• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of biochemjBJ Latest papers and much more!
Biochem J. Oct 1, 1999; 343(Pt 1): 115–124.
PMCID: PMC1220531

Pathway alignment: application to the comparative analysis of glycolytic enzymes.


Comparative analysis of metabolic pathways in different genomes yields important information on their evolution, on pharmacological targets and on biotechnological applications. In this study on glycolysis, three alternative ways of comparing biochemical pathways are combined: (1) analysis and comparison of biochemical data, (2) pathway analysis based on the concept of elementary modes, and (3) a comparative genome analysis of 17 completely sequenced genomes. The analysis reveals a surprising plasticity of the glycolytic pathway. Isoenzymes in different species are identified and compared; deviations from the textbook standard are detailed. Several potential pharmacological targets and by-passes (such as the Entner-Doudoroff pathway) to glycolysis are examined and compared in the different species. Archaean, bacterial and parasite specific adaptations are identified and described.

Full Text

The Full Text of this article is available as a PDF (158K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Bork P, Dandekar T, Diaz-Lazcoz Y, Eisenhaber F, Huynen M, Yuan Y. Predicting function: from genes to genomes and back. J Mol Biol. 1998 Nov 6;283(4):707–725. [PubMed]
  • Koonin EV, Tatusov RL, Galperin MY. Beyond complete genomes: from sequence to structure and function. Curr Opin Struct Biol. 1998 Jun;8(3):355–363. [PubMed]
  • Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science. 1997 Oct 24;278(5338):631–637. [PubMed]
  • Goto S, Bono H, Ogata H, Fujibuchi W, Nishioka T, Sato K, Kanehisa M. Organizing and computing metabolic pathway data in terms of binary relations. Pac Symp Biocomput. 1997:175–186. [PubMed]
  • Galperin MY, Brenner SE. Using metabolic pathway databases for functional annotation. Trends Genet. 1998 Aug;14(8):332–333. [PubMed]
  • Meléndez-Hevia E, Waddell TG, Heinrich R, Montero F. Theoretical approaches to the evolutionary optimization of glycolysis--chemical analysis. Eur J Biochem. 1997 Mar 1;244(2):527–543. [PubMed]
  • Tatusov RL, Mushegian AR, Bork P, Brown NP, Hayes WS, Borodovsky M, Rudd KE, Koonin EV. Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli. Curr Biol. 1996 Mar 1;6(3):279–291. [PubMed]
  • Schuster S, Dandekar T, Fell DA. Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends Biotechnol. 1999 Feb;17(2):53–60. [PubMed]
  • Pfeiffer T, Sánchez-Valdenebro I, Nuño JC, Montero F, Schuster S. METATOOL: for studying metabolic networks. Bioinformatics. 1999 Mar;15(3):251–257. [PubMed]
  • Holländer R. Energy metabolism of some representatives of the Haemophilus group. Antonie Van Leeuwenhoek. 1976;42(4):429–444. [PubMed]
  • Stanton TB. Glucose metabolism and NADH recycling by Treponema hyodysenteriae, the agent of swine dysentery. Appl Environ Microbiol. 1989 Sep;55(9):2365–2371. [PMC free article] [PubMed]
  • Ojcius DM, Degani H, Mispelter J, Dautry-Varsat A. Enhancement of ATP levels and glucose metabolism during an infection by Chlamydia. NMR studies of living cells. J Biol Chem. 1998 Mar 20;273(12):7052–7058. [PubMed]
  • Moulder JW. The relation of the psittacosis group (Chlamydiae) to bacteria and viruses. Annu Rev Microbiol. 1966;20:107–130. [PubMed]
  • Pollack JD, Williams MV, McElhaney RN. The comparative metabolism of the mollicutes (Mycoplasmas): the utility for taxonomic classification and the relationship of putative gene annotation and phylogeny to enzymatic function in the smallest free-living cells. Crit Rev Microbiol. 1997;23(4):269–354. [PubMed]
  • Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, Ketchum KA, Klenk HP, Gill S, Dougherty BA, et al. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature. 1997 Aug 7;388(6642):539–547. [PubMed]
  • Podestá FE, Plaxton WC. Plant cytosolic pyruvate kinase: a kinetic study. Biochim Biophys Acta. 1992 Nov 20;1160(2):213–220. [PubMed]
  • Huynen M, Dandekar T, Bork P. Differential genome analysis applied to the species-specific features of Helicobacter pylori. FEBS Lett. 1998 Apr 10;426(1):1–5. [PubMed]
  • Selkov E, Maltsev N, Olsen GJ, Overbeek R, Whitman WB. A reconstruction of the metabolism of Methanococcus jannaschii from sequence data. Gene. 1997 Sep 15;197(1-2):GC11–GC26. [PubMed]
  • Kengen SW, Tuininga JE, de Bok FA, Stams AJ, de Vos WM. Purification and characterization of a novel ADP-dependent glucokinase from the hyperthermophilic archaeon Pyrococcus furiosus. J Biol Chem. 1995 Dec 22;270(51):30453–30457. [PubMed]
  • Pandolfi PP, Sonati F, Rivi R, Mason P, Grosveld F, Luzzatto L. Targeted disruption of the housekeeping gene encoding glucose 6-phosphate dehydrogenase (G6PD): G6PD is dispensable for pentose synthesis but essential for defense against oxidative stress. EMBO J. 1995 Nov 1;14(21):5209–5215. [PMC free article] [PubMed]
  • van der Oost J, Schut G, Kengen SW, Hagen WR, Thomm M, de Vos WM. The ferredoxin-dependent conversion of glyceraldehyde-3-phosphate in the hyperthermophilic archaeon Pyrococcus furiosus represents a novel site of glycolytic regulation. J Biol Chem. 1998 Oct 23;273(43):28149–28154. [PubMed]
  • Angell S, Schwarz E, Bibb MJ. The glucose kinase gene of Streptomyces coelicolor A3(2): its nucleotide sequence, transcriptional analysis and role in glucose repression. Mol Microbiol. 1992 Oct;6(19):2833–2844. [PubMed]
  • Skarlatos P, Dahl MK. The glucose kinase of Bacillus subtilis. J Bacteriol. 1998 Jun;180(12):3222–3226. [PMC free article] [PubMed]
  • Plumbridge J, Vimr E. Convergent pathways for utilization of the amino sugars N-acetylglucosamine, N-acetylmannosamine, and N-acetylneuraminic acid by Escherichia coli. J Bacteriol. 1999 Jan;181(1):47–54. [PMC free article] [PubMed]
  • Bork P, Sander C, Valencia A. Convergent evolution of similar enzymatic function on different protein folds: the hexokinase, ribokinase, and galactokinase families of sugar kinases. Protein Sci. 1993 Jan;2(1):31–40. [PMC free article] [PubMed]
  • Thomson GJ, Howlett GJ, Ashcroft AE, Berry A. The dhnA gene of Escherichia coli encodes a class I fructose bisphosphate aldolase. Biochem J. 1998 Apr 15;331(Pt 2):437–445. [PMC free article] [PubMed]
  • Hughes NJ, Clayton CL, Chalk PA, Kelly DJ. Helicobacter pylori porCDAB and oorDABC genes encode distinct pyruvate:flavodoxin and 2-oxoglutarate:acceptor oxidoreductases which mediate electron transport to NADP. J Bacteriol. 1998 Mar;180(5):1119–1128. [PMC free article] [PubMed]
  • Romano AH, Conway T. Evolution of carbohydrate metabolic pathways. Res Microbiol. 1996 Jul-Sep;147(6-7):448–455. [PubMed]
  • Gebbia JA, Backenson PB, Coleman JL, Anda P, Benach JL. Glycolytic enzyme operon of Borrelia burgdorferi: characterization and evolutionary implications. Gene. 1997 Apr 1;188(2):221–228. [PubMed]
  • Anda P, Gebbia JA, Backenson PB, Coleman JL, Benach JL. A glyceraldehyde-3-phosphate dehydrogenase homolog in Borrelia burgdorferi and Borrelia hermsii. Infect Immun. 1996 Jan;64(1):262–268. [PMC free article] [PubMed]
  • Schmid R, Bernhardt J, Antelmann H, Völker A, Mach H, Völker U, Hecker M. Identification of vegetative proteins for a two-dimensional protein index of Bacillus subtilis. Microbiology. 1997 Mar;143(Pt 3):991–998. [PubMed]
  • Gay P, Delobbe A. Fructose transport in Bacillus subtilis. Eur J Biochem. 1977 Oct 3;79(2):363–373. [PubMed]
  • Macfadyen LP, Dorocicz IR, Reizer J, Saier MH, Jr, Redfield RJ. Regulation of competence development and sugar utilization in Haemophilus influenzae Rd by a phosphoenolpyruvate:fructose phosphotransferase system. Mol Microbiol. 1996 Sep;21(5):941–952. [PubMed]
  • Porras O, Caugant DA, Lagergård T, Svanborg-Edén C. Application of multilocus enzyme gel electrophoresis to Haemophilus influenzae. Infect Immun. 1986 Jul;53(1):71–78. [PMC free article] [PubMed]
  • Hazell SL, Mendz GL. How Helicobacter pylori works: an overview of the metabolism of Helicobacter pylori. Helicobacter. 1997 Mar;2(1):1–12. [PubMed]
  • Yu JP, Ladapo J, Whitman WB. Pathway of glycogen metabolism in Methanococcus maripaludis. J Bacteriol. 1994 Jan;176(2):325–332. [PMC free article] [PubMed]
  • Krishnan G, Altekar W. An unusual class I (Schiff base) fructose-1,6-bisphosphate aldolase from the halophilic archaebacterium Haloarcula vallismortis. Eur J Biochem. 1991 Jan 30;195(2):343–350. [PubMed]
  • Shieh JS, Whitman WB. Pathway of acetate assimilation in autotrophic and heterotrophic methanococci. J Bacteriol. 1987 Nov;169(11):5327–5329. [PMC free article] [PubMed]
  • Vettakkorumakankav N, Danson MJ, Hough DW, Stevenson KJ, Davison M, Young J. Dihydrolipoamide dehydrogenase from the halophilic archaebacterium Haloferax volcanii: characterization and N-terminal sequence. Biochem Cell Biol. 1992 Jan;70(1):70–75. [PubMed]
  • Hsieh PC, Shenoy BC, Samols D, Phillips NF. Cloning, expression, and characterization of polyphosphate glucokinase from Mycobacterium tuberculosis. J Biol Chem. 1996 Mar 1;271(9):4909–4915. [PubMed]
  • O'Brien WE, Bowien S, Wood HG. Isolation and characterization of a pyrophosphate-dependent phosphofructokinase from Propionibacterium shermanii. J Biol Chem. 1975 Nov 25;250(22):8690–8695. [PubMed]
  • Valverde F, Losada M, Serrano A. Functional complementation of an Escherichia coli gap mutant supports an amphibolic role for NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase of Synechocystis sp. strain PCC 6803. J Bacteriol. 1997 Jul;179(14):4513–4522. [PMC free article] [PubMed]

Articles from Biochemical Journal are provided here courtesy of The Biochemical Society


Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...


  • Cited in Books
    Cited in Books
    PubMed Central articles cited in books
  • PubMed
    PubMed citations for these articles

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...