Molecular Biology

Deep learning-driven insights into super protein complexes for outer membrane protein biogenesis in bacteria

1. Mu Gao
2. Davi Nakajima An
3. Jeffrey Skolnick

• Curated by eLife

  eLife assessment

  In this valuable contribution, the authors apply an artificial intelligence method to predict the three-dimensional structure of complexes of outer membrane proteins of the Gram-negative bacterium E. coli. Some of the cases presented are compelling, as they explain previously published biochemical data and/or reproduce existing structural data.

Reviewed by eLife

m6A modification of U6 snRNA modulates usage of two major classes of pre-mRNA 5’ splice site

1. Matthew T Parker
2. Beth K Soanes
3. Jelena Kusakina
4. Antoine Larrieu
5. Katarzyna Knop
6. Nisha Joy
7. Friedrich Breidenbach
8. Anna V Sherwood
9. Geoffrey J Barton
10. Sebastian M Fica
11. Brendan H Davies
12. Gordon G Simpson

• Curated by eLife

  eLife assessment

  This is an important paper reporting that an adenosine methyltransferase in the model plant Arabidopsis functions to target a key RNA component of the spliceosome, as in fission yeast, and thereby contributes to intron recognition. By contrast, the authors report no major role for the methyltransferase in targeting mRNAs, as reported in previous studies in Arabidopsis. While some of the evidence is convincing, other evidence is incomplete. The conclusions that mRNAs are not a significant target and that specific intronic sequences define sensitivity to the methyltransferase require additional support.

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A cryogenic, coincident fluorescence, electron, and ion beam microscope

1. Daan B Boltje
2. Jacob P Hoogenboom
3. Arjen J Jakobi
4. Grant J Jensen
5. Caspar TH Jonker
6. Max J Kaag
7. Abraham J Koster
8. Mart GF Last
9. Cecilia de Agrela Pinto
10. Jürgen M Plitzko
11. Stefan Raunser
12. Sebastian Tacke
13. Zhexin Wang
14. Ernest B van der Wee
15. Roger Wepf
16. Sander den Hoedt

• Curated by eLife

  eLife assessment

  This paper is of particular interest to researchers who plan to use focused-ion beam scanning electron microscopes (FIB-SEMs) and require fluorescent data to guide the milling process. The authors describe a valuable after-market upgrade that allows fluorescent data acquisition during FIB-milling without stage repositioning. Technical details of the fluorescent module upgrade together with the sample stage redesign are compellingly documented and will enhance the implementation of this important technology.

Reviewed by eLife

The anatomy of transcriptionally active chromatin loops in Drosophila primary spermatocytes using super-resolution microscopy

1. Madeleine L. Ball
2. Stefan A. Koestler
3. Leila Muresan
4. Sohaib Abdul Rehman
5. Kevin O’Holleran
6. Robert White

Reviewed by Review Commons

Structure and flexibility of the yeast NuA4 histone acetyltransferase complex

1. Stefan A Zukin
2. Matthew R Marunde
3. Irina K Popova
4. Katarzyna M Soczek
5. Eva Nogales
6. Avinash B Patel

• Curated by eLife

  eLife assessment

  This manuscript provides insights into the architecture of the yeast histone acetyltransferase complex NuA4 and is of broad interest to those studying transcription and chromatin modification. The cryo-EM data are of very high quality, and enable the authors to devise a structural model that is in much better agreement with biochemical data than previously reported models. This structure represents an important puzzle piece towards a molecular understanding of chromatin modification.

Reviewed by eLife

Nuclear m6A reader YTHDC1 promotes muscle stem cell activation/proliferation by regulating mRNA splicing and nuclear export

1. Yulong Qiao
2. Qiang Sun
3. Xiaona Chen
4. Liangqiang He
5. Di Wang
6. Ruibao Su
7. Yuanchao Xue
8. Hao Sun
9. Huating Wang

• Curated by eLife

  eLife assessment

  This is a valuable study performing elegant experiments making identification of a specific regulator in skeletal muscle regeneration. It will form a foundation for further mechanistic investigation. The work is of importance in the clinical field of muscle injury and regeneration.

Reviewed by eLife

Tup1 is critical for transcriptional repression in Quiescence in S. cerevisiae

1. Thomas B. Bailey
2. Phaedra A. Whitty
3. Eric U. Selker
4. Jeffrey. N. McKnight
5. Laura E. McKnight

Reviewed by Review Commons

A cell wall synthase accelerates plasma membrane partitioning in mycobacteria

1. Takehiro Kado
2. Zarina Akbary
3. Daisuke Motooka
4. Ian L Sparks
5. Emily S Melzer
6. Shota Nakamura
7. Enrique R Rojas
8. Yasu S Morita
9. M Sloan Siegrist

• Curated by eLife

  eLife assessment

  This paper addresses an important question: the relationship between the cell wall and other, primarily lipid, based components of the cell envelope. Building on previous work, the authors provide data suggesting that the activity of a PonA2, non-essential peptidoglycan synthase, promotes membrane partitioning through its role in cell wall synthesis. While the data are consistent with this model, the reviewers felt additional experiments are necessary to fully support the authors' conclusions.

Reviewed by eLife

Perturbed fatty-acid metabolism is linked to localized chromatin hyperacetylation, increased stress-response gene expression and resistance to oxidative stress

1. Jarmila Princová
2. Clàudia Salat-Canela
3. Petr Daněk
4. Anna Marešová
5. Laura de Cubas
6. Jürg Bähler
7. José Ayté
8. Elena Hidalgo
9. Martin Převorovský

Reviewed by Review Commons

Molecular mechanism of Afadin substrate recruitment to the receptor phosphatase PTPRK via its pseudophosphatase domain

1. Iain M Hay
2. Katie E Mulholland
3. Tiffany Lai
4. Stephen C Graham
5. Hayley J Sharpe
6. Janet E Deane

• Curated by eLife

  Evaluation Summary:

  These studies establish a role for the D2 pseudophosphatase domain of the PTPRK receptor-like phosphotyrosine phosphatase in recruiting Afadin, a cell-cell junction protein that is reported to be a PTPRK substrate, for dephosphorylation by the active D1 phosphatase domain. These findings suggest that the D2 pseudophosphatase domains of RPTPKs might have a general function as platforms to recruit specific phosphotyrosine substrates.

  (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 name with the authors.)

Reviewed by eLife