Home LiteratureArticle Details
PMID: 1793334 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

Archives of microbiology ·Vol. 156 ·No. 4 ·1991-00-00 ·Pages 270-6

Ramseier TM, Göttfert M

Abstract

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 RSRj alpha 9 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 RSRj alpha 9 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.

Related Genes
fbc fix nif nod
MeSH Terms
Amino Acid Sequence Base Composition Base Sequence Codon/physiology Cytosine/analysis DNA, Bacterial/chemistry,genetics Genes, Bacterial Guanine/analysis Molecular Sequence Data Nitrogen Fixation/genetics Open Reading Frames Repetitive Sequences, Nucleic Acid Rhizobiaceae/genetics
Chemicals
Codon DNA, Bacterial Guanine Cytosine
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Ramseier T M
Mikrobiologisches Institut, Eidgenössische Technische Hochschule, ETH-Zentrum, Zürich, Switzerland.
Göttfert M
References (39)
39 references, click to expand
  1. Rhizobium japonicum nitrogenase Fe protein gene (nifH).
    J Bacteriol. 1984 Jun;158(3):1005-11 PMID: 6327620
  2. The nifEN genes participating in FeMo cofactor biosynthesis and genes encoding dinitrogenase are part of the same operon in Bradyrhizobium species.
    Mol Gen Genet. 1990 Dec;224(3):413-20 PMID: 2266945
  3. Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes.
    Gene. 1982 Jun;18(3):199-209 PMID: 6751939
  4. 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. 1986 Jun;5(6):1165-73 PMID: 15966104
  5. Nucleotide sequence of the genetic loci encoding subunits of Bradyrhizobium japonicum uptake hydrogenase.
    Proc Natl Acad Sci U S A. 1988 Nov;85(22):8395-9 PMID: 3054886
  6. An unusual gene cluster for the cytochrome bc1 complex in Bradyrhizobium japonicum and its requirement for effective root nodule symbiosis.
    Cell. 1989 May 19;57(4):683-97 PMID: 2541921
  7. Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases.
    Nucleic Acids Res. 1987 Oct 12;15(19):8023-40 PMID: 3118331
  8. Organization and characterization of genes essential for symbiotic nitrogen fixation from Bradyrhizobium japonicum I110.
    J Bacteriol. 1986 Sep;167(3):774-83 PMID: 3462181
  9. The biosynthesis of nitrogenase MoFe protein polypeptides in free-living cultures of Rhizobium japonicum.
    Biochim Biophys Acta. 1979 Dec 17;565(2):365-78 PMID: 518887
  10. The regulatory status of the fixL- and fixJ-like genes in Bradyrhizobium japonicum may be different from that in Rhizobium meliloti.
    Mol Gen Genet. 1991 Jan;225(1):38-48 PMID: 2000090
  11. Role of GC-biased mutation pressure on synonymous codon choice in Micrococcus luteus, a bacterium with a high genomic GC-content.
    Nucleic Acids Res. 1990 Mar 25;18(6):1565-9 PMID: 2326195
  12. Nucleotide sequence analysis of TL-DNA of Agrobacterium rhizogenes agropine type plasmid. Identification of open reading frames.
    J Biol Chem. 1986 Jan 5;261(1):108-21 PMID: 3001043
  13. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes.
    Nucleic Acids Res. 1986 Jul 11;14(13):5125-43 PMID: 3526280
  14. Identification of glyA as a symbiotically essential gene in Bradyrhizobium japonicum.
    Mol Microbiol. 1991 Jan;5(1):39-47 PMID: 2014004
  15. Structure of the Bradyrhizobium japonicum gene hemA encoding 5-aminolevulinic acid synthase.
    Gene. 1987;54(1):133-9 PMID: 3609750
  16. 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. 1991 Sep-Oct;4(5):521-9 PMID: 1799702
  17. Identification of nodS and nodU, two inducible genes inserted between the Bradyrhizobium japonicum nodYABC and nodIJ genes.
    Mol Plant Microbe Interact. 1990 Sep-Oct;3(5):308-16 PMID: 2134855
  18. Discovery and sequence analysis of bacterial genes involved in the biogenesis of c-type cytochromes.
    J Biol Chem. 1991 Apr 25;266(12):7793-803 PMID: 1850420
  19. Rhizobium-legume nodulation: life together in the underground.
    Cell. 1989 Jan 27;56(2):203-14 PMID: 2643474
  20. DNA sequencing with chain-terminating inhibitors.
    Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7 PMID: 271968
  21. The Bradyrhizobium japonicum fixBCX operon: identification of fixX and of a 5' mRNA region affecting the level of the fixBCX transcript.
    Mol Microbiol. 1989 Feb;3(2):141-8 PMID: 2503674
  22. Bradyrhizobium japonicum glnB, a putative nitrogen-regulatory gene, is regulated by NtrC at tandem promoters.
    J Bacteriol. 1989 Oct;171(10):5638-45 PMID: 2793830
  23. Bradyrhizobium japonicum has two differentially regulated, functional homologs of the sigma 54 gene (rpoN).
    J Bacteriol. 1991 Feb;173(3):1125-38 PMID: 1991712
  24. Codon selection in yeast.
    J Biol Chem. 1982 Mar 25;257(6):3026-31 PMID: 7037777
  25. Activation of the Bradyrhizobium japonicum nifH and nifDK operons is dependent on promoter-upstream DNA sequences.
    Nucleic Acids Res. 1986 May 27;14(10):4207-27 PMID: 3086837
  26. Regulation of nitrogen fixation genes.
    Annu Rev Genet. 1986;20:567-91 PMID: 3545064
  27. Codon usage in bacteria: correlation with gene expressivity.
    Nucleic Acids Res. 1982 Nov 25;10(22):7055-74 PMID: 6760125
  28. Codon preferences in free-living microorganisms.
    Microbiol Rev. 1990 Jun;54(2):198-210 PMID: 2194095
  29. Regulation of nod gene expression in Bradyrhizobium japonicum.
    Mol Gen Genet. 1988 Nov;214(3):420-4 PMID: 3146016
  30. Identification of a new Bradyrhizobium japonicum gene (frxA) encoding a ferredoxinlike protein.
    J Bacteriol. 1988 Apr;170(4):1999-2001 PMID: 3350797
  31. Cloning, sequencing, and mutational analysis of the Bradyrhizobium japonicum fumC-like gene: evidence for the existence of two different fumarases.
    J Gen Microbiol. 1991 Apr;137(4):991-1000 PMID: 1856685
  32. Nucleotide sequence of a gene for indole-3-acetamide hydrolase from Bradyrhizobium japonicum.
    Nucleic Acids Res. 1989 Aug 11;17(15):6400 PMID: 2771653
  33. 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. 1987 Oct 26;15(20):8479-99 PMID: 3313281
  34. Proposed regulatory pathway encoded by the nodV and nodW genes, determinants of host specificity in Bradyrhizobium japonicum.
    Proc Natl Acad Sci U S A. 1990 Apr;87(7):2680-4 PMID: 2320582
  35. The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression.
    Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):539-49 PMID: 6694906
  36. Construction of improved M13 vectors using oligodeoxynucleotide-directed mutagenesis.
    Gene. 1983 Dec;26(1):101-6 PMID: 6323249
  37. Genetic analysis of the cytochrome c-aa3 branch of the Bradyrhizobium japonicum respiratory chain.
    Mol Microbiol. 1990 Dec;4(12):2147-57 PMID: 1965217
  38. Repeated sequences similar to insertion elements clustered around the nif region of the Rhizobium japonicum genome.
    J Bacteriol. 1985 May;162(2):535-42 PMID: 2985537
  39. Regulation of the fixA gene and fixBC operon in Bradyrhizobium japonicum.
    J Bacteriol. 1988 Mar;170(3):1205-14 PMID: 3343218
Article Info
Journal
Archives of microbiology
Abbr.
Arch Microbiol
ISSN
0302-8933
DOI
10.1007/BF00262997
Published
1991-00-00
Pages
270-6
Language
English
Region
Germany
NLM ID
0410427
Subset
IM
Databases
GENBANK
M63190, M63191, M63293, M63294, M63295, S57874, S77323, S77325, S86118, S86172
External Links
PubMed source DOI: 10.1007/BF00262997 View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2