Biochemistry

Sec17/Sec18 can support membrane fusion without help from completion of SNARE zippering

1. Hongki Song
2. Thomas L Torng
3. Amy S Orr
4. Axel T Brunger
5. William T Wickner

• Curated by eLife

  Evaluation Summary:

  This is a very important paper that challenges the generally accepted dogma that full zippering of SNARE complexes is essential for intracellular membrane fusion. Previous work had already shown that C-terminal truncation of one SNARE arrested liposome fusion mediated by the yeast vacuolar SNARE complex and that Sec17/Sec18 could rescue fusion, but it was argued that such rescue could arise because Sec17/Sec18 restored C-terminal zippering. This paper now shows that Sec17/Sec18 rescue fusion even when three SNAREs are crippled -by truncation or mutation- to definitively prevent zippering, thus showing that Sec17/18 have a direct, positive role in membrane fusion.

  (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.)

Reviewed by eLife

HPF1 and nucleosomes mediate a dramatic switch in activity of PARP1 from polymerase to hydrolase

1. Johannes Rudolph
2. Genevieve Roberts
3. Uma M Muthurajan
4. Karolin Luger

• Curated by eLife

  Evaluation Summary:

  This manuscript describes a set of biochemical studies on the substrate and reaction specificity of poly(ADP-ribose) polymerase 1 (PARP1), an important antineoplastic drug target and component of DNA damage response. The most significant finding is that histone PARylation factor (HPF1) binding to PARP1 causes a shift from primarily PARylation activity to that of hydrolytic activity, which offers new avenues for understanding and controlling PARP1. While some of the observed effects need a modest amount of further explanation, the findings described in this paper are of broad interest to readers in the fields of DNA damage response, chromatin structure regulation, and to researchers studying PARP1 and issues related to NAD+ metabolism.

  (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

PP2A/B55α substrate recruitment as defined by the retinoblastoma-related protein p107

1. Holly Fowle
2. Ziran Zhao
3. Qifang Xu
4. Jason S Wasserman
5. Xinru Wang
6. Mary Adeyemi
7. Felicity Feiser
8. Alison N Kurimchak
9. Diba Atar
10. Brennan C McEwan
11. Arminja N Kettenbach
12. Rebecca Page
13. Wolfgang Peti
14. Roland L Dunbrack
15. Xavier Graña

Reviewed by eLife

A Liquid-to-Solid Phase Transition Enhances the Catalytic Activity of SARM1

1. Heather S. Loring
2. Paul R. Thompson

• Curated by eLife

  Evaluation Summary:

  This manuscript describes an interesting regulatory mechanism that activates SARM1, an enzyme that degrade NAD+ and promote axon degeneration. Previous structural and biochemical studies mostly focus on how SARM1 is auto-inhibited at basal conditions and this manuscript provides evidences supporting that phase transition could promote its activity, thus providing new understanding about its regulatory mechanism. The finding also enables in vitro assays to be carried out more easily and thus could facilitate the development of small molecule modulators of SARM1 for therapeutics purposes.

  (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

Chromatin structure-dependent histone incorporation revealed by a genome-wide deposition assay

1. Hiroaki Tachiwana
2. Mariko Dacher
3. Kazumitsu Maehara
4. Akihito Harada
5. Yosuke Seto
6. Ryohei Katayama
7. Yasuyuki Ohkawa
8. Hiroshi Kimura
9. Hitoshi Kurumizaka
10. Noriko Saitoh

• Curated by eLife

  Evaluation Summary:

  The method presented in this article is of interest for all fields that interface with chromatin dynamics. It could provide a powerful tool to dissect the mechanisms of chromatin assembly and disassembly genome-wide, and determine how cell cycle and chromatin structure influence these dynamics. However, in the current form, the article falls short of its potential. Further validation of the data, and clarification of its implications is requested.

  (This preprint has been reviewed by eLife. We include the public review 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

Recapitulating the frataxin activation mechanism in an engineered bacterial cysteine desulfurase supports the architectural switch model

1. Shachin Patra
2. Cheng-Wei Lin
3. Manas K. Ghosh
4. Steven M. Havens
5. Seth A. Cory
6. David H. Russell
7. David P. Barondeau

• Curated by eLife

  Summary: This study provides support for a proposed allosteric regulatory mechanism in a human iron-sulfur cluster biosynthesis protein that is linked to the human genetic disorder, Friedrich's Ataxia. In an approach guided by inspection of a structure of the human enzyme, the authors successfully converted a bacterial homolog lacking allosteric regulation into a system that behaves similarly to the human one. The work provides validation of the roles of accessory proteins in activating iron-sulfur cluster biosynthesis machinery. It also could open novel routes for therapeutic intervention in genetic disorders of this process in humans.

  The major concerns about the study center on the significance of the form of the human enzyme structure used as the basis for designing the mutagenesis/activity experiments in the bacterial enzyme. To bolster the underlying framework for the experiment design, the description of the existing human enzyme structures and how exactly they were used to select sites for mutagenesis in the bacterial counterparts should be improved to include more detail and balanced perspective. Experiments are suggested to show that activity enhancement upon addition of accessory proteins is specific to those factors, along with a more comprehensive discussion of the errors and reproducibility in activity measurements. Finally, the significance of the work would be elevated if the authors could use a similar approach to install activating mutations in the human enzyme - particularly if these could overcome the requirement for frataxin.

Reviewed by eLife

SARS-CoV-2 S protein:ACE2 interaction reveals novel allosteric targets

1. Palur V Raghuvamsi
2. Nikhil K Tulsian
3. Firdaus Samsudin
4. Xinlei Qian
5. Kiren Purushotorman
6. Gu Yue
7. Mary M Kozma
8. Wong Y Hwa
9. Julien Lescar
10. Peter J Bond
11. Paul A MacAry
12. Ganesh S Anand

• Curated by eLife

  Summary: This is a timely and interesting exploration of the interaction between the Spike protein of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, and the ACE2 receptor using hydrogen deuterium exchange mass spectrometry and molecular dynamics simulations. The Spike protein consists of two sub-domains S1 and S2 with the S1 needing to be cleaved-off so the S2 can become the fusion protein responsible for getting the SARS-CoV-2 into the cell. Structures are available but they do not shed light on how the protease furin can access the cleavage site between S1 and S2 in order to begin the process of fusion. The results suggest that the Spike-ACE2 interaction induces extremely long-range allosteric effects on the Spike protein that could trigger proteolysis of the Spike protein. Specifically, when ACE2 binds to the Spike protein, a conformational change occurs near the S1/S2 cleavage site, exposing it and likely making it more susceptible to furin cleavage. The binding also dampens exchange in the stalk region of the Spike protein. The authors refer to these regions as "dynamic hotspots in the pre-fusion state". The results of this work have implications for the development of small molecule inhibitors.

  In general, the work is timely, and the results will be of interest to many in the field. The major conclusions of the work are generally supported by the results.

Reviewed by eLife, ScreenIT

A computationally designed fluorescent biosensor for D-serine

1. Vanessa Vongsouthi
2. Jason H. Whitfield
3. Petr Unichenko
4. Joshua A. Mitchell
5. Björn Breithausen
6. Olga Khersonsky
7. Leon Kremers
8. Harald Janovjak
9. Hiromu Monai
10. Hajime Hirase
11. Sarel J. Fleishman
12. Christian Henneberger
13. Colin J. Jackson

• Curated by eLife

  Summary: The reviewers recognize the merits of your work and your efforts to engineer a D-serine selective biosensor. However, they also raise major concerns regarding the experimental design (selection of mutations), methodology and achieved applicability. The reviewers find that the improvement in the selectivity of the engineered construct for the targeted ligand over alternative ligands is modest. They further indicate ambiguities regarding the origin of the ligand-induced fluorescence signal changes of the sensor. Other problematic aspects are the estimation of thermal stabilities and the lack of physiological signals in fluorescence imaging results that could demonstrate applicability to a biological problem.

Reviewed by eLife

Hypoxia-inducible lipid droplet-associated induces DGAT1 and promotes lipid storage in hepatocytes

1. Montserrat A. de la Rosa Rodriguez
2. Lei Deng
3. Anne Gemmink
4. Michel van Weeghel
5. Marie Louise Aoun
6. Christina Warnecke
7. Rajat Singh
8. Jan Willem Borst
9. Sander Kersten

Reviewed by eLife

Rqc1 and other yeast proteins containing highly positively charged sequences are not targets of the RQC complex

1. Géssica C. Barros
2. Rodrigo D. Requião
3. Rodolfo L. Carneiro
4. Claudio A. Masuda
5. Mariana H. Moreira
6. Silvana Rossetto
7. Tatiana Domitrovic
8. Fernando L. Palhano

Reviewed by eLife