Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803

Rajib Saha, Alex T. Verseput, Bertram M. Berla, Thomas J. Mueller, Himadri B. Pakrasi, Costas D. Maranas

Research output: Contribution to journalArticle

53 Citations (Scopus)

Abstract

Cyanobacteria are an important group of photoautotrophic organisms that can synthesize valuable bio-products by harnessing solar energy. They are endowed with high photosynthetic efficiencies and diverse metabolic capabilities that confer the ability to convert solar energy into a variety of biofuels and their precursors. However, less well studied are the similarities and differences in metabolism of different species of cyanobacteria as they pertain to their suitability as microbial production chassis. Here we assemble, update and compare genome-scale models (iCyt773 and iSyn731) for two phylogenetically related cyanobacterial species, namely Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803. All reactions are elementally and charge balanced and localized into four different intracellular compartments (i.e., periplasm, cytosol, carboxysome and thylakoid lumen) and biomass descriptions are derived based on experimental measurements. Newly added reactions absent in earlier models (266 and 322, respectively) span most metabolic pathways with an emphasis on lipid biosynthesis. All thermodynamically infeasible loops are identified and eliminated from both models. Comparisons of model predictions against gene essentiality data reveal a specificity of 0.94 (94/100) and a sensitivity of 1 (19/19) for the Synechocystis iSyn731 model. The diurnal rhythm of Cyanothece 51142 metabolism is modeled by constructing separate (light/dark) biomass equations and introducing regulatory restrictions over light and dark phases. Specific metabolic pathway differences between the two cyanobacteria alluding to different bio-production potentials are reflected in both models.

Original languageEnglish (US)
Article numbere48285
JournalPloS one
Volume7
Issue number10
DOIs
StatePublished - Oct 31 2012

Fingerprint

Cyanothece
Synechocystis sp. PCC 6803
Synechocystis
Cyanobacteria
Solar Energy
Metabolic Networks and Pathways
Biomass
Light
Periplasm
Thylakoids
solar energy
Biofuels
Circadian Rhythm
Metabolism
Cytosol
Solar energy
biochemical pathways
Genes
Genome
Lipids

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Saha, Rajib ; Verseput, Alex T. ; Berla, Bertram M. ; Mueller, Thomas J. ; Pakrasi, Himadri B. ; Maranas, Costas D. / Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803. In: PloS one. 2012 ; Vol. 7, No. 10.
@article{f428ce2daa1a432680c3940284a549f6,
title = "Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803",
abstract = "Cyanobacteria are an important group of photoautotrophic organisms that can synthesize valuable bio-products by harnessing solar energy. They are endowed with high photosynthetic efficiencies and diverse metabolic capabilities that confer the ability to convert solar energy into a variety of biofuels and their precursors. However, less well studied are the similarities and differences in metabolism of different species of cyanobacteria as they pertain to their suitability as microbial production chassis. Here we assemble, update and compare genome-scale models (iCyt773 and iSyn731) for two phylogenetically related cyanobacterial species, namely Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803. All reactions are elementally and charge balanced and localized into four different intracellular compartments (i.e., periplasm, cytosol, carboxysome and thylakoid lumen) and biomass descriptions are derived based on experimental measurements. Newly added reactions absent in earlier models (266 and 322, respectively) span most metabolic pathways with an emphasis on lipid biosynthesis. All thermodynamically infeasible loops are identified and eliminated from both models. Comparisons of model predictions against gene essentiality data reveal a specificity of 0.94 (94/100) and a sensitivity of 1 (19/19) for the Synechocystis iSyn731 model. The diurnal rhythm of Cyanothece 51142 metabolism is modeled by constructing separate (light/dark) biomass equations and introducing regulatory restrictions over light and dark phases. Specific metabolic pathway differences between the two cyanobacteria alluding to different bio-production potentials are reflected in both models.",
author = "Rajib Saha and Verseput, {Alex T.} and Berla, {Bertram M.} and Mueller, {Thomas J.} and Pakrasi, {Himadri B.} and Maranas, {Costas D.}",
year = "2012",
month = "10",
day = "31",
doi = "10.1371/journal.pone.0048285",
language = "English (US)",
volume = "7",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "10",

}

Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803. / Saha, Rajib; Verseput, Alex T.; Berla, Bertram M.; Mueller, Thomas J.; Pakrasi, Himadri B.; Maranas, Costas D.

In: PloS one, Vol. 7, No. 10, e48285, 31.10.2012.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Reconstruction and Comparison of the Metabolic Potential of Cyanobacteria Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803

AU - Saha, Rajib

AU - Verseput, Alex T.

AU - Berla, Bertram M.

AU - Mueller, Thomas J.

AU - Pakrasi, Himadri B.

AU - Maranas, Costas D.

PY - 2012/10/31

Y1 - 2012/10/31

N2 - Cyanobacteria are an important group of photoautotrophic organisms that can synthesize valuable bio-products by harnessing solar energy. They are endowed with high photosynthetic efficiencies and diverse metabolic capabilities that confer the ability to convert solar energy into a variety of biofuels and their precursors. However, less well studied are the similarities and differences in metabolism of different species of cyanobacteria as they pertain to their suitability as microbial production chassis. Here we assemble, update and compare genome-scale models (iCyt773 and iSyn731) for two phylogenetically related cyanobacterial species, namely Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803. All reactions are elementally and charge balanced and localized into four different intracellular compartments (i.e., periplasm, cytosol, carboxysome and thylakoid lumen) and biomass descriptions are derived based on experimental measurements. Newly added reactions absent in earlier models (266 and 322, respectively) span most metabolic pathways with an emphasis on lipid biosynthesis. All thermodynamically infeasible loops are identified and eliminated from both models. Comparisons of model predictions against gene essentiality data reveal a specificity of 0.94 (94/100) and a sensitivity of 1 (19/19) for the Synechocystis iSyn731 model. The diurnal rhythm of Cyanothece 51142 metabolism is modeled by constructing separate (light/dark) biomass equations and introducing regulatory restrictions over light and dark phases. Specific metabolic pathway differences between the two cyanobacteria alluding to different bio-production potentials are reflected in both models.

AB - Cyanobacteria are an important group of photoautotrophic organisms that can synthesize valuable bio-products by harnessing solar energy. They are endowed with high photosynthetic efficiencies and diverse metabolic capabilities that confer the ability to convert solar energy into a variety of biofuels and their precursors. However, less well studied are the similarities and differences in metabolism of different species of cyanobacteria as they pertain to their suitability as microbial production chassis. Here we assemble, update and compare genome-scale models (iCyt773 and iSyn731) for two phylogenetically related cyanobacterial species, namely Cyanothece sp. ATCC 51142 and Synechocystis sp. PCC 6803. All reactions are elementally and charge balanced and localized into four different intracellular compartments (i.e., periplasm, cytosol, carboxysome and thylakoid lumen) and biomass descriptions are derived based on experimental measurements. Newly added reactions absent in earlier models (266 and 322, respectively) span most metabolic pathways with an emphasis on lipid biosynthesis. All thermodynamically infeasible loops are identified and eliminated from both models. Comparisons of model predictions against gene essentiality data reveal a specificity of 0.94 (94/100) and a sensitivity of 1 (19/19) for the Synechocystis iSyn731 model. The diurnal rhythm of Cyanothece 51142 metabolism is modeled by constructing separate (light/dark) biomass equations and introducing regulatory restrictions over light and dark phases. Specific metabolic pathway differences between the two cyanobacteria alluding to different bio-production potentials are reflected in both models.

UR - http://www.scopus.com/inward/record.url?scp=84868275739&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84868275739&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0048285

DO - 10.1371/journal.pone.0048285

M3 - Article

VL - 7

JO - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 10

M1 - e48285

ER -