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

BMC Genomics

Louis A Sherman¹  Richard D Smith⁴  Hugh Mitchell²  Marina Gritsenko⁴  Jyothi Thimmapuram³  Ketaki Bhide³  Jon Jacobs⁴  Galya Orr²  Ronald Taylor²  Meng Lye Markillie²  Xiaohui Zhang¹  David Welkie¹ 

[1] Department of Biological Sciences, Purdue University, West Lafayette, IN, USA;Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA;Bioinformatics Core, Purdue University, West Lafayette, IN, USA;Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA

关键词: CRISPR;    Butanol;    Proteomics;    N₂ fixation;    RNA-Seq;    Cyanobacteria;    Cyanothece;   

Others  :  1121419
DOI  :  10.1186/1471-2164-15-1185

 received in 2014-08-07, accepted in 2014-12-16,  发布年份 2014

【 摘 要 】

Background

Cyanothece 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.

Results

By 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.

Conclusions

This 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.

【 授权许可】

   
2014 Welkie et al.; licensee BioMed Central.

【 图 表 】

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