Function of heterologous and truncated RNase P proteins in Bacillus subtilis

Molecular Microbiology

Volumn 66, Issue 3, 2007, Pages 801-813

  Gößringer, Markus ^a   Hartmann, Roland K ^a  

^a PHILIPPS UNIVERSITY MARBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; RIBONUCLEASE P; RIBONUCLEOPROTEIN A; UNCLASSIFIED DRUG;

ARCHAEBACTERIUM; ARTICLE; BACILLUS SUBTILIS; BACTERIAL GENETICS; BACTERIAL GROWTH; BACTERIAL STRAIN; GENE FUNCTION; GENE INSERTION; GENETIC COMPLEMENTATION; HETEROLOGOUS EXPRESSION; METAL BINDING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FUNCTION; PSYCHROPHILIC BACTERIUM; THERMOACIDOPHILIC BACTERIUM; THERMOPHILIC BACTERIUM;

AMINO ACID SEQUENCE; BACILLUS SUBTILIS; BACTERIAL PROTEINS; BLOTTING, WESTERN; EVOLUTION, MOLECULAR; GENETIC COMPLEMENTATION TEST; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; PHYLOGENY; PROTEIN STRUCTURE, SECONDARY; RIBONUCLEASE P; SEQUENCE DELETION;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 35448968985     PISSN: 0950382X     EISSN: 13652958     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2007.05962.x     Document Type: Article

References (48)

1. Aguiar, P., Beveridge, T.J. Reysenbach, A.L. (2004) Sulfurihydrogenibium azorense, sp. nov., a thermophilic hydrogen-oxidizing microaerophile from terrestrial hot springs in the Azores. Int J Syst Evol Microbiol 54 : 33 39.
2. Andrews, A.J., Hall, T.A. Brown, J.W. (2001) Characterization of RNase P holoenzymes from Methanococcus jannaschii and Methanothermobacter thermoautotrophicus. Biol Chem 382 : 1171 1177.
3. Brown, J.W. (1999) The Ribonuclease P Database. Nucleic Acids Res 27 : 314.
4. Buck, A.H., Kazantsev, A.V., Dalby, A.B. Pace, N.R. (2005a) Structural perspective on the activation of RNAse P RNA by protein. Nat Struct Mol Biol 12 : 958 964.
5. Buck, A.H., Dalby, A.B., Poole, A.W., Kazantsev, A.V. Pace, N.R. (2005b) Protein activation of a ribozyme: the role of bacterial RNase P protein. EMBO J 24 : 3360 3368.
6. Asp. Biochemistry 37 : 9409 9416.
7. Day-Storms, J.J., Niranjanakumari, S. Fierke, C.A. (2004) Ionic interactions between P RNA and P protein in Bacillus subtilis RNase P characterized using a magnetocapture-based assay. RNA 10 : 1595 1608.
8. Fang, X.W., Yang, X.J., Littrell, K., Niranjanakumari, S., Thiyagarajan, P., Fierke, C.A., et al. (2001) The Bacillus subtilis RNase P holoenzyme contains two RNase P RNA and two RNase P protein subunits. RNA 7 : 233 241.
9. Feltens, R., Gößringer, M., Willkomm, D.K., Urlaub, H. Hartmann, R.K. (2003) An unusual mechanism of bacterial gene expression revealed for the RNase P protein of Thermus strains. Proc Natl Acad Sci USA 100 : 5724 5729.
10. Garsoux, G., Lamotte, J., Gerday, C. Feller, G. (2004) Kinetic and structural optimization to catalysis at low temperatures in a psychrophilic cellulase from the Antarctic bacterium Pseudoalteromonas haloplanktis. Biochem J 384 : 247 253.
11. Gopalan, V. (2007) Uniformity amid diversity in RNase P. Proc Natl Acad Sci USA 104 : 2031 2032.
12. Gopalan, V., Baxevanis, A.D., Landsman, D. Altman, S. (1997) Analysis of the functional role of conserved residues in the protein subunit of Ribonuclease P from Escherichia coli. J Mol Biol 267 : 818 829.
13. Gößringer, M., Kretschmer-Kazemi Far, R. Hartmann, R.K. (2006) Analysis of RNase P protein (rnpA) expression in Bacillus subtilis utilizing strains with suppressable rnpA expression. J Bacteriol 188 : 6816 6823.
14. Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N. Altman, S. (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35 : 849 857.
15. Hall, T.A. Brown, J.W. (2001) The ribonuclease P family. Methods Enzymol 341 : 56 77.
16. Hartmann, E. Hartmann, R.K. (2003) The enigma of ribonuclease P evolution. Trends Genet 19 : 561 569.
17. Higgins, D.G., Thompson, J.D. Gibson, T.J. (1996) Using CLUSTAL for multiple sequence alignments. Methods Enzymol 266 : 383 402.
18. Jovanovic, M., Sanchez, R., Altman, S. Gopalan, V. (2002) Elucidation of structure-function relationships in the protein subunit of bacterial RNase P using a genetic complementation approach. Nucleic Acids Res 30 : 5065 5073.
19. Kazantsev, A.V., Krivenko, A.A., Harrington, D.J., Carter, R.J., Holbrook, S.R., Adams, P.D. Pace, N.R. (2003) High-resolution structure of RNase P protein from Thermotoga maritima. Proc Natl Acad Sci USA 100 : 7497 7502.
20. Kim, J.J., Kilani, A.F., Zhan, X., Altman, S. Liu, F. (1997) The protein cofactor allows the sequence of an RNase P ribozyme to diversify by maintaining the catalytically active structure of the enzyme. RNA 3 : 613 623.
21. Kim, M., Hyun Park, B. Lee, Y. (2000) Effects of terminal deletions in C5 protein on promoting RNase P catalysis. Biochem Biophys Res Commun 268 : 118 123.
22. Kirsebom, L.A., Baer, M.F. Altman, S. (1988) Differential effects of mutations in the protein and RNA moieties of RNase P on the efficiency of suppression by various tRNA suppressors. J Mol Biol 204 : 879 888.
23. Kouzuma, Y., Mizoguchi, M., Takagi, H., Fukuhara, H., Tsukamoto, M., Numata, T. Kimura, M. (2003) Reconstitution of archaeal ribonuclease P from RNA and four protein components. Biochem Biophys Res Commun 306 : 666 673.
24. Kurz, J.C. Fierke, C.A. (2002) The affinity of magnesium binding sites in the Bacillus subtilis RNase P x pre-tRNA complex is enhanced by the protein subunit. Biochemistry 41 : 9545 9558.
25. Asp. Biochemistry 37 : 2393 2400.
26. Kyhse-Andersen, J. (1984) Electroblotting of multiple gels: a simple apparatus without buffer tank for rapid transfer of proteins from polyacrylamide to nitrocellulose. J Biochem Biophys Methods 10 : 203 209.
27. Mann, H., Ben-Asouli, Y., Schein, A., Moussa, S. Jarrous, N. (2003) Eukaryotic RNase P: role of RNA and protein subunits of a primordial catalytic ribonucleoprotein in RNA-based catalysis. Mol Cell 12 : 925 935.
28. Marquez, S.M., Harris, J.K., Kelley, S.T., Brown, J.W., Dawson, S.C., Roberts, E.C. Pace, N.R. (2005) Structural implications of novel diversity in eucaryal RNase P RNA. RNA 11 : 739 751.
29. Niranjanakumari, S., Stams, T., Crary, S.M., Christianson, D.W. Fierke, C.A. (1998) Protein component of the ribozyme ribonuclease P alters substrate recognition by directly contacting precursor tRNA. Proc Natl Acad Sci USA 95 : 15212 15217.
30. Niranjanakumari, S., Day-Storms, J.J., Ahmed, M., Hsieh, J., Zahler, N.H., Venters, R.A. Fierke, C.A. (2007) Probing the architecture of the Bacillus subtilis RNase P holoenzyme active site by cross-linking and affinity cleavage. RNA 13 : 521 535.
31. Reich, C., Olsen, G.J., Pace, B. Pace, N.R. (1988) Role of the protein moiety of ribonuclease P, a ribonucleoprotein enzyme. Science 239 : 178 181.
32. Asp bound to the Bacillus subtilis RNase P holoenzyme has an extended conformation. Biochemistry 44 : 16130 16139.
33. Sambrook, J., Fritsch, E.F. Maniatis, T.E. (1989) Molecular Cloning. A Laboratory Manual. Cold Spring Harbor, NY : Cold Spring Harbor Laboratory.
34. Schägger, H. von Jagow, G. (1987) Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Anal Biochem 166 : 368 379.
35. Schedl, P., Primakoff, P. Roberts, J. (1974) Processing of E. coli tRNA precursors. Brookhaven Symp Biol 26 : 53 76.
36. Sharin, E., Schein, A., Mann, H., Ben-Asouli, Y. Jarrous, N. (2005) RNase P: role of distinct protein cofactors in tRNA substrate recognition and RNA-based catalysis. Nucleic Acids Res 33 : 5120 5132.
37. Spitzfaden, C., Nicholson, N., Jones, J.J., Guth, S., Lehr, R., Prescott, C.D., et al. (2000) The structure of ribonuclease P protein from Staphylococcus aureus reveals a unique binding site for single-stranded RNA. J Mol Biol 295 : 105 115.
38. Stams, T., Niranjanakumari, S., Fierke, C. Christianson, D.W. (1998) Ribonuclease P protein structure: evolutionary origins in the translational apparatus. Science 280 : 752 755.
39. Stragier, P., Bonamy, C. Karmazyn-Campelli, C. (1988) Processing of a sporulation sigma factor in Bacillus subtilis: how morphological structure could control gene expression. Cell 52 : 697 704.
40. Sun, L., Campbell, F.E., Zahler, N.H. Harris, M.E. (2006) Evidence that substrate-specific effects of C5 protein lead to uniformity in binding and catalysis by RNase P. EMBO J 25 : 3998 4007.
41. Teeling, H. Gloeckner, F.O. (2006) RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits. BMC Bioinformatics 7 : 66.
42. Tsai, H.Y., Pulukkunat, D.K., Woznick, W.K. Gopalan, V. (2006) Functional reconstitution and characterization of Pyrococcus furiosus RNase P. Proc Natl Acad Sci USA 103 : 16147 16152.
43. Waugh, D.S. Pace, N.R. (1990) Complementation of an RNase P RNA (rnpB) gene deletion in Escherichia coli by homologous genes from distantly related eubacteria. J Bacteriol 172 : 6316 6321.
44. Wegscheid, B., Condon, C. Hartmann, R.K. (2006) Type A and B RNase P RNAs are interchangeable in vivo despite substantial biophysical differences. EMBO Rep 7 : 411 417.
45. Westhof, E., Wesolowski, D. Altman, S. (1996) Mapping in three dimensions of regions in a catalytic RNA protected from attack by an Fe (II) -EDTA reagent. J Mol Biol 258 : 600 613.
46. Wilson, R.C., Bohlen, C.J., Foster, M.P. Bell, C.E. (2006) Structure of Pfu Pop5, an archaeal RNase P protein. Proc Natl Acad Sci USA 103 : 873 878.
47. Xue, G.-P., Johnson, J.S. Dalrymple, B.P. (1999) High osmolarity improves the electro-transformation efficiency of the gram-positive bacteria Bacillus subtilis and Bacillus licheniformes. J Microbiol Methods 34 : 183 191.
48. Zeikus, J.G. Wolfe, R.S. (1972) Methanobacterium thermoautotrophicus sp. n., an anaerobic, autotrophic, extreme thermophile. J Bacteriol 109 : 707 715.