Acclimation of the Global Transcriptome of the Cyanobacterium Synechococcus sp. Strain PCC 7002 to Nutrient Limitations and Different Nitrogen Sources

Abstract

The unicellular, euryhaline cyanobacterium Synechococcus sp. strain PCC 7002 is a model organism for laboratory-based studies of cyanobacterial metabolism and is a potential platform for biotechnological applications. Two of its most notable properties are its exceptional tolerance of high-light intensity and very rapid growth under optimal conditions. In this study, transcription profiling by RNAseq has been used to perform an integrated study of global changes in transcript levels in cells subjected to limitation for the major nutrients CO2, nitrogen, sulfate, phosphate, and iron. Transcriptional patterns for cells grown on nitrate, ammonia, and urea were also studied. Nutrient limitation caused strong decreases of transcript levels of the genes encoding major metabolic pathways, especially for components of the photosynthetic apparatus, CO2 fixation, and protein biosynthesis. Uptake mechanisms for the respective nutrients were strongly up-regulated. The transcription data further suggest that major changes in the composition of the NADH dehydrogenase complex occur upon nutrient limitation. Transcripts for flavoproteins increased strongly when CO2 was limiting. Genes involved in protection from oxidative stress generally showed high, constitutive transcript levels, which possibly explains the high-light tolerance of this organism. The transcriptomes of cells grown with ammonia or urea as nitrogen source showed increased transcript levels for components of the CO2 fixation machinery compared to cells grown with nitrate, but in general transcription differences in cells grown on different N-sources exhibited surprisingly minor differences.

Inference of interactions in cyanobacterial–heterotrophic co-cultures via transcriptome sequencing

“…However, the causative effect of co-cultivation on Fe homeostasis in cyanobacteria is yet to be determined. Although increased Fe availability can be a result of lower demand-for instance, owing to declining photosynthetic activity (Ludwig and Bryant, 2012), the mRNA abundance of Synechococcus 7002 genes involved in photosynthetic metabolism was high across all experimental conditions. A more compelling explanation may be linked to the documented capacity of aerobic heterotrophic microorganisms to produce large quantities of extracellular Fe chelators (Wandersman and Delepelaire, 2004), which can be recognized and transported intracellularly by the cyanobacterium.…”

“…When compared with lactate-grown co-cultures (Supplementary Table S7), Synechococcus 7002 transcription profiles displayed downregulation of photorespiration and carbohydrate metabolism genes during co-culturing with HCO 3 À . These patterns as well as elevated transcript levels of Fe acquisition genes (Table 5) are more likely to be linked to the increased production of light-capturing and photosynthetic machinery (Ludwig and Bryant, 2012;Morrissey and Bowler, 2012) and higher CO 2 availability (Table 1). Similarly, lower mRNA levels of putative nitrile/cyanate, dipeptide and amino acids transporter genes suggested decreased need for additional (organic) carbon sources during photoautotrophic growth of Synechococcus 7002.…”

NtcA is responsible for accumulation of the small isoform of ferredoxin:NADP oxidoreductase

“…Whilst FNR S accumulates under nitrogen starvation, it was not detected under standard conditions. In a recent transcriptome work, the long petH transcript, in addition to the short transcript, was detected under standard conditions (Ludwig & Bryant, 2012;M. Ludwig & D. A. Bryant, personal communication).…”

“…PCC7002 showed that petH transcription proceeds from a proximal transcription start point, located 87 bases upstream from the ORF, under standard conditions, and from a distal transcription start point, located 283 bases upstream from the ORF, operating under nitrogen starvation (Ludwig & Bryant, 2012). We performed Western blots on total extracts from Synechococcus sp.…”

Proteomic analysis of post translational modifications in cyanobacteria

“…strain PCC 7002 (hereafter Synechococcus 7002) [25]. Synechococcus 7002 is a model organism for studying photosynthetic carbon fixation and the development of biofuels [68,69], it can tolerate extremely high-light intensities and high salinity [70]. By using biochemical enrichment of phosphopeptides in combination with MS, we identified 280 unique phosphopeptides from 245 proteins with the determination of 410 Ser/Thr/Tyr phosphorylation sites in Synechococcus 7002 cells grown to early/mid-exponential phase under standard conditions (38°C, 1% (v/v) CO 2 in air, 250 μmol photons m −2 s −1 ).…”