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Miller SC, MacDonald CC, Kellogg MK, Karamysheva ZN, Karamyshev AL. Specialized Ribosomes in Health and Disease. Int J Mol Sci 2023; 24:ijms24076334. [PMID: 37047306 PMCID: PMC10093926 DOI: 10.3390/ijms24076334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
Ribosomal heterogeneity exists within cells and between different cell types, at specific developmental stages, and occurs in response to environmental stimuli. Mounting evidence supports the existence of specialized ribosomes, or specific changes to the ribosome that regulate the translation of a specific group of transcripts. These alterations have been shown to affect the affinity of ribosomes for certain mRNAs or change the cotranslational folding of nascent polypeptides at the exit tunnel. The identification of specialized ribosomes requires evidence of the incorporation of different ribosomal proteins or of modifications to rRNA and/or protein that lead(s) to physiologically relevant changes in translation. In this review, we summarize ribosomal heterogeneity and specialization in mammals and discuss their relevance to several human diseases.
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Affiliation(s)
- Sarah C. Miller
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Clinton C. MacDonald
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Morgana K. Kellogg
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | | | - Andrey L. Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Correspondence: ; Tel.: +1-806-743-4102
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2
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Imamoto JM, Zauhar RJ, Bruist MF. Sarcin/Ricin Domain RNA Retains Its Structure Better Than A-RNA in Adaptively Biased Molecular Dynamics Simulations. J Phys Chem B 2022; 126:10018-10033. [PMID: 36417896 DOI: 10.1021/acs.jpcb.2c05859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Less than one in thirty of the RNA sequences transcribed in humans are translated into protein. The noncoding RNA (ncRNA) functions in catalysis, structure, regulation, and more. However, for the most part, these functions are poorly characterized. RNA is modular and described by motifs that include helical A-RNA with canonical Watson-Crick base-pairing as well as structures with only noncanonical base pairs. Understanding the structure and dynamics of motifs will aid in deciphering functions of specific ncRNAs. We present computational studies on a standard sarcin/ricin domain (SRD), citrus bark cracking viroid SRD, as well as A-RNA. We have applied enhanced molecular dynamics techniques that construct an inverse free-energy surface (iFES) determined by collective variables that monitor base-pairing and backbone conformation. Each SRD RNA is flanked on each side by A-RNA, allowing comparison of the behavior of these motifs in the same molecule. The RNA iFESs have single peaks, indicating that the combined motifs should denature as a single cohesive unit, rather than by regional melting. Local root-mean-square deviation (RMSD) analysis and communication propensity (CProp, variance in distances between residue pairs) reveal distinct motif properties. Our analysis indicates that the standard SRD is more stable than the viroid SRD, which is more stable than A-RNA. Base pairs at SRD to A-RNA transitions have limited flexibility. Application of CProp reveals extraordinary stiffness of the SRD, allowing residues on opposite sides of the motif to sense each other's motions.
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Affiliation(s)
- Jason M Imamoto
- Department of Chemistry and Biochemistry, St. Joseph's University, Philadelphia, Pennsylvania19131, United States
| | - Randy J Zauhar
- Department of Chemistry and Biochemistry, St. Joseph's University, Philadelphia, Pennsylvania19131, United States
| | - Michael F Bruist
- Department of Chemistry and Biochemistry, St. Joseph's University, Philadelphia, Pennsylvania19131, United States
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3
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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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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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Das R, Watkins AM. RiboDraw: semiautomated two-dimensional drawing of RNA tertiary structure diagrams. NAR Genom Bioinform 2021; 3:lqab091. [PMID: 34661102 PMCID: PMC8515840 DOI: 10.1093/nargab/lqab091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 09/06/2021] [Accepted: 10/08/2021] [Indexed: 11/14/2022] Open
Abstract
Publishing, discussing, envisioning, modeling, designing and experimentally determining RNA three-dimensional (3D) structures involve preparation of two-dimensional (2D) drawings that depict critical functional features of the subject molecules, such as noncanonical base pairs and protein contacts. Here, we describe RiboDraw, new software for crafting these drawings. We illustrate the features of RiboDraw by applying it to several RNAs, including the Escherichia coli tRNA-Phe, the P4-P6 domain of Tetrahymena ribozyme, a -1 ribosomal frameshift stimulation element from beet western yellows virus and the 5' untranslated region of SARS-CoV-2. We show secondary structure diagrams of the 23S and 16S subunits of the E. coli ribosome that reflect noncanonical base pairs, ribosomal proteins and structural motifs, and that convey the relative positions of these critical features in 3D space. This software is a MATLAB package freely available at https://github.com/DasLab/RiboDraw.
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Affiliation(s)
- Rhiju Das
- Department of Physics, Stanford University, Stanford, CA 94305, USA
| | - Andrew M Watkins
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
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Seligmann H, Vuillerme N, Demongeot J. Unpredictable, Counter-Intuitive Geoclimatic and Demographic Correlations of COVID-19 Spread Rates. BIOLOGY 2021; 10:623. [PMID: 34356478 PMCID: PMC8301123 DOI: 10.3390/biology10070623] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/16/2021] [Accepted: 06/29/2021] [Indexed: 11/17/2022]
Abstract
We present spread parameters for first and second waves of the COVID-19 pandemic for USA states, and for consecutive nonoverlapping periods of 20 days for the USA and 51 countries across the globe. We studied spread rates in the USA states and 51 countries, and analyzed associations between spread rates at different periods, and with temperature, elevation, population density and age. USA first/second wave spread rates increase/decrease with population density, and are uncorrelated with temperature and median population age. Spread rates are systematically inversely proportional to those estimated 80-100 days later. Ascending/descending phases of the same wave only partially explain this. Directions of correlations with factors such as temperature and median age flip. Changes in environmental trends of the COVID-19 pandemic remain unpredictable; predictions based on classical epidemiological knowledge are highly uncertain. Negative associations between population density and spread rates, observed in independent samples and at different periods, are most surprising. We suggest that systematic negative associations between spread rates 80-100 days apart could result from confinements selecting for greater contagiousness, a potential double-edged sword effect of confinements.
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Affiliation(s)
- Hervé Seligmann
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France;
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem 91404, Israel;
| | - Nicolas Vuillerme
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecom4Health, Faculty of Medicine, University Grenoble Alpes (UGA), 38700 La Tronche, France;
| | - Jacques Demongeot
- The National Natural History Collections, The Hebrew University of Jerusalem, Jerusalem 91404, Israel;
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Demongeot J, Seligmann H. Codon assignment evolvability in theoretical minimal RNA rings. Gene 2020; 769:145208. [PMID: 33031892 DOI: 10.1016/j.gene.2020.145208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 12/28/2022]
Abstract
Genetic code codon-amino acid assignments evolve for 15 (AAA, AGA, AGG, ATA, CGG, CTA, CTG. CTC, CTT, TAA, TAG, TCA, TCG, TGA and TTA (GNN codons notably absent)) among 64 codons (23.4%) across the 31 genetic codes (NCBI list completed with recently suggested green algal mitochondrial genetic codes). Their usage in 25 theoretical minimal RNA rings is examined. RNA rings are designed in silico to code once over the shortest length for all 22 coding signals (start and stop codons and each amino acid according to the standard genetic code). Though designed along coding constraints, RNA rings resemble ancestral tRNA loops, assigning to each RNA ring a putative anticodon, a cognate amino acid and an evolutionary genetic code integration rank for that cognate amino acid. Analyses here show 1. biases against/for evolvable codons in the two first vs last thirds of RNA ring coding sequences, 2. RNA rings with evolvable codons have recent cognates, and 3. evolvable codon and cytosine numbers in RNA ring compositions are positively correlated. Applying alternative genetic codes to RNA rings designed for nonredundant coding according to the standard genetic code reveals unsuspected properties of the standard genetic code and of RNA rings, notably on codon assignment evolvability and the special role of cytosine in relation to codon assignment evolvability and of the genetic code's coding structure.
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Affiliation(s)
- Jacques Demongeot
- Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, F-38700 La Tronche, France
| | - Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, 91404 Jerusalem, Israel.
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Demongeot J, Seligmann H. Comparisons between small ribosomal RNA and theoretical minimal RNA ring secondary structures confirm phylogenetic and structural accretion histories. Sci Rep 2020; 10:7693. [PMID: 32376895 PMCID: PMC7203183 DOI: 10.1038/s41598-020-64627-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 04/01/2020] [Indexed: 12/16/2022] Open
Abstract
Ribosomal RNAs are complex structures that presumably evolved by tRNA accretions. Statistical properties of tRNA secondary structures correlate with genetic code integration orders of their cognate amino acids. Ribosomal RNA secondary structures resemble those of tRNAs with recent cognates. Hence, rRNAs presumably evolved from ancestral tRNAs. Here, analyses compare secondary structure subcomponents of small ribosomal RNA subunits with secondary structures of theoretical minimal RNA rings, presumed proto-tRNAs. Two independent methods determined different accretion orders of rRNA structural subelements: (a) classical comparative homology and phylogenetic reconstruction, and (b) a structural hypothesis assuming an inverted onion ring growth where the three-dimensional ribosome's core is most ancient and peripheral elements most recent. Comparisons between (a) and (b) accretions orders with RNA ring secondary structure scales show that recent rRNA subelements are: 1. more like RNA rings with recent cognates, indicating ongoing coevolution between tRNA and rRNA secondary structures; 2. less similar to theoretical minimal RNA rings with ancient cognates. Our method fits (a) and (b) in all examined organisms, more with (a) than (b). Results stress the need to integrate independent methods. Theoretical minimal RNA rings are potential evolutionary references for any sequence-based evolutionary analyses, independent of the focal data from that study.
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Affiliation(s)
- Jacques Demongeot
- Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecoms4Health, F-38700, La Tronche, France.
| | - Hervé Seligmann
- Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecoms4Health, F-38700, La Tronche, France
- The National Natural History Collections, The Hebrew University of Jerusalem, 91404, Jerusalem, Israel
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Demongeot J, Seligmann H. Accretion history of large ribosomal subunits deduced from theoretical minimal RNA rings is congruent with histories derived from phylogenetic and structural methods. Gene 2020; 738:144436. [PMID: 32027954 DOI: 10.1016/j.gene.2020.144436] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/24/2020] [Accepted: 02/01/2020] [Indexed: 12/17/2022]
Abstract
Accretions of tRNAs presumably formed the large complex ribosomal RNA structures. Similarities of tRNA secondary structures with rRNA secondary structures increase with the integration order of their cognate amino acid in the genetic code, indicating tRNA evolution towards rRNA-like structures. Here analyses rank secondary structure subelements of three large ribosomal RNAs (Prokaryota: Archaea: Thermus thermophilus; Bacteria: Escherichia coli; Eukaryota: Saccharomyces cerevisiae) in relation to their similarities with secondary structures formed by presumed proto-tRNAs, represented by 25 theoretical minimal RNA rings. These ranks are compared to those derived from two independent methods (ranks provide a relative evolutionary age to the rRNA substructure), (a) cladistic phylogenetic analyses and (b) 3D-crystallography where core subelements are presumed ancient and peripheral ones recent. Comparisons of rRNA secondary structure subelements with RNA ring secondary structures show congruence between ranks deduced by this method and both (a) and (b) (more with (a) than (b)), especially for RNA rings with predicted ancient cognate amino acid. Reconstruction of accretion histories of large rRNAs will gain from adequately integrating information from independent methods. Theoretical minimal RNA rings, sequences deterministically designed in silico according to specific coding constraints, might produce adequate scales for prebiotic and early life molecular evolution.
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Affiliation(s)
- Jacques Demongeot
- Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecoms4Health, F-38700 La Tronche, France.
| | - Hervé Seligmann
- Université Grenoble Alpes, Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecoms4Health, F-38700 La Tronche, France; The National Natural History Collections, The Hebrew University of Jerusalem, 91404 Jerusalem, Israel.
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10
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Seligmann H, Warthi G. Chimeric Translation for Mitochondrial Peptides: Regular and Expanded Codons. Comput Struct Biotechnol J 2019; 17:1195-1202. [PMID: 31534643 PMCID: PMC6742854 DOI: 10.1016/j.csbj.2019.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 02/07/2023] Open
Abstract
Frameshifting protein translation occasionally results from insertion of amino acids at isolated mono- or dinucleotide-expanded codons by tRNAs with expanded anticodons. Previous analyses of two different types of human mitochondrial MS proteomic data (Fisher and Waters technologies) detect peptides entirely corresponding to expanded codon translation. Here, these proteomic data are reanalyzed searching for peptides consisting of at least eight consecutive amino acids translated according to regular tricodons, and at least eight adjacent consecutive amino acids translated according to expanded codons. Both datasets include chimerically translated peptides (mono- and dinucleotide expansions, 42 and 37, respectively). The regular tricodon-encoded part of some chimeric peptides corresponds to standard human mitochondrial proteins (mono- and dinucleotide expansions, six (AT6, CytB, ND1, 2xND2, ND5) and one (ND1), respectively). Chimeric translation probably increases the diversity of mitogenome-encoded proteins, putatively producing functional proteins. These might result from translation by tRNAs with expanded anticodons, or from regular tricodon translation of RNAs where transcription/posttranscriptional edition systematically deleted mono- or dinucleotides after each trinucleotide. The pairwise matched combination of adjacent peptide parts translated from regular and expanded codons strengthens the hypothesis that translation of stretches of consecutive expanded codons occurs. Results indicate statistical translation producing distributions of alternative proteins. Genetic engineering should account for potential unexpected, unwanted secondary products.
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Affiliation(s)
- Hervé Seligmann
- The National Natural History Collections, The Hebrew University of Jerusalem, 91404 Jerusalem, Israel
| | - Ganesh Warthi
- Aix-Marseille University, IRD, VITROME, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
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Hartman H, Smith TF. Origin of the Genetic Code Is Found at the Transition between a Thioester World of Peptides and the Phosphoester World of Polynucleotides. Life (Basel) 2019; 9:life9030069. [PMID: 31443422 PMCID: PMC6789786 DOI: 10.3390/life9030069] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/09/2019] [Accepted: 08/14/2019] [Indexed: 11/16/2022] Open
Abstract
The early metabolism arising in a Thioester world gave rise to amino acids and their simple peptides. The catalytic activity of these early simple peptides became instrumental in the transition from Thioester World to a Phosphate World. This transition involved the appearances of sugar phosphates, nucleotides, and polynucleotides. The coupling of the amino acids and peptides to nucleotides and polynucleotides is the origin for the genetic code. Many of the key steps in this transition are seen in the catalytic cores of the nucleotidyltransferases, the class II tRNA synthetases (aaRSs) and the CCA adding enzyme. These catalytic cores are dominated by simple beta hairpin structures formed in the Thioester World. The code evolved from a proto-tRNA, a tetramer XCCA interacting with a proto-aminoacyl-tRNA synthetase (aaRS) activating Glycine and Proline. The initial expanded code is found in the acceptor arm of the tRNA, the operational code. It is the coevolution of the tRNA with the aaRSs that is at the heart of the origin and evolution of the genetic code. There is also a close relationship between the accretion models of the evolving tRNA and that of the ribosome.
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Affiliation(s)
- Hyman Hartman
- Earth, Atmosphere, and Planetary Science Department, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Temple F Smith
- BioMedical Engineering, Boston University, Boston, MA 02215, USA
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Lackmann F, Belikov S, Burlacu E, Granneman S, Wieslander L. Maturation of the 90S pre-ribosome requires Mrd1 dependent U3 snoRNA and 35S pre-rRNA structural rearrangements. Nucleic Acids Res 2019; 46:3692-3706. [PMID: 29373706 PMCID: PMC5909432 DOI: 10.1093/nar/gky036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/15/2018] [Indexed: 01/25/2023] Open
Abstract
In eukaryotes, ribosome biogenesis requires folding and assembly of the precursor rRNA (pre-rRNA) with a large number of proteins and snoRNPs into huge RNA-protein complexes. In spite of intense genetic, biochemical and high-resolution cryo-EM studies in Saccharomyces cerevisiae, information about the structure of the 35S pre-rRNA is limited. To overcome this, we performed high-throughput SHAPE chemical probing on the 35S pre-rRNA within 90S pre-ribosomes. We focused our analyses on external (5′ETS) and internal (ITS1) transcribed spacers as well as the 18S rRNA region. We show that in the 35S pre-rRNA, the central pseudoknot is not formed and the central core of the 18S rRNA is in an open configuration but becomes more constrained in 20S pre-rRNA. The essential ribosome biogenesis protein Mrd1 influences the structure of the 18S rRNA region locally and is involved in organizing the central pseudoknot and surrounding structures. We demonstrate that U3 snoRNA dynamically interacts with the 35S pre-rRNA and that Mrd1 is required for disrupting U3 snoRNA base pairing interactions in the 5′ETS. We propose that the dynamic U3 snoRNA interactions and Mrd1 are essential for establishing the structure of the central core of 18S rRNA that is required for processing and 40S subunit function.
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Affiliation(s)
- Fredrik Lackmann
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Sergey Belikov
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Elena Burlacu
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Sander Granneman
- Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Lars Wieslander
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
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Ariza-Mateos A, Briones C, Perales C, Domingo E, Gómez J. The archaeology of coding RNA. Ann N Y Acad Sci 2019; 1447:119-134. [PMID: 31237363 DOI: 10.1111/nyas.14173] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/18/2019] [Accepted: 05/29/2019] [Indexed: 12/16/2022]
Abstract
Different theories concerning the origin of RNA (and, in particular, mRNA) point to the concatenation and expansion of proto-tRNA-like structures. Different biochemical and biophysical tools have been used to search for ancient-like RNA elements with a specific structure in genomic viral RNAs, including that of the hepatitis C virus, as well as in cellular mRNA populations, in particular those of human hepatocytes. We define this method as "archaeological," and it has been designed to discover evolutionary patterns through a nonphylogenetic and nonrepresentational strategy. tRNA-like elements were found in structurally or functionally relevant positions both in viral RNA and in one of the liver mRNAs examined, the antagonist interferon-alpha subtype 5 (IFNA5) mRNA. Additionally, tRNA-like elements are highly represented within the hepatic mRNA population, which suggests that they could have participated in the formation of coding RNAs in the distant past. Expanding on this finding, we have observed a recurring dsRNA-like motif next to the tRNA-like elements in both viral RNAs and IFNA5 mRNA. This suggested that the concatenation of these RNA motifs was an activity present in the RNA pools that might have been relevant in the RNA world. The extensive alteration of sequences that likely triggered the transition from the predecessors of coding RNAs to the first fully functional mRNAs (which was not the case in the stepwise construction of noncoding rRNAs) hinders the phylogeny-based identification of RNA elements (both sequences and structures) that might have been active before the advent of protein synthesis. Therefore, our RNA archaeological method is presented as a way to better understand the structural/functional versatility of a variety of RNA elements, which might represent "the losers" in the process of RNA evolution as they had to adapt to the selective pressures favoring the coding capacity of the progressively longer mRNAs.
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Affiliation(s)
- Ascensión Ariza-Mateos
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina "López-Neyra" (CSIC), Granada, Spain.,Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Carlos Briones
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Celia Perales
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain.,Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, UAM, Madrid, Spain
| | - Esteban Domingo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Jordi Gómez
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina "López-Neyra" (CSIC), Granada, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
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Clouet-d'Orval B, Batista M, Bouvier M, Quentin Y, Fichant G, Marchfelder A, Maier LK. Insights into RNA-processing pathways and associated RNA-degrading enzymes in Archaea. FEMS Microbiol Rev 2018; 42:579-613. [PMID: 29684129 DOI: 10.1093/femsre/fuy016] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/17/2018] [Indexed: 12/20/2022] Open
Abstract
RNA-processing pathways are at the centre of regulation of gene expression. All RNA transcripts undergo multiple maturation steps in addition to covalent chemical modifications to become functional in the cell. This includes destroying unnecessary or defective cellular RNAs. In Archaea, information on mechanisms by which RNA species reach their mature forms and associated RNA-modifying enzymes are still fragmentary. To date, most archaeal actors and pathways have been proposed in light of information gathered from Bacteria and Eukarya. In this context, this review provides a state of the art overview of archaeal endoribonucleases and exoribonucleases that cleave and trim RNA species and also of the key small archaeal proteins that bind RNAs. Furthermore, synthetic up-to-date views of processing and biogenesis pathways of archaeal transfer and ribosomal RNAs as well as of maturation of stable small non-coding RNAs such as CRISPR RNAs, small C/D and H/ACA box guide RNAs, and other emerging classes of small RNAs are described. Finally, prospective post-transcriptional mechanisms to control archaeal messenger RNA quality and quantity are discussed.
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Affiliation(s)
- Béatrice Clouet-d'Orval
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Manon Batista
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Marie Bouvier
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Yves Quentin
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
| | - Gwennaele Fichant
- Laboratoire de Microbiologie et de Génétique Moléculaires (LMGM), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, 31062 Toulouse, France
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15
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Gómez Ramos LM, Degtyareva NN, Kovacs NA, Holguin SY, Jiang L, Petrov AS, Biesiada M, Hu MY, Purzycka KJ, Arya DP, Williams LD. Eukaryotic Ribosomal Expansion Segments as Antimicrobial Targets. Biochemistry 2017; 56:5288-5299. [PMID: 28895721 DOI: 10.1021/acs.biochem.7b00703] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Diversity in eukaryotic rRNA structure and function offers possibilities of therapeutic targets. Unlike ribosomes of prokaryotes, eukaryotic ribosomes contain species-specific rRNA expansion segments (ESs) with idiosyncratic structures and functions that are essential and specific to some organisms. Here we investigate expansion segment 7 (ES7), one of the largest and most variable expansions of the eukaryotic ribosome. We hypothesize that ES7 of the pathogenic fungi Candida albicans (ES7CA) could be a prototypic drug target. We show that isolated ES7CA folds reversibly to a native-like state. We developed a fluorescence displacement assay using an RNA binding fluorescent probe, F-neo. F-neo binds tightly to ES7CA with a Kd of 2.5 × 10-9 M but binds weakly to ES7 of humans (ES7HS) with a Kd estimated to be greater than 7 μM. The fluorescence displacement assay was used to investigate the affinities of a library of peptidic aminosugar conjugates (PAs) for ES7CA. For conjugates with highest affinities for ES7CA (NeoRH, NeoFH, and NeoYH), the lowest dose needed to induce mortality in C. albicans (minimum inhibitory concentration, MIC) was determined. PAs with the lowest MIC values were tested for cytotoxicity in HEK293T cells. Molecules with high affinity for ES7CA in vitro induce mortality in C. albicans but not in HEK293T cells. The results are consistent with the hypothesis that ESs represent useful targets for chemotherapeutics directed against eukaryotic pathogens.
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Affiliation(s)
- Lizzette M Gómez Ramos
- School of Chemistry and Biochemistry, Georgia Institute of Technology , 315 Ferst Drive NW, Atlanta, Georgia 30332-0363, United States.,School of Chemical and Biomolecular Engineering, Georgia Institute of Technology , 311 Ferst Drive NW, Atlanta, Georgia 30332-0100, United States
| | - Natalya N Degtyareva
- NUBAD, LLC , 900 B West Farris Road, Greenville, South Carolina 29605, United States
| | - Nicholas A Kovacs
- School of Chemistry and Biochemistry, Georgia Institute of Technology , 315 Ferst Drive NW, Atlanta, Georgia 30332-0363, United States
| | - Stefany Y Holguin
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology , 311 Ferst Drive NW, Atlanta, Georgia 30332-0100, United States
| | - Liuwei Jiang
- Department of Chemistry, Clemson University , 436 Hunter Laboratories, Clemson, South Carolina 29634-0973, United States
| | - Anton S Petrov
- School of Chemistry and Biochemistry, Georgia Institute of Technology , 315 Ferst Drive NW, Atlanta, Georgia 30332-0363, United States
| | - Marcin Biesiada
- RNA Structure and Function Laboratory, Institute of Bioorganic Chemistry, Polish Academy of Sciences , Poznan 61-704, Poland
| | - Michael Y Hu
- School of Chemistry and Biochemistry, Georgia Institute of Technology , 315 Ferst Drive NW, Atlanta, Georgia 30332-0363, United States
| | - Katarzyna J Purzycka
- RNA Structure and Function Laboratory, Institute of Bioorganic Chemistry, Polish Academy of Sciences , Poznan 61-704, Poland
| | - Dev P Arya
- NUBAD, LLC , 900 B West Farris Road, Greenville, South Carolina 29605, United States.,Department of Chemistry, Clemson University , 436 Hunter Laboratories, Clemson, South Carolina 29634-0973, United States
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology , 315 Ferst Drive NW, Atlanta, Georgia 30332-0363, United States
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16
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Tomkuvienė M, Ličytė J, Olendraitė I, Liutkevičiūtė Z, Clouet-d'Orval B, Klimašauskas S. Archaeal fibrillarin-Nop5 heterodimer 2'- O-methylates RNA independently of the C/D guide RNP particle. RNA (NEW YORK, N.Y.) 2017; 23:1329-1337. [PMID: 28576826 PMCID: PMC5558902 DOI: 10.1261/rna.059832.116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 05/19/2017] [Indexed: 06/01/2023]
Abstract
Archaeal fibrillarin (aFib) is a well-characterized S-adenosyl methionine (SAM)-dependent RNA 2'-O-methyltransferase that is known to act in a large C/D ribonucleoprotein (RNP) complex together with Nop5 and L7Ae proteins and a box C/D guide RNA. In the reaction, the guide RNA serves to direct the methylation reaction to a specific site in tRNA or rRNA by sequence complementarity. Here we show that a Pyrococcus abyssi aFib-Nop5 heterodimer can alone perform SAM-dependent 2'-O-methylation of 16S and 23S ribosomal RNAs in vitro independently of L7Ae and C/D guide RNAs. Using tritium-labeling, mass spectrometry, and reverse transcription analysis, we identified three in vitro 2'-O-methylated positions in the 16S rRNA of P. abyssi, positions lying outside of previously reported pyrococcal C/D RNP methylation sites. This newly discovered stand-alone activity of aFib-Nop5 may provide an example of an ancestral activity retained in enzymes that were recruited to larger complexes during evolution.
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MESH Headings
- Archaea/genetics
- Archaea/metabolism
- Chromosomal Proteins, Non-Histone/chemistry
- Chromosomal Proteins, Non-Histone/metabolism
- Methylation
- Nucleic Acid Conformation
- Protein Binding
- Protein Multimerization
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Ribonucleoproteins/chemistry
- Ribonucleoproteins/metabolism
- Ribonucleoproteins, Small Nucleolar/chemistry
- Ribonucleoproteins, Small Nucleolar/metabolism
- Substrate Specificity
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Affiliation(s)
- Miglė Tomkuvienė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | - Janina Ličytė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | - Ingrida Olendraitė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Zita Liutkevičiūtė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | - Béatrice Clouet-d'Orval
- Laboratoire de Microbiologie et Génétique Moléculaires UMR 5100, CNRS, Université de Toulouse, F-31062 Toulouse, France
| | - Saulius Klimašauskas
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
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17
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Locati MD, Pagano JFB, Girard G, Ensink WA, van Olst M, van Leeuwen S, Nehrdich U, Spaink HP, Rauwerda H, Jonker MJ, Dekker RJ, Breit TM. Expression of distinct maternal and somatic 5.8S, 18S, and 28S rRNA types during zebrafish development. RNA (NEW YORK, N.Y.) 2017; 23:1188-1199. [PMID: 28500251 PMCID: PMC5513064 DOI: 10.1261/rna.061515.117] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/09/2017] [Indexed: 05/27/2023]
Abstract
There is mounting evidence that the ribosome is not a static translation machinery, but a cell-specific, adaptive system. Ribosomal variations have mostly been studied at the protein level, even though the essential transcriptional functions are primarily performed by rRNAs. At the RNA level, oocyte-specific 5S rRNAs are long known for Xenopus. Recently, we described for zebrafish a similar system in which the sole maternal-type 5S rRNA present in eggs is replaced completely during embryonic development by a somatic-type. Here, we report the discovery of an analogous system for the 45S rDNA elements: 5.8S, 18S, and 28S. The maternal-type 5.8S, 18S, and 28S rRNA sequences differ substantially from those of the somatic-type, plus the maternal-type rRNAs are also replaced by the somatic-type rRNAs during embryogenesis. We discuss the structural and functional implications of the observed sequence differences with respect to the translational functions of the 5.8S, 18S, and 28S rRNA elements. Finally, in silico evidence suggests that expansion segments (ES) in 18S rRNA, previously implicated in ribosome-mRNA interaction, may have a preference for interacting with specific mRNA genes. Taken together, our findings indicate that two distinct types of ribosomes exist in zebrafish during development, each likely conducting the translation machinery in a unique way.
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MESH Headings
- Animals
- Base Pairing
- Base Sequence
- DNA, Ribosomal/genetics
- Embryo, Nonmammalian/cytology
- Embryo, Nonmammalian/metabolism
- Nucleic Acid Conformation
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- RNA, Ribosomal, 28S/genetics
- RNA, Ribosomal, 28S/metabolism
- RNA, Ribosomal, 5.8S/genetics
- RNA, Ribosomal, 5.8S/metabolism
- Ribosomes/metabolism
- Sequence Alignment
- Zebrafish/genetics
- Zebrafish/growth & development
- Zebrafish/metabolism
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Affiliation(s)
- Mauro D Locati
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Johanna F B Pagano
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Geneviève Girard
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Wim A Ensink
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Marina van Olst
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Selina van Leeuwen
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Ulrike Nehrdich
- Department of Molecular Cell Biology, Institute of Biology, Leiden University, Gorlaeus Laboratories-Cell Observatorium, Leiden 2333 CE, the Netherlands
| | - Herman P Spaink
- Department of Molecular Cell Biology, Institute of Biology, Leiden University, Gorlaeus Laboratories-Cell Observatorium, Leiden 2333 CE, the Netherlands
| | - Han Rauwerda
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Martijs J Jonker
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Rob J Dekker
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Timo M Breit
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
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18
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Lupas AN, Alva V. Ribosomal proteins as documents of the transition from unstructured (poly)peptides to folded proteins. J Struct Biol 2017; 198:74-81. [DOI: 10.1016/j.jsb.2017.04.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 04/23/2017] [Accepted: 04/24/2017] [Indexed: 11/16/2022]
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19
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Caetano-Anollés D, Caetano-Anollés G. Commentary: History of the ribosome and the origin of translation. Front Mol Biosci 2017; 3:87. [PMID: 28119917 PMCID: PMC5222800 DOI: 10.3389/fmolb.2016.00087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 12/23/2016] [Indexed: 12/23/2022] Open
Affiliation(s)
- Derek Caetano-Anollés
- Department of Evolutionary Genetics, Max-Planck-Institut für Evolutionsbiologie Plön, Germany
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois Urbana, IL, USA
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20
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Lanier KA, Athavale SS, Petrov AS, Wartell R, Williams LD. Imprint of Ancient Evolution on rRNA Folding. Biochemistry 2016; 55:4603-13. [DOI: 10.1021/acs.biochem.6b00168] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Kathryn A. Lanier
- School of Chemistry and Biochemistry and ‡School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Shreyas S. Athavale
- School of Chemistry and Biochemistry and ‡School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Anton S. Petrov
- School of Chemistry and Biochemistry and ‡School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Roger Wartell
- School of Chemistry and Biochemistry and ‡School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Loren Dean Williams
- School of Chemistry and Biochemistry and ‡School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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