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dc.contributor.authorMotwalli, Olaa Amin
dc.contributor.authorEssack, Magbubah
dc.contributor.authorJankovic, Boris R.
dc.contributor.authorJi, Boyang
dc.contributor.authorLiu, Xinyao
dc.contributor.authorAnsari, Hifzur Rahman
dc.contributor.authorHoehndorf, Robert
dc.contributor.authorGao, Xin
dc.contributor.authorArold, Stefan T.
dc.contributor.authorMineta, Katsuhiko
dc.contributor.authorArcher, John A.C.
dc.contributor.authorGojobori, Takashi
dc.contributor.authorMijakovic, Ivan
dc.contributor.authorBajic, Vladimir B.
dc.date.accessioned2017-01-08T13:05:39Z
dc.date.available2017-01-08T13:05:39Z
dc.date.issued2017-01-05
dc.identifier.citationMotwalli O, Essack M, Jankovic BR, Ji B, Liu X, et al. (2017) In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria. BMC Genomics 18. Available: http://dx.doi.org/10.1186/s12864-016-3389-4.
dc.identifier.issn1471-2164
dc.identifier.doi10.1186/s12864-016-3389-4
dc.identifier.urihttp://hdl.handle.net/10754/622638
dc.description.abstractBackground Finding a source from which high-energy-density biofuels can be derived at an industrial scale has become an urgent challenge for renewable energy production. Some microorganisms can produce free fatty acids (FFA) as precursors towards such high-energy-density biofuels. In particular, photosynthetic cyanobacteria are capable of directly converting carbon dioxide into FFA. However, current engineered strains need several rounds of engineering to reach the level of production of FFA to be commercially viable; thus new chassis strains that require less engineering are needed. Although more than 120 cyanobacterial genomes are sequenced, the natural potential of these strains for FFA production and excretion has not been systematically estimated. Results Here we present the FFA SC (FFASC), an in silico screening method that evaluates the potential for FFA production and excretion of cyanobacterial strains based on their proteomes. A literature search allowed for the compilation of 64 proteins, most of which influence FFA production and a few of which affect FFA excretion. The proteins are classified into 49 orthologous groups (OGs) that helped create rules used in the scoring/ranking of algorithms developed to estimate the potential for FFA production and excretion of an organism. Among 125 cyanobacterial strains, FFASC identified 20 candidate chassis strains that rank in their FFA producing and excreting potential above the specifically engineered reference strain, Synechococcus sp. PCC 7002. We further show that the top ranked cyanobacterial strains are unicellular and primarily include Prochlorococcus (order Prochlorales) and marine Synechococcus (order Chroococcales) that cluster phylogenetically. Moreover, two principal categories of enzymes were shown to influence FFA production the most: those ensuring precursor availability for the biosynthesis of lipids, and those involved in handling the oxidative stress associated to FFA synthesis. Conclusion To our knowledge FFASC is the first in silico method to screen cyanobacteria proteomes for their potential to produce and excrete FFA, as well as the first attempt to parameterize the criteria derived from genetic characteristics that are favorable/non-favorable for this purpose. Thus, FFASC helps focus experimental evaluation only on the most promising cyanobacteria.
dc.description.sponsorshipThis publication is based upon work supported by the King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Awards No URF/1/1976-02 and FCS/1/2448-01.
dc.publisherSpringer Nature
dc.relation.urlhttp://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3389-4
dc.rightsThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectCyanobacteria
dc.subjectFree fatty acids
dc.subjectBiofuel
dc.subjectScreening method
dc.subjectCell factories
dc.subjectBioinformatics
dc.subjectOptimization
dc.subjectComputer science
dc.titleIn silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria
dc.typeArticle
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentSABIC - Corporate Research and Innovation Center (CRI) at KAUST
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentPathogen Genomics Laboratory
dc.identifier.journalBMC Genomics
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionDivision of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Gothenburg, Sweden
kaust.personMotwalli, Olaa Amin
kaust.personEssack, Magbubah
kaust.personJankovic, Boris R.
kaust.personLiu, Xinyao
kaust.personAnsari, Hifzur Rahman
kaust.personHoehndorf, Robert
kaust.personGao, Xin
kaust.personArold, Stefan T.
kaust.personMineta, Katsuhiko
kaust.personArcher, John A.C.
kaust.personGojobori, Takashi
kaust.personBajic, Vladimir B.
kaust.grant.numberURF/1/1976-02
kaust.grant.numberFCS/1/2448-01
dc.relation.isSupplementedByOlaa Motwalli, Magbubah Essack, Jankovic, B., Boyang Ji, Xinyao Liu, Hifzur Ansari, … Bajic, V. (2017). In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria. Figshare. https://doi.org/10.6084/m9.figshare.c.3658880
dc.relation.isSupplementedByDOI:10.6084/m9.figshare.c.3658880
dc.relation.isSupplementedByHANDLE:http://hdl.handle.net/10754/624143
refterms.dateFOA2018-06-14T05:04:02Z


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This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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.
Except where otherwise noted, this item's license is described as This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. 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.