Diurnal Regulation of Cellular Processes in the Cyanobacterium Synechocystis sp. Strain PCC 6803: Insights from Transcriptomic, Fluxomic, and Physiological Analyses

Abstract

Synechocystis sp. strain PCC 6803 is the most widely studied model cyanobacterium, with a well-developed omics level knowledgebase. Like the lifestyles of other cyanobacteria, that of Synechocystis PCC 6803 is tuned to diurnal changes in light intensity. In this study, we analyzed the expression patterns of all of the genes of this cyanobacterium over two consecutive diurnal periods. Using stringent criteria, we determined that the transcript levels of nearly 40% of the genes in Synechocystis PCC 6803 show robust diurnal oscillating behavior, with a majority of the transcripts being upregulated during the early light period. Such transcripts corresponded to a wide array of cellular processes, such as light harvesting, photosynthetic light and dark reactions, and central carbon metabolism. In contrast, transcripts of membrane transporters for transition metals involved in the photosynthetic electron transport chain (e.g., iron, manganese, and copper) were significantly upregulated during the late dark period. Thus, the pattern of global gene expression led to the development of two distinct transcriptional networks of coregulated oscillatory genes. These networks help describe how Synechocystis PCC 6803 regulates its metabolism toward the end of the dark period in anticipation of efficient photosynthesis during the early light period. Furthermore, in silico flux prediction of important cellular processes and experimental measurements of cellular ATP, NADP(H), and glycogen levels showed how this diurnal behavior influences its metabolic characteristics. In particular, NADPH/NADP+ showed a strong correlation with the majority of the genes whose expression peaks in the light. We conclude that this ratio is a key endogenous determinant of the diurnal behavior of this cyanobacterium.

Cellular trade-offs and optimal resource allocation during cyanobacterial diurnal growth

“…measurements over a full diurnal cycle have been conducted yet, several studies have investigated the transcriptome, proteome, and physiology of S. elongatus PCC 7942 and other cyanobacteria over a full 24-h diurnal cycle (9,31,33,34). Published transcriptome studies of cyanobacteria typically show global rhythms in gene expression, including a significant reduction of the transcriptional output during the dark period (33,35,36).…”

“…The observed temporal order is consistent across different cyanobacterial strains: For the cyanobacterium Synechocystis sp. PCC 6803, Saha et al (34) report an upregulation of PSI and PSII transcripts, genes for amino acid metabolism, and genes from the Calvin-Benson cycle at the beginning of the light period, whereas essential genes for glycogen catabolism showed upregulation in the dark period. Behrenfeld et al (39) report that metabolism is dominated by amino acid synthesis between sunrise and noon in a synchronized culture of Prochlorococcus (strain PCC 9511).…”

“…The constant rate of glycogen accumulation through the light period is in excellent agreement with recent data from S. elongatus PCC 7942 (9) and Synechocystis sp. PCC 6803 (34). To verify the robustness of our approach, and because most experimental studies use a square-wave light intensity rather than a sinusoidal function, we also investigate glycogen accumulation using a square-wave light function, resulting in a similar functional form (SI Appendix, Fig.…”

Physical, chemical, and metabolic state sensors expand the synthetic biology toolbox for Synechocystis sp. PCC 6803

“…When utilizing photosynthetic organisms in biotechnology, light is an important physical signal. Synechocystis carries out the majority of its metabolic processes in the light (Saha et al, 2016); therefore, limitations of cellular resources (Cardinale and Arkin, 2012) could be especially acute if the heterologous pathway is expressed during the day. A dark-inducible sensor could also be beneficial for expressing enzymes inactivated by photosynthetic oxygen, including nitrogenase (Stockel et al, 2008) and hydrogenase (Melis et al, 2000).…”

Distinct light-, stress-, and nutrient-dependent regulation of multiple tryptophan-rich sensory protein (TSPO) genes in the cyanobacterium Fremyella diplosiphon

“…PCC 6803, a singlecelled non-chromatically acclimating cyanobacterium, reported oscillation of the expression of the Synechocystis TSPO homolog with peak expression from very early (i.e., from 1 to 3 h) to near the middle (i.e., at 5 h) of the light phase under a 12 h diurnal cycle. 8 We, thus, grew F. diplosiphon cells in diurnal cycles (12 h of white light [WL] at »10 mmol m ¡2 s ¡1 and 12 h of dark) and tested TSPO transcript accumulation. As an initial survey of the potentially distinct regulation of these genes under diurnal conditions, we determined TSPO mRNA levels 12 h into the light period (L12), 12 h into the dark period (D12) and 3 h into the light period (L3) (for schematic see Fig.…”