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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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Specific genes transcriptionally regulated by urea.A) Number of common genes differentially regulated between the mixture N and urea groups compared with the reference nitrate group; B) the pattern of regulation of these common genes.
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pone-0111069-g008: Specific genes transcriptionally regulated by urea.A) Number of common genes differentially regulated between the mixture N and urea groups compared with the reference nitrate group; B) the pattern of regulation of these common genes.

Mentions: The comparison of results for the mixture N and urea groups with the nitrate reference allowed us to find genes for which transcription was specifically regulated by urea. We found 124 common genes differentially regulated between the mixture N and urea groups compared with the reference nitrate group (Figure 8A). These genes are listed in Table S10. Interestingly, the pattern of regulation of gene expression for urea and mixture N-grown cells appeared to be perfectly consistent (Figure 8B). Among these 124 genes, those involved in protein synthesis were well represented (Table 3). The next represented gene categories were nitrogen compound metabolism, protein modification and degradation, DNA and RNA binding, transport, signaling, photosynthesis, glycolysis/gluconeogenesis, and stress. Transcripts encoding argininosuccinate synthase, tryptophan synthase and spermine synthase increased in urea-and mixture-grown cells compared with nitrate-grown cells. Twenty two transcripts encoding proteins that are involved in protein synthesis were induced in urea-and mixture-grown cells.


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)

Specific genes transcriptionally regulated by urea.A) Number of common genes differentially regulated between the mixture N and urea groups compared with the reference nitrate group; B) the pattern of regulation of these common genes.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111069-g008: Specific genes transcriptionally regulated by urea.A) Number of common genes differentially regulated between the mixture N and urea groups compared with the reference nitrate group; B) the pattern of regulation of these common genes.
Mentions: The comparison of results for the mixture N and urea groups with the nitrate reference allowed us to find genes for which transcription was specifically regulated by urea. We found 124 common genes differentially regulated between the mixture N and urea groups compared with the reference nitrate group (Figure 8A). These genes are listed in Table S10. Interestingly, the pattern of regulation of gene expression for urea and mixture N-grown cells appeared to be perfectly consistent (Figure 8B). Among these 124 genes, those involved in protein synthesis were well represented (Table 3). The next represented gene categories were nitrogen compound metabolism, protein modification and degradation, DNA and RNA binding, transport, signaling, photosynthesis, glycolysis/gluconeogenesis, and stress. Transcripts encoding argininosuccinate synthase, tryptophan synthase and spermine synthase increased in urea-and mixture-grown cells compared with nitrate-grown cells. Twenty two transcripts encoding proteins that are involved in protein synthesis were induced in urea-and mixture-grown cells.

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