Bibliography

Bibliography

1. Adrniraal, S. J., Khosla, C., and Walsh, C. T. (2002). The loading and initial

elongation modules of rifamycin synthetase collaborate to produce mixed

aryl ketide products. Biochemistry 41,5313-5324.

2. Admiraal, S. J., Khosla, C., and Walsh, C. T. (2003). A Switch for the

transfer of substrate between nonribosomal peptide and polyketide modules

of the rifamycin synthetase assembly line. J Am Chern Soc 125, 13664-

13665.

3. Admiraal, S. J., Walsh, C. T., and Khosla, C. CWO 1). The loading module of

rifamycin synthetase is an adenylation-thiolation didomain with substrate

tolerance for substituted benzoates. Biochemistry 40,6116-6123.

4. Alberts, A. W., Chen, J., Kuron, G., Hunt, V., Huff, J., Hoffman, C.,

Rothrock, J., Lopez, M., Joshua, H., Harris, E., et al. (1980). Mevinolin: a

highly potent competitive inhibitor of hydroxymethylglutaryl-coenzyme A

reductase and a cholesterol-lowering agent. Proc Natl Acad Sci USA 77,

3957-3961.

5. Andersen, P., Askgaard, D., Ljungqvist, L., Bennedsen, J., and Heron, I.

(1991). Proteins released from Mycobacterium tuberculosis during growth.

Infect Immun 59, 1905-1910.

6. Anderson, M. S., Bulawa, C. E., and Raetz, C. R. (1985). The biosynthesis of

gram-negative endotoxin. Formation of lipid A precursors from UDP­

GlcNAc in extracts of Escherichia coli. J BioI Chern 260, 15536-15541.

7. Anderson, M. S., and Raetz, C. R. (1987). Biosynthesis of lipid A precursors

in Escherichia coli. A cytoplasmic acyltransferase that converts UDP-N­

acetylglucosamine to UDP-3-0-(R-3-hydroxymyristoyl)-N­

acetylglucosamine. J BioI Chern 262,5159-5169.

8. Ansari, M. Z., Yadav, G., Gokhale, R. S., and Mohanty, D. (2004). NRPS­

PKS: a knowledge-based resource for analysis ofNRPS/PKS megasynthases.

Nucleic Acids Res 32, W405-413.

9. Aparicio, J. F., Molnar, I., Schwecke, T., Konig, A., Haydock, S. F., Khaw,

L. E., Staunton, J., and Leadlay, P. F. (1996). Organization of the

biosynthetic gene cluster for rapamycin in Streptomyces hygroscopicus:

220

Bibliography

analysis of the enzymatic domains in the modular po1yketide synthase. Gene

169,9-16.

10. August, P. R., Tang, L., Yo on, Y. 1., Ning, S., Muller, R., Yu, T. W., Taylor,

M., Hoffmann, D., Kim, C. G., Zhang, x., et at. (1998). Biosynthesis of the

ansamycin antibiotic rifamycin: deductions from the molecular analysis of

the rif biosynthetic gene cluster of Amyco1atopsis mediterranei S699. Chern

BioI 5, 69-79.

11. Austin, M. B., and Noel, J. P. (2003). The chalcone synthase superfamily of

type III po1yketide synthases. Nat Prod Rep 20, 79-110.

12. Azad, A. K., Sirakova, T. D., Fernandes, N. D., and Kolattukudy, P. E.

(1997). Gene knockout reveals a novel gene cluster for the synthesis of a

class of cell wall lipids unique to pathogenic mycobacteria. J BioI Chern 272,

16741-16745.

13. Azad, A. K., Sirakova, T. D., Rogers, L. M., and Kolattukudy, P. E. (1996).

Targeted replacement of the mycocerosic acid synthase gene in

Mycobacterium bovis BCG produces a mutant that lacks mycosides. Proc

Natl Acad Sci USA 93, 4787-4792.

14. Banchio, c., and Gramajo, H. (2002). A stationary-phase acyl-coenzyme A

synthetase of Streptomyces coelico10r A3(2) is necessary for the normal

onset of antibiotic production. App1 Environ Microbio1 68, 4240-4246.

15. Banerjee, A., Dubnau, E., Quemard, A., Ba1asubramanian, V., Urn, K. S.,

Wilson, T., Collins, D., de Lisle, G., and Jacobs, W. R., Jr. (1994). inhA, a

gene encoding a target for isoniazid and ethionamide in Mycobacterium

tuberculosis. Science 263,227-230.

16. Bangera, M. G., and Thomashow, L. S. (1999). Identification and

characterization of a gene cluster for synthesis of the po1yketide antibiotic

2,4-diacety1ph10rog1ucino1 from Pseudomonas fluorescens Q2-87. J Bacterio1

181,3155-3163.

17. Barnes, P. F., Chatterjee, D., Abrams, 1. S., Lu, S., Wang, E., Yamamura, M.,

Brennan, P. J., and Modlin, R. L. (1992). Cytokine production induced by

Mycobacterium tuberculosis lipoarabinomannan. Relationship to chemical

structure. J Immuno1149, 541-547.

221

Bibliography

18. Bellizzi, J. J., 3rd, Widom, J., Kemp, C., Lu, J. Y., Das, A. K., Hofmann, S.

L., and Clardy, J. (2000). The crystal structure of palmitoyl protein

thioesterase 1 and the molecular basis of infantile neuronal ceroid

lipofuscinosis. Proc Natl Acad Sci USA 97, 4573-4578.

19. Benning, M. M., Wesenberg, G., Liu, R, Taylor, K. L., Dunaway-Mariano,

D., and Holden, H. M. (1998). The three-dimensional structure of 4-

hydroxybenzoyl-CoA thioesterase from Pseudomonas sp. Strain CBS-3. J

BioI Chern 273,33572-33579.

20. Berg, P. (1956). Acyl adenylates; an enzymatic mechanism of acetate

activation. J BioI Chern 222,991-1013.

21. Bisang, C., Long, P. F., Cortes, J., Westcott, J., Crosby, J., Matharu, A. L.,

Cox, R 1., Simpson, T. J., Staunton, J., and Leadlay, P. F. (1999). A chain

initiation factor common to both modular and aromatic polyketide synthases.

Nature 401, 502-505.

22. Black, P. N., DiRusso, C. c., Metzger, A. K., and Heimert, T. L. (1992).

Cloning, sequencing, and expression of the fadD gene of Escherichia coli

encoding acyl coenzyme A synthetase. J BioI Chern 267, 25513-25520.

23. Bloch, K., and Vance, D. (1977). Control mechanisms in the synthesis of

saturated fatty acids. Annu Rev Biochem 46, 263-298.

24. Boddy, C. N., Schneider, T. L., Hotta, K., Walsh, C. T., and Khosla~ C.

(2003). Epothilone C macrolactonization and hydrolysis are catalyzed by the

isolated thioesterase domain of epothilone polyketide synthase. J Am Chern

Soc 125, 3428-3429.

25. Bradbury, M. G., and Moreno, C. (1993). Effect of lipoarabinomannan and

mycobacteria on tumour necrosis factor production by different populations

of murine macrophages. Clin Exp Immunol94, 57-63.

26. Brennan, P. 1. (2003). Structure, function, and biogenesis of the cell wall of

Mycobacterium tuberculosis. Tuberculosis (Edinb) 83, 91-97.

27. Brennan, P. J., and Nikaido, H. (1995). The envelope of mycobacteria. Annu

Rev Biochem 64, 29-63.

28. Bruner, S. D., Weber, T., Kohli, R M., Schwarzer, D., Marahiel, M. A.,

Walsh, C. T., and Stubbs, M. T. (2002). Structural basis for the cyclization of

222

Bibliography

the lipopeptide antibiotic surf actin by the thioesterase domain SrITE.

Structure (Camb) 10, 301-310.

29. Buckner, J. S., and Kolattukudy, P. E. (1976). One-step purification and

properties of a two-peptide fatty acid synthetase from the uropygial gland of

the goose. Biochemistry 15, 1948-1957.

30. Buckner, J. S., Kolattukudy, P. E., and Rogers, L. (1978). Synthesis of

multimethyl-branched fatty acids by avian and mammalian fatty acid

synthetase and its regulation by malonyl-CoA decarboxylase in the uropygial

gland. Arch Biochem Biophys 186, 152-163.

31. Buglino, J., Onwueme, K. c., Ferreras, J. A., Quadri, L. E., and Lima, C. D.

(2004). Crystal structure of PapA5, a phthiocerol dimycocerosyl transferase

from Mycobacterium tuberculosis. J BioI Chern 279, 30634-30642. Epub

32004 May 30633.

32. Butler, A. R., Bate, N., and Cundliffe, E. (1999). Impact of thioesterase

activity on tylosin biosynthesis in Streptomyces fradiae. Chern BioI 6, 287-

292.

33. Caffrey, P., Bevitt, D. J., Staunton, J., and Leadlay, P. F. (1992).

Identification of DEBS 1, DEBS 2 and DEBS 3, the multienzyme

polypeptides of the erythromycin-producing polyketide synthase from

Saccharopolyspora erythraea. FEBS Lett 304,225-228.

34. Camacho, L. R., Constant, P., Raynaud, C., Laneelle, M. A., Triccas, J. A.,

Gicquel, B., Daffe, M., and Guilhot, C. (2001). Analysis of the phthiocerol

dimycocerosate locus of Mycobacterium tuberculosis. Evidence that this lipid

is involved in the cell wall permeability barrier. J BioI Chern 276, 19845-

19854.

35. Campbell, J. W., and Cronan, J. E., Jr. (2001). Bacterial fatty acid

biosynthesis: targets for antibacterial drug discovery. Annu Rev Microbiol

55, 305-332.

36. Cane, D. E., and Walsh, C. T. (1999). The parallel and convergent universes

of polyketide synthases and nonribosomal peptide synthetases. Chern BioI 6,

R319-325.

223

Bibliography

37. Cane; D. E., Walsh, C. T., and Khosla, C. (1998). Harnessing the

biosynthetic code: combinations, permutations, and mutations. Science 282,

63-68.

38. Carman, G. M., and Zeimetz, G. M. (1996). Regulation of phospholipid

biosynthesis in the yeast Saccharomyces cerevisiae. J BioI Chern 271, 13293-

13296.

39. Carreras, C. W., Gehring, A. M., Walsh, C. T., and Khosla, C. (1997).

Utilization of enzymatically phosphopantetheinylated acyl carrier proteins

and acetyl-acyl carrier proteins by the actinorhodin polyketide synthase.

Biochemistry 36, 11757-11761.

40. Carreras, C. W., and Khosla, C. (1998). Purification and in vitro

reconstitution of the essential protein components of an aromatic polyketide

synthase. Biochemistry 37,2084-2088.

41. Chan, J., Fan, X. D., Hunter, S. W., Brennan, P. J., and Bloom, B. R. (1991).

Lipoarabinomannan, a possible virulence factor involved in persistence of

Mycobacterium tuberculosis within macrophages. Infect Immun 59, 1755-

1761.

42. Chatterjee, D., Roberts, A D., Lowell, K., Brennan, P. J., and Orme, I. .M.

(1992). Structural basis of capacity oflipoarabinomannan to induce secretion

oftumor necrosis factor. Infect Immun 60,1249-1253.

43. Chiu, H. T., Hubbard, B. K., Shah, A. N., Eide, J., Fredenburg, R. A, Walsh,

C. T., and Khosla, C. (2001). Molecular cloning and sequence analysis of the

complestatin biosynthetic gene cluster. Proc Natl Acad Sci USA 98, 8548-

8553.

44. Cole, S. T., Brosch, R., Parkhill, 1., Garnier, T., Churcher, C., Harris, D.,

Gordon, S. V., Eiglmeier, K., Gas, S., Barry, C. E., 3rd, et al. (1998).

Deciphering the biology of Mycobacterium tuberculosis from the complete

genome sequence. Nature 393, 537-544.

45. Constant, P., Perez, E., Malaga, W., Laneelle, M. A., Saurel, 0., Daffe, M.,

and Guilhot, C. (2002). Role of the pks1511 gene in the biosynthesis of

phenolglycolipids in the Mycobacterium tuberculosis complex. Evidence that

all strains synthesize glycosylated p-hydroxybenzoic methly esters and that

. 224

Bibliography

strains devoid of phenolglycolipids harbor a frameshift mutation in the

pks1511 gene. J BioI Chern 277,38148-38158. Epub 32002 Ju138122.

46. Conti, E., Franks, N. P., and Brick, P. (1996). Crystal structure of firefly

luciferase throws light on a superfamily of adenyl ate-forming enzymes.

Structure 4, 287-298.

47. Conti, E., Stachelhaus, T., Marahiel, M. A., and Brick, P. (1997). Structural

basis for the activation of phenylalanine in the non-ribosomal biosynthesis of

gramicidin S. Embo J 16,4174-4183.

48. Converse, S. E., Mougous, J. D., Leavell, M. D., Leary, J. A., Bertozzi, C. R.,

and Cox, J. S. (2003). MmpL8 is required for sulfolipid-l biosynthesis and

Mycobacterium tuberculosis virulence. Proc Natl Acad Sci USA 100, 6121-

6126. Epub 2003 Apr 6130.

49. Corbett, E. L., Watt, C. J., Walker, N., Maher, D., Williams, B. G.,

Raviglione, M. C., and Dye, C. (2003). The growing burden of tuberculosis:

global trends and interactions with the HIV epidemic. Arch Intern Med 163,

1009-1021.

50. Cortes, J., Haydock, S. F., Roberts, G. A., Bevitt, D. J., and Leadlay, P. F.

(1990). An unusually large multifunctional polypeptide in the erythromycin.,.

producing polyketide synthase of Saccharopolyspora erythraea. Nature 348,

176-178.

51. Cortes, 1., Wiesmann, K. E., Roberts, G. A., Brown, M. 1., Staunton, 1., and

Leadlay, P. F. (1995). Repositioning of a domain in a modular polyketide

synthase to promote specific chain cleavage. Science 268, 1487-1489.

52. Cosma, C. L., Humbert, 0., and Ramakrishnan, L. (2004). Superinfecting

mycobacteria home to established tuberculous granulomas. Nat Immunol 5,

828-835. Epub 2004 Jun 2027 ..

53. Cox, J. S., Chen, B., McNeil, M., and Jacobs, W. R., Jr. (1999). Complex

lipid determines tissue-specific replication of Mycobacterium tuberculosis in

mice. Nature 402, 79-83.

54. Daffe, M. (1989). Further specific triglycosyl phenol phthiocerol diester from

Mycobacterium tuberculosis. Biochim Biophys Acta 1002, 257-260.

225

Bibliography

55. Daffe,M. (1991). Further stereochemical studies of phthiocerol and phenol

phthiocerol in mycobacteria. Res Microbiol142, 405-410.

56. Daffe, M., and Draper, P. (1998). The envelope layers of mycobacteria with

reference to their pathogenicity. Adv Microb Physiol 39, 131-203.

57. Daffe, M., and Laneelle, M. A (1988). Distribution of phthiocerol diester,

phenolic mycosides and related compounds in mycobacteria. J Gen Microbiol

134,2049-2055.

58. Daffe, M., and Laneelle, M. A (1989). Diglycosyl phenol phthiocerol diester

of Mycobacterium leprae. Biochim Biophys Acta 1002, 333-337.

59. Daffe, M., Laneelle, M. A, Lacave, C., and Laneelle, G. (1988).

Monoglycosyldiacylphenol-phthiocerol of Mycobacterium tuberculosis and

Mycobacterium bovis. Biochim Biophys Acta 958,443-449.

60. Daffe, M., Laneelle, M. A, and Puzo, G. (1983). Structural elucidation by

field desorption and electron-impact mass spectrometry of the C-mycosides

isolated from Mycobacterium smegmatis. Biochim Biophys Acta 751,439-

443.

61. Daniel, J., Deb, C., Dubey, V. S., Sirakova, T. D., Abomoelak, B.,

Morbidoni, H. R, and Kolattukudy, P. E. (2004). Induction of a novel class

of diacylglycerol acyltransferases and triacylglycerol accumulation in

Mycobacterium tuberculosis as it goes into a dormancy-like state in culture. J

Bacteriol 186, 5017-5030.

62. Deng, L., Mikusova, K., Robuck, K. G., Scherman, M., Brennan, P. 1., and

McNeil, M. R (1995). Recognition of multiple effects of ethambutol on

metabolism of mycobacterial cell envelope. Antimicrob Agents Chemother

39,694-701.

63. Dessen, A, Quemard, A, Blanchard, J. S., Jacobs, W. R, Jr., and

Sacchettini, J. C. (1995). Crystal structure and function of the isoniazid target

of Mycobacterium tuberculosis. Science 267, 1638-1641.

64. Devedjiev, Y., Dauter, Z., Kuznetsov, S. R, Jones, T. L., and Derewenda, Z.

S. (2000). Crystal structure of the human acyl protein thioesterase I· from a

single X-ray data set to 1.5 A Structure Fold Des 8, 1137-1146.

226

Bibliography

65. Dieckmann, R., Lee, Y. 0., van Liempt, H., von Dohren, H., and Kleinkauf,

H. (1995). Expression of an active adenylate-forming domain of peptide

synthetases corresponding to acyl-CoA-synthetases. FEBS Lett 357,212-216.

66. Dieckmann, R., Pavela-Vrancic, M., Pfeifer, E., von Dohren, H., and

Kleinkauf, H. (1997). The adenylation domain of tyrocidine synthetase I-­

structural and functional role of the interdomain linker region and the

(S/T)GT(T/S)GXPKG core sequence. Eur J Biochem 247, 1074-1082.

67. Dieckmann, R., Pavela-Vrancic, M., von Dahren, H., and Kleinkauf, H.

(1999). Probing the domain structure and ligand-induced conformational

changes by limited proteolysis of tyrocidine synthetase 1. J Mol BioI 288,

129-140.

68. Dirusso, C. C., Connell, E. 1., Faergeman, N. J., Knudsen, J., Hansen, J. K.,

and Black, P. N. (2000). Murine FATP alleviates growth and biochemical

deficiencies of yeast fat! Delta strains. Eur J Biochem 267, 4422-4433.

69. DiRusso, C. c., Heimert, T. L., and Metzger, A. K. (1992). Characterization

of FadR, a global transcriptional regulator of fatty acid metabolism in

Escherichia coli. Interaction with the fadB promoter is prevented by long

chain fatty acyl coenzyme A. J BioI Chern 267, 8685-8691.

70. Dixon, R. A. (1999). Plant natural products: the molecular genetic basis of

biosynthetic diversity. Curr Opin BiotechnollO, 192-197.

71. Doi-Katayama, Y., Yoon, Y. J., Choi, C. Y., Yu, T. W., Floss, H. G., and

Hutchinson, C. R. (2000). Thioesterases and the premature termination of

polyketide chain elongation in rifamycin B biosynthesis by Amycolatopsis

mediterranei S699. J Antibiot (Tokyo) 53, 484-495.

72. Domenech, P., Reed, M. B., Dowd, C. S., Manca, C., Kaplan, G., and Barry,

C. E., 3rd (2004). The role of MmpL8 in sulfatide biogenesis and virulence

of Mycobacterium tuberculosis. J BioI Chern 279, 21257-21265. Epub 22004

Mar 21254.

73. Donadio, S., McAlpine, J. B., Sheldon, P. 1., Jackson, M., and Katz, L.

(1993). An erythromycin analog produced by reprogramming of polyketide

synthesis. Proc Natl Acad Sci USA 90, 7119-7123.

227

Bibliography

74. Donadio, S., Staver, M. J., McAlpine, J. B., Swanson, S. J., and Katz, L.

(1991). Modular organization of genes required for complex polyketide

biosynthesis. Science 252,675-679.

75. Dover, L. G., Cerdeno-Tarraga, A. M., Pallen, M. J., Parkhill, J., and Besra,

G. S. (2004). Comparative cell wall core biosynthesis in the mycolated

pathogens, Mycobacterium tuberculosis and Corynebacterium diphtheriae.

FEMS Microbiol Rev 28, 225-250.

76. Du, L., Sanchez, C., Chen, M., Edwards, D. J., and Shen, B. (2000). The

biosynthetic gene cluster for the antitumor drug bleomycin from

Streptomyces' verticillus ATCC 15003 supporting functional interactions

between nonribosomal peptide synthetases and a polyketide synthase. Chern

BioI 7, 623-642.

77. Dubey, V. S., Sirakova, T. D., Cynamon, M. H., and Kolattukudy, P. E.

(2003). Biochemical function of msl5 (pks8 plus pks17) in Mycobacterium

tuberculosis H37Rv: biosynthesis of monomethyl branched unsaturated fatty

acids. J Bacteriol 185, 4620-4625.

78. Dubey, V. S., Sirakova, T. D., and Kolattukudy, P. E. (2002). Disruption of

ms13 abolishes the synthesis of mycolipanoic and mycolipenic acids required

for polyacyltrehalose synthesis in Mycobacterium tuberculosis H37Rv and

causes cell aggregation. Mol Microbio145,-1451-1459.

79. Duitman, E. H., Hamoen, L. W., Rembold, M., Venema, G., Seitz, H.,

Saenger, W., Bernhard, F., Reinhardt, R., Schmidt, M., Ullrich, C., et at.

(1999). The mycosubtilin synthetase of Bacillus subtilis A TCC6633: a

multifunctional hybrid between a peptide synthetase, an amino transferase,

and a fatty acid synthase. Proc Natl Acad Sci USA 96,13294-13299 ..

80. Ehmann, D. E., Shaw-Reid, C. A., Losey, H. C., and Walsh, C. T. (2000).

The EntF and EntE adenylation domains of Escherichia coli enterobactin

synthetase: sequestration and selectivity in acyl-AMP transfers to thiolation

domain cosubstrates. Proc Natl Acad Sci USA 97, 2509-2514.

81. Ellner, J. J., and Daniel, T. M. (1979). Immunosuppression by mycobacterial

arabinomannan. Clin Exp Immuno135, 250-257.

228

Bibliography

82. Eppelmann, K., Stachelhaus, T., and Marahiel, M. A (2002). Exploitation of

the selectivity-conferring code of nonribosomal peptide synthetases for the

rational design of novel peptide antibiotics. Biochemistry 41,9718-9726.

83. Ernst, J. D. (1998). Macrophage receptors for Mycobacterium tuberculosis.

Infect Immun 66, 1277-128l.

84. Fernandes, N. D., and Kolattukudy, P. E. (1998). A newly identified methyl­

branched chain fatty acid synthesizing enzyme from Mycobacterium

tuberculosis var. bovis BCG. J BioI Chern 273, 2823-2828.

85. Ferrer,1. L., Jez, J. M., Bowman, M. E., Dixon, R. A., and Noel, 1. P. (1999).

Structure of chalcone synthase and the molecular basis of plant polyketide

biosynthesis. Nat Struct BioI 6, 775-784.

86. Finking, R., and Marahiel, M. A (2004). BIOSYNTHESIS OF

NONRIBOSOMAL PEPTIDES. Annual Review of Microbiology 58, 453-

488.

87. Finking, R., Mofid, M. R., and Marahiel, M. A (2004). Mutational analysis

of peptidyl carrier protein and acyl carrier protein synthase unveils residues

involved in protein-protein recognition. Biochemistry 43, 8946-8956.

88. Fitzmaurice, A M., and Kolattukudy, P. E. (1997). Open reading frame 3,

which is adjacent to the mycocerosic acid synthase gene, is expressed as an

acyl coenzyme A synthase in Mycobacterium bovis BCG. J Bacteriol 179,

2608-2615.

89. Fitzmaurice, A M., and Kolattukudy, P. E. (1998). An acyl-CoA synthase

(acoas) gene adjacent to the mycocerosic acid synthase (mas) locus is

necessary for mycocerosyllipid synthesis in Mycobacterium tuberculosis var.

bovis BCG. J BioI Chern 273,8033-8039.

90. Fontana, A, Fassina, G., Vita, C., Dalzoppo, D., Zamai, M., and Zambonin,

,M. (1986). Correlation between sites of limited proteolysis and segmental

mobility in thermolysin. Biochemistry 25, 1847-1851.

91. Fontana, A, Polverino de Laureto,P., De Filippis, V., Scaramella, E., and

Zambonin, M. (1997a). Probing the partly folded states of proteins by limited

proteolysis. Fold Des 2, RI7-26.

229

Bibliography

92. Fontana, A., Zambonin, M., Polverino de Laureto, P., De Filippis, V.,

Clementi, A., and Scaramella, E. (1997b). Probing the conformational state

of apomyoglobin by limited proteolysis. J Mol BioI 266, 223-230.

93. Funa, N., Ohnishi, Y., Fujii, 1., Shibuya, M., Ebizuka, Y., and Horinouchi, S.

(1999). A new pathway for polyketide synthesis in microorganisms. Nature

400,897-899.

94. Garbe, T., Harris, D., Vordermeier, M., Lathigra, R., Ivanyi, J., and Young,

D. (1993). Expression of the Mycobacterium tuberculosis 19-kilodalton

antigen in Mycobacterium smegmatis: immunological analysis and evidence

of glycosylation. Infect Immun 61, 260-267.

95. Garnier, T., Eigl~eier, K., Camus, J. C., Medina, N., Mansoor, H., Pryor, M.,

Duthoy, S., Grondin, S., Lacroix, c., Monsempe, C., et al. (2003). The

complete genome sequence of Mycobacterium bovis. Proc Natl Acad Sci U S

A 100, 7877-7882.

96. Gatfield, J., and Pieters, J. (2000). Essential role for cholesterol in entry of

mycobacteria into macrophages. Science 288, 1647-1650.

97. Gehring, A. M., DeMoll, E., Fetherston, J. D., Mori, 1., Mayhew, G. F.,

Blattner, F. R., Walsh, C. T., and Perry, R. D. (1998a). Iron acquisition in

plague: modular logic in enzymatic biogenesis of yersiniabactin by Yersinia

pestis. Chern BioI 5, 573-586.

98. Gehring, A. M., Mori, 1., Perry, R. D., and Walsh, C. T. (1998b). The

nonribosomal peptide synthetase HMWP2 forms a thiazoline ring during

biogenesis of yersiniabactin, an iron-chelating virulence factor of Yersinia

pestis. Biochemistry 37, 11637-11650.

99. Gehring, A. M., Mori, 1., and Walsh, C. T. (1998c). Reconstitution and

characterization of the Escherichia coli enterobactin synthetase from EntB,

EntE, and EntF. Biochemistry 37, 2648-2659.

100. George, K. M., Chatterjee, D., Gunawardana, G., Welty, D., Hayman, J., Lee,

R., and Small, P. L. (1999). Mycolactone:a polyketide toxin from

Mycobacterium ulcerans required for virulence. Science 283, 854-857.

101. Glickman, M. S., and Jacobs, W. R., Jr. (2001). Microbial pathogenesis of

Mycobacterium tuberculosis: dawn of a discipline. CellI 04,477-485.

230

Bibliography

102. Gokhale, R. S., and Tuteja, D. (2001). Biochemistry ofPolyketide Synthases.

In Biotechnology, Rehm,H.-l. & Reed, G, eds. (Weinheim,): WILEY-VCH,

pp.341-372.

103. Gokhale, R. S., Hunziker, D., Cane, D. E., and Khosla, C. (1999a).

Mechanism and specificity of the terminal thioesterase domain from the

erythromycin polyketide synthase. Chern BioI 6, 117-125.

104. Gokhale, R. S., Tsuji, S. Y., Cane, D. E., and Khosla, C. (1999b). Dissecting

and exploiting intermodular communication inpolyketide synthases. Science

284,482-485.

105. Gordon, 1. I., Duronio, R. 1., Rudnick, D. A., Adams, S. P., and Gokel, G. W.

(1991). Protein N-myristoylation. 1 BioI Chern 266,8647-8650.

106. Goren, M. B. (1970a). Sulfolipid I of Mycobacterium tuberculosis, strain

H37Rv. I. Purification and properties. Biochim Biophys Acta 210, 116-126.

107. Goren, M. B. (1970b). Sulfolipid I of Mycobacterium tuberculosis, strain

H37Rv. II. Structural studies. Biochim Biophys Acta 210,127-138.

108. Gu, S., Chen, 1., Dobos, K. M., Bradbury, E. M., Belisle, 1. T., and Chen, X.

(2003). Comprehensive Proteomic Profiling of the Membrane Constituents of

a Mycobacterium tuberculosis Strain. Mol Cell Proteomics 2, 1284-1296.

Epub 2003 Oct 1286.

109. Gulick, A. M., Starai, V. 1., Horswill,' A. R., Hornick, K. M., and Escalante­

Semerena, 1. C. (2003). The 1.75 A crystal structure of acetyl-CoA

synthetase bound to adenosine-5'-propylphosphate and coenzyme A.

Biochemistry 42, 2866-2873.

110. Haydock, S. F., Aparicio, 1. F., Molnar, I., Schwecke, T., Khaw, L. E.,

Konig, A., Marsden, A. F., Galloway, 1. S., Staunton, 1., and Leadlay, P. F.

(1995). Divergent sequence motifs correlated with the substrate specificity of

(methyl)malonyl-CoA:acyl carrier protein transacylase domains in modular

polyketide synthases. FEBS Lett 374,246-248.

111. Haydock, S. F., Dowson, 1. A., Dhillon, N., Roberts, G. A., Cortes, 1., and

Leadlay, P. F. (1991). Cloning and sequence analysis of genes involved in

erythromycin biosynthesis in Saccharopolyspora erythraea: sequence

231

Bibliography

similarities between EryG and a family of S-adenosylmethionine-dependent

methyltransferases. Mol Gen Genet 230, 120-128.

112. Herrmann, J. L., O'Gaora, P., Gallagher, A., Thole, J. E., and Young, D. B.

(1996). Bacterial glycoproteins: a link between glycosylation and proteolytic

cleavage of a 19 kDa antigen from Mycobacterium tuberculosis. Embo J J 5,

3547~3554.

113. Hertz, R., Magenheim, J., Berman, 1., and Bar-Tana, J. (1998). Fatty acyl­

CoA thioesters are ligands of hepatic nuclear factor-4alpha. Nature 392, 512-

516.

114. Hettema, E. H., and Tabak, H. F. (2000). Transport of fatty acids and

metabolites across the peroxisomal membrane. Biochim BiojJhys Acta J 486,

18-27.

115. Hickman, S. P., Chan, J., and Salgame, P. (2002). Mycobacterium

tuberculosis induces differential cytokine production from dendritic cells and

macrophages with divergent effects on naive T cell polarization. J Immunol

J 68, 4636-4642.

116. Hillgartner, F. B., Salati, L. M., and Goodridge, A. G. (1995). Physiological

and molecular mechanisms involved in nutritional regulation of fatty acid

synthesis. Physiol Rev 75,47-76.

117. Hillson, N. J., Balibar, C. J., and Walsh, C. T. (2004). Catalytically Inactive

Condensation Domain C 1 Is Responsible for the Dimerization of the VibF

Subunit of Vibrio bact in Synthetase. Biochemistry 43, 11344-11351.

118. Holmquist, M. (2000). Alpha/Beta-hydrolase fold enzymes: structures,

functions and mechanisms. CUIT Protein Pept Sci J, 209-235.

119. Hopwood, D. A. (1997). Genetic Contributions to Understanding Polyketide

Synthases. Chern Rev 97, 2465-2498.

120. Hopwood, D. A., and Sherman, D. H. (1990). Molecular genetics of

polyketides and its comparison to fatty acid biosynthesis. Annu Rev Genet

24,37-66.

121. Hu, Z., Pfeifer, B. A., Chao, E., Murli, S., Kealey, 1., Carney, J. R., Ashley,

G., Khosla, C., and Hutchinson, C. R. (2003). A specific role of the

232

Bibliography

Saccharopolyspora erythraea thioesterase II gene in the function of modular

polyketide synthases. Microbiology 149, 2213-2225.

122. Huang, W., Jia, J., Edwards, P., Dehesh, K., Schneider, G., and Lindqvist, Y.

(1998). Crystal structure of beta-keto acyl-acyl carrier protein synthase II

from E.coli reveals the molecular architecture of condensing enzymes. Embo

J 17, 1183-1191.

123. Hunter, S. W., and Brennan, P. J. (1990). Evidence for the presence of a

phosphatidylinositol anchor on the lipoarabinomannan and lipomannan of

Mycobacterium tuberculosis. J BioI Chern 265,9272-9279.

124. Hunter, S. W., Gaylord, H., and Brennan, P. J. (1986). Structure and

antigenicity of the phosphorylated lipopolysaccharide antigens from the

leprosy and tubercle bacilli. J BioI Chern 261,12345-12351.

125. Jackson, R. M., Gabb, H. A., and Sternberg, M. J. (1998). Rapid refinement

of protein interfaces incorporating solvation: application to the docking

problem. J Mol BioI 276, 265-285.

126. Jacobsen,1. R., Cane, D. E., and Khosla, C. (1998a). Spontaneous priming of

a downstream module in 6-deoxyerythronolide B synthase leads to

polyketide biosynthesis. Biochemistry 37, 4928-4934.

127. Jacobsen, 1. R., Hutchinson, C. R., Cane, D. E., and Khosla, C. (1997).

Precursor-directed biosynthesis of erythromycin analogs by an engineered

polyketide synthase. Science 277,367-369.

128. Jacobsen,1. R., Keatinge-Clay, A. T, Cane, D. E., and Khosla, C. (1998b).

Precursor-directed biosynthesis of 12-ethyl erythromycin. Bioorg Med Chern

6,1171-1177.

129. Jez,1. M., Austin, M. B., Ferrer, J., Bowman, M. E., Schroder, 1., and Noel,

J. P. (2000). Structural control of polyketide formation in plant-specific

polyketide synthases. Chern BioI 7,919-930.

130. Jiang, D. W., Ingersoll, R., Myler, P. J., and Englund, P. T (2000).

Trypanosoma brucei: four tandemly linked genes for fatty acyl-CoA

synthetases. Exp Parasitol 96, 16-22.

233

Bibliography

131. Jogl, G., and Tong, L. (2003). Crystal structure of carnitine acetyltransferase

and implications for the catalytic mechanism and fatty acid transport. Cell

112,113-122.

132. Kalscheuer, R, and Steinbuchel, A. (2003). A novel bifunctional wax ester

synthase/acyl-CoA:diacylglycerol acyltransferase mediates wax ester and

triacylglycerol biosynthesis in Acinetobacter calcoaceticus ADPI. J BioI

Chern 278, 8075-8082. Epub 2002 Dec 8026.

133. Kaneda, T. (1977). Fatty acids of the genus Bacillus: an example of

branched-chain preference. Bacteriol Rev 41,391-418.

134. Kaneda, T. (1991). Iso- and anteiso-fatty acids in bacteria: biosynthesis,

function, and taxonomic significance. Microbiol Rev 55, 288-302.

135. Kao, C. M., Katz, L., and Khosla, C. (1994). Engineered biosynthesis of a

complete macro lactone in a heterologous host. Science 265, 509-512.

136. Kao, C. M., Luo, G., Katz, L., Cane, D. E., and Khosla, C. (1995).

Manipulation of macrolide ring size by directed mutagenesis of a modular

polyketide synthase. J Am Chern Soc 117, 9105-9106.

137. Kao, C. M., McPherson, M., McDaniel, R N., Fu, H., Cane, D: E., and

Khosla, C. (1997). Gain of Function Mutagenesis of the Erythromycin

Polyketide Synthase. 2. Engineered Biosynthesis of an Eight-Membered Ring

Tetraketide Lactone. J Am Chern Soc 119, 11339-11340.

138. Karakousis, P. C., Bishai, W. R, and Dorman, S. E. (2004). Mycobacterium

tuberculosis cell envelope lipids and the host immune response. Cell

MicrobioI6,105-116.

139. Kawaguchi, A., Tomoda, H., Okuda, S., and Omura, S. (1981). Fatty acid

synthase from Cephalosporium caerulens. Methods Enzymol 71 PtC, 117-

120.

140. Kealey, 1. T., Liu, L., Santi, D. V., Betlach, M. C., and Barr, P. J. (1998).

Production of a polyketide natural product in nonpolyketide-producing

prokaryotic and eukaryotic hosts. Proc Natl Acad Sci USA 95,505-509.

141. Kearney, G. c., Gates, P. 1., Leadlay, P. F., Staunton, 1., and Jones, R.

(1999). Structural elucidation studies of erythromycins by electro spray

234

Bibliography

tandem mass spectrometry II. Rapid Commun Mass Spectrom 13, 1650-

1656.

142. Keating, T. A., Ehmann, D. E., Kohli, R. M., Marshall" C. G., Trauger, J. W.,

and Walsh, C. T. (2001). Chain termination steps in nonribosomal peptide

synthetase assembly lines: directed acyl-S-enzyme breakdown in antibiotic

and siderophore biosynthesis. Chembiochem 2,99-107.

143. Keating, T. A., Marshall, C. G., and Walsh, C. T. (2000a). Reconstitution and

characterization of the Vibrio cholerae vibriobactin synthetase from VibB,

VibE, VibF, and VibH. Biochemistry 39, 15522-15530.

144. Keating, T. A., Marshall, C. G., and Walsh, C. T (2000b). Vibriobactin

biosynthesis in Vibrio cholerae: VibH is an amide synthase homologous to

nonribosomal peptide synthetase condensation domains. Biochemistry 39,

15513-15521.

145. Keating, T. A., Marshall, C. G., Walsh, C. T., and Keating, A. E. (2002). The

structure of VibH represents nonribosomal peptide synthetase condensation,

cyclization and epimerization domains. Nat Struct BioI 9, 522-526.

146. Keating, T. A., Miller, D. A., and Walsh, C. T. (2000c). Expression,

purification, and characterization of HMWP2, a 229 kDa, six domain protein

subunit of Yersiniabactin synthetase. Biochemistry 39, 4729-4739.

147. Keatinge-Clay, A. T., Maltby, D. A., Medzihradszky, K. F., Khosla, c., and

Stroud, R. M. (2004). An antibiotic factory caught in action. Nat Struct Mol

BioI 11 , 888-893. Epub 2004 Aug 2001.

148. Keatinge-CIay, A. T., Shelat, A. A., Savage, D. F., Tsai, S. C., Miercke, L. 1.,

O'Connell, J. D., 3rd, Khosla, C., and Stroud, R. M. (2003). Catalysis,

specificity, and ACP docking site of Streptomyces co eli color malonyl­

CoA:ACP transacylase. Structure (Camb) 11, 147-154.

149. Keller, u., Kleinkauf, H., and Zocher, R. (1984). 4-Methyl-3-

hydroxyanthranilic acid activating enzyme from actinomycin-producing

Streptomyces chrysomallus. Biochemistry 23, 1479-1484.

150. Kennedy, J., Auclair, K., Kendrew, S. G., Park, c., Vederas, J. c., and

Hutchinson, C. R. (1999). Modulation of polyketide synthase activity by

accessory proteins during lovastatin biosynthesis. Science 284, 1368-1372.

235

Bibliography

151. Khosla, C. (2000). Natural product biosynthesis: a new interface between

enzymology and medicine. J Org Chern 65,8127-8133.

152. Khosla, C., Gokhale, R. S., Jacobsen, J. R., and Cane, D. E. (1999).

Tolerance and specificity of polyketide synthases. Annu Rev Biochem 68,

219-253.

153. Kieser, T., Bibb, M. J., Buttner, M. J., Chater, K. F., and Hopwood, D. A.

(2000). Practical Streptomyces Genetics, second edn (Norwich, The John

Innes Foundation).

154. Kim, B. S., Cropp, T. A., Beck, B. J., Sherman, D. H., and Reynolds, K. A.

(2002). Biochemical evidence for an editing role of thioesterase II in the

biosynthesis of the polyketide pikromycin. J BioI Chern 277, 48028-48034.

155. Knoll, L. J., Johnson, D. R., and Gordon, J. 1. (1995). Complementation of

Saccharomyces cerevisiae strains containing fatty acid activation gene (FAA)

deletions with a mammalian acyl-CoA synthetase. J BioI Chern 270, 10861-

10867.

156. Knudsen, J., Jensen, M. v., Hansen, J. K., Faergeman, N. J., Neergaard, T.

B., and Gaigg, B. (1999). Role of acylCoA binding protein in acylCoA

transport, metabolism and cell signaling. Mol Cell Biochem 192, 95-103.

157. Kolattukudy, P. E., Fernandes, N. D., Azad, A. K., Fitzmaurice, A. M., and

Sirakova, T. D. (1997). Biochemistry and molecular genetics of cell-wall

lipid biosynthesis in mycobacteria. Mol Microbiol 24, 263-270.

158. Kolattukudy, P. E., Poulose, A. J., and Buckner, 1. S. (1981). Fatty acid

synthase from the uropygial gland of goose. Methods Enzymol 71 Pt C, 103-

109.

159. Kwon, H. J., Smith, W. C., Xiang, L., and Shen, B. (2001). Cloning and

heterologous expression of the macrotetrolide biosynthetic gene cluster

revealed a novel polyketide synthase that lacks an acyl carrier protein. J Am

Chern Soc 123, 3385-3386.

160. Lambalot, R. H., Gehring, A. M., Flugel, R. S., Zuber, P., LaCelle, M.,

Marahie!, M. A., Reid, R., Khosla, c., and Walsh, C. T. (1996). A new

enzyme superfamily - the phosphopantetheinyl transferases. Chern BioI 3,

923-936.

236

Bibliography

161. Lamichhane, G., Zignol, M., Blades, N. J., Geiman, D. E., Dougherty, A,

Grosset, J., Broman, K. W., and Bishai, W. R. (2003). A postgenomic

method for predicting essential genes at subsaturation levels of mutagenesis:

application to Mycobacterium tuberculosis. Proc Natl Acad Sci D S A 100,

7213-7218. Epub 2003 May 7229.

162. Lathigra, R., Zhang, Y., Hill, M., Garcia, M. J., Jackett, P. S., and Ivanyi, 1.

(1996). Lack of production of the 19-kDa glycolipoprotein in certain strains

of Mycobacterium tuberculosis. Res Microbio1147, 237-249.

163. Lau, 1., Cane, D. E., and Khosla, C. (2000). Substrate specificity of the

loading didomain of the erythromycin polyketide synthase. Biochemistry 39,

10514-10520.

164. Lau, J., Fu, H., Cane, D. E., and Khosla, C. (1999). Dissecting the role of

acyltransferase domains of modular polyketide synthases in the choice and

stereochemical fate of extender units. Biochemistry 38, 1643-1651.

165. Lawson, D. M., Derewenda, n, Serre, L., Ferri, S., Szittner, R., Wei, Y.,

Meighen, E. A, and Derewenda, Z. S. (1994). Structure of a myristoyl-ACP­

specific thioesterase from Vibrio harveyi. Biochemistry 33, 9382-9388.

166. Leslie, A G. (1990). Refined crystal structure of type III chloramphenicol

acetyltransferase at 1.75 A resolution. J Mol Bio12J3, 167-186.

167. Li, J., Derewenda, D., Dauter, Z., Smith, S., and Derewenda, Z. S. (2000).

Crystal structure of the Escherichia coli thioesterase II, a homolog of the

human Nefbinding enzyme. Nat Struct BioI 7, 555-559.

168. Linne, n, Doekel, S., and Marahiel, M. A. (2001). Portability of

epimerization domain and role of peptidyl carrier protein on epimerization

activity in nonribosomal peptide synthetases. Biochemistry 40, 15824-15834.

169. Linne, D., Schwarzer, D., Schroeder, G. N., and Marahiel, M. A. (2004).

Mutational analysis of a type II thioesterase associated with nonribosomal

peptide synthesis. Eur J Biochem 271,1536-1545.

170. Lopez Marin, L. M., Laneelle, M. A, Prome, D., Daffe, M., Laneelle, G., and

Prome, J. C. (1991). Glycopeptidolipids from Mycobacterium fortuitum: a

variant in the structure ofC-mycoside. Biochemistry 30, 10536-10542.

237

Bibliography

171. Lowry, O. H., Rosebrough, N. J., Farr, A L., and Randall, R. J. (1951).

Protein measurement with the Folin phenol reagent. J BioI Chern 193, 265-

275.

172. Lukacin, R., Springob, K., Urbanke, C., Ernwein, C., Schroder, G., Schroder,

J., and Matern, U. (1999). Native acridone synthases I and II from Ruta

graveolens L. form homodimers. FEBS Lett 448, 135-140.

173. Lynen, F. (1980). On the structure of fatty acid synthetase of yeast. Eur J

Biochem 112, 431-442.

174. MacNeil, D. J., Gewain, K. M., Ruby, C. L., Dezeny, G., Gibbons, P. H., and

MacNeil, T. (1992). Analysis of Streptomyces avermitilis genes required for

avermectin biosynthesis utilizing a novel integration vector. Gene 111, 61-68.

175. Marsden, A F., Caffrey, P., Aparicio, J. F., Loughran, M. S;, Staunton, J.,

and Leadlay, P. F. (1994). Stereospecific acyl transfers on the erythromycin­

producing polyketide synthase. Science 263,378-380.

176. Marsden, A F. n. A., Wilkinson, B., Cortés, J. u. s., Dunster, N. J.,

Staunton, J., and Leadlay, P. F. (1998). Engineering Broader Specificity into

an Antibiotic-Producing Polyketide Synthase. Science 279, 199-202.

177. Marshall, C. G., Hillson, N. J., and Walsh, C. T. (2002). Catalytic mapping of

the vibriobactin biosynthetic enzyme VibF. Biochemistry 41,244-250.

178. Martin, J. F., Liras, P., and Demain, A L. (1978). ATP and adenyl ate energy

. charge during phosphate-mediated control of antibiotic synthesis. Biochem

Biophys Res Commun 83, 822-828.

179. May, J. J., Kessler, N., Marahiel, M. A, and Stubbs, M. T. (2002). Crystal

structure of DhbE, an archetype for aryl acid activating domains of modular

nonribosomal peptide synthetases. Proc Nati Acad Sci USA 99, 12120-

12125.

180. McDaniel, R., Ebert-Khosla, S., Hopwood, D. A., and Khosla, C. (1993).

Engineered biosynthesis of novel polyketides. Science 262, 1546-1550.

181. McDaniel, R., Kao, C. M., Hwang, S. J., and Khosla, C. (1997). Engineered

intermodular and intramodular polyketide synthase fusions. Chern BioI 4,

667-674.

238

Bihliography

182. McDaniel, R., Thamchaipenet, A, Gustafsson, C., Fu, H., Betlach, M., and

Ashley, G. (1999). Multiple genetic modifications of the erythromycin

polyketide synthase to produce a library of novel "unnatural" natural

products. Proc Natl Acad sCi USA 96, 1846-185l.

183. Merson-Davies, L. A, and Cundliffe, E. ('1994). Analysis of five tylosin

biosynthetic genes from the tyllBA region of the Streptomyces fradiae

genome. Mol Microbiol13, 349-355.

184. Mofid, M. R., Marahiel, M. A, Ficner, R.,. and Reuter, K. (1999).

Crystallization and preliminary crystallographic studies of Sfp: a

phosphopantetheinyl transferase of modular peptide synthetases. Acta

Crystallogr D BioI Crystallogr 55,1098-1100.

185. Mootz, H. D., and Marahiel, M. A (1997). The tyrocidine biosynthesis

operon of Bacillus brevis: complete nucleotide sequence and biochemical

characterization of functional internal adenylation domains. J Bacteriol 179,

6843-6850.

186. Moreno, C., Mehlert, A, and Lamb, J. (1988). The inhibitory effects of

mycobacterial lipoarabinomannan and polysaccharides upon polyclonal and

monoclonal human T cell proliferation. Clin Exp Immunol 74,206-210.

187. Nau, G. J., Richmond, 1. F., Schlesinger, A., Jennings, E. G., Lander, E. S.,

and Young, R. A (2002). Human macrophage activation programs induced

by bacterial pathogens; Proc Natl Acad Sci USA 99, 1503-1508.

188. Ng, V., Zanazzi, G., Timpl, R., Talts, J. F., Salzer, J. L., Brennan, P. J., and

Rambukkana, A. (2000). Role of the cell wall phenolic glycolipid-1 in the

peripheral nerve predilection of Mycobacterium leprae. Cell 1 03, 511-524.

189. Noss, E. H., Harding, C. V., and Boom, W. H. (2000). Mycobacterium

tuberculosis inhibits MHC class II antigen processing in murine bone marrow

macrophages. Cell Immunol201, 63-74.

190. O'Hagan, D. (1993). Biosynthesis of fatty acid and polyketide metabolites.

Nat Prod Rep 10, 593-624.

191. Oliynyk, M., Brown, M. J., Cortes, J., Staunton, J., and Leadlay, P. F. (1996).

A hybrid modular polyketide synthase obtained by domain swapping. Chern

BioI 3, 833-839.

239

Bibliography

192. Omura, S. (1976). The antibiotic cerulenin, a novel tool for biochemistry as

an inhibitor of fatty acid synthesis. Bacteriol Rev 40,681-697 ..

193. Onwueme, K. C., Ferreras, 1. A., Buglino, J., Lima, C. D., and Quadri, L. E.

(2004). Mycobacterial polyketide-associated proteins are acyltransferases:

proof of principle with Mycobacterium tuberculosis PapAS. Proc Natl Acad

Sci USA 101, 4608-4613. Epub 2004 Mar 4618.

194. Ortalo-Magne, A., Andersen, A. B., and Daffe, M. (1996a). The outermost

capsular arabinomannans and other mannoconjugates of virulent and

avirulent tubercle bacilli. Microbiology 142 ( Pt 4),927-935.

195. Ortalo-Magne, A., Dupont, M. A., Lemassu, A., Andersen, A. B., Gounon,

P., and Daffe, M. (1995). Molecular composition of the outermost capsular

material of the tubercle bacillus. Microbiology 141 (Pt 7), 1609-1620.

196. Ortalo-Magne, A., Lemassu, A., Laneelle, M. A., Bardou, F., Silve, G.,

Gounon, P., Marchal, G., and Daffe, M. (1996b). Identification of the

surface-exposed lipids on the cell envelopes of Mycobacterium tuberculosis

and other mycobacterial species. J Bacteriol178, 456-461.

197. Paniego, N. B., Zuurbier, K. W., Fung, S. Y., van der Heijden, R., Scheffer,

J. J., and Verpoorte, R. (1999). Phlorisovalerophenone synthase, a novel

polyketide synthase from hop (Humulus lupulus L.) cones. Eur J Biochem

262,612-616.

198. Payne, D. J. (2004). The potential of bacterial fatty acid biosynthetic

enzymes as a source of novel antibacterial agents. Drug News Perspect 17,

187-194.

199. Pelludat, C., Rakin, A., Jacobi, C. A., Schubert, S., and Heesemann, 1.

(1998). The yersiniabactin biosynthetic gene cluster of Yersinia

enterocolitica: organization and siderophore-dependent regulation. J

Bacteriol180, 538-546.

200. Perez, E., Constant, P., Laval, F., Lemassu, A., Laneelle, M. A., Daffe, M.,

and Guilhot, C. (2004). Molecular dissection of the role of two

methyltransferases in the biosynthesis of phenolglycolipids and phthiocerol

dimycoserosate in the mycobacterium tuberculosis complex. J BioI Chern 3,

3.

240

Bihliography

201. Pfeifer, B. A., Admiraal, S. J., Gramajo, H., Cane, D. E., and Khosla, C.

(2001). Biosynthesis of complex polyketides in a metabolically engineered

strain of E. coli. Science 291, 1790-1792.

202. Pieper, R., Haese, A., Schroder, W., and Zocher, R. (1995a). Arrangement of

catalytic sites in the multifunctional enzyme enniatin synthetase. Eur J

Biochem 230, 119-126.

203. Pieper, R., Luo, G., Cane, D. E., and Khosla, C. (1995b). Cell-free synthesis

of polyketides by recombinant erythromycin polyketidesynthases. Nature

378,263-266.

204. Pieters, 1., and Gatfield, J. (2002). Hijacking the host: survival of pathogenic

mycobacteria inside macrophages. Trends Microbio110, 142-146.

205. Polverino de Laureto, P., De Filippis, V., Di Bello, M., Zambonin, M., and

Fontana, A. (1995). Probing the molten globule state of alpha-lactalbumin by

limited proteolysis. Biochemistry 34, 12596-12604.

206. Polverino de Laureto, P., Frare, E., Gottardo, R., Van Dael, H., and Fontana,

A. (2002)., Partly folded states of members of the lysozyme/lactalbumin

superfamily: a comparative study by circular dichroism spectroscopy and

limited proteolysis. Protein Sci 11, 2932-2946.

207. Polverino de Laureto, P., Taddei, N., Frare, E., Capanni, C., Costantini, S.,

Zurdo, J., Chiti, F., Dobson, C. M., and Fontana, A. (2003). Protein

aggregation and amyloid fibril formation by an SH3 domain probed by

limited proteolysis. J Mol BioI 334, 129-141.

208. Portevin, D., De Sousa-D'Auria, c., Houssin, C., Grimaldi, c., Chami, M.,

Daffe, M., and Guilhot, C. (2004). A polyketide synthase catalyzes the last

condensation step of mycolic acid biosynthesis in mycobacteria and related

organisms. Proc Natl Acad Sci USA 101, 314-319. Epub 2003 Dec 2026.

209. Pudles, 1., and Lederer, E. (1954). [Isolation and chemical constitution of

coryno-mycolenic acid and of two ketones from lipids of the diphtheria

bacillus.]. Bull Soc Chim BioI (Paris) 36, 759-777.

210. Quadri, L. E., Weinreb, P. H., Lei, M., Nakano, M. M., Zuber, P., and Walsh,

C. T. (1998). Characterization of Sfp, a Bacillus subtilis phosphopantetheinyl

241

Bibliography

transferase for peptidyl carrier protein domains m peptide synthetases.

Biochemistry 37, 1585-1595.

211. Quemard, A., Sacchettini, 1. C., Dessen, A., Vilcheze, c., Bittman, R,

Jacobs, W. R., Jr., and Blanchard, J. S. (1995). Enzymatic characterization of

the target for isoniazid in Mycobacterium tuberculosis. Biochemistry 34,

8235-8241.

212. Rainwater, D. L., and Kolattukudy, P. E. (1983). Synthesis of mycocerosic

acids from methylmalonyl coenzyme A· by cell-free extracts of

Mycobacterium tuberculosis var. bovis BCG. J BioI Chern 258, 2979-2985.

213. Rainwater, D. L., and Kolattukudy, P. E. (1985). Fatty acid biosynthesis in

Mycobacterium tuberculosis var. bovis Bacillus Calmette-Guerin.

Purification and characterization of a novel fatty acid synthase, mycocerosic

acid synthase, which elongates n-fatty acyl-CoA with methylmalonyl-CoA. J

BioI Chern 260,616-623.

214. Reed, M. B., Domenech, P., Manca, C., Su, H., Barczak, A. K., Kreiswirth,

B. N., Kaplan, G., and Barry, C. E., 3rd (2004). A glycolipid of hyper virulent

tuberculosis strains that inhibits the innate immune response. Nature 431, 84-

87.

215. Reeves, C. D., Murli, S., Ashley, G. W., Piagentini, M., Hutchinson, C. R.,

and McDaniel, R. (2001). Alteration of the substrate specificity of a modular

polyketide synthase acyltransferase domain through site-specific mutations.

Biochemistry 40, 15464-15470.

216. Reimmann, C., Patel, H. M., Serino, L., Barone, M., Walsh, C. T., and Haas,

D. (2001). Essential PchG-dependent reduction in pyochelin biosynthesis of

Pseudomonas aeruginosa. J Bacteriol183, 813-820.

217. Reimmann, C., Patel, H. M., Walsh, C. T., and Haas, D. (2004). PchC

thioesterase optimizes nonribosomal biosynthesis of the peptide siderophore

pyochelin in Pseudomonas aeruginosa. J Bacteriol186, 6367-6373.

218. Reuter, K., Mofid, M. R., Marahiel, M. A., and Ficner, R (1999). Crystal

structure of the surf actin synthetase-activating enzyme sfp: a prototype of the

4'-phosphopantetheinyl transferase superfamily. Embo J 18, 6823-6831.

242

Bihliography

219. Rindi, L., Bonanni, D., Lari, N., and Garzelli, C. (2004). Requirement of

gene fadD33 for the growth of Mycobacterium tuberculosis in a hepatocyte

cell line. New Microbiol27, 125-131.

220. Rindi, L., Fattorini, L., Bonanni, D., Iona, E., Freer, G., Tan, D., Deho, G.,

Orefici, G., and Garzelli, C. (2002). Involvement of the fadD33 gene in the

growth of Mycobacterium tuberculosis in the liver of BALB/c mice.

Microbiology 148, 3873-3880.

221. Rock, C. 0., and Cronan, J. E. (1996). Escherichia coli as a model for the

regulation of dissociable (type II) fatty acid biosynthesis. Biochim Biophys

Acta 1302, 1-16.

222. Romain, F., Laqueyrerie, A., Militzer, P., Pescher, P., Chavarot, P.,

Lagranderie, M., Auregan, G., Gheorghiu, M., and Marchal, G.(1993).

Identification of a Mycobacterium bovis BCG 45/47-kilodalton antigen

complex, an immunodominant target for antibody response after

immunization with living bacteria. Infect Immun 61, 742-750.

223. Rossler, H., Rieck, C., Delong, T., Boja, u., and Schweizer, E. (2003).

Functional differentiation and selective inactivation of multiple

Saccharomyces cerevisiae genes involved in very-long-chain fatty acid

synthesis. Mol Genet Genomics 269, 290-298.

224. Rousseau, C., Neyrolles, 0., Bordat, Y., Giroux, S., Sirakova, T. D., Prevost,

M. C., Kolattukudy, P. E., Gicquel, B., and Jackson, M. (2003a). Deficiency

in mycolipenate- and mycosanoate-derived acyltrehaloses enhances early

interactions of Mycobacterium tuberculosis with host cells. Cell Microbiol 5,

405-415.

225. Rousseau, C., Sirakova, T. D., Dubey, V. S., Bordat, Y., Kolattukudy, P. E.,

Gicquel, B., and Jackson, M. (2003b). Virulence attenuation of two Mas-like

polyketide synthase mutants of Mycobacterium tuberculosis. Microbiology

149, 1837-1847.

226. Routaboul, 1. M., Benning, C., Bechtold, N., Caboche, M., and Lepiniec, L.

(1999). The TAG 1 locus of Arabidopsis encodes for a diacylglycerol

acyltransferase. Plant Physiology and Biochemistry 37, 831-840.

243

Bibliography

227. Russell, D. G., Mwandumba, H. C., and Rhoades, E. E. (2002).

Mycobacterium and the coat of many lipids. J Cell Biol158, 421-426.

228. Sambrook, 1., Fritsch, E. F., and Maniatis, T. (1989). Molecular Cloning: A

Laboratory Manual, Second edn (New York, Cold Spring Harbor Laboratory

Press).

229. Sankaranarayanan, R, Saxena, P., Marathe, U. B., Gokhale, R. S.,

Shanmugam, V. M., and Rukmini, R (2004). A novel tunnel III

mycobacterial type III polyketide synthase reveals the structural basis for

generating diverse metabolites. Nat Struct Mol BioI 11 , 894-900.

230. Sassetti, C. M., Boyd, D. H., and Rubin, E. J. (2001). Comprehensive

identification of conditionally essential genes in mycobacteria. Proc Natl

Acad Sci USA 98, 12712-12717. Epub 12001 Oct 12716.

231. Sassetti, C. M., and Rubin, E. 1. (2003). Genetic requirements for

mycobacterial survival during infection. Proc Natl Acad Sci USA 100,

12989-12994. Epub 12003 Oct 12920.

232. Saxena, P., Yadav, G., Mohanty, D., and Gokhale, R. S. (2003). A new

family of type III polyketide synthases in Mycobacterium tuberculosis. J BioI

Chern 278,44780-44790.

233. Schaeffer, M. L., Agnihotri, G., Volker, c., Kallender, H., Brennan, P. J., and

Lonsdale, J. T. (2001). Purification and biochemical characterization of the

Mycobacterium tuberculosis beta-keto acyl-acyl carrier protein synthases

KasA and KasB. J BioI Chern 276,47029-47037.

234. Schlesinger, L. S., and Horwitz, M. A (1991). Phenolic glycolipid-l of

Mycobacterium leprae binds complement component C3 in serum and

mediates phagocytosis by human monocytes. J Exp Med 174, 1031-1038.

235. Schneider, A, and Marahiel, M. A (1998). Genetic evidence "for a role of

thioesterase domains, integrated in or associated with peptide synthetases, in

non-ribosomal peptide biosynthesis in Bacillus subtilis. Arch Microbiol 169,

404-410.

236. Schneider, R, Brors, B., Massow, M., and Weiss, H. (1997). Mitochondrial

fatty acid synthesis: a relic of endosymbiontic origin and a specialized means

for respiration. FEBS Lett 407,249-252.

244

Bibliography

237. Schroder, J., and Schroder, G. (1990). Stilbene and chalcone synthases:

related enzymes with key functions in plant-specific pathways. Z Naturforsch

[C] 45, 1-8.

238. Schwarzer, D., Mootz, H. D., Linne, u., and Marahiel, M. A. (2002).

Regeneration of misprimed nonribosomal peptide synthetases by type II

thioesterases. Proc Natl Acad Sci USA 99, 14083-14088. Epub 12002 Oct

14016.

239. Shockey, J. M., Fulda, M. S., and Browse, J. (2003). Arabidopsis contains a

large superfamily of acyl-activating enzymes. Phylogenetic and biochemical

analysis reveals a new class of acyl-coenzyme a synthetases. Plant Physiol

132, 1065-1076.

240. Shockey, J. M., Fulda, M. S., and Browse, J. A. (2002). Arabidopsis contains

nine long-chain acyl-coenzyme a synthetase genes that participate in fatty

acid and glycerolipid metabolism. Plant Physiol129, 1710-1722.

241. Silakowski, B., Schairer, H. u., Ehret, H., Kunze, B., Weinig, S., Nordsiek,

G., Brandt, P., Blocker, H., Hofie, G., Beyer, S., and Muller, R. (1999). New

lessons for combinatorial biosynthesis from myxobacteria. The myxothiazol

biosynthetic gene cluster of Stigmatella aurantiaca DW4/3-l. J BioI Chern

274,37391-37399.

242. Sirakova, T. D., Dubey, V. S., Cynamon, M. H., and Kolattukudy, P. E.

(2003a). Attenuation of Mycobacterium tuberculosis by disruption of a mas­

like gene or a chalcone synthase-like gene, which causes deficiency III

dimycocerosyl phthiocerol synthesis. J Bacteriol185, 2999-3008.

243. Sirakova, T. D., Dubey, V. S., Kim, H. 1., Cynamon, M. H., and Kolattukudy,

P. E. (2003b). The largest open reading frame (pksI2) in the Mycobacterium

tuberculosis genome is involved in pathogenesis and dimycocerosyl

phthiocerol synthesis. Infect Immun 71, 3794-380 l.

244. Sirakova, T. D., Thirumala, A. K., Dubey, V. S., Sprecher, H., and

Kolattukudy, P. E. (2001). The Mycobacterium tuberculosis pks2 gene

encodes the synthase for the hepta- and octamethyl-branched fatty acids

required for sulfolipid synthesis. J BioI Chern 276, 16833-16839.

245

Bibliography

245. Sly, L. M., Bingley-Wilson, S. M., Reiner, N. E., and McMaster, W. R.

(2003). Survival of Mycobacterium tuberculosis in host macrophages

involves resistance to apoptosis dependent upon induction of antiapoptotic

Bel-2 family member Mel-I. J Immunol170, 430-437.

246. Smith, S. (1994). The animal fatty acid synthase: one gene, one polypeptide,

seven enzymes. Faseb J 8, 1248-1259.

247. Smith, S., Witkowski, A., and Joshi, A. K. (2003). Structural and functional

organization ofthe animal fatty acid synthase. Prog Lipid Res 42, 289-317.

248. Stachelhaus, T., Buser, A., and Marahiel, M. A. (1996). Biochemical

characterization of peptidyl carrier protein (PCP), the thiolation domain of

multifunctional peptide synthetases. Chern BioI 3, 913 -921.

249. Stachelhaus, T., Mootz, H. D., Bergendahl, V., and Marahiel, M. A. (1998).

Peptide bond formation in nonribosomal peptide biosynthesis. Catalytic role

of the condensation domain. J BioI Chern 273, 22773-2278 I.

250. Stachelhaus, T., Mootz, H. D., and Marahiel, M. A. (1999). The specificity­

conferring code of adenylation domains in nonribosomal peptide synthetases.

Chern BioI 6, 493-505.

251. Stachelhaus, T., and Walsh, C. T. (2000). Mutational analysis of the

epimerization domain in the initiation module PheA TE of gramicidin S

synthetase. Biochemistry 39, 5775-5787.

252. Staunton, J., Caffrey, P., Aparicio, J. F., Roberts, G. A., Beth<;ll, S. S., and

Leadlay, P. F. (1996). Evidence for a double-helical structure for modular

polyketide synthases. Nat Struct Bioi 3, 188-192.

253. Stinear, T. P., Mve-Obiang, A., Small, P. L., Frigui, W., Pryor, M. J., Brosch,

R., Jenkin, G. A., Johnson, P. D., Davies, J. K., Lee, R. E., et al. (2004).

Giant plasmid-encoded polyketide synthases produce the macrolide toxin of

Mycobacterium ulcerans. Proc Natl Acad Sci USA 101, 1345-1349. Epub

2004 Jan 1321.

254. Suo, Z., Chen, H., and Walsh, C. T. (2000). Acyl-CoA hydrolysis by the high

molecular weight protein 1 subunit of yersiniabactin synthetase: mutational

evidence for a cascade of four acyl-enzyme intermediates during hydrolytic

editing. Proc Natl Acad Sci USA 97, 14188-14193.

246

Bibliography

255. Suo, Z., Tseng, C. C., and Walsh, C. T. (2001). Purification, priming, and

catalytic acylation of carrier protein domains in the polyketide synthase and

nonribosomal peptidyl synthetase modules of the HMWPI subunit of

yersiniabactin synthetase. Proc Natl Acad Sci USA 98,99-104.

256. Takayama, K., Armstrong, E. L., Kunugi, K. A., and Kilburn, J. O. (1979).

Inhibition by ethambutol of mycolic acid transfer into the cell wall of

Mycobacterium smegmatis. Antimicrob Agents Chern other 16, 240-242.

257. Takayama, K., and Kilburn, J. O. (1989). Inhibition of synthesis of

arabinogalactan by ethambutol in Mycobacterium smegmatis. Antimicrob

Agents Chemother 33, 1493-1499.

258. Ting, L. M., Kim, A. C., Cattamanchi, A., and Ernst, J. D. (1999).

Mycobacterium tuberculosis inhibits IFN-gamma transcriptional responses

without inhibiting activation of STAT 1. J Immunol163, 3898-3906.

259. Tosato, V., Albertini, A. M., Zotti, M., Sonda, S., and Bruschi, C. V. (1997).

Sequence completion, identification and definition of the fengycin operon in

Bacillus subtilis 168. Microbiology 143, 3443-3450.

260. Trauger, J. W., Kohli, R M., Mootz, H. D., Marahiel, M. A., and Walsh, C.

T. (2000). Peptide cyclization catalysed by the thioesterase domain of

tyrocidine synthetase. Nature 407, 215-218.

261. Trivedi, O. A., Arora, P., Sridharan, V., Tickoo, R, Mohanty, D., and

Gokhale, R S. (2004). Enzymic activation and transfer of fatty acids as acyl­

adenylates in mycobacteria. Nature 428, 441-445.

262. Tsai, S. c., Lu, H., Cane, D. E., Khosla, C., and Stroud, R. M. (2002).

Insights into channel architecture and substrate specificity from crystal

structures of two macro cycle-forming thioesterases of modular polyketide

synthases. Biochemistry 41, 12598-12606.

263. Tsai, S. C., Miercke, L. J., Krucinski, J., Gokhale, R, Chen, J. C., Foster, P.

G., Cane, D. E., Khosla, C., and Stroud, R. M. (2001). Crystal structure of the

macro cycle-forming thioesterase domain of the erythromycin polyketide

synthase: versatility from a unique substrate channel. Proc Natl Acad Sci US

A 98, 14808-14813.

247

Bibliography

264. Walsh, C. T. (2004). Polyketide and nonribosomal peptide antibiotics:

modularity and versatility. Science 303, 1805-1810.

265. Walsh, C. T., Chen, H., Keating, T. A., Hubbard, B. K, Losey, H. C., Luo,

L., Marshall, C. G., Miller, D. A., and Patel, H. M. (2001). Tailoring

enzymes that modify nonribosomal peptides during and after chain

elongation on NRPS assembly lines. Curr Opin Chern BioI 5, 525-534.

266. Watanabe, K, Rude, M. A., Walsh, C. T., and Khosla, C. (2003). Engineered

biosynthesis of an ansamycin polyketide precursor in Escherichia coli. Proc

Natl Acad Sci USA 100, 9774-9778.

267. Weber, G., Schorgendorfer, K., Schneider-Scherzer, E., and Leitner, E.

(1994). The peptide synthetase catalyzing cyc1osporine production III

Tolypoc1adium niveum is encoded by a giant 45.8-kilobase open reading

frame. Curr Genet 26, 120-125.

268. Weber, T., Baumgartner, R., Renner, C., Marahiel, M. A., and Holak, T. A.

(2000). Solution structure of PCP, a prototype for the peptidyl carrier

domains of modular peptide synthetases. Structure Fold Des 8, 407-418.

269. Weinreb, P. H., Quadri, L. E., Walsh, C. T., and Zuber, P. (1998).

Stoichiometry and specificity of in vitro phosphopantetheinylation and

amino acylation of the valine-activating module of surf actin synthetase.

Biochemistry 37, 1575-1584.

270. Weissman, K. 1., Kearney, G. C., Leadlay, P. F., and Staunton, 1. (1999).

Structural elucidation studies of polyketide tetrasubstituted delta-lactones by

gas chromatography/tandem mass spectrometry and electro spray mass

spectrometry. Rapid Commun Mass Spectrom 13, 2103-2108.

271. Wiesmann, K E., Cortes, 1., Brown, M. J., Cutter, A. L., Staunton, 1., and

Leadlay, P. F. (1995). Polyketide synthesis in vitro on a modular polyketide

synthase. Chern BioI 2, 583-589.

272. Wright, F., and Bibb, M. 1. (1992). Codon usage III the G+C-rich

Streptomyces genome. Gene 113, 55-65.

273. Wu, N., Cane, D. E., and Khosla, C. (2002). Quantitative analysis of the

relative contributions of donor acyl carrier proteins, acceptor ketosynthases,

248

Bibliography

and linker reglOns to intermodular transfer of intermediates in hybrid

polyketide synthases. Biochemistry 41, 5056-5066.

274. Xue, Y., Zhao, L., Liu, H. W., and Sherman, D. H. (1998). A gene cluster for

macrolide antibiotic biosynthesis in Streptomyces venezuelae: architecture of

metabolic diversity. Proc Natl Acad Sci USA 95, 12111-12116.

275. Yadav, G., Gokhale, R. S., and Mohanty, D. (2003). Computational approach

for prediction of domain organization and substrate specificity of modular

polyketide synthases. J Mol BioI 328, 335-363.'

276. Yalovsky, S., Rodr Guez-Concepcion, M., and Gruissem, W. (1999). Lipid

modifications of proteins - slipping in and out of membranes. Trends Plant

Sci 4, 439-445.

277. Yasuno, R., von Wettstein-Knowles, P., and Wada, H. (2004). Identification

and molecular characterization of the beta-ketoacyl-[acyl carrier protein]

synthase component of the Arabidopsis mitochondrial fatty acid synthase. J

BioI Chern 279, 8242-825l.

278. Yeh, E., Kohli, R. M., Bruner, S. D., and· Walsh, C. T. (2004). Type II

thioesterase restores activity of a NRPS module stalled with an aminoacyl-S­

enzyme that cannot be elongated. Chembiochem 5, 1290-1293.

279. Zhang, Y., Heym, B., Allen, B., Young, D., and Cole, S. (1992). The

catalase-peroxidase gene and isoniazid resistance of Mycobacterium

tuberculosis. Nature 358, 591-593.

280. Zimhony, 0., Cox, J. S., Welch, 1. T., Vilcheze, C., and Jacobs, W. R., Jr.

(2000). Pyrazinamide inhibits the eukaryotic-like fatty acid synthetase I

(FASI) of Mycobacterium tuberculosis. Nat Med 6, 1043-1047.

249