5 Appendix
5.1 List of references
Abdel-Hamid,A.M., Attwood,M.M., and Guest,J.R. (2001) Pyruvate oxidase contributes to the aerobic growth efficiency of Escherichia coli. Microbiology 147: 1483-1498.
Aceti,D.J., and Ferry,J.G. (1988) Purification and characterization of acetate kinase from acetate-grown Methanosarcina thermophila. Evidence for regulation of synthesis. J Biol Chem 263:
15444-15448.
Aly,S., Wagner,K., Keller,C., Malm,S., Malzan,A., Brandau,S. et al. (2006) Oxygen status of lung granulomas in Mycobacterium tuberculosis-infected mice. J Pathol 210: 298-305.
Andersen,K.B., and von Meyenburg,K. (1980) Are growth rates of Escherichia coli in batch cultures limited by respiration? Journal of Bacteriology 144: 114-123.
Andries,K., Verhasselt,P., Guillemont,J., Gohlmann,H.W., Neefs,J.M., Winkler,H. et al. (2005a) A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis. Science 307:
223-227.
Anis,M.M., Fulton,S.A., Reba,S.M., Liu,Y., Harding,C.V., and Boom,W.H. (2008) Modulation of pulmonary dendritic cell function during mycobacterial infection. Infect Immun 76: 671-677.
Armstrong,J.A., and Hart,P.D. (1971) Response of cultured macrophages to Mycobacterium tuberculosis, with observations on fusion of lysosomes with phagosomes. J Exp Med 134: 713-740.
Bange,F.C., Collins,F.M., and Jacobs,W.R., Jr. (1999) Survival of mice infected with Mycobacterium smegmatis containing large DNA fragments from Mycobacterium tuberculosis.
Tuber Lung Dis 79: 171-180.
Becker,J., Klopprogge,C., and Wittmann,C. (2008) Metabolic responses to pyruvate kinase deletion in lysine producing Corynebacterium glutamicum. Microb Cell Fact 7: 8.
Betts,J.C., Lukey,P.T., Robb,L.C., McAdam,R.A., and Duncan,K. (2002) Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling. Mol Microbiol 43: 717-731.
Bloch,H., and Segal,W. (1956) Biochemical differentiation of Mycobacterium tuberculosis grown in vivo and in vitro. J Bacteriol 72: 132-141.
Bogdan,C. (2001) Nitric oxide and the immune response. Nat Immunol 2: 907-916.
Botella,H., Peyron,P., Levillain,F., Poincloux,R., Poquet,Y., Brandli,I. et al. (2011) Mycobacterial p(1)-type ATPases mediate resistance to zinc poisoning in human macrophages.
Cell Host Microbe 10: 248-259.
Böttger,E.C. (1991) Systematics, differentiation, and detection of bacterial infections-- the family Mycobacteriaceae. Immun Infekt 19: 143-152.
Appendix
Brown,T.D., Jones-Mortimer,M.C., and Kornberg,H.L. (1977) The enzymic interconversion of acetate and acetyl-coenzyme A in Escherichia coli. J Gen Microbiol 102: 327-336.
Buchmeier,N., Blanc-Potard,A., Ehrt,S., Piddington,D., Riley,L., and Groisman,E.A. (2000) A parallel intraphagosomal survival strategy shared by mycobacterium tuberculosis and Salmonella enterica. Mol Microbiol 35: 1375-1382.
Calmette A, La vaccination preventive contre la tuberculose par le ''BCG''. 1927. Masson.
Castano-Cerezo,S., Pastor,J.M., Renilla,S., Bernal,V., Iborra,J.L., and Canovas,M. (2009) An insight into the role of phosphotransacetylase (pta) and the acetate/acetyl-CoA node in Escherichia coli. Microb Cell Fact 8: 54.
Chang,D.E., Shin,S., Rhee,J.S., and Pan,J.G. (1999) Acetate metabolism in a pta mutant of oxidase (PoxB) depends on the sigma factor encoded by the rpoS(katF) gene. Mol Microbiol 11:
1019-1028.
Colditz,G.A., Berkey,C.S., Mosteller,F., Brewer,T.F., Wilson,M.E., Burdick,E., and Fineberg,H.V. (1995) The efficacy of bacillus Calmette-Guerin vaccination of newborns and infants in the prevention of tuberculosis: meta-analyses of the published literature. Pediatrics 96:
29-35.
Colditz,G.A., Brewer,T.F., Berkey,C.S., Wilson,M.E., Burdick,E., Fineberg,H.V., and Mosteller,F. (1994) Efficacy of BCG vaccine in the prevention of tuberculosis. Meta-analysis of the published literature. JAMA 271: 698-702.
Cole,S.T., Brosch,R., Parkhill,J., Garnier,T., Churcher,C., Harris,D. et al. (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393: 537-544.
Cruz,R.H., Hoffmann,T., Marino,M., Nedjari,H., Presecan-Siedel,E., Dreesen,O. et al. (2000) Fermentative metabolism of Bacillus subtilis: physiology and regulation of gene expression. J Bacteriol 182: 3072-3080.
Daniel,J., Maamar,H., Deb,C., Sirakova,T.D., and Kolattukudy,P.E. (2011) Mycobacterium tuberculosis uses host triacylglycerol to accumulate lipid droplets and acquires a dormancy-like phenotype in lipid-loaded macrophages. PLoS Pathog 7: e1002093.
Darwin,K.H. (2009) Prokaryotic ubiquitin-like protein (Pup), proteasomes and pathogenesis. Nat Rev Microbiol 7: 485-491.
Dauner,M., Storni,T., and Sauer,U. (2001) Bacillus subtilis metabolism and energetics in carbon-limited and excess-carbon chemostat culture. J Bacteriol 183: 7308-7317.
Appendix
Davies,K.J., Lloyd,D., and Boddy,L. (1989) The effect of oxygen on denitrification in Paracoccus denitrificans and Pseudomonas aeruginosa. J Gen Microbiol 135: 2445-2451.
Davis,J.M., and Ramakrishnan,L. (2009) The role of the granuloma in expansion and dissemination of early tuberculous infection. Cell 136: 37-49.
de Carvalho,L.P., Fischer,S.M., Marrero,J., Nathan,C., Ehrt,S., and Rhee,K.Y. (2010) Metabolomics of Mycobacterium tuberculosis reveals compartmentalized co-catabolism of carbon substrates. Chem Biol 17: 1122-1131.
Diacon,A.H., Donald,P.R., Pym,A., Grobusch,M., Patientia,R.F., Mahanyele,R. et al. (2012) Randomized pilot trial of eight weeks of bedaquiline (TMC207) treatment for multidrug-resistant tuberculosis: long-term outcome, tolerability, and effect on emergence of drug resistance.
Antimicrob Agents Chemother 56: 3271-3276.
Diacon,A.H., Pym,A., Grobusch,M., Patientia,R., Rustomjee,R., Page-Shipp,L. et al. (2009) The diarylquinoline TMC207 for multidrug-resistant tuberculosis. N Engl J Med 360: 2397-2405.
Diekert,G., and Wohlfarth,G. (1994) Metabolism of homocetogens. Antonie Van Leeuwenhoek 66: 209-221.
Domenech,P., and Reed,M.B. (2009) Rapid and spontaneous loss of phthiocerol dimycocerosate (PDIM) from Mycobacterium tuberculosis grown in vitro: implications for virulence studies.
Microbiology 155: 3532-3543.
Dye,C., Scheele,S., Dolin,P., Pathania,V., and Raviglione,M.C. (1999) Consensus statement.
Global burden of tuberculosis: estimated incidence, prevalence, and mortality by country. WHO Global Surveillance and Monitoring Project. JAMA 282: 677-686.
Edson,N.L. (1951) The intermediary metabolism of the mycobacteria. Bacteriol Rev 15: 147-182.
Ehlers,S. Formalpathogenese der tuberkulosen Gewebsveranderungen. (44), 1363-1373. 2003.
Internist.
Ehrt,S., and Schnappinger,D. (2009) Mycobacterial survival strategies in the phagosome:
defence against host stresses. Cell Microbiol 11: 1170-1178.
el-Mansi,E.M., and Holms,W.H. (1989) Control of carbon flux to acetate excretion during growth of Escherichia coli in batch and continuous cultures. J Gen Microbiol 135: 2875-2883.
El-Mansi,M. (2004) Flux to acetate and lactate excretions in industrial fermentations:
physiological and biochemical implications. J Ind Microbiol Biotechnol 31: 295-300.
Eoh,H., and Rhee,K.Y. (2013) Multifunctional essentiality of succinate metabolism in adaptation to hypoxia in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 110: 6554-6559.
Eschbach,M., Schreiber,K., Trunk,K., Buer,J., Jahn,D., and Schobert,M. (2004) Long-term anaerobic survival of the opportunistic pathogen Pseudomonas aeruginosa via pyruvate fermentation. J Bacteriol 186: 4596-4604.
Appendix
Eum,S.Y., Kong,J.H., Hong,M.S., Lee,Y.J., Kim,J.H., Hwang,S.H. et al. (2010) Neutrophils are the predominant infected phagocytic cells in the airways of patients with active pulmonary TB.
Chest 137: 122-128.
Feng,C.G., Kaviratne,M., Rothfuchs,A.G., Cheever,A., Hieny,S., Young,H.A. et al. (2006) NK cell-derived IFN-gamma differentially regulates innate resistance and neutrophil response in T cell-deficient hosts infected with Mycobacterium tuberculosis. J Immunol 177: 7086-7093.
Ferrer,N.L., Gomez,A.B., Neyrolles,O., Gicquel,B., and Martin,C. (2010) Interactions of attenuated Mycobacterium tuberculosis phoP mutant with human macrophages. PLoS One 5:
e12978.
Garton,N.J., Waddell,S.J., Sherratt,A.L., Lee,S.M., Smith,R.J., Senner,C. et al. (2008) Cytological and transcript analyses reveal fat and lazy persister-like bacilli in tuberculous sputum. PLoS Med 5: e75.
Gengenbacher,M., and Kaufmann,S.H. (2012) Mycobacterium tuberculosis: success through dormancy. FEMS Microbiol Rev 36: 514-532.
Gengenbacher,M., Rao,S.P.S., Pethe,K., and Dick,T. (2010) Nutrient-starved, non-replicating Mycobacterium tuberculosis requires respiration, ATP synthase and isocitrate lyase for maintenance of ATP homeostasis and viability. Microbiology 156: 81-87.
Georgellis,D., Kwon,O., and Lin,E.C. (2001) Quinones as the redox signal for the arc two-component system of bacteria. Science 292: 2314-2316.
Gorke,B., and Stulke,J. (2008) Carbon catabolite repression in bacteria: many ways to make the most out of nutrients. Nat Rev Microbiol 6: 613-624.
Gottschalk. Bacterial Metabolism. 2. 1986. Berlin, Heidelberg, New York, Tokyo, Springer.
Gould,T.A., van de,L.H., Munoz-Elias,E.J., McKinney,J.D., and Sacchettini,J.C. (2006) Dual role of isocitrate lyase 1 in the glyoxylate and methylcitrate cycles in Mycobacterium tuberculosis. Mol Microbiol 61: 940-947.
Green,J., and Guest,J.R. (1994) Regulation of transcription at the ndh promoter of Escherichia coli by FNR and novel factors. Mol Microbiol 12: 433-444.
Grundy,F.J., Waters,D.A., Allen,S.H., and Henkin,T.M. (1993a) Regulation of the Bacillus subtilis acetate kinase gene by CcpA. J Bacteriol 175: 7348-7355.
Grundy,F.J., Waters,D.A., Takova,T.Y., and Henkin,T.M. (1993b) Identification of genes involved in utilization of acetate and acetoin in Bacillus subtilis. Mol Microbiol 10: 259-271.
Appendix
Hahn,H..&.R.A.C. Medizinische Mikrobiologie und Infektiologie, chapter "Mykobakterien".
435-455. 2001. Berlin, Heidelberg, New York, London, Paris, Tokyo, Hong Kong, Barcelona, Budapest, Springer Verlag.
Halbedel,S., Eilers,H., Jonas,B., Busse,J., Hecker,M., Engelmann,S., and Stulke,J. (2007) Transcription in Mycoplasma pneumoniae: analysis of the promoters of the ackA and ldh genes.
J Mol Biol 371: 596-607.
Han,K., Lim,H.C., and Hong,J. (1992) Acetic acid formation in Escherichia coli fermentation.
Biotechnol Bioeng 39: 663-671.
Hippocrates. Aphorisms. 400.
Hof,H.D.R. Medizinische Mikrobiologie, chapter "Mykobakterien". 330-339. 2002. Stuttgart, New York, Georg Thieme Verlag.
Hoffmann,T., Frankenberg,N., Marino,M., and Jahn,D. (1998) Ammonification in Bacillus subtilis utilizing dissimilatory nitrite reductase is dependent on resDE. J Bacteriol 180: 186-189.
Hoffmann,T., Troup,B., Szabo,A., Hungerer,C., and Jahn,D. (1995) The anaerobic life of Bacillus subtilis: cloning of the genes encoding the respiratory nitrate reductase system. FEMS Microbiol Lett 131: 219-225.
Holms,H. (1996) Flux analysis and control of the central metabolic pathways in Escherichia coli.
FEMS Microbiol Rev 19: 85-116.
Inui,M., Murakami,S., Okino,S., Kawaguchi,H., Vertes,A.A., and Yukawa,H. (2004) Metabolic analysis of Corynebacterium glutamicum during lactate and succinate productions under oxygen deprivation conditions. J Mol Microbiol Biotechnol 7: 182-196.
Jackson,M., Phalen,S.W., Lagranderie,M., Ensergueix,D., Chavarot,P., Marchal,G. et al. (1999) Persistence and protective efficacy of a Mycobacterium tuberculosis auxotroph vaccine. Infect Immun 67: 2867-2873.
Jackson,M., Stadthagen,G., and Gicquel,B. (2007) Long-chain multiple methyl-branched fatty acid-containing lipids of Mycobacterium tuberculosis: biosynthesis, transport, regulation and biological activities. Tuberculosis (Edinb) 87: 78-86.
Jantama,K., Haupt,M.J., Svoronos,S.A., Zhang,X., Moore,J.C., Shanmugam,K.T., and Ingram,L.O. (2008a) Combining metabolic engineering and metabolic evolution to develop nonrecombinant strains of Escherichia coli C that produce succinate and malate. Biotechnol Bioeng 99: 1140-1153.
Jantama,K., Zhang,X., Moore,J.C., Shanmugam,K.T., Svoronos,S.A., and Ingram,L.O. (2008b) Eliminating side products and increasing succinate yields in engineered strains of Escherichia coli C. Biotechnol Bioeng 101: 881-893.
Jolkver,E., Emer,D., Ballan,S., Kramer,R., Eikmanns,B.J., and Marin,K. (2009) Identification and characterization of a bacterial transport system for the uptake of pyruvate, propionate, and acetate in Corynebacterium glutamicum. J Bacteriol 191: 940-948.
Appendix
Kakuda,H., Shiroishi,K., Hosono,K., and Ichihara,S. (1994) Construction of Pta-Ack pathway deletion mutants of Escherichia coli and characteristic growth profiles of the mutants in a rich medium. Biosci Biotechnol Biochem 58: 2232-2235.
Keren,I., Minami,S., Rubin,E., and Lewis,K. (2011) Characterization and transcriptome analysis of Mycobacterium tuberculosis persisters. MBio 2: e00100-e00111.
Kim,B.H., and Gadd,G.M. (2008) Bacterial Physiology and Metabolism Cambridge University Press.
Kind,S., Jeong,W.K., Schroder,H., Zelder,O., and Wittmann,C. (2010) Identification and elimination of the competing N-acetyldiaminopentane pathway for improved production of diaminopentane by Corynebacterium glutamicum. Appl Environ Microbiol 76: 5175-5180.
King,G.M. (2003) Uptake of carbon monoxide and hydrogen at environmentally relevant concentrations by mycobacteria. Appl Environ Microbiol 69: 7266-7272.
Koch,R. The Nobel Prize in Physiology or Medicine 1905. 1905. Nobelprize.org.
Ref Type: Generic
Koch-Koerfges,A., Pfelzer,N., Platzen,L., Oldiges,M., and Bott,M. (2013) Conversion of Corynebacterium glutamicum from an aerobic respiring to an aerobic fermenting bacterium by inactivation of the respiratory chain. Biochim Biophys Acta.
Kopke,M., Held,C., Hujer,S., Liesegang,H., Wiezer,A., Wollherr,A. et al. (2010) Clostridium ljungdahlii represents a microbial production platform based on syngas. Proc Natl Acad Sci U S A 107: 13087-13092.
Kumar,A., Deshane,J.S., Crossman,D.K., Bolisetty,S., Yan,B.S., Kramnik,I. et al. (2008) Heme oxygenase-1-derived carbon monoxide induces the Mycobacterium tuberculosis dormancy regulon. J Biol Chem 283: 18032-18039.
Lang,V.J., Leystra-Lantz,C., and Cook,R.A. (1987) Characterization of the specific pyruvate transport system in Escherichia coli K-12. J Bacteriol 169: 380-385.
Lee,W., Vanderven,B.C., Fahey,R.J., and Russell,D.G. (2013) Intracellular Mycobacterium tuberculosis Exploits Host-derived Fatty Acids to Limit Metabolic Stress. J Biol Chem 288:
6788-6800.
Lehmann,B.H.N.R.O. Atlas und Grundriss der Bakteriologie und Lehrbuch der speciellen
bakteriologischen Diagnostik. 1896. München, Lehmann.
Levy-Frebault,V.V., and Portaels,F. (1992) Proposed minimal standards for the genus Mycobacterium and for description of new slowly growing Mycobacterium species. Int J Syst Bacteriol 42: 315-323.
Lockhart,E., Green,A.M., and Flynn,J.L. (2006) IL-17 production is dominated by gammadelta T cells rather than CD4 T cells during Mycobacterium tuberculosis infection. J Immunol 177:
4662-4669.
Appendix
Madigan,M.T., Martinko,J.M., Stahl,D.A., and Clark,D.P. Brock Biology of Microorganisms.
2006. Pearson.
Ref Type: Generic
Majewski,R.A., and Domach,M.M. (1990) Simple constrained-optimization view of acetate overflow in E. coli. Biotechnol Bioeng 35: 732-738.
Makinoshima,H., and Glickman,M.S. (2005) Regulation of Mycobacterium tuberculosis cell envelope composition and virulence by intramembrane proteolysis. Nature 436: 406-409.
Malm,S., Tiffert,Y., Micklinghoff,J., Schultze,S., Joost,I., Weber,I. et al. (2009) The roles of the nitrate reductase NarGHJI, the nitrite reductase NirBD and the response regulator GlnR in nitrate assimilation of Mycobacterium tuberculosis. Microbiology 155: 1332-1339.
Maloney,E., Stankowska,D., Zhang,J., Fol,M., Cheng,Q.J., Lun,S. et al. (2009) The two-domain LysX protein of Mycobacterium tuberculosis is required for production of lysinylated phosphatidylglycerol and resistance to cationic antimicrobial peptides. PLoS Pathog 5:
e1000534.
Marrero,J., Rhee,K.Y., Schnappinger,D., Pethe,K., and Ehrt,S. (2010) Gluconeogenic carbon flow of tricarboxylic acid cycle intermediates is critical for Mycobacterium tuberculosis to establish and maintain infection. Proc Natl Acad Sci U S A 107: 9819-9824.
Marrero,J., Trujillo,C., Rhee,K.Y., and Ehrt,S. (2013) Glucose phosphorylation is required for Mycobacterium tuberculosis persistence in mice. PLoS Pathog 9: e1003116.
McKinney,J.D., Honer zu,B.K., Munoz-Elias,E.J., Miczak,A., Chen,B., Chan,W.T. et al. (2000) Persistence of Mycobacterium tuberculosis in macrophages and mice requires the glyoxylate shunt enzyme isocitrate lyase. Nature 406: 735-738.
Meier,A., Kirschner,P., Schroder,K.H., Wolters,J., Kroppenstedt,R.M., and Bottger,E.C. (1993) Mycobacterium intermedium sp. nov. Int J Syst Bacteriol 43: 204-209.
Metchock,B..&.W.Jr.R.J. Mycobacterium, chapter "Mycobacterium". 399-437. 2013. ASM Press, Washington D. C.
Micklinghoff,J.C., Breitinger,K.J., Schmidt,M., Geffers,R., Eikmanns,B.J., and Bange,F.C.
(2009) Role of the transcriptional regulator RamB (Rv0465c) in the control of the glyoxylate cycle in Mycobacterium tuberculosis. J Bacteriol 191: 7260-7269.
Mogues,T., Goodrich,M.E., Ryan,L., LaCourse,R., and North,R.J. (2001) The relative importance of T cell subsets in immunity and immunopathology of airborne Mycobacterium tuberculosis infection in mice. J Exp Med 193: 271-280.
Munoz-Elias,E.J., and McKinney,J.D. (2005) Mycobacterium tuberculosis isocitrate lyases 1 and 2 are jointly required for in vivo growth and virulence. Nat Med 11: 638-644.
Munoz-Elias,E.J., and McKinney,J.D. (2006) Carbon metabolism of intracellular bacteria. Cell Microbiol 8: 10-22.
Murray,P.R., Rosenthal,K.S., and Pfaller,M.A. Medical Microbiology. 2005. Mosby, Elsevier.
Appendix
Nakano,M.M., Dailly,Y.P., Zuber,P., and Clark,D.P. (1997) Characterization of anaerobic fermentative growth of Bacillus subtilis: identification of fermentation end products and genes required for growth. J Bacteriol 179: 6749-6755.
Nakano,M.M., and Zuber,P. (1998) Anaerobic growth of a "strict aerobe" (Bacillus subtilis).
Annu Rev Microbiol 52: 165-190.
Nicas,M., Nazaroff,W.W., and Hubbard,A. (2005) Toward understanding the risk of secondary airborne infection: emission of respirable pathogens. J Occup Environ Hyg 2: 143-154.
Nicholson,T.L., Chiu,K., and Stephens,R.S. (2004) Chlamydia trachomatis lacks an adaptive response to changes in carbon source availability. Infect Immun 72: 4286-4289.
Niederweis,M. (2008) Nutrient acquisition by mycobacteria. Microbiology 154: 679-692.
Niederweis,M., Danilchanka,O., Huff,J., Hoffmann,C., and Engelhardt,H. (2010) Mycobacterial outer membranes: in search of proteins. Trends Microbiol 18: 109-116.
Olszewski,K.L., Mather,M.W., Morrisey,J.M., Garcia,B.A., Vaidya,A.B., Rabinowitz,J.D., and Llinas,M. (2010) Branched tricarboxylic acid metabolism in Plasmodium falciparum. Nature 466: 774-778.
Pandey,A.K., and Sassetti,C.M. (2008) Mycobacterial persistence requires the utilization of host cholesterol. Proc Natl Acad Sci U S A 105: 4376-4380.
Parish,T. (2003) Starvation survival response of Mycobacterium tuberculosis. J Bacteriol 185:
6702-6706.
Park,S.W., Hwang,E.H., Park,H., Kim,J.A., Heo,J., Lee,K.H. et al. (2003) Growth of mycobacteria on carbon monoxide and methanol. J Bacteriol 185: 142-147.
Park,S.W., Song,T., Kim,S.Y., Kim,E., Oh,J.I., Eom,C.Y., and Kim,Y.M. (2007) Carbon monoxide dehydrogenase in mycobacteria possesses a nitric oxide dehydrogenase activity.
Biochem Biophys Res Commun 362: 449-453.
Pasteur,L. (1879) Modern History Sourcebook: Louis Pasteur (1822-1895): Physiological theory of fermentation.
Pavelka,M.S., Jr., and Jacobs,W.R., Jr. (1999) Comparison of the construction of unmarked deletion mutations in Mycobacterium smegmatis, Mycobacterium bovis bacillus Calmette-Guerin, and Mycobacterium tuberculosis H37Rv by allelic exchange. J Bacteriol 181: 4780-4789.
Peirs,P., Lefevre,P., Boarbi,S., Wang,X.M., Denis,O., Braibant,M. et al. (2005) Mycobacterium tuberculosis with disruption in genes encoding the phosphate binding proteins PstS1 and PstS2 is deficient in phosphate uptake and demonstrates reduced in vivo virulence. Infect Immun 73:
1898-1902.
Peng,L., and Shimizu,K. (2003) Global metabolic regulation analysis for Escherichia coli K12 based on protein expression by 2-dimensional electrophoresis and enzyme activity measurement.
Appl Microbiol Biotechnol 61: 163-178.
Appendix
Petrova,O.E., Schurr,J.R., Schurr,M.J., and Sauer,K. (2012) Microcolony formation by the opportunistic pathogen Pseudomonas aeruginosa requires pyruvate and pyruvate fermentation.
Mol Microbiol.
Phue,J.N., Lee,S.J., Kaufman,J.B., Negrete,A., and Shiloach,J. (2010) Acetate accumulation through alternative metabolic pathways in ackA (-) pta (-) poxB (-) triple mutant in E. coli B (BL21). Biotechnol Lett 32: 1897-1903.
Phue,J.N., and Shiloach,J. (2005) Impact of dissolved oxygen concentration on acetate accumulation and physiology of E. coli BL21, evaluating transcription levels of key genes at different dissolved oxygen conditions. Metab Eng 7: 353-363.
Presecan-Siedel,E., Galinier,A., Longin,R., Deutscher,J., Danchin,A., Glaser,P., and Martin-Verstraete,I. (1999) Catabolite regulation of the pta gene as part of carbon flow pathways in Bacillus subtilis. J Bacteriol 181: 6889-6897.
Pruss,B.M., and Wolfe,A.J. (1994) Regulation of acetyl phosphate synthesis and degradation, and the control of flagellar expression in Escherichia coli. Mol Microbiol 12: 973-984.
Rao,S.P., Alonso,S., Rand,L., Dick,T., and Pethe,K. (2008) The protonmotive force is required for maintaining ATP homeostasis and viability of hypoxic, nonreplicating Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 105: 11945-11950.
Rhee,K.Y., de Carvalho,L.P., Bryk,R., Ehrt,S., Marrero,J., Park,S.W. et al. (2011) Central carbon metabolism in Mycobacterium tuberculosis: an unexpected frontier. Trends Microbiol 19:
307-314.
Roberts,G., Vadrevu,I.S., Madiraju,M.V., and Parish,T. (2011) Control of CydB and GltA1 expression by the SenX3 RegX3 two component regulatory system of Mycobacterium tuberculosis. PLoS One 6: e21090.
Rogall,T., Wolters,J., Flohr,T., and Bottger,E.C. (1990) Towards a phylogeny and definition of species at the molecular level within the genus Mycobacterium. Int J Syst Bacteriol 40: 323-330.
Romano,M., and Huygen,K. (2012) An update on vaccines for tuberculosis - there is more to it than just waning of BCG efficacy with time. Expert Opin Biol Ther 12: 1601-1610.
Rothschild,B.M., Martin,L.D., Lev,G., Bercovier,H., Bar-Gal,G.K., Greenblatt,C. et al. (2001) Mycobacterium tuberculosis Complex DNA from an Extinct Bison Dated 17,000 Years before the Present. Clinical Infectious Diseases 33: 305-311.
Runyon,E.H.T.A. Anonymous mycobacteria in pulmonary disease. (43), 273-290. 1959. Med Clin North Am.
Russell,D.G., Barry,C.E., III, and Flynn,J.L. (2010) Tuberculosis: what we don't know can, and does, hurt us. Science 328: 852-856.
Saiki,R.K., Scharf,S., Faloona,F., Mullis,K.B., Horn,G.T., Erlich,H.A., and Arnheim,N. (1985) Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230: 1350-1354.
Appendix
Sambandamurthy,V.K., Wang,X., Chen,B., Russell,R.G., Derrick,S., Collins,F.M. et al. (2002) A pantothenate auxotroph of Mycobacterium tuberculosis is highly attenuated and protects mice against tuberculosis. Nat Med 8: 1171-1174.
Sanger,F., Nicklen,S., and Coulson,A.R. (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74: 5463-5467.
Sassetti,C.M., and Rubin,E.J. (2003) Genetic requirements for mycobacterial survival during infection. Proc Natl Acad Sci U S A 100: 12989-12994.
Sauer,U., and Eikmanns,B.J. (2005) The PEP-pyruvate-oxaloacetate node as the switch point for carbon flux distribution in bacteria. FEMS Microbiol Rev 29: 765-794.
Savvi,S., Warner,D.F., Kana,B.D., McKinney,J.D., Mizrahi,V., and Dawes,S.S. (2008) Functional characterization of a vitamin B12-dependent methylmalonyl pathway in Mycobacterium tuberculosis: implications for propionate metabolism during growth on fatty acids. J Bacteriol 190: 3886-3895.
Schnappinger,D., Ehrt,S., Voskuil,M.I., Liu,Y., Mangan,J.A., Monahan,I.M. et al. (2003) Transcriptional Adaptation of Mycobacterium tuberculosis within Macrophages: Insights into the Phagosomal Environment. J Exp Med 198: 693-704.
Selbitz,H.-J. Medizinische Mikrobiologie, Infektions- und Seuchenlehre, chapter "Bakterielle Krankheiten der Tiere". 555-565. 2002. Enke Verlag, Stuttgart.
Shah,D., Zhang,Z., Khodursky,A., Kaldalu,N., Kurg,K., and Lewis,K. (2006) Persisters: a distinct physiological state of E. coli. BMC Microbiol 6: 53.
Shi,L., Sohaskey,C.D., Kana,B.D., Dawes,S., North,R.J., Mizrahi,V., and Gennaro,M.L. (2005) Changes in energy metabolism of Mycobacterium tuberculosis in mouse lung and under in vitro conditions affecting aerobic respiration. Proc Natl Acad Sci U S A 102: 15629-15634.
Shi,L., Sohaskey,C.D., Pfeiffer,C., Datta,P., Parks,M., McFadden,J. et al. (2010) Carbon flux rerouting during Mycobacterium tuberculosis growth arrest. Mol Microbiol 78: 1199-1215.
Sohaskey,C.D., and Wayne,L.G. (2003) Role of narK2X and narGHJI in hypoxic upregulation of nitrate reduction by Mycobacterium tuberculosis. J Bacteriol 185: 7247-7256.
Sohaskey,C.D. (2008) Nitrate Enhances the Survival of Mycobacterium tuberculosis during Inhibition of Respiration. Journal of Bacteriology 190: 2981-2986.
Somashekar,B.S., Amin,A.G., Rithner,C.D., Troudt,J., Basaraba,R., Izzo,A. et al. (2011) Metabolic profiling of lung granuloma in Mycobacterium tuberculosis infected guinea pigs: ex vivo 1H magic angle spinning NMR studies. J Proteome Res 10: 4186-4195.
Somashekar,B.S., Amin,A.G., Tripathi,P., MacKinnon,N., Rithner,C.D., Shanley,C.A. et al.
(2012) Metabolomic signatures in guinea pigs infected with epidemic-associated W-Beijing strains of Mycobacterium tuberculosis. J Proteome Res 11: 4873-4884.
Stoodley,P., Sauer,K., Davies,D.G., and Costerton,J.W. (2002) Biofilms as complex differentiated communities. Annu Rev Microbiol 56: 187-209.
Appendix
Stover,C.K., de,l.C., V, Fuerst,T.R., Burlein,J.E., Benson,L.A., Bennett,L.T. et al. (1991) New use of BCG for recombinant vaccines. Nature 351: 456-460.
Tailleux,L., Waddell,S.J., Pelizzola,M., Mortellaro,A., Withers,M., Tanne,A. et al. (2008) Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages. PLoS One 3: e1403.
Tan,M.P., Sequeira,P., Lin,W.W., Phong,W.Y., Cliff,P., Ng,S.H. et al. (2010) Nitrate respiration protects hypoxic Mycobacterium tuberculosis against acid- and reactive nitrogen species stresses. PLoS One 5: e13356.
Titgemeyer,F., Amon,J., Parche,S., Mahfoud,M., Bail,J., Schlicht,M. et al. (2007) A genomic view of sugar transport in Mycobacterium smegmatis and Mycobacterium tuberculosis. J Bacteriol 189: 5903-5915.
Tran,S.L., and Cook,G.M. (2005) The F1Fo-ATP synthase of Mycobacterium smegmatis is essential for growth. J Bacteriol 187: 5023-5028.
Unden,G., and Bongaerts,J. (1997) Alternative respiratory pathways of Escherichia coli:
energetics and transcriptional regulation in response to electron acceptors. Biochim Biophys Acta 1320: 217-234.
Valgepea,K., Adamberg,K., Nahku,R., Lahtvee,P.J., Arike,L., and Vilu,R. (2010) Systems biology approach reveals that overflow metabolism of acetate in Escherichia coli is triggered by carbon catabolite repression of acetyl-CoA synthetase. BMC Syst Biol 4: 166.
van der Geize,R., Yam,K., Heuser,T., Wilbrink,M.H., Hara,H., Anderton,M.C. et al. (2007) A gene cluster encoding cholesterol catabolism in a soil actinomycete provides insight into Mycobacterium tuberculosis survival in macrophages. Proc Natl Acad Sci U S A 104: 1947-1952.
Van Dyk,T.K., and LaRossa,R.A. (1987) Involvement of ack-pta operon products in alpha-ketobutyrate metabolism by Salmonella typhimurium. Mol Gen Genet 207: 435-440.
van Hoek,M.J., and Merks,R.M. (2012) Redox balance is key to explaining full vs. partial switching to low-yield metabolism. BMC Syst Biol 6: 22.
Vandal,O.H., Pierini,L.M., Schnappinger,D., Nathan,C.F., and Ehrt,S. (2008) A membrane protein preserves intrabacterial pH in intraphagosomal Mycobacterium tuberculosis. Nat Med 14:
849-854.
Vander,W.C., Pierard,A., Kley-Raymann,M., and Haas,D. (1984) Pseudomonas aeruginosa mutants affected in anaerobic growth on arginine: evidence for a four-gene cluster encoding the arginine deiminase pathway. J Bacteriol 160: 928-934.
Velayati,A.A., Masjedi,M.R., Farnia,P., Tabarsi,P., Ghanavi,J., Ziazarifi,A.H., and Hoffner,S.E.
Velayati,A.A., Masjedi,M.R., Farnia,P., Tabarsi,P., Ghanavi,J., Ziazarifi,A.H., and Hoffner,S.E.