eLife

Latest preprint reviews

1. Single turnover transient state kinetics reveals processive protein unfolding catalyzed by Escherichia coli ClpB

   This article has 3 authors:

   1. Jaskamaljot Kaur Banwait
   2. Liana Islam
   3. Aaron L Lucius

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This valuable study presents the development of a single turnover stopped-flow fluorescence experiment to study the kinetics of substrate unfolding and translocation by the bacterial ClpB disaggregase. Using non-physiological nucleotides to bypass the physiological regulation mechanism of ClpB, the authors convincingly show that the ClpB disaggregase is a processive motor with a slow unfolding step preceding rapid translocation. The results of this analysis are of value for future mechanistic studies on energy-dependent unfolding, degradation, and disaggregation molecular machines.

   Reviewed by eLife

2. PPIscreenML: Structure-based screening for protein-protein interactions using AlphaFold

   This article has 4 authors:

   1. Victoria Mischley
   2. Johannes Maier
   3. Jesse Chen
   4. John Karanicolas

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This study explores simple machine learning frameworks to distinguish between interacting and non-interacting protein pairs, offering solid computational results despite some concerns about dataset generation. The authors demonstrate a modest improvement in AlphaFold-multimers' ability to differentiate these pairs. Using a simple yet sound approach, this work is a valuable contribution to the challenging problem of reconstructing protein-protein interaction networks.

   Reviewed by eLife

3. Dock-and-lock binding of SxIP ligands is required for stable and selective EB1 interactions

   This article has 4 authors:

   1. Teresa Almeida
   2. Eleanor Hargreaves
   3. Tobias Zech
   4. Igor Barsukov

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This study provides important insights into how the EBH domain of microtubule end-binding protein 1 (EB1) interacts with SxIP peptides derived from the MACF plus-end tracking protein. The revised manuscript includes convincing ITC and NMR experiments that clarify the role of flanking residues and address the influence of dimerization and cooperativity on binding. While some mechanistic aspects remain difficult to resolve experimentally, the data and analysis now more clearly justify the proposed "dock-and-lock" model and its interpretive value. This work will be of interest to structural biologists and biophysicists studying microtubule-associated protein interactions.

   Reviewed by eLife

4. Proteomic landscape of tunneling nanotubes reveals CD9 and CD81 tetraspanins as key regulators

   This article has 7 authors:

   1. Roberto Notario Manzano
   2. Thibault Chaze
   3. Eric Rubinstein
   4. Esthel Penard
   5. Mariette Matondo
   6. Chiara Zurzolo
   7. Christel Brou

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     Notario Manzano et al. offer a valuable first analysis of proteins within tunneling nanotubes (TNTs), membranous bridges connecting cells. This work distinguishes TNTs from extracellular vesicles, but further experimental and analytical tools are needed to refine the TNT proteome. Solid data supports a role for tetraspanins CD9 and CD81 in TNT function. The proposed model for CD9 and CD81 is over-interpreted and requires additional evidence for stronger support.

   Reviewed by eLife

5. Treacle’s ability to form liquid-like phase condensates is essential for nucleolar fibrillar center assembly, efficient rRNA transcription and processing, and rRNA gene repair

   This article has 9 authors:

   1. Artem K Velichko
   2. Nadezhda V Petrova
   3. Dmitry A Deriglazov
   4. Anastasia P Kovina
   5. Artem V Luzhin
   6. Eugene P Kazakov
   7. Igor I Kireev
   8. Sergey Razin
   9. Omar L Kantidze

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This important study reveals that the nucleolar protein Treacle undergoes liquid-liquid phase separation in vitro and in vivo. It provides convincing evidence that the ability of Treacle to form phase-separated condensates is necessary for the proper formation of the fibrillar center of the nucleolus, rRNA transcription, and rDNA repair. These findings will be of interest to the communities studying biomolecular condensates, nucleolar organization, and ribosome biogenesis.

   Reviewed by eLife

6. Loss of SPNS1, a lysosomal transporter, in the nervous system causes dysmyelination and white matter dysplasia

   This article has 11 authors:

   1. Yoshinobu Ichimura
   2. Yuki Sugiura
   3. Yoshinori Katsuragi
   4. Yu-Shin Sou
   5. Takefumi Uemura
   6. Naoki Tamura
   7. Satoko Komatsu-Hirota
   8. Takashi Ueno
   9. Masato Koike
   10. Satoshi Waguri
   11. Masaaki Komatsu

   This article has been curated by 1 group:

   • Curated by eLife

     eLife assessment

     This paper presents useful findings on the dysmyelination phenotype of nervous system-specific Spns1 (a lysosomal lipid transporter) knockout mice. While the analysis of the phenotype is solid, the evidence for the underlying mechanisms, especially the molecular function for SPNS1, is incomplete. With more careful interpretation and/or additional experimental data, this work could have implications for understanding lipid transport and lysosomal storage diseases.

   Reviewed by eLife

7. Neuronal migration depends on blood flow in the adult mammalian brain

   This article has 16 authors:

   1. Takashi Ogino
   2. Akari Saito
   3. Masato Sawada
   4. Shoko Takemura
   5. Yuzuki Hara
   6. Kanami Yoshimura
   7. Jiro Nagase
   8. Honomi Kawase
   9. Takamasa Sato
   10. Hiroyuki Inada
   11. Vicente Herranz-Pérez
   12. Yoh-suke Mukouyama
   13. Masatsugu Ema
   14. José Manuel García-Verdugo
   15. Junichi Nabekura
   16. Kazunobu Sawamoto

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This fundamental work provides novel insights into the blood flow-dependent mechanisms of neuronal migration and the role of Gherlin signaling in the adult brain. The authors present convincing evidence that newborn rostral migratory stream (RMS) neurons are closely situated alongside blood vessels, preferentially along arterioles, and that migratory speed is correlated with blood flow. They also provide evidence (in vitro and some in vivo) that Ghrelin from blood is involved in augmenting RMS neuron migration speed.

   Reviewed by eLife

8. Mesolimbic dopamine ramps reflect environmental timescales

   This article has 4 authors:

   1. Joseph R Floeder
   2. Huijeong Jeong
   3. Ali Mohebi
   4. Vijay Mohan K Namboodiri

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     Floeder and colleagues provide an important investigation that describes the experimental conditions that systematically produce "ramps" in dopamine signaling in the striatum. This somewhat nebulous feature of dopamine has been a significant part of recent theoretical and computational debates attempting to formally describe the different timescales on which dopamine functions. The current results are convincing and add context to that ongoing work.

   Reviewed by eLife

9. Secondary structure of the SARS-CoV-2 genome is predictive of nucleotide substitution frequency

   This article has 1 author:

   1. Zach Hensel

   This article has been curated by 1 group:

   • Curated by eLife

     eLife Assessment

     This short manuscript uses mutation counts in phylogenies of millions of SARS-CoV-2 genomes to show that mutation rates systematically differ between regions that are paired or unpaired in the predicted RNA secondary structure of the viral genome. Such an effect of pairing state is not unexpected, but its systematic demonstration using millions of viral genomes is valuable and convincing.

   Reviewed by eLife

10. On the nature of the earliest known lifeforms

    This article has 9 authors:

    1. Dheeraj Kanaparthi
    2. Frances Westall
    3. Marko Lampe
    4. Baoli Zhu
    5. Thomas Boesen
    6. Bettina Scheu
    7. Andreas Klingl
    8. Petra Schwille
    9. Tillmann Lueders

    This article has been curated by 1 group:

    • Curated by eLife

      eLife Assessment

      This provocative manuscript presents important comparisons of the morphologies of Archaean bacterial microfossils to those of microbes transformed under environmental conditions that mimic those present on Earth during the same Eon. The evidence in support of the conclusions is solid. The authors' environmental condition selection for their experiment is justified.

    Reviewed by eLife