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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:
; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
J. Craig Venter Inst., La Jolla, CA (United States); Univ. of California, San Diego, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Inst. of Health (NIH) (United States); Univ. of California (United States); National Science Foundation (NSF)
OSTI Identifier:
1334350
Alternate Identifier(s):
OSTI ID: 1423793
Grant/Contract Number:  
SC0008593; T32GM00724; 2-P3071; MCB1244108
Resource Type:
Journal Article: Published Article
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Volume: 113 Journal Issue: 51; Journal ID: ISSN 0027-8424
Publisher:
Proceedings of the National Academy of Sciences
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; 59 BASIC BIOLOGICAL SCIENCES; cyanobacteria; constraint-based modeling; TCA cycle; photosynthesis; Synechococcus elongatus

Citation Formats

Broddrick, Jared T., Rubin, Benjamin E., Welkie, David G., Du, Niu, Mih, Nathan, Diamond, Spencer, Lee, Jenny J., Golden, Susan S., and Palsson, Bernhard O. Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis. United States: N. p., 2016. Web. doi:10.1073/pnas.1613446113.
Broddrick, Jared T., Rubin, Benjamin E., Welkie, David G., Du, Niu, Mih, Nathan, Diamond, Spencer, Lee, Jenny J., Golden, Susan S., & Palsson, Bernhard O. Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis. United States. https://doi.org/10.1073/pnas.1613446113
Broddrick, Jared T., Rubin, Benjamin E., Welkie, David G., Du, Niu, Mih, Nathan, Diamond, Spencer, Lee, Jenny J., Golden, Susan S., and Palsson, Bernhard O. Thu . "Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis". United States. https://doi.org/10.1073/pnas.1613446113.
@article{osti_1334350,
title = {Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis},
author = {Broddrick, Jared T. and Rubin, Benjamin E. and Welkie, David G. and Du, Niu and Mih, Nathan and Diamond, Spencer and Lee, Jenny J. and Golden, Susan S. and Palsson, Bernhard O.},
abstractNote = {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.},
doi = {10.1073/pnas.1613446113},
url = {https://www.osti.gov/biblio/1334350}, journal = {Proceedings of the National Academy of Sciences of the United States of America},
issn = {0027-8424},
number = 51,
volume = 113,
place = {United States},
year = {2016},
month = {12}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at https://doi.org/10.1073/pnas.1613446113

Citation Metrics:
Cited by: 6 works
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