Synthetic Biology

A molecular proximity sensor based on an engineered, dual-component guide RNA

1. Junhong Choi
2. Wei Chen
3. Hanna Liao
4. Xiaoyi Li
5. Jay Shendure

• Curated by eLife

  eLife Assessment

  This important manuscript describes a creative approach using dual-component gRNAs to create a new class of molecular proximity sensors for genome editing. The authors demonstrate that this tool can be coupled with several different gene editing effectors, showing convincingly that the tool functions as intended. This study not only introduces a first-of-its kind approach, but through careful measurements also enables future further development of the technology.

Reviewed by eLife

De novo-designed minibinders expand the synthetic biology sensing repertoire

1. Zara Y Weinberg
2. Sarah S Soliman
3. Matthew S Kim
4. Devan H Shah
5. Irene P Chen
6. Melanie Ott
7. Wendell A Lim
8. Hana El-Samad

• Curated by eLife

  eLife Assessment

  This study presents a useful investigation of the use of small, de novo-designed protein binding domains (mini-binders) against the Spike protein of SARS-CoV-2 and EGFR, as ligand binding domains on two classes of synthetic receptors, second-generation synNotch (SNIPR) and CAR. The methods and evidence supporting the focused claims are solid. This work will be of interest to synthetic biologists and cell engineers as a starting point to map out the rules for receptor engineering based on mini-binders and ultimately to advance them in biomedical applications.

Reviewed by eLife

A synthetic method to assay polycystin channel biophysics

1. Megan Larmore
2. Orhi Esarte Palomero
3. Neha Kamat
4. Paul G DeCaen

• Curated by eLife

  eLife Assessment

  The authors have developed a valuable approach that employs cell-free expression to reconstitute ion channels into giant unilamellar vesicles for biophysical characterisation. The work is convincing and will be of particular interest to those studying ion channels that primarily occur in organelles and are therefore not amenable to be studied by more traditional methods.

Reviewed by eLife

Light-driven synchronization of optogenetic clocks

1. Maria Cristina Cannarsa
2. Filippo Liguori
3. Nicola Pellicciotta
4. Giacomo Frangipane
5. Roberto Di Leonardo

• Curated by eLife

  eLife assessment

  This study presents a light-entrainable synthetic oscillator in bacteria, the optorepressilator. The authors develop a toolbox using optogenetics that makes the cellular oscillator easily controllable. This toolbox is valuable, contributing both to bioengineering and to the understanding of biological dynamical systems. The comparison with a mathematical model, population, and single-cell measurements demonstrate convincingly that the planned system was achieved and is suitable to control and study biological oscillators.

Reviewed by eLife

Design of highly functional genome editors by modeling the universe of CRISPR-Cas sequences

1. Jeffrey A. Ruffolo
2. Stephen Nayfach
3. Joseph Gallagher
4. Aadyot Bhatnagar
5. Joel Beazer
6. Riffat Hussain
7. Jordan Russ
8. Jennifer Yip
9. Emily Hill
10. Martin Pacesa
11. Alexander J. Meeske
12. Peter Cameron
13. Ali Madani

Reviewed by Arcadia Science

Intracellular Expression of a Fluorogenic DNA Aptamer Using Retron Eco2

1. Mahesh A Vibhute
2. Corbin Machatzke
3. Katrin Bigler
4. Saskia Krümpel
5. Daniel Summerer
6. Hannes Mutschler

• Curated by eLife

  eLife assessment

  This important work introduces a method to express fluorogenic DNA aptamers in E. coli, paving the way for genetically encoded fluorescent DNA. The evidence supporting the conclusions is solid, consisting of comparisons of the aptamer's activity in vitro and within bacterial cells. This advancement described in this study is likely to become a standard technique in the DNA aptamer field, and the work will be of interest and utility to researchers in synthetic biology, molecular imaging, and bacterial genetics fields.

Reviewed by eLife

Targeted protein degradation systems to enhance Wnt signaling

1. Parthasarathy Sampathkumar
2. Heekyung Jung
3. Hui Chen
4. Zhengjian Zhang
5. Nicholas Suen
6. Yiran Yang
7. Zhong Huang
8. Tom Lopez
9. Robert Benisch
10. Sung-Jin Lee
11. Jay Ye
12. Wen-Chen Yeh
13. Yang Li

• Curated by eLife

  eLife assessment

  The manuscript describes a valuable method to boost WNT signaling in a tissue-specific manner. The work extends previous data from the authors based on fusing an RSPO2 mutant protein to an antibody that binds ASGR1/2. In the current manuscript, two new antibodies with similar effects are described, that expand this solid approach and provide alternatives for potential future clinical applications. This manuscript will be of interest to all scientists studying protein engineering and cellular targeting.

Reviewed by eLife

Highly multiplexed design of an allosteric transcription factor to sense novel ligands

1. Kyle K. Nishikawa
2. Jackie Chen
3. Justin F. Acheson
4. Svetlana V. Harbaugh
5. Phil Huss
6. Max Frenkel
7. Nathan Novy
8. Hailey R. Sieren
9. Ella C. Lodewyk
10. Daniel H. Lee
11. Jorge L. Chávez
12. Brian G. Fox
13. Srivatsan Raman

Reviewed by PREreview

Specific Modulation of CRISPR Transcriptional Activators through RNA-Sensing Guide RNAs in Mammalian Cells and Zebrafish Embryos

1. Oana Pelea
2. Sarah Mayes
3. Quentin RV. Ferry
4. Tudor A. Fulga
5. Tatjana Sauka-Spengler

• Curated by eLife

  eLife assessment

  The authors aim to develop a CRISPR system that can be activated upon sensing an RNA. As an initial step to this goal, they describe RNA-sensing guide RNAs for controlled activation of CRISPR modification. Many of the data look convincing and while several steps remain to achieve the stated goal in an in vivo setting and for robust activation by endogenous RNAs, the current work will be important for many in the field.

Reviewed by eLife

Synthetic bacteria with programmed cell targeting and protein injection suppress tumor growth in vivo

1. Alejandro Asensio-Calavia
2. Carmen Mañas
3. Alba Cabrera-Fisac
4. Eva Pico-Sánchez
5. Elena M. Seco
6. Starsha Kolodziej
7. Daniel S. Leventhal
8. José M. Lora
9. Beatriz Álvarez
10. Luis Ángel Fernández

Reviewed by Arcadia Science