Sequencing of regions downstream of addA (98°) and citG (28°) in Bacillus subtilis

Medina, Nadine; Vannier, F.; Roche, Benjamin; Autret, Sabine; Levine, Anna; Séror, Simone J.

doi:10.1099/00221287-143-10-3305

Cited by 5 publications

(1 citation statement)

References 11 publications

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“…The DNA sequence of region VII was homologous to those of DNA repair exonuclease (sbcD) of Bacillus subtilis [30], rhcU of Bradyrhizobium japonicum [31] and orf17 of Streptococcus pneumoniae bacteriophage Cp-1 [32] (Table 4). These genes, except for those from Streptococcus pneumoniae bacteriophage Cp-1, were only predicted based on the DNA sequences.…”

Section: Region VIImentioning

confidence: 99%

Structural evolution of Flavodoxin reductase in <I>Escherichia coli</I>

Ohfuku

Tanaka

Uebayasi

2002

CBIJ

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The three-dimensional structure of Flavodoxin reductase in Escherichia coli had been determined by X-ray crystallography and was found to consist of multi-domains. Then the DNA sequence of Flavodoxin reductase was analyzed by using Markov models, and the sequence was divided into seven regions (I-VII), which corresponded to the structural domains classified based on "Class," derived from the secondary structure, "Architecture," which was derived from the gross orientation of the secondary structures and "Topology," as defined by CATH. In addition, the domains defined by CATH are equivalent to the domains identified by analysis of the X-ray crystallography. A FASTA homology search was done against the DDBJ ALL database with each divided region. Region I+II belongs to the FAD domain, which binds FAD, and its DNA sequence showed homology to that of the FAD binding site of NADPH:ferredoxin reductase of Azotobacter vinelanndii. It is reported that the overall 3D structure was very similar to that of Flavodoxin reductase, since the RMSD between these two proteins was 1.49 Å and the amino acid sequences at the N-termini also showed high homology. Thus there is a correspondence between the 3D structures, amino acid sequences, and the divided sequences of both sequences. The region from IV to VII belongs to the NADP domain, which binds to NADP/NADPH. The DNA sequences of regions IV, V+VI and VII showed respective homology to conjugal transfer gene E (traE) of Escherichia coli pKM101, the czcB gene (cation-proton antipoter) from Ralstonia sp. CH34 pMOL30, and orf17 of Streptococcus pneumoniae Bacteriophage Cp-1, which was predicted as a tail protein. Thus it is suggested that the NADP domain would have been constructed by the fusion of a tail protein from a bacteriophage, the czcB gene and the conjugal transfer gene from a plasmid. Moreover, NADPH:ferredoxin reductase of Azotobacter vinelanndii, which showed homology to the DNA sequence in the region of the FAD domain, was coded on the chromosome. On the contrary, genes homologous to the DNA sequence of the region of the NADP domain were coded on a plasmid or bacteriophage. The structurally divided regions of Flavodoxin reductase were supposed to be comprised of several fragments of DNA sequence whose imprinted structural information might be incorporated as parts of structure from other species.

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Section: Region VIImentioning

confidence: 99%