Difference between revisions of "Stusti 2018"
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= Die Sprache der RNA: Von RNA-Schaltern zu CRISPR/ Cas = | = Die Sprache der RNA: Von RNA-Schaltern zu CRISPR/ Cas = | ||
| − | == What makes RNA such a special molecule – specific chemical and structural features of RNA == | + | == What makes RNA such a special molecule – specific chemical and structural features of RNA: Niklas Kehl == |
<pubmed> 21930584</pubmed> | <pubmed> 21930584</pubmed> | ||
| − | == RNA synthesis – DNA and RNA dependent RNA polymerases and primase during transcription, replication and repair == | + | == RNA synthesis – DNA and RNA dependent RNA polymerases and primase during transcription, replication and repair: Andrea Lehner == |
<pubmed> 24219496 8156586 28979293 26109351</pubmed> | <pubmed> 24219496 8156586 28979293 26109351</pubmed> | ||
| − | == Ribozymes (catalytically active RNAs | + | == Ribozymes (catalytically active RNAs: Christian Thielscher) == |
| − | <pubmed> 21930582</pubmed> | + | <pubmed> 21930582 22454536 14730013 10554775 21930585 6297745</pubmed> |
| − | == The Ribosome - the role and function of ribosomal RNAs and the central dogma of molecular biology == | + | == The Ribosome - the role and function of ribosomal RNAs and the central dogma of molecular biology: Matthias Lenz == |
<pubmed> 18292779 21930591 25500179</pubmed> | <pubmed> 18292779 21930591 25500179</pubmed> | ||
| − | == The Splicosome - the mechanism of mRNA splicing – alternative gene expression, genome size definition and phenotype plasticity == | + | == The Splicosome - the mechanism of mRNA splicing – alternative gene expression, genome size definition and phenotype plasticity: Christian Schneider == |
<pubmed> 24452469,26682498 25798239 </pubmed> | <pubmed> 24452469,26682498 25798239 </pubmed> | ||
| − | + | == Riboregulation and virulence, targeting by antibiotics: Theresia Eisele == | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | == Riboregulation and virulence, targeting by antibiotics == | ||
<pubmed>27651123 26416753 | <pubmed>27651123 26416753 | ||
27120414 27672192 28434876 28529506 28886688</pubmed> | 27120414 27672192 28434876 28529506 28886688</pubmed> | ||
| − | |||
| − | |||
| − | |||
== Riboswitch modeling: Mark Sinzger == | == Riboswitch modeling: Mark Sinzger == | ||
<pubmed>19381267 28591515 27378291</pubmed> | <pubmed>19381267 28591515 27378291</pubmed> | ||
| − | |||
| − | |||
| − | |||
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| − | == The RNA world and evolution == | + | == The RNA world and evolution: Roman Doll == |
<pubmed> 25109990 25385129 25734234 25739364 26439358 17540026 29031737 28657884 19117371</pubmed> | <pubmed> 25109990 25385129 25734234 25739364 26439358 17540026 29031737 28657884 19117371</pubmed> | ||
| − | == RNA modification == | + | == RNA modification: Jan Michel Göring == |
<pubmed> 26189113 26832457 27375676 | <pubmed> 26189113 26832457 27375676 | ||
28264529 28624569</pubmed> | 28264529 28624569</pubmed> | ||
| − | == RNA degradation/processing == | + | == RNA degradation/processing: Lena Kricsfalussy-Hrabar == |
<pubmed> 26096689 28202538 19239894 </pubmed> | <pubmed> 26096689 28202538 19239894 </pubmed> | ||
| − | == Regulation by non-coding RNA == | + | == Regulation by non-coding RNA: Maxin Drömer == |
<pubmed> 18981470 24667238 </pubmed> | <pubmed> 18981470 24667238 </pubmed> | ||
| − | == RNA dependent DNA Polymerases - from telomerase to retroviruses== | + | == RNA dependent DNA Polymerases - from telomerase to retroviruses: Ansgar Stenzel== |
<pubmed> 18972389 26830230 28141967 </pubmed> | <pubmed> 18972389 26830230 28141967 </pubmed> | ||
| − | + | == CRISPR/Cas: Science – the bacterial “immune” system: Maximilian Schreier == | |
| − | |||
| − | |||
| − | == CRISPR/Cas: Science – the bacterial “immune” system == | ||
<pubmed> 29358495 29169146 28375731</pubmed> | <pubmed> 29358495 29169146 28375731</pubmed> | ||
| − | == CRISPR/Cas: Application and groundbreaking perspectives == | + | == CRISPR/Cas: Application and groundbreaking perspectives: Johann Liebeton == |
<pubmed> 26771484 </pubmed> | <pubmed> 26771484 </pubmed> | ||
| − | + | == Synthesis, maturation and function of tRNAs – The wobble hypothesis and specific codon usage as a molecular barrier for horizontal gene transfer: Artur Fornol == | |
| − | |||
| − | |||
| − | == Synthesis, maturation and function of tRNAs – The wobble hypothesis and specific codon usage as a molecular barrier for horizontal gene transfer == | ||
<pubmed> 22016848 26186290 21957054 23166520 21930591</pubmed> | <pubmed> 22016848 26186290 21957054 23166520 21930591</pubmed> | ||
| Line 74: | Line 54: | ||
== Outlook: RNA and SELEX – new prospects and applications for targeted interference with regulatory pathways == | == Outlook: RNA and SELEX – new prospects and applications for targeted interference with regulatory pathways == | ||
<pubmed> 17627883 19943183 </pubmed> | <pubmed> 17627883 19943183 </pubmed> | ||
| + | |||
| + | == RNA-based second messengers: Jörg Stülke == | ||
| + | <pubmed> 28420751 25616065 25682701 25869574 26280533</pubmed> | ||
| + | |||
| + | == Riboswitches: Jörg Stülke == | ||
| + | <pubmed> 27607554 26655897 28121427 29618088 25794618 25794617 25848023 24769284 25571850 25964329 25959893 24816551 25583497 26118534 26494285 28206750 28375729 28396576 28541183 28455443 29537923 27798597 29135333 29420816 28611182</pubmed> | ||
| + | |||
| + | == RNA dependent RNA Polymerases – the RNA replicase == | ||
| + | <pubmed> 29439438 18268843 9878607 </pubmed> | ||
| + | |||
| + | == The mysterious function and role of 6S-RNA and pRNA in bacteria == | ||
| + | <pubmed> 24786589 17383220 24742053 23457253</pubmed> | ||
| + | |||
| + | == RNA thermometers== | ||
| + | <pubmed>25477380 27060146 </pubmed> | ||
Latest revision as of 13:42, 27 July 2018
Contents
- 1 Die Sprache der RNA: Von RNA-Schaltern zu CRISPR/ Cas
- 1.1 What makes RNA such a special molecule – specific chemical and structural features of RNA: Niklas Kehl
- 1.2 RNA synthesis – DNA and RNA dependent RNA polymerases and primase during transcription, replication and repair: Andrea Lehner
- 1.3 Ribozymes (catalytically active RNAs: Christian Thielscher)
- 1.4 The Ribosome - the role and function of ribosomal RNAs and the central dogma of molecular biology: Matthias Lenz
- 1.5 The Splicosome - the mechanism of mRNA splicing – alternative gene expression, genome size definition and phenotype plasticity: Christian Schneider
- 1.6 Riboregulation and virulence, targeting by antibiotics: Theresia Eisele
- 1.7 Riboswitch modeling: Mark Sinzger
- 1.8 The RNA world and evolution: Roman Doll
- 1.9 RNA modification: Jan Michel Göring
- 1.10 RNA degradation/processing: Lena Kricsfalussy-Hrabar
- 1.11 Regulation by non-coding RNA: Maxin Drömer
- 1.12 RNA dependent DNA Polymerases - from telomerase to retroviruses: Ansgar Stenzel
- 1.13 CRISPR/Cas: Science – the bacterial “immune” system: Maximilian Schreier
- 1.14 CRISPR/Cas: Application and groundbreaking perspectives: Johann Liebeton
- 1.15 Synthesis, maturation and function of tRNAs – The wobble hypothesis and specific codon usage as a molecular barrier for horizontal gene transfer: Artur Fornol
- 1.16 Outlook: Finding function in mystery transcripts – eRNAs, long-non coding (lncRNA) and circular RNA (circRNA)
- 1.17 Outlook: RNA and SELEX – new prospects and applications for targeted interference with regulatory pathways
- 1.18 RNA-based second messengers: Jörg Stülke
- 1.19 Riboswitches: Jörg Stülke
- 1.20 RNA dependent RNA Polymerases – the RNA replicase
- 1.21 The mysterious function and role of 6S-RNA and pRNA in bacteria
- 1.22 RNA thermometers
Die Sprache der RNA: Von RNA-Schaltern zu CRISPR/ Cas
What makes RNA such a special molecule – specific chemical and structural features of RNA: Niklas Kehl
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)
Ribozymes (catalytically active RNAs: Christian Thielscher)
The Ribosome - the role and function of ribosomal RNAs and the central dogma of molecular biology: Matthias Lenz
The Splicosome - the mechanism of mRNA splicing – alternative gene expression, genome size definition and phenotype plasticity: Christian Schneider
Riboregulation and virulence, targeting by antibiotics: Theresia Eisele
Juan J Quereda, Pascale Cossart
Regulating Bacterial Virulence with RNA.
Annu Rev Microbiol: 2017, 71;263-280
[PubMed:28886688]
[WorldCat.org]
[DOI]
(I p)
Petra Dersch, Muna A Khan, Sabrina Mühlen, Boris Görke
Roles of Regulatory RNAs for Antibiotic Resistance in Bacteria and Their Potential Value as Novel Drug Targets.
Front Microbiol: 2017, 8;803
[PubMed:28529506]
[WorldCat.org]
[DOI]
(P e)
Hao Wang, Paul A Mann, Li Xiao, Charles Gill, Andrew M Galgoci, John A Howe, Artjohn Villafania, Christopher M Barbieri, Juliana C Malinverni, Xinwei Sher, Todd Mayhood, Megan D McCurry, Nicholas Murgolo, Amy Flattery, Matthias Mack, Terry Roemer
Dual-Targeting Small-Molecule Inhibitors of the Staphylococcus aureus FMN Riboswitch Disrupt Riboflavin Homeostasis in an Infectious Setting.
Cell Chem Biol: 2017, 24(5);576-588.e6
[PubMed:28434876]
[WorldCat.org]
[DOI]
(I p)
Andreas Matern, Danielle Pedrolli, Stephanie Großhennig, Jörgen Johansson, Matthias Mack
Uptake and Metabolism of Antibiotics Roseoflavin and 8-Demethyl-8-Aminoriboflavin in Riboflavin-Auxotrophic Listeria monocytogenes.
J Bacteriol: 2016, 198(23);3233-3243
[PubMed:27672192]
[WorldCat.org]
[DOI]
(I e)
Aaron M Nuss, Ann Kathrin Heroven, Petra Dersch
RNA Regulators: Formidable Modulators of Yersinia Virulence.
Trends Microbiol: 2017, 25(1);19-34
[PubMed:27651123]
[WorldCat.org]
[DOI]
(I p)
Daniel Dar, Maya Shamir, J R Mellin, Mikael Koutero, Noam Stern-Ginossar, Pascale Cossart, Rotem Sorek
Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria.
Science: 2016, 352(6282);aad9822
[PubMed:27120414]
[WorldCat.org]
[DOI]
(I p)
John A Howe, Hao Wang, Thierry O Fischmann, Carl J Balibar, Li Xiao, Andrew M Galgoci, Juliana C Malinverni, Todd Mayhood, Artjohn Villafania, Ali Nahvi, Nicholas Murgolo, Christopher M Barbieri, Paul A Mann, Donna Carr, Ellen Xia, Paul Zuck, Dan Riley, Ronald E Painter, Scott S Walker, Brad Sherborne, Reynalda de Jesus, Weidong Pan, Michael A Plotkin, Jin Wu, Diane Rindgen, John Cummings, Charles G Garlisi, Rumin Zhang, Payal R Sheth, Charles J Gill, Haifeng Tang, Terry Roemer
Selective small-molecule inhibition of an RNA structural element.
Nature: 2015, 526(7575);672-7
[PubMed:26416753]
[WorldCat.org]
[DOI]
(I p)
Riboswitch modeling: Mark Sinzger
The RNA world and evolution: Roman Doll
RNA modification: Jan Michel Göring
RNA degradation/processing: Lena Kricsfalussy-Hrabar
John C Zinder, Christopher D Lima
Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactors.
Genes Dev: 2017, 31(2);88-100
[PubMed:28202538]
[WorldCat.org]
[DOI]
(I p)
Soraya Aït-Bara, Agamemnon J Carpousis
RNA degradosomes in bacteria and chloroplasts: classification, distribution and evolution of RNase E homologs.
Mol Microbiol: 2015, 97(6);1021-135
[PubMed:26096689]
[WorldCat.org]
[DOI]
(I p)
Jonathan Houseley, David Tollervey
The many pathways of RNA degradation.
Cell: 2009, 136(4);763-76
[PubMed:19239894]
[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)
CRISPR/Cas: Application and groundbreaking perspectives: Johann Liebeton
Addison V Wright, James K Nuñez, Jennifer A Doudna
Biology and Applications of CRISPR Systems: Harnessing Nature's Toolbox for Genome Engineering.
Cell: 2016, 164(1-2);29-44
[PubMed:26771484]
[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
RNA-based second messengers: Jörg Stülke
Riboswitches: Jörg Stülke
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]
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(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)
