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Phosphorus deficiency alleviates cyanobacterial iron-limitation through a direct PhoB_x0002_ mediated gene regulation

ABSTRACT: Phosphorus deficiency alleviates cyanobacterial iron-limitation through a direct PhoB_x0002_ mediated gene regulation

PROVIDER: PRJNA1083543 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28219460_1.fastq.gz	Fastqsanger.gz
	SRR28219460_2.fastq.gz	Fastqsanger.gz
	SRR28219461_1.fastq.gz	Fastqsanger.gz
	SRR28219461_2.fastq.gz	Fastqsanger.gz
	SRR28219462_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Phosphorus deficiency alleviates cyanobacterial iron-limitation through a direct PhoB_x0002_ mediated gene regulation

Project description:Iron (Fe) and phosphorus (P) are essential nutrients with close geochemical association. They exist at low concentrations in surface waters and may be co-limiting resources for phytoplankton growth. However, the adaptive strategies of photosynthetic organisms to Fe/P co-limitation remain largely unknown. Here, we show that phosphorus deficiency increases the growth of Fe-limited cyanobacteria through a PhoB-mediated regulatory network. In addition to its well-recognized role in controlling phosphate homeostasis, PhoB regulates key metabolic processes crucial for Fe-limited cyanobacteria, including ROS detoxification and Fe uptake. Transcript abundances of PhoB-targeted genes are enriched in samples from the P-deplete ocean, and a conserved PhoB binding site is widely present in the promoters of the targets, suggesting that the strategy we discovered may be highly conserved. Our findings provide important molecular insights into the response of cyanobacteria to simultaneous Fe/P nutrient limitation and help in understanding how nutrient availability affects primary productivity in aquatic environments.

2024-03-06 | GSE260812 | GEO

Uncovering the mechanisms of phosphorus recycling and lipid class remodeling under P limitation by integration of transcriptomics and lipidomics data of Nannochloropsis oceanica.

Project description:In the present study the effect of phosphorus (P) limitation was investigated in the microalgae Nannochloropsis oceanica. Algal cultures were analysed for transcriptomic and lipidomic changes during P-limited growth, with sample time points: 24h, 48h, 53h, 58h and 70h. The transcriptome data identified unique P acquiring genes and the results were also supported by corresponding changes in the lipidome dataset, which showed a lipid class shift from phospholipids to phosphorus-free lipids under P-limitation. During the exponential growth phase a gradual 6-fold reduction of the cellular P level induced RNA transcripts encoding proteins acquiring P from inorganic and organic sources. For this process 6 novel purple acid phosphatases and 5 unique Pi transporters were identified. Additionally, increased gene expression of 2 triose-phosphate transporters (TPTs) indicated the importance of the carbon-to-phosphorus balance for the plastidial anabolic processes. Phospholipid degradation was shown to be an early response to P limitation, by overexpression of sets of 2 novel glycerophosphoryl diester phosphodiesterases (GDPDs), and 3 patatin-like phospholipases of type A. To compensate for phospholipid degradation, the transcriptome and lipidome level showed increased synthesis of sulfoquinovosyl diacylglycerol (SQDG), and diacylglyceroltrimethylhomoserine (DGTS). Phosphorus limitation triggered the lipid class shift in both the exponential growth phase and the triacylglycerol (TAG) accumulation period to release P and increase the organic C:P ratio.

2017-10-31 | GSE95774 | GEO

Epigenomic variation under iron and phosphorus co-limitation in the globally important Trichodesmium

Project description:We present population-level epigenetic variation in Trichodesmium erythraeum IMS101 associated with steady-state Fe-limitation at two different P concentrations on both short (i.e. 2 months) and long timescales (i.e. ~1 year).

2019-12-15 | GSE101083 | GEO

Transcriptional, metabolic, physiological and developmental responses of switchgrass to phosphorus limitation

Project description:Knowing how switchgrass (Panicum virgatum L.) responds and adapts to phosphorus (P)-limitation will aid efforts to optimize P acquisition and use in this species for sustainable biomass production. This integrative study investigated the impacts of mild, moderate, and severe P-stress on genome transcription and whole-plant metabolism, physiology and development in switchgrass. P-limitation reduced overall plant growth, increased root/shoot ratio, increased root branching at moderate P-stress, and decreased root diameter with increased density and length of root hairs at severe P-stress. RNA-seq analysis revealed thousands of genes that were differentially expressed under moderate and severe P-stress in roots and/or shoots compared to P-replete plants, with many stress-induced genes involved in transcriptional and other forms of regulation, primary and secondary metabolism, transport, and other processes involved in P-acquisition and homeostasis. Amongst the latter were multiple miRNA399 genes and putative targets of these. Metabolite profiling showed that levels of most sugars and sugar alcohols decreased with increasing P stress, while organic and amino acids increased under mild and moderate P-stress in shoots and roots, although this trend reversed under severe P-stress, especially in shoots.

2023-07-13 | GSE237285 | GEO

Transcriptional, metabolic, physiological and developmental responses of switchgrass to phosphorus limitation

Project description:Transcriptional, metabolic, physiological and developmental responses of switchgrass to phosphorus limitation

| PRJNA994525 | ENA

RNA-protein dynamics of high CO2-adapted, iron-phosphorus co-limited Trichodesmium reveals nutrient-limited molecular architecture of a globally significant marine nitrogen fixer in a future ocean

Project description:Our paper presents the results of a study in which we used Illumina RNA-Seq (i.e. transcriptomics) and high-CO2 nutrient limitation experiments to examine transcriptional variation of iron-limited, phosphorus-limited, and iron-phosphorus co-limited cultures following long-term (~7 years) low- (380 µatm CO2) and high-CO2 (750 µatm CO2) selection. Hence, we describe the molecular physiology of the globally-significant, biogeochemically-critical marine cyanobacterium Trichodesmium.

2017-10-23 | GSE94951 | GEO

Phosphorus-Ca2+ signalling in marine diatoms

Project description:Phosphorus is a critical nutrient controlling phytoplankton growth. Availability of this limiting factor can vary significantly in space and time, particularly in dynamic aquatic ecosystems. Diatoms are important eukaryotic phytoplankton that thrive in regions of pulsed phosphate supply, yet little is known of the sensory mechanisms enabling them to detect and rapidly respond to phosphorus availability. Here we show that phosphorus-starved diatoms utilise a novel Ca2+-dependent signalling pathway to sense and regulate cellular recovery following phosphorus resupply. This pathway, which has not previously been described in eukaryotes, is sensitive to sub-micromolar concentrations of phosphate, alongside a range of environmentally relevant phosphorus forms. Using comparative proteomics, we have characterised early adaptations governing diatom cellular recovery from phosphorus limitation. Strikingly, the dominant response was substantial enhancement of nitrogen assimilation proteins. This led to 12-fold increases in absolute nitrate uptake rates, relative to phosphorus-starved cells. Moreover, we find that the novel phosphorus-Ca2+ signalling pathway controls this primary recovery response. Our findings highlight that fundamental cross-talk between the essential nutrients phosphorus and nitrogen drive diatom recovery from phosphorus limitation. Moreover, a novel Ca2+-dependent phosphorus signalling pathway governs such ecological acclimation responses, and is thus likely critical to the success of diatoms in regions of episodic nutrient supply.

2021-02-22 | PXD022586 | Pride

Clostridium difficile response to iron limitation

Project description:Clostridium difficile response to iron limitation

| PRJNA430909 | ENA

Transcription profiling by array of yeast strain FY1679 homozygous for HO deletion by KanMX4 grown in a series of nutrient limited continuous cultures carbon, nitrogen, phosphorus and sulfur limitation to determine genes which are growth rate regulated and those which are nutrient specific regulated

Project description:S. cerevisiae strain FY1679 homozygous for HO deletion by KanMX4 was grown in a series of nutrient limited continuous cultures carbon, nitrogen, phosphorus and sulfur limitation to determine genes which are growth rate regulated and those which are nutrient specific regulated.

2007-05-02 | E-MEXP-115 | biostudies-arrayexpress

Trichodesmium LC-MSMS iron and phosphorous co-limitation in the ocean

Project description:Nitrogen fixation by cyanobacteria supplies critical bioavailable nitrogen to marine ecosystems worldwide; however, field and lab data have demonstrated it to be limited by iron, phosphorus and/or CO2. To address unknown future interactions among these factors, we grew the nitrogen-fixing cyanobacterium Trichodesmium for 1 year under Fe/P co-limitation following 7 years of both low and high CO2 selection. Fe/P co-limited cell lines demonstrated a complex cellular response including increased growth rates, broad proteome restructuring and cell size reductions relative to steady-state growth limited by either Fe or P alone. Fe/P co-limitation increased abundance of a protein containing a conserved domain previously implicated in cell size regulation, suggesting a similar role in Trichodesmium. Increased CO2 further induced nutrient-limited proteome shifts in widespread core metabolisms. Our results thus suggest that N2-fixing microbes may be significantly impacted by interactions between elevated CO2 and nutrient limitation, with broad implications for global biogeochemical cycles in the future ocean. Sample number sample description 1 380-1 2 380-2 3 380-3 4 750-1 5 750-2 6 750-3 7 380-1P 8 380-2P 9 380-3P 10 800-1P 11 800-2P 12 800-3P 13 380-1Fe 14 380-2Fe 15 380-3Fe 16 750-1Fe 17 750-2Fe 18 750-3Fe 19 380-1FeP 20 380-2FeP 21 380-3FeP 22 750-1FeP 23 750-2FeP 24 750-3FeP

2018-08-09 | PXD010515 | Pride

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