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