Untranslated Region of Mrnas As a Site for Ribozyme Cleavage-Dependent Processing and Control in Bacteria
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Intronic Mir-26B Controls Neuronal Differentiation by Repressing Its Host Transcript, Ctdsp2
Downloaded from genesdev.cshlp.org on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press RESEARCH COMMUNICATION CTDSPL. As part of the REST complex, these enzymes Intronic miR-26b controls dephosphorylate the C-terminal domain (CTD) of RNA neuronal differentiation polymerase II (PolII) and thereby inhibit the expression of genes that have an RE1 signature sequence (Yeo et al. by repressing its host 2005; Visvanathan et al. 2007). During neural fate com- ctdsp2 mitment and terminal differentiation, the REST/CTDSP transcript, pathway is gradually inactivated to allow the expression Holger Dill,1 Bastian Linder,1 Alexander Fehr,2 of RE1-containing genes (Ballas et al. 2005; Yeo et al. 3 2005; Visvanathan et al. 2007). Neuronal gene activation and Utz Fischer in mice and humans is known to depend on the action of Department of Biochemistry, Theodor Boveri-Institute, miR-124, which prevents expression of CTDSPs (Lim University of Wu¨ rzburg, D-97074 Wu¨ rzburg, Germany et al. 2005; Conaco et al. 2006; Visvanathan et al. 2007). However, as shown in mice, the neuron-specific miR-124 Differentiation of neural stem cells (NSCs) to neurons is itself repressed by the REST/CTDSP pathway, since all of its loci contain an RE1 (Conaco et al. 2006). As mRNAs requires the activation of genes controlled by the re- often are under the control of a collection of microRNAs pressor element 1 (RE1) silencing transcription factor (miRNAs) (Krek et al. 2005), we therefore hypothesized (REST)/neuron-restrictive silencer factor (NRSF) protein that additional miRNAs might be involved in the regu- complex. Important components of REST/NRSF are phos- lation of CTDSP activity. -
Active State of the Twister Ribozyme in Solution Predicted from Molecular Simulation Colin S
Article pubs.acs.org/JACS Ribozyme Catalysis with a Twist: Active State of the Twister Ribozyme in Solution Predicted from Molecular Simulation Colin S. Gaines and Darrin M. York* Center for Integrative Proteomics Research and Department of Chemistry & Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, New Jersey 08854-8076, United States *S Supporting Information ABSTRACT: We present results from molecular dynamics simulations and free energy calculations of the twister ribozyme at different stages along the reaction path to gain insight into its mechanism. The results, together with recent biochemical experiments, provide support for a mechanism involving general-acid catalysis by a conserved adenine residue in the active site. Although adenine has been previously implicated as a general acid acting through the N1 position in other ribozymes such as the hairpin and VS ribozymes, in the twister ribozyme there may be a twist. Biochemical experiments suggest that general acid catalysis may occur through the N3 position, which has never before been implicated in this role; however, currently, there is a lack of a detailed structural model for the active state of the twister ribozyme in solution that is consistent with these and other experiments. Simulations in a crystalline environment reported here are consistent with X-ray crystallographic data, and suggest that crystal packing contacts trap the RNA in an inactive conformation with U-1 in an extruded state that is incompatible with an in-line attack to the scissile phosphate. Simulations in solution, on the other hand, reveal this region to be dynamic and able to adopt a conformation where U-1 is stacked with G33. -
Twister Ribozymes As Highly Versatile Expression Platforms for Artificial Riboswitches
ARTICLE Received 18 Feb 2016 | Accepted 5 Aug 2016 | Published 27 Sep 2016 DOI: 10.1038/ncomms12834 OPEN Twister ribozymes as highly versatile expression platforms for artificial riboswitches Michele Felletti1,2, Julia Stifel1,2, Lena A. Wurmthaler1,2, Sophie Geiger1 &Jo¨rg S. Hartig1,2 The utilization of ribozyme-based synthetic switches in biotechnology has many advantages such as an increased robustness due to in cis regulation, small coding space and a high degree of modularity. The report of small endonucleolytic twister ribozymes provides new oppor- tunities for the development of advanced tools for engineering synthetic genetic switches. Here we show that the twister ribozyme is distinguished as an outstandingly flexible expression platform, which in conjugation with three different aptamer domains, enables the construction of many different one- and two-input regulators of gene expression in both bacteria and yeast. Besides important implications in biotechnology and synthetic biology, the observed versatility in artificial genetic control set-ups hints at possible natural roles of this widespread ribozyme class. 1 Department of Chemistry, University of Konstanz, Universita¨tsstrae 10, 78457 Konstanz, Germany. 2 Konstanz Research School Chemical Biology (Kors-CB), University of Konstanz, Universita¨tsstrae 10, 78457 Konstanz, Germany. Correspondence and requests for materials should be addressed to J.S.H. (email: [email protected]). NATURE COMMUNICATIONS | 7:12834 | DOI: 10.1038/ncomms12834 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms12834 he family of small endonucleolytic ribozymes is composed organization suggests regulatory functions for the variable of RNA motifs of 50–150 nucleotides (nt) length with domains observed in positions P1 and P5 in several naturally Tintrinsic RNA cleavage activity1. -
Light-Controlled Twister Ribozyme with Single-Molecule Detection Resolves RNA Function in Time and Space
Light-controlled twister ribozyme with single-molecule detection resolves RNA function in time and space Arthur Kormana,1,2, Huabing Sunb,1,3, Boyang Huac, Haozhe Yangb, Joseph N. Capilatob, Rakesh Paulb,4, Subrata Panjad,5, Taekjip Hac,e,f, Marc M. Greenbergb,6, and Sarah A. Woodsond,6 aCell, Molecular, Developmental Biology and Biophysics Program, Johns Hopkins University, Baltimore, MD 21218; bDepartment of Chemistry, Johns Hopkins University, Baltimore, MD 21218; cDepartment of Biophysics and Biochemistry, Johns Hopkins University, Baltimore, MD 21205-2185; dT. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218; eDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218; and fHoward Hughes Medical Institute, Johns Hopkins University, Baltimore, MD 21205 Edited by Michael F. Summers, University of Maryland, Baltimore County, Baltimore, MD, and approved April 3, 2020 (received for review February 22, 2020) Small ribozymes such as Oryza sativa twister spontaneously cleave which limits their use in dynamics experiments (13). Photosolvolysis their own RNA when the ribozyme folds into its active conforma- reactions, such as those involving p-hydroxyphenacyl protecting tion. The coupling between twister folding and self-cleavage has groups (e.g., ref. 1 and Fig. 1A), release their cargo in less than one been difficult to study, however, because the active ribozyme rap- microsecond (13) and should be useful for probing processes oc- idly converts to product. Here, we describe the synthesis of a pho- curring on the submillisecond timescale. We previously employed tocaged nucleotide that releases guanosine within microseconds a UV-activated variant of 1 to temporally modulate RNA base upon photosolvolysis with blue light. -
Synthesis of Orthogonal Transcription- Translation Networks
Synthesis of orthogonal transcription- translation networks Wenlin An and Jason W. Chin1 Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom Edited by Susan Gottesman, National Institutes of Health, Bethesda, MD, and approved April 2, 2009 (received for review January 11, 2009) Orthogonal, parallel and independent, systems are one key foun- O-ribosomes for the translation of an O-mRNA arises from the dation for synthetic biology. The synthesis of orthogonal systems altered 16S rRNA in the O-ribosome that recognizes an altered that are uncoupled from evolutionary constraints, and selectively Shine-Dalgarno sequence in the leader sequence of the O-mRNA abstracted from cellular regulation, is an emerging approach to in the initiation phase of translation (12). In previous work O- making biology more amenable to engineering. Here, we combine ribosomes have been evolved that decode genetic information in orthogonal transcription by T7 RNA polymerase and translation by orthogonal mRNAs in new ways. In combination with orthogonal orthogonal ribosomes (O-ribosomes), creating an orthogonal gene aminoacyl-tRNA synthetases and tRNAs that recognize unnatural expression pathway in Escherichia coli. We design and implement amino acids the evolved O-ribosomes have allowed us to begin to compact, orthogonal gene expression networks. In particular we undo the ‘‘frozen accident’’ of the natural genetic code and direct focus on creating transcription–translation feed-forward loops the efficient incorporation of unnatural amino acids into proteins (FFLs). The transcription–translation FFLs reported cannot be cre- encoded on O-mRNAs (13, 14). O-ribosomes have also been used ated by using the cells’ gene expression machinery and introduce to create new translational Boolean logic functions that would not information-processing delays on the order of hours into gene be possible to create by using the essential cellular ribosome (15) expression. -
Coupling Between Conformational Dynamics and Catalytic Function at the Active Site of the Lead-Dependent Ribozyme
Downloaded from rnajournal.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Coupling between conformational dynamics and catalytic function at the active site of the lead-dependent ribozyme NEIL A. WHITE,1,3 MINAKO SUMITA,1,4 VICTOR E. MARQUEZ,2 and CHARLES G. HOOGSTRATEN1 1Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA 2Chemical Biology Laboratory, Molecular Discovery Program, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland 21702, USA ABSTRACT In common with other self-cleaving RNAs, the lead-dependent ribozyme (leadzyme) undergoes dynamic fluctuations to a chemically activated conformation. We explored the connection between conformational dynamics and self-cleavage func- tion in the leadzyme using a combination of NMR spin-relaxation analysis of ribose groups and conformational restriction via chemical modification. The functional studies were performed with a North-methanocarbacytidine modification that prevents fluctuations to C2′′′′′-endo conformations while maintaining an intact 2′′′′′-hydroxyl nucleophile. Spin-relaxation data demonstrate that the active-site Cyt-6 undergoes conformational exchange attributed to sampling of a minor C2′′′′′- endo state with an exchange lifetime on the order of microseconds to tens of microseconds. A conformationally restricted species in which the fluctuations to the minor species are interrupted shows a drastic decrease in self-cleavage activity. Taken together, these data indicate that dynamic sampling of a minor species at the active site of this ribozyme, and likely of related naturally occurring motifs, is strongly coupled to catalytic function. The combination of NMR dynamics analysis with functional probing via conformational restriction is a general methodology for dissecting dynamics-function relation- ships in RNA. -
A Small Nucleolar RNA Is Processed from an Intron of the Human Gene Encoding Ribosomal Protein $3
Downloaded from genesdev.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press A small nucleolar RNA is processed from an intron of the human gene encoding ribosomal protein $3 Kazimierz Tyc Tycowski, Mei-Di Shu, and Joan A. Steitz Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, Connecticut 06536-0812 USA A human small nucleolar RNA, identified previously in HeLa cells by anti-fibrillarin autoantibody precipitation and termed RNA X, has been characterized. It comprises two uridine-rich variants (148 and 146 nucleotides}, which we refer to as snRNA U15A and U15B. Secondary structure models predict for both variants a U15-specific stem-loop structure, as well as a new structural motif that contains conserved sequences and can also be recognized in the other fibrillarin-associated nucleolar snRNAs, U3, U14, and RNA Y. The single-copy gene for human U15A has been found unexpectedly to reside in intron 1 of the ribosomal protein $3 gene; the U15A sequence appears on the same strand as the $3 mRNA and does not exhibit canonical transcription signals for nuclear RNA polymerases. U15A RNA is processed in vitro from $3 intron 1 transcripts to yield the correct 5' end with a 5'-monophosphate; the in vitro system requires ATP for 3' cleavage, which occurs a few nucleotides downstream of the mature end. The production of a single primary transcript specifying the mRNA for a ribosomal or nucleolar protein and a nucleolar snRNA may constitute a general mechanism for balancing the levels of nucleolar components in vertebrate cells. -
Detecting Rna Folding and Dynamics of the Twister Ribozyme and The
DETECTING RNA FOLDING AND DYNAMICS OF THE TWISTER RIBOZYME AND THE 16S RIBOSOMAL RNA by Arthur Korman A dissertation submitted to Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland October 2019 © 2019 Arthur Korman All Rights Reserved Abstract Ribozymes are ribonucleic acid (RNA) enzymes capable of catalyzing chemical reactions. Their ability to catalyze reactions is dependent on the formation of proper secondary and tertiary folds. RNA folding begins as the nascent RNA is being synthesized. Structures that are formed early by the 5′ RNA will rearrange, allowing for more mature folds to take hold once the full-length RNA is synthesized. The final fold is the result of constant shifts in RNA structure as the RNA travels through its rugged folding pathway, until the full RNA has been synthesized and the RNA has reached its thermodynamically stable structure. In this dissertation, the folding dynamics of two RNAs, the bacterial 16S ribosomal RNA (rRNA) and the twister ribozyme, are studied. The 16S rRNA undergoes many conformational changes during 30S ribosome assembly, including a critical structural rearrangement during late stage of 30S subunit biogenesis between two competing structures, helix 1 and a hypothesized alternative helix 1. Using biochemical and analytical techniques, helix switching that occurs between the competing helical structures during 30S subunit reconstitution is examined. Unlike the large 16S rRNA, the Twister ribozyme is a small RNA that undergoes dynamic structural changes required for self-scission. The folding dynamics of twister RNA were measured in real time using single molecule Förster resonance energy transfer (smFRET). -
Rna Full Form in Telecom
Rna Full Form In Telecom Cantabrigian and juristic Albert never decorticated syne when Walter lute his villains. Christof is sclerotized and pettifogged stochastically while overpriced Laurens bronzings and unifies. Is Jake congenial or bated when slaughters some quadriremes pinions invidiously? Health department full form clusters in isolation measures is often target. Transmission owner plans are huge developments in. And communications Routing and switching Smart grid Telecom VoIP. To maintain on long-term reliability of the BPTF these additional resources must be readily available height in. RNA What does RNA mean Slangorg. Acronyms and Abbreviations of Computer Technology and. The telecom services, forms base pairing. In personal information is for all degradation. RNA proteins and carbohydrates containers multi-head scales frying pans g. Department of Informatics and Telecommunications Postgraduate Program. RNA is the acronym for ribonucleic acid RNA is crazy vital molecule found as your cells and lid is arrange for life Pieces of RNA are used to construct proteins inside then your body so let new cell growth may use place. RT may rise to Contents 1 Arts and media 2 Science and technology 21 Biology and medicine 22 Computing and telecommunications 23 Other. The SIM was initially recognized and declared by the European Telecommunication Standards Institute Function of SIM Card SIM card stores a quote of information. Each guess you're left scouring the internet for the meaning of stuff set of letters. It nuclein because failures can form a billion years service providers have glorified their customers. In a mix in case resources below guidelines at daytona international level agreements that emerges from telecom in this point, but posits that showcases all degradation. -
Light-Controlled Twister Ribozyme with Single-Molecule Detection Resolves RNA Function in Time and Space
Light-controlled twister ribozyme with single-molecule detection resolves RNA function in time and space Arthur Kormana,1,2, Huabing Sunb,1,3, Boyang Huac, Haozhe Yangb, Joseph N. Capilatob, Rakesh Paulb,4, Subrata Panjad,5, Taekjip Hac,e,f, Marc M. Greenbergb,6, and Sarah A. Woodsond,6 aCell, Molecular, Developmental Biology and Biophysics Program, Johns Hopkins University, Baltimore, MD 21218; bDepartment of Chemistry, Johns Hopkins University, Baltimore, MD 21218; cDepartment of Biophysics and Biochemistry, Johns Hopkins University, Baltimore, MD 21205-2185; dT. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218; eDepartment of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218; and fHoward Hughes Medical Institute, Johns Hopkins University, Baltimore, MD 21205 Edited by Michael F. Summers, University of Maryland, Baltimore County, Baltimore, MD, and approved April 3, 2020 (received for review February 22, 2020) Small ribozymes such as Oryza sativa twister spontaneously cleave which limits their use in dynamics experiments (13). Photosolvolysis their own RNA when the ribozyme folds into its active conforma- reactions, such as those involving p-hydroxyphenacyl protecting tion. The coupling between twister folding and self-cleavage has groups (e.g., ref. 1 and Fig. 1A), release their cargo in less than one been difficult to study, however, because the active ribozyme rap- microsecond (13) and should be useful for probing processes oc- idly converts to product. Here, we describe the synthesis of a pho- curring on the submillisecond timescale. We previously employed tocaged nucleotide that releases guanosine within microseconds a UV-activated variant of 1 to temporally modulate RNA base upon photosolvolysis with blue light. -
Review Chemistry and Biology of Self-Cleaving Ribozymes Randi M
TIBS 1181 No. of Pages 14 Review Chemistry and Biology of Self-Cleaving Ribozymes Randi M. Jimenez,1 Julio A. Polanco,1 and Andrej Lupták1,2,3,* Self-cleaving ribozymes were discovered 30 years ago, but their biological Trends fi distribution and catalytic mechanisms are only beginning to be de ned. Each Self-cleaving ribozymes are distributed ribozyme family is defined by a distinct structure, with unique active sites throughout all branches of life. Cur- accelerating the same transesterification reaction across the families. Biochem- rently, there are nine distinct structural motifs that promote self-scission in ical studies show that general acid-base catalysis is the most common mecha- nature. nism of self-cleavage, but metal ions and metabolites can be used as cofactors. The six self-cleaving ribozymes that Ribozymes have been discovered in highly diverse genomic contexts through- have been investigated mechanistically out nature, from viroids to vertebrates. Their biological roles include self- all appear to use a general acid-base scission during rolling-circle replication of RNA genomes, co-transcriptional mechanism for catalysis. Magnesium, or another divalent metal ion, is largely processing of retrotransposons, and metabolite-dependent gene expression used to stabilize the tertiary structures regulation in bacteria. Other examples, including highly conserved mammalian of these ribozymes. ribozymes, suggest that many new biological roles are yet to be discovered. The broad distribution of self-cleaving ribozymes suggests several biological Guiding Principles for Ribozyme Exploration roles. The known functions include RNA processing during rolling-circle Small nucleolytic ribozymes carry out site-specific phosphodiester scission without the need for replication of single-stranded subviral protein chaperones or enzymes. -
KINETICS, THERMODYNAMICS, and DYNAMICS of RIBOZYMES By
KINETICS, THERMODYNAMICS, AND DYNAMICS OF RIBOZYMES By Neil Andrew White A DISSERTATION Submitted to Michigan State University In partial fulfillment of requirements For the degree of Biochemistry and Molecular Biology—Doctor of Philosophy 2016 ABSTRACT KINETICS, THERMODYNAMICS, AND DYNAMICS OF RIBOZYMES By Neil Andrew White RNA transcribed from DNA can be divided into two groups: RNA that codes for protein and RNA that does not code for protein, or so-called non-coding RNA. Non-coding RNA can be further divided into several classes based on function. Non-coding RNAs perform a wide array of functions in living organisms, from gene regulation, to scaffolding, to catalysis. It is amazing that despite RNA having only four, chemically-similar monomers it can have such important, wide-ranging functions. Proteins which also perform wide-ranging functions in organisms have twenty common monomers that are vastly more diverse in terms of chemical or functional groups and structure. How non-coding RNA, specifically catalytic RNA or ribozymes, overcome this inherent lack of chemical and structural diversity to have impressive, intricate structures and function is the focus of this thesis. It is important to study how ribozymes are able to form intricate structure and execute function. They also have potential therapeutic applications, to control RNA viruses like HIV and oncogene transcripts, due to their ability to cleave RNA. Also, they provide a window back to a time described by the RNA World Hypothesis, a time before DNA and proteins, when RNA performed self-replication. Ribozymes overcomes its lack of diversity in monomers by being a dynamic polymer.