Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria

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.

A tightly inducible riboswitch system in <i>Synechocystis</i> sp. PCC 6803

“…In addition, our data imply an issue about this system: the effect of the sequence around the riboswitch. This work contributes to the field of synthetic biology by demonstrating the utility of the theophylline riboswitch to control protein expression in Synechocystis, the most popular cyanobacterial model organism, given the availability of currently more than 860 mutants (Nakamura et al, 1999) and significant resources addressing the systems biology of this strain (Fujisawa et al, 2014;Hernandez-Prieto and Futschik, 2012;Hernandez-Prieto et al, 2014). The vector constructed in this work followed the rational design of a gene expression system in Synechocystis.…”

Next-Generation Sequencing — An Overview of the History, Tools, and “Omic” Applications

“…Systeomics is the integration of genomics, proteomics, metabolomics, and phenomics into a single network system. It is a branch of biology that uses computational techniques to analyze and model how the components of a biological system such as cells or organisms interact with each other to produce the characteristics and behavior of that system [160][161][162]. Systeomics is a biology-based interdisciplinary field applied to biomedical and biological scientific research that focuses on complex interactions within biological systems using a holistic approach.…”

Algal Cell Factories: Approaches, Applications, and Potentials

“…PCC 6803 with a computational metabolic engineering tool called Optknock [68] to enhance astaxanthin production [85]. Recent web-based tools for system biology analysis for cyanobacteria can be found in recent reviews [86] and their application to the synthesis of industrial products was reported [87,88]. …”