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An archaeal ADP-dependent serine kinase involved in cysteine biosynthesis and serine metabolism

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ABSTRACT

Routes for cysteine biosynthesis are still unknown in many archaea. Here we find that the hyperthermophilic archaeon Thermococcus kodakarensis generates cysteine from serine via O-phosphoserine, in addition to the classical route from 3-phosphoglycerate. The protein responsible for serine phosphorylation is encoded by TK0378, annotated as a chromosome partitioning protein ParB. The TK0378 protein utilizes ADP as the phosphate donor, but in contrast to previously reported ADP-dependent kinases, recognizes a non-sugar substrate. Activity is specific towards free serine, and not observed with threonine, homoserine and serine residues within a peptide. Genetic analyses suggest that TK0378 is involved in serine assimilation and clearly responsible for cysteine biosynthesis from serine. TK0378 homologs, present in Thermococcales and Desulfurococcales, are most likely not ParB proteins and constitute a group of kinases involved in serine utilization.

No MeSH data available.


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Ser, Gly or Cys auxotrophy of Thermococcus kodakarensis gene disruptants.Ser or Gly auxotrophy was investigated by cultivating cells in synthetic amino acid medium with (a) or without Ser (b) or with (c) or without Gly (d). Symbols: T. kodakarensis KU216 (open circles), ΔserAΔldhA1ΔldhA2-1 (open triangles), ΔglyA (open squares), Δtdh (grey triangles), ΔglyAΔtdh (black squares). Contribution of the route from 3-phosphoglycerate to Ser biosynthesis was examined in synthetic amino acid medium supplemented with pyruvate and depleted of Ser (e). Contribution of the route from 3-phosphoglycerate to Cys biosynthesis was examined in synthetic amino acid medium depleted of Cys with or without pyruvate (f). (e) Symbols: ΔglyA (open squares), ΔglyAΔserA (black circles), ΔglyAΔldhA1 (grey diamonds), ΔglyAΔldhA2 (black diamonds). (f) Symbols: KU216 host strain (open circles), ΔserK (grey circles), KU216 host strain with pyruvate (grey squares), ΔserK with pyruvate (black triangles). Error bars indicate the standard deviations of three independent culture experiments.
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f5: Ser, Gly or Cys auxotrophy of Thermococcus kodakarensis gene disruptants.Ser or Gly auxotrophy was investigated by cultivating cells in synthetic amino acid medium with (a) or without Ser (b) or with (c) or without Gly (d). Symbols: T. kodakarensis KU216 (open circles), ΔserAΔldhA1ΔldhA2-1 (open triangles), ΔglyA (open squares), Δtdh (grey triangles), ΔglyAΔtdh (black squares). Contribution of the route from 3-phosphoglycerate to Ser biosynthesis was examined in synthetic amino acid medium supplemented with pyruvate and depleted of Ser (e). Contribution of the route from 3-phosphoglycerate to Cys biosynthesis was examined in synthetic amino acid medium depleted of Cys with or without pyruvate (f). (e) Symbols: ΔglyA (open squares), ΔglyAΔserA (black circles), ΔglyAΔldhA1 (grey diamonds), ΔglyAΔldhA2 (black diamonds). (f) Symbols: KU216 host strain (open circles), ΔserK (grey circles), KU216 host strain with pyruvate (grey squares), ΔserK with pyruvate (black triangles). Error bars indicate the standard deviations of three independent culture experiments.

Mentions: T. kodakarensis can grow in a synthetic amino acid medium without Ser (Fig. 5a,b), indicating that this organism can also synthesize Ser from the other 19 amino acids. As a pathway that generates Cys from Ser was identified, we further examined the pathways responsible for the biosynthesis of Ser. There are three established pathways that result in the biosynthesis of Ser (Fig. 1b). One pathway, reported in microorganisms, mammals and plants, generates Ser from 3-phosphoglycerate via Sep, and is called the ‘phosphorylated pathway' for Ser biosynthesis (pathway Ser1) (refs 33, 34, 35, 36, 37). The route from 3-phosphoglycerate to Sep is also utilized for Cys biosynthesis (for example, pathway Cys2 in Fig. 1a). Sep is converted to Ser by phosphoserine phosphatase (SerB). The second pathway is the ‘non-phosphorylated pathway' (pathway Ser2), which is utilized by eukaryotes. Ser is generated from 3-phosphoglycerate via glycerate and hydroxypyruvate, and involves 3-phosphoglycerate phosphatase, glycerate dehydrogenase and serine-pyruvate aminotransferase38. In the third pathway which is found in microorganisms and plants, Ser is generated directly from Gly through the function of glycine/serine hydroxymethyltransferase (GlyA) (pathway Ser3). This conversion is included in the serine pathway in methanotrophic and methyltrophic bacteria which utilize C1 compounds as a carbon source39.


An archaeal ADP-dependent serine kinase involved in cysteine biosynthesis and serine metabolism
Ser, Gly or Cys auxotrophy of Thermococcus kodakarensis gene disruptants.Ser or Gly auxotrophy was investigated by cultivating cells in synthetic amino acid medium with (a) or without Ser (b) or with (c) or without Gly (d). Symbols: T. kodakarensis KU216 (open circles), ΔserAΔldhA1ΔldhA2-1 (open triangles), ΔglyA (open squares), Δtdh (grey triangles), ΔglyAΔtdh (black squares). Contribution of the route from 3-phosphoglycerate to Ser biosynthesis was examined in synthetic amino acid medium supplemented with pyruvate and depleted of Ser (e). Contribution of the route from 3-phosphoglycerate to Cys biosynthesis was examined in synthetic amino acid medium depleted of Cys with or without pyruvate (f). (e) Symbols: ΔglyA (open squares), ΔglyAΔserA (black circles), ΔglyAΔldhA1 (grey diamonds), ΔglyAΔldhA2 (black diamonds). (f) Symbols: KU216 host strain (open circles), ΔserK (grey circles), KU216 host strain with pyruvate (grey squares), ΔserK with pyruvate (black triangles). Error bars indicate the standard deviations of three independent culture experiments.
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f5: Ser, Gly or Cys auxotrophy of Thermococcus kodakarensis gene disruptants.Ser or Gly auxotrophy was investigated by cultivating cells in synthetic amino acid medium with (a) or without Ser (b) or with (c) or without Gly (d). Symbols: T. kodakarensis KU216 (open circles), ΔserAΔldhA1ΔldhA2-1 (open triangles), ΔglyA (open squares), Δtdh (grey triangles), ΔglyAΔtdh (black squares). Contribution of the route from 3-phosphoglycerate to Ser biosynthesis was examined in synthetic amino acid medium supplemented with pyruvate and depleted of Ser (e). Contribution of the route from 3-phosphoglycerate to Cys biosynthesis was examined in synthetic amino acid medium depleted of Cys with or without pyruvate (f). (e) Symbols: ΔglyA (open squares), ΔglyAΔserA (black circles), ΔglyAΔldhA1 (grey diamonds), ΔglyAΔldhA2 (black diamonds). (f) Symbols: KU216 host strain (open circles), ΔserK (grey circles), KU216 host strain with pyruvate (grey squares), ΔserK with pyruvate (black triangles). Error bars indicate the standard deviations of three independent culture experiments.
Mentions: T. kodakarensis can grow in a synthetic amino acid medium without Ser (Fig. 5a,b), indicating that this organism can also synthesize Ser from the other 19 amino acids. As a pathway that generates Cys from Ser was identified, we further examined the pathways responsible for the biosynthesis of Ser. There are three established pathways that result in the biosynthesis of Ser (Fig. 1b). One pathway, reported in microorganisms, mammals and plants, generates Ser from 3-phosphoglycerate via Sep, and is called the ‘phosphorylated pathway' for Ser biosynthesis (pathway Ser1) (refs 33, 34, 35, 36, 37). The route from 3-phosphoglycerate to Sep is also utilized for Cys biosynthesis (for example, pathway Cys2 in Fig. 1a). Sep is converted to Ser by phosphoserine phosphatase (SerB). The second pathway is the ‘non-phosphorylated pathway' (pathway Ser2), which is utilized by eukaryotes. Ser is generated from 3-phosphoglycerate via glycerate and hydroxypyruvate, and involves 3-phosphoglycerate phosphatase, glycerate dehydrogenase and serine-pyruvate aminotransferase38. In the third pathway which is found in microorganisms and plants, Ser is generated directly from Gly through the function of glycine/serine hydroxymethyltransferase (GlyA) (pathway Ser3). This conversion is included in the serine pathway in methanotrophic and methyltrophic bacteria which utilize C1 compounds as a carbon source39.

View Article: PubMed Central - PubMed

ABSTRACT

Routes for cysteine biosynthesis are still unknown in many archaea. Here we find that the hyperthermophilic archaeon Thermococcus kodakarensis generates cysteine from serine via O-phosphoserine, in addition to the classical route from 3-phosphoglycerate. The protein responsible for serine phosphorylation is encoded by TK0378, annotated as a chromosome partitioning protein ParB. The TK0378 protein utilizes ADP as the phosphate donor, but in contrast to previously reported ADP-dependent kinases, recognizes a non-sugar substrate. Activity is specific towards free serine, and not observed with threonine, homoserine and serine residues within a peptide. Genetic analyses suggest that TK0378 is involved in serine assimilation and clearly responsible for cysteine biosynthesis from serine. TK0378 homologs, present in Thermococcales and Desulfurococcales, are most likely not ParB proteins and constitute a group of kinases involved in serine utilization.

No MeSH data available.


Related in: MedlinePlus