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Transcriptomic profiling of an oceanic diatom adapted to Cu deficiency

ABSTRACT: Transcriptomic profiling of an oceanic diatom adapted to Cu deficiency

PROVIDER: PRJNA781117 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16963167_1.fastq.gz	Fastqsanger.gz
	SRR16963167_2.fastq.gz	Fastqsanger.gz
	SRR16963168_1.fastq.gz	Fastqsanger.gz
	SRR16963168_2.fastq.gz	Fastqsanger.gz
	SRR16963169_1.fastq.gz	Fastqsanger.gz

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Transcriptomic profiling of an oceanic diatom adapted to Cu deficiency

Project description:Enhanced vertical stratification brought about by warming of the ocean surface is expected to reduce vertical circulation and nutrient input with knock-on effects for phytoplankton. Increased nutrient limitation is one predicted outcome, but the response of phytoplankton is uncertain because long-term adaptation to nutrient limitation has not been studied. We used Cu as a model catalytic nutrient to explore the adaptive response of an oceanic diatom to continuous nutrient deprivation. Thalassiosira oceanica was maintained under Cu-limiting and sufficient conditions for more than 2000 generations and the evolved populations evaluated for physiological traits in a reciprocal transplant experiment. Adaptation to low Cu concentration increased Cu use efficiency, so that under Cu-limiting conditions T. oceanica maintained significantly faster rates of net C assimilation and growth than the control and ancestral populations.

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Transcriptomic profiling of Cu-regulated genes in an oceanic diatom

Project description:Copper (Cu) plays an essential role in cellular metabolism and limits phytoplankton growth and production in parts of the open sea. Whole transcriptome analysis provides a powerful tool to explore gene expression profiles and cellular metabolic pathways regulated by Cu. In this study, we identified Cu-regulated genes by profiling the transcriptomes of an oceanic diatom, Thalassiosira oceanica 1005, adapted to survive in a Cu-limited and Cu-replete environment. The results provide insights to the mechanisms of adaptation and acclimation of T. oceanica to low Cu environments.

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Project description:Transcriptomic profiling of Cu-regulated genes in an oceanic diatom

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2018-08-21 | PXD009698 | Pride

Transcriptomic characterization of spl7 and Col-0 ecotypes of Arabidopsis reveals new aspects of Fe-Cu crosstalk

Project description:Iron (Fe) and copper (Cu) are essential metal micronutrients that are necessary for many redox reactions. The uptake of these metals is tightly regulated in plants. Some redox processes can alternatively use Fe-containing proteins or Cu-containing proteins, depending on nutritional status. Copper deficiency can rescue a Cucumis melo Fe uptake deficient mutant, and Fe deficiency can result in increased accumulation of Cu. However, the system responsible for Fe-deficiency-regulated Cu-uptake is unknown. To understand the genes and gene networks associated with Fe-deficiency regulated Cu uptake and Fe-Cu cross-talk, we conducted transcriptomic profiling of roots and rosettes of spl7 (a Cu uptake deficient mutant in arabidopsis) and Col-0 (WT) grown under Fe, Cu and simultaneous Fe and Cu deficiency conditions.

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Diatom acclimation to elevated CO2 via novel gene clusters and cAMP-signaling

Project description:Diatoms are responsible for ~40% of marine primary productivity1, fueling the oceanic carbon cycle and contributing to natural carbon sequestration in the deep ocean2. Diatoms rely on energetically expensive carbon concentrating mechanisms (CCMs) to fix carbon efficiently at modern levels of CO23–5. How diatoms may respond over the short and long-term to rising atmospheric CO2 remains an open question. Here we use nitrate-limited chemostats to show that the model diatom Thalassiosira pseudonana rapidly responds to increasing CO2 by differentially expressing gene clusters that regulate transcription and chromosome folding and subsequently reduces transcription of photosynthesis and respiration gene clusters under steady-state elevated CO2. These results suggest that exposure to elevated CO2 first causes a shift in regulation and then a metabolic rearrangement. Genes in one CO2-responsive cluster included CCM and photorespiration genes that share a putative cyclic-AMP responsive cis-regulatory sequence, implying these genes are co-regulated in response to CO2 with cAMP as an intermediate messenger. We verified cAMP-induced down-regulation of CCM gene δ-CA3 in nutrient-replete diatom cultures by inhibiting the hydrolysis of cAMP. These results indicate an important role for cAMP in down-regulating CCM and photorespiration genes under elevated CO2 and provide insights into mechanisms of diatom acclimation in response to climate change.

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Project description:The physiological adaptations of diatoms to cope with Cu limitation are largely unknown. In the present study we investigated the response to Cu limitation in two strains of the model open ocean diatom T. oceanica (CCMP 1003 and CCMP 1005), focusing on physiological and proteomic changes in the photosynthetic apparatus. Our results show remarkable differences between the adaptations of TO05 and TO03 to low Cu, highlighting significant intra specific variations.

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Project description:The transition metal Cu is an essential micronutrient in biological systems. The majority of Cu is taken up into the cell through the Cu transporter CTR1 and thus, deletion of Ctr1 results in Cu deficiency. Here we performed transcriptional profiling of isogenic mouse embryonic fibroblast harboring conditional alleles for Ctr1 floxed out or intact through in vitro administration of doxycycline. The goal was to elucidate gene expression changes upon knockout of Ctr1.

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Genome and low-iron response of an oceanic diatom adapted to chronic iron limitation.

Project description:BACKGROUND:Biogeochemical elemental cycling is driven by primary production of biomass via phototrophic phytoplankton growth, with 40% of marine productivity being assigned to diatoms. Phytoplankton growth is widely limited by the availability of iron, an essential component of the photosynthetic apparatus. The oceanic diatom Thalassiosira oceanica shows a remarkable tolerance to low-iron conditions and was chosen as a model for deciphering the cellular response upon shortage of this essential micronutrient. RESULTS:The combined efforts in genomics, transcriptomics and proteomics reveal an unexpected metabolic flexibility in response to iron availability for T. oceanica CCMP1005. The complex response comprises cellular retrenchment as well as remodeling of bioenergetic pathways, where the abundance of iron-rich photosynthetic proteins is lowered, whereas iron-rich mitochondrial proteins are preserved. As a consequence of iron deprivation, the photosynthetic machinery undergoes a remodeling to adjust the light energy utilization with the overall decrease in photosynthetic electron transfer complexes. CONCLUSIONS:Beneficial adaptations to low-iron environments include strategies to lower the cellular iron requirements and to enhance iron uptake. A novel contribution enhancing iron economy of phototrophic growth is observed with the iron-regulated substitution of three metal-containing fructose-bisphosphate aldolases involved in metabolic conversion of carbohydrates for enzymes that do not contain metals. Further, our data identify candidate components of a high-affinity iron-uptake system, with several of the involved genes and domains originating from duplication events. A high genomic plasticity, as seen from the fraction of genes acquired through horizontal gene transfer, provides the platform for these complex adaptations to a low-iron world.

| S-EPMC3491386 | biostudies-literature

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