Biophysics

Archaeal chromatin ‘slinkies’ are inherently dynamic complexes with deflected DNA wrapping pathways

1. Samuel Bowerman
2. Jeff Wereszczynski
3. Karolin Luger

• Curated by eLife

  Evaluation Summary:

  In their manuscript titled "Archaeal chromatin 'slinkies' are inherently dynamic complexes with deflected DNA wrapping pathways", Bowerman et al. use an elegant combination of cryo-EM, analytical ultracentrifugation and molecular dynamics simulations to investigate the structure and dynamics of archaeal histone — DNA complexes, termed archaeasomes to distinguish them from eukaryotic nucleosomes. This study builds upon the crystal structure of an archaeasome and the functional analysis of its disruption recently published by the same group (Mattiroli et al, 2017) by analyzing the dynamics of this complex and discussing how these dynamics could relate to archaeal genome biology. How chromatin evolved is a fundamental question in biology, marking a striking departure from the bacterial nucleoid. This current manuscript describes a rigorous biophysical study that not only provides substantial new insights into archaeal genome biology but also raises intriguing questions for future study. This manuscript will therefore no doubt be of interest not only to the archaeal research community but also to the field of chromatin biology.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their names with the authors.)

Reviewed by eLife

Ligand Sensing Enhances Bacterial Flagellar Motor Output via Stator Recruitment

1. Farha Naaz
2. Megha Agrawal
3. Soumyadeep Chakraborty
4. Mahesh S. Tirumkudulu
5. K.V. Venkatesh

• Curated by eLife

  Summary: This is an interesting study reporting an increase in the rotation speed of the E. coli flagellar motor upon the sensing of a non-metabolizable glucose analog (2Dg) by the cell. The authors conclude that this increase is due to an increase in the number of torque-generating stator complexes that drive the motor. Knockout of the trg gene abolished this effect, suggesting that sensing of 2Dg by the Trg chemosensor is responsible. Involvement of membrane potential, the PTS pathway, and the chemotaxis response regulator CheY is ruled out. The manuscript is well-written, and the data are convincing. But the mechanism remains unclear.

  Reviewer #3 opted to reveal their name to the authors in the decision letter after review.

Reviewed by eLife

How subtle changes in 3D structure can create large changes in transcription

1. Jordan Xiao
2. Antonina Hafner
3. Alistair N. Boettiger

• Curated by eLife

  Summary: The work describes a simple theoretical model for enhancer action that explains several major controversies in the field of long-range gene regulation and the role of topologically associating domains and insulating boundaries in modulating enhancer-promoter interactions. Further, the model makes predictions that can be experimentally tested. This is valuable for the field of gene regulation.

  Reviewer #2 and Reviewer #3 opted to reveal their name to the authors in the decision letter after review.

Reviewed by eLife

The genotype-phenotype landscape of an allosteric protein

1. Drew S. Tack
2. Peter D. Tonner
3. Abe Pressman
4. Nathanael D. Olson
5. Sasha F. Levy
6. Eugenia F. Romantseva
7. Nina Alperovich
8. Olga Vasilyeva
9. David Ross

Reviewed by Review Commons

Structural characterization of the ANTAR antiterminator domain bound to RNA

1. James L Walshe
2. Rezwan Siddiquee
3. Karishma Patel
4. Sandro F Ataide

• Curated by eLife

  Summary: The reviewers were excited by the structural data, and felt that the structure represents an important advance in our understanding of ANTAR domain proteins. Nonetheless, while the reviewers found the proposed model of ANTAR regulation to be interesting, they raised concerns about the limited evidence in support of this model. In addition to the suggestions in the individual reviews, the authors thought the model could be tested using mutagenesis together with an in vivo or in vitro reporter system, and/or by structural studies of nascent transcripts in transcription complexes with EutV.

Reviewed by eLife

SARS-CoV-2 nucleocapsid protein forms condensates with viral genomic RNA

1. Amanda Jack
2. Luke S. Ferro
3. Michael J. Trnka
4. Eddie Wehri
5. Amrut Nadgir
6. Xammy Nguyenla
7. Katelyn Costa
8. Sarah Stanley
9. Julia Schaletzky
10. Ahmet Yildiz

Reviewed by eLife, ScreenIT

The metal cofactor zinc and interacting membranes modulate SOD1 conformation-aggregation landscape in an in vitro ALS Model

1. Achinta Sannigrahi
2. Sourav Chowdhury
3. Bidisha Das
4. Amrita Banerjee
5. Animesh Halder
6. Athi N. Naganathan
7. Sanat Karmakar
8. Krishnananda Chattopadhyay

Reviewed by eLife

Characterization of the dynamic resting state of a pentameric ligand-gated ion channel by cryo-electron microscopy and simulations

1. U Rovšnik
2. Y Zhuang
3. L Axelsson
4. BO Forsberg
5. V Lim
6. M Carroni
7. C Blau
8. RJ Howard
9. E Lindahl

Reviewed by eLife

Calponin-homology domain mediated bending of membrane-associated actin filaments

1. Saravanan Palani
2. Sayantika Ghosh
3. Esther Ivorra-Molla
4. Scott Clarke
5. Andrejus Suchenko
6. Mohan K Balasubramanian
7. Darius Vasco Köster

Reviewed by eLife

Through-grid wicking enables high-speed cryoEM specimen preparation

1. Yong Zi Tan
2. John L. Rubinstein

Reviewed by eLife