High-Resolution Phenotypic Profiling Defines Genes Essential for Mycobacterial Growth and Cholesterol Catabolism

2010

DG Russell, 2010, My<italic>cobacterium tuberculosis</italic> wears what it eats., Cell Host Microbe, 8, 68, 10.1016/j.chom.2010.06.002

V Badarinarayana, 2001, Selection analyses of insertional mutants using subgenic-resolution arrays., Nat Biotechnol, 19, 1060, 10.1038/nbt1101-1060

J Rengarajan, 2005, Genome-wide requirements for <italic>Mycobacterium tuberculosis</italic> adaptation and survival in macrophages., Proc Natl Acad Sci U S A, 102, 8327, 10.1073/pnas.0503272102

CM Sassetti, 2001, Comprehensive identification of conditionally essential genes in mycobacteria., Proc Natl Acad Sci U S A, 98, 12712, 10.1073/pnas.231275498

CM Sassetti, 2003, Genes required for mycobacterial growth defined by high density mutagenesis., Mol Microbiol, 48, 77, 10.1046/j.1365-2958.2003.03425.x

CA Hutchison, 1999, Global transposon mutagenesis and a minimal Mycoplasma genome., Science, 286, 2165, 10.1126/science.286.5447.2165

MA Jacobs, 2003, Comprehensive transposon mutant library of <italic>Pseudomonas aeruginosa</italic>., Proc Natl Acad Sci U S A, 100, 14339, 10.1073/pnas.2036282100

G Lamichhane, 2003, A postgenomic method for predicting essential genes at subsaturation levels of mutagenesis: application to <italic>Mycobacterium tuberculosis.</italic>, Proc Natl Acad Sci U S A, 100, 7213, 10.1073/pnas.1231432100

DJ Lampe, 1996, A purified mariner transposase is sufficient to mediate transposition in vitro., EMBO J, 15, 5470, 10.1002/j.1460-2075.1996.tb00930.x

EJ Rubin, 1999, In vivo transposition of mariner-based elements in enteric bacteria and mycobacteria., Proc Natl Acad Sci U S A, 96, 1645, 10.1073/pnas.96.4.1645

BJ Akerley, 1998, Systematic identification of essential genes by in vitro mariner mutagenesis., Proc Natl Acad Sci U S A, 95, 8927, 10.1073/pnas.95.15.8927

JC Chang, 2009, igr Genes and Mycobacterium tuberculosis cholesterol metabolism., J Bacteriol, 191, 5232, 10.1128/JB.00452-09

AK Pandey, 2008, Mycobacterial persistence requires the utilization of host cholesterol., Proc Natl Acad Sci U S A, 105, 4376, 10.1073/pnas.0711159105

R Van der Geize, 2007, A gene cluster encoding cholesterol catabolism in a soil actinomycete provides insight into <italic>Mycobacterium tuberculosis</italic> survival in macrophages., Proc Natl Acad Sci U S A, 104, 1947, 10.1073/pnas.0605728104

SM Joshi, 2006, Characterization of mycobacterial virulence genes through genetic interaction mapping., Proc Natl Acad Sci U S A, 103, 11760, 10.1073/pnas.0603179103

NM Nesbitt, 2009, A thiolase of Mycobacterium tuberculosis is required for virulence and production of androstenedione and androstadienedione from cholesterol., Infect Immun, 78, 275, 10.1128/IAI.00893-09

A Brzostek, 2007, Cholesterol oxidase is required for virulence of <italic>Mycobacterium tuberculosis</italic>., FEMS Microbiol Lett, 275, 106, 10.1111/j.1574-6968.2007.00865.x

X Yang, 2007, Rv1106c from <italic>Mycobacterium tuberculosis</italic> is a 3beta-hydroxysteroid dehydrogenase., Biochemistry, 46, 9058, 10.1021/bi700688x

KZ Rosloniec, 2009, Cytochrome P450 125 (CYP125) catalyses C26-hydroxylation to initiate sterol side-chain degradation in <italic>Rhodococcus jostii</italic> RHA1., Mol Microbiol, 74, 1031, 10.1111/j.1365-2958.2009.06915.x

JK Capyk, 2009, Mycobacterial cytochrome p450 125 (cyp125) catalyzes the terminal hydroxylation of c27 steroids., J Biol Chem, 284, 35534, 10.1074/jbc.M109.072132

H Ouellet, 2010, <italic>Mycobacterium tuberculosis</italic> CYP125A1, a steroid C27 monooxygenase that detoxifies intracellularly generated cholest-4-en-3-one., Mol Microbiol, 77, 730, 10.1111/j.1365-2958.2010.07243.x

JB Johnston, 2010, Functional redundancy of steroid C26-monooxygenase activity in <italic>Mycobacterium tuberculosis</italic> revealed by biochemical and genetic analyses., J Biol Chem, 285, 36352, 10.1074/jbc.M110.161117

X Yang, 2009, Cholesterol metabolism increases the metabolic pool of propionate in <italic>Mycobacterium tuberculosis</italic>., Biochemistry, 48, 3819, 10.1021/bi9005418

TA Gould, 2006, Dual role of isocitrate lyase 1 in the glyoxylate and methylcitrate cycles in <italic>Mycobacterium tuberculosis</italic>., Mol Microbiol, 61, 940, 10.1111/j.1365-2958.2006.05297.x

EJ Munoz-Elias, 2005, <italic>Mycobacterium tuberculosis</italic> isocitrate lyases 1 and 2 are jointly required for in vivo growth and virulence., Nat Med, 11, 638, 10.1038/nm1252

JC Micklinghoff, 2009, Role of the transcriptional regulator RamB (Rv0465c) in the control of the glyoxylate cycle in <italic>Mycobacterium tuberculosis</italic>., J Bacteriol, 191, 7260, 10.1128/JB.01009-09

LA Gallagher, 2011, Genome-Scale Identification of Resistance Functions in <italic>Pseudomonas aeruginosa</italic> Using Tn-seq. MBio 2., MBio, 18, e00315

JD Gawronski, 2009, Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung., Proc Natl Acad Sci U S A, 106, 16422, 10.1073/pnas.0906627106

AL Goodman, 2009, Identifying genetic determinants needed to establish a human gut symbiont in its habitat., Cell Host Microbe, 6, 279, 10.1016/j.chom.2009.08.003

GC Langridge, 2009, Simultaneous assay of every <italic>Salmonella Typhi</italic> gene using one million transposon mutants., Genome Res, 19, 2308, 10.1101/gr.097097.109

T van Opijnen, 2009, Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms., Nat Methods, 6, 767, 10.1038/nmeth.1377

M Braunstein, 2001, Two nonredundant SecA homologues function in mycobacteria., J Bacteriol, 183, 6979, 10.1128/JB.183.24.6979-6990.2001

SE Converse, 2003, MmpL8 is required for sulfolipid-1 biosynthesis and <italic>Mycobacterium tuberculosis</italic> virulence., Proc Natl Acad Sci U S A, 100, 6121, 10.1073/pnas.1030024100

I Matsunaga, 2004, <italic>Mycobacterium tuberculosis pks12</italic> produces a novel polyketide presented by CD1c to T cells., J Exp Med, 200, 1559, 10.1084/jem.20041429

JD McKinney, 2000, Persistence of <italic>Mycobacterium tuberculosis</italic> in macrophages and mice requires the glyoxylate shunt enzyme isocitrate lyase., Nature, 406, 735, 10.1038/35021074

VH Ng, 2004, Role of KatG catalase-peroxidase in mycobacterial pathogenesis: countering the phagocyte oxidative burst., Mol Microbiol, 52, 1291, 10.1111/j.1365-2958.2004.04078.x

TP Primm, 2000, The stringent response of <italic>Mycobacterium tuberculosis</italic> is required for long-term survival., J Bacteriol, 182, 4889, 10.1128/JB.182.17.4889-4898.2000

GM Rodriguez, 2002, ideR, An essential gene in <italic>Mycobacterium tuberculosis</italic>: role of IdeR in iron-dependent gene expression, iron metabolism, and oxidative stress response., Infect Immun, 70, 3371, 10.1128/IAI.70.7.3371-3381.2002

Y Hu, 2010, 3-Ketosteroid 9alpha-hydroxylase is an essential factor in the pathogenesis of <italic>Mycobacterium tuberculosis.</italic>, Mol Microbiol, 75, 107, 10.1111/j.1365-2958.2009.06957.x

KC Yam, 2009, Studies of a ring-cleaving dioxygenase illuminate the role of cholesterol metabolism in the pathogenesis of <italic>Mycobacterium tuberculosis</italic>., PLoS Pathog, 5, e1000344, 10.1371/journal.ppat.1000344

J Marrero, 2010, Gluconeogenic carbon flow of tricarboxylic acid cycle intermediates is critical for <italic>Mycobacterium tuberculosis</italic> to establish and maintain infection., Proc Natl Acad Sci U S A, 107, 9819, 10.1073/pnas.1000715107

M Benziman, 1971, Pyruvate-phosphate dikinase and the control of gluconeogenesis in <italic>Acetobacter xylinum.</italic>, J Biol Chem, 246, 57, 10.1016/S0021-9258(18)62531-1

M Osteras, 1997, Increased pyruvate orthophosphate dikinase activity results in an alternative gluconeogenic pathway in <italic>Rhizobium (Sinorhizobium) meliloti</italic>., Microbiology 143 (Pt, 5), 1639

X Yang, 2011, Cholesterol is not an essential source of nutrition for <italic>Mycobacterium tuberculosis</italic> during infection., J Bacteriol, 193, 1473, 10.1128/JB.01210-10

CM Sassetti, 2003, Genetic requirements for mycobacterial survival during infection., Proc Natl Acad Sci U S A, 100, 12989, 10.1073/pnas.2134250100

ST Cole, 1998, Deciphering the biology of <italic>Mycobacterium tuberculosis</italic> from the complete genome sequence [see comments] [published erratum appears in Nature 1998 Nov 12;396(6707):190]., Nature, 393, 537

R Li, 2008, SOAP: short oligonucleotide alignment program., Bioinformatics, 24, 713, 10.1093/bioinformatics/btn025