Next Article in Journal / Special Issue
Advances in Understanding Carboxysome Assembly in Prochlorococcus and Synechococcus Implicate CsoS2 as a Critical Component
Previous Article in Journal / Special Issue
Enhancing Alkane Production in Cyanobacterial Lipid Droplets: A Model Platform for Industrially Relevant Compound Production
Article Menu

Export Article

Open AccessArticle
Life 2015, 5(2), 1127-1140; doi:10.3390/life5021127

Integrated in silico Analyses of Regulatory and Metabolic Networks of Synechococcus sp. PCC 7002 Reveal Relationships between Gene Centrality and Essentiality

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
*
Authors to whom correspondence should be addressed.
Academic Editors: John C. Meeks and Robert Haselkorn
Received: 13 February 2015 / Revised: 17 March 2015 / Accepted: 19 March 2015 / Published: 27 March 2015
(This article belongs to the Special Issue Cyanobacteria: Ecology, Physiology and Genetics)
View Full-Text   |   Download PDF [976 KB, uploaded 27 March 2015]   |  

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 biological principles. View Full-Text
Keywords: cyanobacteria; Synechococcus 7002; gene co-expression network; genome-scale metabolic network; node centrality; gene knock-out simulation; randomization test cyanobacteria; Synechococcus 7002; gene co-expression network; genome-scale metabolic network; node centrality; gene knock-out simulation; randomization test
Figures

Figure 1

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Supplementary material

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Song, H.-S.; McClure, R.S.; Bernstein, H.C.; Overall, C.C.; Hill, E.A.; Beliaev, A.S. Integrated in silico Analyses of Regulatory and Metabolic Networks of Synechococcus sp. PCC 7002 Reveal Relationships between Gene Centrality and Essentiality. Life 2015, 5, 1127-1140.

Show more citation formats Show less citations formats

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Life EISSN 2075-1729 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top