Table 2.
OriBP (origin binding protein) regulators.
| OriBP | Binding sequence and features | Reference |
|---|---|---|
| ESCHERICHIA COLI | ||
| SeqA | 5′-GATC-3′ | Slater et al., 1995; Brendler et al., 1995; Taghbalout et al., 2000; Nievera et al., 2006 |
| (sequestration factor A) | Binds to oriC and inhibits DnaA binding at low affinity sites. | |
| Fis | 5′-GAACAACAGTTGTTC-3′ | Gille et al., 1991; Filutowicz et al., 1992; Ryan et al., 2004 |
| (factor for inversion stimulation) | Binds to single site in oriC and inhibits DnaA binding. | |
| IHF | 5′-GATCAACAACCTG-3′ Binds to single site in oriC, stimulates DnaA binding at low affinity sites. | Filutowicz and Roll, 1990; Polaczek, 1990; Grimwade et al., 2000 |
| (integration host factor) | ||
| HU | Binds non-specifically to oriC and influences: DnaA oligomer stability at oriC, IHF binding, and stability of ds DNA helix. | Bonnefoy and Rouvière-Yaniv, 1992; Hwang and Kornberg, 1992; Ryan et al., 2002 |
| (histone like U-factor) | Interacts with N-terminus of DnaA. | |
| Dps | Binds non-specifically to oriC and interacts with N-terminus of DnaA. | Chodavarapu et al., 2008b |
| (DNA-binding protein from starved cells) | ||
| ArcA | Binds to 13-mer AT-rich repeats, and to DnaA, IHF, IciA binding sites in oriC. | Lee et al., 2001 |
| (aerobic respiration control) | Influences DnaA interaction with AT-rich region. | |
| IciA | Binds to 13-mer AT-rich repeats in oriC and inhibits unwinding. | Hwang and Kornberg, 1990; Thöny et al., 1991; Hwang et al., 1992 |
| (inhibitor of chromosomal initiation) | ||
| CspD | No apparent target sequence, binds exclusively to ssDNA. Inhibits replication initiation. | Yamanaka et al., 2001 |
| (stationary phase-induced, stress response protein in the CspA family) | ||
| Rob | 5′-ATCGCACGATCTGTATACTT-3′ | Skarstad et al., 1993; Martin et al., 1999 |
| (right oriC-binding) | Binds to single site in oriC. No clear function in initiation regulation. | |
| H-NS | 5′-ATGATCGGTGATCCTG-3′ | Kim et al., 2005; Yun et al., 2012a,b |
| (heat-stable nucleoid structural protein) | Binds to single site in oriC. Probably requires both Cnu and/or Hha proteins to bind DNA. | |
| DpiA | Binds to 13-mer AT-rich repeats in oriC. No function in initiation regulation. | Miller et al., 2003 |
| (destabilizer of plasmid inheritance) | ||
| BACILLUS SUBTILIS | ||
| Spo0A | 5′-TG[TA]CGAA-3′ | Strauch et al., 1990; Castilla-Llorente et al., 2006 |
| (sporulation specific sigma factor) | Binds to oriC and inhibits DnaA binding. | |
| CAULOBACTER CRESCENTUS | ||
| CtrA | 5′-TTAA[Nx7]TTAA-3′ | Siam and Marczynski, 2000; Taylor et al., 2011 |
| (cell transcriptional regulator) | Binds to Cori and inhibits DnaA binding. | |
| IHF | 5′-TAACGCTCTGTT-3′ | Siam et al., 2003 |
| (integration host factor) | Binds to single site in Cori, displaces CtrA, which facilitates bending of DNA and promotes chromosome replication. | |
| HELICOBACTER PYLORI | ||
| HP1021 | 5′-TGTT[TA]C[TA]-3 | Donczew et al., 2014a |
| atypical response regulator | Binds to oriC1 and oriC2 and blocks DNA unwinding at the DUE (within the oriC2). | |
| STREPTOMYCES COELICOLOR | ||
| AdpA | 5′-TGGCSNGWWY-3′ | Wolański et al., 2012 |
| (A-factor dependent protein) | Binds to oriC and inhibits DnaA binding. | |
| MYCOBACTERIUM TUBERCULOSIS | ||
| IciA (Rv1985c) | Binds to AT-rich region within oriC and blocks DNA unwinding. | Kumar et al., 2009 |
| (inhibitor of chromosomal initiation) | ||
| MtrA | 5′-GTCACAGCG-3′ Mechanism not known. | Rajagopalan et al., 2010 |
| (Mycobacterium tuberculosis response regulator A) | ||