1
|
Penev PI, McCann HM, Meade CD, Alvarez-Carreño C, Maddala A, Bernier CR, Chivukula VL, Ahmad M, Gulen B, Sharma A, Williams LD, Petrov AS. ProteoVision: web server for advanced visualization of ribosomal proteins. Nucleic Acids Res 2021; 49:W578-W588. [PMID: 33999189 PMCID: PMC8265156 DOI: 10.1093/nar/gkab351] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/11/2021] [Accepted: 04/21/2021] [Indexed: 11/26/2022] Open
Abstract
ProteoVision is a web server designed to explore protein structure and evolution through simultaneous visualization of multiple sequence alignments, topology diagrams and 3D structures. Starting with a multiple sequence alignment, ProteoVision computes conservation scores and a variety of physicochemical properties and simultaneously maps and visualizes alignments and other data on multiple levels of representation. The web server calculates and displays frequencies of amino acids. ProteoVision is optimized for ribosomal proteins but is applicable to analysis of any protein. ProteoVision handles internally generated and user uploaded alignments and connects them with a selected structure, found in the PDB or uploaded by the user. It can generate de novo topology diagrams from three-dimensional structures. All displayed data is interactive and can be saved in various formats as publication quality images or external datasets or PyMol Scripts. ProteoVision enables detailed study of protein fragments defined by Evolutionary Classification of protein Domains (ECOD) classification. ProteoVision is available at http://proteovision.chemistry.gatech.edu/.
Collapse
Affiliation(s)
- Petar I Penev
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Holly M McCann
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Caeden D Meade
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Claudia Alvarez-Carreño
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Aparna Maddala
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Chad R Bernier
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Vasanta L Chivukula
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Maria Ahmad
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Burak Gulen
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Aakash Sharma
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Loren Dean Williams
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Anton S Petrov
- NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| |
Collapse
|
2
|
Abstract
Mitochondrial ribosomes (mitoribosomes) are essential components of all mitochondria that synthesize proteins encoded by the mitochondrial genome. Unlike other ribosomes, mitoribosomes are highly variable across species. The basis for this diversity is not known. Here, we examine the composition and evolutionary history of mitoribosomes across the phylogenetic tree by combining three-dimensional structural information with a comparative analysis of the secondary structures of mitochondrial rRNAs (mt-rRNAs) and available proteomic data. We generate a map of the acquisition of structural variation and reconstruct the fundamental stages that shaped the evolution of the mitoribosomal large subunit and led to this diversity. Our analysis suggests a critical role for ablation and expansion of rapidly evolving mt-rRNA. These changes cause structural instabilities that are “patched” by the acquisition of pre-existing compensatory elements, thus providing opportunities for rapid evolution. This mechanism underlies the incorporation of mt-tRNA into the central protuberance of the mammalian mitoribosome, and the altered path of the polypeptide exit tunnel of the yeast mitoribosome. We propose that since the toolkits of elements utilized for structural patching differ between mitochondria of different species, it fosters the growing divergence of mitoribosomes.
Collapse
Affiliation(s)
- Anton S Petrov
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA
| | - Elizabeth C Wood
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA
| | - Chad R Bernier
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA
| | - Ashlyn M Norris
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA
| | - Alan Brown
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA
| | - Alexey Amunts
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.,Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
3
|
Abstract
The Universal Gene Set of Life (UGSL) is common to genomes of all extant organisms. The UGSL is small, consisting of <100 genes, and is dominated by genes encoding the translation system. Here we extend the search for biological universality to three dimensions. We characterize and quantitate the universality of structure of macromolecules that are common to all of life. We determine that around 90% of prokaryotic ribosomal RNA (rRNA) forms a common core, which is the structural and functional foundation of rRNAs of all cytoplasmic ribosomes. We have established a database, which we call the Sparse and Efficient Representation of the Extant Biology (the SEREB database). This database contains complete and cross-validated rRNA sequences of species chosen, as far as possible, to sparsely and efficiently sample all known phyla. Atomic-resolution structures of ribosomes provide data for structural comparison and validation of sequence-based models. We developed a similarity statistic called pairing adjusted sequence entropy, which characterizes paired nucleotides by their adherence to covariation and unpaired nucleotides by conventional conservation of identity. For canonically paired nucleotides the unit of structure is the nucleotide pair. For unpaired nucleotides, the unit of structure is the nucleotide. By quantitatively defining the common core of rRNA, we systematize the conservation and divergence of the translational system across the tree of life, and can begin to understand the unique evolutionary pressures that cause its universality. We explore the relationship between ribosomal size and diversity, geological time, and organismal complexity.
Collapse
Affiliation(s)
- Chad R Bernier
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332
| | - Anton S Petrov
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332
| | - Nicholas A Kovacs
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332
| | - Petar I Penev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332
| |
Collapse
|
4
|
Bernier CR, Petrov AS, Waterbury CC, Jett J, Li F, Freil LE, Xiong X, Wang L, Migliozzi BLR, Hershkovits E, Xue Y, Hsiao C, Bowman JC, Harvey SC, Grover MA, Wartell ZJ, Williams LD. RiboVision suite for visualization and analysis of ribosomes. Faraday Discuss 2014; 169:195-207. [PMID: 25340471 DOI: 10.1039/c3fd00126a] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
RiboVision is a visualization and analysis tool for the simultaneous display of multiple layers of diverse information on primary (1D), secondary (2D), and three-dimensional (3D) structures of ribosomes. The ribosome is a macromolecular complex containing ribosomal RNA and ribosomal proteins and is a key component of life responsible for the synthesis of proteins in all living organisms. RiboVision is intended for rapid retrieval, analysis, filtering, and display of a variety of ribosomal data. Preloaded information includes 1D, 2D, and 3D structures augmented by base-pairing, base-stacking, and other molecular interactions. RiboVision is preloaded with rRNA secondary structures, rRNA domains and helical structures, phylogeny, crystallographic thermal factors, etc. RiboVision contains structures of ribosomal proteins and a database of their molecular interactions with rRNA. RiboVision contains preloaded structures and data for two bacterial ribosomes (Thermus thermophilus and Escherichia coli), one archaeal ribosome (Haloarcula marismortui), and three eukaryotic ribosomes (Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens). RiboVision revealed several major discrepancies between the 2D and 3D structures of the rRNAs of the small and large subunits (SSU and LSU). Revised structures mapped with a variety of data are available in RiboVision as well as in a public gallery (). RiboVision is designed to allow users to distill complex data quickly and to easily generate publication-quality images of data mapped onto secondary structures. Users can readily import and analyze their own data in the context of other work. This package allows users to import and map data from CSV files directly onto 1D, 2D, and 3D levels of structure. RiboVision has features in rough analogy with web-based map services capable of seamlessly switching the type of data displayed and the resolution or magnification of the display. RiboVision is available at .
Collapse
Affiliation(s)
- Chad R Bernier
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Petrov AS, Bernier CR, Gulen B, Waterbury CC, Hershkovits E, Hsiao C, Harvey SC, Hud NV, Fox GE, Wartell RM, Williams LD. Secondary structures of rRNAs from all three domains of life. PLoS One 2014; 9:e88222. [PMID: 24505437 PMCID: PMC3914948 DOI: 10.1371/journal.pone.0088222] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 01/03/2014] [Indexed: 12/19/2022] Open
Abstract
Accurate secondary structures are important for understanding ribosomes, which are extremely large and highly complex. Using 3D structures of ribosomes as input, we have revised and corrected traditional secondary (2°) structures of rRNAs. We identify helices by specific geometric and molecular interaction criteria, not by co-variation. The structural approach allows us to incorporate non-canonical base pairs on parity with Watson-Crick base pairs. The resulting rRNA 2° structures are up-to-date and consistent with three-dimensional structures, and are information-rich. These 2° structures are relatively simple to understand and are amenable to reproduction and modification by end-users. The 2° structures made available here broadly sample the phylogenetic tree and are mapped with a variety of data related to molecular interactions and geometry, phylogeny and evolution. We have generated 2° structures for both large subunit (LSU) 23S/28S and small subunit (SSU) 16S/18S rRNAs of Escherichia coli, Thermus thermophilus, Haloarcula marismortui (LSU rRNA only), Saccharomyces cerevisiae, Drosophila melanogaster, and Homo sapiens. We provide high-resolution editable versions of the 2° structures in several file formats. For the SSU rRNA, the 2° structures use an intuitive representation of the central pseudoknot where base triples are presented as pairs of base pairs. Both LSU and SSU secondary maps are available (http://apollo.chemistry.gatech.edu/RibosomeGallery). Mapping of data onto 2° structures was performed on the RiboVision server (http://apollo.chemistry.gatech.edu/RiboVision).
Collapse
Affiliation(s)
- Anton S Petrov
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Chad R Bernier
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Burak Gulen
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Chris C Waterbury
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Eli Hershkovits
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Chiaolong Hsiao
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Stephen C Harvey
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Nicholas V Hud
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - George E Fox
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Roger M Wartell
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Loren Dean Williams
- Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America ; School of Chemistry and Biochemistry Georgia Institute of Technology, Atlanta, Georgia, United States of America
| |
Collapse
|
6
|
Petrov AS, Bernier CR, Hershkovits E, Xue Y, Waterbury CC, Hsiao C, Stepanov VG, Gaucher EA, Grover MA, Harvey SC, Hud NV, Wartell RM, Fox GE, Williams LD. Secondary structure and domain architecture of the 23S and 5S rRNAs. Nucleic Acids Res 2013; 41:7522-35. [PMID: 23771137 PMCID: PMC3753638 DOI: 10.1093/nar/gkt513] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We present a de novo re-determination of the secondary (2°) structure and domain architecture of the 23S and 5S rRNAs, using 3D structures, determined by X-ray diffraction, as input. In the traditional 2° structure, the center of the 23S rRNA is an extended single strand, which in 3D is seen to be compact and double helical. Accurately assigning nucleotides to helices compels a revision of the 23S rRNA 2° structure. Unlike the traditional 2° structure, the revised 2° structure of the 23S rRNA shows architectural similarity with the 16S rRNA. The revised 2° structure also reveals a clear relationship with the 3D structure and is generalizable to rRNAs of other species from all three domains of life. The 2° structure revision required us to reconsider the domain architecture. We partitioned the 23S rRNA into domains through analysis of molecular interactions, calculations of 2D folding propensities and compactness. The best domain model for the 23S rRNA contains seven domains, not six as previously ascribed. Domain 0 forms the core of the 23S rRNA, to which the other six domains are rooted. Editable 2° structures mapped with various data are provided (http://apollo.chemistry.gatech.edu/RibosomeGallery).
Collapse
Affiliation(s)
- Anton S. Petrov
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA, Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA, School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA and School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Correspondence may also be addressed to Anton S. Petrov. Tel: +1 404 385 4499; Fax: +1 404 894 7452;
| | - Chad R. Bernier
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA, Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA, School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA and School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Eli Hershkovits
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA, Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA, School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA and School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Yuzhen Xue
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA, Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA, School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA and School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Chris C. Waterbury
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA, Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA, School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA and School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Chiaolong Hsiao
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA, Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA, School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA and School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Victor G. Stepanov
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA, Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA, School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA and School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Eric A. Gaucher
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA, Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA, School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA and School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Martha A. Grover
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA, Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA, School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA and School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Stephen C. Harvey
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA, Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA, School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA and School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Nicholas V. Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA, Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA, School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA and School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Roger M. Wartell
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA, Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA, School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA and School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - George E. Fox
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA, Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA, School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA and School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA, Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA, School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA and School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
- *To whom correspondence should be addressed. Tel: +1 404 894 9752; Fax: +1 404 894 7452;
| |
Collapse
|
7
|
Petrov AS, Bernier CR, Hsiao C, Okafor CD, Tannenbaum E, Stern J, Gaucher E, Schneider D, Hud NV, Harvey SC, Williams LD. RNA-magnesium-protein interactions in large ribosomal subunit. J Phys Chem B 2012; 116:8113-20. [PMID: 22712611 DOI: 10.1021/jp304723w] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Some of the magnesium ions in the ribosome are coordinated by multiple rRNA phosphate groups. These magnesium ions link distal sequences of rRNA, primarily by incorporating phosphate groups into the first coordination shell. Less frequently, magnesium interacts with ribosomal proteins. Ribosomal protein L2 appears to be unique by forming specific magnesium-mediated interactions with rRNA. Using optimized models derived from X-ray structures, we subjected rRNA/magnesium/water/rProtein L2 assemblies to quantum mechanical analysis using the density functional theory and natural energy decomposition analysis. The combined results provide estimates of energies of formation of these assemblies, and allow us to decompose the energies of interaction. The results indicated that RNA immobilizes magnesium by multidentate chelation with phosphate, and that the magnesium ions in turn localize and polarize water molecules, increasing energies and specificities of interaction of these water molecules with L2 protein. Thus, magnesium plays subtle, yet important, roles in ribosomal assembly beyond neutralization of electrostatic repulsion and direct coordination of RNA functional groups.
Collapse
Affiliation(s)
- Anton S Petrov
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Athavale SS, Petrov AS, Hsiao C, Watkins D, Prickett CD, Gossett JJ, Lie L, Bowman JC, O'Neill E, Bernier CR, Hud NV, Wartell RM, Harvey SC, Williams LD. RNA folding and catalysis mediated by iron (II). PLoS One 2012; 7:e38024. [PMID: 22701543 PMCID: PMC3365117 DOI: 10.1371/journal.pone.0038024] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 04/28/2012] [Indexed: 01/06/2023] Open
Abstract
Mg2+ shares a distinctive relationship with RNA, playing important and specific roles in the folding and function of essentially all large RNAs. Here we use theory and experiment to evaluate Fe2+ in the absence of free oxygen as a replacement for Mg2+ in RNA folding and catalysis. We describe both quantum mechanical calculations and experiments that suggest that the roles of Mg2+ in RNA folding and function can indeed be served by Fe2+. The results of quantum mechanical calculations show that the geometry of coordination of Fe2+ by RNA phosphates is similar to that of Mg2+. Chemical footprinting experiments suggest that the conformation of the Tetrahymena thermophila Group I intron P4–P6 domain RNA is conserved between complexes with Fe2+ or Mg2+. The catalytic activities of both the L1 ribozyme ligase, obtained previously by in vitro selection in the presence of Mg2+, and the hammerhead ribozyme are enhanced in the presence of Fe2+ compared to Mg2+. All chemical footprinting and ribozyme assays in the presence of Fe2+ were performed under anaerobic conditions. The primary motivation of this work is to understand RNA in plausible early earth conditions. Life originated during the early Archean Eon, characterized by a non-oxidative atmosphere and abundant soluble Fe2+. The combined biochemical and paleogeological data are consistent with a role for Fe2+ in an RNA World. RNA and Fe2+ could, in principle, support an array of RNA structures and catalytic functions more diverse than RNA with Mg2+ alone.
Collapse
Affiliation(s)
- Shreyas S. Athavale
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Anton S. Petrov
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Chiaolong Hsiao
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Derrick Watkins
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Caitlin D. Prickett
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - J. Jared Gossett
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Lively Lie
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Jessica C. Bowman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Eric O'Neill
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Chad R. Bernier
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Nicholas V. Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Roger M. Wartell
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Stephen C. Harvey
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- NAI Center for Ribosomal Origins and Evolution, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail:
| |
Collapse
|