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RNA-seq gene expression data for Synechococcus sp. WH8102 under continuous high, mid, and low phosphorus treatments in laboratory EFB experiments in 2025

ABSTRACT: Polyphosphate (polyP) is a ubiquitous and evolutionarily conserved form of phosphorus (P) present in all living organisms, yet its role in cellular and biogeochemical P cycling remains poorly constrained. In P-depleted marine environments, polyP consistently represents a larger fraction of total particulate P (TPP) than in P-replete environments. This P deficiency response is paradoxical under the classical view of polyP as a luxury storage compound, highlighting a longstanding unresolved discrepancy. Whether the elevated polyP:TPP ratio reflects active accumulation under P stress or simply the persistence of this intracellular pool has never been directly tested under steady-state conditions. Using continuous cultures of the globally important marine cyanobacterium Synechococcus sp. WH8102, we address this knowledge gap. While P availability strongly affected growth rates, single-cell C:N:P stoichiometry and the expression of P-stress genes, polyP:TPP increased with decreasing growth rate, reproducing the pattern observed in oligotrophic marine environments. This shift was not driven by polyP accumulation; instead, cellular polyP concentrations remained relatively stable across growth rates (ANOVA, p = 0.16), while other intracellular P pools—including RNA, free Pi, ATP and phospholipids—were preferentially depleted with decreasing P availability (ranging from 2.6- to 11.8-fold, respectively), increasing the relative contribution of polyP to total cellular P. Gene expression analysis revealed little transcription differences between polyP-metabolism associated genes. These results indicate that cellular polyP content is maintained independently of growth rate under steady-state conditions, suggesting that P deficiency responses observed in oligotrophic environments and various microorganisms in batch culture reflect slow-growing physiology (differential pool lability over selective polyP retention), with consequences for interpreting particulate P stoichiometry and export.

ORGANISM(S): Parasynechococcus marenigrum WH 8102

PROVIDER: GSE327000 | GEO | 2026/05/05

REPOSITORIES: GEO

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Project description:The genome of the marine Synechococcus sp. WH8102 displays a minimal regulatory network yet physiological and molecular responses of this organism are tuned to episodic limitation for nitrogen and phosphorus. Microarray analyses have demonstrated a key role for the two-component regulatory system, PhoBR, in the regulation of P transport and metabolism in this strain. However, there is some evidence that another regulator, SYNW1019 (designated as ptrA), probably under the control of PhoB, is involved in the wider response to P-depletion. PtrA is one of only two genome encoded DNA binding proteins of the CRP family in Synechococcus sp. WH8102, and a potential transcriptional regulator with homology to NtcA, the global nitrogen regulator in cyanobacteria. To define the precise role of this regulator we constructed a mutant by insertional inactivation and compared the physiology of wild-type Synechcococcus sp. WH8102 with the ptrA mutant under P-replete and P-deplete growth conditions. During P-depletion the ptrA mutant failed to up-regulate phosphatase activity. Microarrays and quantitative RT-PCR indicate that a subset of the Pho regulon is directly controlled by PtrA, including two phosphatase genes (SYNW0196, SYNW2390), a predicted phytase (SYNW0762) and a gene of unknown function (SYNW0165) all of which are highly up regulated during P-limitation. This result was confirmed by electrophoretic mobility shift assays which demonstrated binding of over expressed PtrA to promoter sequences upstream of the induced phosphatases (SYNW0165, SYNW0196 and SYNW2390). This work suggests a two-tiered response to P-depletion in this strain, the first being PhoB-dependent induction of high affinity PO4 transporters, and the second the PtrA-dependent induction of phosphatases for scavenging organic P. The levels of numerous other transcripts are also directly or indirectly controlled by PtrA, including those involved in cell surface modification, metal uptake, photosynthesis, stress responses and other metabolic process, which may indicate a wider role for PtrA in cellular organisation. In an environmental context ptrA is found in a number of picocyanobateria isolated from a range of oceanic provinces, including strains that lack a functional phoBR..These results give broader insight into the regulation of physiological responses that may dictate niche adaptation in genetically diverse lineages of marine Synechococcus, and suggest that signalling networks and coordinated responses to nutrient availability are important, even in oligotrophic ocean environments. In this series gene expression of a ptrA mutant has been analyzed under phosphorus deplete conditions just after the onset of induction of phosphatase activity in wild type. There are six duel-channel slides upon which both ptrA mutant and wild type samples were hybridized. There are three technical replicates for each of two biological replicates including one flip-dye comparison. Each slide contains six replicate spots per gene.

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RNA-seq gene expression data for Synechococcus sp. WH8102 under continuous high, mid, and low phosphorus treatments in laboratory EFB experiments in 2025

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