Biochemistry

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. Daniela Rieger
5. Johanna Frickel
6. Timo Sachsenheimer
7. Christian Lüchtenborg
8. Rico Schieweck
9. Britta Brügger
10. Benedikt Westermann
11. Till Klecker
12. Walter Neupert
13. 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

Filamentation modulates allosteric regulation of PRPS

1. Huan-Huan Hu
2. Guang-Ming Lu
3. Chia-Chun Chang
4. Yilan Li
5. Jiale Zhong
6. Chen-Jun Guo
7. Xian Zhou
8. Boqi Yin
9. Tianyi Zhang
10. Ji-Long Liu

• Curated by eLife

  Evaluation Summary:

  The authors investigated the structure of phosphoribosyl pyrophosphate (PRPP) synthase (PRPPS) from Escherichia coli, a highly conserved enzyme from bacteria to mammals that catalyzes the synthesis of a key common compound for several metabolic pathways. Combining structural data with mutagenesis and activity assays, they demonstrate that the enzyme is regulated differently by allosteric effectors when assembled into one filament form or the other. The strength of the manuscript is the high-quality cryo-EM data, which allows the reconstruction of two different filament forms bound to different ligands.

  (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

Structural basis of a two-antibody cocktail exhibiting highly potent and broadly neutralizing activities against SARS-CoV-2 variants including diverse Omicron sublineages

1. Xiaoman Li
2. Yongbing Pan
3. Qiangling Yin
4. Zejun Wang
5. Sisi Shan
6. Laixing Zhang
7. Jinfang Yu
8. Yuanyuan Qu
9. Lina Sun
10. Fang Gui
11. Jia Lu
12. Zhaofei Jing
13. Wei Wu
14. Tao Huang
15. Xuanling Shi
16. Jiandong Li
17. Xinguo Li
18. Dexin Li
19. Shiwen Wang
20. Maojun Yang
21. Linqi Zhang
22. Kai Duan
23. Mifang Liang
24. Xiaoming Yang
25. Xinquan Wang

Reviewed by ScreenIT

Molecular Investigations of Selected Spike Protein Mutations in SARS-CoV-2: Delta and Omicron Variants and Omicron Subvariants

1. Urmi Roy

Reviewed by ScreenIT