Evaluated articles

Evaluation Summary:

AAA+ ATPases consume chemical energy in form of ATP to catalyze essential cellular reactions. Here, computational and biochemical approaches are used to model how the six subunits of the AAA+ ATPase Rpt1-6 coordinate their enzymatic activity with each other to exert unidirectional pulling forces on target polypeptide chains that promote protein unfolding. Although the technical aspects of the work are sometimes difficult to follow, the findings indicate that the order in which ATPase active sites fire is generally sequential, much like a rotary engine. The system can tolerate "misfires" - instances in which a subunit fails to hydrolyze ATP - by skipping the problematic subunit. The work should appeal to the broad AAA+ community and researchers trying to understand the biophysical principles by which complex biological machines operate.

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

Evaluation Summary:

This work characterizes chromatin compaction in quiescent yeast cells and its role in the repression of gene expression. The authors' findings that chromatin compaction via heterogeneous interactions between nucleosomes directly contributes to transcriptional repression provides a useful conceptual paradigm for studies of quiescence in other organisms.

(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.)

Evaluation Summary:

This study recorded brain activity in monkeys to identify the neural mechanisms underlying an attention-related scalp ERP component that is similar to the human N2pc component. Intriguing evidence was provided that the surface potential was at least partly a result of current flows in the feedback-receiving supragranular and infragranular layers of area V4, not the granular layer that receives feedforward inputs. However, it is not entirely clear if these very interesting intracortical effects are the source of the scalp ERP effects.

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

Evaluation Summary:

This paper performs a systematic analysis of the fitness landscape of the influenza virus protein neuraminidase (NA). The paper analyzes 864 different combinations of mutations, over six genetic backgrounds. The main findings are that the fitness landscape correlates well across genetic backgrounds, and that natural evolution of neuraminidase seems to select for neutrally charged variants.

(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 name with the authors.)

Evaluation Summary:

This work has potential broad interest to both virologists and cell biologists interested in the regulatory functions of promyelocytic leukaemia nuclear bodies (PML-NBs). The authors use a combination of imaging techniques to identify PML, the principal scaffolding protein of PML-NBs, to form a variety of different structures in response to viral infection, immune stimulation, and DNA damage. Thestudy identifies PML to restrict the replication of human cytomegalovirus (HCMV) at multiple stages of infection through the formation of alternate PML-scaffold assemblies.

(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.)

Evaluation Summary:

The formation of the cardiopulmonary circuit is a vital terrestrial adaptation, and precise mechanisms defining how the heart and lung co-develop would be interesting to a broad developmental biology audience. In this manuscript, Rankin et al. propose a nuanced model that bridges previous observations regarding the role of Tbx5 and retinoic acid in forming the cardiopulmonary circuit. This manuscript nicely utilizes forward and reverse genetic approaches in Xenopus model system to rigorously study to describe a Tbx5-Aldh1a2- Shh pathway that leads to reciprocal mesoderm-endoderm interactions and co-induction of segmental heart and lung identities.

(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.)

Evaluation Summary:

The interneuron RIM affects many behaviours in C. elegans. Attempts to understand or manipulate its function have sometimes led to conflicting and difficult to interpret results. Sordillo and Bargmann investigate the role of the RIM in locomotion by manipulating it's signaling properties in multiple ways. The strength of this approach is that targeting multiple biological signaling mechanisms, they are able to conduct a nuanced analysis of RIM's signaling functions that goes beyond simplistic ON/OFF distinctions. They reach two primary conclusions: 1. RIM depolarization extends reversals via synaptic (glutamatergic) and secretory (tyraminergic) signaling; 2. RIM hyperpolarization promotes forward locomotion via electrical signaling through gap junctions. As a result, RIM was shown to act for stabilizing both forward and backward movement, which is important for understanding of C. elegans in general. Also, the implication that interneurons can be multifunctional in this way is intriguing and potentially impactful.

(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.)

Evaluation Summary:

This paper is of potential interest to an audience of biochemists, cell biologists, and structural biologists working in the area of chromosome organization and segregation. A wide range of in vitro methods is used to provide compelling biochemical evidence for the interaction of MatP and ParEC at the hinge of MukB, the condensin of Enterobacteria. However, the evidence supporting the significance of these interactions in vivo is less strong, limiting the biological implications of the elegant biochemical findings.

(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.)

Evaluation Summary:

Post-transcriptional gene regulation mediated by YTH proteins that bind N6-methyladenosine (m6A) in mRNA is a pathway that has emerged of importance in eukaryotic biology. This paper focuses on two evolutionarily close proteins of this family, ETC2 and ETC3 to find redundant, specific and divergent functions. The authors addressed previously contradictory reports regarding the subcellular location of these proteins. The paper is of general interest to scientists within the field of post-transcriptional gene regulation and RNA biology and is not limited to the plant research community. This will advance our understanding of mRNA methylation and its role in plant 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.)

This manuscript was co-submitted with: https://www.biorxiv.org/content/10.1101/2021.04.18.440342v2

Evaluation Summary:

Approaching the search of novel viruses while in an endogenized stage, rather than as free virions, the study by Hackl et al. reveals a large diversity of complete and fragmented virophage genomes - termed EMALEs- scattered throughout the genomes of four strains of the marine protist Cafeteria. Given that the activation of the integrated virophage mavirus during infection by the giant virus, CroV, has been shown to have a protective effect on the Cafeteria population, this study provides a tantalizing window into the traces of virophage-giant virus¬-protist interactions in the marine environment. Given the enormous diversity of virophages and giant viruses that have been found in metagenomes with no known hosts, this study is a step towards deciphering the biology of these viruses.

(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.)

Evaluation Summary:

Gene regulation triggered by recognising N6-methyladenosine (m6A) by RNA-binding proteins emerged as a fundamental process for development and adaptation in most eukaryotes. This paper is of interest to scientists within the field of post-transcriptional gene regulation and RNA biology. In a deep and thorough analysis, the authors resolved previously contradictory reports of sequence motifs associated with methylation sites in messenger RNAs and shed light on the proteins that recognise this modification.

(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.)

This manuscript was co-submitted with: https://www.biorxiv.org/content/10.1101/2021.08.01.454660v1

Evaluation Summary:

This work combines elegant experimental approaches with modelling predictions to study of metabolic adaptations in the bacterium Cupriavidus necator, a microorganism of interest given its metabolic versatility and potential industrial applications. This manuscript will be interesting for microbiologists and systems biologists who want to understand how protein production and economy and enzyme utilization differs in a versatile microorganism in different conditions.

(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.)

Evaluation Summary:

This manuscript will be of interest to immunologists studying mechanisms of thymic central tolerance. The study elegantly makes use of multiple genetic mouse models to generate data supporting the conclusion that different dendritic cell subsets in the thymus capture self-antigens from distinct subsets of thymic epithelial cells. However, some key conclusions are not entirely novel, and the final model, as currently presented, draws from only selective analyses and thus may not accurately reflect the antigen transfer between thymic epithelial cell and dendritic cell subsets that promote central tolerance.

(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.)

Evaluation Summary:

The authors report continuum electrostatics, molecular dynamics and QM/MM simulations to probe the protonation pattern of key residues in anion channelrhodopsin (GtACR1). The findings provide new mechanistic insights into the gating mechanism of GtACR1, and the study will be of potential interest for the community focused on biophysical chemistry, protein simulations and optogenetics. More generally, the study helps highlight that due to potential compensatory effects, care needs to be exercised when interpreting absorption spectra of mutant 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.)

Evaluation Summary:

This study describes the addition of peptide immunoprecipitation by means of SISCAPA technology to the Sars-Cov2 mass spectrometry-based diagnostics toolbox. While MS-based viral detection has been described by several other groups, the presented method enriches SARS-CoV-2 peptides from clinical samples, thus enhancing the sensitivity and addressing one of the major limitations of this new method for viral diagnostics. The work is straightforward and of potentially great importance to the field. It shows beyond any doubt that mass spectrometry can become a clinically applied diagnostic instrument to detect (viral) infection.

(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.)

Evaluation Summary:

This manuscript introduces a novel method for the monitoring of immune dynamics from blood, based on a measurement of the burden of cell-free DNA derived from seven key immune cell types in blood. The authors demonstrate the possibility to quantify the specific amounts of cell-free DNA by assaying cell-type specific CpG methylation marks via a targeted DNA sequencing assay. Assays of specific immune cell counts in blood are commonplace in modern diagnostic medicine. Rather than counting cells, the assay reported in this manuscript measures the burden of DNA released by dying immune cells, and this new assay may provide information about the immune system beyond what is possible with mere cell counting. The authors test their assay in three different settings (vaccination, inflammation and cancer), and provide significant support for the utility of their assay for immune monitoring in health and disease.

(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.)

Evaluation Summary:

The goal of this study was to test whether multiple attempts at suppressing the retrieval of an (emotional) memory is associated with degradation of the representation of information in the brain about such memories. A combination of sophisticated computational modelling in fMRI reveals that neural representations of previously suppressed memories are sustainably weakened during memory retrieval attempts. This manuscript is of interest for neuroscientists in the field of motivated forgetting and memory control.

(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.)

Evaluation Summary:

In this interesting study, the authors combined Brillouin microscopy with Optical Diffraction Tomography and epi-fluorescence imaging to investigate physical properties of biological materials including nucleoplasm, cytoplasm, phase-separated organelles, and adipocytes. The results are largely convincing and offer interesting insights into the material properties of these subcellular structures.

(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.)

Evaluation Summary:

In large nervous systems such as mammalian cortex excitatory synapses are stochastic and the probability of release of neurotransmitter can be modulated by plasticity and neural activity. This paper presents a simple biologically plausible mechanism that regulates the probability of release during learning. Using network simulations the authors show that this can result in more energy efficient processing of learned stimuli by enhancing the reliability of important connections, with lower expected rates of transmission at less important synapses.

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.

Evaluation Summary:

This paper investigates the evolutionary path of Escherichia coli resistance to the antibiotic trimethoprim. The authors show that adaptive mutations that accumulate early are often not in the drug target itself, but rather mutations that lead to transcriptional up-regulation of the drug target. Higher-level resistance can then evolve due to the addition of mutations in the drug target; however, at lower drug concentrations, cells are more likely to accumulate mutations that reverse the fitness defect associated with the initially acquired mutations. Overall, this study shows that regulatory mutations can play a major role in the evolution of antibiotic resistance in bacterial populations, and that the evolutionary path is influenced by the level of drug exposure.

(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. Reviewers #1 , #2, and #3 agreed to share their names with the authors.)