Archives of Microbiology

, Volume 156, Issue 4, pp 270–276 | Cite as

Codon usage and G+C content in Bradyrhizobium japonicum genes are not uniform

  • Tom M. Ramseier
  • Michael Göttfert
Original Papers


To date, the sequences of 45 Bradyrhizobium japonicum genes are known. This provides sufficient information to determine their codon usage and G+C content. Surprisingly, B. japonicum nodulation and NifA-regulated genes were found to have a less biased codon usage and a lower G+C content than genes not belonging to these two groups. Thus, the coding regions of nodulation genes and NifA-regulated genes could hardly be identified in codon preference plots whereas this was not difficult with other genes. The codon frequency table of the highly biased genes was used in a codon preference plot to analyze the RSRjα9 sequence which is an insertion sequence (IS)-like element. The plot helped identify a new open reading frame (ORF355) that escaped previous detection because of two sequencing errors. These were now corrected. The deduced gene product of ORF355 in RSRjα9 showed extensive similarity to a putative protein encoded by an ORF in the T-DNA of Agrobacterium rhizogenes. The DNA sequences bordering both ORFs showed inverted repeats and potential target site duplications which supported the assumption that they were IS-like elements.

Key words

Coding regions Codon frequency table IS-like elements Nitrogen fixation Nodulation Repeated sequence Bradyrhizobium japonicum 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Acuña G, Ebeling S, Hennecke H (1991) Cloning, sequencing, and mutational analysis of the Bradyrhizobium japonicum fumC-like gene: evidence for the existence of two different fumarases. J Gen Microbiol 137:991–1000Google Scholar
  2. Aguilar OM, Taormino J, Thöny B, Ramseier T, Hennecke H, Szalay AA (1990) The nifEN genes participating in FeMo cofactor biosynthesis and genes encoding dinitrogenase are part of the same operon in Bradyrhizobium species. Mol Gen Genet 224:413–420Google Scholar
  3. Alvarez-Morales A, Betancourt-Alvarez M, Kaluza K, Hennecke H (1986) Activation of the Bradyrhizobium japonicum nifH and nifDK operons is dependent on promoter-upstream DNA sequences. Nucleic Acids Res 14:4207–4227Google Scholar
  4. Andersson SGE, Kurland CG (1990) Codon preference in free-living microorganisms. Microbiol Rev 54:198–210Google Scholar
  5. Anthamatten D, Hennecke H (1991) The regulatory status of the fixL- and fixJ-like genes in Bradyrhizobium japonicum may be different from that in Rhizobium meliloti. Mol Gen Genet 225:38–48Google Scholar
  6. Banfalvi Z, Nieuwkoop A, Schell M, Besl L, Stacey G (1988) Regulation of nod gene expression in Bradyrhizobium japonicum. Mol Gen Genet 214:420–424Google Scholar
  7. Bennetzen JL, Hall BD (1982) Codon selection in yeast. J Biol Chem 257:3026–3031Google Scholar
  8. Bott M, Bolliger M, Hennecke H (1990) Genetic analysis of the cytochrome c-aa 3 branch of the Bradyrhizobium japonicum respiratory chain. Mol Microbiol 4:2147–2157Google Scholar
  9. Carlson TA, Chelm BK (1986) Apparent eucaryotic origin of glutamine synthetase II from the bacterium Bradyrhizobium japonicum. Nature 322:568–570Google Scholar
  10. Ebeling S, Noti JD, Hennecke H (1988) Identification of a new Bradyrhizobium japonicum gene (frxA) encoding a ferredoxinlike protein. J Bacteriol 170:1999–2001Google Scholar
  11. Fischer H-M, Alvarez-Morales A, Hennecke H (1986) The pleiotropic nature of symbiotic regulatory mutants: Bradyrhizobium japonicum nifA gene is involved in control of nif gene expression and formation of determinate symbiosis. EMBO J 5:1165–1173Google Scholar
  12. Fuhrmann M, Hennecke H (1984) Rhizobium japonicum nitrogenase Fe protein gene (nifH). J Bacteriol 158:1005–1011Google Scholar
  13. Göttfert M, Grob P, Hennecke H (1990a) Proposed regulatory pathway encoded by the nodV and nodW genes, determinants of host specificity in Bradyrhizobium japonicum. Proc Natl Acad Sci USA 87:2680–2684Google Scholar
  14. Göttfert M, Hitz S, Hennecke H (1990b) Identification of nodS and nodU, two inducible genes inserted between the Bradyrhizobium japonicum nodYABC and nodIJ genes. Mol Plant-Microbe Interact 3:308–316Google Scholar
  15. Gouy M, Gautier C (1982) Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res 10:7055–7074Google Scholar
  16. Gribskov M, Devereux J, Burgess RR (1984) The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression. Nucleic Acids Res 12:539–549Google Scholar
  17. Grosjean H, Fiers W (1982) Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. Gene 18:199–209Google Scholar
  18. Gubler M, Hennecke H (1988) Regulation of the fixA gene and fixBC operon in Bradyrhizobium japonicum. J Bacteriol 170:1205–1214Google Scholar
  19. Gubler M, Hürcher T, Hennecke H (1989) The Bradyrhizobium japonicum fixBCX operon: identification of fixX and of a 5′ mRNA region affecting the level of the fixBCX transcript. Mol Microbiol 3:141–148Google Scholar
  20. Gussin GN, Ronson CW, Ausubel FM (1986) Regulation of nitrogen fixation genes. Annu Rev Genet 20:567–591Google Scholar
  21. Hennecke H, Kaluza K, Thöny B, Fuhrmann M, Ludwig W, Stackebrandt E (1985) Concurrent evolution of nitrogenase genes and 16S rRNA in Rhizobium species and other nitrogen fixing bacteria. Arch Microbiol 142:342–348Google Scholar
  22. Jordan DC (1982) Transfer of Rhizobium japonicum Buchanan 1980 to Bradyrhizobium gen. nov., a genus of slow-growing root nodule bacteria from leguminous plants. Int J Syst Bacteriol 32:136–139Google Scholar
  23. Kaluza K, Hennecke H (1984) Fine structure analysis of the nifDK operon encoding the α and β subunits of dinitrogenase from Rhizobium japonicum. Mol Gen Genet 196:35–42Google Scholar
  24. Kaluza K, Hahn M, Hennecke H (1985) Repeated sequences similar to insertion elements clustered around the nif region of the Rhizobium japonicum genome. J Bacteriol 162:535–542Google Scholar
  25. Krishnan HB, Pueppke S (1991) Repetitive sequences with homology to Bradyrhizobium japonicum DNA and the T-DNA of Agrobacterium rhizogenes are closely linked to nodABC of Rhizobium fredii USDA257. Mol Plant-Microbe Interact (in press)Google Scholar
  26. Kullik I, Fritsche S, Knobel H, Sanjuan J, Hennecke H, Fischer HM (1991) Bradyrhizobium japonicum has two differently regulated functional homologs of the σ 54 gene (rpoN). J Bacteriol 173:1125–1138Google Scholar
  27. Long SR (1989) Rhizobium-legume nodulation: life together in the underground. Cell 56:203–214Google Scholar
  28. Martin GB, Thomashow MF, Chelm BK (1989) Bradyrhizobium japonicum glnB, a putative nitrogen-regulatory gene, is regulated by NtrC at tandem promoters. J Bacteriol 171:5638–5645Google Scholar
  29. McClung CR, Somerville JE, Guerinot M-L, Chelm BK (1987) Structure of the Bradyrhizobium japonicum gene hemA encoding δ-aminolevulinic acid synthase. Gene 54:133–139Google Scholar
  30. Norrander J, Kempe T, Messing J (1983) Construction of improved M13 vectors using oligodeoxynucleotide-directed mutagenesis. Gene 26:101–106Google Scholar
  31. Noti JD, Folkerts O, Turken AN, Szalay AA (1986) Organization and characterization of genes essential for symbiotic nitrogen fixation from Bradyrhizobium japonicum I110. J Bacteriol 167:774–783Google Scholar
  32. Ohama T, Muto A, Osawa S (1990) Role of GC-biased mutation pressure on synonymous codon choice in Microeoccus luteus, a bacterium with a high genomic GC-content. Nucleic Acids Res 18:1565–1569Google Scholar
  33. Ramseier TM, Winteler HV, Hennecke H (1991) Discovery and sequence analysis of bacterial genes involved in the biogenesis of c-type cytochromes. J Biol Chem 266:7793–7803Google Scholar
  34. Rossbach S, Hennecke H (1991) Identification of glyA as a symbiotically essential gene in Bradyrhizobium japonicum. Mol Microbiol 5:39–47Google Scholar
  35. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467Google Scholar
  36. Sayavedra-Soto LA, Powell GK, Evans HJ, Morris RO (1988) Nucleotide sequence of the genetic loci encoding subunits of Bradyrhizobium japonicum uptake hydrogenase. Proc Natl Acad Sci USA 85:8395–8399Google Scholar
  37. Scott DB, Hennecke H, Lim ST (1979) The biosynthesis of nitrogenase MoFe protein polypeptides in free-living cultures of Rhizobium japonicum. Biochim Biophys Acta 565:365–378Google Scholar
  38. Sekine M, Watanabe K, Syono K (1988) Nucleotide sequence of a gene for indole-3-acetamide hydrolase from Bradyrhizobium japonicum. Nucleic Acids Res 17:6400Google Scholar
  39. Sharp PM, Tuohy TMF, Mosurski KR (1986) Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes. Nucleic Acids Res 14:5125–5143Google Scholar
  40. Shields DC, Sharp PM (1987) Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases. Nucleic Acids Res 15:8023–8040Google Scholar
  41. Slightom JL, Durand-Tardif M, Jouanin L, Tepfer D (1986) Nucleotide sequence analysis of TL-DNA of Agrobacterium rhizogenes agropine type plasmid. J Biol Chem 261:108–121Google Scholar
  42. Thöny B, Kaluza K, Hennecke H (1985) Structural and functional homology between the α and β subunits of the nitrogenase MoFe protein as revealed by sequencing the Rhizobium japonicum nifK gene. Mol Gen Genet 198:441–448Google Scholar
  43. Thöny B, Fischer H-M, Anthamatten D, Bruderer T, Hennecke H (1987) The symbiotic nitrogen fixation regulatory operon (fixRnifA) of Bradyrhizobium japonicum is expressed aerobically and is subject to a novel, nifA-independent type of activation. Nucleic Acids Res 15:8479–8499Google Scholar
  44. Thöny-Meyer L, Stax D, Hennecke H (1989) An unusual gene cluster for the cytochrome bc 1 complex in Bradyrhizobium japonicum and its requirement for effective root nodule symbiosis. Cell 57:683–697Google Scholar

Copyright information

© Springer-Verlag 1991

Authors and Affiliations

  • Tom M. Ramseier
    • 1
  • Michael Göttfert
    • 1
  1. 1.Mikrobiologisches Institut, Eidgenössische Technische HochschuleETH-ZentrumZürichSwitzerland

Personalised recommendations