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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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Proposed model showing the urea cycle, nitrate transport and assimilation, and the glutamine-glutamate cycle.Enzymes that are involved in these pathways are labeled with colors that indicate the fold change (log2) in their transcript levels in urea-grown cells relative to nitrate-grown cells (color code is provided in the figure). NRT, nitrate transporter; NR nitrate reductase; NAR1, nitrite transporter; NasB, NADPH nitrite reductase; GS, glutamine synthetase; Fd-GOGAT, ferredoxin-dependent glutamate synthase; CPS, carbamoyl phosphate synthase; OTC, ornithine transcarboxylase; AsuS, argininosuccinate synthase; ASL, argininosuccinate lyase; ARG, arginase; Ure, urease; DUR, urea transporter.
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pone-0111069-g006: Proposed model showing the urea cycle, nitrate transport and assimilation, and the glutamine-glutamate cycle.Enzymes that are involved in these pathways are labeled with colors that indicate the fold change (log2) in their transcript levels in urea-grown cells relative to nitrate-grown cells (color code is provided in the figure). NRT, nitrate transporter; NR nitrate reductase; NAR1, nitrite transporter; NasB, NADPH nitrite reductase; GS, glutamine synthetase; Fd-GOGAT, ferredoxin-dependent glutamate synthase; CPS, carbamoyl phosphate synthase; OTC, ornithine transcarboxylase; AsuS, argininosuccinate synthase; ASL, argininosuccinate lyase; ARG, arginase; Ure, urease; DUR, urea transporter.

Mentions: Compared with cells that were grown on urea, 142 transcripts were upregulated 2-fold or greater in cells that were grown on nitrate, and 180 transcripts were downregulated 2-fold or greater in cells that were grown on nitrate (Table S4). Approximately 24% of differentially expressed genes could not be assigned a function because the reference genes represented hypothetical or predicted protein or showed no database homology. Transcripts encoding nitrate high affinity transporter, nitrite transporter NAR1, formate/nitrite transporter, and ammonium transporter increased when A. anophagefferens cells were grown on nitrate compared with urea. Transcripts encoding a putative nitrate reductase, NADPH nitrite reductase and glutamine synthetase increased in cells that were grown on nitrate compared with cells that were grown on urea (Fig. 6). Notably, 4 transcripts that were involved in OUC showed 2.0- to 2.6-fold upregulation in urea-grown cells relative to nitrate-grown cells (Table S4, Fig. 6). Thirty nine transcripts encoding proteins that were involved in protein synthesis showed 2.0- to 3.6-fold upregulation in urea-grown cells relative to nitrate-grown cells (Table S4). There were 11 transcripts encoding enzymes that were involved in amino acid synthesis that were upregulated in urea-grown cells relative to nitrate-grown cells. Levels of transcripts encoding proteins that were involved in photosynthesis and central carbon metabolism displayed difference in cells that were grown on urea and nitrate (Table S4, Fig. 7).


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)

Proposed model showing the urea cycle, nitrate transport and assimilation, and the glutamine-glutamate cycle.Enzymes that are involved in these pathways are labeled with colors that indicate the fold change (log2) in their transcript levels in urea-grown cells relative to nitrate-grown cells (color code is provided in the figure). NRT, nitrate transporter; NR nitrate reductase; NAR1, nitrite transporter; NasB, NADPH nitrite reductase; GS, glutamine synthetase; Fd-GOGAT, ferredoxin-dependent glutamate synthase; CPS, carbamoyl phosphate synthase; OTC, ornithine transcarboxylase; AsuS, argininosuccinate synthase; ASL, argininosuccinate lyase; ARG, arginase; Ure, urease; DUR, urea transporter.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111069-g006: Proposed model showing the urea cycle, nitrate transport and assimilation, and the glutamine-glutamate cycle.Enzymes that are involved in these pathways are labeled with colors that indicate the fold change (log2) in their transcript levels in urea-grown cells relative to nitrate-grown cells (color code is provided in the figure). NRT, nitrate transporter; NR nitrate reductase; NAR1, nitrite transporter; NasB, NADPH nitrite reductase; GS, glutamine synthetase; Fd-GOGAT, ferredoxin-dependent glutamate synthase; CPS, carbamoyl phosphate synthase; OTC, ornithine transcarboxylase; AsuS, argininosuccinate synthase; ASL, argininosuccinate lyase; ARG, arginase; Ure, urease; DUR, urea transporter.
Mentions: Compared with cells that were grown on urea, 142 transcripts were upregulated 2-fold or greater in cells that were grown on nitrate, and 180 transcripts were downregulated 2-fold or greater in cells that were grown on nitrate (Table S4). Approximately 24% of differentially expressed genes could not be assigned a function because the reference genes represented hypothetical or predicted protein or showed no database homology. Transcripts encoding nitrate high affinity transporter, nitrite transporter NAR1, formate/nitrite transporter, and ammonium transporter increased when A. anophagefferens cells were grown on nitrate compared with urea. Transcripts encoding a putative nitrate reductase, NADPH nitrite reductase and glutamine synthetase increased in cells that were grown on nitrate compared with cells that were grown on urea (Fig. 6). Notably, 4 transcripts that were involved in OUC showed 2.0- to 2.6-fold upregulation in urea-grown cells relative to nitrate-grown cells (Table S4, Fig. 6). Thirty nine transcripts encoding proteins that were involved in protein synthesis showed 2.0- to 3.6-fold upregulation in urea-grown cells relative to nitrate-grown cells (Table S4). There were 11 transcripts encoding enzymes that were involved in amino acid synthesis that were upregulated in urea-grown cells relative to nitrate-grown cells. Levels of transcripts encoding proteins that were involved in photosynthesis and central carbon metabolism displayed difference in cells that were grown on urea and nitrate (Table S4, Fig. 7).

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