Difference between revisions of "Stusti 2018"

From SubtiWiki
Jump to: navigation, search
Line 28: Line 28:
 
== Riboswitches ==
 
== Riboswitches ==
 
<pubmed>    27607554      26655897   28121427      29618088 25794618    25794617 25848023    24769284 25571850   25964329   26118534 26494285 28206750  28375729    28396576    28541183    28455443   29537923      27798597 29135333  29420816  28611182</pubmed>
 
<pubmed>    27607554      26655897   28121427      29618088 25794618    25794617 25848023    24769284 25571850   25964329   26118534 26494285 28206750  28375729    28396576    28541183    28455443   29537923      27798597 29135333  29420816  28611182</pubmed>
 +
 +
== Riboswitch modeling: Mark Sinzger ==
 +
<pubmed>29939019 19381267 28591515 27378291</pubmed>
  
 
== Protein- or tRNA-controlled RNA switches ==
 
== Protein- or tRNA-controlled RNA switches ==

Revision as of 09:03, 16 July 2018

Contents

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

What makes RNA such a special molecule – specific chemical and structural features of RNA


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


Ribozymes (catalytically active RNAs) (Intro)


The Ribosome - the role and function of ribosomal RNAs and the central dogma of molecular biology

Meredith Root-Bernstein, Robert Root-Bernstein
The ribosome as a missing link in the evolution of life.
J Theor Biol: 2015, 367;130-158
[PubMed:25500179] [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)

Thomas A Steitz
A structural understanding of the dynamic ribosome machine.
Nat Rev Mol Cell Biol: 2008, 9(3);242-53
[PubMed:18292779] [WorldCat.org] [DOI] (I p)


The Splicosome - the mechanism of mRNA splicing – alternative gene expression, genome size definition and phenotype plasticity


Protein independent ribozymes – about Hammerhead, Varkud satellite, hairpin ribozyme & Co


RNA-based second messengers

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
##Title##
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)


Riboregulation and virulence, targeting by antibiotics


Riboswitches


Riboswitch modeling: Mark Sinzger


Protein- or tRNA-controlled RNA switches

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)

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)

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)


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)


The RNA world and evolution


RNA modification


RNA degradation/processing


Regulation by non-coding RNA



RNA dependent DNA Polymerases - from telomerase to retroviruses


RNA dependent RNA Polymerases – the RNA replicase


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


CRISPR/Cas: Application and groundbreaking perspectives


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


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


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


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