title: In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria.
abstract: 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.
  
  
  
  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.
  
  
  
  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.
authors.affiliation: Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
authors.forename: Olaa
authors.initials: O
authors.lastname: Motwalli
authors.affiliation: Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
authors.forename: Magbubah
authors.initials: M
authors.lastname: Essack
authors.affiliation: Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
authors.forename: Boris R
authors.initials: BR
authors.lastname: Jankovic
authors.affiliation: Division of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden.
authors.forename: Boyang
authors.initials: B
authors.lastname: Ji
authors.affiliation: SABIC Corporate Research and Development (CRD), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
authors.forename: Xinyao
authors.initials: X
authors.lastname: Liu
authors.affiliation: Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
authors.forename: Hifzur Rahman
authors.initials: HR
authors.lastname: Ansari
authors.affiliation: Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
authors.forename: Robert
authors.initials: R
authors.lastname: Hoehndorf
authors.affiliation: Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
authors.forename: Xin
authors.initials: X
authors.lastname: Gao
authors.affiliation: Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
authors.forename: Stefan T
authors.initials: ST
authors.lastname: Arold
authors.affiliation: Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
authors.forename: Katsuhiko
authors.initials: K
authors.lastname: Mineta
authors.affiliation: Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
authors.forename: John A C
authors.initials: JA
authors.lastname: Archer
authors.affiliation: Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.
authors.forename: Takashi
authors.initials: T
authors.lastname: Gojobori
authors.affiliation: Division of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296, Gothenburg, Sweden.
authors.forename: Ivan
authors.initials: I
authors.lastname: Mijakovic
authors.affiliation: Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia. vladimir.bajic@kaust.edu.sa.
authors.forename: Vladimir B
authors.initials: VB
authors.lastname: Bajic
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D000458:Cyanobacteria / Q000145:classification / Q000235:genetics* / Q000378:metabolism*; D005230:Fatty Acids, Nonesterified / Q000096:biosynthesis*; D053858:Metabolic Networks and Pathways; D010788:Photosynthesis; D010802:Phylogeny; D020543:Proteome; D040901:Proteomics / Q000379:methods
chemical_list: D005230:Fatty Acids, Nonesterified; D020543:Proteome
keywords: Biofuel; Bioinformatics; Cell factories; Computer science; Cyanobacteria; Free fatty acids; Optimization; Screening method