Stusti 2018

Die Sprache der RNA: Von RNA-Schaltern zu CRISPR/ Cas

RNA synthesis – DNA and RNA dependent RNA polymerases and primase during transcription, replication and repair: Andrea Lehner

Savio T de Farias, Ariosvaldo P Dos Santos Junior, Thais G Rêgo, Marco V José
Origin and Evolution of RNA-Dependent RNA Polymerase.
Front Genet: 2017, 8;125
[PubMed:28979293] [WorldCat.org] [DOI] (P e)

Thomas A Guilliam, Benjamin A Keen, Nigel C Brissett, Aidan J Doherty
Primase-polymerases are a functionally diverse superfamily of replication and repair enzymes.
Nucleic Acids Res: 2015, 43(14);6651-64
[PubMed:26109351] [WorldCat.org] [DOI] (I p)

Maria L Kireeva, Mikhail Kashlev, Zachary F Burton
RNA polymerase structure, function, regulation, dynamics, fidelity, and roles in gene expression.
Chem Rev: 2013, 113(11);8325-30
[PubMed:24219496] [WorldCat.org] [DOI] (I p)

S Buratowski
The basics of basal transcription by RNA polymerase II.
Cell: 1994, 77(1);1-3
[PubMed:8156586] [WorldCat.org] [DOI] (P p)

Riboswitch modeling: Mark Sinzger

Christopher Schneider, Leo Bronstein, Jascha Diemer, Heinz Koeppl, Beatrix Suess
ROC'n'Ribo: Characterizing a Riboswitching Expression System by Modeling Single-Cell Data.
ACS Synth Biol: 2017, 6(7);1211-1224
[PubMed:28591515] [WorldCat.org] [DOI] (I p)

Marco Barsacchi, Eva Maria Novoa, Manolis Kellis, Alessio Bechini
SwiSpot: modeling riboswitches by spotting out switching sequences.
Bioinformatics: 2016, 32(21);3252-3259
[PubMed:27378291] [WorldCat.org] [DOI] (I p)

Chase L Beisel, Christina D Smolke
Design principles for riboswitch function.
PLoS Comput Biol: 2009, 5(4);e1000363
[PubMed:19381267] [WorldCat.org] [DOI] (I p)

Regulation by non-coding RNA: Maxin Drömer

Yvonne Göpel, Muna A Khan, Boris Görke
Ménage à trois: post-transcriptional control of the key enzyme for cell envelope synthesis by a base-pairing small RNA, an RNase adaptor protein, and a small RNA mimic.
RNA Biol: 2014, 11(5);433-42
[PubMed:24667238] [WorldCat.org] [DOI] (I p)

Boris Görke, Jörg Vogel
Noncoding RNA control of the making and breaking of sugars.
Genes Dev: 2008, 22(21);2914-25
[PubMed:18981470] [WorldCat.org] [DOI] (P p)

RNA dependent DNA Polymerases - from telomerase to retroviruses: Ansgar Stenzel

R Alex Wu, Heather E Upton, Jacob M Vogan, Kathleen Collins
Telomerase Mechanism of Telomere Synthesis.
Annu Rev Biochem: 2017, 86;439-460
[PubMed:28141967] [WorldCat.org] [DOI] (I p)

Yoshiko Maida, Mami Yasukawa, Kenkichi Masutomi
De Novo RNA Synthesis by RNA-Dependent RNA Polymerase Activity of Telomerase Reverse Transcriptase.
Mol Cell Biol: 2016, 36(8);1248-59
[PubMed:26830230] [WorldCat.org] [DOI] (I e)

George Tzertzinis, Stanley Tabor, Nicole M Nichols
RNA-dependent DNA polymerases.
Curr Protoc Mol Biol: 2008, Chapter 3;Unit3.7
[PubMed:18972389] [WorldCat.org] [DOI] (I p)

CRISPR/Cas: Science – the bacterial “immune” system: Maximilian Schreier

Yoshizumi Ishino, Mart Krupovic, Patrick Forterre
History of CRISPR-Cas from Encounter with a Mysterious Repeated Sequence to Genome Editing Technology.
J Bacteriol: 2018, 200(7);
[PubMed:29358495] [WorldCat.org] [DOI] (I e)

Lina M Leon, Senén D Mendoza, Joseph Bondy-Denomy
How bacteria control the CRISPR-Cas arsenal.
Curr Opin Microbiol: 2018, 42;87-95
[PubMed:29169146] [WorldCat.org] [DOI] (I p)

Fuguo Jiang, Jennifer A Doudna
CRISPR-Cas9 Structures and Mechanisms.
Annu Rev Biophys: 2017, 46;505-529
[PubMed:28375731] [WorldCat.org] [DOI] (I p)

Synthesis, maturation and function of tRNAs – The wobble hypothesis and specific codon usage as a molecular barrier for horizontal gene transfer: Artur Fornol

Tessa E F Quax, Nico J Claassens, Dieter Söll, John van der Oost
Codon Bias as a Means to Fine-Tune Gene Expression.
Mol Cell: 2015, 59(2);149-61
[PubMed:26186290] [WorldCat.org] [DOI] (I p)

Sibah Alkatib, Lars B Scharff, Marcelo Rogalski, Tobias T Fleischmann, Annemarie Matthes, Stefanie Seeger, Mark A Schöttler, Stephanie Ruf, Ralph Bock
The contributions of wobbling and superwobbling to the reading of the genetic code.
PLoS Genet: 2012, 8(11);e1003076
[PubMed:23166520] [WorldCat.org] [DOI] (I p)

Tamir Tuller
Codon bias, tRNA pools and horizontal gene transfer.
Mob Genet Elements: 2011, 1(1);75-77
[PubMed:22016848] [WorldCat.org] [DOI] (P p)

Richard Giegé, Frank Jühling, Joern Pütz, Peter Stadler, Claude Sauter, Catherine Florentz
Structure of transfer RNAs: similarity and variability.
Wiley Interdiscip Rev RNA: 2012, 3(1);37-61
[PubMed:21957054] [WorldCat.org] [DOI] (I p)

Ingo Wohlgemuth, Corinna Pohl, Joerg Mittelstaet, Andrey L Konevega, Marina V Rodnina
Evolutionary optimization of speed and accuracy of decoding on the ribosome.
Philos Trans R Soc Lond B Biol Sci: 2011, 366(1580);2979-86
[PubMed:21930591] [WorldCat.org] [DOI] (I p)

Outlook: Finding function in mystery transcripts – eRNAs, long-non coding (lncRNA) and circular RNA (circRNA)

Shahnaz Haque, Lorna W Harries
Circular RNAs (circRNAs) in Health and Disease.
Genes (Basel): 2017, 8(12);
[PubMed:29182528] [WorldCat.org] [DOI] (P e)

Feng Liu
Enhancer-derived RNA: A Primer.
Genomics Proteomics Bioinformatics: 2017, 15(3);196-200
[PubMed:28533025] [WorldCat.org] [DOI] (I p)

Kuei-Yang Hsiao, H Sunny Sun, Shaw-Jenq Tsai
Circular RNA - New member of noncoding RNA with novel functions.
Exp Biol Med (Maywood): 2017, 242(11);1136-1141
[PubMed:28485684] [WorldCat.org] [DOI] (I p)

Yiwen Fang, Melissa J Fullwood
Roles, Functions, and Mechanisms of Long Non-coding RNAs in Cancer.
Genomics Proteomics Bioinformatics: 2016, 14(1);42-54
[PubMed:26883671] [WorldCat.org] [DOI] (I p)

Tae-Kyung Kim, Martin Hemberg, Jesse M Gray
Enhancer RNAs: a class of long noncoding RNAs synthesized at enhancers.
Cold Spring Harb Perspect Biol: 2015, 7(1);a018622
[PubMed:25561718] [WorldCat.org] [DOI] (I e)

Kevin C Wang, Howard Y Chang
Molecular mechanisms of long noncoding RNAs.
Mol Cell: 2011, 43(6);904-14
[PubMed:21925379] [WorldCat.org] [DOI] (I p)

Outlook: RNA and SELEX – new prospects and applications for targeted interference with regulatory pathways

Sujin Jeong, Seung Ryul Han, Young Ju Lee, Seong-Wook Lee
Selection of RNA aptamers specific to active prostate-specific antigen.
Biotechnol Lett: 2010, 32(3);379-85
[PubMed:19943183] [WorldCat.org] [DOI] (I p)

Regina Stoltenburg, Christine Reinemann, Beate Strehlitz
SELEX--a (r)evolutionary method to generate high-affinity nucleic acid ligands.
Biomol Eng: 2007, 24(4);381-403
[PubMed:17627883] [WorldCat.org] [DOI] (P p)

RNA-based second messengers: Jörg Stülke

Jan Gundlach, Christina Herzberg, Volkhard Kaever, Katrin Gunka, Tamara Hoffmann, Martin Weiß, Johannes Gibhardt, Andrea Thürmer, Dietrich Hertel, Rolf Daniel, Erhard Bremer, Fabian M Commichau, Jörg Stülke
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Sci Signal: 2017, 10(475);
[PubMed:28420751] [WorldCat.org] [DOI] (I e)

Christopher P Jones, Adrian R Ferré-D'Amaré
Recognition of the bacterial alarmone ZMP through long-distance association of two RNA subdomains.
Nat Struct Mol Biol: 2015, 22(9);679-85
[PubMed:26280533] [WorldCat.org] [DOI] (I p)

Fabian M Commichau, Achim Dickmanns, Jan Gundlach, Ralf Ficner, Jörg Stülke
A jack of all trades: the multiple roles of the unique essential second messenger cyclic di-AMP.
Mol Microbiol: 2015, 97(2);189-204
[PubMed:25869574] [WorldCat.org] [DOI] (I p)

Renée J St-Onge, Henry J Haiser, Mary R Yousef, Emma Sherwood, Natalia Tschowri, Mahmoud Al-Bassam, Marie A Elliot
Nucleotide second messenger-mediated regulation of a muralytic enzyme in Streptomyces.
Mol Microbiol: 2015, 96(4);779-95
[PubMed:25682701] [WorldCat.org] [DOI] (I p)

Gregory S Ducker, Joshua D Rabinowitz
ZMP: a master regulator of one-carbon metabolism.
Mol Cell: 2015, 57(2);203-4
[PubMed:25616065] [WorldCat.org] [DOI] (I p)

Riboswitches: Jörg Stülke

Stefan Schwenk, Alexandra Moores, Irene Nobeli, Timothy D McHugh, Kristine B Arnvig
Cell-wall synthesis and ribosome maturation are co-regulated by an RNA switch in Mycobacterium tuberculosis.
Nucleic Acids Res: 2018, 46(11);5837-5849
[PubMed:29618088] [WorldCat.org] [DOI] (I p)

Laurène Bastet, Pierre Turcotte, Joseph T Wade, Daniel A Lafontaine
Maestro of regulation: Riboswitches orchestrate gene expression at the levels of translation, transcription and mRNA decay.
RNA Biol: 2018, 15(6);679-682
[PubMed:29537923] [WorldCat.org] [DOI] (I p)

Marc Vogel, Julia E Weigand, Britta Kluge, Manuel Grez, Beatrix Suess
A small, portable RNA device for the control of exon skipping in mammalian cells.
Nucleic Acids Res: 2018, 46(8);e48
[PubMed:29420816] [WorldCat.org] [DOI] (I p)

Etienne B Greenlee, Shira Stav, Ruben M Atilho, Kenneth I Brewer, Kimberly A Harris, Sarah N Malkowski, Gayan Mirihana Arachchilage, Kevin R Perkins, Madeline E Sherlock, Ronald R Breaker
Challenges of ligand identification for the second wave of orphan riboswitch candidates.
RNA Biol: 2018, 15(3);377-390
[PubMed:29135333] [WorldCat.org] [DOI] (I p)

James W Nelson, Ronald R Breaker
The lost language of the RNA World.
Sci Signal: 2017, 10(483);
[PubMed:28611182] [WorldCat.org] [DOI] (I e)

Hannah Steinert, Florian Sochor, Anna Wacker, Janina Buck, Christina Helmling, Fabian Hiller, Sara Keyhani, Jonas Noeske, Steffen Grimm, Martin M Rudolph, Heiko Keller, Rachel Anne Mooney, Robert Landick, Beatrix Suess, Boris Fürtig, Jens Wöhnert, Harald Schwalbe
Pausing guides RNA folding to populate transiently stable RNA structures for riboswitch-based transcription regulation.
Elife: 2017, 6;
[PubMed:28541183] [WorldCat.org] [DOI] (I e)

Joseph E Wedekind, Debapratim Dutta, Ivan A Belashov, Jermaine L Jenkins
Metalloriboswitches: RNA-based inorganic ion sensors that regulate genes.
J Biol Chem: 2017, 292(23);9441-9450
[PubMed:28455443] [WorldCat.org] [DOI] (I p)

Phillip J McCown, Keith A Corbino, Shira Stav, Madeline E Sherlock, Ronald R Breaker
Riboswitch diversity and distribution.
RNA: 2017, 23(7);995-1011
[PubMed:28396576] [WorldCat.org] [DOI] (I p)

Christopher P Jones, Adrian R Ferré-D'Amaré
Long-Range Interactions in Riboswitch Control of Gene Expression.
Annu Rev Biophys: 2017, 46;455-481
[PubMed:28375729] [WorldCat.org] [DOI] (I p)

Maja Etzel, Mario Mörl
Synthetic Riboswitches: From Plug and Pray toward Plug and Play.
Biochemistry: 2017, 56(9);1181-1198
[PubMed:28206750] [WorldCat.org] [DOI] (I p)

Svetlana V Harbaugh, Michael S Goodson, Kateri Dillon, Sarah Zabarnick, Nancy Kelley-Loughnane
Riboswitch-Based Reversible Dual Color Sensor.
ACS Synth Biol: 2017, 6(5);766-781
[PubMed:28121427] [WorldCat.org] [DOI] (I p)

Kyle E Watters, Eric J Strobel, Angela M Yu, John T Lis, Julius B Lucks
Cotranscriptional folding of a riboswitch at nucleotide resolution.
Nat Struct Mol Biol: 2016, 23(12);1124-1131
[PubMed:27798597] [WorldCat.org] [DOI] (I p)

Anna V Sherwood, Tina M Henkin
Riboswitch-Mediated Gene Regulation: Novel RNA Architectures Dictate Gene Expression Responses.
Annu Rev Microbiol: 2016, 70;361-74
[PubMed:27607554] [WorldCat.org] [DOI] (I p)

Aiming Ren, Yi Xue, Alla Peselis, Alexander Serganov, Hashim M Al-Hashimi, Dinshaw J Patel
Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch.
Cell Rep: 2015, 13(9);1800-13
[PubMed:26655897] [WorldCat.org] [DOI] (I p)

Danielle Biscaro Pedrolli, Christian Kühm, Daniel C Sévin, Michael P Vockenhuber, Uwe Sauer, Beatrix Suess, Matthias Mack
A dual control mechanism synchronizes riboflavin and sulphur metabolism in Bacillus subtilis.
Proc Natl Acad Sci U S A: 2015, 112(45);14054-9
[PubMed:26494285] [WorldCat.org] [DOI] (I p)

Aiming Ren, Kanagalaghatta R Rajashankar, Dinshaw J Patel
Global RNA Fold and Molecular Recognition for a pfl Riboswitch Bound to ZMP, a Master Regulator of One-Carbon Metabolism.
Structure: 2015, 23(8);1375-1381
[PubMed:26118534] [WorldCat.org] [DOI] (I p)

Mingxu You, Jacob L Litke, Samie R Jaffrey
Imaging metabolite dynamics in living cells using a Spinach-based riboswitch.
Proc Natl Acad Sci U S A: 2015, 112(21);E2756-65
[PubMed:25964329] [WorldCat.org] [DOI] (I p)

Jinwei Zhang, Adrian R Ferré-D'Amaré
Structure and mechanism of the T-box riboswitches.
Wiley Interdiscip Rev RNA: 2015, 6(4);419-33
[PubMed:25959893] [WorldCat.org] [DOI] (I p)

James W Nelson, Narasimhan Sudarsan, Grace E Phillips, Shira Stav, Christina E Lünse, Phillip J McCown, Ronald R Breaker
Control of bacterial exoelectrogenesis by c-AMP-GMP.
Proc Natl Acad Sci U S A: 2015, 112(17);5389-94
[PubMed:25848023] [WorldCat.org] [DOI] (I p)

Michael Dambach, Melissa Sandoval, Taylor B Updegrove, Vivek Anantharaman, L Aravind, Lauren S Waters, Gisela Storz
The ubiquitous yybP-ykoY riboswitch is a manganese-responsive regulatory element.
Mol Cell: 2015, 57(6);1099-1109
[PubMed:25794618] [WorldCat.org] [DOI] (I p)

Kazuhiro Furukawa, Arati Ramesh, Zhiyuan Zhou, Zasha Weinberg, Tenaya Vallery, Wade C Winkler, Ronald R Breaker
Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and control expression of heavy metal transporters.
Mol Cell: 2015, 57(6);1088-1098
[PubMed:25794617] [WorldCat.org] [DOI] (I p)

Anna V Sherwood, Frank J Grundy, Tina M Henkin
T box riboswitches in Actinobacteria: translational regulation via novel tRNA interactions.
Proc Natl Acad Sci U S A: 2015, 112(4);1113-8
[PubMed:25583497] [WorldCat.org] [DOI] (I p)

José A L da Silva
From the RNA world to the RNA/protein world: contribution of some riboswitch-binding species?
J Theor Biol: 2015, 370;197-201
[PubMed:25571850] [WorldCat.org] [DOI] (I p)

Tina M Henkin
The T box riboswitch: A novel regulatory RNA that utilizes tRNA as its ligand.
Biochim Biophys Acta: 2014, 1839(10);959-963
[PubMed:24816551] [WorldCat.org] [DOI] (P p)

Arati Ramesh, Wade C Winkler
Metabolite-binding ribozymes.
Biochim Biophys Acta: 2014, 1839(10);989-994
[PubMed:24769284] [WorldCat.org] [DOI] (P p)

RNA dependent RNA Polymerases – the RNA replicase

Sangita Venkataraman, Burra V L S Prasad, Ramasamy Selvarajan
RNA Dependent RNA Polymerases: Insights from Structure, Function and Evolution.
Viruses: 2018, 10(2);
[PubMed:29439438] [WorldCat.org] [DOI] (I e)

Kenneth K S Ng, Jamie J Arnold, Craig E Cameron
Structure-function relationships among RNA-dependent RNA polymerases.
Curr Top Microbiol Immunol: 2008, 320;137-56
[PubMed:18268843] [WorldCat.org] [DOI] (P p)

E K O'Reilly, C C Kao
Analysis of RNA-dependent RNA polymerase structure and function as guided by known polymerase structures and computer predictions of secondary structure.
Virology: 1998, 252(2);287-303
[PubMed:9878607] [WorldCat.org] [DOI] (P p)

The mysterious function and role of 6S-RNA and pRNA in bacteria

Benedikt Steuten, Philipp G Hoch, Katrin Damm, Sabine Schneider, Karen Köhler, Rolf Wagner, Roland K Hartmann
Regulation of transcription by 6S RNAs: insights from the Escherichia coli and Bacillus subtilis model systems.
RNA Biol: 2014, 11(5);508-21
[PubMed:24786589] [WorldCat.org] [DOI] (I p)

Amy T Cavanagh, Karen M Wassarman
6S RNA, a global regulator of transcription in Escherichia coli, Bacillus subtilis, and beyond.
Annu Rev Microbiol: 2014, 68;45-60
[PubMed:24742053] [WorldCat.org] [DOI] (I p)

Amy T Cavanagh, Karen M Wassarman
6S-1 RNA function leads to a delay in sporulation in Bacillus subtilis.
J Bacteriol: 2013, 195(9);2079-86
[PubMed:23457253] [WorldCat.org] [DOI] (I p)

Karen M Wassarman
6S RNA: a small RNA regulator of transcription.
Curr Opin Microbiol: 2007, 10(2);164-8
[PubMed:17383220] [WorldCat.org] [DOI] (P p)

RNA thermometers

Johanna Roßmanith, Franz Narberhaus
Exploring the modular nature of riboswitches and RNA thermometers.
Nucleic Acids Res: 2016, 44(11);5410-23
[PubMed:27060146] [WorldCat.org] [DOI] (I p)

Satya Narayan, Mamta H Kombrabail, Sudipta Das, Himanshu Singh, Kandala V R Chary, Basuthkar J Rao, Guruswamy Krishnamoorthy
Site-specific fluorescence dynamics in an RNA 'thermometer' reveals the role of ribosome binding in its temperature-sensitive switch function.
Nucleic Acids Res: 2015, 43(1);493-503
[PubMed:25477380] [WorldCat.org] [DOI] (I p)