Standardization in synthetic biology: an engineering discipline coming of age

Abstract

Akin to other engineering disciplines, extensive standardization will undoubtedly speed-up and reduce the cost of bioprocess development. In this respect, further implementation of synthetic biology standards will be crucial for the field in order to redeem its promise, i.e. to enable predictable forward engineering.

A Synthetic Approach Allows Rapid Characterization of the Maize Nuclear Auxin Response Circuit

“…Most of these students were participants in several semesters of course-based undergraduate research experiences. This type of undergraduate-focused synthetic biology research experience offers an exciting way to acquaint young scientists with plant synthetic biology and could be readily adapted to focus on the standardization and characterization of parts for use in synthetic biology, an area of continuing concern (Decoene et al, 2018).…”

Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria

“…Apart from advances in genome and metabolic engineering techniques, the positive impact of standardization on the SynBio field should not be underestimated, as it boosts interoperability, reproducibility of results, and reduces redundant work 29 . Although the level of standardization within SynBio is still far below those of the hard sciences, large efforts led by the National Institute of Standards and Technology, the iGEM foundation and several other organizations are putting us on the right track for the future by the creation of biological part databases, software for circuit design and standards for data representation and communication 29 . However, standardized biological parts and constructs, transparent data sharing and standard operating procedures (SOPs) are largely missing for non-model species.…”

“…The SEVA 3.0 database offers a wide array of replicative and integrative ‘SEVA plasmids’ following a uniform design and nomenclature, some of them endowed with expression systems that are commonly used by the Pseudomonas community 31 . Besides the SEVA repository, several databases are available with biological parts for both Gram-negative and Gram-positive organisms 29 , but unfortunately, dedicated parts and repositories for Gram-positive organisms remain scarce. In recent years, progress in this field has been made by developments including the iGEM Registry Probiotic Collection 32 and the Bacillus BioBrick Box 2.0 33 .…”

“…The vast majority of parts have been developed for E. coli and are barely validated nor characterized in other hosts. Moreover, even for this reference strain species, standardization of parts is still an illusion, as no clear consensus exists on characterization protocols for parts, let alone on standard units for the quantification of transcriptional and translational activity 29 . Therefore, biological parts cannot be reliably compared and as a consequence, researchers still tend to construct genetic circuits with parts they are familiar with rather than those possessing the optimal features to reach their goal.…”

The art of vector engineering: towards the construction of next‐generation genetic tools

“…Thus, we have reached a state in which modular vector or high-throughput assembled constructs, from vectors to genomes, can be easily designed and assembled through computational and experimental tools (Casini et al, 2015;Woodruff et al, 2017). However, it is clear that this powerful design and build process was not followed by the standardization of biological parts that ultimately compose those systems (Decoene et al, 2017). The lack of biological information regarding the behaviour of simple genetic features such as promoters, terminators and origins of replication hinders the potential of engineering living organisms.…”