Quantitative Proteomics of Intracellular Campylobacter jejuni Reveals Metabolic Reprogramming
Figure 3
Cellular overview of C. jejuni metabolic pathways.
Metabolic pathways are grouped into different general functional categories as indicated. Protein transporters are located at the double peripheral lines representing the bacterial membrane structure. Within individual pathways, symbols represent metabolites and connecting lines denote respective enzymes that catalyze the inter-conversion of those metabolites. Most enzymes are color-coded in the following fashion: blue indicates mapped proteins in pathways present in the C. jejuni proteome, grey indicates those not found in the annotated genome, bold green represents those proteins whose expression levels were lower at 20 h of infection relative to 2 h of infection, and bold red corresponds to up-regulated proteins at 20 h of infection. Description of individually numbered pathways is as follows: 1. a, flavin biosynthesis; b, methylerythritol phosphate pathway; c, tetrapyrrole biosynthesis; d, ubiquinone-8 biosynthesis; e, di-trans, poly-cis-undecaprenyl phosphate biosynthesis; f, pantothenate biosynthesis I; g, chlorophyllide a biosynthesis I; h, TCA cycle; i, tetrahydrofolate biosynthesis; j, thiamine biosynthesis I; k, pyridoxal 5′-phosphate biosynthesis; l, coenzyme M biosynthesis; m, 6-hydroxymethyl-dihydropterin diphosphate biosynthesis; n, NAD biosynthesis I; o, folate transformations p. phosphate acquisition I; q, NAD phosphorylation and dephosphorylation; r, acyl carrier protein metabolism; s, formyl THF biosynthesis I; t, thioredoxin pathway; u, NAD salvage pathway II; v, biotin biosynthesis; w, menaquinone-8 biosynthesis; x, biotin biosynthesis; y, heme biosynthesis from uroporphyrinogen-III II; z, trans, trans-farnesyl diphosphate biosynthesis; aa, glutathionylspermidine biosynthesis; ab, NAD salvage pathway I; ac, geranyldiphosphate biosynthesis. 2. a, histidine biosynthesis; b, lysine biosynthesis I; c, valine biosynthesis; d, isoleucine biosynthesis I; e, threonine biosynthesis from homoserine; f, homocysteine biosynthesis; g, homoserine biosynthesis; h, ornithine biosynthesis; i, tryptophan biosynthesis; j, proline biosynthesis I; k, S-adenosyl-L-methionine cycle I; l, serine biosynthesis; m, alanine biosynthesis; n, tyrosine biosynthesis I; o, alanine biosynthesis III; p, selenocysteine biosynthesis I; q, glutamate biosynthesis; r, protein citrullination; s, cysteine biosynthesis I; t, L-glutamine biosynthesis II; u, glutamine biosynthesis I; 3. a, palmitate biosynthesis II; b, CMP-KDO biosynthesis I; c, biotin-carboxyl carrier protein assembly; d, fatty acid biosynthesis initiation III; e, CDP-diacylglycerol biosynthesis I; f, fatty acid biosynthesis initiation II; g, cyclopropane fatty acid (CFA) biosynthesis; h, CDP-diacylglycerol biosynthesis II; i, cis-vaccenate biosynthesis; j, phospholipid biosynthesis I; k, stearate biosynthesis II; l, fatty acid elongation-saturated. 4. a, (5R)-carbapenem biosynthesis; b, hyperforin biosynthesis; c, myo-inositol biosynthesis. 5. a, respiration (anaerobic); b, aerobic respiration-electron donor II. 6. a. homolactic fermentation; b. (S)-acetoin biosynthesis; c. (R)-acetoin biosynthesis I d. mixed acid fermentation; e. pyruvate fermentation to acetate; f. pyruvate fermentation to lactate. 7. a, 5-aminoimidazole ribonucleotide biosynthesis I; b, uridine-5′-phosphate biosynthesis c, adenosine nucleotides de novo biosynthesis; d, guanosine nucleotides de novo biosynthesis; e, pyrimidine deoxyribonucleotides de novo biosynthesis; f, salvage pathways of pyrimidine ribonucleotides; g, salvage pathways of guanine, xanthine, and their nucleosides; h, salvage pathways of purine and pyrimidine nucleotides; i, salvage pathways of purine and pyrimidine nucleotides; j, salvage pathways of purine and pyrimidine nucleotides; k, salvage pathways of purine and pyrimidine nucleotides; l, salvage pathways of purine and pyrimidine nucleotides. 8. a, autoinducer AI-2 biosynthesis I; b, PRPP biosynthesis I. 9. ppGpp biosynthesis. 10. a, chorismate biosynthesis I; b, 3-dehydroquinate biosynthesis I. 11. IAA biosynthesis V. 12. putrescine biosynthesis II. 13. a, UDP-N-acetylmuramoyl-pentapeptide biosynthesis I (generic); b, superpathway of KDO2-lipid A biosynthesis; c, peptidoglycan biosynthesis III; d, UDP-N-acetylmuramoyl-pentapeptide biosynthesis III (meso-DAP); e, enterobacterial common antigen biosynthesis; f, O-antigen biosynthesis; g, dTDP-L-rhamnose biosynthesis I; h, UDP-N-acetyl-D-glucosamine biosynthesis I. 14. a, purine degradation II (anaerobic); b, purine degradation III (anaerobic); c, formaldehyde oxidation V (tetrahydrofolate pathway); d, reductive monocarboxylic acid cycle; e, formaldehyde assimilation I (serine pathway). 15. a, aspartate-glutamate-proline degradation; b, tyrosine degradation I; c, arginine degradation IV; d, aspartate degradation II; e, proline degradation II; f, L-serine degradation; g, lysine degradation I; h, glutamine degradation II; i, citrulline degradation; j, proline degradation I; k, phenylalanine degradation (aerobic); l, asparagine degradation I. 16. tRNA charging pathway. 17. a, gluconeogenesis I; b, colanic acid building blocks biosynthesis; c, colanic acid building blocks biosynthesis; d, GDP-mannose biosynthesis; e, ADP-L-glycero-beta-D-manno-heptose biosynthesis; f, CMP-KDO biosynthesis II; g, GDP-glucose biosynthesis; h, GDP-D-rhamnose biosynthesis; i, glycogen degradation I; j, CMP-N-acetylneuraminate biosynthesis II. 18. a, protocatechuate degradation I; b, methylgallate degradation; c, protocatechuate degradation III; d, orthanilate degradation; e, cyanurate degradation; f, anthranilate degradation I (aerobic). 19. a, galactose degradation I; b, glycogen degradation II; c, glucose and glucose-1 phosphate degradation. 20. a, glycolate and glyoxylate degradation I; b, pyruvate fermentation to acetate VII; c, glycolate and glyoxylate degradation II; d, acetate conversion to acetyl-CoA. 21. a, pentose phosphate pathway (non-oxidative branch); b, pentose phosphate pathway (partial). 22. a, glycolysis I b. glycolysis II. 23. a, seed germination protein turnover; b, wound-induced proteolysis I. 24. fatty acid and lipids degradation. 25. a, sulfate activation for sulfonation, b, nitrate reduction III; c, nitrate reduction IV. Open triangles: Amino acids; open squares: carbohydrates; open rhomboids: proteins; vertical ovals: purines; horizontal ovals: pyrimidines; inverted triangles: cofactors; T:tRNAs; open circles: other; closed symbols indicate phosphorylated forms. (Note: this data has been deposited in the BioCyc home page [http://biocyc.org/] where it can be seen in an interactive fashion).