Amino Acid biosynthesis pathways in diatoms

Abstract

Amino acids are not only building blocks for proteins but serve as precursors for the synthesis of many metabolites with multiple functions in growth and other biological processes of a living organism. The biosynthesis of amino acids is tightly connected with central carbon, nitrogen and sulfur metabolism. Recent publication of genome sequences for two diatoms Thalassiosira pseudonana and Phaeodactylum tricornutum created an opportunity for extensive studies on the structure of these metabolic pathways. Based on sequence homology found in the analyzed diatomal genes, the biosynthesis of amino acids in diatoms seems to be similar to higher plants. However, one of the most striking differences between the pathways in plants and in diatomas is that the latter possess and utilize the urea cycle. It serves as an important anaplerotic pathway for carbon fixation into amino acids and other N-containing compounds, which are essential for diatom growth and contribute to their high productivity.

Figure 1

The pathway of glycine and two pathways of serine synthesis. A. Glycine and serine synthesis as part of the photorespiration. B. A non-photorespiratory pathway of serine synthesis. Reactions denoted as numbers are catalyzed by following enzymes:(1) ribulose-1,5-bisphosphate carboxylase oxygenase, (2) phosphoglycolate phosphatase, (3) glyoxylate synthase, (4) alanine:glyoxylate aminotransferase / serine:glyoxylate aminotransferase, (5) glycine decarboxylase + serine hydroxymethyl-transferase, (6) hydroxypyruvate reductase, (7) glycerate kinase, (8) 3-phoshoglycerate dehydrogenase, (9) phosphoserine transaminase, (10) phosphoserine phosphatase. Abbreviations used: 3-PGA, 3-phosphoglycerate; RuBP, ribulose-1,5-bisphosphate.

Figure 2

The pathway of cysteine synthesis. Reactions denoted as numbers are catalyzed by following enzymes: (1) ATP sulfurylase, (2) adenosine 5′-phosphosulfate kinase, (3) adenosine 5′-phosphosulfate reductase, (4) 3′-phospho-adenosine 5′-phosphosulfate reductase, (5) sulfite reductase, (6) O-acetyl(thiol)lyase, (7) serine acetyltransferase. Abbreviations used: APS, adenosine 5′-phosphosulfate; PAPS, 3′-phospho-adenosine 5′-phosphosulfate.

Figure 3

Pathways of lysine, methionine and threonine synthesis. Reactions denoted as numbers are catalyzed by following enzymes: (1) aspartate kinase, (2) aspartate semialdehyde dehydrogenase, (3) homoserine dehydrogenase, (4) homoserine kinase, (5) cystathionine-γ-synthase,(6) cystathionine-β-lyase, (7) methionine synthase, (8) threonine synthase, (9) dihydrodipicolinate synthase, (10) dihydrodipicolinate reductase, (11) LL-diaminopimelate aminotransferase, (12) diaminopimelate epimerase, (13) diaminopimelate epimerase, (14) asparagine synthetase, (15) ammonia:aspartate ligase.

Figure 4

Pathways of isoleucine, valine and leucine synthesis. Reactions denoted as numbers are catalyzed by following enzymes: (1) threonine deaminase, (2) 2-aceto-2-hydroxy-butyrate synthase, (3) ketol-acid reductoisomerase, (4) dihydroxy-acid dehydratase, (5) branched-chain amino acid transaminase, (6) 2-isopropylmalate synthase, (7) isopropylmalate isomerase, (8) 3-isopropylmalate dehydrogenase. Abbreviations used: 2-OG, 2-oxoglutarate; spont., spontaneous.

Figure 5

Pathways of aromatic amino acids synthesis. Reactions denoted as numbers are catalyzed by following enzymes: (1) 2-dehydro-3-deoxyphosphoheptonate aldolase, (2) dehydroquinate synthase, (3) 3-dehydroquinate dehydratase, (4) shikimate-NADP oxidoreductase, (5) shikimate kinase, (6) 5-enolpyruvylshikimate-3-phosphate synthase, (7) chorismate synthase, (8) chorismate mutase, (9) prephenate dehydrogenase, (10) phenylalanine:2-oxoglutarate transaminases, (11) phenylalanine 4-monooxygenase, (12) anthranilate synthase, (13) anthranilate phosphoribosyltransferase, (14) phosphoribosylanthranilate isomerase, (15) indole-3-glycerolphosphate synthase, (16) tryptophan synthase.

Figure 6

Pathway of histidine synthesis. Reactions denoted as numbers are catalyzed by the following enzymes: (1) ribose-phosphate diphosphokinase, (2) ATP phosphoribosyltransferase, (3) phosphoribosyl-ATP pyrophosphatase / phosphoribosyl-AMP cyclohydrolase,(4) phosphoribosylformiminoAICAR-P isomerase, (5) imidazole glycerol phosphate synthase, (6) imidazoleglycerol-phosphate dehydratase,(7) enzyme histidinol-phosphate transaminase, (8) histidinol phosphate phosphatase, (9) histidinol dehydrogenase. Abbreviations used: 2-OG, 2-oxoglutarate.

Figure 7

Pathways of arginine and proline synthesis. Reactions denoted as numbers are catalyzed by following enzymes: (1) carbamoyl-phosphate synthase, (2) ornithine carbamoyltransferase, (3) argininosuccinate synthase, (4) argininosuccinate lyase, (5) arginase, (6) N-acetylglutamate syntase (7) N-acetylglutamate kinase, (8) N-acetylglutamyl reductase, (9) acetylornithine transaminase, (10) amidoacylase, (11) urease, (12) ornithine-delta-transaminase,(13) + (14) pyrroline-5-carboxylate synthetase, (15) spontaneous, (16) pyrroline-5-carboxylate reductase.