Molecular Biology

Ensemble refinement of mismodeled cryo-EM RNA structures using all-atom simulations

1. Elisa Posani
2. Pavel Janoš
3. Daniel Haack
4. Navtej Toor
5. Massimiliano Bonomi
6. Alessandra Magistrato
7. Giovanni Bussi

Reviewed by PREreview

Genetic stability of Mycobacterium smegmatis under the stress of first-line antitubercular agents

1. Dániel Molnár
2. Éva Viola Surányi
3. Tamás Trombitás
4. Dóra Füzesi
5. Rita Hirmondó
6. Judit Toth

• Curated by eLife

  eLife Assessment

  This useful study reports on the impact of antibiotic pressure on the genomic stability of the mc2155 strain of Mycobacterium smegmatis, a model for Mycobacterium tuberculosis. The findings of the study indicate that exposure to antibiotics did not lead to the development of new adaptive mutations in controlled laboratory environments, challenging the notion that antibiotic resistance arises from drug-induced microevolution. The genomic analysis provides detailed insights into the stability of M. smegmatis following exposure to standard TB treatment antibiotics, and the evidence suggesting that antibiotic pressure does not contribute to the emergence of new adaptive mutations is solid.

Reviewed by eLife

Robust single-nucleus RNA sequencing reveals depot-specific cell population dynamics in adipose tissue remodeling during obesity

1. Jisun So
2. Olivia Strobel
3. Jamie Wann
4. Kyungchan Kim
5. Avishek Paul
6. Dominic J Acri
7. Luke C Dabin
8. Jungsu Kim
9. Gang Peng
10. Hyun Cheol Roh

• Curated by eLife

  eLife Assessment

  So et al. present an optimized protocol for single-nuclei RNA sequencing of adipose tissue in mice, ensuring better RNA quality and nuclei integrity. The authors use this protocol to explore the cellular landscape in both lean and diet-induced obese mice, identifying a dysfunctional hypertrophic adipocyte subpopulation linked to obesity. The data analyses are solid, and the findings are supported by the evidence presented. This study provides valuable information for the field of adipose tissue biology and will be particularly helpful for researchers using single-nuclei transcriptomics in various tissues.

Reviewed by eLife

Perturbations in eIF3 subunit stoichiometry alter expression of ribosomal proteins and key components of the MAPK signaling pathways

1. Anna Herrmannová
2. Jan Jelínek
3. Klára Pospíšilová
4. Farkas Kerényi
5. Tomáš Vomastek
6. Kathleen Watt
7. Jan Brábek
8. Mahabub Pasha Mohammad
9. Susan Wagner
10. Ivan Topisirovic
11. Leoš Shivaya Valášek

• Curated by eLife

  eLife Assessment

  This study demonstrates mRNA-specific regulation of translation by subunits of the eukaryotic initiation factor complex 3 (eIF3) using convincing methods, data, and analyses. The investigations have generated important information that will be of interest to biologists studying translation regulation. However, the physiological significance of the gene expression changes that were observed is not clear.

Reviewed by eLife

Molecular basis of neurodegeneration in a mouse model of Polr3-related disease

1. Robyn D Moir
2. Emilio Merheb
3. Violeta Chitu
4. E Richard Stanley
5. Ian M Willis

• Curated by eLife

  eLife Assessment

  This study provides important insights into the mechanistic basis of neurological manifestations of RNA polymerase III-related disease by creating a mutant mouse to dissect transcriptional changes. The data provide compelling evidence for disease progression initiated by a global reduction in tRNA levels leading to integrated stress and innate immune responses and neuronal loss. The work will be of interest to those engaged in the study of chromosome biology, developmental biology and neurodegeneration.

Reviewed by eLife

RNA tertiary structure and conformational dynamics revealed by BASH MaP

1. Maxim Oleynikov
2. Samie R Jaffrey

• Curated by eLife

  eLife Assessment

  This important work substantially advances our understanding of RNA structure analysis by introducing an innovative method that extends DMS probing to include guanosine residues, thereby enhancing our ability to detect complex tertiary interactions. The evidence supporting the conclusions is compelling, with detailed analyses demonstrating the method's capacity to differentiate structural contexts and improve RNA structure predictions. This work will be of broad interest to RNA structural biology, biochemistry, and biophysics researchers.

Reviewed by eLife

UBR4 regulates a MetAP2-dependent Arg/N-degron pathway

1. Evan J. Morrison
2. Emma Horton
3. Olivia S. Rissland

Reviewed by Life Science Editors Foundation

Localized molecular chaperone synthesis maintains neuronal dendrite proteostasis

1. Célia Alecki
2. Javeria Rizwan
3. Phuong Le
4. Suleima Jacob-Tomas
5. Mario Fernandez-Comaduran
6. Morgane Verbrugghe
7. Jia Ming Stella Xu
8. Sandra Minotti
9. James Lynch
10. Tad Wu
11. Heather Durham
12. Gene W. Yeo
13. Maria Vera

Reviewed by Life Science Editors Foundation

Evidence for a role of human blood-borne factors in mediating age-associated changes in molecular circadian rhythms

1. Jessica E Schwarz
2. Antonijo Mrčela
3. Nicholas F Lahens
4. Yongjun Li
5. Cynthia Hsu
6. Gregory R Grant
7. Carsten Skarke
8. Shirley L Zhang
9. Amita Sehgal

• Curated by eLife

  eLife Assessment

  The authors tested the hypothesis that age-dependent factors in human sera affect the core circadian clock or its outputs in cultured fibroblasts, and they provide compelling evidence that genes involved in the cell cycle and transcription/translation remain rhythmic in both conditions, genes associated with oxidative phosphorylation and Alzheimer's Disease lose rhythmicity in the aged condition, while the expression of cycling genes associated with cholesterol biosynthesis increase in the cells entrained with old serum. Together, the findings suggest that yet to be identified age-dependent blood-borne factors affect circadian rhythms in the periphery. The paper provides fundamental insights and a possible explanation for previous observations showing that circadian gene expression in peripheral tissues tends to dampen or phase-shift with age.

Reviewed by eLife

Human DCP1 is crucial for mRNA decapping and possesses paralog-specific gene regulating functions

1. Ting-Wen Chen
2. Hsiao-Wei Liao
3. Michelle Noble
4. Jing-Yi Siao
5. Yu-Hsuan Cheng
6. Wei-Chung Chiang
7. Yi-Tzu Lo
8. Chung-Te Chang

• Curated by eLife

  eLife Assessment

  This study attempts to understand the functional roles of the human DCP1 paralogs in regulating RNA decay by DCP2. Using a combination of cellular-based assays and in vitro assays, the authors conclude that DCP1a/b plays a role in regulating DCP2 activity. While this revised version presents some new and interesting observations on human DCP1, the underlying data to support its claims remain incomplete. Overall, these results will be useful to the RNA community.

Reviewed by eLife