Table 2.

Comparison between DnaA and theta A Rep-mediated replication initiation^a

Feature	DnaA	Rep	References
Structural domains	HTH domain	Winged helix domain	143, 144
DNA cognate site	DnaA box	Iterons	8, 43
Number of nucleotides bound	3	3	22, 144, 145
DNA melting	AT-rich DUE	AT-rich DUE	14, 20, 21, 146
Can bind within single-stranded region of melted DUE	Yes	Yes	22, 145, 147
ATP binding to replication initiator required for DNA melting	Yes, used to regulate the timing	No, instead timing regulated by transcriptional autoregulation, monomer concentration and activation, and handcuffing	48, 49, 148
Presence of high- and low-affinity binding motifs in the ori	Yes, role in controlling oligomerization	No	20, 32
Melting assisted by NAPS; DnaA binding to origin of replication enhanced by the presence of NAPS IHF and HU	Yes	Sometimes	46, 149–151
Role in recruitment of replisome	Yes	Yes	26, 28, 49, 103, 136, 144, 152
Role in transcriptional autoregulation	No	Sometimes	44, 153
Formation of dimers in solution	No	Yesb	44, 153, 154

^a Largely based on reference 8.

^b pAMbeta1 is the exception (72).