Study on the effect of environmental changes to the photosynthesis of microalgae and cyanobacteria

Abstract

Microalgae and cyanobacteria are photosynthetic microorganisms that possesses advantageous characteristics to be a potential bio-feedstock for biofuel and biochemical. However, current level of productivity from microalgae does not match up to their potentials due to the growth retardation in different and uncontrollable environmental stresses. Here, this study reports the response of three photosynthetic micro-organisms to different environmental stress such as nitrogen deprivation and temperature fluctuation which ultimately leads to the understanding of how photosynthetic machineries are repressed.

To understand the effect of nitrogen deprivation on the growth of microalgae, Dunaliella tertiolecta LB999 were cultivated under the combination of different light intensity and nitrogen level. Using transcriptome sequencing and transcriptome de novo assembly, genes that respond to both light and nitrogen with an opposite mode of action were investigated. This investigation showed that chlorophyll synthesis, tetrahydrofolate mediated C1 metabolism and GS/GOGAT nitrogen assimilation pathways are repressed in nitrogen deficient condition and upregulated in high-light condition. Glutamate is competitively used in all related pathways, which indicate that the glutamate level in the cells plays a regulatory role.

To understand the effect of temperature changes, Tetraselmis KCTC12432BP, a microalgae strain that show broad temperature tolerance range was cultivated under different temperature of 10°C, 20°C and 30°C. The functional enrichment analysis performed on the differentially expressed genes to different temperatures revealed that upregulated genes in low temperature were enriched in the plastid while the upregulated genes in high temperature were enriched in the mitochondria. In particular, the electron transport chain in the thylakoid and mitochondria showed distinct response which suggests an organelle level response to different temperature stresses. This data indicates that the low energy state of Tetraselmis under repressed photosynthesis by different temperature stress is compensated by the increased in photosynthetic electron transport chain (PETC) in low temperature, while the even more repressed photosynthesis in high temperature lead to energy salvation by using beta oxidation and mitochondrial oxidative phosphorylation to survive.

To further investigate the change in photosynthetic apparatus to low temperature, cyanobacteria model organism Synechocystis sp. PCC6803 was analyzed using RNA-seq and ribo-seq. Similar to the results from Tetraselmis, the genes composing the PETC were up-regulated, however, the reduced plastoquinone pool remained charged. Investigation of the genome-wide translation level by ribo-seq showed that several subunits of cytochrome b6f complex and ferredoxin complex were repressed at the translation level. Further investigation shows that low temperature globally inhibits translation deficiency. Along with increased ribosome occupancy near the 5’UTR and approximately 50 nt downstream of the start codon the translation initiation factor S1, elongation factor Ts, elongation factor P and RNA helicase crhR were down-regulated either in both transcription and translational level or in translational level.

As a model organism of cyanobacteria, Synechocystis sp. PCC6803’s transcription architecture have been vastly studied for small RNA, anti-sense RNA and transcription start sites. However, the 3’ UTR and terminators of Synechocystis have not been identified. To this end, the 3’ UTR and terminators of Synechocystis were investigated by term-seq which may elucidate translation regulatory mechanisms. A total of 1,017 termination sites were identified, where 755, 104, 68, 79 and 11 were localized at gene 3’ ends, intragenic region, anti-sense direction, 5’UTR and intergenic regions, respectively. Secondary structure prediction and motif searching abled the prediction of the terminator strength of primary terminators. In particular, terminators with C-rich motif found at the intragenic region showed an enrichment of proline-rich amino acids which suggests that the ribosome pausing leads to intragenic transcription termination. Furthermore, due to the proline’s role trans-membrane alpha helix, genes intragenic termination occurrence were strongly enriched in photosynthetic membrane proteins.