Designer proteins for bottom-up synthetic biology

2017 ◽  
pp. 115-154
Author(s):  
Maxim G. Ryadnov
Keyword(s):  
Synthetic Biology ◽  
Bottom Up ◽  
Designer Proteins

Evolving protocells to prototissues: rational design of a missing link

2013 ◽  
Vol 41 (5) ◽  
pp. 1159-1165 ◽  
Author(s):  
Shiksha Mantri ◽  
K. Tanuj Sapra
Keyword(s):  
Synthetic Biology ◽  
Rational Design ◽  
Structural Elements ◽  
Bottom Up ◽  
Missing Link ◽  
Hierarchical Assembly ◽  
Artificial Cell

Realization of a functional artificial cell, the so-called protocell, is a major challenge posed by synthetic biology. A subsequent goal is to use the protocellular units for the bottom-up assembly of prototissues. There is, however, a looming chasm in our knowledge between protocells and prototissues. In the present paper, we give a brief overview of the work on protocells to date, followed by a discussion on the rational design of key structural elements specific to linking two protocellular bilayers. We propose that designing synthetic parts capable of simultaneous insertion into two bilayers may be crucial in the hierarchical assembly of protocells into a functional prototissue.

scholarly journals Microfluidic platform enables tailored translocation and reaction cascades in nanoliter droplet networks

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Simon Bachler ◽  
Dominik Haidas ◽  
Marion Ort ◽  
Todd A. Duncombe ◽  
Petra S. Dittrich
Keyword(s):  
Synthetic Biology ◽  
Lipid Membranes ◽  
Bottom Up ◽  
Microfluidic Platform ◽  
Alpha Hemolysin ◽  
Droplet Interface Bilayer ◽  
Translocation Experiments ◽  
Fluorescent Molecules ◽  
Reaction Cascades ◽  
Minimal Cells

AbstractIn the field of bottom-up synthetic biology, lipid membranes are the scaffold to create minimal cells and mimic reactions and processes at or across the membrane. In this context, we employ here a versatile microfluidic platform that enables precise positioning of nanoliter droplets with user-specified lipid compositions and in a defined pattern. Adjacent droplets make contact and form a droplet interface bilayer to simulate cellular membranes. Translocation of molecules across membranes are tailored by the addition of alpha-hemolysin to selected droplets. Moreover, we developed a protocol to analyze the translocation of non-fluorescent molecules between droplets with mass spectrometry. Our method is capable of automated formation of one- and two-dimensional droplet networks, which we demonstrated by connecting droplets containing different compound and enzyme solutions to perform translocation experiments and a multistep enzymatic cascade reaction across the droplet network. Our platform opens doors for creating complex artificial systems for bottom-up synthetic biology.

Bottom-Up Synthetic Biology: Engineering in a Tinkerer’s World

Science ◽  
2011 ◽  
Vol 333 (6047) ◽  
pp. 1252-1254 ◽  
Author(s):  
Petra Schwille
Keyword(s):  
Synthetic Biology ◽  
Life Science ◽  
Biological Systems ◽  
Living Systems ◽  
Design Features ◽  
Literal Interpretation ◽  
Bottom Up ◽  
Systematic Construction ◽  
Science Discipline ◽  
Recent Developments

How synthetic can “synthetic biology” be? A literal interpretation of the name of this new life science discipline invokes expectations of the systematic construction of biological systems with cells being built module by module—from the bottom up. But can this possibly be achieved, taking into account the enormous complexity and redundancy of living systems, which distinguish them quite remarkably from design features that characterize human inventions? There are several recent developments in biology, in tight conjunction with quantitative disciplines, that may bring this literal perspective into the realm of the possible. However, such bottom-up engineering requires tools that were originally designed by nature’s greatest tinkerer: evolution.

scholarly journals Simultaneous monitoring of transcription and translation in mammalian cell-free expression in bulk and in cell-sized droplets

2018 ◽  
Vol 3 (1) ◽  
Author(s):  
Shue Wang ◽  
Sagardip Majumder ◽  
Nicholas J Emery ◽  
Allen P Liu
Keyword(s):  
Synthetic Biology ◽  
Real Time ◽  
Protein Dynamics ◽  
Mammalian Cell ◽  
Locked Nucleic Acid ◽  
Free Expression ◽  
Reporter Protein ◽  
Bottom Up ◽  
Lna Probe

Abstract Transcription and translation are two critical processes during eukaryotic gene expression that regulate cellular activities. The development of mammalian cell-free expression (CFE) systems provides a platform for studying these two critical processes in vitro for bottom-up synthetic biology applications such as construction of an artificial cell. Moreover, real-time monitoring of the dynamics of synthesized mRNA and protein is key to characterize and optimize gene circuits before implementing in living cells or in artificial cells. However, there are few tools for measurement of mRNA and protein dynamics in mammalian CFE systems. Here, we developed a locked nucleic acid (LNA) probe for monitoring transcription in a HeLa-based CFE system in real-time. By using this LNA probe in conjunction with a fluorescent reporter protein, we were able to simultaneously monitor mRNA and protein dynamics in bulk reactions and cell-sized single-emulsion droplets. We found rapid production of mRNA transcripts that decreased over time as protein production ensued in bulk reactions. Our results also showed that transcription in cell-sized droplets has different dynamics compared to the transcription in bulk reactions. The use of this LNA probe in conjunction with fluorescent proteins in HeLa-based mammalian CFE system provides a versatile in vitro platform for studying mRNA dynamics for bottom-up synthetic biology applications.

Living Technology: Exploiting Life's Principles in Technology

2010 ◽  
Vol 16 (1) ◽  
pp. 89-97 ◽  
Author(s):  
Mark A. Bedau ◽  
John S. McCaskill ◽  
Norman H. Packard ◽  
Steen Rasmussen
Keyword(s):  
Synthetic Biology ◽  
Artificial Life ◽  
Evolvable Hardware ◽  
Top Down ◽  
Bottom Up ◽  
Chemical Systems ◽  
The Social ◽  
Living Organisms ◽  
Electronic Chemical ◽  
Core Features

The concept of living technology—that is, technology that is based on the powerful core features of life—is explained and illustrated with examples from artificial life software, reconfigurable and evolvable hardware, autonomously self-reproducing robots, chemical protocells, and hybrid electronic-chemical systems. We define primary (secondary) living technology according as key material components and core systems are not (are) derived from living organisms. Primary living technology is currently emerging, distinctive, and potentially powerful, motivating this review. We trace living technology's connections with artificial life (soft, hard, and wet), synthetic biology (top-down and bottom-up), and the convergence of nano-, bio-, information, and cognitive (NBIC) technologies. We end with a brief look at the social and ethical questions generated by the prospect of living technology.

scholarly journals Construction of membrane-bound artificial cells using microfluidics: a new frontier in bottom-up synthetic biology

2016 ◽  
Vol 44 (3) ◽  
pp. 723-730 ◽  
Author(s):  
Yuval Elani
Keyword(s):  
Synthetic Biology ◽  
High Throughput ◽  
Lipid Membranes ◽  
Spatial Organization ◽  
Building Blocks ◽  
Artificial Cells ◽  
Bottom Up ◽  
Grand Challenges ◽  
New Frontier ◽  
Membrane Bound

The quest to construct artificial cells from the bottom-up using simple building blocks has received much attention over recent decades and is one of the grand challenges in synthetic biology. Cell mimics that are encapsulated by lipid membranes are a particularly powerful class of artificial cells due to their biocompatibility and the ability to reconstitute biological machinery within them. One of the key obstacles in the field centres on the following: how can membrane-based artificial cells be generated in a controlled way and in high-throughput? In particular, how can they be constructed to have precisely defined parameters including size, biomolecular composition and spatial organization? Microfluidic generation strategies have proved instrumental in addressing these questions. This article will outline some of the major principles underpinning membrane-based artificial cells and their construction using microfluidics, and will detail some recent landmarks that have been achieved.

scholarly journals An in vitro synthetic biology platform for emerging industrial biomanufacturing: Bottom-up pathway design

2018 ◽  
Vol 3 (3) ◽  
pp. 186-195 ◽  
Author(s):  
Ting Shi ◽  
Pingping Han ◽  
Chun You ◽  
Yi-Heng P. Job Zhang
Keyword(s):  
Synthetic Biology ◽  
Bottom Up
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