eLife

Latest preprint reviews

1. Post-translational flavinylation is associated with diverse extracytosolic redox functionalities throughout bacterial life

   This article has 5 authors:

   1. Raphaël Méheust
   2. Shuo Huang
   3. Rafael Rivera-Lugo
   4. Jillian F. Banfield
   5. Samuel H. Light

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     Light and coworkers provide evidence from mining 31,910 prokaryotic genomes for the widespread occurrence of extracytosolic flavinylated FMN-binding domains in bacteria. They discovered extracytosolic flavinylation of five protein classes potentially involved in transmembrane electron transfer. The study also proposes new connections between respiration and iron assimilation and identifies two novel substrates of ApbE enzymes. This work should inspire further work in the fields of redox enzymology and bioenergetics to characterize the suggested involvement of flavinylated protein complexes in prokaryotes.

     (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, Reviewer #2 and Reviewer #3 agreed to share their names with the authors.)

   Reviewed by eLife

2. Contingency and chance erase necessity in the experimental evolution of ancestral proteins

   This article has 5 authors:

   1. Victoria Cochran Xie
   2. Jinyue Pu
   3. Brian P.H. Metzger
   4. Joseph W. Thornton
   5. Bryan C. Dickinson

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This manuscript, which will be of interest to students of evolution and anybody interested in protein function, uses an original, clever, high throughput, and rapid experimental protein evolution method to assess the roles and contributions of contingency, chance, and necessity in the evolution of protein-protein interactions. The authors focus on the animal BCL-2 protein family and on the evolution of their binding properties to two proteins, NOXA and BID. Using several replicates and several starting points, they found little predictability between replicates of single starting points and among those from multiple starting points, indicating that there is no single pathway through sequence space to the selected function, and that historical contingency is the primary cause of protein evolution here. The presented results convincingly illustrate the potential of this novel technology for future work in directed protein evolution.

     (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

3. Differential conditioning produces merged long-term memory in Drosophila

   This article has 4 authors:

   1. Bohan Zhao
   2. Jiameng Sun
   3. Qian Li
   4. Yi Zhong

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This work reveals a novel form of Drosophila long-term memory (LTM) that is of potential interest to most neuroscientists working on various animals. While classical protein-synthesis-dependent LTM forms only after repetitive spaced trials of olfactory conditioning, the authors discovered that flies also form a "blurred" or "vague" protein-synthesis-dependent LTM which distinguishes the experienced two odors from the third naive odor after single-trial training. This merged LTM lacking the event details likely occurs in most animals since long-lasting memory of occasional threatening experiences for future escape behavior is crucial for survival.

     (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 agreed to share their name with the authors.)

   Reviewed by eLife

4. Allosteric communication in DNA polymerase clamp loaders relies on a critical hydrogen-bonded junction

   This article has 8 authors:

   1. Subu Subramanian
   2. Kent Gorday
   3. Kendra Marcus
   4. Matthew R Orellana
   5. Peter Ren
   6. Xiao Ran Luo
   7. Michael E O'Donnell
   8. John Kuriyan

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper will be of interest not only to scientists working in the primary field of DNA replication, but also to molecular biologists employing deep mutagenesis as well as structural biologists interested in the functions of the broader class of AAA+ ATPase molecular machines. The work examines relationships between protein sequence, structure and function in the bacteriophage T4 clamp-clamp loader complex, a highly studied AAA+ ATPase that deposits ring-shaped proteins onto DNA to support DNA polymerase processivity and DNA replication. The clamp loader system is revealed to have a high tolerance to amino acid substitution, with little correlation between permitted substitutions and phylogenetic variation. A hitherto unrecognized residue in the clamp loader, which appears to be shared among certain AAA+ ATPase members, is identified as critical for the maintenance of a functional structure and for allosteric coupling. The key claims of the paper are well supported by the data presented, and the employed methodology has undergone rigorous validation. Although a few control studies are still needed, this is a novel and significant paper overall.

     (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 agreed to share their name with the authors.)

   Reviewed by eLife

5. Structural Basis for Allosteric Control of the SERCA-Phospholamban Membrane Complex by Ca ²⁺ and cAMP-dependent Phosphorylation

   This article has 11 authors:

   1. Daniel K. Weber
   2. Máximo Sanz-Hernández
   3. U. Venkateswara Reddy
   4. Songlin Wang
   5. Erik K. Larsen
   6. Tata Gopinath
   7. Martin Gustavsson
   8. Razvan L. Cornea
   9. David D. Thomas
   10. Alfonso De Simone
   11. Gianluigi Veglia

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     There are many of membrane-embedded mini-proteins, which fulfill a large range of regulatory functions. One of them is phospholamban, a single transmembrane helix protein that regulates the sarcoplasmic reticulum Ca2+-ATPase by binding in the membrane. The work presented here combines new experiments with computer simulations with the aim of arriving at a more definitive answer to the long-standing mechanistic question of how exactly phosphorylation of phospholamban modulates its regulatory behavior. In this manuscript, an allosteric mechanism is presented, which could be of general importance for the whole family of these mini-proteins.

     (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 agreed to share their name with the authors.)

   Reviewed by eLife

6. Diversity of excitatory release sites

   This article has 6 authors:

   1. Maria Rita Karlocai
   2. Judit Heredi
   3. Tünde Benedek
   4. Noemi Holderith
   5. Andrea Lorincz
   6. Zoltan Nusser

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     The authors study how individual synapses can compute information by tuning the properties of the individual components that drive synaptic communication between neurons. Using cutting edge physiology and morphology they show that the reliability of synaptic communication depends not only on how many units drive synaptic communication, but also the authors suggest that individual units vary in their quantitative molecular composition.

     (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 #2 agreed to share their name with the authors.)

   Reviewed by eLife

7. 7-Dehydrocholesterol-derived oxysterols cause neurogenic defects in Smith-Lemli-Opitz syndrome

   This article has 6 authors:

   1. Hideaki Tomita
   2. Kelly M Hines
   3. Josi M Herron
   4. Amy Li
   5. David W Baggett
   6. Libin Xu

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper will be of interest to developmental biologists and neuroscientists as it aims to resolve the unknown mechanism by which loss of a key enzyme in cholesterol biosynthesis results in neurodevelopmental defects. It provides a conceptual framework for understanding how altered lipid metabolism can impact brain development. Many of the key claims of the paper are well-supported, but reasonable alternative explanations remain.

     (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 agreed to share their name with the authors.)

   Reviewed by eLife

8. A Brownian ratchet model for DNA loop extrusion by the cohesin complex

   This article has 5 authors:

   1. Torahiko L Higashi
   2. Georgii Pobegalov
   3. Minzhe Tang
   4. Maxim I Molodtsov
   5. Frank Uhlmann

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This work combines experiments and simulations together with previously reported biophysical and structural observations to develop a structure-based model that provides mechanistic insight into the two functions of cohesin: cohesion and loop extrusion. This intriguing and informative manuscript will be of broad interest to those working in the fields of chromatin structure, chromosome biology and molecular machines. While the data and analysis support the authors' conclusions, the presentation of the work can be improved for clarity.

     (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. The reviewers remained anonymous to the authors.)

   Reviewed by eLife

9. Sustained expression of unc-4 homeobox gene and unc-37/Groucho in postmitotic neurons specifies the spatial organization of the cholinergic synapses in C. elegans

   This article has 6 authors:

   1. Mizuki Kurashina
   2. Jane Wang
   3. Jeffrey Lin
   4. Kathy Kyungeun Lee
   5. Arpun Johal
   6. Kota Mizumoto

   This article has been curated by 1 group:

   • Curated by eLife

     Evaluation Summary:

     This paper is of potential interest to a broad audience of neuroscientists, as it adds to our growing understanding of transcriptional mechanisms that regulate neural connectivity. Specifically, the paper provides support for the idea that transcriptional pathways previously implicated in neuronal cell fate determination can have independent roles in specifying connectivity between neurons. The study is highly technically innovative and cleverly uses a set of newly developed tools to analyze the developmental time window over which transcriptional activity is required to achieve to proper connectivity. However, the paper falls a little short in defining specific mechanisms involved downstream of the transcription factors themselves.

     (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. The reviewers remained anonymous to the authors.)

   Reviewed by eLife

10. Single-cell analysis of the ventricular-subventricular zone reveals signatures of dorsal and ventral adult neurogenesis

    This article has 11 authors:

    1. Arantxa Cebrian-Silla
    2. Marcos Assis Nascimento
    3. Stephanie A Redmond
    4. Benjamin Mansky
    5. David Wu
    6. Kirsten Obernier
    7. Ricardo Romero Rodriguez
    8. Susana Gonzalez-Granero
    9. Jose Manuel García-Verdugo
    10. Daniel A Lim
    11. Arturo Álvarez-Buylla

    This article has been curated by 1 group:

    • Curated by eLife

      Evaluation Summary:

      Redmond et al. use single-cell and single-nucleus RNA-sequencing to reveal the molecular heterogeneity that underlies regional differences in neural stem cells in the adult mouse. Prior work had separate subventricular stem cells as type A and B. By generating bulk and single cell transcriptome sequence data, the authors identified a distinct subtype of both A and B cells that differentiate into dorsal and ventral identities. They also identify a set of genes that constitute a conserved molecular signature of these cell types.

      (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 #2 agreed to share their name with the authors.)

    Reviewed by eLife