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Mishra RK, Sharma P, Khaja FT, Uday AB, Hussain T. Cryo-EM structure of wheat ribosome reveals unique features of the plant ribosomes. Structure 2024:S0969-2126(24)00045-5. [PMID: 38458197 DOI: 10.1016/j.str.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/16/2023] [Accepted: 02/12/2024] [Indexed: 03/10/2024]
Abstract
Plants being sessile organisms exhibit unique features in ribosomes, which might aid in rapid gene expression and regulation in response to varying environmental conditions. Here, we present high-resolution structures of the 60S and 80S ribosomes from wheat, a monocot staple crop plant (Triticum aestivum). While plant ribosomes have unique plant-specific rRNA modification (Cm1847) in the peptide exit tunnel (PET), the zinc-finger motif in eL34 is absent, and uL4 is extended, making an exclusive interaction network. We note differences in the eL15-helix 11 (25S) interaction, eL6-ES7 assembly, and certain rRNA chemical modifications between monocot and dicot ribosomes. In eukaryotes, we observe highly conserved rRNA modification (Gm75) in 5.8S rRNA and a flipped base (G1506) in PET. These features are likely involved in sensing or stabilizing nascent chain. Finally, we discuss the importance of the universal conservation of three consecutive rRNA modifications in all ribosomes for their interaction with A-site aminoacyl-tRNA.
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Affiliation(s)
- Rishi Kumar Mishra
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru PIN-560012, India
| | - Prafful Sharma
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru PIN-560012, India
| | - Faisal Tarique Khaja
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru PIN-560012, India
| | - Adwaith B Uday
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru PIN-560012, India
| | - Tanweer Hussain
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru PIN-560012, India.
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2
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Hariharan N, Ghosh S, Palakodeti D. The story of rRNA expansion segments: Finding functionality amidst diversity. Wiley Interdiscip Rev RNA 2023; 14:e1732. [PMID: 35429135 DOI: 10.1002/wrna.1732] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 02/24/2022] [Accepted: 03/19/2022] [Indexed: 01/31/2023]
Abstract
Expansion segments (ESs) are multinucleotide insertions present across phyla at specific conserved positions in eukaryotic rRNAs. ESs are generally absent in bacterial rRNAs with some exceptions, while the archaeal rRNAs have microexpansions at regions that coincide with those of eukaryotic ESs. Although there is an increasing prominence of ribosomes, especially the ribosomal proteins, in fine-tuning gene expression through translation regulation, the role of rRNA ESs is relatively underexplored. While rRNAs have been established as the major catalytic hub in ribosome function, the presence of ESs widens their scope as a species-specific regulatory hub of protein synthesis. In this comprehensive review, we have elaborately discussed the current understanding of the functional aspects of rRNA ESs of cytoplasmic eukaryotic ribosomes and discuss their past, present, and future. This article is categorized under: RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems Translation > Ribosome Structure/Function Translation > Regulation.
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Affiliation(s)
- Nivedita Hariharan
- Technologies for the Advancement of Science, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India.,The University of Trans-disciplinary Health Sciences and Technology, Bangalore, India
| | - Sumana Ghosh
- Manipal Academy of Higher Education, Manipal, India
| | - Dasaradhi Palakodeti
- Technologies for the Advancement of Science, Institute for Stem Cell Science and Regenerative Medicine (inStem), Bangalore, India
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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Mestre-Fos S, Ito C, Moore CM, Reddi AR, Williams LD. Human ribosomal G-quadruplexes regulate heme bioavailability. J Biol Chem 2020; 295:14855-14865. [PMID: 32817343 PMCID: PMC7606673 DOI: 10.1074/jbc.ra120.014332] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/06/2020] [Indexed: 12/13/2022] Open
Abstract
The in vitro formation of stable G-quadruplexes (G4s) in human rRNA was recently reported. However, their formation in cells and their cellular roles were not resolved. Here, by taking a chemical biology approach that integrates results from immunofluorescence, G4 ligands, heme-affinity reagents, and a genetically encoded fluorescent heme sensor, we report that human ribosomes can form G4s in vivo that regulate heme bioavailability. Immunofluorescence experiments indicate that the vast majority of extra-nuclear G4s are associated with rRNA. Moreover, titrating human cells with a G4 ligand alters the ability of ribosomes to bind heme and disrupts cellular heme bioavailability as measured by a genetically encoded fluorescent heme sensor. Overall, these results suggest that ribosomes play a role in regulating heme homeostasis.
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Affiliation(s)
- Santi Mestre-Fos
- Center for the Origin of Life, Georgia Institute of Technology, Atlanta, Georgia, USA; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA; Parker Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Chieri Ito
- Center for the Origin of Life, Georgia Institute of Technology, Atlanta, Georgia, USA; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA; Parker Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Courtney M Moore
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA; Parker Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Amit R Reddi
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA; Parker Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA.
| | - Loren Dean Williams
- Center for the Origin of Life, Georgia Institute of Technology, Atlanta, Georgia, USA; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA; Parker Petit Institute of Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA.
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Mestre-Fos S, Penev PI, Suttapitugsakul S, Hu M, Ito C, Petrov AS, Wartell RM, Wu R, Williams LD. G-Quadruplexes in Human Ribosomal RNA. J Mol Biol 2019; 431:1940-55. [PMID: 30885721 DOI: 10.1016/j.jmb.2019.03.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 11/20/2022]
Abstract
rRNA is the single most abundant polymer in most cells. Mammalian rRNAs are nearly twice as large as those of prokaryotes. Differences in rRNA size are due to expansion segments, which contain extended tentacles in metazoans. Here we show that the terminus of an rRNA tentacle of Homo sapiens contains 10 tandem G-tracts that form highly stable G-quadruplexes in vitro. We characterized rRNA of the H. sapiens large ribosomal subunit by computation, circular dichroism, UV melting, fluorescent probes, nuclease accessibility, electrophoretic mobility shifts, and blotting. We investigated Expansion Segment 7 (ES7), oligomers derived from ES7, intact 28S rRNA, 80S ribosomes, and polysomes. We used mass spectrometry to identify proteins that bind to rRNA G-quadruplexes in cell lysates. These proteins include helicases (DDX3, CNBP, DDX21, DDX17) and heterogeneous nuclear ribonucleoproteins. Finally, by multiple sequence alignments, we observe that G-quadruplex-forming sequences are a general feature of LSU rRNA of Chordata but not, as far as we can tell, of other species. Chordata ribosomes present polymorphic tentacles with the potential to switch between inter- and intramolecular G-quadruplexes. To our knowledge, G-quadruplexes have not been reported previously in ribosomes.
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Parker MS, Balasubramaniam A, Parker SL. The Expansion Segments of Human 28S rRNA Match MicroRNAs Much Above 18S rRNA or Core Segments. Microrna 2018; 7:128-137. [PMID: 29595121 DOI: 10.2174/2211536607666180328120018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/14/2018] [Accepted: 03/20/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND The size of eukaryotic 25-28S rRNAs shows a progressive phylogenetically linked increase which is pronounced in mammals, and especially in hominids. The increase is confined to specific expansion segments, inserted at points that are highly conserved from yeast to man. These segments also show a progressive increase in nucleotide bias, mostly the GC bias. Substantial parts of the large expansion segments 7, 15 and 27 of 28S rRNA are known to be exposed at the ribosome surface, with no clear association with ribosomal proteins. These segments could bind extraneous RNAs and proteins to support regulatory events. METHODS This study examined the possible canonical matching of human 28S rRNA and 18S rRNA segments with 2586 human microRNAs. This was compared with matching of the microRNAs to sectors of 18810 human mRNAs. RESULTS The overall matching was rather similar across 18S rRNA segments and core segments of 28S rRNA. However, the expansion segments of 28S rRNA (abbreviated ESL) collectively have a much higher (up to two-fold) capacity for the canonical association with microRNAs. This is pronounced in large ESL, and is found to strongly relate to the GC content of microRNAs. CONCLUSION Oligonucleotides and microRNAs of high GC content through a strong canonical hydrogen bonding could have large activity in regulation of subcellular RNAs. In view of the considerable abundance of ribosomal RNAs in many mammalian tissues, ESL could constitute an important component of microRNA balance, possibly serving to lower the availability of GC-rich microRNAs (and thereby help conservation of GC-rich mRNAs).
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Affiliation(s)
- Michael S Parker
- Department of Microbiology and Molecular Cell Sciences, University of Memphis, Memphis, TN 38152, United States
| | | | - Steven L Parker
- Department of Pharmacology, University of Tennessee Health Science Center, Memphis, TN 38163, United States
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Abstract
The secondary structure of ribosomal RNA (rRNA) is largely conserved across all kingdoms of life. However, eukaryotes have evolved extra blocks of rRNA sequences, relative to those of prokaryotes, called expansion segments (ES). A thorough characterization of the potential roles of ES remains to be done, possibly because of limitations in the availability of robust systems to study rRNA mutants. We sought to systematically investigate the potential functions, if any, of the ES in 25S rRNA of Saccharomyces cerevisiae by deletion mutagenesis. We deleted 14 of the 16 different eukaryote-specific ES in yeast 25S rRNA individually and assayed their phenotypes. Our results show that all but two of the ES tested are necessary for optimal growth and are required for production of 25S rRNA, suggesting that ES play roles in ribosome biogenesis. Further, we classified expansion segments into groups that participate in early nucleolar, middle, and late nucleoplasmic steps of ribosome biogenesis, by assaying their pre-rRNA processing phenotypes. This study is the first of its kind to systematically identify the functions of eukaryote-specific expansion segments by showing that they play roles in specific steps of ribosome biogenesis. The catalog of phenotypes we identified, combined with previous investigations of the roles ribosomal proteins in large subunit biogenesis, leads us to infer that assembling ribosomes are composed of distinct RNA and protein structural neighborhood clusters that participate in specific steps of ribosome biogenesis.
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Affiliation(s)
- Madhumitha Ramesh
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15232, USA
| | - John L Woolford
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15232, USA
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Chandramouli P, Topf M, Ménétret JF, Eswar N, Gutell RR, Sali A, Akey CW. Structure of the mammalian 80S ribosome at 8.7 A resolution. Structure 2008; 16:535-48. [PMID: 18400176 PMCID: PMC2775484 DOI: 10.1016/j.str.2008.01.007] [Citation(s) in RCA: 121] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 01/03/2008] [Accepted: 01/26/2008] [Indexed: 01/12/2023]
Abstract
In this paper, we present a structure of the mammalian ribosome determined at approximately 8.7 A resolution by electron cryomicroscopy and single-particle methods. A model of the ribosome was created by docking homology models of subunit rRNAs and conserved proteins into the density map. We then modeled expansion segments in the subunit rRNAs and found unclaimed density for approximately 20 proteins. In general, many conserved proteins and novel proteins interact with expansion segments to form an integrated framework that may stabilize the mature ribosome. Our structure provides a snapshot of the mammalian ribosome at the beginning of translation and lends support to current models in which large movements of the small subunit and L1 stalk occur during tRNA translocation. Finally, details are presented for intersubunit bridges that are specific to the eukaryotic ribosome. We suggest that these bridges may help reset the conformation of the ribosome to prepare for the next cycle of chain elongation.
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Affiliation(s)
- Preethi Chandramouli
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany St., Boston, Massachusetts 02118, USA
| | - Maya Topf
- School of Crystallography, Birkbeck, University of London, Malet Street, London WC1E 7HX
| | - Jean-François Ménétret
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany St., Boston, Massachusetts 02118, USA
| | - Narayanan Eswar
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, QB3 at Mission Bay, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA
| | - Robin R. Gutell
- The Institute for Cellular and Molecular Biology, The University of Texas at Austin, TX 78712, USA
| | - Andrej Sali
- Department of Biopharmaceutical Sciences, California Institute for Quantitative Biomedical Research, QB3 at Mission Bay, University of California at San Francisco, 1700 4th Street, San Francisco, CA 94158, USA
| | - Christopher W. Akey
- Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany St., Boston, Massachusetts 02118, USA
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