Biochemistry

Toxin-based screening of C-terminal tags in Escherichia coli reveals the exceptional potency of ssrA-like degrons

1. Patrick C. Beardslee
2. Karl R. Schmitz

• Curated by eLife

  eLife assessment

  This important study employs an innovative genetic selection-based approach to identify short peptide sequences that target bacterial proteins for degradation. Using random mutagenesis they identified 5 amino acid long "degrons" that target the toxin VapC for degradation permitting survival. They provide compelling data that degrons ending in Ala-Ala are selectively recognized by the ClpXP protease and identify the sequence FKLVA as a particularly significant target. As a whole, there is enthusiasm about the author's findings, although there are also some improvements that could be made to increase the clarity and impact, mostly in the form of revisions to the text.

Reviewed by eLife

Nucleotide binding to the ATP-cone in anaerobic ribonucleotide reductases allosterically regulates activity by modulating substrate binding

1. Ornella Bimai
2. Ipsita Banerjee
3. Inna Rozman Grinberg
4. Ping Huang
5. Lucas Hultgren
6. Simon Ekström
7. Daniel Lundin
8. Britt-Marie Sjöberg
9. Derek T Logan

• Curated by eLife

  eLife assessment

  This study advances our understanding of the allosteric regulation of anaerobic ribonucleotide reductases (RNRs) by nucleotides, providing valuable new structural insight into class III RNRs containing ATP cones. The cryo-EM structural characterization of the system is solid, but some open questions remain about the interpretation of activity/binding assays and the HDX-MS results that have been newly incorporated compared to a previous version. The work will be of interest to biochemists and structural biologists working on ribonucleotide reductases and other allosterically regulated enzymes.

Reviewed by eLife

Allosteric activation of the co-receptor BAK1 by the EFR receptor kinase initiates immune signaling

1. Henning Mühlenbeck
2. Yuko Tsutsui
3. Mark A Lemmon
4. Kyle W Bender
5. Cyril Zipfel

• Curated by eLife

  eLife assessment

  This manuscript reports important in vitro biochemical and in planta experiments to study the receptor activation mechanism of plant membrane receptor kinase complexes with non-catalytic intracellular kinase domains. Several lines of evidence convincingly show that one such putative pseudokinase, the immune receptor EFR achieves an active conformation following phosphorylation by a co-receptor kinase, and then in turn activates the co-receptor kinase allosterically to enable it to phosphorylate down-stream signaling components. This manuscript will be of interest to scientists focusing on cell signalling and allosteric regulation.

Reviewed by eLife

Fitness landscape of substrate-adaptive mutations in evolved amino acid-polyamine-organocation transporters

1. Foteini Karapanagioti
2. Úlfur Águst Atlason
3. Dirk J Slotboom
4. Bert Poolman
5. Sebastian Obermaier

• Curated by eLife

  eLife assessment

  This important manuscript describes experimental evolution experiments using a novel genetic system in yeast, showing that solute carrier transporters can incorporate additional functionality through the introduction of point mutations to either the ligand binding site or gating helices. These findings provide convincing evidence to establish that for Amino Acid transporters of the APC-type family, evolution to recognize new substrates passes through generalist intermediates that can transport most amino acids.

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Deep Mutagenesis of a Transporter for Uptake of a Non-Native Substrate Identifies Conformationally Dynamic Regions

1. Heather J Ellis
2. Matthew Chan
3. Balaji Selvam
4. Evan Walter
5. Christine A Devlin
6. Steven K Szymanski
7. Loren Keith Henry
8. Diwakar Shukla
9. Erik Procko

• Curated by eLife

  eLife assessment

  Serotonin is an important neurotransmitter and its synaptic concentration is controlled by re-uptake by the sodium-coupled serotonin transporter SERT. The manuscript by Chan et al reports results from a systematic deep mutagenesis approach to study the surface expression and APP+ (5HT analogue) transport mechanism of the human serotonin transporter. The authors complement this experimental evidence with large-scale molecular simulations of the transporter in the presence of APP+. The use of deep mutagenesis and large-scale adaptive sampling simulations is impressive, and could contribute to understanding the structural requirements for folding and how transporters evolve to recognize different substrates.

Reviewed by eLife

Bacterial exonuclease III expands its enzymatic activities on single-stranded DNA

1. Hao Wang
2. Chen Ye
3. Qi Lu
4. Zhijie Jiang
5. Chao Jiang
6. Chun Zhou
7. Na Li
8. Caiqiao Zhang
9. Guoping Zhao
10. Min Yue
11. Yan Li

• Curated by eLife

  eLife assessment

  This manuscript highlights single-stranded DNA exo- and endo-nuclease activities of ExoIII as a potential caveat and an underestimated source of decreased efficiency in its use in biosensor assays. The data present solid evidence for the ssDNA nuclease activity of ExoIII and identifies residues that contribute to it. The findings are useful, but some aspects in the study remain incomplete.

Reviewed by eLife

Ligand response of guanidine-IV riboswitch at single-molecule level

1. Lingzhi Gao
2. Dian Chen
3. Yu Liu

• Curated by eLife

  eLife assessment

  This study presents valuable findings on the ligand- and ion-dependent structural dynamics of a transcriptional riboswitch. The single-molecule data presented are solid and prompts intriguing hypotheses and models, which will undoubtedly stimulate future structural analyses. These findings are of considerable interest to biochemists and biophysicists engaged in the study of RNA structure and riboswitch mechanisms.

Reviewed by eLife

Mapping protein-metabolite interactions in E. coli by integrating chromatographic techniques and co-fractionation mass spectrometry

1. Mateusz Wagner
2. Jieun Kang
3. Catherine Mercado
4. Venkatesh P. Thirumalaikumar
5. Michal Gorka
6. Hanne Zillmer
7. Jingzhe Guo
8. Romina I. Minen
9. Caroline F. Plecki
10. Katayoon Dehesh
11. Frank C. Schroeder
12. Dirk Walther
13. Aleksandra Skirycz

Reviewed by Review Commons

Alzheimer’s disease linked Aβ42 exerts product feedback inhibition on γ-secretase impairing downstream cell signaling

1. Katarzyna Marta Zoltowska
2. Utpal Das
3. Sam Lismont
4. Thomas Enzlein
5. Masato Maesako
6. Mei CQ Houser
7. Maria Luisa Franco
8. Burcu Özcan
9. Diana Gomes Moreira
10. Dmitry Karachentsev
11. Ann Becker
12. Carsten Hopf
13. Marçal Vilar
14. Oksana Berezovska
15. William Mobley
16. Lucía Chávez-Gutiérrez

• Curated by eLife

  eLife assessment

  In this manuscript, the authors tested the hypothesis that Aβ42 toxicity arises from its proven affinity for γ-secretases. The authors provide useful findings, showing convincingly that human Abeta42 inhibits gamma-secretase activity. The data will be of interest to all scientists working on neurodegenerative diseases.

Reviewed by eLife

A robust method for measuring aminoacylation through tRNA-Seq

1. Kristian Davidsen
2. Lucas B Sullivan

• Curated by eLife

  eLife assessment

  This valuable paper presents a new protocol for quantifying tRNA aminoacylation levels by deep sequencing. The improved methods for discrimination of aminoacyl-tRNAs from non-acylated tRNAs, more efficient splint-assisted ligation to modify the tRNAs' ends for the following RT-PCR reaction, along with the use of an error-tolerating mapping algorithm to map the tRNA sequencing reads provide new tools for anyone interested in tRNA concentrations and functional states in different cells and organisms. The results and conclusions are solid, with well-designed tests to optimize the protocol under different conditions.

Reviewed by eLife