1
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Villanueva CD, Bohunická M, Johansen JR. We are doing it wrong: Putting homology before phylogeny in cyanobacterial taxonomy. JOURNAL OF PHYCOLOGY 2024. [PMID: 39152777 DOI: 10.1111/jpy.13491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 07/11/2024] [Accepted: 07/18/2024] [Indexed: 08/19/2024]
Abstract
The rapid expansion of whole genome sequencing in bacterial taxonomy has revealed deep evolutionary relationships and speciation signals, but assembly methods often miss true nucleotide diversity in the ribosomal operons. Though it lacks sufficient phylogenetic signal at the species level, the 16S ribosomal RNA gene is still much used in bacterial taxonomy. In cyanobacterial taxonomy, comparisons of 16S-23S Internal Transcribed Spacer (ITS) regions are used to bridge this information gap. Although ITS rRNA region analyses are routinely being used to identify species, researchers often do not identify orthologous operons, which leads to improper comparisons. No method for delineating orthologous operon copies from paralogous ones has been established. A new method for recognizing orthologous ribosomal operons by quantifying the conserved paired nucleotides in a helical domain of the ITS, has been developed. The D1' Index quantifies differences in the ratio of pyrimidines to purines in paired nucleotide sequences of this helix. Comparing 111 operon sequences from 89 strains of Brasilonema, four orthologous operon types were identified. Plotting D1' Index values against the length of helices produced clear separation of orthologs. Most orthologous operons in this study were observed both with and without tRNA genes present. We hypothesize that genomic rearrangement, not gene duplication, is responsible for the variation among orthologs. This new method will allow cyanobacterial taxonomists to utilize ITS rRNA region data more correctly, preventing erroneous taxonomic hypotheses. Moreover, this work could assist genomicists in identifying and preserving evident sequence variability in ribosomal operons, which is an important proxy for evolution in prokaryotes.
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Affiliation(s)
- Chelsea D Villanueva
- Department of Biological, Geological, & Environmental Sciences, Cleveland State University, Cleveland, Ohio, USA
- Department of Biology, John Carroll University, University Heights, Ohio, USA
| | - Markéta Bohunická
- Department of Biology, Faculty of Science, University of Hradec Králové, Hradec Králové, Czech Republic
| | - Jeffrey R Johansen
- Department of Biology, John Carroll University, University Heights, Ohio, USA
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2
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Kofman C, Willi JA, Karim AS, Jewett MC. Ribosome Pool Engineering Increases Protein Biosynthesis Yields. ACS CENTRAL SCIENCE 2024; 10:871-881. [PMID: 38680563 PMCID: PMC11046459 DOI: 10.1021/acscentsci.3c01413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 05/01/2024]
Abstract
The biosynthetic capability of the bacterial ribosome motivates efforts to understand and harness sequence-optimized versions for synthetic biology. However, functional differences between natively occurring ribosomal RNA (rRNA) operon sequences remain poorly characterized. Here, we use an in vitro ribosome synthesis and translation platform to measure protein production capabilities of ribosomes derived from all unique combinations of 16S and 23S rRNAs from seven distinct Escherichia coli rRNA operon sequences. We observe that polymorphisms that distinguish native E. coli rRNA operons lead to significant functional changes in the resulting ribosomes, ranging from negligible or low gene expression to matching the protein production activity of the standard rRNA operon B sequence. We go on to generate strains expressing single rRNA operons and show that not only do some purified in vivo expressed homogeneous ribosome pools outperform the wild-type, heterogeneous ribosome pool but also that a crude cell lysate made from the strain expressing only operon A ribosomes shows significant yield increases for a panel of medically and industrially relevant proteins. We anticipate that ribosome pool engineering can be applied as a tool to increase yields across many protein biomanufacturing systems, as well as improve basic understanding of ribosome heterogeneity and evolution.
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Affiliation(s)
- Camila Kofman
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Jessica A. Willi
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Ashty S. Karim
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C. Jewett
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department
of Bioengineering, Stanford University, Stanford California 94305, United States
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3
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Höfler S, Duss O. Interconnections between m 6A RNA modification, RNA structure, and protein-RNA complex assembly. Life Sci Alliance 2024; 7:e202302240. [PMID: 37935465 PMCID: PMC10629537 DOI: 10.26508/lsa.202302240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/09/2023] Open
Abstract
Protein-RNA complexes exist in many forms within the cell, from stable machines such as the ribosome to transient assemblies like the spliceosome. All protein-RNA assemblies rely on spatially and temporally coordinated interactions between specific proteins and RNAs to achieve a functional form. RNA folding and structure are often critical for successful protein binding and protein-RNA complex formation. RNA modifications change the chemical nature of a given RNA and often alter its folding kinetics. Both these alterations can affect how and if proteins or other RNAs can interact with the modified RNA and assemble into complexes. N6-methyladenosine (m6A) is the most common base modification on mRNAs and regulatory noncoding RNAs and has been shown to impact RNA structure and directly modulate protein-RNA interactions. In this review, focusing on the mechanisms and available quantitative information, we discuss first how the METTL3/14 m6A writer complex is specifically targeted to RNA assisted by protein-RNA and other interactions to enable site-specific and co-transcriptional RNA modification and, once introduced, how the m6A modification affects RNA folding and protein-RNA interactions.
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Affiliation(s)
- Simone Höfler
- https://ror.org/03mstc592 Structural and Computational Biology Unit, EMBL Heidelberg, Heidelberg, Germany
| | - Olivier Duss
- https://ror.org/03mstc592 Structural and Computational Biology Unit, EMBL Heidelberg, Heidelberg, Germany
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4
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Wonderlick DR, Widom JR, Harms MJ. Disentangling contact and ensemble epistasis in a riboswitch. Biophys J 2023; 122:1600-1612. [PMID: 36710492 PMCID: PMC10183321 DOI: 10.1016/j.bpj.2023.01.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/09/2023] [Accepted: 01/24/2023] [Indexed: 01/29/2023] Open
Abstract
Mutations introduced into macromolecules often exhibit epistasis, where the effect of one mutation alters the effect of another. Knowing the mechanisms that lead to epistasis is important for understanding how macromolecules work and evolve, as well as for effective macromolecular engineering. Here, we investigate the interplay between "contact epistasis" (epistasis arising from physical interactions between mutated residues) and "ensemble epistasis" (epistasis that occurs when a mutation redistributes the conformational ensemble of a macromolecule, thus changing the effect of the second mutation). We argue that the two mechanisms can be distinguished in allosteric macromolecules by measuring epistasis at differing allosteric effector concentrations. Contact epistasis manifests as nonadditivity in the microscopic equilibrium constants describing the conformational ensemble. This epistatic effect is independent of allosteric effector concentration. Ensemble epistasis manifests as nonadditivity in thermodynamic observables-such as ligand binding-that are determined by the distribution of ensemble conformations. This epistatic effect strongly depends on allosteric effector concentration. Using this framework, we experimentally investigated the origins of epistasis in three pairwise mutant cycles introduced into the adenine riboswitch aptamer domain by measuring ligand binding as a function of allosteric effector concentration. We found evidence for both contact and ensemble epistasis in all cycles. Furthermore, we found that the two mechanisms of epistasis could interact with each other. For example, in one mutant cycle we observed 6 kcal/mol of contact epistasis in a microscopic equilibrium constant. In that same cycle, the maximum epistasis in ligand binding was only 1.5 kcal/mol: shifts in the ensemble masked the contribution of contact epistasis. Finally, our work yields simple heuristics for identifying contact and ensemble epistasis based on measurements of a biochemical observable as a function of allosteric effector concentration.
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Affiliation(s)
- Daria R Wonderlick
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon
| | - Julia R Widom
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon; Institute for Molecular Biology, University of Oregon, Eugene, Oregon; Oregon Center for Optical, Molecular, & Quantum Science, University of Oregon, Eugene, Oregon
| | - Michael J Harms
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon; Institute for Molecular Biology, University of Oregon, Eugene, Oregon.
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5
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Hughes LA, Rudler DL, Siira SJ, McCubbin T, Raven SA, Browne JM, Ermer JA, Rientjes J, Rodger J, Marcellin E, Rackham O, Filipovska A. Copy number variation in tRNA isodecoder genes impairs mammalian development and balanced translation. Nat Commun 2023; 14:2210. [PMID: 37072429 PMCID: PMC10113395 DOI: 10.1038/s41467-023-37843-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/29/2023] [Indexed: 04/20/2023] Open
Abstract
The number of tRNA isodecoders has increased dramatically in mammals, but the specific molecular and physiological reasons for this expansion remain elusive. To address this fundamental question we used CRISPR editing to knockout the seven-membered phenylalanine tRNA gene family in mice, both individually and combinatorially. Using ATAC-Seq, RNA-seq, ribo-profiling and proteomics we observed distinct molecular consequences of single tRNA deletions. We show that tRNA-Phe-1-1 is required for neuronal function and its loss is partially compensated by increased expression of other tRNAs but results in mistranslation. In contrast, the other tRNA-Phe isodecoder genes buffer the loss of each of the remaining six tRNA-Phe genes. In the tRNA-Phe gene family, the expression of at least six tRNA-Phe alleles is required for embryonic viability and tRNA-Phe-1-1 is most important for development and survival. Our results reveal that the multi-copy configuration of tRNA genes is required to buffer translation and viability in mammals.
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Affiliation(s)
- Laetitia A Hughes
- Harry Perkins Institute of Medical Research, Perth, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Danielle L Rudler
- Harry Perkins Institute of Medical Research, Perth, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Stefan J Siira
- Harry Perkins Institute of Medical Research, Perth, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Tim McCubbin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, 4072, QLD, Australia
| | - Samuel A Raven
- Harry Perkins Institute of Medical Research, Perth, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Jasmin M Browne
- Harry Perkins Institute of Medical Research, Perth, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Judith A Ermer
- Harry Perkins Institute of Medical Research, Perth, WA, Australia
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, 6009, Australia
| | - Jeanette Rientjes
- Monash Genome Modification Platform, Monash University, 35 Rainforest Walk, Clayton, VIC, 3800, Australia
| | - Jennifer Rodger
- School of Biological Sciences (Physiology), The University of Western Australia, Crawley, WA, 6009, Australia
- Perron Institute for Neurological and Translational Sciences, Nedlands, WA, 6009, Australia
| | - Esteban Marcellin
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, 4072, QLD, Australia
- Queensland Metabolomics and Proteomics (Q-MAP), The University of Queensland, Brisbane, 4072, QLD, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, Perth, WA, Australia.
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia.
- Curtin Medical School, Curtin University, Bentley, WA, 6102, Australia.
- Curtin Health Innovation Research Institute, Curtin University, Bentley, WA, 6102, Australia.
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, Australia.
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, Perth, WA, Australia.
- ARC Centre of Excellence in Synthetic Biology, QEII Medical Centre, Nedlands, WA, 6009, Australia.
- Centre for Medical Research, The University of Western Australia, QEII Medical Centre, Nedlands, WA, 6009, Australia.
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, Australia.
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6
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Hart SM, Banal JL, Castellanos MA, Markova L, Vyborna Y, Gorman J, Häner R, Willard AP, Bathe M, Schlau-Cohen GS. Activating charge-transfer state formation in strongly-coupled dimers using DNA scaffolds. Chem Sci 2022; 13:13020-13031. [PMID: 36425503 PMCID: PMC9667922 DOI: 10.1039/d2sc02759c] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/04/2022] [Indexed: 09/16/2023] Open
Abstract
Strongly-coupled multichromophoric assemblies orchestrate the absorption, transport, and conversion of photonic energy in natural and synthetic systems. Programming these functionalities involves the production of materials in which chromophore placement is precisely controlled. DNA nanomaterials have emerged as a programmable scaffold that introduces the control necessary to select desired excitonic properties. While the ability to control photophysical processes, such as energy transport, has been established, similar control over photochemical processes, such as interchromophore charge transfer, has not been demonstrated in DNA. In particular, charge transfer requires the presence of close-range interchromophoric interactions, which have a particularly steep distance dependence, but are required for eventual energy conversion. Here, we report a DNA-chromophore platform in which long-range excitonic couplings and short-range charge-transfer couplings can be tailored. Using combinatorial screening, we discovered chromophore geometries that enhance or suppress photochemistry. We combined spectroscopic and computational results to establish the presence of symmetry-breaking charge transfer in DNA-scaffolded squaraines, which had not been previously achieved in these chromophores. Our results demonstrate that the geometric control introduced through the DNA can access otherwise inaccessible processes and program the evolution of excitonic states of molecular chromophores, opening up opportunities for designer photoactive materials for light harvesting and computation.
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Affiliation(s)
- Stephanie M Hart
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - James L Banal
- Department of Biological Engineering, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Maria A Castellanos
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Larysa Markova
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3, CH-3012 Bern Switzerland
| | - Yuliia Vyborna
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3, CH-3012 Bern Switzerland
| | - Jeffrey Gorman
- Department of Biological Engineering, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Robert Häner
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3, CH-3012 Bern Switzerland
| | - Adam P Willard
- Department of Chemistry, Massachusetts Institute of Technology Cambridge MA 02139 USA
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology Cambridge MA 02139 USA
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7
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Zhu L, Jiang H, Cao S, Unarta IC, Gao X, Huang X. Critical role of backbone coordination in the mRNA recognition by RNA induced silencing complex. Commun Biol 2021; 4:1345. [PMID: 34848812 PMCID: PMC8632932 DOI: 10.1038/s42003-021-02822-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/26/2021] [Indexed: 01/02/2023] Open
Abstract
Despite its functional importance, the molecular mechanism underlying target mRNA recognition by Argonaute (Ago) remains largely elusive. Based on extensive all-atom molecular dynamics simulations, we constructed quasi-Markov State Model (qMSM) to reveal the dynamics during recognition at position 6-7 in the seed region of human Argonaute 2 (hAgo2). Interestingly, we found that the slowest mode of motion therein is not the gRNA-target base-pairing, but the coordination of the target phosphate groups with a set of positively charged residues of hAgo2. Moreover, the ability of Helix-7 to approach the PIWI and MID domains was found to reduce the effective volume accessible to the target mRNA and therefore facilitate both the backbone coordination and base-pair formation. Further mutant simulations revealed that alanine mutation of the D358 residue on Helix-7 enhanced a trap state to slow down the loading of target mRNA. Similar trap state was also observed when wobble pairs were introduced in g6 and g7, indicating the role of Helix-7 in suppressing non-canonical base-paring. Our study pointed to a general mechanism for mRNA recognition by eukaryotic Agos and demonstrated the promise of qMSM in investigating complex conformational changes of biomolecular systems.
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Affiliation(s)
- Lizhe Zhu
- Warshel Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong, 518172, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hanlun Jiang
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Department of Biochemistry, Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Siqin Cao
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Ilona Christy Unarta
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xin Gao
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
| | - Xuhui Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
- Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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8
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Hurst T, Chen SJ. Deciphering nucleotide modification-induced structure and stability changes. RNA Biol 2021; 18:1920-1930. [PMID: 33586616 DOI: 10.1080/15476286.2021.1882179] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Nucleotide modification in RNA controls a bevy of biological processes, including RNA degradation, gene expression, and gene editing. In turn, misregulation of modified nucleotides is associated with a host of chronic diseases and disorders. However, the molecular mechanisms driving these processes remain poorly understood. To partially address this knowledge gap, we used alchemical and temperature replica exchange molecular dynamics (TREMD) simulations on an RNA duplex and an analogous hairpin to probe the structural effects of modified and/or mutant nucleotides. The simulations successfully predict the modification/mutation-induced relative free energy change for complementary duplex formation, and structural analyses highlight mechanisms driving stability changes. Furthermore, TREMD simulations for a hairpin-forming RNA with and without modification provide reliable estimations of the energy landscape. Illuminating the impact of methylated and/or mutated nucleotides on the structure-function relationship and the folding energy landscape, the simulations provide insights into modification-induced alterations to the folding mechanics of the hairpin. The results here may be biologically significant as hairpins are widespread structure motifs that play critical roles in gene expression and regulation. Specifically, the tetraloop of the probed hairpin is phylogenetically abundant, and the stem mirrors a miRNA seed region whose modification has been implicated in epilepsy pathogenesis.
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Affiliation(s)
- Travis Hurst
- Department of Physics, Department of Biochemistry, and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
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9
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Seelam Prabhakar P, Takyi NA, Wetmore SD. Posttranscriptional modifications at the 37th position in the anticodon stem-loop of tRNA: structural insights from MD simulations. RNA (NEW YORK, N.Y.) 2021; 27:202-220. [PMID: 33214333 PMCID: PMC7812866 DOI: 10.1261/rna.078097.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/16/2020] [Indexed: 06/11/2023]
Abstract
Transfer RNA (tRNA) is the most diversely modified RNA. Although the strictly conserved purine position 37 in the anticodon stem-loop undergoes modifications that are phylogenetically distributed, we do not yet fully understand the roles of these modifications. Therefore, molecular dynamics simulations are used to provide molecular-level details for how such modifications impact the structure and function of tRNA. A focus is placed on three hypermodified base families that include the parent i6A, t6A, and yW modifications, as well as derivatives. Our data reveal that the hypermodifications exhibit significant conformational flexibility in tRNA, which can be modulated by additional chemical functionalization. Although the overall structure of the tRNA anticodon stem remains intact regardless of the modification considered, the anticodon loop must rearrange to accommodate the bulky, dynamic hypermodifications, which includes changes in the nucleotide glycosidic and backbone conformations, and enhanced or completely new nucleobase-nucleobase interactions compared to unmodified tRNA or tRNA containing smaller (m1G) modifications at the 37th position. Importantly, the extent of the changes in the anticodon loop is influenced by the addition of small functional groups to parent modifications, implying each substituent can further fine-tune tRNA structure. Although the dominant conformation of the ASL is achieved in different ways for each modification, the molecular features of all modified tRNA drive the ASL domain to adopt the functional open-loop conformation. Importantly, the impact of the hypermodifications is preserved in different sequence contexts. These findings highlight the likely role of regulating mRNA structure and translation.
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MESH Headings
- Adenosine/analogs & derivatives
- Adenosine/metabolism
- Anticodon/chemistry
- Anticodon/genetics
- Anticodon/metabolism
- Base Pairing
- Base Sequence
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Isopentenyladenosine/chemistry
- Isopentenyladenosine/metabolism
- Molecular Dynamics Simulation
- Nucleic Acid Conformation
- Nucleosides/chemistry
- Nucleosides/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Transfer, Lys/chemistry
- RNA, Transfer, Lys/genetics
- RNA, Transfer, Lys/metabolism
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/genetics
- RNA, Transfer, Phe/metabolism
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Affiliation(s)
- Preethi Seelam Prabhakar
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Nathania A Takyi
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
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10
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Yu J. From Mutation Signature to Molecular Mechanism in the RNA World: A Case of SARS-CoV-2. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:627-639. [PMID: 32739507 PMCID: PMC7391168 DOI: 10.1016/j.gpb.2020.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/10/2020] [Accepted: 07/23/2020] [Indexed: 02/07/2023]
Affiliation(s)
- Jun Yu
- China National Center for Bioinformation, Beijing 100101, China; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100190, China.
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11
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Abstract
Base pairing plays a pivotal role in DNA functions and replication fidelity. But while the complementarity between Watson-Crick matched bases is generally believed to arise from the different number of hydrogen bonds in G|C pairs versus A|T, the energetics of these interactions are heavily renormalized by the aqueous solvent. Employing large-scale Monte Carlo simulations, we have extracted the solvent contribution to the free energy for canonical and some noncanonical and stacked base pairs. For all of them, the solvent's contribution to the base pairing free energy is exclusively destabilizing. While the direct hydrogen bonding interactions in the G|C pair is much stronger than A|T, the thermodynamic resistance produced by the solvent also pushes back much stronger against G|C compared to A|T, generating an only ∼1 kcal/mol free energy difference between them. We have profiled the density of water molecules in the solvent adjacent to the bases and observed a "freezing" behavior where waters are recruited into the gap between the bases to compensate for the unsatisfied hydrogen bonds between them. A very small number of water molecules that are associated with the Watson-Crick donor/acceptor atoms turn out to be responsible for the majority of the solvent's thermodynamic resistance to base pairing. The absence or presence of these near-field waters can be used to enhance fidelity during DNA replication.
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12
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Savage JC, Davare MA, Shinde U. Subtle sequence variations alter tripartite complex kinetics and G-quadruplex dynamics in RNA aptamer Broccoli. Chem Commun (Camb) 2020; 56:2634-2637. [PMID: 32016232 DOI: 10.1039/c9cc09375c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Though extensively utilized, the fluorescent RNA aptamer Broccoli is poorly characterized with an unknown structure. Spectroscopic and kinetic investigations of tripartite complex formation reveal surprising differences between Broccoli and Spinach aptamers despite extreme sequence conservation. Our studies highlight how subtle sequence variations impart functional consequences of G-quadruplex-cation interactions in RNA.
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Affiliation(s)
- Jonathan C Savage
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA.
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13
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Thermodynamic control of -1 programmed ribosomal frameshifting. Nat Commun 2019; 10:4598. [PMID: 31601802 PMCID: PMC6787027 DOI: 10.1038/s41467-019-12648-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/11/2019] [Indexed: 12/18/2022] Open
Abstract
mRNA contexts containing a 'slippery' sequence and a downstream secondary structure element stall the progression of the ribosome along the mRNA and induce its movement into the -1 reading frame. In this study we build a thermodynamic model based on Bayesian statistics to explain how -1 programmed ribosome frameshifting can work. As training sets for the model, we measured frameshifting efficiencies on 64 dnaX mRNA sequence variants in vitro and also used 21 published in vivo efficiencies. With the obtained free-energy difference between mRNA-tRNA base pairs in the 0 and -1 frames, the frameshifting efficiency of a given sequence can be reproduced and predicted from the tRNA-mRNA base pairing in the two frames. Our results further explain how modifications in the tRNA anticodon modulate frameshifting and show how the ribosome tunes the strength of the base-pair interactions.
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14
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Strebitzer E, Rangadurai A, Plangger R, Kremser J, Juen MA, Tollinger M, Al‐Hashimi HM, Kreutz C. 5-Oxyacetic Acid Modification Destabilizes Double Helical Stem Structures and Favors Anionic Watson-Crick like cmo 5 U-G Base Pairs. Chemistry 2018; 24:18903-18906. [PMID: 30300940 PMCID: PMC6348377 DOI: 10.1002/chem.201805077] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Indexed: 01/20/2023]
Abstract
Watson-Crick like G-U mismatches with tautomeric Genol or Uenol bases can evade fidelity checkpoints and thereby contribute to translational errors. The 5-oxyacetic acid uridine (cmo5 U) modification is a base modification at the wobble position on tRNAs and is presumed to expand the decoding capability of tRNA at this position by forming Watson-Crick like cmo5 Uenol -G mismatches. A detailed investigation on the influence of the cmo5 U modification on structural and dynamic features of RNA was carried out by using solution NMR spectroscopy and UV melting curve analysis. The introduction of a stable isotope labeled variant of the cmo5 U modifier allowed the application of relaxation dispersion NMR to probe the potentially formed Watson-Crick like cmo5 Uenol -G base pair. Surprisingly, we find that at neutral pH, the modification promotes transient formation of anionic Watson-Crick like cmo5 U- -G, and not enolic base pairs. Our results suggest that recoding is mediated by an anionic Watson-Crick like species, as well as bring an interesting aspect of naturally occurring RNA modifications into focus-the fine tuning of nucleobase properties leading to modulation of the RNA structural landscape by adoption of alternative base pairing patterns.
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Affiliation(s)
- Elisabeth Strebitzer
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80/826020InnsbruckAustria
| | - Atul Rangadurai
- Department of Biochemistry and Department of ChemistryDuke University School of Medicine, Nanaline H. Duke Building307 Research DriveDurhamNC27710USA
| | - Raphael Plangger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80/826020InnsbruckAustria
| | - Johannes Kremser
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80/826020InnsbruckAustria
| | - Michael Andreas Juen
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80/826020InnsbruckAustria
| | - Martin Tollinger
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80/826020InnsbruckAustria
| | - Hashim M. Al‐Hashimi
- Department of Biochemistry and Department of ChemistryDuke University School of Medicine, Nanaline H. Duke Building307 Research DriveDurhamNC27710USA
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnrain 80/826020InnsbruckAustria
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15
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Tanzer A, Hofacker IL, Lorenz R. RNA modifications in structure prediction - Status quo and future challenges. Methods 2018; 156:32-39. [PMID: 30385321 DOI: 10.1016/j.ymeth.2018.10.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 10/12/2018] [Accepted: 10/26/2018] [Indexed: 01/01/2023] Open
Abstract
Chemical modifications of RNA nucleotides change their identity and characteristics and thus alter genetic and structural information encoded in the genomic DNA. tRNA and rRNA are probably the most heavily modified genes, and often depend on derivatization or isomerization of their nucleobases in order to correctly fold into their functional structures. Recent RNomics studies, however, report transcriptome wide RNA modification and suggest a more general regulation of structuredness of RNAs by this so called epitranscriptome. Modification seems to require specific substrate structures, which in turn are stabilized or destabilized and thus promote or inhibit refolding events of regulatory RNA structures. In this review, we revisit RNA modifications and the related structures from a computational point of view. We discuss known substrate structures, their properties such as sub-motifs as well as consequences of modifications on base pairing patterns and possible refolding events. Given that efficient RNA structure prediction methods for canonical base pairs have been established several decades ago, we review to what extend these methods allow the inclusion of modified nucleotides to model and study epitranscriptomic effects on RNA structures.
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Affiliation(s)
- Andrea Tanzer
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Waehringerstrasse 17, 1090 Vienna, Austria
| | - Ivo L Hofacker
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Waehringerstrasse 17, 1090 Vienna, Austria; Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Waehringerstrasse 29, 1090 Vienna, Austria
| | - Ronny Lorenz
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Waehringerstrasse 17, 1090 Vienna, Austria
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16
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Nigita G, Distefano R, Veneziano D, Romano G, Rahman M, Wang K, Pass H, Croce CM, Acunzo M, Nana-Sinkam P. Tissue and exosomal miRNA editing in Non-Small Cell Lung Cancer. Sci Rep 2018; 8:10222. [PMID: 29976955 PMCID: PMC6033928 DOI: 10.1038/s41598-018-28528-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 06/15/2018] [Indexed: 01/11/2023] Open
Abstract
RNA editing in microRNAs has been recently proposed as a novel biomarker in cancer. Here, we investigated RNA editing by leveraging small-RNA sequencing data from 87 NSCLC (Non-Small Cell Lung Cancer) samples paired with normal lung tissues from The Cancer Genome Atlas (TCGA) combined with 26 plasma-derived exosome samples from an independent cohort. Using both the editing levels and microRNA editing expression, we detected deregulated microRNA editing events between NSCLC tumor and normal tissues. Interestingly, and for the first time, we also detected editing sites in the microRNA cargo of circulating exosomes, providing the potential to non-invasively discriminate between normal and tumor samples. Of note, miR-411-5p edited in position 5 was significantly dysregulated in tissues as well as in exosomes of NSCLC patients, suggesting a potential targetome shift relevant to lung cancer biology.
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Affiliation(s)
- Giovanni Nigita
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Rosario Distefano
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Dario Veneziano
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Giulia Romano
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Mohammad Rahman
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Kai Wang
- Institute for System Biology, Seattle, WA, USA
| | - Harvey Pass
- Department of Cardiothoracic Surgery, New York University Cancer Center, New York, NY, USA
| | - Carlo M Croce
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
| | - Mario Acunzo
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, USA.
| | - Patrick Nana-Sinkam
- Division of Pulmonary Diseases and Critical Care Medicine, Virginia Commonwealth University, Richmond, VA, USA.
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17
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Héliou A, Budday D, Fonseca R, van den Bedem H. Fast, clash-free RNA conformational morphing using molecular junctions. Bioinformatics 2018; 33:2114-2122. [PMID: 28334257 DOI: 10.1093/bioinformatics/btx127] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 03/11/2017] [Indexed: 12/20/2022] Open
Abstract
Motivation Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. Results Despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble. Here we present a kinematics-based procedure to morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes. We represent an RNA as a kinematic linkage, with fixed groups of atoms as rigid bodies and rotatable bonds as degrees of freedom. Our procedure maintains RNA secondary structure by treating hydrogen bonds between base pairs as constraints. The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation space, where motions are largely governed by molecular junctions of unpaired nucleotides. On a large benchmark set, we show that our morphing procedure compares favorably to peer algorithms, and can approach goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms. Our results suggest that molecular junctions can modulate 3D structural rearrangements, while secondary structure elements guide large parts of the molecule along the transition to the correct final conformation. Availability and Implementation The source code, binaries and data are available at https://simtk.org/home/kgs . Contact amelie.heliou@polytechnique.edu or vdbedem@stanford.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Amélie Héliou
- LIX, Ecole Polytechnique, CNRS, Inria, Université Paris-Saclay, Palaiseau, France
| | - Dominik Budday
- Chair of Applied Dynamics, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Rasmus Fonseca
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.,Biosciences Division, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA
| | - Henry van den Bedem
- Biosciences Division, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA
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18
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RNA editing by ADAR1 leads to context-dependent transcriptome-wide changes in RNA secondary structure. Nat Commun 2017; 8:1440. [PMID: 29129909 PMCID: PMC5682290 DOI: 10.1038/s41467-017-01458-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 09/19/2017] [Indexed: 11/09/2022] Open
Abstract
Adenosine deaminase acting on RNA 1 (ADAR1) is the master RNA editor, catalyzing the deamination of adenosine to inosine. RNA editing is vital for preventing abnormal activation of cytosolic nucleic acid sensing pathways by self-double-stranded RNAs. Here we determine, by parallel analysis of RNA secondary structure sequencing (PARS-seq), the global RNA secondary structure changes in ADAR1 deficient cells. Surprisingly, ADAR1 silencing resulted in a lower global double-stranded to single-stranded RNA ratio, suggesting that A-to-I editing can stabilize a large subset of imperfect RNA duplexes. The duplexes destabilized by editing are composed of vastly complementary inverted Alus found in untranslated regions of genes performing vital biological processes, including housekeeping functions and type-I interferon responses. They are predominantly cytoplasmic and generally demonstrate higher ribosomal occupancy. Our findings imply that the editing effect on RNA secondary structure is context dependent and underline the intricate regulatory role of ADAR1 on global RNA secondary structure.
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19
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Agris PF, Eruysal ER, Narendran A, Väre VYP, Vangaveti S, Ranganathan SV. Celebrating wobble decoding: Half a century and still much is new. RNA Biol 2017; 15:537-553. [PMID: 28812932 PMCID: PMC6103715 DOI: 10.1080/15476286.2017.1356562] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/04/2017] [Accepted: 07/06/2017] [Indexed: 10/25/2022] Open
Abstract
A simple post-transcriptional modification of tRNA, deamination of adenosine to inosine at the first, or wobble, position of the anticodon, inspired Francis Crick's Wobble Hypothesis 50 years ago. Many more naturally-occurring modifications have been elucidated and continue to be discovered. The post-transcriptional modifications of tRNA's anticodon domain are the most diverse and chemically complex of any RNA modifications. Their contribution with regards to chemistry, structure and dynamics reveal individual and combined effects on tRNA function in recognition of cognate and wobble codons. As forecast by the Modified Wobble Hypothesis 25 years ago, some individual modifications at tRNA's wobble position have evolved to restrict codon recognition whereas others expand the tRNA's ability to read as many as four synonymous codons. Here, we review tRNA wobble codon recognition using specific examples of simple and complex modification chemistries that alter tRNA function. Understanding natural modifications has inspired evolutionary insights and possible innovation in protein synthesis.
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Affiliation(s)
- Paul F. Agris
- The RNA Institute, State University of New York, Albany, NY, USA
- Department of Biology, State University of New York, Albany, NY, USA
- Department of Chemistry, State University of New York, Albany, NY, USA
| | - Emily R. Eruysal
- Department of Biology, State University of New York, Albany, NY, USA
| | - Amithi Narendran
- Department of Biology, State University of New York, Albany, NY, USA
| | - Ville Y. P. Väre
- Department of Biology, State University of New York, Albany, NY, USA
| | - Sweta Vangaveti
- The RNA Institute, State University of New York, Albany, NY, USA
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20
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Sochacka E, Lodyga-Chruscinska E, Pawlak J, Cypryk M, Bartos P, Ebenryter-Olbinska K, Leszczynska G, Nawrot B. C5-substituents of uridines and 2-thiouridines present at the wobble position of tRNA determine the formation of their keto-enol or zwitterionic forms - a factor important for accuracy of reading of guanosine at the 3΄-end of the mRNA codons. Nucleic Acids Res 2017; 45:4825-4836. [PMID: 28088758 PMCID: PMC5416851 DOI: 10.1093/nar/gkw1347] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 12/30/2016] [Indexed: 12/19/2022] Open
Abstract
Modified nucleosides present in the wobble position of the tRNA anticodons regulate protein translation through tuning the reading of mRNA codons. Among 40 of such nucleosides, there are modified uridines containing either a sulfur atom at the C2 position and/or a substituent at the C5 position of the nucleobase ring. It is already evidenced that tRNAs with 2-thiouridines at the wobble position preferentially read NNA codons, while the reading mode of the NNG codons by R5U/R5S2U-containing anticodons is still elusive. For a series of 18 modified uridines and 2-thiouridines, we determined the pKa values and demonstrated that both modifying elements alter the electron density of the uracil ring and modulate the acidity of their N3H proton. In aqueous solutions at physiological pH the 2-thiouridines containing aminoalkyl C5-substituents are ionized in ca. 50%. The results, confirmed also by theoretical calculations, indicate that the preferential binding of the modified units bearing non-ionizable 5-substituents to guanosine in the NNG codons may obey the alternative C-G-like (Watson–Crick) mode, while binding of those bearing aminoalkyl C5-substituents (protonated under physiological conditions) and especially those with a sulfur atom at the C2 position, adopt a zwitterionic form and interact with guanosine via a ‘new wobble’ pattern.
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Affiliation(s)
- Elzbieta Sochacka
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Elzbieta Lodyga-Chruscinska
- Institute of General Food Chemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Justyna Pawlak
- Institute of General Food Chemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Marek Cypryk
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Paulina Bartos
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Katarzyna Ebenryter-Olbinska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.,Department of Computer Modeling, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Grazyna Leszczynska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Barbara Nawrot
- Department of Computer Modeling, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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21
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Väre VYP, Eruysal ER, Narendran A, Sarachan KL, Agris PF. Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function. Biomolecules 2017; 7:E29. [PMID: 28300792 PMCID: PMC5372741 DOI: 10.3390/biom7010029] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/06/2017] [Accepted: 03/06/2017] [Indexed: 12/21/2022] Open
Abstract
RNAs are central to all gene expression through the control of protein synthesis. Four major nucleosides, adenosine, guanosine, cytidine and uridine, compose RNAs and provide sequence variation, but are limited in contributions to structural variation as well as distinct chemical properties. The ability of RNAs to play multiple roles in cellular metabolism is made possible by extensive variation in length, conformational dynamics, and the over 100 post-transcriptional modifications. There are several reviews of the biochemical pathways leading to RNA modification, but the physicochemical nature of modified nucleosides and how they facilitate RNA function is of keen interest, particularly with regard to the contributions of modified nucleosides. Transfer RNAs (tRNAs) are the most extensively modified RNAs. The diversity of modifications provide versatility to the chemical and structural environments. The added chemistry, conformation and dynamics of modified nucleosides occurring at the termini of stems in tRNA's cloverleaf secondary structure affect the global three-dimensional conformation, produce unique recognition determinants for macromolecules to recognize tRNAs, and affect the accurate and efficient decoding ability of tRNAs. This review will discuss the impact of specific chemical moieties on the structure, stability, electrochemical properties, and function of tRNAs.
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Affiliation(s)
- Ville Y P Väre
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Emily R Eruysal
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Amithi Narendran
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Kathryn L Sarachan
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Paul F Agris
- The RNA Institute, Departments of Biological Sciences and Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
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22
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Nigita G, Acunzo M, Romano G, Veneziano D, Laganà A, Vitiello M, Wernicke D, Ferro A, Croce CM. microRNA editing in seed region aligns with cellular changes in hypoxic conditions. Nucleic Acids Res 2016; 44:6298-308. [PMID: 27298257 PMCID: PMC4994866 DOI: 10.1093/nar/gkw532] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 05/31/2016] [Accepted: 06/01/2016] [Indexed: 12/22/2022] Open
Abstract
RNA editing is a finely tuned, dynamic mechanism for post-transcriptional gene regulation that has been thoroughly investigated in the last decade. Nevertheless, RNA editing in non-coding RNA, such as microRNA (miRNA), have caused great debate and have called for deeper investigation. Until recently, in fact, inadequate methodologies and experimental contexts have been unable to provide detailed insights for further elucidation of RNA editing affecting miRNAs, especially in cancer.In this work, we leverage on recent innovative bioinformatics approaches applied to a more informative experimental context in order to analyze the variations in miRNA seed region editing activity during a time course of a hypoxia-exposed breast cancer cell line. By investigating its behavior in a dynamic context, we found that miRNA editing events in the seed region are not depended on miRNA expression, unprecedentedly providing insights on the targetome shifts derived from these modifications. This reveals that miRNA editing acts under the influence of environmentally induced stimuli.Our results show a miRNA editing activity trend aligning with cellular pathways closely associated to hypoxia, such as the VEGF and PI3K/Akt pathways, providing important novel insights on this poorly elucidated phenomenon.
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Affiliation(s)
- Giovanni Nigita
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Mario Acunzo
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Giulia Romano
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Dario Veneziano
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Alessandro Laganà
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA
| | - Marika Vitiello
- Department of Clinicaland Molecular Biomedicine, University of Catania, Catania 95125, Italy
| | - Dorothee Wernicke
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Alfredo Ferro
- Department of Structural & Functional Biology, University 'Federico II' of Naples, Naples 80126, Italy
| | - Carlo M Croce
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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23
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van der Gulik PTS, Hoff WD. Anticodon Modifications in the tRNA Set of LUCA and the Fundamental Regularity in the Standard Genetic Code. PLoS One 2016; 11:e0158342. [PMID: 27454314 PMCID: PMC4959769 DOI: 10.1371/journal.pone.0158342] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 06/14/2016] [Indexed: 11/19/2022] Open
Abstract
Based on (i) an analysis of the regularities in the standard genetic code and (ii) comparative genomics of the anticodon modification machinery in the three branches of life, we derive the tRNA set and its anticodon modifications as it was present in LUCA. Previously we proposed that an early ancestor of LUCA contained a set of 23 tRNAs with unmodified anticodons that was capable of translating all 20 amino acids while reading 55 of the 61 sense codons of the standard genetic code (SGC). Here we use biochemical and genomic evidence to derive that LUCA contained a set of 44 or 45 tRNAs containing 2 or 3 modifications while reading 59 or 60 of the 61 sense codons. Subsequent tRNA modifications occurred independently in the Bacteria and Eucarya, while the Archaea have remained quite close to the tRNA set as it was present in LUCA.
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Affiliation(s)
| | - Wouter D. Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, 74078, United States of America
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma, 74078, United States of America
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24
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Vincent AT, Emond-Rheault JG, Barbeau X, Attéré SA, Frenette M, Lagüe P, Charette SJ. Antibiotic resistance due to an unusual ColE1-type replicon plasmid in Aeromonas salmonicida. Microbiology (Reading) 2016; 162:942-953. [DOI: 10.1099/mic.0.000286] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Antony T. Vincent
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, QC, Canada, G1V 4G5
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC, Canada, G1V 0A6
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6
| | - Jean-Guillaume Emond-Rheault
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC, Canada, G1V 0A6
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, QC, Canada, G1V 4G5
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6
| | - Xavier Barbeau
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC, Canada, G1V 0A6
- Département de Chimie, Université Laval, Québec, Canada
| | - Sabrina A. Attéré
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC, Canada, G1V 0A6
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, QC, Canada, G1V 4G5
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6
| | - Michel Frenette
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6
- Groupe de Recherche en Écologie Buccale (GREB), Faculté de médecine dentaire, Université Laval, Quebec City, QC, Canada, G1V 0A6
| | - Patrick Lagüe
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC, Canada, G1V 0A6
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6
| | - Steve J. Charette
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, QC, Canada, G1V 0A6
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, QC, Canada, G1V 4G5
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, QC, Canada G1V 0A6
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Fei J, Cui XB, Wang JN, Dong K, Chen SY. ADAR1-Mediated RNA Editing, A Novel Mechanism Controlling Phenotypic Modulation of Vascular Smooth Muscle Cells. Circ Res 2016; 119:463-9. [PMID: 27199464 DOI: 10.1161/circresaha.116.309003] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 05/19/2016] [Indexed: 11/16/2022]
Abstract
RATIONALE Vascular smooth muscle cell (SMC) phenotypic modulation is characterized by the downregulation of SMC contractile genes. Platelet-derived growth factor-BB, a well-known stimulator of SMC phenotypic modulation, downregulates SMC genes via posttranscriptional regulation. The underlying mechanisms, however, remain largely unknown. OBJECTIVE To establish RNA editing as a novel mechanism controlling SMC phenotypic modulation. METHODS AND RESULTS Precursor mRNAs (pre-mRNA) of SMC myosin heavy chain and smooth muscle α-actin were accumulated while their mature mRNAs were downregulated during SMC phenotypic modulation, suggesting an abnormal splicing of the pre-mRNAs. The abnormal splicing resulted from SMC marker pre-mRNA editing that was facilitated by adenosine deaminase acting on RNA 1 (ADAR1), an enzyme converting adenosines to inosines (A→I editing) in RNA sequences. ADAR1 expression inversely correlated with SMC myosin heavy chain and smooth muscle α-actin levels; knockdown of ADAR1 restored SMC myosin heavy chain and smooth muscle α-actin expression in phenotypically modulated SMC, and editase domain mutation diminished the ADAR1-mediated abnormal splicing of SMC marker pre-mRNAs. Moreover, the abnormal splicing/editing of SMC myosin heavy chain and smooth muscle α-actin pre-mRNAs occurred during injury-induced vascular remodeling. Importantly, heterozygous knockout of ADAR1 dramatically inhibited injury-induced neointima formation and restored SMC marker expression, demonstrating a critical role of ADAR1 in SMC phenotypic modulation and vascular remodeling in vivo. CONCLUSIONS Our results unraveled a novel molecular mechanism, that is, pre-mRNA editing, governing SMC phenotypic modulation.
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Affiliation(s)
- Jia Fei
- From the Department of Physiology and Pharmacology, University of Georgia, Athens (J.F., X.-B.C., J.-N.W., K.D., S.-Y.C.); and Institute of Clinical Medicine, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei, China (J.-N.W., S.-Y.C.)
| | - Xiao-Bing Cui
- From the Department of Physiology and Pharmacology, University of Georgia, Athens (J.F., X.-B.C., J.-N.W., K.D., S.-Y.C.); and Institute of Clinical Medicine, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei, China (J.-N.W., S.-Y.C.)
| | - Jia-Ning Wang
- From the Department of Physiology and Pharmacology, University of Georgia, Athens (J.F., X.-B.C., J.-N.W., K.D., S.-Y.C.); and Institute of Clinical Medicine, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei, China (J.-N.W., S.-Y.C.)
| | - Kun Dong
- From the Department of Physiology and Pharmacology, University of Georgia, Athens (J.F., X.-B.C., J.-N.W., K.D., S.-Y.C.); and Institute of Clinical Medicine, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei, China (J.-N.W., S.-Y.C.)
| | - Shi-You Chen
- From the Department of Physiology and Pharmacology, University of Georgia, Athens (J.F., X.-B.C., J.-N.W., K.D., S.-Y.C.); and Institute of Clinical Medicine, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei, China (J.-N.W., S.-Y.C.).
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26
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Lamichhane TN, Arimbasseri AG, Rijal K, Iben JR, Wei FY, Tomizawa K, Maraia RJ. Lack of tRNA-i6A modification causes mitochondrial-like metabolic deficiency in S. pombe by limiting activity of cytosolic tRNATyr, not mito-tRNA. RNA (NEW YORK, N.Y.) 2016; 22:583-96. [PMID: 26857223 PMCID: PMC4793213 DOI: 10.1261/rna.054064.115] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/28/2015] [Indexed: 05/17/2023]
Abstract
tRNA-isopentenyl transferases (IPTases) are highly conserved enzymes that form isopentenyl-N(6)-A37 (i6A37) on subsets of tRNAs, enhancing their translation activity. Nuclear-encoded IPTases modify select cytosolic (cy-) and mitochondrial (mt-) tRNAs. Mutation in human IPTase, TRIT1, causes disease phenotypes characteristic of mitochondrial translation deficiency due to mt-tRNA dysfunction. Deletion of the Schizosaccharomyces pombe IPTase (tit1-Δ) causes slow growth in glycerol, as well as in rapamycin, an inhibitor of TOR kinase that maintains metabolic homeostasis. Schizosaccharomyces pombe IPTase modifies three different cy-tRNAs(Ser) as well as cy-tRNA(Tyr), cy-tRNA(Trp), and mt-tRNA(Trp). We show that lower ATP levels in tit1-Δ relative to tit1(+) cells are also more decreased by an inhibitor of oxidative phosphorylation, indicative of mitochondrial dysfunction. Here we asked if the tit1-Δ phenotypes are due to hypomodification of cy-tRNA or mt-tRNA. A cytosol-specific IPTase that modifies cy-tRNA, but not mt-tRNA, fully rescues the tit1-Δ phenotypes. Moreover, overexpression of cy-tRNAs also rescues the phenotypes, and cy-tRNA(Tyr) alone substantially does so. Bioinformatics indicate that cy-tRNA(Tyr) is most limiting for codon demand in tit1-Δ cells and that the cytosolic mRNAs most loaded with Tyr codons encode carbon metabolilizing enzymes, many of which are known to localize to mitochondria. Thus, S. pombe i6A37 hypomodification-associated metabolic deficiency results from hypoactivity of cy-tRNA, mostly tRNA(Tyr), and unlike human TRIT1-deficiency does not impair mitochondrial translation due to mt-tRNA hypomodification. We discuss species-specific aspects of i6A37. Specifically relevant to mitochondria, we show that its hypermodified version, ms2i6A37 (2-methylthiolated), which occurs on certain mammalian mt-tRNAs (but not cy-tRNAs), is not found in yeast.
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Affiliation(s)
- Tek N Lamichhane
- Section on Molecular and Cell Biology, Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Aneeshkumar G Arimbasseri
- Section on Molecular and Cell Biology, Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Keshab Rijal
- Section on Molecular and Cell Biology, Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - James R Iben
- Molecular Genetics Laboratory, Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Fan Yan Wei
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, 860-0862 Kumamoto, Japan
| | - Kazuhito Tomizawa
- Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, 860-0862 Kumamoto, Japan
| | - Richard J Maraia
- Section on Molecular and Cell Biology, Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA Commissioned Corps, US Public Health Service, Rockville, Maryland 20016, USA
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27
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Leeder WM, Voigt C, Brecht M, Göringer HU. The RNA chaperone activity of the Trypanosoma brucei editosome raises the dynamic of bound pre-mRNAs. Sci Rep 2016; 6:19309. [PMID: 26782631 PMCID: PMC4726059 DOI: 10.1038/srep19309] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/09/2015] [Indexed: 12/27/2022] Open
Abstract
Mitochondrial transcript maturation in African trypanosomes requires an RNA editing reaction that is characterized by the insertion and deletion of U-nucleotides into otherwise non-functional mRNAs. The reaction is catalyzed by editosomes and requires guide (g)RNAs as templates. Recent data demonstrate that the binding of pre-edited mRNAs to editosomes is followed by a chaperone-type RNA remodeling reaction. Here we map the changes in RNA folding using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE). We demonstrate that pre-mRNAs in their free state adopt intricately folded, highly stable 2D-structures. Editosome binding renders the pre-mRNAs to adopt 2D-conformations of reduced stabilities. On average about 30% of the nucleotides in every pre-mRNA are affected with a prevalence for U-nucleotides. The data demonstrate that the chaperone activity acts by increasing the flexibility of U-residues to lower their base-pairing probability. This results in a simplified RNA folding landscape with a reduced energy barrier to facilitate the binding of gRNAs. The data provide a first rational for the enigmatic U-specificity of the editing reaction.
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MESH Headings
- G-Quadruplexes
- Genes, Mitochondrial
- Nucleic Acid Conformation
- Protein Binding
- Protozoan Proteins/metabolism
- RNA Editing
- RNA Precursors/chemistry
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA, Guide, Kinetoplastida/chemistry
- RNA, Guide, Kinetoplastida/genetics
- RNA, Guide, Kinetoplastida/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Protozoan
- RNA-Binding Proteins/metabolism
- Thermodynamics
- Trypanosoma brucei brucei/genetics
- Trypanosoma brucei brucei/metabolism
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Affiliation(s)
- W.-Matthias Leeder
- Molecular Genetics, Darmstadt University of Technology, Schnittspahnstraße 10, 64287 Darmstadt, Germany
| | - Christin Voigt
- Molecular Genetics, Darmstadt University of Technology, Schnittspahnstraße 10, 64287 Darmstadt, Germany
| | - Michael Brecht
- Molecular Genetics, Darmstadt University of Technology, Schnittspahnstraße 10, 64287 Darmstadt, Germany
| | - H. Ulrich Göringer
- Molecular Genetics, Darmstadt University of Technology, Schnittspahnstraße 10, 64287 Darmstadt, Germany
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28
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Crescenzo-Chaigne B, Barbezange C, Frigard V, Poulain D, van der Werf S. Chimeric NP non coding regions between type A and C influenza viruses reveal their role in translation regulation. PLoS One 2014; 9:e109046. [PMID: 25268971 PMCID: PMC4182659 DOI: 10.1371/journal.pone.0109046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 09/01/2014] [Indexed: 12/14/2022] Open
Abstract
Exchange of the non coding regions of the NP segment between type A and C influenza viruses was used to demonstrate the importance not only of the proximal panhandle, but also of the initial distal panhandle strength in type specificity. Both elements were found to be compulsory to rescue infectious virus by reverse genetics systems. Interestingly, in type A influenza virus infectious context, the length of the NP segment 5' NC region once transcribed into mRNA was found to impact its translation, and the level of produced NP protein consequently affected the level of viral genome replication.
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Affiliation(s)
- Bernadette Crescenzo-Chaigne
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, Paris, France
- Unité Mixte de Recherche 3569, Centre National de la Recherche Scientifique, Paris, France
| | - Cyril Barbezange
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, Paris, France
- Unité Mixte de Recherche 3569, Centre National de la Recherche Scientifique, Paris, France
| | - Vianney Frigard
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, Paris, France
- Unité Mixte de Recherche 3569, Centre National de la Recherche Scientifique, Paris, France
| | - Damien Poulain
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, Paris, France
- Unité Mixte de Recherche 3569, Centre National de la Recherche Scientifique, Paris, France
| | - Sylvie van der Werf
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, Paris, France
- Unité Mixte de Recherche 3569, Centre National de la Recherche Scientifique, Paris, France
- Université Paris Diderot Sorbonne Paris Cité, Paris, France
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29
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Conformational entropy of the RNA phosphate backbone and its contribution to the folding free energy. Biophys J 2014; 106:1497-507. [PMID: 24703311 DOI: 10.1016/j.bpj.2014.02.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 01/15/2014] [Accepted: 02/12/2014] [Indexed: 01/16/2023] Open
Abstract
While major contributors to the free energy of RNA tertiary structures such as basepairing, base-stacking, and charge and counterion interactions have been studied extensively, little is known about the intrinsic free energy of the backbone. To assess the magnitude of the entropic strains along the phosphate backbone and their impact on the folding free energy, we have formulated a mathematical treatment for computing the volume of the main-chain torsion-angle conformation space between every pair of nucleobases along any sequence to compute the corresponding backbone entropy. To validate this method, we have compared the computed conformational entropies against a statistical free energy analysis of structures in the crystallographic database from several-thousand backbone conformations between nearest-neighbor nucleobases as well as against extensive computer simulations. Using this calculation, we analyzed the backbone entropy of several ribozymes and riboswitches and found that their entropic strains are highly localized along their sequences. The total entropic penalty due to steric congestions in the backbone for the native fold can be as high as 2.4 cal/K/mol per nucleotide for these medium and large RNAs, producing a contribution to the overall free energy of up to 0.72 kcal/mol per nucleotide. For these RNAs, we found that low-entropy high-strain residues are predominantly located at loops with tight turns and at tertiary interaction platforms with unusual structural motifs.
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30
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Vik ES, Nawaz MS, Strøm Andersen P, Fladeby C, Bjørås M, Dalhus B, Alseth I. Endonuclease V cleaves at inosines in RNA. Nat Commun 2014; 4:2271. [PMID: 23912683 PMCID: PMC3741635 DOI: 10.1038/ncomms3271] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 07/09/2013] [Indexed: 01/05/2023] Open
Abstract
Endonuclease V orthologues are highly conserved proteins found in all kingdoms of life. While the prokaryotic enzymes are DNA repair proteins for removal of deaminated adenosine (inosine) from the genome, no clear role for the eukaryotic counterparts has hitherto been described. Here we report that human endonuclease V (ENDOV) and also Escherichia coli endonuclease V are highly active ribonucleases specific for inosine in RNA. Inosines are normal residues in certain RNAs introduced by specific deaminases. Adenosine-to-inosine editing is essential for proper function of these transcripts and defects are linked to various human disease. Here we show that human ENDOV cleaves an RNA substrate containing inosine in a position corresponding to a biologically important site for deamination in the Gabra-3 transcript of the GABA(A) neurotransmitter. Further, human ENDOV specifically incises transfer RNAs with inosine in the wobble position. This previously unknown RNA incision activity may suggest a role for endonuclease V in normal RNA metabolism.
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Affiliation(s)
- Erik Sebastian Vik
- Department of Microbiology, Oslo University Hospital HF and University of Oslo, Rikshospitalet, PO Box 4950 Nydalen, 0424 Oslo, Norway
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31
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Structural determinants for ligand capture by a class II preQ1 riboswitch. Proc Natl Acad Sci U S A 2014; 111:E663-71. [PMID: 24469808 DOI: 10.1073/pnas.1400126111] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Prequeuosine (preQ1) riboswitches are RNA regulatory elements located in the 5' UTR of genes involved in the biosynthesis and transport of preQ1, a precursor of the modified base queuosine universally found in four tRNAs. The preQ1 class II (preQ1-II) riboswitch regulates preQ1 biosynthesis at the translational level. We present the solution NMR structure and conformational dynamics of the 59 nucleotide Streptococcus pneumoniae preQ1-II riboswitch bound to preQ1. Unlike in the preQ1 class I (preQ1-I) riboswitch, divalent cations are required for high-affinity binding. The solution structure is an unusual H-type pseudoknot featuring a P4 hairpin embedded in loop 3, which forms a three-way junction with the other two stems. (13)C relaxation and residual dipolar coupling experiments revealed interhelical flexibility of P4. We found that the P4 helix and flanking adenine residues play crucial and unexpected roles in controlling pseudoknot formation and, in turn, sequestering the Shine-Dalgarno sequence. Aided by divalent cations, P4 is poised to act as a "screw cap" on preQ1 recognition to block ligand exit and stabilize the binding pocket. Comparison of preQ1-I and preQ1-II riboswitch structures reveals that whereas both form H-type pseudoknots and recognize preQ1 using one A, C, or U nucleotide from each of three loops, these nucleotides interact with preQ1 differently, with preQ1 inserting into different grooves. Our studies show that the preQ1-II riboswitch uses an unusual mechanism to harness exquisite control over queuosine metabolism.
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32
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Crescenzo-Chaigne B, Barbezange C, van der Werf S. The Panhandle formed by influenza A and C virus NS non-coding regions determines NS segment expression. PLoS One 2013; 8:e81550. [PMID: 24348921 PMCID: PMC3858493 DOI: 10.1371/journal.pone.0081550] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 10/23/2013] [Indexed: 11/18/2022] Open
Abstract
Exchange of the extremities of the NS segment of type A and C influenza viruses in reverse genetics systems was used to assess their putative role in type specificity. Restoration of each specific proximal panhandle was mandatory to allow the rescue of viruses with heterotypic extremities. Moreover, the transcription level of the modified segment seemed to be directly affected by the distal panhandle strength.
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Affiliation(s)
- Bernadette Crescenzo-Chaigne
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, Paris, France
- Unité Mixte de Recherche 3569, Centre National de la Recherche Scientifique, Paris, France
- Unité de Génétique Moléculaire des Virus à ARN, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Cyril Barbezange
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, Paris, France
- Unité Mixte de Recherche 3569, Centre National de la Recherche Scientifique, Paris, France
- Unité de Génétique Moléculaire des Virus à ARN, Université Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Sylvie van der Werf
- Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, Paris, France
- Unité Mixte de Recherche 3569, Centre National de la Recherche Scientifique, Paris, France
- Unité de Génétique Moléculaire des Virus à ARN, Université Paris Diderot Sorbonne Paris Cité, Paris, France
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33
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Harrison JG, Zheng YB, Beal PA, Tantillo DJ. Computational approaches to predicting the impact of novel bases on RNA structure and stability. ACS Chem Biol 2013; 8:2354-9. [PMID: 24063428 DOI: 10.1021/cb4006062] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The use of computational modeling techniques to gain insight into nucleobase interactions has been a challenging endeavor to date. Accurate treatment requires the tackling of many challenges but also holds the promise of great rewards. The development of effective computational approaches to predict the binding affinities of nucleobases and analogues can, for example, streamline the process of developing novel nucleobase modifications, which should facilitate the development of new RNAi-based therapeutics. This brief review focuses on available computational approaches to predicting base pairing affinity in RNA-based contexts such as nucleobase-nucleobase interactions in duplexes and nucleobase-protein interactions. The challenges associated with such modeling along with potential future directions for the field are highlighted.
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Affiliation(s)
- Jason G. Harrison
- Department of Chemistry, University of California−Davis, Davis, California 95616, United States
| | - Yvonne B. Zheng
- Department of Chemistry, University of California−Davis, Davis, California 95616, United States
| | - Peter A. Beal
- Department of Chemistry, University of California−Davis, Davis, California 95616, United States
| | - Dean J. Tantillo
- Department of Chemistry, University of California−Davis, Davis, California 95616, United States
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34
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Rios AC, Tor Y. On the Origin of the Canonical Nucleobases: An Assessment of Selection Pressures across Chemical and Early Biological Evolution. Isr J Chem 2013; 53:469-483. [PMID: 25284884 PMCID: PMC4181368 DOI: 10.1002/ijch.201300009] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The native bases of RNA and DNA are prominent examples of the narrow selection of organic molecules upon which life is based. How did nature "decide" upon these specific heterocycles? Evidence suggests that many types of heterocycles could have been present on the early Earth. It is therefore likely that the contemporary composition of nucleobases is a result of multiple selection pressures that operated during early chemical and biological evolution. The persistence of the fittest heterocycles in the prebiotic environment towards, for example, hydrolytic and photochemical assaults, may have given some nucleobases a selective advantage for incorporation into the first informational polymers. The prebiotic formation of polymeric nucleic acids employing the native bases remains, however, a challenging problem to reconcile. Hypotheses have proposed that the emerging RNA world may have included many types of nucleobases. This is supported by the extensive utilization of non-canonical nucleobases in extant RNA and the resemblance of many of the modified bases to heterocycles generated in simulated prebiotic chemistry experiments. Selection pressures in the RNA world could have therefore narrowed the composition of the nucleic acid bases. Two such selection pressures may have been related to genetic fidelity and duplex stability. Considering these possible selection criteria, the native bases along with other related heterocycles seem to exhibit a certain level of fitness. We end by discussing the strength of the N-glycosidic bond as a potential fitness parameter in the early DNA world, which may have played a part in the refinement of the alphabetic bases.
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Affiliation(s)
- Andro C. Rios
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358 (USA), phone: (+1) 8585346401, fax: (+1) 858534 0202
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358 (USA), phone: (+1) 8585346401, fax: (+1) 858534 0202
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35
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Zhu S, Xiang JF, Chen T, Chen LL, Yang L. Prediction of constitutive A-to-I editing sites from human transcriptomes in the absence of genomic sequences. BMC Genomics 2013; 14:206. [PMID: 23537002 PMCID: PMC3637798 DOI: 10.1186/1471-2164-14-206] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 03/21/2013] [Indexed: 02/28/2023] Open
Abstract
Background Adenosine-to-inosine (A-to-I) RNA editing is recognized as a cellular mechanism for generating both RNA and protein diversity. Inosine base pairs with cytidine during reverse transcription and therefore appears as guanosine during sequencing of cDNA. Current approaches of RNA editing identification largely depend on the comparison between transcriptomes and genomic DNA (gDNA) sequencing datasets from the same individuals, and it has been challenging to identify editing candidates from transcriptomes in the absence of gDNA information. Results We have developed a new strategy to accurately predict constitutive RNA editing sites from publicly available human RNA-seq datasets in the absence of relevant genomic sequences. Our approach establishes new parameters to increase the ability to map mismatches and to minimize sequencing/mapping errors and unreported genome variations. We identified 695 novel constitutive A-to-I editing sites that appear in clusters (named “editing boxes”) in multiple samples and which exhibit spatial and dynamic regulation across human tissues. Some of these editing boxes are enriched in non-repetitive regions lacking inverted repeat structures and contain an extremely high conversion frequency of As to Is. We validated a number of editing boxes in multiple human cell lines and confirmed that ADAR1 is responsible for the observed promiscuous editing events in non-repetitive regions, further expanding our knowledge of the catalytic substrate of A-to-I RNA editing by ADAR enzymes. Conclusions The approach we present here provides a novel way of identifying A-to-I RNA editing events by analyzing only RNA-seq datasets. This method has allowed us to gain new insights into RNA editing and should also aid in the identification of more constitutive A-to-I editing sites from additional transcriptomes.
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Affiliation(s)
- Shanshan Zhu
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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36
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Alon S, Mor E, Vigneault F, Church GM, Locatelli F, Galeano F, Gallo A, Shomron N, Eisenberg E. Systematic identification of edited microRNAs in the human brain. Genome Res 2012; 22:1533-40. [PMID: 22499667 PMCID: PMC3409266 DOI: 10.1101/gr.131573.111] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Adenosine-to-inosine (A-to-I) editing modifies RNA transcripts from their genomic blueprint. A prerequisite for this process is a double-stranded RNA (dsRNA) structure. Such dsRNAs are formed as part of the microRNA (miRNA) maturation process, and it is therefore expected that miRNAs are affected by A-to-I editing. Editing of miRNAs has the potential to add another layer of complexity to gene regulation pathways, especially if editing occurs within the miRNA–mRNA recognition site. Thus, it is of interest to study the extent of this phenomenon. Current reports in the literature disagree on its extent; while some reports claim that it may be widespread, others deem the reported events as rare. Utilizing a next-generation sequencing (NGS) approach supplemented by an extensive bioinformatic analysis, we were able to systematically identify A-to-I editing events in mature miRNAs derived from human brain tissues. Our algorithm successfully identified many of the known editing sites in mature miRNAs and revealed 17 novel human sites, 12 of which are in the recognition sites of the miRNAs. We confirmed most of the editing events using in vitro ADAR overexpression assays. The editing efficiency of most sites identified is very low. Similar results are obtained for publicly available data sets of mouse brain-regions tissues. Thus, we find that A-to-I editing does alter several miRNAs, but it is not widespread.
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Affiliation(s)
- Shahar Alon
- Department of Neurobiology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
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37
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Cantara WA, Bilbille Y, Kim J, Kaiser R, Leszczyńska G, Malkiewicz A, Agris PF. Modifications Modulate Anticodon Loop Dynamics and Codon Recognition of E. coli tRNAArg1,2. J Mol Biol 2012; 416:579-97. [DOI: 10.1016/j.jmb.2011.12.054] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Revised: 12/13/2011] [Accepted: 12/27/2011] [Indexed: 10/14/2022]
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38
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Vendeix FAP, Murphy FV, Cantara WA, Leszczyńska G, Gustilo EM, Sproat B, Malkiewicz A, Agris PF. Human tRNA(Lys3)(UUU) is pre-structured by natural modifications for cognate and wobble codon binding through keto-enol tautomerism. J Mol Biol 2011; 416:467-85. [PMID: 22227389 DOI: 10.1016/j.jmb.2011.12.048] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 12/14/2011] [Accepted: 12/23/2011] [Indexed: 10/14/2022]
Abstract
Human tRNA(Lys3)(UUU) (htRNA(Lys3)(UUU)) decodes the lysine codons AAA and AAG during translation and also plays a crucial role as the primer for HIV-1 (human immunodeficiency virus type 1) reverse transcription. The posttranscriptional modifications 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)U(34)), 2-methylthio-N(6)-threonylcarbamoyladenosine (ms(2)t(6)A(37)), and pseudouridine (Ψ(39)) in the tRNA's anticodon domain are critical for ribosomal binding and HIV-1 reverse transcription. To understand the importance of modified nucleoside contributions, we determined the structure and function of this tRNA's anticodon stem and loop (ASL) domain with these modifications at positions 34, 37, and 39, respectively (hASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37);Ψ(39)). Ribosome binding assays in vitro revealed that the hASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37);Ψ(39) bound AAA and AAG codons, whereas binding of the unmodified ASL(Lys3)(UUU) was barely detectable. The UV hyperchromicity, the circular dichroism, and the structural analyses indicated that Ψ(39) enhanced the thermodynamic stability of the ASL through base stacking while ms(2)t(6)A(37) restrained the anticodon to adopt an open loop conformation that is required for ribosomal binding. The NMR-restrained molecular-dynamics-derived solution structure revealed that the modifications provided an open, ordered loop for codon binding. The crystal structures of the hASL(Lys3)(UUU)-mcm(5)s(2)U(34);ms(2)t(6)A(37);Ψ(39) bound to the 30S ribosomal subunit with each codon in the A site showed that the modified nucleotides mcm(5)s(2)U(34) and ms(2)t(6)A(37) participate in the stability of the anticodon-codon interaction. Importantly, the mcm(5)s(2)U(34)·G(3) wobble base pair is in the Watson-Crick geometry, requiring unusual hydrogen bonding to G in which mcm(5)s(2)U(34) must shift from the keto to the enol form. The results unambiguously demonstrate that modifications pre-structure the anticodon as a key prerequisite for efficient and accurate recognition of cognate and wobble codons.
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Affiliation(s)
- Franck A P Vendeix
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA.
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Allnér O, Nilsson L. Nucleotide modifications and tRNA anticodon-mRNA codon interactions on the ribosome. RNA (NEW YORK, N.Y.) 2011; 17:2177-2188. [PMID: 22028366 PMCID: PMC3222130 DOI: 10.1261/rna.029231.111] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 09/14/2011] [Indexed: 05/31/2023]
Abstract
We have carried out molecular dynamics simulations of the tRNA anticodon and mRNA codon, inside the ribosome, to study the effect of the common tRNA modifications cmo(5)U34 and m(6)A37. In tRNA(Val), these modifications allow all four nucleotides to be successfully read at the wobble position in a codon. Previous data suggest that entropic effects are mainly responsible for the extended reading capabilities, but detailed mechanisms have remained unknown. We have performed a wide range of simulations to elucidate the details of these mechanisms at the atomic level and quantify their effects: extensive free energy perturbation coupled with umbrella sampling, entropy calculations of tRNA (free and bound to the ribosome), and thorough structural analysis of the ribosomal decoding center. No prestructuring effect on the tRNA anticodon stem-loop from the two modifications could be observed, but we identified two mechanisms that may contribute to the expanded decoding capability by the modifications: The further reach of the cmo(5)U34 allows an alternative outer conformation to be formed for the noncognate base pairs, and the modification results in increased contacts between tRNA, mRNA, and the ribosome.
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Affiliation(s)
- Olof Allnér
- Department of Biosciences and Nutrition, Center for Biosciences, Karolinska Institutet, SE-141 83 Huddinge, Sweden
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Center for Biosciences, Karolinska Institutet, SE-141 83 Huddinge, Sweden
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The human mitochondrial tRNAMet: structure/function relationship of a unique modification in the decoding of unconventional codons. J Mol Biol 2010; 406:257-74. [PMID: 21168417 DOI: 10.1016/j.jmb.2010.11.042] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 11/18/2010] [Accepted: 11/22/2010] [Indexed: 11/21/2022]
Abstract
Human mitochondrial mRNAs utilize the universal AUG and the unconventional isoleucine AUA codons for methionine. In contrast to translation in the cytoplasm, human mitochondria use one tRNA, hmtRNA(Met)(CAU), to read AUG and AUA codons at both the peptidyl- (P-), and aminoacyl- (A-) sites of the ribosome. The hmtRNA(Met)(CAU) has a unique post-transcriptional modification, 5-formylcytidine, at the wobble position 34 (f(5)C(34)), and a cytidine substituting for the invariant uridine at position 33 of the canonical U-turn in tRNAs. The structure of the tRNA anticodon stem and loop domain (hmtASL(Met)(CAU)), determined by NMR restrained molecular modeling, revealed how the f(5)C(34) modification facilitates the decoding of AUA at the P- and the A-sites. The f(5)C(34) defined a reduced conformational space for the nucleoside, in what appears to have restricted the conformational dynamics of the anticodon bases of the modified hmtASL(Met)(CAU). The hmtASL(Met)(CAU) exhibited a C-turn conformation that has some characteristics of the U-turn motif. Codon binding studies with both Escherichia coli and bovine mitochondrial ribosomes revealed that the f(5)C(34) facilitates AUA binding in the A-site and suggested that the modification favorably alters the ASL binding kinetics. Mitochondrial translation by many organisms, including humans, sometimes initiates with the universal isoleucine codons AUU and AUC. The f(5)C(34) enabled P-site codon binding to these normally isoleucine codons. Thus, the physicochemical properties of this one modification, f(5)C(34), expand codon recognition from the traditional AUG to the non-traditional, synonymous codons AUU and AUC as well as AUA, in the reassignment of universal codons in the mitochondria.
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Cantara WA, Crain PF, Rozenski J, McCloskey JA, Harris KA, Zhang X, Vendeix FAP, Fabris D, Agris PF. The RNA Modification Database, RNAMDB: 2011 update. Nucleic Acids Res 2010; 39:D195-201. [PMID: 21071406 PMCID: PMC3013656 DOI: 10.1093/nar/gkq1028] [Citation(s) in RCA: 636] [Impact Index Per Article: 45.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Since its inception in 1994, The RNA Modification Database (RNAMDB, http://rna-mdb.cas.albany.edu/RNAmods/) has served as a focal point for information pertaining to naturally occurring RNA modifications. In its current state, the database employs an easy-to-use, searchable interface for obtaining detailed data on the 109 currently known RNA modifications. Each entry provides the chemical structure, common name and symbol, elemental composition and mass, CA registry numbers and index name, phylogenetic source, type of RNA species in which it is found, and references to the first reported structure determination and synthesis. Though newly transferred in its entirety to The RNA Institute, the RNAMDB continues to grow with two notable additions, agmatidine and 8-methyladenosine, appended in the last year. The RNA Modification Database is staying up-to-date with significant improvements being prepared for inclusion within the next year and the following year. The expanded future role of The RNA Modification Database will be to serve as a primary information portal for researchers across the entire spectrum of RNA-related research.
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Affiliation(s)
- William A Cantara
- The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY 12222, USA
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