Biochemistry

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.

Reviewed by eLife

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

Molecular determinants of Neu5Ac binding to tripartite ATP independent periplasmic (TRAP) transporter

1. Parveen Goyal
2. KanagaVijayan Dhanabalan
3. Mariafrancesca Scalise
4. Rosmarie Friemann
5. Cesare Indiveri
6. Renwick CJ Dobson
7. Kutti R Vinothkumar
8. Ramaswamy Subramanian

• Curated by eLife

  eLife assessment

  This valuable work provides novel insights into the substrate binding mechanism of a tripartite ATP-independent periplasmic (TRAP) transporter. The structural analysis is convincing, but evidence to support some of the conclusions regarding the mechanism is incomplete. This study will be of interest to the membrane transport and bacterial biochemistry communities.

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

Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase

1. Roberto Efraín Díaz
2. Andrew K Ecker
3. Galen J Correy
4. Pooja Asthana
5. Iris D Young
6. Bryan Faust
7. Michael C Thompson
8. Ian B Seiple
9. Steven Van Dyken
10. Richard M Locksley
11. James S Fraser

• Curated by eLife

  eLife assessment

  This structural and biochemical study of the mouse homolog of acidic mammalian chitinase (AMCase) enhances our understanding of the pH-dependent activity and catalytic properties of mouse AMCase, and it sheds light on its adaptation to different physiological pH environments. The methods and analysis of data are solid, providing several lines of evidence to support the development of mechanistic hypotheses. While the findings and interpretation will be valuable to those studying AMCase in mice, the broader significance, including extension of the results to other species including human, remain less clear.

Reviewed by eLife

Prominin 1 and Tweety Homology 1 both induce extracellular vesicle formation

1. Tristan A. Bell
2. Bridget E. Luce
3. Pusparanee Hakim
4. Virly Y. Ananda
5. Hiba Dardari
6. Tran H. Nguyen
7. Arezu Monshizadeh
8. Luke H. Chao

Reviewed by Review Commons