Alignment of the predicted amino acid sequence of SLC4s in P. tricornutum and T. pseudonana, and two human SLC4s. from Mechanisms of carbon dioxide acquisition and CO₂ sensing in marine diatoms: a gateway to carbon metabolism

The black and gray boxes indicate putative transmembrane helices (TM1-TM14) predicted by TMHMM and SOSUI, and the putative first methionine, respectively. ☆ and * show the three CO2 responsive PtSLC4s and putative chloroplast membranes-localized DIC transporters, respectively

Proportionate abundances of the picocyanobacteria <i>Prochlorococcus</i> and <i>Synechococcus</i> among cyanobacteria and other microorganisms in the Indian Ocean sorted by size fractionation.

<p>The total number of genes taxonomically referring to picocyanobacteria and other microbes are given per size fraction at the Indian Ocean stations GS108, GS110, GS112, GS117 and GS122.</p

Unrooted picocyanobacterial gene trees inferred using maximum likelihood of sampled in the Indian Ocean (GOSII), and the Atlantic and Pacific Oceans (GOSI).

<p>Sampling locations (colored dots), and taxonomy (colored edges). (A) Pcb/IsiA, light-harvesting chlorophyll-binding peptides. (B) Light-harvesting phycobilisome ß-subunits (<i>cpe</i>, <i>cpc</i>, <i>apc</i>). (C) Light-harvesting phycobilisome α-subunits (<i>cpe</i>, <i>cpc</i>, <i>apc</i>). Scale bar indicates expected number of substitutions per site.</p

Map of Indian Ocean indicating metagenomic sampling stations along the east-west equatorial transect in GOSII.

<p>Map of Indian Ocean indicating metagenomic sampling stations along the east-west equatorial transect in GOSII.</p

Chloroplastic ornithine cycle as revealed by the model.

<p>Metabolic network usage of a chloroplastic ornithine cycle is shown under a saturating photon constraint of 16 mM allowing maximum carbon uptake. Minor reactants and products are omitted for visual clarity (i.e., water, protons and phosphate). Metabolite and reaction abbreviation suffixes indicate cellular compartment; c, cytosol; h, chloroplast; m, mitochondria. Reversible reactions are indicated by arrowheads at both ends. The filled arrowhead indicates the direction in which the reaction is running, i.e. from substrate (open arrowhead) to product (filled arrowhead). Abbreviations used: ACOAT, acetylornithine transaminase; AGK, acetylglutamate kinase; AGPR, N-acetyl-δ-glutamyl-phosphate reductase; GACT, glutamate N-acetyltransferase; GLNA, glutamine synthase; GLTS, glutamate synthase (ferredoxin dependent); GLUDH2, glutamine dehydrogenase (NAD dependent); GLUSA, glutamate semialdehyde degradation (spontaneous); OAT, ornithine aminotransferase; P5CDH, 1-pyrroline-5-carboxylate dehydrogenase; acorn, N-acetylornithine; acglu, N-acetyl-L-glutamate; acg5p, N-acetyl-L-glutamate 5-phosphate; acg5sa, N-Acetyl-L-glutamate 5-semialdehyde; adp, ADP; akg, α-ketoglutarate; atp, ATP; fdxox, ferredoxin (oxidized); fdxrd, ferredoxin (reduced); gln__L, L-glutamine; glu__L, L-glutamate; glu5sa, L-glutamate 5-semialdehyde; nad, NAD⁺; nadh, NADH; nadp, NADP⁺; nadph, NADPH; nh4, ammonium ion; orn, ornithine; 1pyr5c, (S)-1-Pyrroline-5-carboxylate.</p

Genes in reconstruction over predicted genes in genome against genome size for selected eukaryotic metabolic reconstructions.

<p>The three reconstructions with the highest ratio of genes in reconstruction per genes in genome are highlighted. bna572+ has a comparable ratio as <i>i</i>LB1025 and <i>i</i>LB1027_lipid, <i>i</i>TO977 has a higher ratio. Compared to <i>i</i>TO977 and bna572+, <i>i</i>LB1025 and <i>i</i>LB1027_lipid contain more reactions. The number of reactions in the respective reconstructions is used to scale the circle diameters. Note the discontinuous x-axis. Abbreviations: AraGEM: <i>Arabidopsis thaliana</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0155038#pone.0155038.ref073" target="_blank">73</a>]; bna572+: <i>Brassica napus</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0155038#pone.0155038.ref074" target="_blank">74</a>]; AlgaGEM: <i>Chlamydomonas reinhardtii</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0155038#pone.0155038.ref075" target="_blank">75</a>]; <i>i</i>RC1080: <i>Chlamydomonas reinhardtii</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0155038#pone.0155038.ref039" target="_blank">39</a>]; <i>i</i>RS1563: <i>Zea mays</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0155038#pone.0155038.ref076" target="_blank">76</a>]; <i>i</i>LB1025 and <i>i</i>LB1027_lipid: <i>Phaeodactylum tricornutum</i>, this study; <i>i</i>TO977: <i>Saccharomyces cerevisiae</i> Sc288 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0155038#pone.0155038.ref077" target="_blank">77</a>]; Recon2: <i>Homo sapiens</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0155038#pone.0155038.ref078" target="_blank">78</a>]; <i>i</i>MM1415: <i>Mus musculus</i> [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0155038#pone.0155038.ref079" target="_blank">79</a>].</p

Characteristics of available models for <i>Phaeodactylum tricornutum</i>.

<p>Characteristics of available models for <i>Phaeodactylum tricornutum</i>.</p

Light-dependent carbon partitioning.

<p>(A) Simulations indicated as photon uptake exceeds carbon uptake, excess redox potential is stored in triacylglycerol. The saturation of carbon uptake is shown in black. (B) Percent of carbon fixed in TAG against percent of metabolite flow through NADHOR (vNADHOR; EC 1.6.5.3,1.6.99.3) over metabolite flow through PSI (vPSI; EC 1.97.1.2) at a super-saturating photon uptake of 22 mM. According to our simulations TAG accumulation is inversely proportional to energetic coupling. TAG accumulation is prohibited when at least 35% of photosynthetically fixed electrons are redirected to the mitochondria.</p

Metabolic network reconstruction workflow.

<p>In step one we obtained a draft reconstruction based on <i>P</i>. <i>tricornutum</i>’s genome annotation and reference reconstructions. This draft reconstruction was manually curated using several resources such as an improved genome annotation, subcellular localization predictions and external databases. All reactions were elementally and charge balanced, QC/QA was performed and a biomass objective function was defined before transforming the reconstruction into a computational model. In an iterative process, the <i>in silico</i> predictions are compared with experimental observations to validate and improve the metabolic model.</p

Photosynthetic electron flow constraints as determined by Bailleul <i>et al</i>. [83].

<p>Photosynthetic electron flow constraints as determined by Bailleul <i>et al</i>. [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0155038#pone.0155038.ref083" target="_blank">83</a>].</p