Whole-cell response of the pennate diatom
            <i>Phaeodactylum tricornutum</i>
            to iron starvation

Allen, Andrew E.; LaRoche, Julie; Maheswari, Uma; Lommer, Markus; Schauer, Nicolas; Lopez, Pascal J.; Finazzi, Guido; Fernie, Alisdair R.; Bowler, Chris

doi:10.1073/pnas.0711370105

Cited by 393 publications

(536 citation statements)

References 48 publications

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“…Lastly, iron starvation-induced protein (ISIP2A, Fc 272749) was elevated by 1.6-fold. Studies in the temperate diatom P. tricornutum found this gene transcript to be highly increased under iron starvation (Allen et al, 2008). Genomic annotation in the multicellular brown algae Ectocarpus siliculosus (Cock et al, 2010) identified a Fc272749 homolog as a probable high-CO 2 inducible periplasmic protein (Supplemental Table S5).…”

Section: General Stress Response Proteinsmentioning

confidence: 99%

Proteomic Analysis of a Sea-Ice Diatom: Salinity Acclimation Provides New Insight into the Dimethylsulfoniopropionate Production Pathway

et al. 2011

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Dimethylsulfoniopropionate (DMSP) plays important roles in oceanic carbon and sulfur cycling and may significantly impact climate. It is a biomolecule synthesized from the methionine (Met) pathway and proposed to serve various physiological functions to aid in environmental stress adaptation through its compatible solute, cryoprotectant, and antioxidant properties. Yet, the enzymes and mechanisms regulating DMSP production are poorly understood. This study utilized a proteomics approach to investigate protein changes associated with salinity-induced DMSP increases in the model sea-ice diatom Fragilariopsis cylindrus (CCMP 1102). We hypothesized proteins associated with the Met-DMSP biosynthesis pathway would increase in relative abundance when challenged with elevated salinity. To test this hypothesis axenic log-phase cultures initially grown at a salinity of 35 were gradually shifted to a final salinity of 70 over a 24-h period. Intracellular DMSP was measured and two-dimensional gel electrophoresis was used to identify protein changes at 48 h after the shift. Intracellular DMSP increased by approximately 85% in the hypersaline cultures. One-third of the proteins increased under high salinity were associated with amino acid pathways. Three protein isoforms of S-adenosylhomo-cysteine hydrolase, which synthesizes a Met precursor, increased 1.8-to 2.1-fold, two isoforms of S-adenosyl Met synthetase increased 1.9-to 2.5-fold, and S-adenosyl Met methyltransferase increased by 2.8-fold, suggesting active methyl cycle proteins are recruited in the synthesis of DMSP. Proteins from the four enzyme classes of the proposed algal Met transaminase DMSP pathway were among the elevated proteins, supporting our hypothesis and providing candidate genes for future characterization studies.

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Section: General Stress Response Proteinsmentioning

confidence: 99%

Proteomic Analysis of a Sea-Ice Diatom: Salinity Acclimation Provides New Insight into the Dimethylsulfoniopropionate Production Pathway

et al. 2011

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“…Particularly striking was the 5-10-fold enrichment of acetyl-CoA carboxylase (ACAC, Figure 4b), which catalyzes one of the initial steps in fatty acid biosynthesis. Diatoms accumulate lipids under nutrient-limited conditions (N, Si or Fe; Roessler, 1988;Mock and Kroon, 2002a;Allen et al, 2008), particularly relevant in light of enriched transport functions (see following section).…”

Section: Variation In Diatom Metabolic Pathways Across Communitiesmentioning

confidence: 99%

Metatranscriptomes reveal functional variation in diatom communities from the Antarctic Peninsula

et al. 2015

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Functional genomics of diatom-dominated communities from the Antarctic Peninsula was studied using comparative metatranscriptomics. Samples obtained from diatom-rich communities in the Bransfield Strait, the western Weddell Sea and sea ice in the Bellingshausen Sea/Wilkins Ice Shelf yielded more than 500K pyrosequencing reads that were combined to produce a global metatranscriptome assembly. Multi-gene phylogenies recovered three distinct communities, and diatom-assigned contigs further indicated little read-sharing between communities, validating an assembly-based annotation and analysis approach. Although functional analysis recovered a core of abundant shared annotations that were expressed across the three diatom communities, over 40% of annotations (but accounting for o10% of sequences) were community-specific. The two pelagic communities differed in their expression of N-metabolism and acquisition genes, which was almost absent in post-bloom conditions in the Weddell Sea community, while enrichment of transporters for ammonia and urea in Bransfield Strait diatoms suggests a physiological stance towards acquisition of reduced N-sources. The depletion of carbohydrate and energy metabolism pathways in sea ice relative to pelagic communities, together with increased light energy dissipation (via LHCSR proteins), photorespiration, and NO 3 − uptake and utilization all pointed to irradiance stress and/or inorganic carbon limitation within sea ice. Ice-binding proteins and cold-shock transcription factors were also enriched in sea ice diatoms. Surprisingly, the abundance of gene transcripts for the translational machinery tracked decreasing environmental temperature across only a 4°C range, possibly reflecting constraints on translational efficiency and protein production in cold environments.

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“…The products of BCAA degradation can be converted to malate by the TCA cycle. Malate produced in mitochondria could be transported into plastids by the malate:aspartate shuttle (Allen et al, 2008) and sequentially converted to pyruvate then acetyl-CoA for fatty acid biosynthesis (Figure 7). Neuronal networks based on SignalP weakly indicated the presence of a signal peptide encoded at the 59-end of the P. tricornutum gene encoding NADP(+)-malic enzyme (ME2; ProtID_51970) gene.…”

Section: Bcca Catabolism Affects Tag Biosynthesismentioning

confidence: 99%

Methylcrotonyl-CoA Carboxylase Regulates Triacylglycerol Accumulation in the Model Diatom Phaeodactylum tricornutum

et al. 2014

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The model marine diatom Phaeodactylum tricornutum can accumulate high levels of triacylglycerols (TAGs) under nitrogen depletion and has attracted increasing attention as a potential system for biofuel production. However, the molecular mechanisms involved in TAG accumulation in diatoms are largely unknown. Here, we employed a label-free quantitative proteomics approach to estimate differences in protein abundance before and after TAG accumulation. We identified a total of 1193 proteins, 258 of which were significantly altered during TAG accumulation. Data analysis revealed major changes in proteins involved in branched-chain amino acid (BCAA) catabolic processes, glycolysis, and lipid metabolic processes. Subsequent quantitative RT-PCR and protein gel blot analysis confirmed that four genes associated with BCAA degradation were significantly upregulated at both the mRNA and protein levels during TAG accumulation. The most significantly upregulated gene, encoding the b-subunit of methylcrotonyl-CoA carboxylase (MCC2), was selected for further functional studies. Inhibition of MCC2 expression by RNA interference disturbed the flux of carbon (mainly in the form of leucine) toward BCAA degradation, resulting in decreased TAG accumulation. MCC2 inhibition also gave rise to incomplete utilization of nitrogen, thus lowering biomass during the stationary growth phase. These findings help elucidate the molecular and metabolic mechanisms leading to increased lipid production in diatoms.

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Whole-cell response of the pennate diatom Phaeodactylum tricornutum to iron starvation

Cited by 393 publications

References 48 publications

Proteomic Analysis of a Sea-Ice Diatom: Salinity Acclimation Provides New Insight into the Dimethylsulfoniopropionate Production Pathway

Proteomic Analysis of a Sea-Ice Diatom: Salinity Acclimation Provides New Insight into the Dimethylsulfoniopropionate Production Pathway

Metatranscriptomes reveal functional variation in diatom communities from the Antarctic Peninsula

Methylcrotonyl-CoA Carboxylase Regulates Triacylglycerol Accumulation in the Model Diatom Phaeodactylum tricornutum

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