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De novo assembly of Aureococcus anophagefferens transcriptomes reveals diverse responses to the low nutrient and low light conditions present during blooms.

Frischkorn KR, Harke MJ, Gobler CJ, Dyhrman ST - Front Microbiol (2014)

Bottom Line: On average, 93% of significantly upregulated transcripts recovered by genome mapping were present in the significantly upregulated pool from both de novo assembly methods.A comparison of this transcriptome to the nutrient regulated transcriptional response of CCMP 1984 identified conserved responses between these two strains.These analyses reveal the transcriptional underpinnings of physiological shifts that could contribute to the ecological success of this species in situ: organic matter processing, metal detoxification, lipid restructuring, and photosynthetic apparatus turnover.

View Article: PubMed Central - PubMed

Affiliation: Department of Earth and Environmental Sciences and the Lamont-Doherty Earth Observatory, Columbia University Palisades, NY, USA.

ABSTRACT
Transcriptome profiling was performed on the harmful algal bloom-forming pelagophyte Aureococcus anophagefferens strain CCMP 1850 to assess responses to common stressors for dense phytoplankton blooms: low inorganic nitrogen concentrations, low inorganic phosphorus concentrations, low light levels, and a replete control. The de novo assemblies of pooled reads from all treatments reconstructed ~54,000 transcripts using Trinity, and ~31,000 transcripts using ABySS. Comparison to the strain CCMP 1984 genome showed that the majority of the gene models were present in both de novo assemblies and that roughly 95% of contigs from both assemblies mapped to the genome, with Trinity capturing slightly more genome content. Sequence reads were mapped back to the de novo assemblies as well as the gene models and differential expression was analyzed using a Bayesian approach called Analysis of Sequence Counts (ASC). On average, 93% of significantly upregulated transcripts recovered by genome mapping were present in the significantly upregulated pool from both de novo assembly methods. Transcripts related to the transport and metabolism of nitrogen were upregulated in the low nitrogen treatment, transcripts encoding enzymes that hydrolyze organic phosphorus or relieve arsenic toxicity were upregulated in the low phosphorus treatment, and transcripts for enzymes that catabolize organic compounds, restructure lipid membranes, or are involved in sulfolipid biosynthesis were upregulated in the low light treatment. A comparison of this transcriptome to the nutrient regulated transcriptional response of CCMP 1984 identified conserved responses between these two strains. These analyses reveal the transcriptional underpinnings of physiological shifts that could contribute to the ecological success of this species in situ: organic matter processing, metal detoxification, lipid restructuring, and photosynthetic apparatus turnover.

No MeSH data available.


Related in: MedlinePlus

Schematic cell model illustrating the potential role of the transcripts highlighted in this study. Localization of the proteins depicted is for clarity and is not meant to represent actual protein localization in the cell. Proteins with black dashed lines represent transcripts that were detected in transcriptomes but were not significantly differentially expressed relative to the control. AAP, Amino acid permease; ACP, Acid phosphatase; ALP, Alkaline phosphatase; AMT, Ammonia transporter; APR, Adenosine-5′-phosphosulfate reductase, ARG, arginase; ArsA, Arsenite trasnlocating ATPase; ArsB, Arsenite efflux protein; ArsC, Arsenate reductase; DUR, Urea transporter; FDS, Formamidase; FGS, Ferredoxin-dependent glutamate synthase; GPX, Glutathione peroxidase; GST, Glutathione S Transferase; HIP, Histidine phosphatase; LHC, Light harvesting complex; LPL, Lysophospholipase; NAR, Nitrite transporter; NIA, Nitrate reductase; NII, Nitrite reductase; NRT, Nitrate transporter; NTD, 5′-Nucleotidase; P4-85, PHO pathway; PEP, Peptidase; PEPyr, Phosphoenolpyruvate; PPL, Patatin-like phospholipase; PTA, Phosphate transporter; SQD, SQD1 (sulfolipid biosynthesis gene); STP, Serine/threonine phosphatase; SUP, Sulfate permease; SUR, Sulfate reductase; UDPG, UDP-glucose; URE, Urease; VTC, Vacuolar transport chaperone (VTC4); XUV, Xanthine/uracil/Vitamin C permease.
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Figure 4: Schematic cell model illustrating the potential role of the transcripts highlighted in this study. Localization of the proteins depicted is for clarity and is not meant to represent actual protein localization in the cell. Proteins with black dashed lines represent transcripts that were detected in transcriptomes but were not significantly differentially expressed relative to the control. AAP, Amino acid permease; ACP, Acid phosphatase; ALP, Alkaline phosphatase; AMT, Ammonia transporter; APR, Adenosine-5′-phosphosulfate reductase, ARG, arginase; ArsA, Arsenite trasnlocating ATPase; ArsB, Arsenite efflux protein; ArsC, Arsenate reductase; DUR, Urea transporter; FDS, Formamidase; FGS, Ferredoxin-dependent glutamate synthase; GPX, Glutathione peroxidase; GST, Glutathione S Transferase; HIP, Histidine phosphatase; LHC, Light harvesting complex; LPL, Lysophospholipase; NAR, Nitrite transporter; NIA, Nitrate reductase; NII, Nitrite reductase; NRT, Nitrate transporter; NTD, 5′-Nucleotidase; P4-85, PHO pathway; PEP, Peptidase; PEPyr, Phosphoenolpyruvate; PPL, Patatin-like phospholipase; PTA, Phosphate transporter; SQD, SQD1 (sulfolipid biosynthesis gene); STP, Serine/threonine phosphatase; SUP, Sulfate permease; SUR, Sulfate reductase; UDPG, UDP-glucose; URE, Urease; VTC, Vacuolar transport chaperone (VTC4); XUV, Xanthine/uracil/Vitamin C permease.

Mentions: The response to the low P treatment featured the significant upregulation of transcripts responsible for phosphate transport and the hydrolysis of DOP including several phosphatases and a 5′-nucleotidase (Figure 4; Table 6), concurrent with an increase in alkaline phosphatase activity. Transcripts for components of a PHO-like (Toh-e et al., 1981) P regulatory signaling cascade were found to be upregulated under low P (Figure 4; Table 6), as was a vacuolar transport chaperone 4 (VTC4) with homology to a eukaryotic polyphosphate polymerase (Hothorn et al., 2009) (Figure 4; Table 6). Transcripts encoding components of an arsenite detoxification pathway including an arsenite transporting ATPase and a glutathione S-transferase were also significantly upregulated (Figure 4; Table 6). An arsenate reductase was identified in the transcriptome, but was not significantly upregulated in the low P treatment relative to the replete control.


De novo assembly of Aureococcus anophagefferens transcriptomes reveals diverse responses to the low nutrient and low light conditions present during blooms.

Frischkorn KR, Harke MJ, Gobler CJ, Dyhrman ST - Front Microbiol (2014)

Schematic cell model illustrating the potential role of the transcripts highlighted in this study. Localization of the proteins depicted is for clarity and is not meant to represent actual protein localization in the cell. Proteins with black dashed lines represent transcripts that were detected in transcriptomes but were not significantly differentially expressed relative to the control. AAP, Amino acid permease; ACP, Acid phosphatase; ALP, Alkaline phosphatase; AMT, Ammonia transporter; APR, Adenosine-5′-phosphosulfate reductase, ARG, arginase; ArsA, Arsenite trasnlocating ATPase; ArsB, Arsenite efflux protein; ArsC, Arsenate reductase; DUR, Urea transporter; FDS, Formamidase; FGS, Ferredoxin-dependent glutamate synthase; GPX, Glutathione peroxidase; GST, Glutathione S Transferase; HIP, Histidine phosphatase; LHC, Light harvesting complex; LPL, Lysophospholipase; NAR, Nitrite transporter; NIA, Nitrate reductase; NII, Nitrite reductase; NRT, Nitrate transporter; NTD, 5′-Nucleotidase; P4-85, PHO pathway; PEP, Peptidase; PEPyr, Phosphoenolpyruvate; PPL, Patatin-like phospholipase; PTA, Phosphate transporter; SQD, SQD1 (sulfolipid biosynthesis gene); STP, Serine/threonine phosphatase; SUP, Sulfate permease; SUR, Sulfate reductase; UDPG, UDP-glucose; URE, Urease; VTC, Vacuolar transport chaperone (VTC4); XUV, Xanthine/uracil/Vitamin C permease.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
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Figure 4: Schematic cell model illustrating the potential role of the transcripts highlighted in this study. Localization of the proteins depicted is for clarity and is not meant to represent actual protein localization in the cell. Proteins with black dashed lines represent transcripts that were detected in transcriptomes but were not significantly differentially expressed relative to the control. AAP, Amino acid permease; ACP, Acid phosphatase; ALP, Alkaline phosphatase; AMT, Ammonia transporter; APR, Adenosine-5′-phosphosulfate reductase, ARG, arginase; ArsA, Arsenite trasnlocating ATPase; ArsB, Arsenite efflux protein; ArsC, Arsenate reductase; DUR, Urea transporter; FDS, Formamidase; FGS, Ferredoxin-dependent glutamate synthase; GPX, Glutathione peroxidase; GST, Glutathione S Transferase; HIP, Histidine phosphatase; LHC, Light harvesting complex; LPL, Lysophospholipase; NAR, Nitrite transporter; NIA, Nitrate reductase; NII, Nitrite reductase; NRT, Nitrate transporter; NTD, 5′-Nucleotidase; P4-85, PHO pathway; PEP, Peptidase; PEPyr, Phosphoenolpyruvate; PPL, Patatin-like phospholipase; PTA, Phosphate transporter; SQD, SQD1 (sulfolipid biosynthesis gene); STP, Serine/threonine phosphatase; SUP, Sulfate permease; SUR, Sulfate reductase; UDPG, UDP-glucose; URE, Urease; VTC, Vacuolar transport chaperone (VTC4); XUV, Xanthine/uracil/Vitamin C permease.
Mentions: The response to the low P treatment featured the significant upregulation of transcripts responsible for phosphate transport and the hydrolysis of DOP including several phosphatases and a 5′-nucleotidase (Figure 4; Table 6), concurrent with an increase in alkaline phosphatase activity. Transcripts for components of a PHO-like (Toh-e et al., 1981) P regulatory signaling cascade were found to be upregulated under low P (Figure 4; Table 6), as was a vacuolar transport chaperone 4 (VTC4) with homology to a eukaryotic polyphosphate polymerase (Hothorn et al., 2009) (Figure 4; Table 6). Transcripts encoding components of an arsenite detoxification pathway including an arsenite transporting ATPase and a glutathione S-transferase were also significantly upregulated (Figure 4; Table 6). An arsenate reductase was identified in the transcriptome, but was not significantly upregulated in the low P treatment relative to the replete control.

Bottom Line: On average, 93% of significantly upregulated transcripts recovered by genome mapping were present in the significantly upregulated pool from both de novo assembly methods.A comparison of this transcriptome to the nutrient regulated transcriptional response of CCMP 1984 identified conserved responses between these two strains.These analyses reveal the transcriptional underpinnings of physiological shifts that could contribute to the ecological success of this species in situ: organic matter processing, metal detoxification, lipid restructuring, and photosynthetic apparatus turnover.

View Article: PubMed Central - PubMed

Affiliation: Department of Earth and Environmental Sciences and the Lamont-Doherty Earth Observatory, Columbia University Palisades, NY, USA.

ABSTRACT
Transcriptome profiling was performed on the harmful algal bloom-forming pelagophyte Aureococcus anophagefferens strain CCMP 1850 to assess responses to common stressors for dense phytoplankton blooms: low inorganic nitrogen concentrations, low inorganic phosphorus concentrations, low light levels, and a replete control. The de novo assemblies of pooled reads from all treatments reconstructed ~54,000 transcripts using Trinity, and ~31,000 transcripts using ABySS. Comparison to the strain CCMP 1984 genome showed that the majority of the gene models were present in both de novo assemblies and that roughly 95% of contigs from both assemblies mapped to the genome, with Trinity capturing slightly more genome content. Sequence reads were mapped back to the de novo assemblies as well as the gene models and differential expression was analyzed using a Bayesian approach called Analysis of Sequence Counts (ASC). On average, 93% of significantly upregulated transcripts recovered by genome mapping were present in the significantly upregulated pool from both de novo assembly methods. Transcripts related to the transport and metabolism of nitrogen were upregulated in the low nitrogen treatment, transcripts encoding enzymes that hydrolyze organic phosphorus or relieve arsenic toxicity were upregulated in the low phosphorus treatment, and transcripts for enzymes that catabolize organic compounds, restructure lipid membranes, or are involved in sulfolipid biosynthesis were upregulated in the low light treatment. A comparison of this transcriptome to the nutrient regulated transcriptional response of CCMP 1984 identified conserved responses between these two strains. These analyses reveal the transcriptional underpinnings of physiological shifts that could contribute to the ecological success of this species in situ: organic matter processing, metal detoxification, lipid restructuring, and photosynthetic apparatus turnover.

No MeSH data available.


Related in: MedlinePlus