A highly conserved transcriptional repressor controls a large regulon involved in lipid degradation in Mycobacterium smegmatis and Mycobacterium tuberculosis

Abstract

Summary The Mycobacterium tuberculosis TetR‐type regulator Rv3574 has been implicated in pathogenesis as it is induced in vivo , and genome‐wide essentiality studies show it is required for infection. As the gene is highly conserved in the mycobacteria, we deleted the Rv3574 orthologue in Mycobacterium smegmatis ( MSMEG_6042 ) and used real‐time quantitative polymerase chain reaction and microarray analyses to show that it represses the transcription both of itself and of a large number of genes involved in lipid metabolism. We identified a conserved motif within its own promoter (TnnAACnnGTTnnA) and showed that it binds as a dimer to 29 bp probes containing the motif. We found 16 and 31 other instances of the motif in intergenic regions of M. tuberculosis and M. smegmatis respectively. Combining the results of the microarray studies with the motif analyses, we predict that Rv3574 directly controls the expression of 83 genes in M. smegmatis , and 74 in M. tuberculosis . Many of these genes are known to be induced by growth on cholesterol in rhodococci, and palmitate in M. tuberculosis . We conclude that this regulator, designated elsewhere as kstR , controls the expression of genes used for utilizing diverse lipids as energy sources, possibly imported through the mce4 system.

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References 60

1. 1.

   Alderwick LJ, Radmacher E, Seidel M, Gande R, Hitcher PG, Morris HR, Dell A, Sahm H, Eggeling L, Besra GS. Deletion of Cg-emb in corynebacterianeae leads to a novel truncated cell wall arabinogalactan, whereas inactivation of Cg-ubiA results in an arabinan-deficient mutant with a cell wall galactan core. J Biol Chem. 2005;280:32362-32371.

   Not in our library10.1074/jbc.m506339200

2. 2.

   Anderton MC, Bhakta S, Besra GS, Jeavons P, Eltis LD, Sim E. Characterization of the putative operon containing arylamine N-acetyltransferase (nat) in Mycobacterium bovis BCG. Mol Microbiol. 2006;59:181-192.

   Not in our library10.1111/j.1365-2958.2005.04945.x

3. 3.

   Ando M, Yoshimatsu T, Ko C, Converse PJ, Bishai WR. Deletion of Mycobacterium tuberculosis sigma factor E results in delayed time to death with bacterial persistence in the lungs of aerosol-infected mice. Infect Immun. 2003;71:7170-7172.

   Not in our library10.1128/iai.71.12.7170-7172.2003

4. 4.

   Arruda S, Bomfim G, Knights R, Huima-Byron T, Riley LW. Cloning of an M. tuberculosis DNA fragment associated with entry and survival inside cells. Science. 1993;261:1454-1457.

   Not in our library10.1126/science.8367727

5. 5.

   Bailey TL, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol. 1994;2:28-36.

   Not in our library

6. 6.

   Bailey TL, Gribskov M. Combining evidence using p-values: application to sequence homology searches. Bioinformatics. 1998;14:48-54.

   Not in our library10.1093/bioinformatics/14.1.48

7. 7.

   Baulard AR, Betts JC, Engohang-Ndong J, Quan S, McAdam RA, Brennan PJ, et al. Activation of the pro-drug ethionamide is regulated in mycobacteria. J Biol Chem. 2000;275:28326-28331.

   Not in our library10.1074/jbc.m003744200

8. 8.

   Benjamini Y, Hochberg Y. Controlling false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc B. 1995;75:289-300.

   Not in our library

9. 9.

   Bhakta S, Besra GS, Upton AM, Parish T, Sholto-Douglas-Vernon C, Gibson KJ, et al. Arylamine N-acetyltransferase is required for synthesis of mycolic acids and complex lipids in Mycobacterium bovis BCG and represents a novel drug target. J Exp Med. 2004;199:1191-1199.

   Not in our library10.1084/jem.20031956

10. 10.

    Bishai W. Lipid lunch for persistent pathogen. Nature. 2000;406:683-685.

    Not in our library10.1038/35021159

11. 11.

    Burguiere A, Hitchen PG, Dover LG, Kremer L, Ridell M, Alexander DC, Liu J, Morris HR, Minnikin DE, Dell A, Besra GS. LosA, a key glycosyltransferase involved in the biosynthesis of a novel family of glycosylated acyltrehalose lipooligosaccharides from Mycobacterium marinum. J Biol Chem. 2005;280:42124-42133.

    Not in our library10.1074/jbc.m507500200

12. 12.

    Calamita H, Ko C, Tyagi S, Yoshimatsu T, Morrison NE, Bishai WR. The Mycobacterium tuberculosis SigD sigma factor controls the expression of ribosome-associated gene products in stationary phase and is required for full virulence. Cell Microbiol. 2005;7:233-244.

    Not in our library10.1111/j.1462-5822.2004.00454.x

13. 13.

    Camus JC, Pryor MJ, Medigue C, Cole ST. Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. Microbiology. 2002;148:2967-2973.

    Not in our library10.1099/00221287-148-10-2967

14. 14.

    Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, Parkhill J. ACT: the Artemis Comparison Tool. Bioinformatics. 2005;21:3422-3423.

    Not in our library10.1093/bioinformatics/bti553

15. 15.

    Casali N, Konieczny M, Schmidt MA, Riley LW. Invasion activity of a Mycobacterium tuberculosis peptide presented by the Escherichia coli AIDA autotransporter. Infect Immun. 2002;70:6846-6852.

    Not in our library10.1128/iai.70.12.6846-6852.2002

16. 16.

    Chang JC, Harik NS, Liao RP, Sherman DR. Identification of mycobacterial genes that alter growth and pathology in macrophages and in mice. J Infect Dis. 2007.

    Not in our library10.1086/520089

17. 17.

    Chen P, Ruiz RE, Li Q, Silver RF, Bishai WR. Construction and characterization of a Mycobacterium tuberculosis mutant lacking the alternate sigma factor gene, sigF. Infect Immun. 2000;68:5575-5580.

    Not in our library10.1128/iai.68.10.5575-5580.2000

18. 18.

    Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998;393:537-544.

    Not in our library10.1038/31159

19. 19.

    Corbett EL, Watt CJ, Walker N, Maher D, Williams BG, Raviglione MC, Dye C. The growing burden of tuberculosis: global trends and interactions with the HIV epidemic. Arch Intern Med. 2003;163:1009-1021.

    Not in our library10.1001/archinte.163.9.1009

20. 20.

    Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Res. 2004;14:1188-1190.

    Not in our library10.1101/gr.849004

21. 21.

    Dobson G, Minnikin DE, Minnikin SM, Parlett JH, Goodfellow M, Ridell MMM, Goodfellow M, Minnikin DE. Systematic analysis of complex mycobacterial lipids. Chemical Methods in Bacterial Systematics. 1985;237-265.

    Not in our library

22. 22.

    Dover LG, Corsino PE, Daniels IR, Cocklin SL, Tatituri V, Besra GS, Futterer K. Crystal structure of the TetR/CamR family repressor Mycobacterium tuberculosis EthR implicated in ethionamide resistance. J Mol Biol. 2004;340:1095-1105.

    Not in our library10.1016/j.jmb.2004.06.003

23. 23.

    Frenois F, Engohang-Ndong J, Locht C, Baulard AR, Villeret V. Structure of EthR in a ligand bound conformation reveals therapeutic perspectives against tuberculosis. Mol Cell. 2004;16:301-307.

    Not in our library10.1016/j.molcel.2004.09.020

24. 24.

    Gatfield J, Pieters J. Essential role for cholesterol in entry of mycobacteria into macrophages. Science. 2000;288:1647-1650.

    Not in our library10.1126/science.288.5471.1647

25. 25.

    Gomez M, Smith I, Hatfull GF, Jacobs WR. Determinants of mycobacterial gene expression. Molecular Genetics of Mycobacteria. 2000;111-129.

    Not in our library

26. 26.

    Grkovic S, Brown MH, Roberts NJ, Paulsen IT, Skurray RA. QacR is a repressor protein that regulates expression of the Staphylococcus aureus multidrug efflux pump QacA. J Biol Chem. 1998;273:18665-18673.

    Not in our library10.1074/jbc.273.29.18665

27. 27.

    Huffman JL, Brennan RG. Prokaryotic transcription regulators: more than just the helix-turn-helix motif. Curr Opin Struct Biol. 2002;12:98-106.

    Not in our library10.1016/s0959-440x(02)00295-6

28. 28.

    Joshi SM, Pandey AK, Capite N, Fortune SM, Rubin EJ, Sassetti CM. Characterization of mycobacterial virulence genes through genetic interaction mapping. Proc Natl Acad Sci USA. 2006;103:11760-11765.

    Not in our library10.1073/pnas.0603179103

29. 29.

    Kendall SL, Rison SC, Movahedzadeh F, Frita R, Stoker NG. What do microarrays really tell us about M. tuberculosis? Trends Microbiol. 2004;12:537-544.

    Not in our library10.1016/j.tim.2004.10.005

30. 30.

    Malhotra V, Sharma D, Ramanathan VD, Shakila H, Saini DK, Chakravorty S, et al. Disruption of response regulator gene, devR, leads to attenuation in virulence of Mycobacterium tuberculosis. FEMS Microbiol Lett. 2004;231:237-245.

    Not in our library10.1016/s0378-1097(04)00002-3

31. 31.

    Martin C, Williams A, Hernandez-Pando R, Cardona PJ, Gormley E, Bordat Y, et al. The live Mycobacterium tuberculosis phoP mutant strain is more attenuated than BCG and confers protective immunity against tuberculosis in mice and guinea pigs. Vaccine. 2006;24:3408-3419.

    Not in our library10.1016/j.vaccine.2006.03.017

32. 32.

    McKinney JD, Honer zu Bentrup K, Munoz-Elias EJ, Miczak A, Chen B, Chan WT, et al. Persistence of Mycobacterium tuberculosis in macrophages and mice requires the glyoxylate shunt enzyme isocitrate lyase. Nature. 2000;406:735-738.

    Not in our library10.1038/35021074

33. 33.

    Mitra D, Saha B, Das D, Wiker HG, Das AK. Correlating sequential homology of Mce1A, Mce2A, Mce3A and Mce4A with their possible functions in mammalian cell entry of Mycobacterium tuberculosis performing homology modeling. Tuberculosis (Edinb). 2005;85:337-345.

    Not in our library10.1016/j.tube.2005.08.010

34. 34.

    Orth P, Schnappinger D, Hillen W, Saenger W, Hinrichs W. Structural basis of gene regulation by the tetracycline inducible Tet repressor-operator system. Nat Struct Biol. 2000;7:215-219.

    Not in our library10.1038/73324

35. 35.

    Parish T, Stoker NG. Electroporation of mycobacteria. Meth Mol Biol. 1998;101:129-144.

    Not in our library10.1385/0-89603-471-2:129

36. 36.

    Parish T, Smith DA, Roberts G, Betts J, Stoker NG. The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence. Microbiology. 2003;149:1423-1435.

    Not in our library10.1099/mic.0.26245-0

37. 37.

    Parish T, Stoker NG. Use of a flexible cassette method to generate a double unmarked Mycobacterium tuberculosis tlyA plcABC mutant by gene replacement. Microbiology. 2000;146:1969-1975.

    Not in our library10.1099/00221287-146-8-1969

38. 38.

    Perez E, Samper S, Bordas Y, Guilhot C, Gicquel B, Martin C. An essential role for phoP. Mycobacterium tuberculosis virulence. Mol Microbiol. 2001;41:179-187.

    Not in our library10.1046/j.1365-2958.2001.02500.x

39. 39.

    Ramos JL, Martinez-Bueno M, Molina-Henares AJ, Teran W, Watanabe K, Zhang X, et al. The TetR family of transcriptional repressors. Microbiol Mol Biol Rev. 2005;69:326-356.

    Not in our library10.1128/mmbr.69.2.326-356.2005

40. 40.

    Rao V, Gao F, Chen B, Jacobs WR, Glickman MS. Trans-cyclopropanation of mycolic acids on trehalose dimycolate suppresses Mycobacterium tuberculosis-induced inflammation and virulence. J Clin Invest. 2006;116:1660-1667.

    Not in our library10.1172/jci27335

41. 41.

    Rengarajan J, Bloom BR, Rubin EJ. Genome-wide requirements for Mycobacterium tuberculosis adaptation and survival in macrophages. Proc Natl Acad Sci USA. 2005;102:8327-8332.

    Not in our library10.1073/pnas.0503272102

42. 42.

    Reuter M, Kupper D, Meisel A, Schroeder C, Kruger DH. Cooperative binding properties of restriction endonuclease EcoRII with DNA recognition sites. J Biol Chem. 1998;273:8294-8300.

    Not in our library10.1074/jbc.273.14.8294

43. 43.

    Rickman L, Saldanha JW, Hunt DM, Hoar DN, Colston MJ, Millar JB, Buxton RS. A two-component signal transduction system with a PAS domain-containing sensor is required for virulence of Mycobacterium tuberculosis in mice. Biochem Biophys Res Commun. 2004;314:259-267.

    Not in our library10.1016/j.bbrc.2003.12.082

44. 44.

    Rosas-Magallanes V, Stadthagen-Gomez G, Rauzier J, Barreiro LB, Tailleux L, Boudou F, et al. Signature-tagged transposon mutagenesis identifies novel Mycobacterium tuberculosis genes involved in the parasitism of human macrophages. Infect Immun. 2007;75:504-507.

    Not in our library10.1128/iai.00058-06

45. 45.

    Russell DG, Mwandumba HC, Rhoades EE. Mycobacterium and the coat of many lipids. J Cell Biol. 2002;158:421-426.

    Not in our library10.1083/jcb.200205034

46. 46.

    Sandy J, Mushtaq A, Kawamura A, Sinclair J, Sim E, Noble M. The structure of arylamine N-acetyltransferase from Mycobacterium smegmatis – an enzyme which inactivates the anti-tubercular drug, isoniazid. J Mol Biol. 2002;318:1071-1083.

    Not in our library10.1016/s0022-2836(02)00141-9

47. 47.

    Santangelo MP, Goldstein J, Alito A, Gioffre A, Caimi K, Zabal O, et al. Negative transcriptional regulation of the mce3 operon in Mycobacterium tuberculosis. Microbiology. 2002;148:2997-3006.

    Not in our library10.1099/00221287-148-10-2997

48. 48.

    Sassetti CM, Rubin EJ. Genetic requirements for mycobacterial survival during infection. Proc Natl Acad Sci USA. 2003;100:12989-12994.

    Not in our library10.1073/pnas.2134250100

49. 49.

    Schnappinger D, Ehrt S, Voskuil MI, Liu Y, Mangan JA, Monahan IM, et al. Transcriptional adaptation of Mycobacterium tuberculosis within macrophages: insights into the phagosomal environment. J Exp Med. 2003;198:693-704.

    Not in our library10.1084/jem.20030846

50. 50.

    Schumacher MA, Miller MC, Grkovic S, Brown MH, Skurray RA, Brennan RG. Structural mechanisms of QacR induction and multidrug recognition. Science. 2001;294:2158-2163.

    Not in our library10.1126/science.1066020

51. 51.

    Smyth GK, Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W. Limma: linear models for microarray data. Bioinformatics and Computational Biology Solutions Using R and Bioconductor. 2005;397-420.

    Not in our library

52. 52.

    Snapper SB, Melton RE, Mustafa S, Kieser T, Jacobs WR. Isolation and characterization of efficient plasmid transformation mutants of Mycobacterium smegmatis. Mol Microbiol. 1990;4:1911-1919.

    Not in our library10.1111/j.1365-2958.1990.tb02040.x

53. 53.

    Sun R, Converse PJ, Ko C, Tyagi S, Morrison NE, Bishai WR. Mycobacterium tuberculosis ECF sigma factor sigC is required for lethality in mice and for the conditional expression of a defined gene set. Mol Microbiol. 2004;52:25-38.

    Not in our library10.1111/j.1365-2958.2003.03958.x

54. 54.

    Talaat AM, Lyons R, Howard ST, Johnston SA. The temporal expression profile of Mycobacterium tuberculosis infection in mice. Proc Natl Acad Sci USA. 2004;101:4602-4607.

    Not in our library10.1073/pnas.0306023101

55. 55.

    Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22:4673-4680.

    Not in our library10.1093/nar/22.22.4673

56. 56.

    Uchida Y, Casali N, White A, Morici L, Kendall LV, Riley LW. Accelerated immunopathological response of mice infected with Mycobacterium tuberculosis disrupted in the mce1 operon negative transcriptional regulator. Cell Microbiol. 2007;9:1275-1283.

    Not in our library10.1111/j.1462-5822.2006.00870.x

57. 57.

    Van der Geize R, Yam K, Heuser T, Wilbrink MH, Hara H, Anderton MC, et al. A gene cluster encoding cholesterol catabolism in a soil actinomycete provides insight into Mycobacterium tuberculosis survival in macrophages. Proc Natl Acad Sci USA. 2007;104:1947-1952.

    Not in our library10.1073/pnas.0605728104

58. 58.

    Walters SB, Dubnau E, Kolesnikova I, Laval F, Daffe M, Smith I. The Mycobacterium tuberculosis PhoPR two-component system regulates genes essential for virulence and complex lipid biosynthesis. Mol Microbiol. 2006;60:312-330.

    Not in our library10.1111/j.1365-2958.2006.05102.x

59. 59.

    Wernisch L, Kendall SL, Soneji S, Wietzorrek A, Parish T, Hinds J, et al. Analysis of whole-genome microarray replicates using mixed models. Bioinformatics. 2003;19:53-61.

    Not in our library10.1093/bioinformatics/19.1.53

60. 60.

    Zahrt TC, Deretic V. Mycobacterium tuberculosis signal transduction system required for persistent infections. Proc Natl Acad Sci USA. 2001;98:12706-12711.

    Not in our library10.1073/pnas.221272198

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