Interactions of the Transcription Machinery with DNA Damage in Prokaryotes

DNA damage can influence interactions between the transcription machinery and the DNA template (reviewed in Refs. 1 and 2) This has been investigated in phage, prokaryotic, and eukaryotic systems. Many studies have focused on how DNA damage can influence the ability of RNA polymerase to either bypass a specific lesion or become arrested at the damaged site (1). The behavior of RNA polymerase elongation complexes at damaged sites is generally thought to play an important role in mechanisms underlying the DNA repair pathway termed transcription-coupled repair (TCR) (2-4). In this chapter, the influence of different types of DNA damage on RNA polymerase progression and how this may impact mechanisms of TCR are described with an emphasis on studies performed in prokaryotic systems.