Synthesis and selection of de novo proteins that bind and impede cellular functions of an essential mycobacterial protein

Applied and Environmental Microbiology

Volumn 73, Issue 4, 2007, Pages 1320-1331

  Rao, Alka ^a   Ram, Geeta ^a   Saini, Adesh Kumar ^b   Vohra, Reena ^b   Kumar, Krishan ^a   Singh, Yogendra ^b   Ranganathan, Anand ^a  

^a INTERNATIONAL CENTRE FOR GENETIC ENGINEERING AND BIOTECHNOLOGY   (Italy)

^b CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

CELLULAR FUNCTIONS; PATHOGENS; PROTEIN LIBRARIES;

AMINO ACIDS; BACTERIA; BIOASSAY; CELLS; GROWTH KINETICS; SYNTHESIS (CHEMICAL);

PROTEINS;

HISTONE; PROTEIN DERIVATIVE; PROTEIN HUPB; UNCLASSIFIED DRUG;

BACTERIUM; GENE EXPRESSION; PATHOGEN; PEPTIDE; PROTEIN; TUBERCULOSIS;

AMINO ACID SEQUENCE; ARTICLE; CELL DAMAGE; CIRCULAR DICHROISM; MYCOBACTERIUM SMEGMATIS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PEPTIDE SYNTHESIS; PROTEIN PROTEIN INTERACTION; PROTEIN SYNTHESIS; TRANSMISSION ELECTRON MICROSCOPY;

BACTERIAL PHYSIOLOGY; BACTERIAL PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; HISTONES; MYCOBACTERIUM; PROTEIN BINDING;

BACTERIA (MICROORGANISMS); CORYNEBACTERINEAE; MYCOBACTERIUM SMEGMATIS; MYCOBACTERIUM TUBERCULOSIS;

EID: 33847182056     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.02461-06     Document Type: Article

References (54)

1. Barberis, A., J. Pearlberg, N. Simkovich, S. Farrell, P. Reinagel, C. Bamdad, G. Sigal, and M. Ptashne. 1995. Contact with a component of the polymerase II holoenzyme suffices for gene activation. Cell 81:359-368.
2. Begg, K. J., and W. D. Donachie. 1985. Cell shape and division in Escherichia coli: experiments with shape and division mutants. J. Bacteriol. 163:615-622.
3. Blum, J. H., S. L. Dove, A. Hochschild, and J. J. Mekalanos. 2000. Isolation of peptide aptamers that inhibit intracellular processes. Proc. Natl. Acad. Sci. USA 97:2241-2246.
4. Butz, K., C. Denk, B. Fitscher, I. Crnkovic-Mertens, A. Ullmann, C. H. Schroder, and F. Hoppe-Seyler. 2001. Peptide aptamers targeting the hepatitis B virus core protein: a new class of molecules with antiviral activity. Oncogene 20:6579-6586.
5. Chattopadhyay, A., S. A. Tate, R. W. Beswick, S. D. Wagner, and P. K. Ferrigno. 2005. A peptide aptamer to antagonize BCL-6 function. Oncogene 25:2223-2233.
6. Chopra, S., and A. Ranganathan. 2003. Protein evolution by "codon shuffling": a novel method for generating highly variant mutant libraries by assembly of hexamer DNA duplexes. Chem. Biol. 10:917-926.
7. Colas, P., B. Cohen, T. Jessen, I. Grishina, J. McCoy, and R. Brent. 1996. Genetic selection of peptide aptamers that recognize and inhibit cyclin-dependent kinase 2. Nature 380:548-550.
8. Cole, S. T., R. Brosch, J. Parkhill, T. Garnier, C. Churcher, D. Harris, S. V. Gordon, K. Eiglmeier, S. Gas, C. E. Barry III, F. Tekaia, K. Badcock, D. Basham, D. Brown, T. Chillingworth, R. Connor, R. Davies, K. Devlin, T. Feltwell, S. Gentles, N. Hamlin, S. Holroyd, T. Hornsby, K. Jagels, A. Krogh, J. McLean, S. Moule, L. Murphy, K. Oliver, J. Osborne, M. A. Quail, M. A. Rajandream, J. Rogers, S. Rutter, K. Seeger, J. Skelton, R. Squares, S. Squares, J. E. Sulston, K. Taylor, S. Whitehead, and B. G. Barrell. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537-544.
9. Corey, M. J., and E. Corey. 1996. On the failure of de novo-designed peptides as biocatalysts. Proc. Natl. Acad. Sci. USA 93:11428-11434.
10. Dahiyat, B. I., and S. L. Mayo. 1997. De novo protein design: fully automated sequence selection. Science 278:82-87.
11. DasGupta, S. K., S. Jain, D. Kaushal, and A. K. Tyagi. 1998. Expression systems for study of mycobacterial gene regulation and development of recombinant BCG vaccines. Biochem. Biophys. Res. Commun. 246:797-804.
12. Deol, P., R. Vohra, A. K. Saini, A. Singh, H. Chandra, P. Chopra, T. K. Das, A. K. Tyagi, and Y. Singh. 2005. Role of Mycobacterium tuberculosis Ser/Thr kinase PknF: implications in glucose transport and cell division. J. Bacteriol. 187:3415-3420.
13. Dove, S. L., J. K. Joung, and A. Hochschild. 1997. Activation of prokaryotic transcription through arbitrary protein-protein contacts. Nature 386:627-630.
14. Eiden, L. E. 2005. Fusion polypeptides that inhibit exocytosis: fusing aptamer and cell-penetrating peptide technologies and pharmacologies. Mol. Pharmacol. 67:980-982.
15. Gazzard, B. 2001. Tuberculosis, HIV and the developing world. Clin. Med. 1:62-68.
16. Glickman, S. W., E. B. Rasiel, C. D. Hamilton, A. Kubataev, and K. A. Schulman. 2006. A portfolio model of drug development for tuberculosis. Science 311:1246-1247.
17. Grass, J. A., M. E. Boyer, S. Pal, J. Wu, M. J. Weiss, and E. H. Bresnick. 2003. GATA-1-dependent transcriptional repression of GATA-2 via disruption of positive autoregulation and domain-wide chromatin remodeling. Proc. Natl. Acad. Sci. USA 100:8811-8816.
18. Hashimoto, Y., A. Q. Khan, and T. Ezaki. 1996. Positive autoregulation of vipR expression in ViaB region-encoded Vi antigen of Salmonella typhi. J. Bacteriol. 178:1430-1436.
19. Hatfull, F., and W. R. Jacobs, Jr. 2000. Molecular genetics of mycobacteria. American Society for Microbiology, Washington, DC.
20. Haydel, S. E., W. H. Benjamin, N. E. Dunlap, and J. E. Clark-Curtiss. 2002. Expression, autoregulation, and DNA binding properties of the Mycobacterium tuberculosis TrcR response regulator. J. Bacteriol. 184:2192-2203.
21. Kamtekar, S., J. M. Schiffer, H. Xiong, J. M. Babik, and M. H. Hecht. 1993. Protein design by binary patterning of polar and nonpolar amino acids. Science 262:1680-1685.
22. Keefe, A. D., and J. W. Szostak. 2001. Functional proteins from a random-sequence library. Nature 410:715-718.
23. Kiel, C., T. Selzer, Y. Shaul, G. Schreiber, and C. Herrmann. 2004. Electrostatically optimized Ras-binding Ral guanine dissociation stimulator mutants increase the rate of association by stabilizing the encounter complex. Proc. Natl. Acad. Sci. USA 101:9223-9228.
24. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680-685.
25. Lee, B. H., B. Murugasu-Oei, and T. Dick. 1998. Upregulation of a histone-like protein in dormant Mycobacterium smegmatis. Mol. Gen. Genet. 260: 475-479.
26. Marques, M. A., S. Mahapatra, E. N. Sarno, S. Santos, J. S. Spencer, P. J. Brennan, and M. C. Pessolani. 2001. Further biochemical characterization of Mycobacterium leprae laminin-binding proteins. Braz. J. Med. Biol. Res. 34:463-470.
27. Miller, J. H. 1972. Experiments in molecular genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
28. Miller, L. P., J. T. Crawford, and T. M. Shinnick. 1994. The rpoB gene of Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 38:805-811.
29. Moffet, D. A., and M. H. Hecht. 2001. De novo proteins from combinatorial libraries. Chem. Rev. 101:3191-3203.
30. Ohlstein, E. H., R. R. Ruffolo, and J. D. Elliott. 2000. Drug discovery in the next millennium. Annu. Rev. Pharmacol. Toxicol. 40:177-191.
31. Onyebujoh, P., A. Zumla, I. Ribeiro, R. Rustomjee, P. Mwaba, M. Gomes, and J. M. Grange. 2005. Treatment of tuberculosis: present status and future prospects. Bull. W. H. O. 83:857-865.
32. Panyim, S., and R. Chalkley. 1971. The molecular weights of vertebrate histones exploiting a modified sodium dodecyl sulfate electrophoretic method. J. Biol. Chem. 246:7557-7560.
33. Prabhakar, S., P. S. Annapurna, N. K. Jain, A. B. Dey, J. S. Tyagi, and H. K. Prasad. 1998. Identification of an immunogenic histone-like protein (HLPMt) of Mycobacterium tuberculosis. Tuber. Lung Dis. 79:43-53.
34. Prijambada, I. D., T. Yomo, F. Tanaka, T. Kawama, K. Yamamoto, A. Hasegawa, Y. Shima, S. Negoro, and I. Urabe. 1996. Solubility of artificial proteins with random sequences. FEBS Lett. 382:21-25.
35. Rao, A., S. Chopra, G. Ram, A. Gupta, and A. Ranganathan. 2005. Application of the "codon-shuffling" method. Synthesis and selection of de novo proicins as antibacterials. J. Biol. Chem. 280:23605-23614.
36. Rao, A., and A. Ranganathan. 2004. Interaction studies on proteins encoded by the phthiocerol dimycocerosate locus of Mycobacterium tuberculosis. Mol. Genet. Genomics 272:571-579.
37. Regan, L., and W. F. DeGrado. 1988. Characterization of a helical protein designed from first principles. Science 241:976-978.
38. Rengarajan, J., B. R. Bloom, and E. J. Rubin. 2005. Genome-wide requirements for Mycobacterium tuberculosis adaptation and survival in macrophages. Proc. Natl. Acad. Sci. USA 102:8327-8332.
39. Roberts, R. W. 1999. Totally in vitro protein selection using mRNA-protein fusions and ribosome display. Curr. Opin. Chem. Biol. 3:268-273.
40. Rodi, D. J., and L. Makowski. 1999. Phage-display technology-finding a needle in a vast molecular haystack. Curr. Opin. Biotechnol. 10:87-93.
41. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
42. Sassetti, C. M., D. H. Boyd, and E. J. Rubin. 2001. Comprehensive identification of conditionally essential genes in mycobacteria. Proc. Natl. Acad. Sci. USA 98:12712-12717.
43. Sassetti, C. M., D. H. Boyd, and E. J. Rubin. 2003. Genes required for mycobacterial growth defined by high density mutagenesis. Mol. Microbiol. 48:77-84.
44. Sassetti, C. M., and E. J. Rubin. 2003. Genetic requirements for mycobacterial survival during infection. Proc. Natl. Acad. Sci. USA 100:12989-12994.
45. Schreiber, G., and A. R. Fersht. 1996. Rapid, electrostatically assisted association of proteins. Nat. Struct. Biol. 3:427-431.
46. Shires, K., and L. Steyn. 2001. The cold-shock stress response in Mycobacterium smegmatis induces the expression of a histone-like protein. Mol. Microbiol. 39:994-1009.
47. Sinha, N., and S. J. Smith-Gill. 2002. Electrostatics in protein binding and function. Curr. Protein Pept. Sci. 3:601-614.
48. Soares de Lima, C., L. Zulianello, M. A. Marques, H. Kim, M. I. Portugal, S. L. Antunes, F. D. Menozzi, T. H. Ottenhoff, P. J. Brennan, and M. C. Pessolani. 2005. Mapping the laminin-binding and adhesive domain of the cell surface-associated Hlp/LBP protein from Mycobacterium leprae. Microbes. Infect. 7:1097-1109.
49. Taylor, S. V., K. U. Walter, P. Kast, and D. Hilvert. 2001. Searching sequence space for protein catalysts. Proc. Natl. Acad. Sci. USA 98:10596-10601.
50. Turgay, K., J. Hahn, J. Burghoorn, and, and D. Dubnau. 1998. Competence in Bacillus subtilis is controlled by regulated proteolysis of a transcription factor. EMBO J. 17:6730-6738.
51. Wade, R. C., R. R. Gabdoulline, S. K. Ludemann, and V. Lounnas. 1998. Electrostatic steering and ionic tethering in enzyme-ligand binding: insights from simulations. Proc. Natl. Acad. Sci. USA 95:5942-5949.
52. Williams, B. G., R. Granich, L. S. Chauhan, N. S. Dharmshaktu, and C. Dye. 2005. The impact of HIV/AIDS on the control of tuberculosis in India. Proc. Natl. Acad. Sci. USA 102:9619-9624.
53. Woodman, R., J. T. Yeh, S. Laurenson, and P. Ko-Ferrigno. 2005. Design and validation of a neutral protein scaffold for the presentation of peptide aptamers. J. Mol. Biol. 352:1118-1133.
54. Zhang, C. C. 1993. A gene encoding a protein related to eukaryotic protein kinases from the filamentous heterocystous cyanobacterium Anabaena PCC7120. Proc. Natl. Acad. Sci. USA 90:11840-11844.