Issue 8, 2011
From the journal:

Molecular BioSystems

A model of cyclic transcriptomic behavior in the cyanobacterium Cyanothece sp. ATCC 51142†

Jason E. McDermott,*a   Christopher S. Oehmen,a   Lee Ann McCue,a   Eric Hill,b   Daniel M. Choi,a   Jana Stöckel,c   Michelle Liberton,c   Himadri B. Pakrasic  and  Louis A. Shermand  

* Corresponding authors

a Computational Biology and Bioinformatics Group, Pacific Northwest National Laboratory, MSIN: J4-33, 902 Battelle Boulevard, PO Box 999, Richland, USA
E-mail: Jason.McDermott@pnl.gov
Fax: 509-372-4720
Tel: 509-372-4360

b Microbiology, Pacific Northwest National Laboratory, Richland, USA

c Department of Biology, Washington University, St. Louis, USA

d Department of Biological Sciences, Purdue University, West Lafayette, USA

Abstract

Systems biology attempts to reconcile large amounts of disparate data with existing knowledge to provide models of functioning biological systems. The cyanobacterium Cyanothece sp. ATCC 51142 is an excellent candidate for such systems biology studies because: (i) it displays tight functional regulation between photosynthesis and nitrogen fixation; (ii) it has robust cyclic patterns at the genetic, protein and metabolomic levels; and (iii) it has potential applications for bioenergy production and carbon sequestration. We have represented the transcriptomic data from Cyanothece 51142 under diurnal light/dark cycles as a high-level functional abstraction and describe development of a predictive in silico model of diurnal and circadian behavior in terms of regulatory and metabolic processes in this organism. We show that incorporating network topology into the model improves performance in terms of our ability to explain the behavior of the system under new conditions. The model presented robustly describes transcriptomic behavior of Cyanothece 51142 under different cyclic and non-cyclic growth conditions, and represents a significant advance in the understanding of gene regulation in this important organism.

Graphical abstract: A model of cyclic transcriptomic behavior in the cyanobacterium Cyanothece sp. ATCC 51142

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Article information

DOI
https://doi.org/10.1039/C1MB05006K
Article type
Paper
Submitted
06 Jan 2011
Accepted
28 May 2011
First published
23 Jun 2011

Mol. BioSyst., 2011,7, 2407-2418

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A model of cyclic transcriptomic behavior in the cyanobacterium Cyanothece sp. ATCC 51142

J. E. McDermott, C. S. Oehmen, L. A. McCue, E. Hill, D. M. Choi, J. Stöckel, M. Liberton, H. B. Pakrasi and L. A. Sherman, Mol. BioSyst., 2011, 7, 2407 DOI: 10.1039/C1MB05006K

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