Biochemistry

What AlphaFold tells us about cohesin’s retention on and release from chromosomes

1. Kim A Nasmyth
2. Byung-Gil Lee
3. Maurici Brunet Roig
4. Jan Löwe

• Curated by eLife

  eLife assessment

  This important study makes use of AlphaFold2 to predict the models of tens of cohesin subcomplexes from different species. The models, which are in most cases consistent with published cohesin variants with compromised in vitro and in vivo cohesin activity, provide convincing evidence that leads to testable hypotheses of cohesin dynamics and regulation. More broadly, this study serves as an example of how to use AlphaFold2 to build models of protein complexes that involve the docking of flexible regions to globular domains.

Reviewed by eLife

Engineered Active Zymogen of Microbial Transglutaminase

1. Ryutaro Ariyoshi
2. Takashi Matsuzaki
3. Ryo Sato
4. Kosuke Minamihata
5. Kounosuke Hayashi
6. Rie Wakabayashi
7. Masahiro Goto
8. Noriho Kamiya

Reviewed by Arcadia Science

Structural basis of EHEP-mediated offense against phlorotannin-induced defense from brown algae to protect akuBGL activity

1. Xiaomei Sun
2. Yuxin Ye
3. Naofumi Sakurai
4. Hang Wang
5. Koji Kato
6. Jian Yu
7. Keizo Yuasa
8. Akihiko Tsuji
9. Min Yao

• Curated by eLife

  eLife assessment

  This important study presents convincing evidence on how the sea slug Aplysia kurodai optimizes its digestion of brown algae, in a classical predator-prey 'arms race' at the molecular level. The experimental protein structures and enzyme assays provide support for the claims of how A. kurodai avoids inhibition by algal compounds, and also hold promise for biotechnological applications.

Reviewed by eLife

The structural basis for deubiquitination by the fingerless USP-type effector TssM

1. Thomas Hermanns
2. Matthias Uthoff
3. Ulrich Baumann
4. Kay Hofmann

Reviewed by Review Commons

Structural foundation for the role of enterococcal PrgB in conjugation, biofilm formation, and virulence

1. Wei-Sheng Sun
2. Lena Lassinantti
3. Michael Järvå
4. Andreas Schmitt
5. Josy ter Beek
6. Ronnie P-A Berntsson

• Curated by eLife

  eLife assessment

  This study presents valuable structural data for the bacterial adhesin PrgB, an atypical microbial cell surface-anchored polypeptide that binds DNA. There is convincing support for the claims regarding the overall function and importance of individual domains, which integrate a wide range of new and previously published experimental data. The structure-based model of PrgB molecular activity will be impactful in the field of bacterial adhesins, conjugation, and biofilm formation, especially because it focuses on a clinically relevant Gram-positive pathogen, whereas most work in the field has been focused on Gram-negative model systems.

Reviewed by eLife

Vibrio cholerae’s ToxRS bile sensing system

1. Nina Gubensäk
2. Theo Sagmeister
3. Christoph Buhlheller
4. Bruno Di Geronimo
5. Gabriel E Wagner
6. Lukas Petrowitsch
7. Melissa A Gräwert
8. Markus Rotzinger
9. Tamara M Ismael Berger
10. Jan Schäfer
11. Isabel Usón
12. Joachim Reidl
13. Pedro A Sánchez-Murcia
14. Klaus Zangger
15. Tea Pavkov-Keller

• Curated by eLife

  eLife assessment

  This study provides important insights into the structural biology and molecular mechanism of the sensory proteins ToxR/S that are associated with survival and virulence of the cholera pathogen. The structural studies are solid and supported by a series of biophysical experiments revealing a split, periplasmic protein binding interface for bile acid. The results are of interest to both protein biochemistry and pharmacology, potentially opening new routes for intervention in cholera disease.

Reviewed by eLife

Indole produced during dysbiosis mediates host–microorganism chemical communication

1. Rui-Qiu Yang
2. Yong-Hong Chen
3. Qin-yi Wu
4. Jie Tang
5. Shan-Zhuang Niu
6. Qiu Zhao
7. Yi-Cheng Ma
8. Cheng-Gang Zou

• Curated by eLife

  eLife assessment

  This fundamental study provides compelling evidence for a new mechanism of host-microbe interaction, with indole, produced by proliferating bacteria in the C. elegans digestive system, signalling through the host via the transcription factor DAF-16 to induce the expression of genes controlling bacterial growth in the gut. The work is relevant to a wide audience as it invites deeper research into this mechanism, while also serving as a template for similar microbiome/host interactions in other systems.

Reviewed by eLife

Mechanism of substrate binding and transport in BASS transporters

1. Patrick Becker
2. Fiona Naughton
3. Deborah Brotherton
4. Raul Pacheco-Gomez
5. Oliver Beckstein
6. Alexander D Cameron

• Curated by eLife

  eLife assessment

  The manuscript represents an important contribution to an ongoing discussion about the substrate binding site and mechanism of the Bile Acid Sodium Symporter (BASS) family of transporters. Structural and biochemical analysis of a bacterial homolog, ASTBnm, in complex with its native substrate (not bile acids, but a vitamin A precursor, pantoate) show a new binding site that is consistent with classical proposals for elevator-type transport mechanisms. Molecular dynamics (MD) simulations highlight the improved stability for the substrate in the active site when ions are present, suggesting a binding order during the transport cycle. The structural studies, binding assays, and MD simulations are convincing.

Reviewed by eLife

The neuronal calcium sensor NCS-1 regulates the phosphorylation state and activity of the Gα chaperone and GEF Ric-8A

1. Daniel Muñoz-Reyes
2. Levi J McClelland
3. Sandra Arroyo-Urea
4. Sonia Sánchez-Yepes
5. Juan Sabín
6. Sara Pérez-Suárez
7. Margarita Menendez
8. Alicia Mansilla
9. Javier García-Nafría
10. Stephen Sprang
11. Maria Jose Sanchez-Barrena

• Curated by eLife

  eLife assessment

  This important study reports biochemical and structural experiments that were carried out to determine the molecular basis of calcium-sensitive regulation of the guanine exchange factor Ric8A by the neuronal calcium sensor 1 (NCS-1). Structural and biochemical evidence for the NCS-1/Ric8A interface is convincing, but evidence for the full-length interactions is incomplete due to the low resolution of cryo-EM maps. This work will have important implications for scientists interested in G-protein signaling and molecular interactions that contribute to synapse function.

Reviewed by eLife

Structural rather than catalytic role for mitochondrial respiratory chain supercomplexes

1. Michele Brischigliaro
2. Alfredo Cabrera-Orefice
3. Susanne Arnold
4. Carlo Viscomi
5. Massimo Zeviani
6. Erika Fernández-Vizarra

• Curated by eLife

  eLife assessment

  This study presents valuable findings on the organization of respiratory chain complexes in mitochondria. It provides solid evidence that respiratory supercomplex formation in the fruit fly does not impact respiratory function, suggesting the role of these complexes is structural, rather than catalytic. However, whether the conclusions extend to other species requires further evidence. This manuscript will be of broad interest to the field of mitochondrial bioenergetics.

Reviewed by eLife