How to make a minimal genome for synthetic minimal cell

Abstract

As a key focus of synthetic biology, building a minimal artificial cell has given rise to many discussions. A synthetic minimal cell will provide an appropriate chassis to integrate functional synthetic parts, devices and systems with functions that cannot generally be found in nature. The design and construction of a functional minimal genome is a key step while building such a cell/ chassis since all the cell functions can be traced back to the genome. Kinds of approaches, based on bioinformatics and molecular biology, have been developed and proceeded to derive essential genes and minimal gene sets for the synthetic minimal genome. Experiments about streamlining genomes of model bacteria revealed genome reduction led to unanticipated beneficial properties, such as high electroporation efficiency and accurate propagation of recombinant genes and plasmids that were unstable in other strains. Recent achievements in chemical synthesis technology for large DNA segments together with the rapid development of the wholegenome sequencing, have transferred synthesis of genes to assembly of the whole genomes based on oligonucleotides, and thus created strong preconditions for synthesis of artificial minimal genome. Here in this article, we review briefly the history and current state of research in this field and summarize the main methods for making a minimal genome. We also discuss the impacts of minimized genome on metabolism and regulation of artificial cell.

Realizing Microbial Evolution

“…And by comparing the genes common to the first two fully sequenced bacterial genomes (H. influenzae and M. genitalium; Fig. 1A), the absolute minimal gene set sufficient for cellular life was estimated to number 256 genes (Mushegian and Koonin 1996), which matched well with some of the lower estimates obtained through largescale gene disruptions in various bacterial species (see Table 2 in Zhang et al 2010 for a compilation of these studies).…”

Can Graphene Bilayers Be the Membrane Mimetic Materials?

“…In other words, there is a problem of reinterpretation of a "minimal cell" not as a cell with a minimal genome [15][16][17][18][19][20][21] and a corresponding nucleotide metabolism [22][23][24], but as a supramolecular structure built up with membranes with the properties which as a whole are necessary and sufficient for the operation of the functionally-minimal cell or its model. To date there are several papers considering the above problem, but the solutions proposed there imply conventional phospholipids already adapted to perform the functions simulated instead of the artificial membrane mimetic materials.…”

Synthetic biology: From the first synthetic cell to see its current situation and future development

“…It should be noted that here the "minimal genome" is not an absolute concept but a relative concept in comparison to natural genomes. Usually the living condition and research objective help define the boundary of a minimal genome [10]. It is hard to get a universal chassis suitable for different research or application purposes.…”

“…Comparative genomics [31,32], large-scale gene inactivation experiments [33][34][35][36][37][38], and network-based prediction [39] have been used to identify essential genes. Studies related to essential genes have been reviewed in refs [10,40]. After experimental identification, results show that even in the genome of M. genitalium, there are about 100 protein coding genes regarded as non-essential [34].…”