Metabolic and Transcriptional Profiles of Dunaliella viridis Supplemented With Ammonium Derived From Glutamine

Dums, Jacob T.; Murphree, Colin A.; Vasani, Naresh; Young, Danielle Yvonne; Sederoff, Heike

doi:10.3389/fmars.2018.00311

Cited by 6 publications

(5 citation statements)

References 61 publications

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“…Based on expression profiles, the ammonium transporter was up-regulated while the nitrate transporters and nitrate reduction genes were downregulated. A recent transcriptome from Dunaliella viridis shows the same expression pattern when cells are grown with NH 4 + as a nitrogen source (Dums et al, 2018), which might suggests a difference in nitrogen source between the different datasets used. However, the study done with salt tolerance in tomato shows ammonium transporter up-regulation and nitrate transporter down-regulation under salt stress (Abouelsaad et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

Integration of Cross Species RNA-seq Meta-Analysis and Machine-Learning Models Identifies the Most Important Salt Stress–Responsive Pathways in Microalga Dunaliella

et al. 2019

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Photosynthetic microalgae are potentially yielding sources of different high-value secondary metabolites. Salinity is a complex stress that influences various metaboliterelated pathways in microalgae. To obtain a clear view of the underlying metabolic pathways and resolve contradictory information concerning the transcriptional regulation of Dunaliella species in salt stress conditions, RNA-seq meta-analysis along with systems levels analysis was conducted. A p-value combination technique with Fisher method was used for cross species meta-analysis on the transcriptomes of two Dunaliella salina and Dunaliella tertiolecta species. The potential functional impacts of core meta-genes were surveyed based on gene ontology and network analysis. In the current study, the integration of supervised machine-learning algorithms with RNA-seq meta-analysis was performed. The analysis shows that the lipid and nitrogen metabolism, structural proteins of photosynthesis apparatus, chaperone-mediated autophagy, and ROS-related genes are the keys and core elements of the Dunaliella salt stress response system. Cross-talk between Ca 2+ signal transduction, lipid accumulation, and ROS signaling network in salt stress conditions are also proposed. Our novel approach opens new avenues for better understanding of microalgae stress response mechanisms and for selection of candidate gene targets for metabolite production in microalgae.

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Section: Discussionmentioning

confidence: 99%

Integration of Cross Species RNA-seq Meta-Analysis and Machine-Learning Models Identifies the Most Important Salt Stress–Responsive Pathways in Microalga Dunaliella

et al. 2019

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“…Interestingly, the magnitude of difference in the relative expression of NR in NO spiked subcultures decreased over time in cultures grown on nitrate alone (Experiment 1), indicating potential feedback inhibition from downstream products 33,34 . Glutamine, for example, has been shown to inhibit transcription of NR in Nicotiana plumbaginifolia 35 , while glutamine-derived ammonium downregulated NR in Dunaliella viridis 36 .…”

Section: Discussionmentioning

confidence: 99%

Effects of nitrate and ammonium on assimilation of nitric oxide by Heterosigma akashiwo

Healey

Flood

Bock

et al. 2023

Sci Rep

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The harmful alga Heterosigma akashiwo possesses a hybrid nitrate reductase (NR) enzyme, NR2-2/2HbN, which has the potential to convert NO to nitrate for assimilation into biomass. In previous research, NR transcription in H. akashiwo was induced by nitrate while NR activity was inhibited by ammonium. Here, the capacity of H. akashiwo to use NO in the presence of nitrate and/or ammonium was investigated to understand the regulation of NO assimilation. Continuous cultures of H. akashiwo were acclimated to growth on nitrate, ammonium, or a mixture of both. Aliquots from these cultures were spiked with 15N-labeled NO. The expression of genes involved in nitrogen assimilation was evaluated, as well as nitrate reductase activity and assimilation of 15N-labeled nitrogen into algal biomass. Results showed that NO induced expression and activity of NR, and upregulated expression of GOGAT regardless of the presence of other inorganic nitrogen sources, while GS expression decreased over time. Furthermore, 15NO uptake and assimilation was significantly higher in cultures acclimated for growth on ammonium compared to cultures acclimated for growth on nitrate alone. Assimilation of NO may provide H. akashiwo with a competitive advantage in N-poor environments or areas with elevated NO.

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“…The processed reads were subjected to de novo assembly using Trinity (v2.4.0) software 15 using default parameters. Protein orthology was determined using Blastx (cutoff value of 6) against C. reinhardtii and D. salina proteins ( https://phytozome.jgi.doe.gov/ ) as described by Dums et al 16 . The best hits were extracted with in-house python scripts (Supplementary File S1 ).…”

Section: Methodsmentioning

confidence: 99%

Weighted gene co-expression network analysis of the salt-responsive transcriptomes reveals novel hub genes in green halophytic microalgae Dunaliella salina

Panahi

Hejazi

2021

Sci Rep

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Despite responses to salinity stress in Dunaliella salina, a unicellular halotolerant green alga, being subject to extensive study, but the underlying molecular mechanism remains unknown. Here, Empirical Bayes method was applied to identify the common differentially expressed genes (DEGs) between hypersaline and normal conditions. Then, using weighted gene co-expression network analysis (WGCNA), which takes advantage of a graph theoretical approach, highly correlated genes were clustered as a module. Subsequently, connectivity patterns of the identified modules in two conditions were surveyed to define preserved and non-preserved modules by combining the Zsummary and medianRank measures. Finally, common and specific hub genes in non-preserved modules were determined using Eigengene-based module connectivity or module membership (kME) measures and validation was performed by using leave-one-out cross-validation (LOOCV). In this study, the power of beta = 12 (scale-free R2 = 0.8) was selected as the soft-thresholding to ensure a scale-free network, which led to the identification of 15 co-expression modules. Results also indicate that green, blue, brown, and yellow modules are non-preserved in salinity stress conditions. Examples of enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in non-preserved modules are Sulfur metabolism, Oxidative phosphorylation, Porphyrin and chlorophyll metabolism, Vitamin B6 metabolism. Moreover, the systems biology approach was applied here, proposed some salinity specific hub genes, such as radical-induced cell death1 protein (RCD1), mitogen-activated protein kinase kinase kinase 13 (MAP3K13), long-chain acyl-CoA synthetase (ACSL), acetyl-CoA carboxylase, biotin carboxylase subunit (AccC), and fructose-bisphosphate aldolase (ALDO), for the development of metabolites accumulating strains in D. salina.

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Metabolic and Transcriptional Profiles of Dunaliella viridis Supplemented With Ammonium Derived From Glutamine

Cited by 6 publications

References 61 publications

Integration of Cross Species RNA-seq Meta-Analysis and Machine-Learning Models Identifies the Most Important Salt Stress–Responsive Pathways in Microalga Dunaliella

Integration of Cross Species RNA-seq Meta-Analysis and Machine-Learning Models Identifies the Most Important Salt Stress–Responsive Pathways in Microalga Dunaliella

Effects of nitrate and ammonium on assimilation of nitric oxide by Heterosigma akashiwo

Weighted gene co-expression network analysis of the salt-responsive transcriptomes reveals novel hub genes in green halophytic microalgae Dunaliella salina

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