Integrating metabolic pathway fluxes with gene-to-enzyme expression rates

Comparative Biochemistry and Physiology - B Biochemistry and Molecular Biology

Volumn 120, Issue 1, 1998, Pages 17-26

  Hochachka, P W ^a   McClelland, G B ^a   Burness, G P ^a   Staples, J F ^b   Suarez, R K ^b  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Enzyme expression; Gene expression; Isoform expression; Metabolic regulation; Symmorphosis

Indexed keywords

GLYCOLYTIC ENZYME;

ADAPTATION; ENERGY METABOLISM; FEEDBACK SYSTEM; GENE EXPRESSION; GLYCOLYSIS; HUMAN; METABOLIC REGULATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; REVIEW; TRANSCRIPTION REGULATION;

EID: 0031851438     PISSN: 03050491     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0305-0491(98)00019-4     Document Type: Article

References (79)

1. Argiles JM, Lopez-Soriano FJ. The ubiquitin-dependent proteolytic pathway in skeletal muscle: Its role in pathological states. Trends Pharm Sci 1996;17:223-6.
2. Arthur PG, Hogan MC, Wagner PD, Hochachka PW. Modelling the effects of hypoxia on ATP turnover in exercising muscle. J Appl Physiol 1992;73:737-60.
3. Atkinson DE. Cellular Energy Metabolism and its Regulation. New York: Academic Press, 1977.
4. Atkinson DE. Control of Metabolic Processes. New York:Plenum, 1990: 11-27.
5. Bachurski CJ, Theodorakis NG, Coulson RMR, Cleveland DW. An amino-terminal tetrapeptide specifies cotranslational degradation of β-tubulin but not α-tubulin mRNAs. Mol Cell Biol 1994;14:4076-86.
6. Balban RS. Regulation of oxidative phosphorylation in the mammalian cell. Am J Physiol 1990;258:C377-89.
7. Baldwin KM, Winder WW, Terjung RL, Holloszy JO. Glycolytic enzymes in different types of skeletal muscle: Adaptation to exercise. Am J Physiol 1973;225:962-6.
8. Beelman CA, Stevens A, Caponigro G, LaGrandeur TE, Hatfield L, Fortner DW, Parker R. An essential component of the decapping enzyme required for normal rates of mRNA turnover. Nature 1996;382:642-6.
9. Betts DF, Srivastava DK. The rationalization of high enzyme concentrations in metabolic pathways such as glycolysis. J Theor Biol 1991;151:155-67.
10. + ATPase in resting and stimulated electric organ of the electric fish Narcine brasiliensis. J Biol Chem 1991;266:10254-9.
11. + ATPase in Narcine brasiliensis. Proc Natl Acad Sci USA 1990;87:1247-51.
12. Brand MD. Control analysis of energy metabolism in mitochondria. Biochem Soc Trans 1995;23:371-6.
13. Brand MD. Regulation analysis of energy metabolism. J Exp Biol 1997;200:193-202.
14. Brown ED, Wood JM. Conformational change and membrane association of the PutA protein are coincident with reduction of its FAD cofactor for proline. J Biol Chem 1993;268:8972-9.
15. Bryant JA, Ibrhaim A, Brice DC, Fitchet PN, Wang XW, Anderson LE. Does a glycolytic enzyme also participate directly in DNA replication? SEB Abstracts C8 1997;6:107-8.
16. Bunn HF, Poyton RO. Oxygen sensing and molecular adaptation to hypoxia. Physiol Rev 1996;76:839-85.
17. 31P NMR. Fed Proc 1986;45:2915-20.
18. Czyzyk-Kreska MF, Dominski Z, Kole R, Millhorn DE. Hypoxia stimulates binding of a cytoplasmic protein to a pyrimidine-rich sequence in the 3′-untranslated region of rat tyrosine hydroxylase mRNA. J Biol Chem 1994;269:9940-5.
19. Darville MI, Antoine IV, Martens-Stritjhagen JR, Dupriez VI, Rousseau G. An E2F-dependent late-serum-response promoter in a gene that controls glycolysis. Oncogene 1995;11:1509-17.
20. Diamond J, Hammond K. The matches achieved by natural selection between biological capacities and their natural loads. Experientia 1992;48:551-7.
21. Dobson GP, Hochachka PW. Role of glycolysis in adenylate depletion and repletion during work and recovery in teleost white muscle. J Exp Biol 1987;129:125-40.
22. Ebert BL, Gleadle JM, O'Rourke JF, Bartlett SM, Poulton J, Ratcliffe PJ. Isoenzyme-specific regulation of genes involved in energy metabolism by hypoxia: Similarities with the regulation of erythropoietin. Biochem J 1996;313:809-14.
23. Fell DA, Thomas ST. Physiological control of metabolic flux: The requirements for multisite regulation. Biochem J 1995;311:35-9.
24. Fersht A. Enzyme Structure and Mechanism. Reading: Freeman, 1985:1-282.
25. Firth JD, Ebert BL, Ratcliffe PJ. Hypoxic regulation of LDH A: Interaction between hypoxia inducible factor 1 and cAMP response elements. J Biol Chem 1995;270:21021-7.
26. From AHL, Zimmer SD, Michurski SP, Mohanakrishnan P, Ulstad VK, Thomas WJ, Ugurbil K. Regulation of oxidative phosphorylation in the intact cell. Biochemistry 1990;29:3733-43.
27. Gallie DR, Feder JN, Schimke RT, Walbot V. Post-transcriptional regulation in higher eukaryotes: The role of the reporter gene in controlling expression. Mol Gen Genet 1991;228:258-64.
28. Goodridge AG. Dietary regulation of gene expression: Enzymes involved in carbohydrate and lipid metabolism. Annu Rev Nutr 1987;7:157-85.
29. Grabarek Z, Tao T, Gergely J. Molecular mechanism of troponin-C function. J Muscle Res Cell Motil 1992;13:383-93.
30. Guppy M, Hulbert WC, Hochachka PW. Metabolic sources of heat and power in tuna muscles. II. Enzyme and metabolite profiles. J Exp Biol 1979;82:303-20.
31. Harvey WR, Wieczorek H. Animal plasma membrane energization by chemiosmotic H + V ATPases control. J Exp Biol 1997;200:203-16.
32. Hochachka PW. Living Without Oxygen. Cambridge, MA: Harvard University Press, 1980:1-181.
33. Hochachka PW. Muscles and Molecular and Metabolic Machines. Boca Raton, FL: CRC Press, 1994:1-157.
34. Hochachka PW, Matheson GO. Regulation of ATP turnover over broad dynamic muscle work ranges. J Appl Physiol 1992;73:570-5.
35. Hochachka PW, Buck LT, Doll C, Land SC. Unifying theory of hypoxia tolerance: Molecular/metabolic defense and rescue mechanisms for surviving oxygen lack. Proc Natl Acad Sci USA 1996;93:9493-9.
36. Hochstrasser M. Protein degradation or regulation: Ub the judge. Cell 1996;84:813-5.
37. Jiang B-H, Rue E, Wang GL, Roe R, Semenza GL. Dimerization, DNA binding, and transactivation properties of hypoxiainducible factor 1. J Biol Chem 1996;271:17771-8.
38. Kashiwaya Y, Sato K, Tshuchiya N, Thomas S, Fell DA, Veech RL, Passonneau JV. Control of glucose utilization in working perfused rat heart. J Biol Chem 1994;269:25502-14.
39. Kollia P, Fibach E, Najjar SM, Schechter A, Noguchi CT. Modifications of RNA processing modulate the expression of hemoglobin genes. Proc Natl Acad Sci USA 1996;93:5693-8.
40. Kushmerick MJ, Meyer RA, Brown TR. Regulation of oxygen consumption in fast- and slow-twitch muscle. Am J Physiol 1992;263:C598-606.
41. Loughna PT, Brownson C. Two myogenic regulatory factor transcripts exhibit muscle-specific responses to disuse and passive stretch in adult rats. FEBS Lett 1996;390:304-6.
42. 2+ transport and matrix Ca in signal transduction in mammalian tissues. Biochim Biophys Acta 1990;1018:287-91.
43. Molkentin JD, Black BL, Martin JF, Olson EN. Cooperative activation of muscle gene expression by MEF2 and myogenic bHLH proteins. Cell 1995;83:1125-36.
44. Moyes CC, Mathieu-Costello O, Tsuchya N, Filburn CF, Hansford RG. Mitochondrial biogenesis in myogenesis. Physiologist 1996;39:71.
45. Muro-Pastor AM, Maloy S. Proline dehydrogenase activity of the transcriptional repressor PutA is required for induction of the put operon by proline. J Biol Chem 1995;270:9819-27.
46. Murphy BJ, Robin ED, Tapper DP, Wong RJ, Clayton DA. Hypoxic coordinate regulation of mitochondrial enzymes in mammalian cells. Science 1984;223:707-9.
47. Nair KS, Schwenk WF. Factors controlling muscle protein synthesis and degradation. Curr Opin Neurol 1994;7:471-4.
48. Norris AJ, Martin SS, Harita T, Nelson JG, Vollenweider P, Gustafson TA, Mueckler M, Rose DW, Olefsky JM. Evidence for an insulin substrate 1 independent insulin signaling pathway that mediates insulin responsive glucose transporter (GLUT4) translocation. Proc Natl Acad Sci USA 1996;93:8401-6.
49. Parkhouse WS, Dobson GP, Hochachka PW. Control of glycogenolysis in rainbow trout muscle during exercise. Can J Zool 1988;66:345-51.
50. Patel MS, Harris RA. Mammalian α-keto acid dehydrogenase complexes: Gene regulation and genetic defects. FASEB J 1995;9:1161-72.
51. Robin ED, Murphy BJ, Theodore J. Coordinate regulation of glycolysisn by hypoxia in mammalian cells. J Cell Physiol 1984;118:287-90.
52. Rowan AN, Newsholme EA. Changes in the contents of adenine nucleotides and intermediates of glycolysis and the citric acid cycle in flight muscle of the locust upon flight and the relationship to the control of the cycle. Biochem J 1979;178:209-16.
53. Sacktor B. Biochemical adaptations for flight in the insects. Biochem Soc Symp 1976;41:111-31.
54. Semenza GL, Roth PH, Fang H-M, Wang GL. Transcriptional regulation of genes encoding glycolytic enzymes by hypoxia inducible factor 1. J Biol Chem 1994;269:23757-63.
55. Simoneau J-A, Pette D. Species-specific effects of chronic stimulation upon tibialis anterior muscle in mouse, rat, guinea pig, and rabbit. Pflug Arch 1988;412:86-92.
56. Simoneau J-A, Hood DA, Pette D. Species-specific responses in enzyme activities of anaerobic and aerobic energy metabolism to increased contractile activity. Int Series Sports Sci 1990;21:95-104.
57. Srivastava DK, Bernhard SA. Metabolite transfer via enzyme - enzyme complexes. Science 1986;234:1080-6.
58. Staples JF, Suarez RK. Honeybee flight muscle phosphogluco-seisomerase: Matching enzyme capacities to flux requirements at a near-equilibrium reaction. J Exp Biol 1997;200:1247-54.
59. Suarez RK Hummingbird flight: Sustaining the highest massspecific metabolic rates among vertebrates. Experientia 1992;48:565-70.
60. Suarez RK, Lighton JRB, Joos B, Roberts SP, Harrison JF. Energy metabolism, enzymatic flux capacities, and metabolic flux rates in flying honeybees. Proc Natl Acad Sci USA 1996;93:12616-20.
61. Suarez RK, Staples JF, Lighton JRB, West TG. Relationships between enzymatic flux capacities and metabolic flux rates: nonequilibrium reactions in glycolysis. Proc Natl Acad Sci USA accepted for publication, 1997;94:7065-9.
62. Taylor CR, Weibel ER, Weber J-M, Vock R, Hoppeler J, Roberts TJ, Brichon G. Design of the oxygen and substrate pathways. I. Model and strategy to test symmorphosis in a network structure. J Exp Biol 1996;199:1643-9.
63. Taylor CR, Weibel ER, Karas RH, Hoppeler H. Adaptive variation in the mammalian respiratory system in relation to energy demand. Respir Physiol 1987;69:1-127.
64. Taylor CR, Maloiy GMO, Weibel ER, Langman VA, Kamau JMZ, Seeherman HJ, Heglund NC. Design of the mammalian respiratory system. III. Scaling maximum aerobic capacity to body mass: Wild and domestic mammals. Respir Physiol 1981;44:25-37.
65. Thoms S, Fell DA. Design of metabolic control for large flux changes. J Theor Biol 1996;182:285-98.
66. Viru A. Molecular cellular mechanisms of training effects. J Sports Med Phys Fit 1994;34:309-22.
67. Wang GL, Semenza GL. J Biol Chem 1995;270:1230-7.
68. Wang GL, Jiang B-H, Rue EA, Semenza GL. Hypoxia inducible factor 1 is a basic-helix-loop-helix-PAS heterodimer regulated by cellular oxygen tension. Proc Natl Acad Sci USA 1995;92:5510-4.
69. Webster KA, Murphy BJ. Regulation of tissue-specific glycolytic isozyme genes: Coordinate response to oxygen availability in myogenic cells. Can J Zool 1988;66:1046-58.
70. Webster KA, Gunning P, Hardeman E, Wallace DC, Kedes L. Coordinate reciprocal trends in glycolytic and mitochondrial transcript accumulations during the in vitro differentiation of human myoblasts. J Cell Physiol 1990;142:566-73.
71. 31P NMR spectroscopy. J Comp Physiol B 1991;161:247-56.
72. Weibel ER, Taylor CR, Hoppeler H. The concept of symmorphosis: A testable hypothesis of structure-function relationships. Proc Natl Acad Sci USA 1991;88:10357-61.
73. Weibel ER, Taylor CR, Weber J-M, Vock R, Roberts TJ, Hoppeler H. Design of the oxygen and substrate pathways. VII. Different structural limits for oxygen and substrates to muscle and mitochondria. J Exp Biol 1996;199:1699-709.
74. Williams RS, Neufer PD. Regulation of gene expression in skeletal muscle by contractile activity. Handb Physiol Sect 1996;12:1124-50.
75. Zorio DAR, Cheng NN, Blumenthal T, Spieth J. Operons as a common form of chromosomal organization in C. elegans. Nature 1994;372:270-2.
76. Burness GP, Hochachka PW and Moyes CD. Molecular basis of scaling of glycolytic enzymes in fish. FASEB J 1998; A3944.
77. Segal JA, Crawford DL, LDH β expression: the mechanism of altered gene expression in acclimation and evolutionary adaptation. Am J Physiol 1994, 267, R1150-3.
78. Yang TH and Somero GN. Fasting reduces protein and messenger RNA concentrations for lactate dehydrogenase but not for actin in white muscle of scorpion fish (Scorpanena guttata, Teleostei) Mol Marine Biol Biotech 1996a, 153-61.
79. Yang TH and Somero GN. Activity of lactate dehydrogenase but not its concentration of messenger RNA increase with body size in barred sand bass, Paralabrax nebulifer (Teleostei) Biol Bull 1996b; 191, 155-8.