Mining Environmental Plasmids for Synthetic Biology Parts and Devices

Abstract

The scientific and technical ambition of contemporary synthetic biology is the engineering of biological objects with a degree of predictability comparable to those made through electric and industrial manufacturing. To this end, biological parts with given specifications are sequence-edited, standardized, and combined into devices, which are assembled into complete systems. This goal, however, faces the customary context dependency of biological ingredients and their amenability to mutation. Biological orthogonality (i.e., the ability to run a function in a fashion minimally influenced by the host) is thus a desirable trait in any deeply engineered construct. Promiscuous conjugative plasmids found in environmental bacteria have evolved precisely to autonomously deploy their encoded activities in a variety of hosts, and thus they become excellent sources of basic building blocks for genetic and metabolic circuits. In this article we review a number of such reusable functions that originated in environmental plasmids and keep their properties and functional parameters in a variety of hosts. The properties encoded in the corresponding sequences include inter alia origins of replication, DNA transfer machineries, toxin-antitoxin systems, antibiotic selection markers, site-specific recombinases, effector-dependent transcriptional regulators (with their cognate promoters), and metabolic genes and operons. Several of these sequences have been standardized as BioBricks and/or as components of the SEVA (Standard European Vector Architecture) collection. Such formatting facilitates their physical composability, which is aimed at designing and deploying complex genetic constructs with new-to-nature properties.

Environmental Galenics: large-scale fortification of extant microbiomes with engineered bioremediation agents

“…This raises an interesting question on the design of universal expression systems for securing activity of the GoIs in any biological host—or using SynBio jargon, engineering orthogonal heterologous expression [ 155 ]. Transcription and translation signals of promiscuous mobile elements look like a good source of parts for engineering equally unrestrained expression devices [ 156 ]. Along the line, platforms based on viral promoters and polymerases have been proposed to this end [ 157 ].…”

Genetic Circuit Design in Rhizobacteria

“…However, rhizobacterial circuit design can be hampered by the limited host range of common plasmid origins of replication. Plasmid-based circuits that use the E. coli -functional ColE1 and p15A origins cannot be directly ported into most rhizobacteria [ 76 ]. Furthermore, plasmid instability in the absence of antibiotics—a scenario often encountered during plant colonization by rhizobacteria—may lead to circuit failure due to cell division-driven plasmid loss [ 77 ].…”

Introduction to Systems and Synthetic Biology in Hydrocarbon Microbiology: Applications

“…Many promiscuous mobile genetic elements have in fact evolved to move between different hosts with a minimum or interference with the innate enzymatic and regulatory network. On this basis, many of them have been re-purposed as constituents of a plethora of synthetic circuits [23]. Understanding structural and functional features of genes that are specific of naturally promiscuous plasmids will surely reveal new principles of great utility for engineering new live systems.…”