Sequence variability of the 40-kDa outer membrane proteins of Fusobacterium nucleatum strains and a model for the topology of the proteins

Abstract

The complete nucleotide sequences of the fomA genes encoding the 40-kDa outer membrane proteins (OMPs) of strains ATCC 10953 and ATCC 25586 of Fusobacterium nucleatum were determined using the genomic DNA, or DNA fragments ligated into a vector plasmid, as template in a polymerase chain reaction. The deduced amino acid sequences of these two proteins were aligned with the amino acid sequence of the corresponding protein of F. nucleatum strain Fev1 and examined for conserved/variable polypeptide segments. A model for the topology of the 40-kDa OMPs is proposed on the basis of this alignment and application of the structural principles derived for OMPs of Escherichia coli. According to this model, sixteen polypeptide segments, which are highly conserved, traverse the outer membrane, thereby creating eight external loops, most of which are highly variable.