Transcriptomic and proteomic dynamics in the metabolism of a diazotrophic cyanobacterium, Cyanothece sp. PCC 7822 during a diurnal light-dark cycle.

David Welkie,Ronald Taylor,Xiaohui Zhang,Hugh Mitchell,Meng Lye Markillie,Ketaki Bhide,Jon Jacobs,Louis A Sherman,Marina Gritsenko,Richard D Smith,Galya Orr,Jyothi Thimmapuram

doi:10.1186/1471-2164-15-1185

Abstract

BackgroundCyanothece sp. PCC 7822 is an excellent cyanobacterial model organism with great potential to be applied as a biocatalyst for the production of high value compounds. Like other unicellular diazotrophic cyanobacterial species, it has a tightly regulated metabolism synchronized to the light–dark cycle. Utilizing transcriptomic and proteomic methods, we quantified the relationships between transcription and translation underlying central and secondary metabolism in response to nitrogen free, 12 hour light and 12 hour dark conditions.ResultsBy combining mass-spectrometry based proteomics and RNA-sequencing transcriptomics, we quantitatively measured a total of 6766 mRNAs and 1322 proteins at four time points across a 24 hour light–dark cycle. Photosynthesis, nitrogen fixation, and carbon storage relevant genes were expressed during the preceding light or dark period, concurrent with measured nitrogenase activity in the late light period. We describe many instances of disparity in peak mRNA and protein abundances, and strong correlation of light dependent expression of both antisense and CRISPR-related gene expression. The proteins for nitrogenase and the pentose phosphate pathway were highest in the dark, whereas those for glycolysis and the TCA cycle were more prominent in the light. Interestingly, one copy of the psbA gene encoding the photosystem II (PSII) reaction center protein D1 (psbA4) was highly upregulated only in the dark. This protein likely cannot catalyze O2 evolution and so may be used by the cell to keep PSII intact during N2 fixation. The CRISPR elements were found exclusively at the ends of the large plasmid and we speculate that their presence is crucial to the maintenance of this plasmid.ConclusionsThis investigation of parallel transcriptional and translational activity within Cyanothece sp. PCC 7822 provided quantitative information on expression levels of metabolic pathways relevant to engineering efforts. The identification of expression patterns for both mRNA and protein affords a basis for improving biofuel production in this strain and for further genetic manipulations. Expression analysis of the genes encoded on the 6 plasmids provided insight into the possible acquisition and maintenance of some of these extra-chromosomal elements.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1185) contains supplementary material, which is available to authorized users.

Highlights

IntroductionThe ability to utilize carbon acquired from the atmosphere as feedstock along with energy provided by light to produce valuable chemicals and fuels (e.g. ethanol, butanol, hydrogen gas, and fatty acid methyl esters) is even more appealing in diazotrophic strains, since they can grow in the absence of combined nitrogen
Our results provide a better understanding of metabolism of Cyanothece 7822 in light and dark conditions and how the metabolic partitioning can be of importance for biofuel production
On the third day of exponential growth, cells were collected for RNAsequencing (RNA-seq) and proteomics at four time points across the light/dark cycle

Summary

Introduction

The ability to utilize carbon acquired from the atmosphere as feedstock along with energy provided by light to produce valuable chemicals and fuels (e.g. ethanol, butanol, hydrogen gas, and fatty acid methyl esters) is even more appealing in diazotrophic strains, since they can grow in the absence of combined nitrogen. Members of Cyanothece have well-defined rhythms when grown under N2-fixing conditions, using light/dark or continuous light illumination [3]. During the light phase of growth, light energy is utilized in photosynthesis to secure and store CO2 in intracellular carbohydrate granules. Photosynthesis shuts down and respiration utilizes the glucose stored in carbohydrate granules to produce energy and to consume intracellular oxygen. This enables the O2-sensitive nitrogenase to function properly during the dark period. The nitrogenase enzymes allow the cell to fix atmospheric nitrogen, a process which releases high levels of hydrogen gas [4]

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