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      Production of ent-kaurene from lignocellulosic hydrolysate in Rhodosporidium toruloides

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          Abstract

          Background

          Rhodosporidium toruloides has emerged as a promising host for the production of bioproducts from lignocellulose, in part due to its ability to grow on lignocellulosic feedstocks, tolerate growth inhibitors, and co-utilize sugars and lignin-derived monomers. Ent-kaurene derivatives have a diverse range of potential applications from therapeutics to novel resin-based materials.

          Results

          The Design, Build, Test, and Learn (DBTL) approach was employed to engineer production of the non-native diterpene ent-kaurene in R. toruloides. Following expression of kaurene synthase (KS) in R. toruloides in the first DBTL cycle, a key limitation appeared to be the availability of the diterpene precursor, geranylgeranyl diphosphate (GGPP). Further DBTL cycles were carried out to select an optimal GGPP synthase and to balance its expression with KS, requiring two of the strongest promoters in R. toruloides, ANT (adenine nucleotide translocase) and TEF1 (translational elongation factor 1) to drive expression of the KS from Gibberella fujikuroi and a mutant version of an FPP synthase from Gallus gallus that produces GGPP. Scale-up of cultivation in a 2 L bioreactor using a corn stover hydrolysate resulted in an ent-kaurene titer of 1.4 g/L.

          Conclusion

          This study builds upon previous work demonstrating the potential of R. toruloides as a robust and versatile host for the production of both mono- and sesquiterpenes, and is the first demonstration of the production of a non-native diterpene in this organism.

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          Most cited references37

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          Skyline: an open source document editor for creating and analyzing targeted proteomics experiments.

          Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. It is open source and freely available for academic and commercial use. The Skyline user interface simplifies the development of mass spectrometer methods and the analysis of data from targeted proteomics experiments performed using selected reaction monitoring (SRM). Skyline supports using and creating MS/MS spectral libraries from a wide variety of sources to choose SRM filters and verify results based on previously observed ion trap data. Skyline exports transition lists to and imports the native output files from Agilent, Applied Biosystems, Thermo Fisher Scientific and Waters triple quadrupole instruments, seamlessly connecting mass spectrometer output back to the experimental design document. The fast and compact Skyline file format is easily shared, even for experiments requiring many sample injections. A rich array of graphs displays results and provides powerful tools for inspecting data integrity as data are acquired, helping instrument operators to identify problems early. The Skyline dynamic report designer exports tabular data from the Skyline document model for in-depth analysis with common statistical tools. Single-click, self-updating web installation is available at http://proteome.gs.washington.edu/software/skyline. This web site also provides access to instructional videos, a support board, an issues list and a link to the source code project.
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            High-density cultivation of oleaginous yeast Rhodosporidium toruloides Y4 in fed-batch culture

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              Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools

              The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about ‘legacy’ parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects.
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                Author and article information

                Contributors
                jmgladden@lbl.gov
                Journal
                Microb Cell Fact
                Microb. Cell Fact
                Microbial Cell Factories
                BioMed Central (London )
                1475-2859
                5 February 2020
                5 February 2020
                2020
                : 19
                : 24
                Affiliations
                [1 ]Department of Energy, Agile BioFoundry, Emeryville, CA 94608 USA
                [2 ]GRID grid.474523.3, ISNI 0000000403888279, Department of Biomass Science and Conversion Technology, , Sandia National Laboratories, ; 7011 East Ave, Livermore, CA 94550 USA
                [3 ]GRID grid.184769.5, ISNI 0000 0001 2231 4551, Advanced Biofuels and Bioproducts Process Development Unit, , Lawrence Berkeley National Laboratory, ; Emeryville, CA 94608 USA
                [4 ]GRID grid.184769.5, ISNI 0000 0001 2231 4551, Biological Systems and Engineering Division, , Lawrence Berkeley National Laboratory, ; Berkeley, CA 94720 USA
                [5 ]GRID grid.451303.0, ISNI 0000 0001 2218 3491, Earth and Biological Sciences Directorate, , Pacific Northwest National Laboratory, ; Richland, WA 99354 USA
                [6 ]GRID grid.451303.0, ISNI 0000 0001 2218 3491, Energy and Environment Directorate, , Pacific Northwest National Laboratory, ; Richland, WA 99354 USA
                [7 ]GRID grid.47840.3f, ISNI 0000 0001 2181 7878, QB3-Berkeley, University of California, ; Berkeley, CA 94704 USA
                Author information
                http://orcid.org/0000-0002-6985-2485
                Article
                1293
                10.1186/s12934-020-1293-8
                7003354
                32024522
                dc94d614-bdea-4a77-8413-0bd7133c4818
                © The Author(s) 2020

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                : 5 September 2019
                : 23 January 2020
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/100011735, Bioenergy Technologies Office;
                Award ID: DE-AC02-05CH11231
                Categories
                Research
                Custom metadata
                © The Author(s) 2020

                Biotechnology
                rhodotorula,mevalonate pathway,diterpene,geranylgeranyl pyrophosphate synthase,mutant farnesyl pyrophosphate synthase,metabolic engineering

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