Biochemistry

Pseudomonas aeruginosa C-Terminal Processing Protease CtpA Assembles into a Hexameric Structure That Requires Activation by a Spiral-Shaped Lipoprotein-Binding Partner

1. Hao-Chi Hsu
2. Michelle Wang
3. Amanda Kovach
4. Andrew J. Darwin
5. Huilin Li

• Curated by eLife

  Evaluation Summary:

  This paper demonstrates an inactive protease in Pseudomonas aeruginosa, CtpA, is regulated by am outer membrane lipoprotein LbcA. Using crystallization and EM strategies, they also provide a complex structure; however, the precise mechanism of regulation is speculative due to the flexible arrangement of protein domains.

  (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.)

Reviewed by eLife

Conformational transitions of the Spindly adaptor underlie its interaction with Dynein and Dynactin

1. Ennio A. d’Amico
2. Misbha Ud Din Ahmad
3. Verena Cmentowski
4. Mathias Girbig
5. Franziska Müller
6. Sabine Wohlgemuth
7. Andreas Brockmeyer
8. Stefano Maffini
9. Petra Janning
10. Ingrid R. Vetter
11. Andrew P. Carter
12. Anastassis Perrakis
13. Andrea Musacchio

Reviewed by Review Commons

A feed-forward pathway drives LRRK2 kinase membrane recruitment and activation

1. Edmundo G Vides
2. Ayan Adhikari
3. Claire Y Chiang
4. Pawel Lis
5. Elena Purlyte
6. Charles Limouse
7. Justin L Shumate
8. Elena Spínola-Lasso
9. Herschel S Dhekne
10. Dario R Alessi
11. Suzanne R Pfeffer

• Curated by eLife

  Evaluation Summary:

  This paper, which is of interest to membrane biologists and colleagues in signal transduction, examines the interesting question of whether LRRK2 recruitment to membranes may regulate its activity. Membrane association involves binding to membrane-tethered Rab GTPases via LRRK2's armadillo domain, and the authors propose an elegant feedforward mechanism to describe how recruitment could lead to Rab phosphorylation, but not all features of the feed-forward model are directly supported by data.

  (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

Redox-controlled reorganization and flavin strain within the ribonucleotide reductase R2b–NrdI complex monitored by serial femtosecond crystallography

1. Juliane John
2. Oskar Aurelius
3. Vivek Srinivas
4. Patricia Saura
5. In-Sik Kim
6. Asmit Bhowmick
7. Philipp S Simon
8. Medhanjali Dasgupta
9. Cindy Pham
10. Sheraz Gul
11. Kyle D Sutherlin
12. Pierre Aller
13. Agata Butryn
14. Allen M Orville
15. Mun Hon Cheah
16. Shigeki Owada
17. Kensuke Tono
18. Franklin D Fuller
19. Alexander Batyuk
20. Aaron S Brewster
21. Nicholas K Sauter
22. Vittal K Yachandra
23. Junko Yano
24. Ville RI Kaila
25. Jan Kern
26. Hugo Lebrette
27. Martin Högbom

• Curated by eLife

  Evaluation Summary:

  The manuscript will be of interest to a broad audience in structural biology, biochemistry, and enzymology. The work demonstrates the use of a cutting-edge approach in protein crystallography to investigate and visualize the complex mechanism of an enzyme, the paradigm being Mn-dependent ribonucleotide reductase R2b in complex with flavin-bound NrdI at different redox states. The work is timely and has implications for future investigation of complex biochemical processes.

  (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

Structures of NF-κB p52 homodimer-DNA complexes rationalize binding mechanisms and transcription activation

1. Wenfei Pan
2. Vladimir A Meshcheryakov
3. Tianjie Li
4. Yi Wang
5. Gourisankar Ghosh
6. Vivien Ya-Fan Wang

• Curated by eLife

  Evaluation Summary:

  This manuscript provides a detailed structural and biophysical characterization of several complexes of the p52 homodimer of NF kB and different DNA binding sites. The main topic is the investigation of why the central base pair(s) have a strong influence on the transcriptional activity of the homodimer. The authors correlate structural changes with measurements of kinetic on and off rates to develop a model that explains the differences in activity. The paper is of interest to all working on understanding how transcriptional activity is regulated.

  (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.)

Reviewed by eLife

A second DNA binding site on RFC facilitates clamp loading at gapped or nicked DNA

1. Xingchen Liu
2. Christl Gaubitz
3. Joshua Pajak
4. Brian A Kelch

• Curated by eLife

  Evaluation Summary:

  Replication Factor C (RFC) is known to play a role in both DNA replication and DNA repair by loading a protein clamp called PCNA onto DNA junctions with a 3'-recessed end. The current paper elegantly demonstrates that RFC has a second DNA binding site that recognizes a single strand-double strand DNA with a 5'-recessed junction. The paper reports a series of interesting structures and confirms binding to both short gapped DNA and nicked DNA by RFC, causing local unwinding DNA at the ssDNA/dsDNA junctions. The paper, which is of interest to colleagues studying DNA replication and repair, should be improved through a few clarifications.

  (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.)

Reviewed by eLife

The UbiB family member Cqd1 forms a novel membrane contact site in mitochondria

1. Siavash Khosravi
2. Xenia Chelius
3. Ann-Katrin Unger
4. Johanna Frickel
5. Timo Sachsenheimer
6. Christian Lüchtenborg
7. Rico Schieweck
8. Britta Brügger
9. Benedikt Westermann
10. Till Klecker
11. Walter Neupert
12. Max E. Harner

Reviewed by Review Commons

Cytosolic aspartate aminotransferase moonlights as a ribosome-binding modulator of Gcn2 activity during oxidative stress

1. Robert A Crawford
2. Mark P Ashe
3. Simon J Hubbard
4. Graham D Pavitt

• Curated by eLife

  Evaluation Summary:

  Using mass spectrometry, Crawford et al. identify aspartate aminotransferase 2 (Aat2) as a protein whose polysome-association is increased under oxidative stress in yeast. Aat2 deletion sensitizes yeast to oxidative stress, which is paralleled by an aberrantly elevated integrated stress response, although polysome-association of Aat2 and its effect on oxidative stress response are independent of its aminotransferase activity. This provides evidence that metabolic enzymes may "moonlight" as post-transcriptional regulators. The study will appeal to experts in the fields of biochemistry, genetics, cellular and molecular biology. The presented data mostly support the authors' conclusions, but there are a few technical issues that should be addressed. These include corroborating Aat2:ribosome association and characterizing the effects of non-catalytic Aat2 mutants on the integrated stress response.

  (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

Mitochondrial redox adaptations enable alternative aspartate synthesis in SDH-deficient cells

1. Madeleine L Hart
2. Evan Quon
3. Anna-Lena BG Vigil
4. Ian A Engstrom
5. Oliver J Newsom
6. Kristian Davidsen
7. Pia Hoellerbauer
8. Samantha M Carlisle
9. Lucas B Sullivan

• Curated by eLife

  Evaluation Summary:

  Hart et al show that loss of mitochondrial complex I rescues succinate dehydrogenase deficient (SDH) cells. The experiments are well performed and the phenotype is potentially very interesting to researchers of cancer metabolism. The authors propose that rescue of SDH deficiency by complex I inhibition is caused by an increase in mitochondrial NADH which leads to a restoration of aspartate levels, which in turn rescues proliferation. To support the model, the authors do demonstrate that there are possible correlations of this phenotype to restored aspartate biosynthesis. However, they do not unambiguously establish a mechanism that fully defines how complex I inhibition rescues the proliferation of SDH deficient cells.

  (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

Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro

1. Ruchi Yadav
2. Valentine V. Courouble
3. Sanjay K. Dey
4. Jerry Joe E. K. Harrison
5. Jennifer Timm
6. Jesse B. Hopkins
7. Ryan L. Slack
8. Stefan G. Sarafianos
9. Francesc X. Ruiz
10. Patrick R. Griffin
11. Eddy Arnold

Reviewed by ScreenIT