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Understanding strategy of nitrate and urea assimilation in a Chinese strain of Aureococcus anophagefferens through RNA-seq analysis.

Dong HP, Huang KX, Wang HL, Lu SH, Cen JY, Dong YL - PLoS ONE (2014)

Bottom Line: Moreover, transcripts for synthesis of proteins, glutamate-derived amino acids, spermines and sterols were upregulated by urea.Transcripts encoding key enzymes that are involved in the ornithine-urea and TCA cycles were differentially regulated by urea and nitrogen concentration, which suggests that the OUC may be linked to the TCA cycle and involved in reallocation of intracellular carbon and nitrogen.These genes regulated by urea may be crucial for the rapid proliferation of A. anophagefferens when urea is provided as the N source.

View Article: PubMed Central - PubMed

Affiliation: Research Center for Harmful Algae and Marine Biology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China.

ABSTRACT
Aureococcus anophagefferens is a harmful alga that dominates plankton communities during brown tides in North America, Africa, and Asia. Here, RNA-seq technology was used to profile the transcriptome of a Chinese strain of A. anophagefferens that was grown on urea, nitrate, and a mixture of urea and nitrate, and that was under N-replete, limited and recovery conditions to understand the molecular mechanisms that underlie nitrate and urea utilization. The number of differentially expressed genes between urea-grown and mixture N-grown cells were much less than those between urea-grown and nitrate-grown cells. Compared with nitrate-grown cells, mixture N-grown cells contained much lower levels of transcripts encoding proteins that are involved in nitrate transport and assimilation. Together with profiles of nutrient changes in media, these results suggest that A. anophagefferens primarily feeds on urea instead of nitrate when urea and nitrate co-exist. Furthermore, we noted that transcripts upregulated by nitrate and N-limitation included those encoding proteins involved in amino acid and nucleotide transport, degradation of amides and cyanates, and nitrate assimilation pathway. The data suggest that A. anophagefferens possesses an ability to utilize a variety of dissolved organic nitrogen. Moreover, transcripts for synthesis of proteins, glutamate-derived amino acids, spermines and sterols were upregulated by urea. Transcripts encoding key enzymes that are involved in the ornithine-urea and TCA cycles were differentially regulated by urea and nitrogen concentration, which suggests that the OUC may be linked to the TCA cycle and involved in reallocation of intracellular carbon and nitrogen. These genes regulated by urea may be crucial for the rapid proliferation of A. anophagefferens when urea is provided as the N source.

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Photosystem II efficiency (Fv/Fm).A) A. anophagefferens cultures grown on urea, nitrate, and a mixture of urea and nitrate at the 6-, 9- and 10-day sampling points; B) A. anophagefferens cultures grown under nitrogen-replete (Nr), limited (Nli) and recovery conditions. Nir and Nur represent nitrate and urea addition, respectively. Nli was compared with Nr while Nir and Nur were compared with Nli. Significance values were expressed as follows: * P <0.05, ** P <0.001. Error bars represent standard deviation of the mean for the three biological replicates.
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pone-0111069-g002: Photosystem II efficiency (Fv/Fm).A) A. anophagefferens cultures grown on urea, nitrate, and a mixture of urea and nitrate at the 6-, 9- and 10-day sampling points; B) A. anophagefferens cultures grown under nitrogen-replete (Nr), limited (Nli) and recovery conditions. Nir and Nur represent nitrate and urea addition, respectively. Nli was compared with Nr while Nir and Nur were compared with Nli. Significance values were expressed as follows: * P <0.05, ** P <0.001. Error bars represent standard deviation of the mean for the three biological replicates.

Mentions: For A. anophagefferens cells that were grown on different N sources, the cell density increased quickly during the first 5 days (exponential phase growth) (Fig. 1A). Maximum growth rates (calculated for days 1 to 5) were observed in cultures grown on urea (0.30 d−1), followed by the mixture of urea and nitrate (0.26 d−1), and nitrate (0.21 d−1) (Fig. 1C). However, there were no significant differences between the maximum growth rates. For cultures with nitrate, the cell density continued to increase after day 5, whereas the cell density did not increase in cultures with urea and mixture N. From day 7 to day 10, the cell density remained at the same level, and the density in all cultures tended to be consistent. The Fv/Fm (Maximum photochemical efficiency of PSII) of cultures from days 6, 9 and 10 was determined, and no significant difference was observed among the three N sources (Fig. 2A). Interestingly, the light-saturated electron transport rate (ETRmax) and electron transport efficiency (ETE) tended to increase gradually from day 6 to day 10 in cultures with urea, whereas these values appeared to drop from day 6 to day 10 in cultures with nitrate and mixture N (Fig. 3). On day 10, ETRmax and ETE of cultures with urea were higher than those values of cultures with the other N sources. In addition, it is noted that the profile of urea concentration as a function of day in cultures with mixture N was extremely similar to that in cultures with urea, whereas no significant decrease was observed in NO3− concentration in cultures with mixture N (Fig. 4), which suggested that A. anophagefferens may primarily utilize N from urea instead of nitrate in the mixture N media.


Understanding strategy of nitrate and urea assimilation in a Chinese strain of Aureococcus anophagefferens through RNA-seq analysis.

Dong HP, Huang KX, Wang HL, Lu SH, Cen JY, Dong YL - PLoS ONE (2014)

Photosystem II efficiency (Fv/Fm).A) A. anophagefferens cultures grown on urea, nitrate, and a mixture of urea and nitrate at the 6-, 9- and 10-day sampling points; B) A. anophagefferens cultures grown under nitrogen-replete (Nr), limited (Nli) and recovery conditions. Nir and Nur represent nitrate and urea addition, respectively. Nli was compared with Nr while Nir and Nur were compared with Nli. Significance values were expressed as follows: * P <0.05, ** P <0.001. Error bars represent standard deviation of the mean for the three biological replicates.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4206512&req=5

pone-0111069-g002: Photosystem II efficiency (Fv/Fm).A) A. anophagefferens cultures grown on urea, nitrate, and a mixture of urea and nitrate at the 6-, 9- and 10-day sampling points; B) A. anophagefferens cultures grown under nitrogen-replete (Nr), limited (Nli) and recovery conditions. Nir and Nur represent nitrate and urea addition, respectively. Nli was compared with Nr while Nir and Nur were compared with Nli. Significance values were expressed as follows: * P <0.05, ** P <0.001. Error bars represent standard deviation of the mean for the three biological replicates.
Mentions: For A. anophagefferens cells that were grown on different N sources, the cell density increased quickly during the first 5 days (exponential phase growth) (Fig. 1A). Maximum growth rates (calculated for days 1 to 5) were observed in cultures grown on urea (0.30 d−1), followed by the mixture of urea and nitrate (0.26 d−1), and nitrate (0.21 d−1) (Fig. 1C). However, there were no significant differences between the maximum growth rates. For cultures with nitrate, the cell density continued to increase after day 5, whereas the cell density did not increase in cultures with urea and mixture N. From day 7 to day 10, the cell density remained at the same level, and the density in all cultures tended to be consistent. The Fv/Fm (Maximum photochemical efficiency of PSII) of cultures from days 6, 9 and 10 was determined, and no significant difference was observed among the three N sources (Fig. 2A). Interestingly, the light-saturated electron transport rate (ETRmax) and electron transport efficiency (ETE) tended to increase gradually from day 6 to day 10 in cultures with urea, whereas these values appeared to drop from day 6 to day 10 in cultures with nitrate and mixture N (Fig. 3). On day 10, ETRmax and ETE of cultures with urea were higher than those values of cultures with the other N sources. In addition, it is noted that the profile of urea concentration as a function of day in cultures with mixture N was extremely similar to that in cultures with urea, whereas no significant decrease was observed in NO3− concentration in cultures with mixture N (Fig. 4), which suggested that A. anophagefferens may primarily utilize N from urea instead of nitrate in the mixture N media.

Bottom Line: Moreover, transcripts for synthesis of proteins, glutamate-derived amino acids, spermines and sterols were upregulated by urea.Transcripts encoding key enzymes that are involved in the ornithine-urea and TCA cycles were differentially regulated by urea and nitrogen concentration, which suggests that the OUC may be linked to the TCA cycle and involved in reallocation of intracellular carbon and nitrogen.These genes regulated by urea may be crucial for the rapid proliferation of A. anophagefferens when urea is provided as the N source.

View Article: PubMed Central - PubMed

Affiliation: Research Center for Harmful Algae and Marine Biology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Jinan University, Guangzhou, China.

ABSTRACT
Aureococcus anophagefferens is a harmful alga that dominates plankton communities during brown tides in North America, Africa, and Asia. Here, RNA-seq technology was used to profile the transcriptome of a Chinese strain of A. anophagefferens that was grown on urea, nitrate, and a mixture of urea and nitrate, and that was under N-replete, limited and recovery conditions to understand the molecular mechanisms that underlie nitrate and urea utilization. The number of differentially expressed genes between urea-grown and mixture N-grown cells were much less than those between urea-grown and nitrate-grown cells. Compared with nitrate-grown cells, mixture N-grown cells contained much lower levels of transcripts encoding proteins that are involved in nitrate transport and assimilation. Together with profiles of nutrient changes in media, these results suggest that A. anophagefferens primarily feeds on urea instead of nitrate when urea and nitrate co-exist. Furthermore, we noted that transcripts upregulated by nitrate and N-limitation included those encoding proteins involved in amino acid and nucleotide transport, degradation of amides and cyanates, and nitrate assimilation pathway. The data suggest that A. anophagefferens possesses an ability to utilize a variety of dissolved organic nitrogen. Moreover, transcripts for synthesis of proteins, glutamate-derived amino acids, spermines and sterols were upregulated by urea. Transcripts encoding key enzymes that are involved in the ornithine-urea and TCA cycles were differentially regulated by urea and nitrogen concentration, which suggests that the OUC may be linked to the TCA cycle and involved in reallocation of intracellular carbon and nitrogen. These genes regulated by urea may be crucial for the rapid proliferation of A. anophagefferens when urea is provided as the N source.

Show MeSH
Related in: MedlinePlus