Structural heterogeneity in the intrinsically disordered RNA polymerase II C-terminal domain

Nature Communications
Bede PortzDavid S Gilmour

Abstract

RNA polymerase II contains a repetitive, intrinsically disordered, C-terminal domain (CTD) composed of heptads of the consensus sequence YSPTSPS. The CTD is heavily phosphorylated and serves as a scaffold, interacting with factors involved in transcription initiation, elongation and termination, RNA processing and chromatin modification. Despite being a nexus of eukaryotic gene regulation, the structure of the CTD and the structural implications of phosphorylation are poorly understood. Here we present a biophysical and biochemical interrogation of the structure of the full length CTD of Drosophila melanogaster, which we conclude is a compact random coil. Surprisingly, we find that the repetitive CTD is structurally heterogeneous. Phosphorylation causes increases in radius, protein accessibility and stiffness, without disrupting local structural heterogeneity. Additionally, we show the human CTD is also structurally heterogeneous and able to substitute for the D. melanogaster CTD in supporting fly development to adulthood. This finding implicates conserved structural organization, not a precise array of heptad motifs, as important to CTD function.

References

Dec 11, 1992·Journal of Medicinal Chemistry·M M Harding
Nov 1, 1992·Journal of Molecular Evolution·E Barron-Casella, J L Corden
Jan 1, 1995·Archives of Virology·G A SmithK C Reed
May 10, 1996·Journal of Molecular Biology·G D MeredithR D Kornberg
Mar 23, 2002·Protein Science : a Publication of the Protein Society·Vladimir N Uversky
Mar 20, 2003·Journal of Proteome Research·Olga TcherkasskayaVladimir N Uversky
May 15, 2003·Proceedings of the National Academy of Sciences of the United States of America·Karim-Jean ArmachePatrick Cramer
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Jun 3, 2004·Genome Research·Gavin E CrooksSteven E Brenner
Aug 18, 2004·Proceedings of the National Academy of Sciences of the United States of America·Jonathan E KohnKevin W Plaxco
Jan 25, 2005·Nature Structural & Molecular Biology·Christian G NobleAndres Ramos
Mar 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Johannes BischofKonrad Basler
May 25, 2007·Proceedings of the National Academy of Sciences of the United States of America·Mikael BorgHue Sun Chan
Feb 13, 2008·The Journal of Chemical Physics·Sebastian MeierStephan Grzesiek
May 13, 2008·Trends in Genetics : TIG·Rob D ChapmanDirk Eick
Sep 29, 2011·Molecular BioSystems·Pau Bernadó, Dmitri I Svergun
Nov 3, 2011·Current Protein & Peptide Science·Veronique Receveur-Brechot, Dominique Durand
May 17, 2012·Nature Communications·Nadine CzudnochowskiMatthias Geyer
Jul 24, 2012·Methods in Molecular Biology·Angelo FontanaErica Frare
Feb 8, 2013·G3 : Genes - Genomes - Genetics·John Roote, Andreas Prokop
Apr 9, 2013·Nature Structural & Molecular Biology·Kuang-Lei TsaiFrancisco J Asturias
Aug 1, 2013·Proceedings of the National Academy of Sciences of the United States of America·Rahul K Das, Rohit V Pappu
Aug 21, 2013·Chemical Reviews·Dirk Eick, Matthias Geyer
Apr 9, 2014·Proceedings of the National Academy of Sciences of the United States of America·Chunlin Yang, John W Stiller
Jun 27, 2014·Nature Protocols·Soren SkouNozomi Ando
Apr 1, 2012·Journal of Applied Crystallography·Maxim V PetoukhovDmitri I Svergun
Jan 21, 2016·Nature·Carrie BerneckyPatrick Cramer
Jan 23, 2016·Molecular Cell·Roland SchüllerDirk Eick

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Citations

Oct 27, 2017·Proceedings of the National Academy of Sciences of the United States of America·Olga JasnovidovaRichard Stefl
Jan 19, 2018·Annual Review of Biophysics·Alex S Holehouse, Rohit V Pappu
Jan 13, 2018·PLoS Genetics·Encarnación Rodríguez-CazorlaAntonio Vera
May 14, 2020·Transcription·Danielle E LyonsMelanie Ott
Aug 22, 2018·Nature Structural & Molecular Biology·Marc BoehningMarkus Zweckstetter
Oct 28, 2019·International Journal of Molecular Sciences·Aneta Tarczewska, Beata Greb-Markiewicz
Oct 21, 2020·Emerging Topics in Life Sciences·Erik W Martin, Alex S Holehouse
Feb 7, 2021·Molecular Cell·Prashant RawatRitwick Sawarkar
Mar 8, 2020·Archives of Biochemistry and Biophysics·Andrea Soranno
Oct 11, 2017·Biophysical Journal·Eric B GibbsScott A Showalter
Mar 8, 2021·Journal of Molecular Biology·Mukesh Kumar Venkat RamaniYan Zhang
May 16, 2018·Journal of Molecular Biology·Anuradha MittalRohit V Pappu
Jun 17, 2020·Molecular Cell·Porfirio Quintero-CadenaPaul W Sternberg
Jul 9, 2021·Current Research in Structural Biology·Juliane F RipkaLaura S Itzhaki
May 19, 2021·Cold Spring Harbor Perspectives in Biology·Feiyue Lu, Timothée Lionnet
Oct 27, 2021·The FEBS Journal·Élie LambertFrançois Robert

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Methods Mentioned

BETA
nuclear
circular dichroism
X-ray
size
size exclusion chromatography
gel filtration
PCR

Software Mentioned

BioXtas RAW
ptmRS
Proteome Discoverer
Weblogo
BOXSHADE
Ensemble Optimization Method ( EOM )
CRYSOL
PyMol
MUSCLE
EOM

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