Additional file 1 of Highly flexible metabolism of the marine euglenozoan protist Diplonema papillatum
Creators: name: Škodová-Sveráková, Ingrid
name: Záhonová, Kristína
name: Juricová, Valéria
name: Danchenko, Maksym
name: Moos, Martin
name: Baráth, Peter
name: Prokopchuk, Galina
name: Butenko, Anzhelika
name: Lukáčová, Veronika
name: Kohútová, Lenka
name: Bučková, Barbora
name: Horák, Aleš
name: Faktorová, Drahomíra
name: Horváth, Anton
name: Šimek, Petr
name: Lukeš, Julius
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Physiology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Computational Biology

description: Additional file 1: Fig. S1. LC-HRMS metabolic profiles. Characteristic (a) posESI HRMS and (b) negESI HRMS metabolic signatures for the D. papillatum cell extracts grown in rich normoxic (R+), rich hypoxic (R-), nutrient poor normoxic (P+), and nutrient poor hypoxic (P-) conditions. 3-Ala, 3-alanine; Ac-Carn, acyl-carnitine; Acyl-Me-Tau, acyl-methyl-taurines (taurates); Ade, adenine; Ado, adenosine; Ala, alanine; Arg, arginine; Arg, arginine; DMSP, 3-dimethylsulfoniopropionate; FA, fatty acid; GMAB, glyceromethyl-3-alanine betaine; Gln, glutamine; GPC, glycerophosphocholine; GSH, glutathione; HRMS, high resolution mass spectrometry; Ile, isoleucine; Betaine LP, betaine-lipids; Lys, lysine; Mal, malate; MeTau, N-methyltaurine; negESI, negative electrospray ionization; Orn, ornithine; PA, phosphatidic acid; PC, phosphatidylcholine; PE, phosphatidylethanolamine; Pro, proline; posESI, positive electrospray ionization; PS, phosphatidylserine; Tau, taurine; Tre, trehalose; Val, valine. Fig. S2. Sequences of phosphofructokinase (PFK) and pyrophosphate-fructose phosphotransferase (PFP). (a) Alignment of PFK1 shows that the sequence previously identified [13] was truncated at its N-terminus. Moreover, predicted protein domains classify it as PFP rather than PFK. (b) Alignment of PFK2 identified in this and previous study [13]. (c) Sequence of PFP identified only in this study. Color boxes correspond to predicted protein domains as in different databases as explained in graphical legend. Fig. S3. 14C-proline (Pro) and 14C-glucose (Glu) uptake in D. papillatum. (a) Cultures of 5 × 106 cells were fed with 14C-Pro and 14C-Glu in poor medium under aerobic conditions. Shown are autoradiograms of separated proteins, monosaccharides, lipids, and fatty acids. (b) Cells were cultivated for 24 h in the presence of radioactive glucose in rich (R) and poor (P) medium under aerobic (+) and hypoxic (-) conditions. (c) Cells were placed into sea salt solution supplemented with radioactive glucose and cultured for 12 h. The amount of isotope was determined with scintillation counter as disintegrations per minute (DPM) in 1 ml of growth medium containing 5 × 106 cells and cellular lysates. Fig. S4. Heatmaps of proteins involved in transcription (a), translation (b), and detoxifying systems (c). Abbreviations: rich medium (R), poor medium (P), aerobic conditions (+) hypoxic conditions (-). Fig. S5. Phylogenetic analysis of D. papillatum opine dehydrogenase. The Maximum Likelihood phylogenetic tree was estimated under the LG + G4 model (chosen as best-fitting model) with ultrafast bootstrapping. Support values are shown when ≥75%.