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 CO(2), 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, CO(2) 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 CO(2) 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 CO(2) fixation machinery compared to cells grown with nitrate, but in general transcription differences in cells grown on different N-sources exhibited surprisingly minor differences.

Keywords: RNAseq; cyanobacteria; nitrogen source; nutrient limitation; photosynthesis; transcription profiling.

Figure 1

Changes in the relative transcript abundance upon nutrient limitation. The scatter plots show the relative transcript abundances (A) when grown with low CO₂ supply and after (B) nitrogen, (C) sulfur, (D) phosphate, and (E) iron deprivation compared to that for “standard” growth conditions (mean of three biological replicates). The gray lines give 2-fold changes in either direction. Selected genes are identified by name/locus tag number.

Figure 2

Overview over the regulation pattern in response to nutrient limitations for a selection of cellular components. The figure summarizes the general regulation pattern in response to limitation of CO₂, nitrogen, sulfur, phosphorus, and iron. The changes of the relative mRNA levels under the respective nutrient limitation are compared to “standard” growth conditions. These ratios are displayed for genes coding for a selection of cellular functions, among these the photosystems (PSI, PSII; for PSII the three psbA genes were disregarded since they replace each other in response to different conditions), phycobilisomes, the phycobilisome degradation protein NblA, components of the photosynthetic electron transport chain, the carboxysome, the Calvin–Benson–Bassham cycle, the NADH dehydrogenase complex, the F₀F₁ type ATP synthase, the terminal oxidases, and the ribosome. Further, the genes coding for uptake systems for ammonia, nitrate, sulfate, phosphate (pstABCS), and iron (all genes listed in Table S3 in Supplementary Material except those for regulation, siderophore biosynthesis, and Fe–S cluster assembly) are shown. The nitrate and nitrite reductases and the glutamine synthetases (glnA, glnN), the siderophore biosynthesis (SYNPCC7002_G0019-G0023), and Fe–S cluster assembly (sufBCDS) are highlighted. Finally, the changes in the transcript levels of two flavoproteins, the superoxide dismutase, and catalase are given.

Figure 3

Differences in the relative transcript abundance in cultures grown with different nitrogen sources. The scatter plots show the relative transcript abundances of a culture grown with (A) ammonia and (B) urea as nitrogen source compared to a culture grown with nitrogen. (C) Shows a comparison of the relative transcript levels in a culture grown with urea as nitrogen source compared to ammonia. The gray lines give 2-fold changes in either direction. Selected genes are identified by name/locus tag number.

Figure 4

Overview over the regulation pattern for a selection of cellular components when the culture was grown on different nitrogen sources. This figure gives an overview of the transcription pattern in response to growth with nitrate, ammonia, and urea as nitrogen source. The changes of the relative mRNA levels are comparisons of ammonia or urea-grown cultures to a nitrate-grown culture and of a urea-grown culture compared to a culture grown with ammonia as nitrogen source. These ratios are displayed for genes coding for a selection of cellular functions, see Figure 2.