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Title: Integrated in silico analyses of regulatory and metabolic networks of Synechococcus sp. PCC 7002 reveal relationships between gene centrality and essentiality

Abstract

Cyanobacteria dynamically relay environmental inputs to intracellular adaptations through a coordinated adjustment of photosynthetic efficiency and carbon processing rates. The output of such adaptations is reflected through changes in transcriptional patterns and metabolic flux distributions that ultimately define growth strategy. To address interrelationships between metabolism and regulation, we performed integrative analyses of metabolic and gene co-expression networks in a model cyanobacterium, Synechococcus sp. PCC 7002. Centrality analyses using the gene co-expression network identified a set of key genes, which were defined here as ‘topologically important.’ Parallel in silico gene knock-out simulations, using the genome-scale metabolic network, classified what we termed as ‘functionally important’ genes, deletion of which affected growth or metabolism. A strong positive correlation was observed between topologically and functionally important genes. Functionally important genes exhibited variable levels of topological centrality; however, the majority of topologically central genes were found to be functionally essential for growth. Subsequent functional enrichment analysis revealed that both functionally and topologically important genes in Synechococcus sp. PCC 7002 are predominantly associated with translation and energy metabolism, two cellular processes critical for growth. This research demonstrates how synergistic network-level analyses can be used for reconciliation of metabolic and gene expression data to uncover fundamental biologicalmore » principles.« less

Authors:
; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1182919
Report Number(s):
PNNL-SA-109173
KP1601010
Grant/Contract Number:  
AC05-76RL01830
Resource Type:
Accepted Manuscript
Journal Name:
Life, 5(2):1127-1140
Additional Journal Information:
Journal Name: Life, 5(2):1127-1140
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; silico analyses; metabolic networks; synechococcus sp. PCC 7002

Citation Formats

Song, Hyun-Seob, McClure, Ryan S., Bernstein, Hans C., Overall, Christopher C., Hill, Eric A., and Beliaev, Alex S. Integrated in silico analyses of regulatory and metabolic networks of Synechococcus sp. PCC 7002 reveal relationships between gene centrality and essentiality. United States: N. p., 2015. Web. doi:10.3390/life5021127.
Song, Hyun-Seob, McClure, Ryan S., Bernstein, Hans C., Overall, Christopher C., Hill, Eric A., & Beliaev, Alex S. Integrated in silico analyses of regulatory and metabolic networks of Synechococcus sp. PCC 7002 reveal relationships between gene centrality and essentiality. United States. https://doi.org/10.3390/life5021127
Song, Hyun-Seob, McClure, Ryan S., Bernstein, Hans C., Overall, Christopher C., Hill, Eric A., and Beliaev, Alex S. Fri . "Integrated in silico analyses of regulatory and metabolic networks of Synechococcus sp. PCC 7002 reveal relationships between gene centrality and essentiality". United States. https://doi.org/10.3390/life5021127. https://www.osti.gov/servlets/purl/1182919.
@article{osti_1182919,
title = {Integrated in silico analyses of regulatory and metabolic networks of Synechococcus sp. PCC 7002 reveal relationships between gene centrality and essentiality},
author = {Song, Hyun-Seob and McClure, Ryan S. and Bernstein, Hans C. and Overall, Christopher C. and Hill, Eric A. and Beliaev, Alex S.},
abstractNote = {Cyanobacteria dynamically relay environmental inputs to intracellular adaptations through a coordinated adjustment of photosynthetic efficiency and carbon processing rates. The output of such adaptations is reflected through changes in transcriptional patterns and metabolic flux distributions that ultimately define growth strategy. To address interrelationships between metabolism and regulation, we performed integrative analyses of metabolic and gene co-expression networks in a model cyanobacterium, Synechococcus sp. PCC 7002. Centrality analyses using the gene co-expression network identified a set of key genes, which were defined here as ‘topologically important.’ Parallel in silico gene knock-out simulations, using the genome-scale metabolic network, classified what we termed as ‘functionally important’ genes, deletion of which affected growth or metabolism. A strong positive correlation was observed between topologically and functionally important genes. Functionally important genes exhibited variable levels of topological centrality; however, the majority of topologically central genes were found to be functionally essential for growth. Subsequent functional enrichment analysis revealed that both functionally and topologically important genes in Synechococcus sp. PCC 7002 are predominantly associated with translation and energy metabolism, two cellular processes critical for growth. This research demonstrates how synergistic network-level analyses can be used for reconciliation of metabolic and gene expression data to uncover fundamental biological principles.},
doi = {10.3390/life5021127},
journal = {Life, 5(2):1127-1140},
number = ,
volume = ,
place = {United States},
year = {Fri Mar 27 00:00:00 EDT 2015},
month = {Fri Mar 27 00:00:00 EDT 2015}
}

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journal, January 2007


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journal, February 2013


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journal, January 1962


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journal, September 2006


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journal, July 2014

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  • Frontiers in Genetics, Vol. 5
  • DOI: 10.3389/fgene.2014.00191

Effect of mono- and dichromatic light quality on growth rates and photosynthetic performance of Synechococcus sp. PCC 7002
journal, September 2014

  • Bernstein, Hans C.; Konopka, Allan; Melnicki, Matthew R.
  • Frontiers in Microbiology, Vol. 5
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Works referencing / citing this record:

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