Biophysics

Spurious regulatory connections dictate the expression‐fitness landscape of translation factors

1. Jean‐Benoît Lalanne
2. Darren J Parker
3. Gene‐Wei Li

Reviewed by Review Commons

Conformational dynamics of auto-inhibition in the ER calcium sensor STIM1

1. Stijn van Dorp
2. Ruoyi Qiu
3. Ucheor B Choi
4. Minnie M Wu
5. Michelle Yen
6. Michael Kirmiz
7. Axel T Brunger
8. Richard S Lewis

• Curated by eLife

  Evaluation Summary:

  This study uses complementary approaches to advance our mechanistic understanding of STIM1 activation, with elegant single molecule methods providing new details on STIM1 structure and dynamics. Full length STIM1 in a cellular environment was probed by crosslinking, but the same has not yet been possible with single-molecule Förster resonance energy transfer (smFRET).

  (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

Voltage-clamp fluorometry analysis of structural rearrangements of ATP-gated channel P2X2 upon hyperpolarization

1. Rizki Tsari Andriani
2. Yoshihiro Kubo

• Curated by eLife

  Evaluation Summary:

  This study will be of broad interest to ion channel researchers interested in understanding the fundamental mechanisms of voltage-sensing. The researchers use a novel approach to determine the mechanism of voltage-sensing in a channel that lacks a canonical voltage-sensing domain.

  (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 #3 agreed to share their names with the authors.)

Reviewed by eLife

The propofol binding sites of prokaryotic voltage-gated sodium channels

1. Elaine Yang
2. Weiming Bu
3. Antonio Suma
4. Vincenzo Carnevale
5. Kimberly C. Grasty
6. Patrick Loll
7. Kellie Woll
8. Natarajan Bhanu
9. Benjamin A. Garcia
10. Roderic G. Eckenhoff
11. Manuel Covarrubias

Reviewed by eLife

Confinement discerns swarmers from planktonic bacteria

1. Weijie Chen
2. Neha Mani
3. Hamid Karani
4. Hao Li
5. Sridhar Mani
6. Jay X Tang

• Curated by eLife

  Summary: In this paper, the authors proposed a new approach by mounting a PDMS microwells of specific sizes on agar surface to confine swarming and planktonic SM3 cells. They found swarming bacteria exhibit a "single-swirl" motion pattern and concentrated planktonic bacteria exhibit "multi-swirls" motion pattern in the diameter range of 31-90 μm. The phase diagram shows that in smaller wells concentrated planktonic SM3 forms a single vortex and in larger wells swarming SM3 also breaks into mesoscale vortices.

  In addition, they conducted systematic experiments to explore parameters defining the divergence of motion patterns in confinement including cell density, cell length, cell speed and surfactant. They concluded that the single swirl pattern depends on cohesive cell-cell interaction mediated by biochemical factors removable through matrix dilution.

  This paper gives a new method to discern swarmers from planktonic bacteria and carefully studies the factors that influence the formation of bacterial vortices under restriction.

Reviewed by eLife

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. KV 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 Yupeng 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. Nathan 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