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Whole-cell response to nitrogen deprivation in the diatom Phaeodactylum tricornutum.

Alipanah L, Rohloff J, Winge P, Bones AM, Brembu T - J. Exp. Bot. (2015)

Bottom Line: Physiological and metabolite measurements indicated that the photosynthetic capacity and chlorophyll content of the cells decreased, while neutral lipids increased in N-deprived cultures.Following N deprivation, reduced biosynthesis and increased recycling of N compounds like amino acids, proteins, and nucleic acids was observed at the transcript level.The majority of the genes associated with photosynthesis and chlorophyll biosynthesis were also repressed.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway.

No MeSH data available.


Cellular pathways and processes related to N metabolism under N deprivation in P. tricornutum. Metabolites detected are indicated by a blue box frame. Red, blue, and black text indicate up-, down-, and no regulation of pathways, genes, or metabolites by N deprivation, respectively. Amino acids are indicated by a yellow background. Red arrows depict gene transcripts found to be upregulated. Fd-GOGAT, ferredoxin-dependent glutamate synthase; GSII, ferredoxin-dependent glutamine synthetase; Fd-NiR, ferredoxin-dependent nitrite reductase; GDH, glutamate dehydrogenase; GSIII, bacterial-origin glutamine synthetase; IDH, isocitrate dehydrogenase; NADPH-GOGAT, NAD(P)H-dependent glutamate synthase; NAD(P)H-NiR, NAD(P)H-dependent nitrite reductase; NR, nitrate reductase.
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Figure 5: Cellular pathways and processes related to N metabolism under N deprivation in P. tricornutum. Metabolites detected are indicated by a blue box frame. Red, blue, and black text indicate up-, down-, and no regulation of pathways, genes, or metabolites by N deprivation, respectively. Amino acids are indicated by a yellow background. Red arrows depict gene transcripts found to be upregulated. Fd-GOGAT, ferredoxin-dependent glutamate synthase; GSII, ferredoxin-dependent glutamine synthetase; Fd-NiR, ferredoxin-dependent nitrite reductase; GDH, glutamate dehydrogenase; GSIII, bacterial-origin glutamine synthetase; IDH, isocitrate dehydrogenase; NADPH-GOGAT, NAD(P)H-dependent glutamate synthase; NAD(P)H-NiR, NAD(P)H-dependent nitrite reductase; NR, nitrate reductase.

Mentions: Transcriptional responses to N deprivation of P. tricornutum showed that uptake, assimilation, and scavenging mechanisms were activated (Fig. 5). In our experiment, transcript levels of genes involved in NO3–, NH4+, and urea transport were upregulated (Fig. 4 and Supplementary Dataset S1, available at JXB online). Of four ammonium transporters detected in our microarray data, three were upregulated. The induction of a nitrate transporter (Phatr2_54101) was confirmed by qRT-PCR (Supplementary Fig. S2). Increased transcription of genes encoding nitrate reductase (NR) and both NAD(P)H- and Fd-dependent nitrite reductase was observed at 72h after deprivation (Figs 4 and 5). Interestingly, two genes encoding molybdopterin biosynthesis proteins were induced (Supplementary Dataset S1). These enzymes might be orthologues of the Arabidopsis thaliana cofactor of NR and xanthine dehydrogenase CNX5 and CNX2, respectively (Schwarz and Mendel, 2006). The biosynthesis of molybdenum cofactor (Moco), which forms the active site of molybdenum (Mo) enzymes in eukaryotes, involves six enzymes. The qRT-PCR result also confirmed upregulation of the CNX5 orthologue (Phatr2_34373; Supplementary Fig. S2). None of the genes encoding plastidial GSII/Fd-GOGAT and mitochondrial GSIII (GLNA), which are required for ammonium assimilation, were regulated (P<0.05). However, increased transcript levels of two different isoforms of NAD(P)H-dependent glutamate synthase (NADPH-GOGAT, GltD and GltX) were observed in N-deprived cells (Fig. 5). Glutamate dehydrogenase (GDH) is another enzyme that catalyses the reversible conversion of 2-oxoglutarate (2-OG) to glutamate. We observed increased expression of an NADP-GDH (Phatr2_13951; Fig. 5 and Supplementary Dataset S1).


Whole-cell response to nitrogen deprivation in the diatom Phaeodactylum tricornutum.

Alipanah L, Rohloff J, Winge P, Bones AM, Brembu T - J. Exp. Bot. (2015)

Cellular pathways and processes related to N metabolism under N deprivation in P. tricornutum. Metabolites detected are indicated by a blue box frame. Red, blue, and black text indicate up-, down-, and no regulation of pathways, genes, or metabolites by N deprivation, respectively. Amino acids are indicated by a yellow background. Red arrows depict gene transcripts found to be upregulated. Fd-GOGAT, ferredoxin-dependent glutamate synthase; GSII, ferredoxin-dependent glutamine synthetase; Fd-NiR, ferredoxin-dependent nitrite reductase; GDH, glutamate dehydrogenase; GSIII, bacterial-origin glutamine synthetase; IDH, isocitrate dehydrogenase; NADPH-GOGAT, NAD(P)H-dependent glutamate synthase; NAD(P)H-NiR, NAD(P)H-dependent nitrite reductase; NR, nitrate reductase.
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Related In: Results  -  Collection

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Figure 5: Cellular pathways and processes related to N metabolism under N deprivation in P. tricornutum. Metabolites detected are indicated by a blue box frame. Red, blue, and black text indicate up-, down-, and no regulation of pathways, genes, or metabolites by N deprivation, respectively. Amino acids are indicated by a yellow background. Red arrows depict gene transcripts found to be upregulated. Fd-GOGAT, ferredoxin-dependent glutamate synthase; GSII, ferredoxin-dependent glutamine synthetase; Fd-NiR, ferredoxin-dependent nitrite reductase; GDH, glutamate dehydrogenase; GSIII, bacterial-origin glutamine synthetase; IDH, isocitrate dehydrogenase; NADPH-GOGAT, NAD(P)H-dependent glutamate synthase; NAD(P)H-NiR, NAD(P)H-dependent nitrite reductase; NR, nitrate reductase.
Mentions: Transcriptional responses to N deprivation of P. tricornutum showed that uptake, assimilation, and scavenging mechanisms were activated (Fig. 5). In our experiment, transcript levels of genes involved in NO3–, NH4+, and urea transport were upregulated (Fig. 4 and Supplementary Dataset S1, available at JXB online). Of four ammonium transporters detected in our microarray data, three were upregulated. The induction of a nitrate transporter (Phatr2_54101) was confirmed by qRT-PCR (Supplementary Fig. S2). Increased transcription of genes encoding nitrate reductase (NR) and both NAD(P)H- and Fd-dependent nitrite reductase was observed at 72h after deprivation (Figs 4 and 5). Interestingly, two genes encoding molybdopterin biosynthesis proteins were induced (Supplementary Dataset S1). These enzymes might be orthologues of the Arabidopsis thaliana cofactor of NR and xanthine dehydrogenase CNX5 and CNX2, respectively (Schwarz and Mendel, 2006). The biosynthesis of molybdenum cofactor (Moco), which forms the active site of molybdenum (Mo) enzymes in eukaryotes, involves six enzymes. The qRT-PCR result also confirmed upregulation of the CNX5 orthologue (Phatr2_34373; Supplementary Fig. S2). None of the genes encoding plastidial GSII/Fd-GOGAT and mitochondrial GSIII (GLNA), which are required for ammonium assimilation, were regulated (P<0.05). However, increased transcript levels of two different isoforms of NAD(P)H-dependent glutamate synthase (NADPH-GOGAT, GltD and GltX) were observed in N-deprived cells (Fig. 5). Glutamate dehydrogenase (GDH) is another enzyme that catalyses the reversible conversion of 2-oxoglutarate (2-OG) to glutamate. We observed increased expression of an NADP-GDH (Phatr2_13951; Fig. 5 and Supplementary Dataset S1).

Bottom Line: Physiological and metabolite measurements indicated that the photosynthetic capacity and chlorophyll content of the cells decreased, while neutral lipids increased in N-deprived cultures.Following N deprivation, reduced biosynthesis and increased recycling of N compounds like amino acids, proteins, and nucleic acids was observed at the transcript level.The majority of the genes associated with photosynthesis and chlorophyll biosynthesis were also repressed.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway.

No MeSH data available.