Synthetic alienation of microbial organisms by using genetic code engineering: Why and how?

Abstract

The main goal of synthetic biology (SB) is the creation of biodiversity applicable for biotechnological needs, while xenobiology (XB) aims to expand the framework of natural chemistries with the non-natural building blocks in living cells to accomplish artificial biodiversity. Protein and proteome engineering, which overcome limitation of the canonical amino acid repertoire of 20 (+2) prescribed by the genetic code by using non-canonic amino acids (ncAAs), is one of the main focuses of XB research. Ideally, estranging the genetic code from its current form via systematic introduction of ncAAs should enable the development of bio-containment mechanisms in synthetic cells potentially endowing them with a "genetic firewall" i.e. orthogonality which prevents genetic information transfer to natural systems. Despite rapid progress over the past two decades, it is not yet possible to completely alienate an organism that would use and maintain different genetic code associations permanently. In order to engineer robust bio-contained life forms, the chemical logic behind the amino acid repertoire establishment should be considered. Starting from recent proposal of Hartman and Smith about the genetic code establishment in the RNA world, here the authors mapped possible biotechnological invasion points for engineering of bio-contained synthetic cells equipped with non-canonical functionalities.

Exploring hydrophobicity limits of polyproline helix with oligomeric octahydroindole‐2‐carboxylic acid

“…5 In our opinion, the most interesting case reported to date is the "lipophilic polyproline-II structure" constructed by Martin et al 6 In particular, NMR investigations of an oligomeric sis, prior to the α-helix and much earlier than the hydrophobic motif was recruited by nature. 19 This follows the GC-GCA-GCAU scheme of the genetic code evolution as recently summarized by Hartman and Smith. 20,21 Owing to its semiextended nature, the P II protein domains are predictably highly solvent exposed in aqueous media.…”

“…Four to six milligrams of a substrate was mixed with octan-1-ol (1.00 mL) and deionized water (1.00 mL), and this mixture was shaken for 12 to 24 hours at 298 ± 2 K. In the NMR tubes, 0.30 mL of each phase was used, and these solutions were diluted by 0.30 mL of acetonitrile-d 3 . 1 H, 19 F, and inverse-gated decoupled 19 F{ 1 H} NMR measurements were performed at 298 K in datasets with identical starting settings, using calibrated 90°pulses. Only zero-order phases were readjusted for reprocessing between equivalent water and octan-1-ol phase spectra.…”

“…With these peptides, we then measured octan-1-ol/water partitioning values. In this case, concentration in the phases was measured by using 19 F NMR detection. Results demonstrate that the oligoprolines have a better preference towards aqueous medium, with a steady decrease of the logP at higher oligomeric numbers.…”

Auxotrophy to Xeno-DNA: an exploration of combinatorial mechanisms for a high-fidelity biosafety system for synthetic biology applications

“…The term ‘xenobiology’ has experienced significant semantic shift over the last few decades [ 163 – 165 ]. Kubyshkin et al define xenobiology as an approach to expand the framework of natural chemistries with non-natural building blocks in living cells to accomplish artificial biodiversity [ 50 ]. Therefore, one key aspect of xenobiology is the search for alternative chemistry for nucleic acids, proteins and other cellular components and functions.…”

“…Interesting in terms of biosafety are rare cases, where replicating systems escaped this system and modified their genetic code [ 47 – 49 ]. Modifications to this universal genetic code pose a powerful biosafety mechanism [ 50 ]. Therefore, xenobiology-based containment is another way to prevent the successful transfer of information from another species.…”