Abstract
The DNA sequence of the Micrococcus luteus str operon, which includes genes for ribosomal proteins S12 (str or rpsL) and S7 (rpsG) and elongation factors (EF) G (fus) and Tu (tuf), has been determined and compared with the corresponding sequence of Escherichia coli to estimate the effect of high genomic G + C content (74%) of M. luteus on the codon usage pattern. The gene organization in this operon and the deduced amino acid sequence of each corresponding protein are well conserved between the two species. The mean G + C content of the M. luteus str operon is 67%, which is much higher than that of E. coli (51%). The codon usage pattern of M. luteus is very different from that of E. coli and extremely biased to the use of G and C in silent positions. About 95% (1,309 of 1,382) of codons have G or C at the third position. Codon GUG is used for initiation of S12, EF-G, and EF-Tu, and AUG is used only in S7, whereas GUG initiates only one of the EF-Tu's in E. coli. UGA is the predominant termination codon in M. luteus, in contrast to UAA in E. coli.
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- An G., Friesen J. D. The nucleotide sequence of tufB and four nearby tRNA structural genes of Escherichia coli. Gene. 1980 Dec;12(1-2):33–39. doi: 10.1016/0378-1119(80)90013-x. [DOI] [PubMed] [Google Scholar]
- Bibb M. J., Bibb M. J., Ward J. M., Cohen S. N. Nucleotide sequences encoding and promoting expression of three antibiotic resistance genes indigenous to Streptomyces. Mol Gen Genet. 1985;199(1):26–36. doi: 10.1007/BF00327505. [DOI] [PubMed] [Google Scholar]
- Brown N. L., Ford S. J., Pridmore R. D., Fritzinger D. C. Nucleotide sequence of a gene from the Pseudomonas transposon Tn501 encoding mercuric reductase. Biochemistry. 1983 Aug 16;22(17):4089–4095. doi: 10.1021/bi00286a015. [DOI] [PubMed] [Google Scholar]
- 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]
- Chen E. Y., Seeburg P. H. Supercoil sequencing: a fast and simple method for sequencing plasmid DNA. DNA. 1985 Apr;4(2):165–170. doi: 10.1089/dna.1985.4.165. [DOI] [PubMed] [Google Scholar]
- Dekio S., Yamasaki R., Jidoi J., Hori H., Osawa S. Secondary structure and phylogeny of Staphylococcus and Micrococcus 5S rRNAs. J Bacteriol. 1984 Jul;159(1):233–237. doi: 10.1128/jb.159.1.233-237.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ghosh H. P., Söll D., Khorana H. G. Studies on polynucleotides. LXVII. Initiation of protein synthesis in vitro as studied by using ribopolynucleotides with repeating nucleotide sequences as messengers. J Mol Biol. 1967 Apr 28;25(2):275–298. doi: 10.1016/0022-2836(67)90142-8. [DOI] [PubMed] [Google Scholar]
- Godson G. N., Vapnek D. A simple method of preparing large amounts of phiX174 RF 1 supercoiled DNA. Biochim Biophys Acta. 1973 Apr 11;299(4):516–520. doi: 10.1016/0005-2787(73)90223-2. [DOI] [PubMed] [Google Scholar]
- Holmes D. S., Quigley M. A rapid boiling method for the preparation of bacterial plasmids. Anal Biochem. 1981 Jun;114(1):193–197. doi: 10.1016/0003-2697(81)90473-5. [DOI] [PubMed] [Google Scholar]
- Hori H., Osawa S. Evolutionary change in 5S rRNA secondary structure and a phylogenic tree of 352 5S rRNA species. Biosystems. 1986;19(3):163–172. doi: 10.1016/0303-2647(86)90037-7. [DOI] [PubMed] [Google Scholar]
- Jaurin B., Cohen S. N. Streptomyces contain Escherichia coli-type A + T-rich promoters having novel structural features. Gene. 1985;39(2-3):191–201. doi: 10.1016/0378-1119(85)90313-0. [DOI] [PubMed] [Google Scholar]
- Jukes T. H., Bhushan V. Silent nucleotide substitutions and G + C content of some mitochondrial and bacterial genes. J Mol Evol. 1986;24(1-2):39–44. doi: 10.1007/BF02099949. [DOI] [PubMed] [Google Scholar]
- Kagawa Y., Nojima H., Nukiwa N., Ishizuka M., Nakajima T., Yasuhara T., Tanaka T., Oshima T. High guanine plus cytosine content in the third letter of codons of an extreme thermophile. DNA sequence of the isopropylmalate dehydrogenase of Thermus thermophilus. J Biol Chem. 1984 Mar 10;259(5):2956–2960. [PubMed] [Google Scholar]
- Kloos W. E. Factors affecting transformation of Micrococcus lysodeikticus. J Bacteriol. 1969 Jun;98(3):1397–1399. doi: 10.1128/jb.98.3.1397-1399.1969. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kloos W. E., Schultes L. M. Transformation in Micrococcus lysodeikticus. J Gen Microbiol. 1969 Feb;55(2):307–317. doi: 10.1099/00221287-55-2-307. [DOI] [PubMed] [Google Scholar]
- Korneluk R. G., Quan F., Gravel R. A. Rapid and reliable dideoxy sequencing of double-stranded DNA. Gene. 1985;40(2-3):317–323. doi: 10.1016/0378-1119(85)90055-1. [DOI] [PubMed] [Google Scholar]
- Maniatis T., Hardison R. C., Lacy E., Lauer J., O'Connell C., Quon D., Sim G. K., Efstratiadis A. The isolation of structural genes from libraries of eucaryotic DNA. Cell. 1978 Oct;15(2):687–701. doi: 10.1016/0092-8674(78)90036-3. [DOI] [PubMed] [Google Scholar]
- Mizusawa S., Nishimura S., Seela F. Improvement of the dideoxy chain termination method of DNA sequencing by use of deoxy-7-deazaguanosine triphosphate in place of dGTP. Nucleic Acids Res. 1986 Feb 11;14(3):1319–1324. doi: 10.1093/nar/14.3.1319. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Moran C. P., Jr, Johnson W. C., Losick R. Close contacts between sigma 37-RNA polymerase and a Bacillus subtilis chromosomal promoter. J Mol Biol. 1982 Dec 15;162(3):709–713. doi: 10.1016/0022-2836(82)90399-0. [DOI] [PubMed] [Google Scholar]
- Muto A., Kawauchi Y., Yamao F., Osawa S. Preferential use of A- and U-rich codons for Mycoplasma capricolum ribosomal proteins S8 and L6. Nucleic Acids Res. 1984 Nov 12;12(21):8209–8217. doi: 10.1093/nar/12.21.8209. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Muto A., Osawa S. The guanine and cytosine content of genomic DNA and bacterial evolution. Proc Natl Acad Sci U S A. 1987 Jan;84(1):166–169. doi: 10.1073/pnas.84.1.166. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Nellen W., Gallwitz D. Actin genes and actin messenger RNA in Acanthamoeba castellanii. Nucleotide sequence of the split actin gene I. J Mol Biol. 1982 Jul 25;159(1):1–18. doi: 10.1016/0022-2836(82)90028-6. [DOI] [PubMed] [Google Scholar]
- Post L. E., Nomura M. DNA sequences from the str operon of Escherichia coli. J Biol Chem. 1980 May 25;255(10):4660–4666. [PubMed] [Google Scholar]
- Reddy P., Peterkofsky A., McKenney K. Translational efficiency of the Escherichia coli adenylate cyclase gene: mutating the UUG initiation codon to GUG or AUG results in increased gene expression. Proc Natl Acad Sci U S A. 1985 Sep;82(17):5656–5660. doi: 10.1073/pnas.82.17.5656. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Robbins P. W., Trimble R. B., Wirth D. F., Hering C., Maley F., Maley G. F., Das R., Gibson B. W., Royal N., Biemann K. Primary structure of the Streptomyces enzyme endo-beta-N-acetylglucosaminidase H. J Biol Chem. 1984 Jun 25;259(12):7577–7583. [PubMed] [Google Scholar]
- Smith H. O., Danner D. B., Deich R. A. Genetic transformation. Annu Rev Biochem. 1981;50:41–68. doi: 10.1146/annurev.bi.50.070181.000353. [DOI] [PubMed] [Google Scholar]
- Thompson C. J., Gray G. S. Nucleotide sequence of a streptomycete aminoglycoside phosphotransferase gene and its relationship to phosphotransferases encoded by resistance plasmids. Proc Natl Acad Sci U S A. 1983 Sep;80(17):5190–5194. doi: 10.1073/pnas.80.17.5190. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Westpheling J., Ranes M., Losick R. RNA polymerase heterogeneity in Streptomyces coelicolor. Nature. 1985 Jan 3;313(5997):22–27. doi: 10.1038/313022a0. [DOI] [PubMed] [Google Scholar]
- 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]
- Yokota T., Sugisaki H., Takanami M., Kaziro Y. The nucleotide sequence of the cloned tufA gene of Escherichia coli. Gene. 1980 Dec;12(1-2):25–31. doi: 10.1016/0378-1119(80)90012-8. [DOI] [PubMed] [Google Scholar]
- Zalacain M., González A., Guerrero M. C., Mattaliano R. J., Malpartida F., Jiménez A. Nucleotide sequence of the hygromycin B phosphotransferase gene from Streptomyces hygroscopicus. Nucleic Acids Res. 1986 Feb 25;14(4):1565–1581. doi: 10.1093/nar/14.4.1565. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zengel J. M., Archer R. H., Lindahl L. The nucleotide sequence of the Escherichia coli fus gene, coding for elongation factor G. Nucleic Acids Res. 1984 Feb 24;12(4):2181–2192. doi: 10.1093/nar/12.4.2181. [DOI] [PMC free article] [PubMed] [Google Scholar]