The long journey towards standards for engineering biosystems

Beal, Jacob; Goñi-Moreno, Ángel; Myers, Chris J.; Hecht, Ariel; Vicente, María del Carmen de; Parco, María; Schmidt, Markus; Timmis, Kenneth N.; Baldwin, Geoff; Friedrichs, Steffi; Freemont, Paul S.; Kiga, Daisuke; Ordozgoiti, Elena; Rennig, Maja; Leonardo, Rios; Tanner, Kristie; Lorenzo, Vı́ctor de; Porcar, Manuel

doi:10.15252/embr.202050521

Cited by 53 publications

(36 citation statements)

References 11 publications

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“…1 and explained in detail above. As is also the case of other standards, this particular choice will certainly limit flexibility but will foster interoperability, parameterization and comparative metrology (42,43). The work above exemplifies how the same device, still after formatting, may go through successive, improved versions of the same functional DNA segments even if a prefixed arrangement is kept constant.…”

Section: Discussionmentioning

confidence: 98%

Standardization of inducer-activated broad host range expression modules: Debugging and refactoring an alkane-responsive AlkS/P_alkBdevice

Arce-Rodríguez

Benedetti

Silva‐Rocha

2020

Preprint

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Although inducible heterologous expression systems have been available since the birth of recombinant DNA technology, the diversity of devices and genetic architectures of the corresponding vectors have often resulted in a lack of reproducibility and interoperability. In an effort to increase predictability of expression of genes of interest in a variety of possible bacterial hosts we propose a composition standard for debugging and reassembling all regulatory parts that participate in the performance of such devices. As a case study we address the n-octane and dicyclopropyl ketone (DCPK)-inducible PalkB promoter of the alkane biodegradation pOCT plasmid of Pseudomonas putida. The standardized expression module consisted of an edited alkS regulatory gene that is divergently expressed and separated of PalkB by a synthetic DNA buffer sequence. The native DNA sequence of the structural alkS gene was modified to alleviate the catabolite repression exerted by some carbon and nitrogen sources through the Crc/Hfq complex of some hosts. The PalkB promoter along with the alkS variants were then formatted as SEVA (Standard European Vector Architecture) cargoes and their activity parameters in P. putida determined with GFP and luminiscent reporters. The thereby refactored system showed improvements in various features desirable in conditional expression modules: inducibility, capacity, noise reduction and on/off ratio. When applied to other promoter/regulator pairs, the compositional standard thereby implemented in the AlkS/PalkB module will enable more complex genetic programming in non-model bacteria.

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Section: Discussionmentioning

confidence: 98%

Standardization of inducer-activated broad host range expression modules: Debugging and refactoring an alkane-responsive AlkS/P_alkBdevice

Arce-Rodríguez

Benedetti

Silva‐Rocha

2020

Preprint

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“…These efforts will be further complicated by the fact that numerous evolutionary routes will likely have to be explored to arrive at a more viable one. Therefore, to facilitate reproducibility and distribution of materials between different groups working on this unifying goal, it would be beneficial to establish or improve platforms for standard part repository ( Beal et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Roadmap to Building a Cell: An Evolutionary Approach

Abil

Danelon

2020

Front. Bioeng. Biotechnol.

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Laboratory synthesis of an elementary biological cell from isolated components may aid in understanding of the fundamental principles of life and will provide a platform for a range of bioengineering and medical applications. In essence, building a cell consists in the integration of cellular modules into system's level functionalities satisfying a definition of life. To achieve this goal, we propose in this perspective to undertake a semirational, system's level evolutionary approach. The strategy would require iterative cycles of genetic integration of functional modules, diversification of hereditary information, compartmentalized gene expression, selection/screening, and possibly, assistance from open-ended evolution. We explore the underlying challenges to each of these steps and discuss possible solutions toward the bottom-up construction of an artificial living cell.

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“…Although titers achieved with R. toruloides to date are lower than those achieved with the model yeast S. cerevisiae, several researchers have developed CRISPR-Cas9 based genome editing methods for R. toruloides, offering increased integration efficiency and targeted multiplex genome editing (Jiao et al, 2019;Otoupal et al, 2019;Schultz et al, 2019). The application of such tools and development of synthetic biology standards (Beal et al, 2020) to construct heterologous pathways for isoprenoid jet fuel candidate biosynthesis has the potential to boost titers from lignocellulose derived feedstocks significantly, thereby improving the economic feasibility of microbial biojet fuel production.…”

Section: Lignocellulosic Biomassmentioning

confidence: 99%

Sustainable Production of Microbial Isoprenoid Derived Advanced Biojet Fuels Using Different Generation Feedstocks: A Review

Walls

Rios‐Solis

2020

Front. Bioeng. Biotechnol.

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As the fastest mode of transport, the aircraft is a major driver for globalization and economic growth. The development of alternative advanced liquid fuels is critical to sustainable development within the sector. Such fuels should be compatible with existing infrastructure and derived from second generation feedstocks to avoid competition with food markets. With properties similar to petroleum based fuels, isoprenoid derived compounds such as limonene, bisabolane, farnesane, and pinene dimers are of increasing interest as "drop-in" replacement jet fuels. In this review potential isoprenoid derived jet fuels and progress toward their microbial production was discussed in detail. Although substantial advancements have been achieved, the use of first generation feedstocks remains ubiquitous. Lignocellulosic biomass is the most abundant raw material available for biofuel production, however, technological constraints associated with its pretreatment and saccharification hinder its economic feasibility for low-value commodity production. Non-conventional microbes with novel characteristics including cellulolytic bacteria and fungi capable of highly efficient lignocellulose degradation and xylose fermenting oleaginous yeast with enhanced ligninassociated inhibitor tolerance were investigated as alternatives to traditional model hosts. Finally, innovative bioprocessing methods including consolidated bioprocessing and sequential bioreactor approaches, with potential to capitalize on such unique natural capabilities were considered.

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The long journey towards standards for engineering biosystems

Abstract: Synthetic biology needs to adopt sound scientific and industry‐like standards in order to achieve its ambitious goals of efficient and accurate engineering of biological systems.

Cited by 53 publications

References 11 publications

Standardization of inducer-activated broad host range expression modules: Debugging and refactoring an alkane-responsive AlkS/P_alkBdevice

Standardization of inducer-activated broad host range expression modules: Debugging and refactoring an alkane-responsive AlkS/P_alkBdevice

Roadmap to Building a Cell: An Evolutionary Approach

Sustainable Production of Microbial Isoprenoid Derived Advanced Biojet Fuels Using Different Generation Feedstocks: A Review

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The long journey towards standards for engineering biosystems

Abstract: Synthetic biology needs to adopt sound scientific and industry‐like standards in order to achieve its ambitious goals of efficient and accurate engineering of biological systems.

Cited by 53 publications

References 11 publications

Standardization of inducer-activated broad host range expression modules: Debugging and refactoring an alkane-responsive AlkS/PalkBdevice

Standardization of inducer-activated broad host range expression modules: Debugging and refactoring an alkane-responsive AlkS/PalkBdevice

Roadmap to Building a Cell: An Evolutionary Approach

Sustainable Production of Microbial Isoprenoid Derived Advanced Biojet Fuels Using Different Generation Feedstocks: A Review

Contact Info

Product

Resources

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Standardization of inducer-activated broad host range expression modules: Debugging and refactoring an alkane-responsive AlkS/P_alkBdevice

Standardization of inducer-activated broad host range expression modules: Debugging and refactoring an alkane-responsive AlkS/P_alkBdevice