Skip to main content
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1997 Jul;179(14):4567–4574. doi: 10.1128/jb.179.14.4567-4574.1997

A novel ribosome-associated protein is important for efficient translation in Escherichia coli.

G O Bylund 1, B C Persson 1, L A Lundberg 1, P M Wikström 1
PMCID: PMC179293  PMID: 9226267

Abstract

Previously, we showed that strains which have been deleted for the 21K gene (hereafter called yfjA), of the trmD operon, encoding a 21-kDa protein (21K protein) have an approximately fivefold-reduced growth rate in rich medium. Here we show that such mutants show an up to sevenfold reduced growth rate in minimal medium, a twofold-lower cell yield-to-carbon source concentration ratio, and a reduced polypeptide chain growth rate of beta-galactosidase. Suppressor mutations that increased the growth rate and translational efficiency of a delta yfjA mutant were localized to the 3' part of rpsM, encoding ribosomal protein S13. The 21K protein was shown to have affinity for free 30S ribosomal subunits but not for 70S ribosomes. Further, the 21K protein seems to contain a KH domain and a KOW motif, both suggested to be involved in binding of RNA. These findings suggest that the 21K protein is essential for a proper function of the ribosome and is involved in the maturation of the ribosomal 30S subunits or in translation initiation.

Full Text

The Full Text of this article is available as a PDF (638.5 KB).

Selected References

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

  1. BERTANI G. Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J Bacteriol. 1951 Sep;62(3):293–300. doi: 10.1128/jb.62.3.293-300.1951. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bachmann B. J. Linkage map of Escherichia coli K-12, edition 8. Microbiol Rev. 1990 Jun;54(2):130–197. doi: 10.1128/mr.54.2.130-197.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Björk G. R. E. coli ribosomal protein operons: the case of the misplaced genes. Cell. 1985 Aug;42(1):7–8. doi: 10.1016/s0092-8674(85)80093-3. [DOI] [PubMed] [Google Scholar]
  4. Björk G. R., Ericson J. U., Gustafsson C. E., Hagervall T. G., Jönsson Y. H., Wikström P. M. Transfer RNA modification. Annu Rev Biochem. 1987;56:263–287. doi: 10.1146/annurev.bi.56.070187.001403. [DOI] [PubMed] [Google Scholar]
  5. Björk G. R., Wikström P. M., Byström A. S. Prevention of translational frameshifting by the modified nucleoside 1-methylguanosine. Science. 1989 May 26;244(4907):986–989. doi: 10.1126/science.2471265. [DOI] [PubMed] [Google Scholar]
  6. Boileau G., Butler P., Hershey J. W., Traut R. R. Direct cross-links between initiation factors 1, 2, and 3 and ribosomal proteins promoted by 2-iminothiolane. Biochemistry. 1983 Jun 21;22(13):3162–3170. doi: 10.1021/bi00282a020. [DOI] [PubMed] [Google Scholar]
  7. Buck M., Connick M., Ames B. N. Complete analysis of tRNA-modified nucleosides by high-performance liquid chromatography: the 29 modified nucleosides of Salmonella typhimurium and Escherichia coli tRNA. Anal Biochem. 1983 Feb 15;129(1):1–13. doi: 10.1016/0003-2697(83)90044-1. [DOI] [PubMed] [Google Scholar]
  8. Byström A. S., Hjalmarsson K. J., Wikström P. M., Björk G. R. The nucleotide sequence of an Escherichia coli operon containing genes for the tRNA(m1G)methyltransferase, the ribosomal proteins S16 and L19 and a 21-K polypeptide. EMBO J. 1983;2(6):899–905. doi: 10.1002/j.1460-2075.1983.tb01519.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Coffman R. L., Norris T. E., Koch A. L. Chain elongation rate of messenger and polypeptides in slowly growing Escherichia coli. J Mol Biol. 1971 Aug 28;60(1):1–19. doi: 10.1016/0022-2836(71)90442-6. [DOI] [PubMed] [Google Scholar]
  10. Ericson J. U., Björk G. R. Pleiotropic effects induced by modification deficiency next to the anticodon of tRNA from Salmonella typhimurium LT2. J Bacteriol. 1986 Jun;166(3):1013–1021. doi: 10.1128/jb.166.3.1013-1021.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Faxén M., Walles-Granberg A., Isaksson L. A. Antisuppression by a mutation in rpsM(S13) giving a shortened ribosomal protein S13. Biochim Biophys Acta. 1994 May 17;1218(1):27–34. doi: 10.1016/0167-4781(94)90097-3. [DOI] [PubMed] [Google Scholar]
  12. Gehrke C. W., Kuo K. C., McCune R. A., Gerhardt K. O., Agris P. F. Quantitative enzymatic hydrolysis of tRNAs: reversed-phase high-performance liquid chromatography of tRNA nucleosides. J Chromatogr. 1982 Jul 9;230(2):297–308. [PubMed] [Google Scholar]
  13. Gibson T. J., Thompson J. D., Heringa J. The KH domain occurs in a diverse set of RNA-binding proteins that include the antiterminator NusA and is probably involved in binding to nucleic acid. FEBS Lett. 1993 Jun 21;324(3):361–366. doi: 10.1016/0014-5793(93)80152-k. [DOI] [PubMed] [Google Scholar]
  14. Hagervall T. G., Tuohy T. M., Atkins J. F., Björk G. R. Deficiency of 1-methylguanosine in tRNA from Salmonella typhimurium induces frameshifting by quadruplet translocation. J Mol Biol. 1993 Aug 5;232(3):756–765. doi: 10.1006/jmbi.1993.1429. [DOI] [PubMed] [Google Scholar]
  15. Heilek G. M., Noller H. F. Directed hydroxyl radical probing of the rRNA neighborhood of ribosomal protein S13 using tethered Fe(II). RNA. 1996 Jun;2(6):597–602. [PMC free article] [PubMed] [Google Scholar]
  16. Heimark R. L., Kahan L., Johnston K., Hershey J. W., Traut R. R. Cross-linking of initiation factor IF3 to proteins of the Escherichia coli 30 S ribosomal subunit. J Mol Biol. 1976 Aug 5;105(2):219–230. doi: 10.1016/0022-2836(76)90108-x. [DOI] [PubMed] [Google Scholar]
  17. Held W. A., Nomura M. Escherichia coli 30 S ribosomal proteins uniquely required for assembly. J Biol Chem. 1975 Apr 25;250(8):3179–3184. [PubMed] [Google Scholar]
  18. Hopfield J. J. Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc Natl Acad Sci U S A. 1974 Oct;71(10):4135–4139. doi: 10.1073/pnas.71.10.4135. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Kennell D., Riezman H. Transcription and translation initiation frequencies of the Escherichia coli lac operon. J Mol Biol. 1977 Jul;114(1):1–21. doi: 10.1016/0022-2836(77)90279-0. [DOI] [PubMed] [Google Scholar]
  20. Kohara Y., Akiyama K., Isono K. The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell. 1987 Jul 31;50(3):495–508. doi: 10.1016/0092-8674(87)90503-4. [DOI] [PubMed] [Google Scholar]
  21. Kulakauskas S., Wikström P. M., Berg D. E. Efficient introduction of cloned mutant alleles into the Escherichia coli chromosome. J Bacteriol. 1991 Apr;173(8):2633–2638. doi: 10.1128/jb.173.8.2633-2638.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Kyrpides N. C., Woese C. R., Ouzounis C. A. KOW: a novel motif linking a bacterial transcription factor with ribosomal proteins. Trends Biochem Sci. 1996 Nov;21(11):425–426. doi: 10.1016/s0968-0004(96)30036-4. [DOI] [PubMed] [Google Scholar]
  23. Linder P., Lasko P. F., Ashburner M., Leroy P., Nielsen P. J., Nishi K., Schnier J., Slonimski P. P. Birth of the D-E-A-D box. Nature. 1989 Jan 12;337(6203):121–122. doi: 10.1038/337121a0. [DOI] [PubMed] [Google Scholar]
  24. Liu M. Y., Yang H., Romeo T. The product of the pleiotropic Escherichia coli gene csrA modulates glycogen biosynthesis via effects on mRNA stability. J Bacteriol. 1995 May;177(10):2663–2672. doi: 10.1128/jb.177.10.2663-2672.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Mullis K. B., Faloona F. A. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol. 1987;155:335–350. doi: 10.1016/0076-6879(87)55023-6. [DOI] [PubMed] [Google Scholar]
  26. Neidhardt F. C., Bloch P. L., Pedersen S., Reeh S. Chemical measurement of steady-state levels of ten aminoacyl-transfer ribonucleic acid synthetases in Escherichia coli. J Bacteriol. 1977 Jan;129(1):378–387. doi: 10.1128/jb.129.1.378-387.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Neidhardt F. C., Bloch P. L., Smith D. F. Culture medium for enterobacteria. J Bacteriol. 1974 Sep;119(3):736–747. doi: 10.1128/jb.119.3.736-747.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Ninio J. Kinetic amplification of enzyme discrimination. Biochimie. 1975;57(5):587–595. doi: 10.1016/s0300-9084(75)80139-8. [DOI] [PubMed] [Google Scholar]
  29. Osswald M., Döring T., Brimacombe R. The ribosomal neighbourhood of the central fold of tRNA: cross-links from position 47 of tRNA located at the A, P or E site. Nucleic Acids Res. 1995 Nov 25;23(22):4635–4641. doi: 10.1093/nar/23.22.4635. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Osswald M., Greuer B., Brimacombe R., Stöffler G., Bäumert H., Fasold H. RNA-protein cross-linking in Escherichia coli 30S ribosomal subunits; determination of sites on 16S RNA that are cross-linked to proteins S3, S4, S5, S7, S8, S9, S11, S13, S19 and S21 by treatment with methyl p-azidophenyl acetimidate. Nucleic Acids Res. 1987 Apr 24;15(8):3221–3240. doi: 10.1093/nar/15.8.3221. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Persson B. C., Bylund G. O., Berg D. E., Wikström P. M. Functional analysis of the ffh-trmD region of the Escherichia coli chromosome by using reverse genetics. J Bacteriol. 1995 Oct;177(19):5554–5560. doi: 10.1128/jb.177.19.5554-5560.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Pohl T., Wittmann-Liebold B. Identification of a cross-link in the Escherichia coli ribosomal protein pair S13-S19 at the amino acid level. J Biol Chem. 1988 Mar 25;263(9):4293–4301. [PubMed] [Google Scholar]
  33. Powers T., Stern S., Changchien L. M., Noller H. F. Probing the assembly of the 3' major domain of 16 S rRNA. Interactions involving ribosomal proteins S2, S3, S10, S13 and S14. J Mol Biol. 1988 Jun 20;201(4):697–716. doi: 10.1016/0022-2836(88)90468-8. [DOI] [PubMed] [Google Scholar]
  34. Putnam S. L., Koch A. L. Complications in the simplest cellular enzyme assay: lysis of Escherichia coli for the assay of beta-galactosidase. Anal Biochem. 1975 Feb;63(2):350–360. doi: 10.1016/0003-2697(75)90357-7. [DOI] [PubMed] [Google Scholar]
  35. Ruusala T., Ehrenberg M., Kurland C. G. Is there proofreading during polypeptide synthesis? EMBO J. 1982;1(6):741–745. doi: 10.1002/j.1460-2075.1982.tb01240.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Rydén-Aulin M., Shaoping Z., Kylsten P., Isaksson L. A. Ribosome activity and modification of 16S RNA are influenced by deletion of ribosomal protein S20. Mol Microbiol. 1993 Mar;7(6):983–992. doi: 10.1111/j.1365-2958.1993.tb01190.x. [DOI] [PubMed] [Google Scholar]
  37. Saiki R. K., Scharf S., Faloona F., Mullis K. B., Horn G. T., Erlich H. A., Arnheim N. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science. 1985 Dec 20;230(4732):1350–1354. doi: 10.1126/science.2999980. [DOI] [PubMed] [Google Scholar]
  38. Schleif R., Hess W., Finkelstein S., Ellis D. Induction kinetics of the L-arabinose operon of Escherichia coli. J Bacteriol. 1973 Jul;115(1):9–14. doi: 10.1128/jb.115.1.9-14.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Schwarzbauer J., Craven G. R. Evidence that E. coli ribosomal protein S13 has two separable functional domains involved in 16S RNA recognition and protein S19 binding. Nucleic Acids Res. 1985 Sep 25;13(18):6767–6786. doi: 10.1093/nar/13.18.6767. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Siomi H., Matunis M. J., Michael W. M., Dreyfuss G. The pre-mRNA binding K protein contains a novel evolutionarily conserved motif. Nucleic Acids Res. 1993 Mar 11;21(5):1193–1198. doi: 10.1093/nar/21.5.1193. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Thompson R. C., Stone P. J. Proofreading of the codon-anticodon interaction on ribosomes. Proc Natl Acad Sci U S A. 1977 Jan;74(1):198–202. doi: 10.1073/pnas.74.1.198. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Toone W. M., Rudd K. E., Friesen J. D. deaD, a new Escherichia coli gene encoding a presumed ATP-dependent RNA helicase, can suppress a mutation in rpsB, the gene encoding ribosomal protein S2. J Bacteriol. 1991 Jun;173(11):3291–3302. doi: 10.1128/jb.173.11.3291-3302.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Tyers M., Tokiwa G., Futcher B. Comparison of the Saccharomyces cerevisiae G1 cyclins: Cln3 may be an upstream activator of Cln1, Cln2 and other cyclins. EMBO J. 1993 May;12(5):1955–1968. doi: 10.1002/j.1460-2075.1993.tb05845.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. VOGEL H. J., BONNER D. M. Acetylornithinase of Escherichia coli: partial purification and some properties. J Biol Chem. 1956 Jan;218(1):97–106. [PubMed] [Google Scholar]
  45. Wikström P. M., Byström A. S., Björk G. R. Non-autogenous control of ribosomal protein synthesis from the trmD operon in Escherichia coli. J Mol Biol. 1988 Sep 5;203(1):141–152. doi: 10.1016/0022-2836(88)90098-8. [DOI] [PubMed] [Google Scholar]
  46. Wilson I. A., Niman H. L., Houghten R. A., Cherenson A. R., Connolly M. L., Lerner R. A. The structure of an antigenic determinant in a protein. Cell. 1984 Jul;37(3):767–778. doi: 10.1016/0092-8674(84)90412-4. [DOI] [PubMed] [Google Scholar]
  47. Wower J., Malloy T. A., 4th, Hixson S. S., Zimmermann R. A. Probing tRNA binding sites on the Escherichia coli 30 S ribosomal subunit with photoreactive analogs of the anticodon arm. Biochim Biophys Acta. 1990 Aug 27;1050(1-3):38–44. doi: 10.1016/0167-4781(90)90138-r. [DOI] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES