Testing Theoretical Minimal Genomes Using Whole-Cell Models.

The minimal gene set for life has often been theorized, with at least ten produced for (). Due to the difficulty of using in the lab, combined with its long replication time of 12-15 h, none of these theoretical minimal genomes have been tested, even with modern techniques. The publication of the whole-cell model provided the first opportunity to test them, simulating the genome edits .

Minimal Genome Design Algorithms Using Whole-Cell Models.

Synthetic biologists engineer cells and cellular functions using design-build-test cycles; when the task is to extensively engineer entire genomes, the lack of appropriate design tools and biological knowledge about each gene in a cell can lengthen the process, requiring time-consuming and expensive experimental iterations.Whole-cell models represent a new avenue for genome design; the bacteria Mycoplasma genitalium has the first (and currently only published) whole-cell model which combines 28 cellular submodels and represents the integrated functions of every gene and molecule in a cell.We created two minimal genome design algorithms, GAMA and Minesweeper, that produced 1000s of in silico minimal genomes by running simulations on multiple supercomputers.

Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology.

Computer-aided design (CAD) for synthetic biology promises to accelerate the rational and robust engineering of biological systems. It requires both detailed and quantitative mathematical and experimental models of the processes to (re)design biology, and software and tools for genetic engineering and DNA assembly. Ultimately, the increased precision in the design phase will have a dramatic impact on the production of designer cells and organisms with bespoke functions and increased modularity.

Author Correction: Designing minimal genomes using whole-cell models.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Designing minimal genomes using whole-cell models.

In the future, entire genomes tailored to specific functions and environments could be designed using computational tools. However, computational tools for genome design are currently scarce. Here we present algorithms that enable the use of design-simulate-test cycles for genome design, using genome minimisation as a proof-of-concept.

Genome-driven cell engineering review: and metabolic and genome engineering.

Producing 'designer cells' with specific functions is potentially feasible in the near future. Recent developments, including whole-cell models, genome design algorithms and gene editing tools, have advanced the possibility of combining biological research and mathematical modelling to further understand and better design cellular processes. In this review, we will explore computational and experimental approaches used for metabolic and genome design.