Biochemistry

  1. Gut Microbe-Derived Trimethylamine Shapes Circadian Rhythms Through the Host Receptor TAAR5

    1. Kala K Mahen
    2. William J Massey
    3. Danny Orabi
    4. Amanda L Brown
    5. Thomas C Jaramillo
    6. Amy C Burrows
    7. Anthony J Horak
    8. Sumita Dutta
    9. Marko Mrdjen
    10. Nour Mouannes
    11. Venkateshwari Varadharajan
    12. Lucas J Osborn
    13. Xiayan Ye
    14. Dante M Yarbrough
    15. Treg Grubb
    16. Natalie Zajczenko
    17. Rachel Hohe
    18. Rakhee Banerjee
    19. Pranavi Linga
    20. Dev Laungani
    21. Adeline M Hajjar
    22. Naseer Sangwan
    23. Mohammed Dwidar
    24. Jennifer A Buffa
    25. Garth R Swanson
    26. Zeneng Wang
    27. J Mark Brown

    • Curated by eLife

      eLife Assessment

      This study presents an important finding linking the bacterial metabolite trimethylamine and its receptor to circadian rhythms and olfaction. The current evidence supporting the claims of the authors is compelling. This work will be of broad interest to researchers interested in nutrition, microbial metabolism, circadian rhythms, and host-microbiome interactions.

    Reviewed by eLife

    9 evaluationsAppears in 1 listLatest version Latest activity

  2. ATP-independent phosphate recycling on AGC kinase activation loops induced by alkali metal ions

    1. Koji Kubouchi
    2. Hideyuki Mukai

    • Curated by eLife

      eLife Assessment

      AGC kinases, such as PKN1, are regulated by activation loop phosphorylation. This paper reports that exposing cells to high concentrations of monovalent cations induces rapid activation loop dephosphorylation, with rapid re-phosphorylation when physiological salt is restored. Re-phosphorylation is apparently independent of ATP or candidate kinases, and the paper presents an extraordinary and unconventional mechanism involving phosphate exchange between the activation loop and an unknown acceptor molecule. The findings are intriguing and the approach is logical, but the evidence is incomplete and the significance unclear until the biochemical mechanism is identified.

    Reviewed by eLife

    5 evaluationsAppears in 1 listLatest version Latest activity

  3. Viral proteins activate PARIS-mediated tRNA degradation and viral tRNAs rescue infection

    1. Nathaniel Burman
    2. Svetlana Belukhina
    3. Florence Depardieu
    4. Royce A. Wilkinson
    5. Mikhail Skutel
    6. Andrew Santiago-Frangos
    7. Ava B. Graham
    8. Alexei Livenskyi
    9. Anna Chechenina
    10. Natalia Morozova
    11. Trevor Zahl
    12. William S. Henriques
    13. Murat Buyukyoruk
    14. Christophe Rouillon
    15. Lena Shyrokova
    16. Tatsuaki Kurata
    17. Vasili Hauryliuk
    18. Konstantin Severinov
    19. Justine Groseille
    20. Agnès Thierry
    21. Romain Koszul
    22. Florian Tesson
    23. Aude Bernheim
    24. David Bikard
    25. Blake Wiedenheft
    26. Artem Isaev

    Reviewed by Rapid Reviews Infectious Diseases

    5 evaluationsAppears in 1 listLatest version Latest activity

  4. Kinesin-1 conformational dynamics are controlled by a cargo-sensitive TPR switch

    1. Shivam Shukla
    2. Jessica A Cross
    3. Monika Kish
    4. Sathish KN Yadav
    5. Johannes F Weijman
    6. Laura O’Regan
    7. Judith Mantell
    8. Ufuk Borucu
    9. Xiyue Leng
    10. Christiane Schaffitzel
    11. Jonathan J Phillips
    12. Derek N Woolfson
    13. Mark P Dodding

    • Curated by eLife

      eLife Assessment

      The manuscript by Shukla et al. provides important mechanistic insights into kinesin-1 autoinhibition and cargo-mediated activation. Using a convincing combination of protein engineering, computational modeling, biophysical assays, HDX-MS, and electron microscopy, the authors reveal how cargo binding induces an allosteric transition that propagates to the motor domains and enhances MAP7 binding. Despite limitations arising from conformational heterogeneity and structural resolution, the study presents a unified mechanism for kinesin-1 activation that will be of broad interest to the motor protein, structural biology, and cell biology communities.

    Reviewed by eLife

    4 evaluationsAppears in 1 listLatest version Latest activity

  5. UV irradiation alters TFAM binding to mitochondrial DNA

    1. Dillon E King
    2. Emily E Beard
    3. Matthew J Satusky
    4. Ian Ryde
    5. Alex George
    6. Caitlin Johnson
    7. Emma L Dolan
    8. Yuning Zhang
    9. Wei Zhu
    10. Hunter Wilkins
    11. Evan Corden
    12. Susan K Murphy
    13. Dorothy Erie
    14. Raluca Gordân
    15. Joel N Meyer

    • Curated by eLife

      eLife Assessment

      Mitochondrial DNA (mtDNA) exhibits a degree of resistance to mutagenesis under genotoxic stress, and this study on the mitochondrial Transcription Factor A (TFAM) presents valuable data concerning the possible mechanisms involved. The presented data are solid, technically rigorous, and consistent with established literature findings. The experiments are well-executed, providing reliable evidence on the change of TFAM-DNA interactions following UVC irradiation. However, the evidence is inadequate to support the primary claims.

    Reviewed by eLife

    4 evaluationsAppears in 1 listLatest version Latest activity

  6. A high-resolution analysis of arrestin2 interactions responsible for CCR5 endocytosis

    1. Ivana Petrovic
    2. Samit Desai
    3. Polina Isaikina
    4. Layara Akemi Abiko
    5. Anne Spang
    6. Stephan Grzesiek

    • Curated by eLife

      eLife Assessment

      The authors investigate arrestin2-mediated CCR5 endocytosis in the context of clathrin and AP2 contributions. Using an extensive set of NMR experiments, and supported by microscopy and other biophysical assays, the authors provide compelling data on the roles of AP2 and clathrin in CCR5 endocytosis. This important work will appeal to an audience beyond those studying chemokine receptors, including those studying GPCR regulation and trafficking. The distinct role of AP2 and not clathrin will be of particular interest to those studying GPCR internalization mechanisms.

    Reviewed by eLife

    9 evaluationsAppears in 1 listLatest version Latest activity

  7. Aggregation-Dependent Epitope Sequence and Modification Fingerprints of Anti-Aβ Antibodies

    1. Ivan Talucci
    2. Timon Leske
    3. Hans-Wolfgang Klafki
    4. Mohammed Mehedi Hassan
    5. Annik Steiert
    6. Barbara Morgado
    7. Sebastian Bothe
    8. Lars van Werven
    9. Thomas Liepold
    10. Jochen Walter
    11. Hermann Schindelin
    12. Jens Wiltfang
    13. Oliver Wirths
    14. Olaf Jahn
    15. Hans Michael Maric

    • Curated by eLife

      eLife Assessment

      Antibodies that selectively bind distinct amyloid-beta variants are vital tools for Alzheimer's disease research. This valuable manuscript aims to delineate the epitope specificity in a panel of anti-amyloid-beta antibodies, including some with clinical relevance. The experiments were rigorously conducted, employing an interesting combination of established and state-of-the-art methodologies, yielding convincing findings.

    Reviewed by eLife

    6 evaluationsAppears in 1 listLatest version Latest activity

  8. Investigation of All Disease-Relevant Lysine Acetylation Sites in α-Synuclein Enabled by Non-canonical Amino Acid Mutagenesis

    1. Marie Shimogawa
    2. Ming-Hao Li
    3. Grace Shin Hye Park
    4. Jennifer Ramirez
    5. Hudson Lee
    6. Paris R Watson
    7. Swati Sharma
    8. Zongtao Lin
    9. Chao Peng
    10. Virginia M.-Y Lee
    11. Benjamin A Garcia
    12. David W Christianson
    13. Elizabeth Rhoades
    14. David Eliezer
    15. E James Petersson

    • Curated by eLife

      eLife Assessment

      This valuable work provides new insights into the role of lysine acetylation of alpha-synuclein, the protein involved in Parkinson's Disease. The evidence is mostly solid, but the claims around the potential disease relevance based on seeding assays and structural work need to be toned down, or else supported by additional experimental evidence. Overall, the work will be of interest to researchers in the fields of protein biophysics and post-translational modifications, as well as Parkinson's Disease.

    Reviewed by eLife

    5 evaluationsAppears in 1 listLatest version Latest activity

  9. Profiling of terminating ribosomes reveals translational control at stop codons

    1. Longfei Jia
    2. Yuanhui Mao
    3. Saori Uematsu
    4. Xinyi Ashley Liu
    5. Leiming Dong
    6. Leonardo Henrique França de Lima
    7. Shu-Bing Qian

    • Curated by eLife

      eLife Assessment

      This manuscript reports on the application of ribosome profiling (EZRA-seq and eRF1-seq) combined with massively parallel reporter assays to identify and characterize a GA-rich element associated with ribosome pausing during translation termination. While the development of eRF1-seq is useful and the identification of GA-rich elements upstream of stop codons is convincing, the level of support for other claims is inadequate. Specifically, the evidence that GA-rich sequences upstream of stop codons can base-pair with the 3′ end of 18S rRNA to prolong ribosome dwell time, and the evidence that Rps26 interferes with this interaction to regulate translation termination, are not adequate.

    Reviewed by eLife

    6 evaluationsAppears in 1 listLatest version Latest activity

  10. Inhibition of NF-κB Signaling by the Reactive Glycolytic Metabolite Methylglyoxal

    1. Caroline Stanton
    2. Woojin Choi
    3. R. Luke Wiseman
    4. Michael J. Bollong

    Reviewed by preLights

    1 evaluationAppears in 1 listLatest version Latest activity
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