In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria

Handle URI:
http://hdl.handle.net/10754/622638
Title:
In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria
Authors:
Motwalli, Olaa Amin ( 0000-0002-3392-5734 ) ; Essack, Magbubah ( 0000-0003-2709-5356 ) ; Jankovic, Boris R.; Ji, Boyang; Liu, Xinyao; Ansari, Hifzur Rahman ( 0000-0002-0646-1743 ) ; Hoehndorf, Robert ( 0000-0001-8149-5890 ) ; Gao, Xin ( 0000-0002-7108-3574 ) ; Arold, Stefan T. ( 0000-0001-5278-0668 ) ; Mineta, Katsuhiko ( 0000-0002-4727-045X ) ; Archer, John A.C. ( 0000-0002-3302-3933 ) ; Gojobori, Takashi ( 0000-0001-7850-1743 ) ; Mijakovic, Ivan; Bajic, Vladimir B. ( 0000-0001-5435-4750 )
Abstract:
Background 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.
KAUST Department:
Computational Bioscience Research Center (CBRC); SABIC - Corporate Research and Innovation Center (CRI) at KAUST; Biological and Environmental Sciences and Engineering (BESE) Division; Pathogen Genomics Laboratory
Citation:
Motwalli 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.
Publisher:
Springer Nature
Journal:
BMC Genomics
KAUST Grant Number:
URF/1/1976-02; FCS/1/2448-01
Issue Date:
5-Jan-2017
DOI:
10.1186/s12864-016-3389-4
Type:
Article
ISSN:
1471-2164
Sponsors:
This 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.
Is Supplemented By:
Olaa 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; DOI:10.6084/m9.figshare.c.3658880; HANDLE:http://hdl.handle.net/10754/624143
Additional Links:
http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3389-4
Appears in Collections:
Articles; Computational Bioscience Research Center (CBRC); Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorMotwalli, Olaa Aminen
dc.contributor.authorEssack, Magbubahen
dc.contributor.authorJankovic, Boris R.en
dc.contributor.authorJi, Boyangen
dc.contributor.authorLiu, Xinyaoen
dc.contributor.authorAnsari, Hifzur Rahmanen
dc.contributor.authorHoehndorf, Roberten
dc.contributor.authorGao, Xinen
dc.contributor.authorArold, Stefan T.en
dc.contributor.authorMineta, Katsuhikoen
dc.contributor.authorArcher, John A.C.en
dc.contributor.authorGojobori, Takashien
dc.contributor.authorMijakovic, Ivanen
dc.contributor.authorBajic, Vladimir B.en
dc.date.accessioned2017-01-08T13:05:39Z-
dc.date.available2017-01-08T13:05:39Z-
dc.date.issued2017-01-05en
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.en
dc.identifier.issn1471-2164en
dc.identifier.doi10.1186/s12864-016-3389-4en
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.en
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.en
dc.publisherSpringer Natureen
dc.relation.urlhttp://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3389-4en
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.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectCyanobacteriaen
dc.subjectFree fatty acidsen
dc.subjectBiofuelen
dc.subjectScreening methoden
dc.subjectCell factoriesen
dc.subjectBioinformaticsen
dc.subjectOptimizationen
dc.subjectComputer scienceen
dc.titleIn silico screening for candidate chassis strains of free fatty acid-producing cyanobacteriaen
dc.typeArticleen
dc.contributor.departmentComputational Bioscience Research Center (CBRC)en
dc.contributor.departmentSABIC - Corporate Research and Innovation Center (CRI) at KAUSTen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.contributor.departmentPathogen Genomics Laboratoryen
dc.identifier.journalBMC Genomicsen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionDivision of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Gothenburg, Swedenen
kaust.authorMotwalli, Olaa Aminen
kaust.authorEssack, Magbubahen
kaust.authorJankovic, Boris R.en
kaust.authorLiu, Xinyaoen
kaust.authorAnsari, Hifzur Rahmanen
kaust.authorHoehndorf, Roberten
kaust.authorGao, Xinen
kaust.authorArold, Stefan T.en
kaust.authorMineta, Katsuhikoen
kaust.authorArcher, John A.C.en
kaust.authorGojobori, Takashien
kaust.authorBajic, Vladimir B.en
kaust.grant.numberURF/1/1976-02en
kaust.grant.numberFCS/1/2448-01en
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.3658880en
dc.relation.isSupplementedByDOI:10.6084/m9.figshare.c.3658880en
dc.relation.isSupplementedByHANDLE:http://hdl.handle.net/10754/624143en
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