Abstract
Cyanobacteria are essential primary producers in marine ecosystems, playing an important role in both carbon and nitrogen cycles. In the last decade, various genome sequencing and metagenomic projects have generated large amounts of genetic data for cyanobacteria. This wealth of data provides researchers with a new basis for the study of molecular adaptation, ecology and evolution of cyanobacteria, as well as for developing biotechnological applications. It also facilitates the use of multiplex techniques, i.e., expression profiling by high-throughput technologies such as microarrays, RNA-seq, and proteomics. However, exploration and analysis of these data is challenging, and often requires advanced computational methods. Also, they need to be integrated into our existing framework of knowledge to use them to draw reliable biological conclusions. Here, systems biology provides important tools. Especially, the construction and analysis of molecular networks has emerged as a powerful systems-level framework, with which to integrate such data, and to better understand biological relevant processes in these organisms. In this review, we provide an overview of the advances and experimental approaches undertaken using multiplex data from genomic, transcriptomic, proteomic, and metabolomic studies in cyanobacteria. Furthermore, we summarize currently available web-based tools dedicated to cyanobacteria, i.e., CyanoBase, CyanoEXpress, ProPortal, Cyanorak, CyanoBIKE, and CINPER. Finally, we present a case study for the freshwater model cyanobacteria, Synechocystis sp. PCC6803, to show the power of meta-analysis, and the potential to extrapolate acquired knowledge to the ecologically important marine cyanobacteria genus, Prochlorococcus.
Highlights
Cyanobacteria have a unique position in the living world, as they are the only prokaryotes capable of performing oxygenic photosynthesis
To facilitate the visualization of these results, we built a small network with the identified genes connected to ferric uptake regulator (Fur), the main transcription factor involved in iron adaptation for Synechocystis and Prochlorococcus (Figures 5A,B)
PMM0370 is part of the cynABDS operon and displays a common expression response to nitrogen limitation together with co-localized genes (Kamennaya and Post, 2011).To compare our regulatory network based on conservation of gene expression, with an automatically generated network, we created one with the keyword set to Fur, using CINPER with Synechocystis 6803 as the reference organism, and Prochlorococcus MED4 as the target (Figure 5C)
Summary
Cyanobacteria have a unique position in the living world, as they are the only prokaryotes capable of performing oxygenic photosynthesis. The data obtained from a natural population showed a great genomic diversity compared with model Synechococcus strains isolated from the same environment, stressing the importance www.frontiersin.org of horizontal gene transfer in natural populations (Palenik et al, 2009). Only two studies have systematically combined available gene expression data for cyanobacteria to obtain a systems level overview.
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