Abstract
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.
Highlights
Cyanobacteria are considered to be among the oldest organisms evolutionarily, given that putative microfossils attributed to cyanobacteria are 3.5 billion years old [1]
Caution should be taken in interpreting these results, since they may represent sequencing artifacts [27]. We tested these assumptions by examining the structural annotation of existing genes, their 59 start sites
Cyanobacteria, Synechocystis, have been shown to acclimate in alkaline pH by spending energy to acquire and concentrate scarce CO2 and bicarbonate, allowing them to grow and outcompete other photosynthesizers at high pH. Consistent with these studies, we found that Synechococcus gene sets related to cell wall biosynthesis and cell motility/signal transduction were enriched with upregulated genes under alkaline pH stress at 1-h and that gene sets for energy production and translation were upregulated at 24-h
Summary
Cyanobacteria are considered to be among the oldest organisms evolutionarily, given that putative microfossils attributed to cyanobacteria are 3.5 billion years old [1]. 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. 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 [2,3]. They have attracted a great deal of attention because of their potential for photobiological production of biofuels and carbon sequestration [2,3] Because of their great importance, the complete sequence of their genomes were among the first photosynthetic bacteria to be elucidated [4,5]. Synechococcus is an obligate photoautotroph [6], while Synechocystis is a facultative photoautotroph [7]
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