Date Published: October 23, 2014
Publisher: Public Library of Science
Author(s): Konstantinos Billis, Maria Billini, H. James Tripp, Nikos C. Kyrpides, Konstantinos Mavromatis, Wolfgang R. Hess.
Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803 are model cyanobacteria from which the metabolism and adaptive responses of other cyanobacteria are inferred. Using stranded and 5′ enriched libraries, we measured the gene expression response of cells transferred from reference conditions to stress conditions of decreased inorganic carbon, increased salinity, increased pH, and decreased illumination at 1-h and 24-h after transfer. We found that the specific responses of the two strains were by no means identical. Transcriptome profiles allowed us to improve the structural annotation of the genome i.e. identify possible missed genes (including anti-sense), alter gene coordinates and determine transcriptional units (operons). Finally, we predicted associations between proteins of unknown function and biochemical pathways by revealing proteins of known functions that are co-regulated with the unknowns. Future studies of these model organisms will benefit from the cataloging of their responses to environmentally relevant stresses, and improvements in their genome annotations found here.
Cyanobacteria are considered to be among the oldest organisms evolutionarily, given that putative microfossils attributed to cyanobacteria are 3.5 billion years old . Synechocystis sp. strain 6803 (referred hereafter as Synechocystis) and Synechococcus sp. PCC 7942 (referred hereafter as Synechococcus) are two of the most well-studied cyanobacterial model organisms. Like other cyanobacteria, these organisms are capable of oxygenic photosynthesis. Most recently, they have attracted a great deal of attention because of their potential for photobiological production of biofuels and carbon sequestration , . Because of their great importance, the complete sequence of their genomes were among the first photosynthetic bacteria to be elucidated , . Despite their similarities, both strains exhibit a number of differences in their response to environmental stresses. For example, even though Synechocystis and Synechococcus are both freshwater unicellular strains, Synechocystis can tolerate elevated concentrations of NaCl better than Synechococcus. Furthermore, Synechococcus is an obligate photoautotroph , while Synechocystis is a facultative photoautotroph .
In this report we have employed an Illumina RNA-seq study for an in depth analysis of the transcriptome of the two cyanobacteria Synechococcus and Synechocystis. Using this data we were able to verify and improve the structural annotation of both genomes by detecting new transcripts located in the intergenic regions. Additionally gene annotations in Synechoccocus were improved based on 5′ enriched libraries evidence, and transcriptional units (operons) were identified containing two genes on average. The identification of genes with similar expression profiles under the conditions examined allowed us to link genes with undetermined function to annotated ones and their corresponding pathways.