Synthetic Biology

Heterogeneity of the GFP fitness landscape and data-driven protein design

1. Louisa Gonzalez Somermeyer
2. Aubin Fleiss
3. Alexander S Mishin
4. Nina G Bozhanova
5. Anna A Igolkina
6. Jens Meiler
7. Maria-Elisenda Alaball Pujol
8. Ekaterina V Putintseva
9. Karen S Sarkisyan
10. Fyodor A Kondrashov

• Curated by eLife

  Evaluation Summary:

  The manuscript dives into how protein structure/function robustness to mutation or polymorphism relates across evolutionary distance. The work indicates that evolutionarily related genes will have different shapes of robustness to variation, and that this will not necessarily track with phylogenetic relationships. The conclusions have potential ramifications for protein engineering, protein structure as well as population genetics and phylogenetics.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

A scalable pipeline for SARS-CoV-2 replicon construction based on de-novo synthesis

1. Ahmet C. Berkyurek
2. Elian Lee
3. Omer Weissbrod
4. Roni Rasnic
5. Ilaria Falciatori
6. Siyuan Chen
7. Yaniv Erlich

Reviewed by ScreenIT

Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic host

1. Francesca D'Angelo
2. Elena Fernández-Fueyo
3. Pierre Simon Garcia
4. Helena Shomar
5. Martin Pelosse
6. Rita Rebelo Manuel
7. Ferhat Büke
8. Siyi Liu
9. Niels van den Broek
10. Nicolas Duraffourg
11. Carol de Ram
12. Martin Pabst
13. Emmanuelle Bouveret
14. Simonetta Gribaldo
15. Béatrice Py
16. Sandrine Ollagnier de Choudens
17. Frédéric Barras
18. Gregory Bokinsky

• Curated by eLife

  Evaluation Summary:

  Three of Nature's life-sustaining processes, respiration, photosynthesis, and nitrogen fixation, all rely on proteins (Fe-S protein) that contain simple inorganic cofactors constructed of Fe and S (Fe-S clusters). Fe-S proteins also participate in a huge and diverse array of metabolic processes. As such there has been considerable interest over the past two decades towards understanding how Fe-S clusters are formed and distributed to their cognate proteins. A related issue, the topic of the present work, is: why is it that many Fe-S proteins from diverse microbial species cannot be heterologously produced in Escherichia coli in active forms? This issue is of considerable interest not only from the perspective of microbial Fe-S proteins but also for heterologous expression of active eukaryotic Fe-S proteins. The study provides insights on the phylogenetic and biosynthetic limitations concerning formation of functional heterologously expressed Fe-S proteins.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 and Reviewer #2 agreed to share their name with the authors.)

Reviewed by eLife

Modular, robust, and extendible multicellular circuit design in yeast

1. Alberto Carignano
2. Dai Hua Chen
3. Cannon Mallory
4. R Clay Wright
5. Georg Seelig
6. Eric Klavins

• Curated by eLife

  Evaluation Summary:

  In this manuscript, the authors address important problems in the field of synthetic biology about scalability, robustness, and modularity. They used multiple strains to build gene circuits and demonstrate the modular composition of strain circuits with an automated design strategy to achieve a target behavior from a large space of possible functional circuit architectures. The major claims of the manuscript are well supported by solid quantitative data and systematic mathematical modeling analysis, and the approaches used are thoughtful and rigorous. This paper is of interest to synthetic biologists within the field of designing community-level behaviors, such as distributed computing, in multicellular consortia.

  (This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. The reviewers remained anonymous to the authors.)

Reviewed by eLife

Integrated autolysis, DNA hydrolysis and precipitation enables an improved bioprocess for Q-Griffithsin, a broad-spectrum antiviral and clinical-stage anti-COVID-19 candidate

1. John S. Decker
2. Romel Menacho-Melgar
3. Michael D. Lynch

Reviewed by ScreenIT

Production and secretion of functional full-length SARS-CoV-2 spike protein in Chlamydomonas reinhardtii

1. Anna Kiefer
2. Justus Niemeyer
3. Anna Probst
4. Gerhard Erkel
5. Michael Schroda

Reviewed by ScreenIT

Predictive profiling of SARS-CoV-2 variants by deep mutational learning

1. Joseph M. Taft
2. Cédric R. Weber
3. Beichen Gao
4. Roy A. Ehling
5. Jiami Han
6. Lester Frei
7. Sean W. Metcalfe
8. Alexander Yermanos
9. William Kelton
10. Sai T. Reddy

Reviewed by ScreenIT

Peptide–Antibody Fusions Engineered by Phage Display Exhibit an Ultrapotent and Broad Neutralization of SARS-CoV-2 Variants

1. Jonathan M. Labriola
2. Shane Miersch
3. Gang Chen
4. Chao Chen
5. Alevtina Pavlenco
6. Reza Saberianfar
7. Francesca Caccuri
8. Alberto Zani
9. Nitin Sharma
10. Annie Feng
11. Daisy W. Leung
12. Arnaldo Caruso
13. Giuseppe Novelli
14. Gaya K. Amarasinghe
15. Sachdev S. Sidhu

Reviewed by ScreenIT

Proof of concept continuous event logging in living cells

1. Andrey Shur
2. Richard M. Murray

Reviewed by ScreenIT

A humanized nanobody phage display library yields potent binders of SARS CoV-2 spike

1. Ying Fu
2. Juliana da Fonseca Rezende e Mello
3. Bryan D. Fleming
4. Alex Renn
5. Catherine Z. Chen
6. Xin Hu
7. Miao Xu
8. Kirill Gorshkov
9. Quinlin Hanson
10. Wei Zheng
11. Emily M. Lee
12. Lalith Perera
13. Robert Petrovich
14. Manisha Pradhan
15. Richard T. Eastman
16. Zina Itkin
17. Thomas B. Stanley
18. Allen Hsu
19. Venkata Dandey
20. Kedar Sharma
21. William Gillette
22. Troy Taylor
23. Nitya Ramakrishnan
24. Shelley Perkins
25. Dominic Esposito
26. Eunkeu Oh
27. Kimihiro Susumu
28. Mason Wolak
29. Marc Ferrer
30. Matthew D. Hall
31. Mario J. Borgnia
32. Anton Simeonov

Reviewed by ScreenIT