Standards not that standard
- Cristina Vilanova†1,
- Kristie Tanner†1,
- Pedro Dorado-Morales1,
- Paula Villaescusa1,
- Divya Chugani1,
- Alba Frías1,
- Ernesto Segredo1,
- Xavier Molero1,
- Marco Fritschi1,
- Lucas Morales1,
- Daniel Ramón2,
- Carlos Peña3,
- Juli Peretó1, 4 and
- Manuel Porcar1, 5Email author
© Vilanova et al. 2015
Received: 6 August 2015
Accepted: 16 September 2015
Published: 1 October 2015
There is a general assent on the key role of standards in Synthetic Biology. In two consecutive letters to this journal, suggestions on the assembly methods for the Registry of standard biological parts have been described. We fully agree with those authors on the need of a more flexible building strategy and we highlight in the present work two major functional challenges standardization efforts have to deal with: the need of both universal and orthogonal behaviors. We provide experimental data that clearly indicate that such engineering requirements should not be taken for granted in Synthetic Biology.
Letter to the editor
Synthetic Biology, as an engineering approach to biotechnology, requires standard biological parts in order to overcome the limitations of assay-and-error strategies widely used in regular biotechnology. Indeed, tinkering may be sophisticated enough for successfully accomplishing simple genetic modifications, but metabolic engineering, let alone genome “programming”, require a basic toolbox of reliable standard biological parts to be combined into progressively increasing levels of complexity. In two recent letters published in this journal, concerns on the constraints of the Registry of Standard Biological parts associated to the limitations of 3A assembly methods have been highlighted [1, 2]. The Registry is indeed a valuable tool for synthetic biologists as a comprehensive catalog of biological parts, which can be physically obtained from it, combined in silico with the aid of ad-hoc software tools (http://sbolstandard.org/), and finally assembled to yield complex biological circuits with, in principle, predictable behaviors. However, as an analysis of the use of the Registry by iGEM participants demonstrates, there is a surprisingly limited reuse of biological parts .
In the present letter, we want to contribute to this debate on the challenges of biological standards by critically revising engineering assumptions in E. coli bioengineering (http://2014.igem.org/Team:Valencia_Biocampus). Of those assumptions, there are two key concepts linked to standardization that are often incorrectly taken for granted: universality and orthogonality. The first notion refers to the standard behavior (when “standard” is used as an adjective it is usually synonymous to “universal”); in other words, biological parts are expected to display the same or very similar outputs independently of the biological system they are placed into. The second concept, orthogonality, relates to the independent behavior of biological parts.
The cellular phenomena underlying the lack of standard and orthogonal behavior of the Biobrick parts we tested might range from differences in protein maturation times  and impact on biosynthetic burden  to context –upstream and downstream sequences effects– dependencies  as well as to stochastic effects or intrinsic and extrinsic noise ; and references therein].
The fact that the tested genetic modifications proved weak standards in terms of universality and orthogonality does not necessarily imply the impossibility of engineering a particular strain in a predictable way, but it poses enormous difficulties in engineering strains on the basis of the work done on other strains, particularly taking into account that only a fraction of the genome is shared by all E. coli strains . This suggests the need of a strain-by-strain both modelling and experimental previous effort. On the other hand, taking advantage of biological flexibility can be used in order to set up more robust devices, such as the use of bacterial haemoglobin to enhance production of foreign fluorescent proteins , tuning intracellular physical distances between the regulator source and the target promoter for selecting a given level of noise in Synthetic Biology constructs , or designing synthetic constructs imposing a minimal burden to the host cells .
There is a general assent in the Synthetic Biology community on the need of collections of biological parts, in which engineering features (universality, stability, orthogonality, among others; ) should be checked and unambiguously quantified as a basic prerequisite for obtaining predictable and scalable designs. Systematic failures and difficulties to meet engineering standards might not constitute the most prized result in terms of publication purposes, but we strongly believe that a comprehensive view on the standardization failures of today is the strongest path towards the development of fully standard and orthogonal biological parts in the future.
Valencia-Biocampus iGEM 2014 Team was supported by the European Projects ST-Flow and ERA-SynBio, Biopolis SL (Parc Científic de la Universitat de València) and the University of València through the International Excellence Campus and Col · legi Major Rector Peset. We are especially indebted to Rafael García-Martínez (OPEX, Oficina per a les Polítiques d’Excel · lència, Universitat de València) and Soledat Rubio (Càtedra de Divulgació de la Ciència de la Universitat de València) for their constant encouragement and support. We also thank the proteomics service (SCSIE) of the Universitat de València for their technical support. CV is a recipient of a FPU fellowship from the MECD Spanish Ministry.
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