Literature DB >> 33650488

Archaeal chromatin 'slinkies' are inherently dynamic complexes with deflected DNA wrapping pathways.

Samuel Bowerman1, Jeff Wereszczynski2, Karolin Luger1.   

Abstract

Eukaryotes and many archaea package their DNA with histones. While the four eukaryotic histones wrap ~147 DNA base pairs into nucleosomes, archaeal histones form 'nucleosome-like' complexes that continuously wind between 60 and 500 base pairs of DNA ('archaeasomes'), suggested by crystal contacts and analysis of cellular chromatin. Solution structures of large archaeasomes (>90 DNA base pairs) have never been directly observed. Here, we utilize molecular dynamics simulations, analytical ultracentrifugation, and cryoEM to structurally characterize the solution state of archaeasomes on longer DNA. Simulations reveal dynamics of increased accessibility without disruption of DNA-binding or tetramerization interfaces. Mg2+ concentration influences compaction, and cryoEM densities illustrate that DNA is wrapped in consecutive substates arranged 90o out-of-plane with one another. Without ATP-dependent remodelers, archaea may leverage these inherent dynamics to balance chromatin packing and accessibility.
© 2021, Bowerman et al.

Entities:  

Keywords:  AUC; archaea; chromosomes; cryo-EM; gene expression; histone; molecular biophysics; molecular dynamics; none; nucleosome; structural biology

Mesh:

Substances:

Year:  2021        PMID: 33650488      PMCID: PMC7990501          DOI: 10.7554/eLife.65587

Source DB:  PubMed          Journal:  Elife        ISSN: 2050-084X            Impact factor:   8.140


  50 in total

1.  Crystal structures of recombinant histones HMfA and HMfB from the hyperthermophilic archaeon Methanothermus fervidus.

Authors:  K Decanniere; A M Babu; K Sandman; J N Reeve; U Heinemann
Journal:  J Mol Biol       Date:  2000-10-13       Impact factor: 5.469

2.  Reconstitution of nucleosome core particles from recombinant histones and DNA.

Authors:  Pamela N Dyer; Raji S Edayathumangalam; Cindy L White; Yunhe Bao; Srinivas Chakravarthy; Uma M Muthurajan; Karolin Luger
Journal:  Methods Enzymol       Date:  2004       Impact factor: 1.600

Review 3.  The histone tails of the nucleosome.

Authors:  K Luger; T J Richmond
Journal:  Curr Opin Genet Dev       Date:  1998-04       Impact factor: 5.578

4.  Reversible oligonucleosome self-association: dependence on divalent cations and core histone tail domains.

Authors:  P M Schwarz; A Felthauser; T M Fletcher; J C Hansen
Journal:  Biochemistry       Date:  1996-04-02       Impact factor: 3.162

5.  Multi-scale architecture of archaeal chromosomes.

Authors:  Naomichi Takemata; Stephen D Bell
Journal:  Mol Cell       Date:  2020-12-30       Impact factor: 17.970

6.  The conformation of the histone H3 tail inhibits association of the BPTF PHD finger with the nucleosome.

Authors:  Emma A Morrison; Samuel Bowerman; Kelli L Sylvers; Jeff Wereszczynski; Catherine A Musselman
Journal:  Elife       Date:  2018-04-12       Impact factor: 8.140

7.  Exploring protein native states and large-scale conformational changes with a modified generalized born model.

Authors:  Alexey Onufriev; Donald Bashford; David A Case
Journal:  Proteins       Date:  2004-05-01

8.  Structure of histone-based chromatin in Archaea.

Authors:  Francesca Mattiroli; Sudipta Bhattacharyya; Pamela N Dyer; Alison E White; Kathleen Sandman; Brett W Burkhart; Kyle R Byrne; Thomas Lee; Natalie G Ahn; Thomas J Santangelo; John N Reeve; Karolin Luger
Journal:  Science       Date:  2017-08-11       Impact factor: 47.728

9.  Chromatin is an ancient innovation conserved between Archaea and Eukarya.

Authors:  Ron Ammar; Dax Torti; Kyle Tsui; Marinella Gebbia; Tanja Durbic; Gary D Bader; Guri Giaever; Corey Nislow
Journal:  Elife       Date:  2012-12-13       Impact factor: 8.140

10.  The Cdc45/RecJ-like protein forms a complex with GINS and MCM, and is important for DNA replication in Thermococcus kodakarensis.

Authors:  Mariko Nagata; Sonoko Ishino; Takeshi Yamagami; Hiromi Ogino; Jan-Robert Simons; Tamotsu Kanai; Haruyuki Atomi; Yoshizumi Ishino
Journal:  Nucleic Acids Res       Date:  2017-10-13       Impact factor: 16.971

View more
  10 in total

1.  Profile of Karolin Luger.

Authors:  Jennifer Viegas
Journal:  Proc Natl Acad Sci U S A       Date:  2022-08-08       Impact factor: 12.779

2.  Columnar structure of human telomeric chromatin.

Authors:  Aghil Soman; Sook Yi Wong; Nikolay Korolev; Wahyu Surya; Simon Lattmann; Vinod K Vogirala; Qinming Chen; Nikolay V Berezhnoy; John van Noort; Daniela Rhodes; Lars Nordenskiöld
Journal:  Nature       Date:  2022-09-14       Impact factor: 69.504

3.  A proposed unified mitotic chromosome architecture.

Authors:  John Sedat; Angus McDonald; Herbert Kasler; Eric Verdin; Hu Cang; Muthuvel Arigovindan; Cornelis Murre; Michael Elbaum
Journal:  Proc Natl Acad Sci U S A       Date:  2022-05-11       Impact factor: 12.779

4.  The structure of a virus-encoded nucleosome.

Authors:  Marco Igor Valencia-Sánchez; Stephen Abini-Agbomson; Miao Wang; Rachel Lee; Nikita Vasilyev; Jenny Zhang; Pablo De Ioannes; Bernard La Scola; Paul Talbert; Steve Henikoff; Evgeny Nudler; Albert Erives; Karim-Jean Armache
Journal:  Nat Struct Mol Biol       Date:  2021-04-29       Impact factor: 15.369

5.  Extended Archaeal Histone-Based Chromatin Structure Regulates Global Gene Expression in Thermococcus kodakarensis.

Authors:  Travis J Sanders; Fahad Ullah; Alexandra M Gehring; Brett W Burkhart; Robert L Vickerman; Sudili Fernando; Andrew F Gardner; Asa Ben-Hur; Thomas J Santangelo
Journal:  Front Microbiol       Date:  2021-05-13       Impact factor: 5.640

6.  Deep Conservation of Histone Variants in Thermococcales Archaea.

Authors:  Kathryn M Stevens; Antoine Hocher; Tobias Warnecke
Journal:  Genome Biol Evol       Date:  2022-01-04       Impact factor: 3.416

7.  A proposed unified interphase nucleus chromosome structure: Preliminary preponderance of evidence.

Authors:  John Sedat; Angus McDonald; Hu Cang; Joseph Lucas; Muthuvel Arigovindan; Zvi Kam; Cornelis Murre; Michael Elbaum
Journal:  Proc Natl Acad Sci U S A       Date:  2022-06-24       Impact factor: 12.779

Review 8.  Archaea: The Final Frontier of Chromatin.

Authors:  Shawn P Laursen; Samuel Bowerman; Karolin Luger
Journal:  J Mol Biol       Date:  2020-12-29       Impact factor: 5.469

Review 9.  Single-Molecule/Cell Analyses Reveal Principles of Genome-Folding Mechanisms in the Three Domains of Life.

Authors:  Hugo Maruyama; Takayuki Nambu; Chiho Mashimo; Toshinori Okinaga; Kunio Takeyasu
Journal:  Int J Mol Sci       Date:  2021-12-14       Impact factor: 5.923

10.  Virus-encoded histone doublets are essential and form nucleosome-like structures.

Authors:  Yang Liu; Hugo Bisio; Chelsea Marie Toner; Sandra Jeudy; Nadege Philippe; Keda Zhou; Samuel Bowerman; Alison White; Garrett Edwards; Chantal Abergel; Karolin Luger
Journal:  Cell       Date:  2021-07-22       Impact factor: 41.582

  10 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.