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Fry M. The discovery of archaea: from observed anomaly to consequential restructuring of the phylogenetic tree. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2024; 46:16. [PMID: 38530473 PMCID: PMC10965645 DOI: 10.1007/s40656-024-00616-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 02/14/2024] [Indexed: 03/28/2024]
Abstract
Observational and experimental discoveries of new factual entities such as objects, systems, or processes, are major contributors to some advances in the life sciences. Yet, whereas discovery of theories was extensively deliberated by philosophers of science, very little philosophical attention was paid to the discovery of factual entities. This paper examines historical and philosophical aspects of the experimental discovery by Carl Woese of archaea, prokaryotes that comprise one of the three principal domains of the phylogenetic tree. Borrowing Kuhn's terminology, this discovery of a major biological entity was made during a 'normal science' project of building molecular taxonomy for prokaryotes. Unexpectedly, however, an observed anomaly instigated the discovery of archaea. Substantiation of the existence of the new archaeal entity and consequent reconstruction of the phylogenetic tree prompted replacement of a long-held model of a prokarya and eukarya bipartite tree of life by a new model of a tripartite tree comprising of bacteria, archaea, and eukarya. This paper explores the history and philosophical implications of the progression of Woese's project from normal science to anomaly-instigated model-changing discovery. It is also shown that the consequential discoveries of RNA splicing and of ribozymes were similarly prompted by unexpected irregularities during normal science activities. It is thus submitted that some discoveries of factual biological entities are triggered by unforeseen observational or experimental anomalies.
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Affiliation(s)
- Michael Fry
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Efron St., Bat Galim, POB 9649, Haifa, 31096, Israel.
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2
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Lyerly HK. Self-replicating messenger RNA based cancer immunotherapy. Cancer Gene Ther 2023:10.1038/s41417-023-00619-w. [PMID: 37147521 PMCID: PMC10161175 DOI: 10.1038/s41417-023-00619-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/20/2023] [Accepted: 04/18/2023] [Indexed: 05/07/2023]
Affiliation(s)
- Herbert Kim Lyerly
- Center for Applied Therapeutics, Duke University School of Medicine, Durham, NC, 27710, USA.
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3
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Plattner H. Ciliate Research. From Myth to Trendsetting Science. J Eukaryot Microbiol 2022; 69:e12926. [PMID: 35608570 DOI: 10.1111/jeu.12926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/18/2022] [Accepted: 05/18/2022] [Indexed: 11/28/2022]
Abstract
This special issue of the Journal of Eukaryotic Microbiology (JEM) summarizes achievements obtained by generations of researchers with ciliates in widely different disciplines. In fact, ciliates range among the first cells seen under the microscope centuries ago. Their beauty made them an object of scientia amabilis and their manifold reactions made them attractive for college experiments and finally challenged causal analyses at the cellular level. Some of this work was honored by a Nobel Prize. Some observations yielded a baseline for additional novel discoveries, occasionally facilitated by specific properties of some ciliates. This also offers some advantage in the exploration of closely related parasites (malaria). Articles contributed here by colleagues from all over the world encompass a broad spectrum of ciliate life, from genetics to evolution, from molecular cell biology to ecology, from intercellular signaling to epigenetics etc. This introductory chapter, largely based on my personal perception, aims at integrating work presented in this special issue of JEM into a broader historical context up to current research.
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Askenase PW. Ancient Evolutionary Origin and Properties of Universally Produced Natural Exosomes Contribute to Their Therapeutic Superiority Compared to Artificial Nanoparticles. Int J Mol Sci 2021; 22:1429. [PMID: 33572657 PMCID: PMC7866973 DOI: 10.3390/ijms22031429] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022] Open
Abstract
Extracellular vesicles (EVs), such as exosomes, are newly recognized fundamental, universally produced natural nanoparticles of life that are seemingly involved in all biologic processes and clinical diseases. Due to their universal involvements, understanding the nature and also the potential therapeutic uses of these nanovesicles requires innovative experimental approaches in virtually every field. Of the EV group, exosome nanovesicles and larger companion micro vesicles can mediate completely new biologic and clinical processes dependent on the intercellular transfer of proteins and most importantly selected RNAs, particularly miRNAs between donor and targeted cells to elicit epigenetic alterations inducing functional cellular changes. These recipient acceptor cells are nearby (paracrine transfers) or far away after distribution via the circulation (endocrine transfers). The major properties of such vesicles seem to have been conserved over eons, suggesting that they may have ancient evolutionary origins arising perhaps even before cells in the primordial soup from which life evolved. Their potential ancient evolutionary attributes may be responsible for the ability of some modern-day exosomes to withstand unusually harsh conditions, perhaps due to unique membrane lipid compositions. This is exemplified by ability of the maternal milk exosomes to survive passing the neonatal acid/enzyme rich stomach. It is postulated that this resistance also applies to their durable presence in phagolysosomes, thus suggesting a unique intracellular release of their contained miRNAs. A major discussed issue is the generally poorly realized superiority of these naturally evolved nanovesicles for therapies when compared to human-engineered artificial nanoparticles, e.g., for the treatment of diseases like cancers.
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Affiliation(s)
- Phillip W Askenase
- Department of Internal Medicine, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
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5
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Scossa F, Fernie AR. The evolution of metabolism: How to test evolutionary hypotheses at the genomic level. Comput Struct Biotechnol J 2020; 18:482-500. [PMID: 32180906 PMCID: PMC7063335 DOI: 10.1016/j.csbj.2020.02.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 01/21/2023] Open
Abstract
The origin of primordial metabolism and its expansion to form the metabolic networks extant today represent excellent systems to study the impact of natural selection and the potential adaptive role of novel compounds. Here we present the current hypotheses made on the origin of life and ancestral metabolism and present the theories and mechanisms by which the large chemical diversity of plants might have emerged along evolution. In particular, we provide a survey of statistical methods that can be used to detect signatures of selection at the gene and population level, and discuss potential and limits of these methods for investigating patterns of molecular adaptation in plant metabolism.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), Via Ardeatina 546, 00178 Rome, Italy
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
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6
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Duan J, Wang X, Kizer ME. Biotechnological and Therapeutic Applications of Natural Nucleic Acid Structural Motifs. Top Curr Chem (Cham) 2020; 378:26. [PMID: 32067108 DOI: 10.1007/s41061-020-0290-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/11/2020] [Indexed: 11/28/2022]
Abstract
Genetic information and the blueprint of life are stored in the form of nucleic acids. The primary sequence of DNA, read from the canonical double helix, provides the code for RNA and protein synthesis. Yet these already-information-rich molecules have higher-order structures which play critical roles in transcription and translation. Uncovering the sequences, parameters, and conditions which govern the formation of these structural motifs has allowed researchers to study them and to utilize them in biotechnological and therapeutic applications in vitro and in vivo. This review covers both DNA and RNA structural motifs found naturally in biological systems including catalytic nucleic acids, non-coding RNA, aptamers, G-quadruplexes, i-motifs, and Holliday junctions. For each category, an overview of the structural characteristics, biological prevalence, and function will be discussed. The biotechnological and therapeutic applications of these structural motifs are highlighted. Future perspectives focus on the addition of proteins and unnatural modifications to enhance structural stability for greater applicability.
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Affiliation(s)
- Jinwei Duan
- Department of Chemistry and Materials Science, College of Sciences, Chang'an University, Xi'an, 710064, Shaanxi, People's Republic of China.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Xing Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Megan E Kizer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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Dexter JP, Prabakaran S, Gunawardena J. A Complex Hierarchy of Avoidance Behaviors in a Single-Cell Eukaryote. Curr Biol 2019; 29:4323-4329.e2. [PMID: 31813604 DOI: 10.1016/j.cub.2019.10.059] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/21/2019] [Accepted: 10/29/2019] [Indexed: 11/29/2022]
Abstract
Complex behavior is associated with animals with nervous systems, but decision-making and learning also occur in non-neural organisms [1], including singly nucleated cells [2-5] and multi-nucleate synctia [6-8]. Ciliates are single-cell eukaryotes, widely dispersed in aquatic habitats [9], with an extensive behavioral repertoire [10-13]. In 1906, Herbert Spencer Jennings [14, 15] described in the sessile ciliate Stentor roeseli a hierarchy of responses to repeated stimulation, which are among the most complex behaviors reported for a singly nucleated cell [16, 17]. These results attracted widespread interest [18, 19] and exert continuing fascination [7, 20-22] but were discredited during the behaviorist orthodoxy by claims of non-reproducibility [23]. These claims were based on experiments with the motile ciliate Stentor coeruleus. We acquired and maintained the correct organism in laboratory culture and used micromanipulation and video microscopy to confirm Jennings' observations. Despite significant individual variation, not addressed by Jennings, S. roeseli exhibits avoidance behaviors in a characteristic hierarchy of bending, ciliary alteration, contractions, and detachment, which is distinct from habituation or conditioning. Remarkably, the choice of contraction versus detachment is consistent with a fair coin toss. Such behavioral complexity may have had an evolutionary advantage in protist ecosystems, and the ciliate cortex may have provided mechanisms for implementing such behavior prior to the emergence of multicellularity. Our work resurrects Jennings' pioneering insights and adds to the list of exceptional features, including regeneration [24], genome rearrangement [25], codon reassignment [26], and cortical inheritance [27], for which the ciliate clade is renowned.
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Affiliation(s)
- Joseph P Dexter
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA; Neukom Institute for Computational Science, Dartmouth College, 27 North Main Street, Hanover, NH 03755, USA
| | - Sudhakaran Prabakaran
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Jeremy Gunawardena
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.
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Gustmann H, Segler ALJ, Gophane DB, Reuss AJ, Grünewald C, Braun M, Weigand JE, Sigurdsson ST, Wachtveitl J. Structure guided fluorescence labeling reveals a two-step binding mechanism of neomycin to its RNA aptamer. Nucleic Acids Res 2019; 47:15-28. [PMID: 30462266 PMCID: PMC6326822 DOI: 10.1093/nar/gky1110] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/22/2018] [Indexed: 12/12/2022] Open
Abstract
The ability of the cytidine analog Çmf to act as a position specific reporter of RNA-dynamics was spectroscopically evaluated. Çmf-labeled single- and double-stranded RNAs differ in their fluorescence lifetimes, quantum yields and anisotropies. These observables were also influenced by the nucleobases flanking Çmf. This conformation and position specificity allowed to investigate the binding dynamics and mechanism of neomycin to its aptamer N1 by independently incorporating Çmf at four different positions within the aptamer. Remarkably fast binding kinetics of neomycin binding was observed with stopped-flow measurements, which could be satisfactorily explained with a two-step binding. Conformational selection was identified as the dominant mechanism.
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Affiliation(s)
- Henrik Gustmann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Anna-Lena J Segler
- Science Institute, University of Iceland, Dunhaga 3, 107 Reykjavik, Iceland
| | | | - Andreas J Reuss
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Christian Grünewald
- Institute for Organic Chemistry and Chemical Biology, Goethe-University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Markus Braun
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
| | - Julia E Weigand
- Department of Biology, Technical University Darmstadt, Schnittspahnstraße 10, 64287 Darmstadt, Germany
| | | | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt am Main, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany
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Demongeot J, Norris V. Emergence of a "Cyclosome" in a Primitive Network Capable of Building "Infinite" Proteins. Life (Basel) 2019; 9:E51. [PMID: 31216720 PMCID: PMC6617141 DOI: 10.3390/life9020051] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/08/2019] [Accepted: 06/13/2019] [Indexed: 01/02/2023] Open
Abstract
We argue for the existence of an RNA sequence, called the AL (for ALpha) sequence, which may have played a role at the origin of life; this role entailed the AL sequence helping generate the first peptide assemblies via a primitive network. These peptide assemblies included "infinite" proteins. The AL sequence was constructed on an economy principle as the smallest RNA ring having one representative of each codon's synonymy class and capable of adopting a non-functional but nevertheless evolutionarily stable hairpin form that resisted denaturation due to environmental changes in pH, hydration, temperature, etc. Long subsequences from the AL ring resemble sequences from tRNAs and 5S rRNAs of numerous species like the proteobacterium, Rhodobacter sphaeroides. Pentameric subsequences from the AL are present more frequently than expected in current genomes, in particular, in genes encoding some of the proteins associated with ribosomes like tRNA synthetases. Such relics may help explain the existence of universal sequences like exon/intron frontier regions, Shine-Dalgarno sequence (present in bacterial and archaeal mRNAs), CRISPR and mitochondrial loop sequences.
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Affiliation(s)
- Jacques Demongeot
- Faculty of Medicine, Université Grenoble Alpes, AGEIS EA 7407 Tools for e-Gnosis Medical, 38700 La Tronche, France.
| | - Vic Norris
- Laboratory of Microbiology Signals and Microenvironment, Université de Rouen, 76821 Mont-Saint-Aignan CEDEX, France.
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10
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The Nefarious Nexus of Noncoding RNAs in Cancer. Int J Mol Sci 2018; 19:ijms19072072. [PMID: 30018188 PMCID: PMC6073630 DOI: 10.3390/ijms19072072] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 07/12/2018] [Indexed: 02/07/2023] Open
Abstract
The past decade has witnessed enormous progress, and has seen the noncoding RNAs (ncRNAs) turn from the so-called dark matter RNA to critical functional molecules, influencing most physiological processes in development and disease contexts. Many ncRNAs interact with each other and are part of networks that influence the cell transcriptome and proteome and consequently the outcome of biological processes. The regulatory circuits controlled by ncRNAs have become increasingly more relevant in cancer. Further understanding of these complex network interactions and how ncRNAs are regulated, is paving the way for the identification of better therapeutic strategies in cancer.
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11
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Suess B, Kemmerer K, Weigand JE. Splicing and Alternative Splicing Impact on Gene Design. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Beatrix Suess
- Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Katrin Kemmerer
- Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Julia E. Weigand
- Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
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12
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Multiplicity of phenotypes and RNA evolution. J Theor Biol 2018; 447:139-146. [PMID: 29567324 DOI: 10.1016/j.jtbi.2018.03.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 03/09/2018] [Accepted: 03/19/2018] [Indexed: 11/20/2022]
Abstract
Motivation Motoo Kimura's neutral theory stipulates that evolution is predominantly driven by neutral mutations. RNA, realizing both genotype (its linear sequence of nucleotides) as well as phenotype (its folded secondary structure) represents a particularly well suited test bed for studying neutrality. This leads to neutral networks of RNA secondary structures, i.e. sets of sequences all of which folding into a fixed phenotype and whose organization plays a crucial role for neutral evolution. In this paper we bring a new perspective to the neutral theory by studying the consequences of the mostly ignored fact that the genotype-to-phenotype map for RNA is often one-to-many. In fact 29.5% of random RNA sequences realize more than one phenotype (minimum free energy structure). We call two genotypes to be quasineutral if their sets of associated phenotypes have non-empty intersection. Results We show that even though the energy profile of quasineutral mutations is almost identical to the neutral ones, a walk in the genotype space whose consecutive steps are quasineutral, can percolate phenotype space and so such walks bridge between neutral and random walks. This provides further evidence that evolution is continuous. We also study how these drift walks transition between neutral networks.
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13
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Kumar VA. Evolution of specific 3'-5'-linkages in RNA in pre-biotic soup: a new hypothesis. Org Biomol Chem 2018; 14:10123-10133. [PMID: 27714238 DOI: 10.1039/c6ob01796g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
This article reviews the different possibilities towards progression of the formation of DNA/RNA in the chemical world, before life, in enzyme-free conditions. The advent of deoxyribo- and ribopentose-sugars, nucleosides, nucleotides and oligonucleotides in the prebiotic soup is briefly discussed. Further, the formation of early single stranded oligomers, base-pairing possibilities and information transfer based on the stability parameters of the derived duplexes is reviewed. Each theory has its own merits and demerits which we have elaborated upon. Lastly, using clues from this literature, a possible explanation for the specific 3'-5'-linkages in RNA is proposed.
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Affiliation(s)
- Vaijayanti A Kumar
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road, Pune, 411008, India.
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Affiliation(s)
- F. Paul Doerder
- Department of Biological, Geological and Environmental Sciences; Cleveland State University; Cleveland Ohio 44115 USA
| | - Joseph Frankel
- Department of Biology; University of Iowa; Iowa City Iowa 52242 USA
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15
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Use of a Fluorescent Aptamer RNA as an Exonic Sequence to Analyze Self-Splicing Ability of aGroup I Intron from Structured RNAs. BIOLOGY 2016; 5:biology5040043. [PMID: 27869660 PMCID: PMC5192423 DOI: 10.3390/biology5040043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 11/17/2022]
Abstract
Group I self-splicing intron constitutes an important class of functional RNA molecules that can promote chemical transformation. Although the fundamental mechanism of the auto-excision from its precursor RNA has been established, convenient assay systems for its splicing activity are still useful for a further understanding of its detailed mechanism and of its application. Because some host RNA sequences, to which group I introns inserted form stable three-dimensional (3D) structures, the effects of the 3D structures of exonic elements on the splicing efficiency of group I introns are important but not a fully investigated issue. We developed an assay system for group I intron self-splicing by employing a fluorescent aptamer RNA (spinach RNA) as a model exonic sequence inserted by the Tetrahymena group I intron. We investigated self-splicing of the intron from spinach RNA, serving as a model exonic sequence with a 3D structure.
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16
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Gebetsberger J, Micura R. Unwinding the twister ribozyme: from structure to mechanism. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [PMID: 27863022 PMCID: PMC5408937 DOI: 10.1002/wrna.1402] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 09/12/2016] [Accepted: 10/10/2016] [Indexed: 11/12/2022]
Abstract
The twister ribozyme motif has been identified by bioinformatic means very recently. Currently, four crystal structures with ordered active sites together with a series of chemical and biochemical data provide insights into how this RNA accomplishes its efficient self‐cleavage. Of particular interest for a mechanistic proposal are structural distinctions observed in the active sites that concern the conformation of the U‐A cleavage site dinucleotide (in‐line alignment of the attacking 2′‐O nucleophile to the to‐be‐cleaved P—O5′ bond versus suboptimal alignments) as well as the presence/absence of Mg2+ ions at the scissile phosphate. All structures support the notion that an active site guanine and the conserved adenine at the cleavage site are important contributors to cleavage chemistry, likely being involved in general acid base catalysis. Evidence for innersphere coordination of a Mg2+ ion to the pro‐S nonbridging oxygen of the scissile phosphate stems from two of the four crystal structures. Together with the finding of thio/rescue effects for phosphorothioate substrates, this suggests the participation of divalent ions in the overall catalytic strategy employed by twister ribozymes. In this context, it is notable that twister retains wild‐type activity when the phylogenetically conserved stem P1 is deleted, able to cleave a single nucleotide only. WIREs RNA 2017, 8:e1402. doi: 10.1002/wrna.1402 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Jennifer Gebetsberger
- Institute of Organic Chemistry, Leopold-Franzens University and Center of Molecular Biosciences Innsbruck CMBI, Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Leopold-Franzens University and Center of Molecular Biosciences Innsbruck CMBI, Innsbruck, Austria
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17
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Guerrier S, Plattner H, Richardson E, Dacks JB, Turkewitz AP. An evolutionary balance: conservation vs innovation in ciliate membrane trafficking. Traffic 2016; 18:18-28. [PMID: 27696651 DOI: 10.1111/tra.12450] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/20/2016] [Accepted: 09/20/2016] [Indexed: 12/15/2022]
Abstract
As most of eukaryotic diversity lies in single-celled protists, they represent unique opportunities to ask questions about the balance of conservation and innovation in cell biological features. Among free-living protists the ciliates offer ease of culturing, a rich array of experimental approaches, and versatile molecular tools, particularly in Tetrahymena thermophila and Paramecium tetraurelia. These attributes have been exploited by researchers to analyze a wealth of cellular structures in these large and complex cells. This mini-review focuses on 3 aspects of ciliate membrane dynamics, all linked with endolysosomal trafficking. First is nutrition based on phagocytosis and maturation of food vacuoles. Secondly, we discuss regulated exocytosis from vesicles that have features of both dense core secretory granules but also lysosome-related organelles. The third topic is the targeting, breakdown and resorption of parental nuclei in mating partners. For all 3 phenomena, it is clear that elements of the canonical membrane-trafficking system have been retained and in some cases repurposed. In addition, there is evidence that recently evolved, lineage-specific proteins provide determinants in these pathways.
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Affiliation(s)
| | - Helmut Plattner
- Department of Biology, University of Konstanz, Konstanz, Germany
| | | | - Joel B Dacks
- Department of Cell Biology, University of Alberta, Canada
| | - Aaron P Turkewitz
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois
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18
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Ništiar F, Rácz O, Brenišin M. Can imprinting play a role in the response of Tetrahymena pyriformis to toxic substance exposure? ENVIRONMENTAL EPIGENETICS 2016; 2:dvw010. [PMID: 29492290 PMCID: PMC5804524 DOI: 10.1093/eep/dvw010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 06/08/2023]
Abstract
Among protozoa, Tetrahymena pyriformis is the most commonly ciliated model used for laboratory research. All living organisms need to adapt to ever changing adverse conditions in order to survive. This article focuses on the phenomenon that exposure to toxic doses of the toxicants protects against a normally harmful dose of the same stressor. This first encounter by toxicant provokes the phenomenon of epigenetical imprinting, by which the reaction of the cell is quantitatively modified. This modification is transmitted to the progeny generations. The experiments demonstrate the possibility of epigenetic effects at a unicellular level and call attention to the possibility that the character of unicellular organisms has changed through to the present day due to an enormous amount of non-physiological imprinter substances in their environment. The results point to the validity of epigenetic imprinting effects throughout the animal world. Imprinting in Tetrahymena was likely the first epigenetic phenomenon which was justified at cellular level. It is very useful for the unicellular organisms, as it helps to avoid dangerous molecules more easily or to find useful ones and by this contributes to the permanence of the population's life.
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Affiliation(s)
- František Ništiar
- Department of Pathological Physiology, Faculty of Medicine, P. J. Šafárik University, Košice, Slovak Republic
| | - Oliver Rácz
- Department of Pathological Physiology, Faculty of Medicine, P. J. Šafárik University, Košice, Slovak Republic
| | - Marek Brenišin
- Department of Pathological Physiology, Faculty of Medicine, P. J. Šafárik University, Košice, Slovak Republic
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19
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Affiliation(s)
- Amanda Solem
- Department of Biology, Hastings College, Hastings, Nebraska, USA
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
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Swadling JB, Wright DW, Suter JL, Coveney PV. Structure, dynamics, and function of the hammerhead ribozyme in bulk water and at a clay mineral surface from replica exchange molecular dynamics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:2493-2501. [PMID: 25647546 DOI: 10.1021/la503685t] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Compared with proteins, the relationship between structure, dynamics, and function of RNA enzymes (known as ribozymes) is far less well understood, despite the fact that ribozymes are found in many organisms and are often conceived as "molecular fossils" of the first self-replicating molecules to have arisen on Earth. To investigate how ribozymal function is governed by structure and dynamics, we study the full hammerhead ribozyme in bulk water and in an aqueous clay mineral environment by computer simulation using replica-exchange molecular dynamics. Through extensive sampling of the major conformational states of the hammerhead ribozyme, we are able to show that the hammerhead manifests a free-energy landscape reminiscent of that which is well known in proteins, exhibiting a "funnel" topology that guides the ribozyme into its globally most stable conformation. The active-site geometry is found to be closely correlated to the tertiary structure of the ribozyme, thereby reconciling conflicts between previously proposed mechanisms for the self-scission of the hammerhead. The conformational analysis also accounts for the differences reported experimentally in the catalytic activity of the hammerhead ribozyme, which is reduced when interacting with clay minerals as compared with bulk water.
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Affiliation(s)
- Jacob B Swadling
- Centre for Computational Science, Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AJ, United Kingdom
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21
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Moran JV. 2013 Curt Stern Award Address. Am J Hum Genet 2014; 94:340-8. [PMID: 24607386 DOI: 10.1016/j.ajhg.2014.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 01/28/2014] [Indexed: 11/29/2022] Open
Affiliation(s)
- John V Moran
- Departments of Human Genetics and Internal Medicine, 1241 East Catherine Street, University of Michigan Medical School, Ann Arbor, MI 48109-5618, USA; Howard Hughes Medical Institute.
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22
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Curtis EA, Liu DR. Discovery of widespread GTP-binding motifs in genomic DNA and RNA. ACTA ACUST UNITED AC 2013; 20:521-32. [PMID: 23601641 DOI: 10.1016/j.chembiol.2013.02.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 01/22/2013] [Accepted: 02/25/2013] [Indexed: 12/20/2022]
Abstract
Biological RNAs that bind small molecules have been implicated in a variety of regulatory and catalytic processes. Inspired by these examples, we used in vitro selection to search a pool of genome-encoded RNA fragments for naturally occurring GTP aptamers. Several aptamer classes were identified, including one (the "G motif") with a G-quadruplex structure. Further analysis revealed that most RNA and DNA G-quadruplexes bind GTP. The G motif is abundant in eukaryotes, and the human genome contains ~75,000 examples with dissociation constants comparable to the GTP concentration of a eukaryotic cell (~300 μM). G-quadruplexes play roles in diverse cellular processes, and our findings raise the possibility that GTP may play a role in the function of these elements. Consistent with this possibility, the sequence requirements of several classes of regulatory G-quadruplexes parallel those of GTP binding.
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Affiliation(s)
- Edward A Curtis
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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23
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Verification of epigenetic inheritance in a unicellular model system: multigenerational effects of hormonal imprinting. Cell Biol Int 2012; 36:951-9. [DOI: 10.1042/cbi20110677] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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24
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Abstract
Ciliated protozoa of the genus Tetrahymena have provided a uniquely enabling platform for monumental discoveries in the molecular biology of the nucleus.
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Affiliation(s)
- Thoru Pederson
- Program in Cell and Developmental Dynamics, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
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25
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Obermayer B, Frey E. Error thresholds for self- and cross-specific enzymatic replication. J Theor Biol 2010; 267:653-62. [DOI: 10.1016/j.jtbi.2010.09.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Revised: 07/28/2010] [Accepted: 09/09/2010] [Indexed: 11/26/2022]
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26
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27
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Klemm CM, Berthelmann A, Neubacher S, Arenz C. Short and Efficient Synthesis of Alkyne-Modified Amino Glycoside Building Blocks. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900076] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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28
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29
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Corey DR. Chemical modification: the key to clinical application of RNA interference? J Clin Invest 2008; 117:3615-22. [PMID: 18060019 DOI: 10.1172/jci33483] [Citation(s) in RCA: 221] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
RNA interference provides a potent and specific method for controlling gene expression in human cells. To translate this potential into a broad new family of therapeutics, it is necessary to optimize the efficacy of the RNA-based drugs. As discussed in this Review, it might be possible to achieve this optimization using chemical modifications that improve their in vivo stability, cellular delivery, biodistribution, pharmacokinetics, potency, and specificity.
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Affiliation(s)
- David R Corey
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9041, USA.
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30
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Silvestre DAMM, Fontanari JF. Preservation of information in a prebiotic package model. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 75:051909. [PMID: 17677100 DOI: 10.1103/physreve.75.051909] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2006] [Indexed: 05/16/2023]
Abstract
The coexistence between different informational molecules has been the preferred mode to circumvent the limitation posed by imperfect replication on the amount of information stored by each of these molecules. Here we reexamine a classic package model in which distinct information carriers or templates are forced to coexist within vesicles, which in turn can proliferate freely through binary division. The combined dynamics of vesicles and templates is described by a multitype branching process which allows us to write equations for the average number of the different types of vesicles as well as for their extinction probabilities. The threshold phenomenon associated with the extinction of the vesicle population is studied quantitatively using finite-size scaling techniques. We conclude that the resultant coexistence is too frail in the presence of parasites and so confinement of templates in vesicles without an explicit mechanism of cooperation does not resolve the information crisis of prebiotic evolution.
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Affiliation(s)
- Daniel A M M Silvestre
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
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31
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Juranek SA, Lipps HJ. New Insights into the Macronuclear Development in Ciliates. INTERNATIONAL REVIEW OF CYTOLOGY 2007; 262:219-51. [PMID: 17631190 DOI: 10.1016/s0074-7696(07)62005-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
During macronuclear differentiation in ciliated protozoa, most amazing "DNA gymnastics" takes place, which includes DNA excision, DNA elimination, DNA reorganization, and DNA-specific amplification. Although the morphological events occurring during macronuclear development are well described, a detailed knowledge of the molecular mechanisms and the regulation of this differentiation process is still missing. However, recently several models have been proposed for the molecular regulation of macronuclear differentiation, but these models have yet to be verified experimentally. The scope of this review is to summarize recent discoveries in different ciliate species and to compare and discuss the different models proposed. Results obtained in these studies are not only relevant for our understanding of nuclear differentiation in ciliates, but also for cellular differentiation in eukaryotic organisms in general as well as for other disciplines such as bioinformatics and computational biology.
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Affiliation(s)
- Stefan A Juranek
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Rockefeller University, New York, New York 10021, USA
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32
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Bundschuh R, Gerland U. Dynamics of intramolecular recognition: base-pairing in DNA/RNA near and far from equilibrium. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2006; 19:319-29. [PMID: 16520899 DOI: 10.1140/epje/i2005-10061-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2005] [Accepted: 01/30/2006] [Indexed: 05/07/2023]
Abstract
The physics of the base-pairing interaction in DNA and RNA molecules plays a fundamental role in biology. Past experimental and theoretical research has led to a fairly complete and quantitative understanding of the equilibrium properties such as the different phases, the melting behavior, and the response to slow stretching. The non-equilibrium behavior is even richer than might be expected on the basis of thermodynamics. However, the non-equilibrium behavior is also far less understood. Here, we review different theoretical approaches to the study of base-pairing thermodynamics and kinetics, and illustrate the rich phenomenology with several examples that use these approaches.
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Affiliation(s)
- R Bundschuh
- Department of Physics, The Ohio State University, Columbus, OH 43210-1117, USA.
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33
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Lawrence MS, Bartel DP. New ligase-derived RNA polymerase ribozymes. RNA (NEW YORK, N.Y.) 2005; 11:1173-80. [PMID: 15987804 PMCID: PMC1370801 DOI: 10.1261/rna.2110905] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2005] [Accepted: 05/20/2005] [Indexed: 05/03/2023]
Abstract
The search is underway for a catalytic RNA molecule capable of self-replication. Finding such a ribozyme would lend crucial support to the RNA World hypothesis, which holds that very early life-forms relied on RNA for both replicating and storing genetic information. We previously reported an RNA polymerase isolated from a pool of variants of an existing RNA ligase ribozyme. Here we report eight additional ligase-derived polymerase ribozymes isolated from this pool. Because each of them is a new potential starting point for further in vitro evolution and engineering, together they substantially enrich the set of candidates from which an RNA replicase ribozyme might eventually emerge.
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Affiliation(s)
- Michael S Lawrence
- Whitehead Institute for Biomedical Research/Biology Department, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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Rahman L, Bliskovski V, Kaye FJ, Zajac-Kaye M. Evolutionary conservation of a 2-kb intronic sequence flanking a tissue-specific alternative exon in the PTBP2 gene. Genomics 2004; 83:76-84. [PMID: 14667811 DOI: 10.1016/s0888-7543(03)00207-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
nPTB is a member of the polypyrimidine tract-binding (PTB) protein family, which participates in alternative pre-mRNA processing. Tissue-specific splicing of exon 10 in nPTB (HGMW-approved symbol PTBP2) may play an important role in regulating the functional activity of nPTB in neuronal versus nonneuronal cells. In this study, we found that 297 consecutive intronic nucleotides flanking this alternatively spliced exon 10 were identical between human, green monkey, mouse, rat, and pig, while 207 consecutive intronic nucleotides were identical between human and bird DNA. In addition, a 2-kb sequence spanning this intron region showed 85 and 70% conservation in mammal and bird DNA, respectively. Unexpected intergenic sequence conservation between human and mouse genomes has recently been identified. We have now identified intragenic (intronic) sequence conservation from mammals to birds. The striking conservation of this large segment of flanking intronic sequence suggests an important role in tissue-specific splice site selection and may function in regulating the production of functional nPTB.
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Affiliation(s)
- Lambratu Rahman
- Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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35
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Yen L, Svendsen J, Lee JS, Gray JT, Magnier M, Baba T, D'Amato RJ, Mulligan RC. Exogenous control of mammalian gene expression through modulation of RNA self-cleavage. Nature 2004; 431:471-6. [PMID: 15386015 DOI: 10.1038/nature02844] [Citation(s) in RCA: 208] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Accepted: 07/14/2004] [Indexed: 12/24/2022]
Abstract
Recent studies on the control of specific metabolic pathways in bacteria have documented the existence of entirely RNA-based mechanisms for controlling gene expression. These mechanisms involve the modulation of translation, transcription termination or RNA self-cleavage through the direct interaction of specific intracellular metabolites and RNA sequences. Here we show that an analogous RNA-based gene regulation system can effectively be designed for mammalian cells via the incorporation of sequences encoding self-cleaving RNA motifs into the transcriptional unit of a gene or vector. When correctly positioned, the sequences lead to potent inhibition of gene or vector expression, owing to the spontaneous cleavage of the RNA transcript. Administration of either oligonucleotides complementary to regions of the self-cleaving motif or a specific small molecule results in the efficient induction of gene expression, owing to inhibition of self-cleavage of the messenger RNA. Efficient regulation of transgene expression is shown in a variety of mammalian cell lines and live animals. In conjunction with other emerging technologies, this methodology may be particularly applicable to the development of gene regulation systems tailored to any small inducer molecule, and provide a novel means of biological sensing in vivo that may have an important application in the regulated delivery of protein therapeutics.
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Affiliation(s)
- Laising Yen
- Department of Genetics, Harvard Institute of Human Genetics, Harvard Medical School, and Division of Molecular Medicine, Children's Hospital, Boston, Massachusetts 02115, USA
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36
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Fillingham JS, Chilcoat ND, Turkewitz AP, Orias E, Reith M, Pearlman RE. Analysis of expressed sequence tags (ESTs) in the ciliated protozoan Tetrahymena thermophila. J Eukaryot Microbiol 2002; 49:99-107. [PMID: 12043965 DOI: 10.1111/j.1550-7408.2002.tb00350.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
To assess the utility of expressed sequence tag (EST) sequencing as a method of gene discovery in the ciliated protozoan Tetrahymena thermophila, we have sequenced either the 5' or 3' ends of 157 clones chosen at random from two cDNA libraries constructed from the mRNA of vegetatively growing cultures. Of 116 total non-redundant clones, 8.6% represented genes previously cloned in Tetrahymena. Fifty-two percent had significant identity to genes from other organisms represented in GenBank, of which 92% matched human proteins. Intriguing matches include an opioid-regulated protein, a glutamate-binding protein for an NMDA-receptor, and a stem-cell maintenance protein. Eleven-percent of the non-Tetrahymena specific matches were to genes present in humans and other mammals but not found in other model unicellular eukaryotes, including the completely sequenced Saccharomyces cerevisiae. Our data reinforce the fact that Tetrahymena is an excellent unicellular model system for studying many aspects of animal biology and is poised to become an important model system for genome-scale gene discovery and functional analysis.
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37
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Hutton JC. Tetrahymena: the key to the genetic analysis of the regulated pathway of polypeptide secretion? Proc Natl Acad Sci U S A 1997; 94:10490-2. [PMID: 9380665 PMCID: PMC33770 DOI: 10.1073/pnas.94.20.10490] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- J C Hutton
- Barbara Davis Center for Childhood Diabetes, University of Colorado Health Sciences Center, Denver, CO 80262, USA.
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38
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Thaler DS, Liu S, Tombline G. Extending the chemistry that supports genetic information transfer in vivo: phosphorothioate DNA, phosphorothioate RNA, 2'-O-methyl RNA, and methylphosphonate DNA. Proc Natl Acad Sci U S A 1996; 93:1352-6. [PMID: 8577768 PMCID: PMC40084 DOI: 10.1073/pnas.93.3.1352] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
DNA and RNA are the polynucleotides known to carry genetic information in life. Chemical variants of DNA and RNA backbones have been used in structure-function and biosynthesis studies in vitro, and in antisense pharmacology, where their properties of nuclease resistance and enhanced cellular uptake are important. This study addressed the question of whether the base(s) attached to artificial backbones encodes genetic information that can be transferred in vivo. Oligonucleotides containing chemical variants of DNA or RNA were used as primers for site-specific mutagenesis of bacteriophage f1. Progeny phage were scored both genetically and physically for the inheritance of information originally encoded by bases attached to the nonstandard backbones. Four artificial backbone chemistries were tested: phosphorothioate DNA, phosphorothioate RNA, 2'-O-methyl RNA and methylphosphonate DNA. All four were found capable of faithful information transfer from their attached bases when one or three artificial positions were flanked by normal DNA. Among oligonucleotides composed entirely of nonstandard backbones, only phosphorothioate DNA supported genetic information transfer in vivo.
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Affiliation(s)
- D S Thaler
- Laboratory of Molecular Genetics and Informatics, Rockefeller University, New York, NY 10021-6399, USA
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39
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Abstract
The potential roles of members of the fibroblast growth factor family in tumor angiogenesis and metastasis and their mechanisms of release from cells are discussed. Furthermore, we review methods of therapeutic targeting of these polypeptides. In particular, we focus on the possibility to inhibit fibroblast growth factors with drugs that mimic heparin-like cellular binding sites and thus can interfere with growth factor receptor recognition. In addition, we discuss antibodies, antisense oligodeoxynucleotides, and ribozymes as approaches to inhibit production and activity of these growth factors.
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Affiliation(s)
- A Wellstein
- Department of Pharmacology, Georgetown University, Washington D.C. 20007, USA
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40
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Abstract
Surface technologies based upon selection of ligands from combinatorial libraries herald a revolution in molecular research and drug discovery. Molecular diversity is generated by random combinations of monomeric building blocks to form polymeric conformers that constitute 'shape libraries'. The media for exploring surfaces of target molecules include synthetic or biological polymers consisting of natural or modified amino acids, nucleotides, carbohydrates and other organic materials. Targets can be any biological surface, including enzymes, antibodies, receptors and other regulatory molecules. The power of combinatorial selection is in finding conceptual leads for designing high-affinity ligands and effector molecules for the analysis and manipulation of biochemical interactions.
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Affiliation(s)
- D J Kenan
- Department of Microbiology, Duke University Medical Center, Durham, NC 27710
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