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ELUCIDATING GENE SIGNATURES THAT CONTROL THE CIRCADIAN RHYTHM IN CYANOBACTERIA USING BIOINFORMATICS METHODS

By Tulip Nandu, Meeta Pradhan and Mathew J. Palakal

Abstract

poster abstractBackground: The daily light-dark cycle govern rhythmic changes in the behavior and physiology of most species. This circadian rhythm, or bi-ological “clock,” allows the organism to anticipate and prepare for the changes in the physical environment that are associated with day and night, thereby ensuring that the organism carry our specific processes at the right time of the day. Studies have found that the internal clock con-sists of an array of genes and the protein products they encode, which regulate various physiological processes throughout the body. Cyanothece sp. ATCC 51142 is an organism that has both photosynthetic (producing oxygen) and nitrogen fixing ability. The N2-fixing enzyme, nitrogenase, is highly sensitive to oxygen for which it has developed a temporal regula-tion in which N2 fixation and photosynthesis occur at different times throughout a diurnal cycle with very high levels of CO2 fixation during the light and high levels of N2 fixation in the dark. The mechanisms underly-ing the circadian rhythm and the signature genes elucidating this mecha-nism are addressed in this research. Objective: The objective is to integrate gene expression data with da-ta and knowledge from prior studies using bibliomics techniques, in the de novo construction of quasi-complete transcriptional regulatory networks to identify gene signatures in functional motifs and elucidate their role in circadian rhythms in cyanothece sp. ATCC 51142. Methodology: The sequence data of Transcription profiling time se-ries of cyanothece sp. ATCC 51142 grown in 12-hour light/12 hour dark then 24 h light from Array Express was used to construct the initial global regulatory network. Different network topological features (degree, betweeness and eccentricity) are used to identify the signature pathways during the day and night. The genes of the global regulatory network were used to construct networks of homologous species. The functions of the already known genes in well-studied homologous species were mapped to the function of the unannotated genes of cynaothece sp. ATCC 51142. Results: We have identified significant (p<0.05) signature pathways like photosynthesis, pantothenate and CoA biosynthesis and Glyoxylate and dicarboxylate metabolism that operate during the day. And during the night, pathways such as ribosome, riboflavin metabolism, and fatty acid biosynthesis sulfur metabolism were found to be significant (p<0.05). We will further investigate the genes that were already known to be significant using cyanobase database in a particular biological path-way and the novel genes that are identified by bibliomics approach

Topics: rhythmic changes, physiology, CIRCADIAN RHYTHM, behavior, GENE SIGNATURES
Publisher: Office of the Vice Chancellor for Research
Year: 2012
OAI identifier: oai:scholarworks.iupui.edu:1805/7837
Provided by: IUPUIScholarWorks

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