A strong sequence homology exists between the major RNA polymerase sigma factors of Bacillus subtilis and Escherichia coli.

The Bacillus subtilis rpoD gene has been sequenced and the primary structure of its product deduced. The molecular weight calculated for the sigma 43 is 42,828. The DNA and protein sequences of sigma 43 exhibit extensive homology to the Escherichia coli rpoD gene and its sigma 70 product, especially in the C-terminal two-thirds of the sequence. Other proteins exhibiting partial homology with sigma 43 include the E. coli nusA protein, the E. coli htpR (heat-shock regulatory gene) product sigma 32, and specific DNA-binding proteins. No amino acid homology was found between sigma 43 and B. subtilis phage SP01 sigma gp28, phage T7 RNA polymerase, or E. coli DNA primase. The gene exhibits a strong ribosomal binding site and a typical rho-independent transcription terminator sequence. A typical transcription terminator sequence was not observed upstream from the sigma 43 gene. The sigma 43 gene may be part of an operon, resembling the situation found in the E. coli sigma operon.