In silico construction of the carbon fixation pathway in Synechococcus sp. WH8102

Because the carbon fixation pathway plays an essential role in the primary production and natural carbon recycling process, and because the genome of the marine cyanobacterial Synechococcus sp. WH8102 (SYNWH8102) was recently sequenced, SYNWH8102 was chosen to further our understanding of the interaction and regulation of the carbon fixation pathway at the molecular level. In this abstract, we present the predicted carbon fixation pathway in SYNWH8102 as a result of our recently developed computational protocol for inference of regulatory and signaling pathways. The results of our pathway prediction include: (a) Major components of the carbon fixation pathway reported in the literature are present in SYNWH8102. (b) Approximately, 48 new candidates are added into the network from the results of the pathway expansion step. (c) Additionally, our in-house motif finding program, CUBIC, found several motifs that are present in the promoter regions of multiple genes involved in this pathway, suggesting that these genes are transcriptionally co-regulated.

[1]  F. Tabita,et al.  The molecular regulation of the reductive pentose phosphate pathway in Proteobacteria and Cyanobacteria , 1996, Archives of Microbiology.

[2]  M. Badger,et al.  CO2 concentrating mechanisms in cyanobacteria: molecular components, their diversity and evolution. , 2003, Journal of experimental botany.

[3]  Grant Heffelfinger,et al.  An overview of the Sandia national laboratories genomes to life project, "carbon sequestration in Synechococcus sp.: from molecular machines to hierarchical modeling" , 2002, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

[4]  Ying Xu,et al.  Identification of Regulatory Binding Sites Using Minimum Spanning Trees , 2003, Pacific Symposium on Biocomputing.

[5]  F. Tabita,et al.  Localization and mapping of CO2 fixation genes within two gene clusters in Rhodobacter sphaeroides , 1988, Journal of bacteriology.

[6]  Tao Jiang,et al.  Computational inference of regulatory pathways in microbes , 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

[7]  F. Tabita.  Molecular and cellular regulation of autotrophic carbon dioxide fixation in microorganisms. , 1988, Microbiological reviews.

[8]  R. Figge,et al.  Characterization and analysis of an NAD(P)H dehydrogenase transcriptional regulator critical for the survival of cyanobacteria facing inorganic carbon starvation and osmotic stress , 2001, Molecular microbiology.

[9]  Tao Jiang,et al.  Operon prediction by comparative genomics: an application to the Synechococcus sp. WH8102 genome. , 2004, Nucleic acids research.