title: Codon usage and G + C content in Bradyrhizobium japonicum genes are not uniform.
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.
authors.affiliation: Mikrobiologisches Institut, Eidgenössische Technische Hochschule, ETH-Zentrum, Zürich, Switzerland.
authors.forename: T M
authors.initials: TM
authors.lastname: Ramseier
authors.forename: M
authors.initials: M
authors.lastname: Göttfert
mesh_terms: D000595:Amino Acid Sequence; D001482:Base Composition; D001483:Base Sequence; D003062:Codon / Q000502:physiology*; D003596:Cytosine / Q000032:analysis; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics; D005798:Genes, Bacterial; D006147:Guanine / Q000032:analysis; D008969:Molecular Sequence Data; D009586:Nitrogen Fixation / Q000235:genetics; D016366:Open Reading Frames; D012091:Repetitive Sequences, Nucleic Acid; D012230:Rhizobiaceae / Q000235:genetics*
chemical_list: D003062:Codon; D004269:DNA, Bacterial; D006147:Guanine; D003596:Cytosine