title: Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis.
abstract: The model cyanobacterium, Synechococcus elongatus PCC 7942, is a genetically tractable obligate phototroph that is being developed for the bioproduction of high-value chemicals. Genome-scale models (GEMs) have been successfully used to assess and engineer cellular metabolism; however, GEMs of phototrophic metabolism have been limited by the lack of experimental datasets for model validation and the challenges of incorporating photon uptake. Here, we develop a GEM of metabolism in S. elongatus using random barcode transposon site sequencing (RB-TnSeq) essential gene and physiological data specific to photoautotrophic metabolism. The model explicitly describes photon absorption and accounts for shading, resulting in the characteristic linear growth curve of photoautotrophs. GEM predictions of gene essentiality were compared with data obtained from recent dense-transposon mutagenesis experiments. This dataset allowed major improvements to the accuracy of the model. Furthermore, discrepancies between GEM predictions and the in vivo dataset revealed biological characteristics, such as the importance of a truncated, linear TCA pathway, low flux toward amino acid synthesis from photorespiration, and knowledge gaps within nucleotide metabolism. Coupling of strong experimental support and photoautotrophic modeling methods thus resulted in a highly accurate model of S. elongatus metabolism that highlights previously unknown areas of S. elongatus biology.
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093.|Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093.
authors.forename: Jared T
authors.initials: JT
authors.lastname: Broddrick
authors.affiliation: Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093.|Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093.
authors.forename: Benjamin E
authors.initials: BE
authors.lastname: Rubin
authors.affiliation: Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093.
authors.forename: David G
authors.initials: DG
authors.lastname: Welkie
authors.affiliation: Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093.|Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA 92037.
authors.forename: Niu
authors.initials: N
authors.lastname: Du
authors.affiliation: Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093.
authors.forename: Nathan
authors.initials: N
authors.lastname: Mih
authors.affiliation: Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093.
authors.forename: Spencer
authors.initials: S
authors.lastname: Diamond
authors.affiliation: Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093.
authors.forename: Jenny J
authors.initials: JJ
authors.lastname: Lee
authors.affiliation: Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093; sgolden@ucsd.edu.|Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093.
authors.forename: Susan S
authors.initials: SS
authors.lastname: Golden
authors.affiliation: Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093.|Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093.
authors.forename: Bernhard O
authors.initials: BO
authors.lastname: Palsson
mesh_terms: D002244:Carbon / Q000378:metabolism; D002734:Chlorophyll / Q000737:chemistry; D002952:Citric Acid Cycle; D000458:Cyanobacteria / Q000235:genetics* / Q000378:metabolism; D005786:Gene Expression Regulation; D020043:Genes, Essential; D016678:Genome; D016296:Mutagenesis; D009711:Nucleotides / Q000378:metabolism; D016366:Open Reading Frames; D017785:Photons; D010788:Photosynthesis; D046940:Synechococcus / Q000235:genetics* / Q000378:metabolism
chemical_list: D009711:Nucleotides; D002734:Chlorophyll; D002244:Carbon
keywords: Synechococcus elongatus; TCA cycle; constraint-based modeling; cyanobacteria; photosynthesis