The Essential Unknowns/About

Essential unknowns

The essential unknown genes (also referred to as the essential unknowns) in the context of the minimal cell, are the genes that must be present in the genome of the organism in order for organism to survive. These genes produce proteins or RNAs with function essential for the viability of the organism, including enzymatic, regulatory, and structural functions [1].

Essentiality, quasi-essentiality, and nonessentiality

Based on the essentiality, the genes of an organism can be classified into the following categories:

1. Essential genes: If the gene is inactivated or excluded from the genome by mutation, the cell cannot be propagated, although it may divide or grow until the gene product is sufficiently diluted across the progeny. This happens, if the function that the gene product performs is not supplied by any other gene present in the cell [1].
   
2. Nonessential genes: If the gene can be excised from the genome, or inactivated without decreasing the growth rate (or fitness) of the cell. In such case, gene either specifies a nonessential function, or its function can be supplied sufficiently by another gene in the cell [1].
   
3. Quasi-essential genes: If the inactivation of disruption of a gene leads to the impaired growth. The decrease in the fitness can vary, for instance, depending on the number and the character of the other genes involved in the provision of a given function [1].
4. Synthetically lethal genes: In the case of multiple genes supplying the same function, knock-out of a single gene does not lead to non-viability of the cell (for example, if such pair of genes code for the protein processing an essential amino acid). However, if both genes are disrupted, the cell loses its viability. As the majority of the studies on the essential genes are knock-out studies, this adds an additional layer of complexity.

Difficulties with determination of the essentiality

Determination of the essentiality brings in several challenges. For example, majority of the gene essentiality studies is conducted using the single gene knock-outs (such as

Minimal cell

The minimal cell is, by definition, the unicellular organism with genome containing only the essential genes required for the growth in under ideal laboratory conditions, in the stress-free environment (i. e. in the absence of the pathogens), with all the nutrients provided by the growth media [1]. Such organism contains all the machinery required for the independent cellular life (in contrast to viruses). However, deletion or inactivation of any of the genes in such minimal cell would lead to the loss of its viability after the gene cannot be propagated across the next generations [1]. Such cell would represent the most simple, yet fully-functional biological system, somehow analogous to the Hydrogen atom in the context of Chemistry: just as the investigation of the Hydrogen atom provides the physicists and chemists with insights into the behavior of the matter, we hope that the minimal cell can provide us with the full understanding of the processes required for the existence of life [1].

Minimal cells in nature

The Mycoplasmas are the natural minimal cells that we understand the most in detail [3]. These parasitic bacteria have a several important properties that make them good candidates for the minimal genome research, such as absence of a cell wall, simplicity of metabolism, and, most importantly, small genomes. The small size of their genome results from the stress-free environment where they reside [1]. The species used the most frequently for the research of the minimal genome are M. pneumoniae, M. mycoides and M. genitalium, which has the smallest genome, with only 583 000 base pairs (583 kbp) encoding 482 genes. Read more about Mycoplasmas.

Synthetic minimal cell: JCVI-syn3.0

Despite its small genome size, M. genitalium does not represent the minimal cell. In 2016, Hutchinson et al. used the design-build-test cycle to construct JCVI-syn3.0 based on the genome of M. mycoides. The genome of JCVI-syn3.0 contains 531 kbp and encodes for 473 genes and is smaller than the genome of any other independently self-replicating organism found in nature [2]. You can read the original paper describing the design and construction of JCVI-syn3.0 of Hutchinson et al. here

References

[1] Glass, J., Merryman, C., Wise, K., Hutchison, C. and Smith, H. (2017). Minimal Cells—Real and Imagined. Cold Spring Harbor Perspectives in Biology, 9(12), p.a023861.
[2] Hutchison, C., Chuang, R., Noskov, V., Assad-Garcia, N., Deerinck, T., Ellisman, M., Gill, J., Kannan, K., Karas, B., Ma, L., Pelletier, J., Qi, Z., Richter, R., Strychalski, E., Sun, L., Suzuki, Y., Tsvetanova, B., Wise, K., Smith, H., Glass, J., Merryman, C., Gibson, D. and Venter, J. (2016). Design and synthesis of a minimal bacterial genome. Science, 351(6280), pp.aad6253-aad6253.
[3] Baldwin, G., Bayer, T., Dickinson, R., Ellis, T., Freemont, P., Kitney, R., Polizzi, K. and Stan, G. (2015). Synthetic biology - A primer (Revised edition). London: Imperial College Press.
[4] Juhas, M., Eberl, L. and Glass, J. (2011). Essence of life: essential genes of minimal genomes. Trends in Cell Biology, 21(10), pp.562-568.