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The second wave of synthetic biology: from modules to systems

Key Points

  • In the 'first wave' of synthetic biology, researchers developed basic elements and modules that allowed transcriptional, translational and post-translational control of cellular processes.

  • The 'second wave' of synthetic biology, in which researchers must integrate these basic elements and modules to create systems-level circuitry, presents new challenges. Traditional principles for systems engineering must be supplemented with approaches that attend to details of biological systems and contexts.

  • Several groups have developed small synthetic systems, including multicellular synthetic ecosystems in bacteria, yeast and mammalian cells; application-orientated systems, such as bacteria that sense and destroy tumours and organisms that produce drug precursors; and initial development of minimized cellular genomes.

  • Many open questions and challenges remain, including the development of readily characterized, standardized and modular components; substantially reducing or exploiting biological noise in synthetic systems; determining the usefulness of innate or engineered epigenetic cellular functions; improving and creating new computational tools and programming abstractions for modelling and designing more complex systems; and determining safety issues and resolutions for clinical manifestations of synthetic biological systems.

Abstract

Synthetic biology is a research field that combines the investigative nature of biology with the constructive nature of engineering. Efforts in synthetic biology have largely focused on the creation and perfection of genetic devices and small modules that are constructed from these devices. But to view cells as true 'programmable' entities, it is now essential to develop effective strategies for assembling devices and modules into intricate, customizable larger scale systems. The ability to create such systems will result in innovative approaches to a wide range of applications, such as bioremediation, sustainable energy production and biomedical therapies.

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Figure 1: Modules based on transcriptional, translational and post-translational control.
Figure 2: The progression of synthetic biology.
Figure 3: Synthetic multicellular systems.

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Acknowledgements

We apologize to those colleagues whose work we do not directly cite owing to space limitations. We especially thank T. Dan-Cohen for critically reading the manuscript and providing much needed feedback and edits. We thank C. DeHart for her ideas and feedback. We would also like to thank past and present members of the Weiss laboratory for engaging daily discussions and for fostering a creative research environment. The Weiss laboratory is supported by the National Institutes of Health, the National Science Foundation, the Army Research Office and the Office of Naval Research.

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Bartel laboratory introduction to 21U-RNAs

BioJade

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Deepak laboratory downloads

Deepak laboratory syntax guide

ESSA

Gene Design

Genetdes

GenoCAD

iGEM

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OpenCell

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OpenWetWare BioBrick standard

PROTDES

Registry of Standard Biological Parts

RNAdraw

RNAstructure

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RNA world

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SynBioSS

Tinkercell

UNAFold software

Vienna RNA package

Glossary

Ribosome binding sites

A messenger RNA sequence that is recognized by the ribosome for protein translation initiation.

Directed evolution

An adaptation of the natural process of evolution — consisting of mutation and selection — to laboratory settings, in which the goal is to customize the behaviours of individual proteins as well as whole pathways for specific functions.

Burnt pancake problem

The challenge of this problem is to develop an efficient mathematical sorting algorithm that reverses the sequence of elements with as few reversals as possible. This problem adds complexity by assigning a sidedness to each element: each element has a burnt side, and the final objective is to have all of these 'burnt' sides facing down.

Boolean logic

The mathematical foundation for digital systems describing rules for input–output functions. Basic operations include AND, OR, NOT and NOR (NOT OR), and can be combined to form arbitrarily complex expressions.

RNA aptamer

An oligonucleotide that specifically binds a small molecule. DNA aptamers also exist.

AHL

(Acyl-homoserine lactone.) A class of small signalling molecule that is commonly used in bacterial quorum sensing pathways.

Quorum sensing

Density-dependent bacterial behaviour that is regulated by cell–cell communication.

CcdB

A toxic protein that targets the Escherichia coli DNA gyrase, a bacterial topoisomerase II.

Commensalism

Non-competitive existence and growth.

Amensalism

The presence of one organism adversely affects the other.

Mutualism

The presence of each organism benefits the other.

Parasitism

One organism enables the other to survive at the expense of the first organism.

Third party inducible parasitism

One organism directs a second organism to allow a third organism to act as a parasite.

Integrin receptor

A human cell surface receptor that interacts with several components of the extracellular matrix, including fibronectin.

BioBrick standard

A set of rules that define the assembly of DNA pieces or parts such that parts can be easily combined to form more complex parts.

Global transposon mutagenesis

A top-down method by which non-essential genes in the chromosome of an organism are identified using random transposon insertion. Viable insertions are then sequenced.

PoPs

(Polymerase operations per second.) A measurement of the transcriptional activity of a gene that is defined as the number of RNA polymerase molecules passing a predefined point on the DNA each second.

Long terminal repeat

A sequence of DNA found in retroviruses that flanks genes. The sequence aids the process of integrating the retroviral DNA into the host genome.

Global sensitivity analysis

A quantitative evaluation of how perturbations in system components affect the overall behaviour of a system (for example, analysing how a change in the DNA-binding constant of a transcription factor affects the overall gene expression output of signal transduction pathway).

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Purnick, P., Weiss, R. The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol 10, 410–422 (2009). https://doi.org/10.1038/nrm2698

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