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In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria
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, ph...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5217662/ https://www.ncbi.nlm.nih.gov/pubmed/28056772 http://dx.doi.org/10.1186/s12864-016-3389-4 |
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author | Motwalli, Olaa Essack, Magbubah Jankovic, Boris R. Ji, Boyang Liu, Xinyao Ansari, Hifzur Rahman Hoehndorf, Robert Gao, Xin Arold, Stefan T. Mineta, Katsuhiko Archer, John A. C. Gojobori, Takashi Mijakovic, Ivan Bajic, Vladimir B. |
author_facet | Motwalli, Olaa Essack, Magbubah Jankovic, Boris R. Ji, Boyang Liu, Xinyao Ansari, Hifzur Rahman Hoehndorf, Robert Gao, Xin Arold, Stefan T. Mineta, Katsuhiko Archer, John A. C. Gojobori, Takashi Mijakovic, Ivan Bajic, Vladimir B. |
author_sort | Motwalli, Olaa |
collection | PubMed |
description | 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3389-4) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5217662 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-52176622017-01-09 In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria Motwalli, Olaa Essack, Magbubah Jankovic, Boris R. Ji, Boyang Liu, Xinyao Ansari, Hifzur Rahman Hoehndorf, Robert Gao, Xin Arold, Stefan T. Mineta, Katsuhiko Archer, John A. C. Gojobori, Takashi Mijakovic, Ivan Bajic, Vladimir B. BMC Genomics Methodology Article 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3389-4) contains supplementary material, which is available to authorized users. BioMed Central 2017-01-05 /pmc/articles/PMC5217662/ /pubmed/28056772 http://dx.doi.org/10.1186/s12864-016-3389-4 Text en © The Author(s). 2017 Open AccessThis 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. |
spellingShingle | Methodology Article Motwalli, Olaa Essack, Magbubah Jankovic, Boris R. Ji, Boyang Liu, Xinyao Ansari, Hifzur Rahman Hoehndorf, Robert Gao, Xin Arold, Stefan T. Mineta, Katsuhiko Archer, John A. C. Gojobori, Takashi Mijakovic, Ivan Bajic, Vladimir B. In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria |
title | In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria |
title_full | In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria |
title_fullStr | In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria |
title_full_unstemmed | In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria |
title_short | In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria |
title_sort | in silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5217662/ https://www.ncbi.nlm.nih.gov/pubmed/28056772 http://dx.doi.org/10.1186/s12864-016-3389-4 |
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