Skip to main content
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1989 Sep 25;17(18):7469–7486. doi: 10.1093/nar/17.18.7469

Cloning and analysis of the spc ribosomal protein operon of Bacillus subtilis: comparison with the spc operon of Escherichia coli.

T M Henkin 1, S H Moon 1, L C Mattheakis 1, M Nomura 1
PMCID: PMC334824  PMID: 2508062

Abstract

A segment of Bacillus subtilis chromosomal DNA homologous to the Escherichia coli spc ribosomal protein operon was isolated using cloned E. coli rplE (L5) DNA as a hybridization probe. DNA sequence analysis of the B. subtilis cloned DNA indicated a high degree of conservation of spc operon ribosomal protein genes between B. subtilis and E. coli. This fragment contains DNA homologous to the promoter-proximal region of the spc operon, including coding sequences for ribosomal proteins L14, L24, L5, S14, and part of S8; the organization of B. subtilis genes in this region is identical to that found in E. coli. A region homologous to the E. coli L16, L29 and S17 genes, the last genes of the S10 operon, was located upstream from the gene for L14, the first gene in the spc operon. Although the ribosomal protein coding sequences showed 40-60% amino acid identity with E. coli sequences, we failed to find sequences which would form a structure resembling the E. coli target site for the S8 translational repressor, located near the beginning of the L5 coding region in E. coli, in this region or elsewhere in the B. subtilis spc DNA.

Full text

PDF

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Band L., Yansura D. G., Henner D. J. Construction of a vector for cloning promoters in Bacillus subtilis. Gene. 1983 Dec;26(2-3):313–315. doi: 10.1016/0378-1119(83)90204-4. [DOI] [PubMed] [Google Scholar]
  2. Boylan S. A., Suh J. W., Thomas S. M., Price C. W. Gene encoding the alpha core subunit of Bacillus subtilis RNA polymerase is cotranscribed with the genes for initiation factor 1 and ribosomal proteins B, S13, S11, and L17. J Bacteriol. 1989 May;171(5):2553–2562. doi: 10.1128/jb.171.5.2553-2562.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Cerretti D. P., Dean D., Davis G. R., Bedwell D. M., Nomura M. The spc ribosomal protein operon of Escherichia coli: sequence and cotranscription of the ribosomal protein genes and a protein export gene. Nucleic Acids Res. 1983 May 11;11(9):2599–2616. doi: 10.1093/nar/11.9.2599. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cerretti D. P., Mattheakis L. C., Kearney K. R., Vu L., Nomura M. Translational regulation of the spc operon in Escherichia coli. Identification and structural analysis of the target site for S8 repressor protein. J Mol Biol. 1988 Nov 20;204(2):309–329. doi: 10.1016/0022-2836(88)90578-5. [DOI] [PubMed] [Google Scholar]
  5. Côté J. C., Wu R. Sequence of the chloroplast rps14 gene encoding the chloroplast ribosomal protein S14 from rice. Nucleic Acids Res. 1989 Feb 25;17(4):1780–1780. doi: 10.1093/nar/17.4.1780. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Dabbs E. R. Arrangement of loci within the principal cluster of ribosomal protein genes of Bacillus subtilis. Mol Gen Genet. 1983;192(1-2):124–130. doi: 10.1007/BF00327657. [DOI] [PubMed] [Google Scholar]
  7. Dabbs E. R. Mapping of the genes for Bacillus subtilis ribosomal proteins S6 and S16: comparison of the chromosomal distribution of ribosomal protein genes in this bacterium with the distribution in Escherichia coli. Mol Gen Genet. 1983;192(3):386–390. doi: 10.1007/BF00392179. [DOI] [PubMed] [Google Scholar]
  8. Dabbs E. R. Order of ribosomal protein genes in the Rif cluster of Bacillus subtilis is identical to that of Escherichia coli. J Bacteriol. 1984 Aug;159(2):770–772. doi: 10.1128/jb.159.2.770-772.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Dean D., Nomura M. Feedback regulation of ribosomal protein gene expression in Escherichia coli. Proc Natl Acad Sci U S A. 1980 Jun;77(6):3590–3594. doi: 10.1073/pnas.77.6.3590. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Dean D., Yates J. L., Nomura M. Escherichia coli ribosomal protein S8 feedback regulates part of spc operon. Nature. 1981 Jan 1;289(5793):89–91. doi: 10.1038/289089a0. [DOI] [PubMed] [Google Scholar]
  11. Feinberg A. P., Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem. 1983 Jul 1;132(1):6–13. doi: 10.1016/0003-2697(83)90418-9. [DOI] [PubMed] [Google Scholar]
  12. Ferrari F. A., Trach K., Hoch J. A. Sequence analysis of the spo0B locus reveals a polycistronic transcription unit. J Bacteriol. 1985 Feb;161(2):556–562. doi: 10.1128/jb.161.2.556-562.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Graves M. C., Rabinowitz J. C. In vivo and in vitro transcription of the Clostridium pasteurianum ferredoxin gene. Evidence for "extended" promoter elements in gram-positive organisms. J Biol Chem. 1986 Aug 25;261(24):11409–11415. [PubMed] [Google Scholar]
  14. Green C. J., Stewart G. C., Hollis M. A., Vold B. S., Bott K. F. Nucleotide sequence of the Bacillus subtilis ribosomal RNA operon, rrnB. Gene. 1985;37(1-3):261–266. doi: 10.1016/0378-1119(85)90281-1. [DOI] [PubMed] [Google Scholar]
  15. Gregory R. J., Cahill P. B., Thurlow D. L., Zimmermann R. A. Interaction of Escherichia coli ribosomal protein S8 with its binding sites in ribosomal RNA and messenger RNA. J Mol Biol. 1988 Nov 20;204(2):295–307. doi: 10.1016/0022-2836(88)90577-3. [DOI] [PubMed] [Google Scholar]
  16. Henkin T. M., Chambliss G. H. Genetic mapping of a mutation causing an alteration in Bacillus subtilis ribosomal protein S4. Mol Gen Genet. 1984;193(2):364–369. doi: 10.1007/BF00330694. [DOI] [PubMed] [Google Scholar]
  17. Henkin T. M., Sonenshein A. L. Mutations of the Escherichia coli lacUV5 promoter resulting in increased expression in Bacillus subtilis. Mol Gen Genet. 1987 Oct;209(3):467–474. doi: 10.1007/BF00331151. [DOI] [PubMed] [Google Scholar]
  18. Higo K., Held W., Kahan L., Nomura M. Functional correspondence between 30S ribosomal proteins of Escherichia coli and Bacillus stearothermophilus. Proc Natl Acad Sci U S A. 1973 Mar;70(3):944–948. doi: 10.1073/pnas.70.3.944. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Higo K., Otaka E., Osawa S. Purification and characterization of 30S ribosomal proteins from Bacillus subtilis: correlation to Escherichia coli 30S proteins. Mol Gen Genet. 1982;185(2):239–244. doi: 10.1007/BF00330792. [DOI] [PubMed] [Google Scholar]
  20. Hori H., Higo K., Osawa S. The rates of evolution in some ribosomal components. J Mol Evol. 1977 May 13;9(3):191–201. doi: 10.1007/BF01796108. [DOI] [PubMed] [Google Scholar]
  21. Kimura M., Kimura J., Ashman K. The complete primary structure of ribosomal proteins L1, L14, L15, L23, L24 and L29 from Bacillus stearothermophilus. Eur J Biochem. 1985 Aug 1;150(3):491–497. doi: 10.1111/j.1432-1033.1985.tb09049.x. [DOI] [PubMed] [Google Scholar]
  22. Lindahl L., Zengel J. M. Ribosomal genes in Escherichia coli. Annu Rev Genet. 1986;20:297–326. doi: 10.1146/annurev.ge.20.120186.001501. [DOI] [PubMed] [Google Scholar]
  23. Mattheakis L. C., Nomura M. Feedback regulation of the spc operon in Escherichia coli: translational coupling and mRNA processing. J Bacteriol. 1988 Oct;170(10):4484–4492. doi: 10.1128/jb.170.10.4484-4492.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Mattheakis L., Vu L., Sor F., Nomura M. Retroregulation of the synthesis of ribosomal proteins L14 and L24 by feedback repressor S8 in Escherichia coli. Proc Natl Acad Sci U S A. 1989 Jan;86(2):448–452. doi: 10.1073/pnas.86.2.448. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Messing J. New M13 vectors for cloning. Methods Enzymol. 1983;101:20–78. doi: 10.1016/0076-6879(83)01005-8. [DOI] [PubMed] [Google Scholar]
  26. Moriya S., Ogasawara N., Yoshikawa H. Structure and function of the region of the replication origin of the Bacillus subtilis chromosome. III. Nucleotide sequence of some 10,000 base pairs in the origin region. Nucleic Acids Res. 1985 Apr 11;13(7):2251–2265. doi: 10.1093/nar/13.7.2251. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Mougel M., Eyermann F., Westhof E., Romby P., Expert-Bezançon A., Ebel J. P., Ehresmann B., Ehresmann C. Binding of Escherichia coli ribosomal protein S8 to 16 S rRNA. A model for the interaction and the tertiary structure of the RNA binding site. J Mol Biol. 1987 Nov 5;198(1):91–107. doi: 10.1016/0022-2836(87)90460-8. [DOI] [PubMed] [Google Scholar]
  28. Nomura M., Traub P., Bechmann H. Hybrid 30S ribosomal particles reconstituted from components of different bacterial origins. Nature. 1968 Aug 24;219(5156):793–799. doi: 10.1038/219793b0. [DOI] [PubMed] [Google Scholar]
  29. Olins P. O., Nomura M. Translational regulation by ribosomal protein S8 in Escherichia coli: structural homology between rRNA binding site and feedback target on mRNA. Nucleic Acids Res. 1981 Apr 10;9(7):1757–1764. doi: 10.1093/nar/9.7.1757. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Piggot P. J., Hoch J. A. Revised genetic linkage map of Bacillus subtilis. Microbiol Rev. 1985 Jun;49(2):158–179. doi: 10.1128/mr.49.2.158-179.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Post L. E., Arfsten A. E., Reusser F., Nomura M. DNA sequences of promoter regions for the str and spc ribosomal protein operons in E. coli. Cell. 1978 Sep;15(1):215–229. doi: 10.1016/0092-8674(78)90096-x. [DOI] [PubMed] [Google Scholar]
  32. Sor F., Nomura M. Cloning and DNA sequence determination of the L11 ribosomal protein operon of Serratia marcescens and Proteus vulgaris: translational feedback regulation of the Escherichia coli L11 operon by heterologous L1 proteins. Mol Gen Genet. 1987 Nov;210(1):52–59. doi: 10.1007/BF00337758. [DOI] [PubMed] [Google Scholar]
  33. Suh J. W., Boylan S. A., Price C. W. Gene for the alpha subunit of Bacillus subtilis RNA polymerase maps in the ribosomal protein gene cluster. J Bacteriol. 1986 Oct;168(1):65–71. doi: 10.1128/jb.168.1.65-71.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Thomas M. S., Bedwell D. M., Nomura M. Regulation of alpha operon gene expression in Escherichia coli. A novel form of translational coupling. J Mol Biol. 1987 Jul 20;196(2):333–345. doi: 10.1016/0022-2836(87)90694-2. [DOI] [PubMed] [Google Scholar]
  35. Ueguchi C., Wittekind M., Nomura M., Akiyama Y., Ito K. The secY-rpmJ region of the spc ribosomal protein operon in Escherichia coli: structural alterations affecting secY expression. Mol Gen Genet. 1989 May;217(1):1–5. doi: 10.1007/BF00330934. [DOI] [PubMed] [Google Scholar]
  36. Wada A., Sako T. Primary structures of and genes for new ribosomal proteins A and B in Escherichia coli. J Biochem. 1987 Mar;101(3):817–820. doi: 10.1093/jb/101.3.817. [DOI] [PubMed] [Google Scholar]
  37. Woese C. R., Gutell R., Gupta R., Noller H. F. Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. Microbiol Rev. 1983 Dec;47(4):621–669. doi: 10.1128/mr.47.4.621-669.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Yanisch-Perron C., Vieira J., Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985;33(1):103–119. doi: 10.1016/0378-1119(85)90120-9. [DOI] [PubMed] [Google Scholar]
  39. Yates J. L., Arfsten A. E., Nomura M. In vitro expression of Escherichia coli ribosomal protein genes: autogenous inhibition of translation. Proc Natl Acad Sci U S A. 1980 Apr;77(4):1837–1841. doi: 10.1073/pnas.77.4.1837. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Zimmermann R. A., Mackie G. A., Muto A., Garrett R. A., Ungewickell E., Ehresmann C., Stiegler P., Ebel J. P., Fellner P. Location and characteristics of ribosomal protein binding sites in the 16S RNA of Escherichia coli. Nucleic Acids Res. 1975 Feb;2(2):279–302. doi: 10.1093/nar/2.2.279. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Zurawski G., Zurawski S. M. Structure of the Escherichia coli S10 ribosomal protein operon. Nucleic Acids Res. 1985 Jun 25;13(12):4521–4526. doi: 10.1093/nar/13.12.4521. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES