folding of the ∼350-nucleotide rRNA, we carried out extensive coarse-grained molecular simulations spanning Mg2+ concentration between 0 and 30 mM. The Mg2+ dependence of the radius of gyration shows that globally the rRNA folds cooperatively. Surprisingly, various structural elements order at different Mg2+ concentrations, indicative of the heterogeneous assembly even within a single domain of the rRNA. Binding of Mg2+ ions is highly specific, with successive ion condensation resulting in nucleation of tertiary structures. We also predict the Mg2+-dependent protection factors, measurable in hydroxyl radical footprinting experiments, which corroborate the specificity of Mg2+-induced folding. The simulations, which agree quantitatively with several experiments on the folding of a three-way junction, show that its folding is preceded by formation of other tertiary contacts in the central junction. Our work provides a starting point in simulating the early events in the assembly of the small subunit of the ribosome.
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35
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Gay DM, Lund AH, Jansson MD. Translational control through ribosome heterogeneity and functional specialization. Trends Biochem Sci 2021; 47:66-81. [PMID: 34312084 DOI: 10.1016/j.tibs.2021.07.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/18/2021] [Accepted: 07/01/2021] [Indexed: 12/31/2022]
Abstract
The conceptual origins of ribosome specialization can be traced back to the earliest days of molecular biology. Yet, this field has only recently begun to gather momentum, with numerous studies identifying distinct heterogeneous ribosome populations across multiple species and model systems. It is proposed that some of these compositionally distinct ribosomes may be functionally specialized and able to regulate the translation of specific mRNAs. Identification and functional characterization of specialized ribosomes has the potential to elucidate a novel layer of gene expression control, at the level of translation, where the ribosome itself is a key regulatory player. In this review, we discuss different sources of ribosome heterogeneity, evidence for ribosome specialization, and also the future directions of this exciting field.
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Affiliation(s)
- David M Gay
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anders H Lund
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
| | - Martin D Jansson
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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36
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Sweeney BA, Hoksza D, Nawrocki EP, Ribas CE, Madeira F, Cannone JJ, Gutell R, Maddala A, Meade CD, Williams LD, Petrov AS, Chan PP, Lowe TM, Finn RD, Petrov AI. R2DT is a framework for predicting and visualising RNA secondary structure using templates. Nat Commun 2021; 12:3494. [PMID: 34108470 PMCID: PMC8190129 DOI: 10.1038/s41467-021-23555-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 05/04/2021] [Indexed: 02/05/2023] Open
Abstract
Non-coding RNAs (ncRNA) are essential for all life, and their functions often depend on their secondary (2D) and tertiary structure. Despite the abundance of software for the visualisation of ncRNAs, few automatically generate consistent and recognisable 2D layouts, which makes it challenging for users to construct, compare and analyse structures. Here, we present R2DT, a method for predicting and visualising a wide range of RNA structures in standardised layouts. R2DT is based on a library of 3,647 templates representing the majority of known structured RNAs. R2DT has been applied to ncRNA sequences from the RNAcentral database and produced >13 million diagrams, creating the world's largest RNA 2D structure dataset. The software is amenable to community expansion, and is freely available at https://github.com/rnacentral/R2DT and a web server is found at https://rnacentral.org/r2dt .
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Affiliation(s)
- Blake A Sweeney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - David Hoksza
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Eric P Nawrocki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Carlos Eduardo Ribas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Fábio Madeira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Jamie J Cannone
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Robin Gutell
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Aparna Maddala
- School of Chemistry and Biochemistry, Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Caeden D Meade
- School of Chemistry and Biochemistry, Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anton S Petrov
- School of Chemistry and Biochemistry, Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Patricia P Chan
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Anton I Petrov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.
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37
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An K, Zhou JB, Xiong Y, Han W, Wang T, Ye ZQ, Wu YD. Computational Studies of the Structural Basis of Human RPS19 Mutations Associated With Diamond-Blackfan Anemia. Front Genet 2021; 12:650897. [PMID: 34108988 PMCID: PMC8181406 DOI: 10.3389/fgene.2021.650897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/28/2021] [Indexed: 11/13/2022] Open
Abstract
Diamond-Blackfan Anemia (DBA) is an inherited rare disease characterized with severe pure red cell aplasia, and it is caused by the defective ribosome biogenesis stemming from the impairment of ribosomal proteins. Among all DBA-associated ribosomal proteins, RPS19 affects most patients and carries most DBA mutations. Revealing how these mutations lead to the impairment of RPS19 is highly demanded for understanding the pathogenesis of DBA, but a systematic study is currently lacking. In this work, based on the complex structure of human ribosome, we comprehensively studied the structural basis of DBA mutations of RPS19 by using computational methods. Main structure elements and five conserved surface patches involved in RPS19-18S rRNA interaction were identified. We further revealed that DBA mutations would destabilize RPS19 through disrupting the hydrophobic core or breaking the helix, or perturb the RPS19-18S rRNA interaction through destroying hydrogen bonds, introducing steric hindrance effect, or altering surface electrostatic property at the interface. Moreover, we trained a machine-learning model to predict the pathogenicity of all possible RPS19 mutations. Our work has laid a foundation for revealing the pathogenesis of DBA from the structural perspective.
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Affiliation(s)
- Ke An
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Jing-Bo Zhou
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yao Xiong
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Wei Han
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Tao Wang
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Zhi-Qiang Ye
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Yun-Dong Wu
- State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
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38
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Aquino GRR, Krogh N, Hackert P, Martin R, Gallesio JD, van Nues RW, Schneider C, Watkins NJ, Nielsen H, Bohnsack KE, Bohnsack MT. RNA helicase-mediated regulation of snoRNP dynamics on pre-ribosomes and rRNA 2'-O-methylation. Nucleic Acids Res 2021; 49:4066-4084. [PMID: 33721027 PMCID: PMC8053091 DOI: 10.1093/nar/gkab159] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 02/23/2021] [Accepted: 02/26/2021] [Indexed: 12/18/2022] Open
Abstract
RNA helicases play important roles in diverse aspects of RNA metabolism through their functions in remodelling ribonucleoprotein complexes (RNPs), such as pre-ribosomes. Here, we show that the DEAD box helicase Dbp3 is required for efficient processing of the U18 and U24 intron-encoded snoRNAs and 2′-O-methylation of various sites within the 25S ribosomal RNA (rRNA) sequence. Furthermore, numerous box C/D snoRNPs accumulate on pre-ribosomes in the absence of Dbp3. Many snoRNAs guiding Dbp3-dependent rRNA modifications have overlapping pre-rRNA basepairing sites and therefore form mutually exclusive interactions with pre-ribosomes. Analysis of the distribution of these snoRNAs between pre-ribosome-associated and ‘free’ pools demonstrated that many are almost exclusively associated with pre-ribosomal complexes. Our data suggest that retention of such snoRNPs on pre-ribosomes when Dbp3 is lacking may impede rRNA 2′-O-methylation by reducing the recycling efficiency of snoRNPs and by inhibiting snoRNP access to proximal target sites. The observation of substoichiometric rRNA modification at adjacent sites suggests that the snoRNPs guiding such modifications likely interact stochastically rather than hierarchically with their pre-rRNA target sites. Together, our data provide new insights into the dynamics of snoRNPs on pre-ribosomal complexes and the remodelling events occurring during the early stages of ribosome assembly.
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Affiliation(s)
- Gerald Ryan R Aquino
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, 3B Blegdamsvej, 2200N Copenhagen, Denmark
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Roman Martin
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Jimena Davila Gallesio
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Robert W van Nues
- Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Claudia Schneider
- Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Nicholas J Watkins
- Biosciences Institute, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, 3B Blegdamsvej, 2200N Copenhagen, Denmark.,Genomics group, Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Humboldtallee 23, 37073 Göttingen, Germany.,Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
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39
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Breuer R, Gomes-Filho JV, Randau L. Conservation of Archaeal C/D Box sRNA-Guided RNA Modifications. Front Microbiol 2021; 12:654029. [PMID: 33776983 PMCID: PMC7994747 DOI: 10.3389/fmicb.2021.654029] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/19/2021] [Indexed: 12/18/2022] Open
Abstract
Post-transcriptional modifications fulfill many important roles during ribosomal RNA maturation in all three domains of life. Ribose 2'-O-methylations constitute the most abundant chemical rRNA modification and are, for example, involved in RNA folding and stabilization. In archaea, these modification sites are determined by variable sets of C/D box sRNAs that guide the activity of the rRNA 2'-O-methyltransferase fibrillarin. Each C/D box sRNA contains two guide sequences that can act in coordination to bridge rRNA sequences. Here, we will review the landscape of archaeal C/D box sRNA genes and their target sites. One focus is placed on the apparent accelerated evolution of guide sequences and the varied pairing of the two individual guides, which results in different rRNA modification patterns and RNA chaperone activities.
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Affiliation(s)
| | | | - Lennart Randau
- Prokaryotic RNA Biology, Philipps-Universität Marburg, Marburg, Germany
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40
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Specificity of RNA Folding and Its Association with Evolutionarily Adaptive mRNA Secondary Structures. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:882-900. [PMID: 33607297 PMCID: PMC9403030 DOI: 10.1016/j.gpb.2019.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 08/03/2019] [Accepted: 11/08/2019] [Indexed: 11/23/2022]
Abstract
The secondary structure is a fundamental feature of both noncoding and messenger RNAs. However, our understanding of the secondary structure of mRNA, especially that of the coding regions, remains elusive, likely due to translation and the lack of RNA-binding proteins that sustain the consensus structure, such as those that bind to noncoding RNA. Indeed, mRNA has recently been found to adopt diverse alternative structures, the overall functional significance of which remains untested. We hereby approached this problem by estimating the folding specificity, i.e., the probability that a fragment of RNA folds back to the same partner once refolded. We showed that the folding specificity of mRNA is lower than that of noncoding RNA and exhibits moderate evolutionary conservation. Notably, we found that specific rather than alternative folding is likely evolutionarily adaptive since specific folding is frequently associated with functionally important genes or sites within a gene. Additional analysis in combination with ribosome density suggests the ability to modulate ribosome movement as one potential functional advantage provided by specific folding. Our findings revealed a novel facet of the RNA structurome with important functional and evolutionary implications and indicated a potential method for distinguishing the mRNA secondary structures maintained by natural selection from molecular noise.
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41
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Zhang Y, De Laurentiis E, Bohnsack KE, Wahlig M, Ranjan N, Gruseck S, Hackert P, Wölfle T, Rodnina MV, Schwappach B, Rospert S. Ribosome-bound Get4/5 facilitates the capture of tail-anchored proteins by Sgt2 in yeast. Nat Commun 2021; 12:782. [PMID: 33542241 PMCID: PMC7862611 DOI: 10.1038/s41467-021-20981-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 01/05/2021] [Indexed: 02/03/2023] Open
Abstract
The guided entry of tail-anchored proteins (GET) pathway assists in the posttranslational delivery of tail-anchored proteins, containing a single C-terminal transmembrane domain, to the ER. Here we uncover how the yeast GET pathway component Get4/5 facilitates capture of tail-anchored proteins by Sgt2, which interacts with tail-anchors and hands them over to the targeting component Get3. Get4/5 binds directly and with high affinity to ribosomes, positions Sgt2 close to the ribosomal tunnel exit, and facilitates the capture of tail-anchored proteins by Sgt2. The contact sites of Get4/5 on the ribosome overlap with those of SRP, the factor mediating cotranslational ER-targeting. Exposure of internal transmembrane domains at the tunnel exit induces high-affinity ribosome binding of SRP, which in turn prevents ribosome binding of Get4/5. In this way, the position of a transmembrane domain within nascent ER-targeted proteins mediates partitioning into either the GET or SRP pathway directly at the ribosomal tunnel exit. The guided entry of tail-anchored proteins (GET) pathway assists in the delivery of such proteins to the ER. Here, the authors reveal that the pathway components Get4/5 probe a region near the ribosomal exit tunnel. Upon emergence of a client protein, Get4/5 recruits Sgt2 and initiates the targeting phase of the pathway.
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Affiliation(s)
- Ying Zhang
- Institute of Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Evelina De Laurentiis
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Mascha Wahlig
- Institute of Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Namit Ranjan
- Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Simon Gruseck
- Institute of Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Tina Wölfle
- Institute of Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Marina V Rodnina
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Göttingen, Germany.,Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Blanche Schwappach
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany. .,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Göttingen, Germany.
| | - Sabine Rospert
- Institute of Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany.
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42
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Bud23 promotes the final disassembly of the small subunit Processome in Saccharomyces cerevisiae. PLoS Genet 2020; 16:e1009215. [PMID: 33306676 PMCID: PMC7758049 DOI: 10.1371/journal.pgen.1009215] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 12/23/2020] [Accepted: 10/21/2020] [Indexed: 01/18/2023] Open
Abstract
The first metastable assembly intermediate of the eukaryotic ribosomal small subunit (SSU) is the SSU Processome, a large complex of RNA and protein factors that is thought to represent an early checkpoint in the assembly pathway. Transition of the SSU Processome towards continued maturation requires the removal of the U3 snoRNA and biogenesis factors as well as ribosomal RNA processing. While the factors that drive these events are largely known, how they do so is not. The methyltransferase Bud23 has a role during this transition, but its function, beyond the nonessential methylation of ribosomal RNA, is not characterized. Here, we have carried out a comprehensive genetic screen to understand Bud23 function. We identified 67 unique extragenic bud23Δ-suppressing mutations that mapped to genes encoding the SSU Processome factors DHR1, IMP4, UTP2 (NOP14), BMS1 and the SSU protein RPS28A. These factors form a physical interaction network that links the binding site of Bud23 to the U3 snoRNA and many of the amino acid substitutions weaken protein-protein and protein-RNA interactions. Importantly, this network links Bud23 to the essential GTPase Bms1, which acts late in the disassembly pathway, and the RNA helicase Dhr1, which catalyzes U3 snoRNA removal. Moreover, particles isolated from cells lacking Bud23 accumulated late SSU Processome factors and ribosomal RNA processing defects. We propose a model in which Bud23 dissociates factors surrounding its binding site to promote SSU Processome progression. Ribosomes are the molecular machines that synthesize proteins and are composed of a large and a small subunit which carry out the essential functions of polypeptide synthesis and mRNA decoding, respectively. Ribosome production is tightly linked to cellular growth as cells must produce enough ribosomes to meet their protein needs. However, ribosome assembly is a metabolically expensive pathway that must be balanced with other cellular energy needs and regulated accordingly. In eukaryotes, the small subunit (SSU) Processome is a metastable intermediate that ultimately progresses towards a mature SSU through the release of biogenesis factors. The decision to progress the SSU Processome is thought to be an early checkpoint in the SSU assembly pathway, but insight into the mechanisms of progression is needed. Previous studies suggest that Bud23 plays an uncharacterized role during SSU Processome progression. Here, we used a genetic approach to understand its function and found that Bud23 is connected to a network of SSU Processome factors that stabilize the particle. Interestingly, two of these factors are enzymes that are needed for progression. We conclude that Bud23 promotes the release of factors surrounding its binding site to induce structural rearrangements during the progression of the SSU Processome.
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43
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Choudhury P, Kretschmer J, Hackert P, Bohnsack KE, Bohnsack MT. The DExD box ATPase DDX55 is recruited to domain IV of the 28S ribosomal RNA by its C-terminal region. RNA Biol 2020; 18:1124-1135. [PMID: 33048000 PMCID: PMC8244758 DOI: 10.1080/15476286.2020.1829366] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
RNA helicases contribute to diverse aspects of RNA metabolism through their functions in re-arranging RNA structures. Identification of the remodelling targets of RNA helicases is a critical step in elucidating their cellular functions. Here, we show that, in contrast to many other ribosome biogenesis factors, the DExD box ATPase DDX55 predominantly localizes to the nucleoplasm and we identify a nuclear localization signal within the C-terminal region of the protein. DDX55 associates with pre-ribosomal subunits in human cells and is required for maturation of large subunit pre-rRNAs. Interestingly, in vitro analyses show that DDX55 selectively associates with double-stranded RNA substrates, which also stimulate its ATPase activity, and our data suggest that the C-terminal region of DDX55 contributes to this substrate specificity. The C-terminal region of DDX55 is also necessary for recruitment of the helicase to pre-ribosomes and, using in vivo crosslinking, we reveal a binding site for DDX55 in helix H62 of the 28S ribosomal RNA. Taken together, these data highlight the importance of the C-terminal region of DDX55 in substrate specificity and recruitment, and identify domain IV as a potential remodelling target of DDX55 during LSU biogenesis.
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Affiliation(s)
- Priyanka Choudhury
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany
| | - Jens Kretschmer
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Centre Göttingen, Göttingen, Germany.,Göttingen Center for Molecular Biosciences, Georg-August University, Göttingen, Germany
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44
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Calvet LE, Matviienko S, Ducluzaux P. Network theory of the bacterial ribosome. PLoS One 2020; 15:e0239700. [PMID: 33017414 PMCID: PMC7535068 DOI: 10.1371/journal.pone.0239700] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 09/08/2020] [Indexed: 02/07/2023] Open
Abstract
In the past two decades, research into the biochemical, biophysical and structural properties of the ribosome have revealed many different steps of protein translation. Nevertheless, a complete understanding of how they lead to a rapid and accurate protein synthesis still remains a challenge. Here we consider a coarse network analysis in the bacterial ribosome formed by the connectivity between ribosomal (r) proteins and RNAs at different stages in the elongation cycle. The ribosomal networks are found to be dis-assortative and small world, implying that the structure allows for an efficient exchange of information between distant locations. An analysis of centrality shows that the second and fifth domains of 23S rRNA are the most important elements in all of the networks. Ribosomal protein hubs connect to much fewer nodes but are shown to provide important connectivity within the network (high closeness centrality). A modularity analysis reveals some of the different functional communities, indicating some known and some new possible communication pathways Our mathematical results confirm important communication pathways that have been discussed in previous research, thus verifying the use of this technique for representing the ribosome, and also reveal new insights into the collective function of ribosomal elements.
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Affiliation(s)
- Laurie E. Calvet
- CNRS, Centre de Nanosciences et Nanotechnologies, Université Paris-Saclay, Palaiseau, France
- * E-mail:
| | - Serhii Matviienko
- CNRS, Centre de Nanosciences et Nanotechnologies, Université Paris-Saclay, Palaiseau, France
| | - Pierre Ducluzaux
- CNRS, Centre de Nanosciences et Nanotechnologies, Université Paris-Saclay, Palaiseau, France
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45
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Kater L, Mitterer V, Thoms M, Cheng J, Berninghausen O, Beckmann R, Hurt E. Construction of the Central Protuberance and L1 Stalk during 60S Subunit Biogenesis. Mol Cell 2020; 79:615-628.e5. [PMID: 32668200 DOI: 10.1016/j.molcel.2020.06.032] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/13/2020] [Accepted: 06/18/2020] [Indexed: 12/15/2022]
Abstract
Ribosome assembly is driven by numerous assembly factors, including the Rix1 complex and the AAA ATPase Rea1. These two assembly factors catalyze 60S maturation at two distinct states, triggering poorly understood large-scale structural transitions that we analyzed by cryo-electron microscopy. Two nuclear pre-60S intermediates were discovered that represent previously unknown states after Rea1-mediated removal of the Ytm1-Erb1 complex and reveal how the L1 stalk develops from a pre-mature nucleolar to a mature-like nucleoplasmic state. A later pre-60S intermediate shows how the central protuberance arises, assisted by the nearby Rix1-Rea1 machinery, which was solved in its pre-ribosomal context to molecular resolution. This revealed a Rix12-Ipi32 tetramer anchored to the pre-60S via Ipi1, strategically positioned to monitor this decisive remodeling. These results are consistent with a general underlying principle that temporarily stabilized immature RNA domains are successively remodeled by assembly factors, thereby ensuring failsafe assembly progression.
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Affiliation(s)
- Lukas Kater
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany
| | - Valentin Mitterer
- Biochemie-Zentrum der Universität Heidelberg, 69120 Heidelberg, Germany
| | - Matthias Thoms
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany; Biochemie-Zentrum der Universität Heidelberg, 69120 Heidelberg, Germany
| | - Jingdong Cheng
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany
| | - Otto Berninghausen
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany
| | - Roland Beckmann
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, Feodor-Lynen-Str. 25, University of Munich, 81377 Munich, Germany.
| | - Ed Hurt
- Biochemie-Zentrum der Universität Heidelberg, 69120 Heidelberg, Germany.
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46
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Kramer MC, Janssen KA, Palos K, Nelson ADL, Vandivier LE, Garcia BA, Lyons E, Beilstein MA, Gregory BD. N 6-methyladenosine and RNA secondary structure affect transcript stability and protein abundance during systemic salt stress in Arabidopsis. PLANT DIRECT 2020; 4:e00239. [PMID: 32724893 PMCID: PMC7379018 DOI: 10.1002/pld3.239] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/05/2020] [Accepted: 06/11/2020] [Indexed: 05/22/2023]
Abstract
After transcription, a messenger RNA (mRNA) is further post-transcriptionally regulated by several features including RNA secondary structure and covalent RNA modifications (specifically N6-methyladenosine, m6A). Both RNA secondary structure and m6A have been demonstrated to regulate mRNA stability and translation and have been independently linked to plant responses to soil salinity levels. However, the effect of m6A on regulating RNA secondary structure and the combinatorial interplay between these two RNA features during salt stress response has yet to be studied. Here, we globally identify RNA-protein interactions and RNA secondary structure during systemic salt stress. This analysis reveals that RNA secondary structure changes significantly during salt stress, and that it is independent of global changes in RNA-protein interactions. Conversely, we find that m6A is anti-correlated with RNA secondary structure in a condition-dependent manner, with salt-specific m6A correlated with a decrease in mRNA secondary structure during salt stress. Taken together, we suggest that salt-specific m6A deposition and the associated loss of RNA secondary structure results in increases in mRNA stability for transcripts encoding abiotic stress response proteins and ultimately increases in protein levels from these stabilized transcripts. In total, our comprehensive analyses reveal important post-transcriptional regulatory mechanisms involved in plant long-term salt stress response and adaptation.
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Affiliation(s)
- Marianne C. Kramer
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPAUSA
- Cell and Molecular Biology Graduate GroupPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Kevin A. Janssen
- Department of Biochemistry and BiophysicsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
- Epigenetics InstitutePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
- Biochemistry and Molecular Biophysics Graduate GroupUniversity of PennsylvaniaPAUSA
| | - Kyle Palos
- School of Plant SciencesUniversity of ArizonaTucsonAZUSA
| | | | - Lee E. Vandivier
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPAUSA
- Cell and Molecular Biology Graduate GroupPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Benjamin A. Garcia
- Department of Biochemistry and BiophysicsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
- Epigenetics InstitutePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Eric Lyons
- School of Plant SciencesUniversity of ArizonaTucsonAZUSA
- CyVerseUniversity of ArizonaTucsonAZUSA
| | | | - Brian D. Gregory
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPAUSA
- Cell and Molecular Biology Graduate GroupPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
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47
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Shigematsu M, Kirino Y. Oxidative stress enhances the expression of 2',3'-cyclic phosphate-containing RNAs. RNA Biol 2020; 17:1060-1069. [PMID: 32397797 DOI: 10.1080/15476286.2020.1766861] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Eukaryotic cells equip robust systems to respond to stress conditions. In stressed mammalian cells, angiogenin endoribonuclease cleaves anticodon-loops of tRNAs to generate tRNA halves termed tRNA-derived stress-induced RNAs (tiRNAs), which promote stress granule formation and regulate translation. The 5'-tiRNAs (5'-tRNA halves) contain a 2',3'-cyclic phosphate (cP) and thus belong to cP-containing RNAs (cP-RNAs). The cP-RNAs form a hidden layer of the transcriptome because standard RNA-seq cannot amplify and sequence them. In this study, we performed genome-wide analyses of short cP-RNA transcriptome in oxidative stress-exposed human cells. Using cP-RNA-seq that can specifically sequence cP-RNAs, we identified tiRNAs and numerous other cP-RNAs that are mainly derived from rRNAs and mRNAs. Although tiRNAs were produced from a wide variety of tRNA species, abundant species of tiRNAs were derived from a focal-specific subset of tRNAs. Regarding rRNA- and mRNA-derived cP-RNAs, determination of the processing sites of substrate RNAs revealed highly specific RNA cleavage events between pyrimidines and adenosine in generation of those cP-RNAs. Those cP-RNAs were derived from specific loci of substrate RNAs rather than from the overall region, implying that cP-RNAs are produced by regulated biogenesis pathways and not by random degradation events. We experimentally confirmed the identified sequences to be expressed as cP-RNAs in the cells, and their expressions were upregulated upon induction of oxidative stress. These analyses of the cP-RNA transcriptome unravel an abundant class of short ncRNAs that accumulate in cells under oxidative stress.
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Affiliation(s)
- Megumi Shigematsu
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University , Philadelphia, Pennsylvania, USA
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University , Philadelphia, Pennsylvania, USA
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48
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Bowman JC, Petrov AS, Frenkel-Pinter M, Penev PI, Williams LD. Root of the Tree: The Significance, Evolution, and Origins of the Ribosome. Chem Rev 2020; 120:4848-4878. [PMID: 32374986 DOI: 10.1021/acs.chemrev.9b00742] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The ribosome is an ancient molecular fossil that provides a telescope to the origins of life. Made from RNA and protein, the ribosome translates mRNA to coded protein in all living systems. Universality, economy, centrality and antiquity are ingrained in translation. The translation machinery dominates the set of genes that are shared as orthologues across the tree of life. The lineage of the translation system defines the universal tree of life. The function of a ribosome is to build ribosomes; to accomplish this task, ribosomes make ribosomal proteins, polymerases, enzymes, and signaling proteins. Every coded protein ever produced by life on Earth has passed through the exit tunnel, which is the birth canal of biology. During the root phase of the tree of life, before the last common ancestor of life (LUCA), exit tunnel evolution is dominant and unremitting. Protein folding coevolved with evolution of the exit tunnel. The ribosome shows that protein folding initiated with intrinsic disorder, supported through a short, primitive exit tunnel. Folding progressed to thermodynamically stable β-structures and then to kinetically trapped α-structures. The latter were enabled by a long, mature exit tunnel that partially offset the general thermodynamic tendency of all polypeptides to form β-sheets. RNA chaperoned the evolution of protein folding from the very beginning. The universal common core of the ribosome, with a mass of nearly 2 million Daltons, was finalized by LUCA. The ribosome entered stasis after LUCA and remained in that state for billions of years. Bacterial ribosomes never left stasis. Archaeal ribosomes have remained near stasis, except for the superphylum Asgard, which has accreted rRNA post LUCA. Eukaryotic ribosomes in some lineages appear to be logarithmically accreting rRNA over the last billion years. Ribosomal expansion in Asgard and Eukarya has been incremental and iterative, without substantial remodeling of pre-existing basal structures. The ribosome preserves information on its history.
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Affiliation(s)
- Jessica C Bowman
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Anton S Petrov
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Moran Frenkel-Pinter
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Petar I Penev
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Loren Dean Williams
- Center for the Origins of Life, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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49
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Cao L, Zhao C, Wang C, Qin H, Qin Q, Tao M, Zhang C, Zhao R, Liu S. Evolutionary dynamics of 18S and 5S rDNA in autotriploid Carassius auratus. Gene 2020; 737:144433. [PMID: 32014563 DOI: 10.1016/j.gene.2020.144433] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 01/30/2020] [Indexed: 02/06/2023]
Abstract
The Carassius auratus (crucian carp) complex of the Dongting water system exhibits coexistence of diploid and triploid forms. As reported, triploid C. auratus is autotriploid origin. Ribosomal DNA (rDNA) with evolutionary conservation is widely used to study polyploidization. Here, we investigated genomic and transcribed rDNA sequences (18S and 5S) in diploid (2nCC, 2n = 100) and triploid (3nCC, 3n = 150) C. auratus. The results showed that the genetic traits and expression of 18S and 5S rDNA from 2nCC individuals were identified in 3nCC individuals. Moreover, pseudogenization of rDNA (18S and 5S) sequences were also observed in both 2nCC and 3nCC individuals, but expression of these variants was not detected. Based on the transcribed rDNA consensus sequence between 2nCC and 3nCC individuals, the functional secondary structures of 18S rRNA (expansion segments, ES6S) and 5S rRNA were predicted. These data demonstrated that complex evolutionary dynamics existed in the rDNA family of C. auratus. The evolutionary conservation of rDNA revealed that autotriploidization could not induce the divergence in Carassius taxa of the Dongting water system. These observations will expand our knowledge of the evolutionary dynamics of the rDNA family in vertebrates.
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Affiliation(s)
- Liu Cao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha 410081, Hunan, PR China; College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Chun Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha 410081, Hunan, PR China; College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Chongqing Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha 410081, Hunan, PR China; College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Huan Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha 410081, Hunan, PR China; College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha 410081, Hunan, PR China; College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha 410081, Hunan, PR China; College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha 410081, Hunan, PR China; College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Rurong Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha 410081, Hunan, PR China; College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha 410081, Hunan, PR China; College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, PR China.
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50
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Braun CM, Hackert P, Schmid CE, Bohnsack MT, Bohnsack KE, Perez-Fernandez J. Pol5 is required for recycling of small subunit biogenesis factors and for formation of the peptide exit tunnel of the large ribosomal subunit. Nucleic Acids Res 2020; 48:405-420. [PMID: 31745560 PMCID: PMC7145529 DOI: 10.1093/nar/gkz1079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 01/24/2023] Open
Abstract
More than 200 assembly factors (AFs) are required for the production of ribosomes in yeast. The stepwise association and dissociation of these AFs with the pre-ribosomal subunits occurs in a hierarchical manner to ensure correct maturation of the pre-rRNAs and assembly of the ribosomal proteins. Although decades of research have provided a wealth of insights into the functions of many AFs, others remain poorly characterized. Pol5 was initially classified with B-type DNA polymerases, however, several lines of evidence indicate the involvement of this protein in ribosome assembly. Here, we show that depletion of Pol5 affects the processing of pre-rRNAs destined for the both the large and small subunits. Furthermore, we identify binding sites for Pol5 in the 5' external transcribed spacer and within domain III of the 25S rRNA sequence. Consistent with this, we reveal that Pol5 is required for recruitment of ribosomal proteins that form the polypeptide exit tunnel in the LSU and that depletion of Pol5 impairs the release of 5' ETS fragments from early pre-40S particles. The dual functions of Pol5 in 60S assembly and recycling of pre-40S AFs suggest that this factor could contribute to ensuring the stoichiometric production of ribosomal subunits.
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Affiliation(s)
- Christina M Braun
- Department of Biochemistry III, University of Regensburg, Universitätstrasse 31, 93053 Regensburg, Germany
| | - Philipp Hackert
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Catharina E Schmid
- Department of Biochemistry III, University of Regensburg, Universitätstrasse 31, 93053 Regensburg, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany.,Göttingen Center for Molecular Biosciences, Georg-August University, Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Jorge Perez-Fernandez
- Department of Biochemistry III, University of Regensburg, Universitätstrasse 31, 93053 Regensburg, Germany
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