A cryptic plastid and a novel mitochondrial plasmid in Leucomyxa plasmidifera gen. and sp. nov. (Ochrophyta) push the frontiers of organellar biology - PubMed

Figure 5.

Bioinformatic reconstruction of the L. plasmidifera plastid and its main metabolic pathways. The reconstruction is based on the data presented in electronic supplementary material, table S5. For simplicity, all the putative plastid-localized reactions are shown such as to taking place in the plastid stroma, but it is likely that some of them (e.g. the haem synthesis pathway, see main text) occur in the periplastidial space (between the second and third plastid envelope membrane). The pathways are distinguished by different colours of the intermediates and final products. Arrows with solid lines indicate a chemical transformation (reaction), with the respective enzymes catalysing the reaction indicated in ovals adjacent to the arrows (for the meaning of the abbreviations used see below). The crossed arrows in grey (to tryptophan, phenylalanine & tyrosine, galactolipids and cysteine) highlights the apparent lack of these common plastidial biosynthetic branches in L. plasmidifera, whereas the dotted arrow with a question mark leading from 5,10-methylene-THF to 10-formyl-THF indicates that the metabolic link is expected but could not be reconstructed by our analyses. The green question mark at the synthesis of formylmethionyl-tRNA indicates that the process is expected to take place in the L. plasmidifera plastid but not directly supported by results of localization predictions for the respective enzyme (FMT). Arrows with dashed lines indicate transport of the particular compound between cellular compartments (for simplicity, the presumed import of diacylglycerol for SQDG biosynthesis from the ER is not illustrated). The complexes of the molecular machinery for the import of nuclear genome-encoded proteins into the plastid that have at least some of their subunits discernible in the transcriptome data from L. plasmidifera, are illustrated in association with the respective membrane bounding the plastid (SEC61, protein translocon at the ER; SELMA, translocon in the periplastidial membrane; TOC, translocon of the outer envelope membrane; TIC, translocon of the inner envelope membrane). Enzyme abbreviations are as follows. Haem synthesis—HemA, glutamyl tRNA reductase; HemL, glutamate-1-semialdehyde 2,1-aminomutase; HemB, porphobilinogen synthase; HemC, hydroxymethylbilane synthase; HemD, uroporphyrinogen III synthase; HemE, uroporphyrinogen decarboxylase; HemF, coproporphyrinogen III oxidase; HemY, protoporphyrinogen/coproporphyrinogen III oxidase; HemH, protoporphyrin/coproporphyrin ferrochelatase. Tocotrienol synthesis—PAH, phenylalanine-4-hydroxylase; TAT, tyrosine aminotransferase; HPD, 4-hydroxyphenylpyruvate dioxygenase; VTE2, homogentisate phytyltransferase/homogentisate geranylgeranyltransferase; VTE1, tocopherol cyclase; VTE3, MPBQ/MSBQ methytransferase. SQDG (sulphoquinovosyldiacylglycerol) synthesis—UGP2, UTP-glucose-1-phosphate uridylyltransferase; USP, UDP-sugar pyrophosphorylase; PHD1, plastid type UDP-glucose epimerase; PAPSS, 3'-phosphoadenosine 5'-phosphosulfate synthase; CysC, adenylylsulfate kinase; CysH, PAPS reductase; Trx, thioredoxin; TRR, thioredoxin reductase; SQD1, UDP-sulfoquinovose synthase; SQD2, sulfoquinovosyltransferase. Shikimate pathway—DAHP, 3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase; DHQS, 3-dehydroquinate synthase; DHQD, 3-dehydroquinate dehydratase; SDH, shikimate dehydrogenase; SK, shikimate kinase); EPSP, 5-enolpyruvylshikimate-3-phosphate synthetase; CS, chorismate synthase. Folate synthesis—ADCS, 4-amino-4-deoxychorismate synthase; ADCL, 4-amino-4-deoxychorismate lyase; DHPS, dihydropteroate synthase (the activity conferred by the protein FolKP, which may in fact localize to the mitochondrion in L. plasmidifera), DHFS, dihydrofolate synthase (the activity conferred by the protein FolC1). Folate-based one-carbon metabolism—SHMT, serine hydroxymethyltransferase; FMT, methionyl tRNA formyltransferase. GluRS, glutamyl tRNA synthetase; MetRS, methionyl tRNA synthetase. Protein sequences corresponding to the enzymes and additional details are provided in electronic supplementary material, table S5.