Other proteins are required, including HU, IHF, and RNA polymerase. DnaA protects initiator RNA from degradation by RNase H. DNA methylation is also involved in origin of replication and DnaA production. Methylation affects binding of DNA to membrane, expression of dnaA gene, and initiation of replication. DnaA is synthesized and initiation occurs. Termination is bidirectional as well.
Reaction is biochemically simple, yet topologically complex.
1. locate proper start sites, 2. separate the DNA strands locally to read the base information on template strand, 3. move helically down template while releasing mRNA strand for translation by ribosomes, and 4. terminate transcription only at appropriate sites. The core polymerase is catalytically active and can synthesize RNA, but does not properly initiate synthesis at specific sites. RNA polymerase moves along template strand in the 3' to 5' direction while synthesizing RNA in the 5' to 3' direction. Different types of sigma factors recognize different promoter sequences, and hence can change the pattern of gene expression of cell by altering the pattern of RNA synthesis. Sigma is free to bind to core and initiate new round of transcription initiation.