Table 1.
Quantitative partitioning of DNA-binding protein activity
| Protein | Function | Size of PAmCherry-Labeled Protein or Protein Complex (kDa)a | Molecules/Cell | D∗mobile (μm2/s) | Dfree (μm2/s) | % Long-Lived DNA-Bound Molecules | % Transient DNA- Bound Molecules | % Freely Diffusing Molecules | Copy Number Reference |
|---|---|---|---|---|---|---|---|---|---|
| MukBEF (MukB subunit) | chromosome organization | 1,006 (dimer of dimers) | 100 | 0.44 (0.43–0.46) | 1.2 (1.1–1.3) | 58 (56–61) | 24 (21–25) | 18 (17–20) | Badrinarayanan et al., 2012 |
| RNA polymerase (β’ subunit) | transcription | 478 (holoenzyme) | 4,000 | 0.36 (0.36–0.37) | 2.7 (2.5–2.8) | 45 (43–46) | 48 (46–50) | 7 (68) | Bakshi et al., 2013; Stracy et al., 2015 |
| DNA gyrase (GyrA subunit) | supercoiling | 424 (heterotetramer) | 600 | 0.35 (0.34–0.36) | 2.4b (0.7–4.2) | 55 (53–57) | 38b (29–47) | 7b (0–15) | Stracy et al., 2019 |
| Topoisomerase IV (ParC subunit) | supercoiling/decatenation | 366 (heterotetramer) | 80 | 0.40 (0.39–0.41) | 2.7b (1.0–4.5) | 37 (35–40) | 52b (41–65) | 11b (0–20) | Zawadzki et al., 2015 |
| UvrA | DNA repair | 270 (dimer) | 80 | 0.36 (0.33–0.38) | 3.4b (1.7–5.1) | 43 (42–46) | 51b (43–58) | 6b (0–12) | Stracy et al., 2016 |
| MutS | DNA repair | 248 (dimer) | 100 | 0.37 (0.35–0.39) | 3.7b (1.9–5.5) | 26 (24–29) | 68b (63–76) | 6b (0–9) | Uphoff et al., 2016 |
| Lac repressor (LacI) | gene regulation | 220 (tetramer) | 40 | 0.40 (0.39–0.43) | 3.3 (3.1–3.5) | 41 (37–46) | 55 (50–60) | 4 (3–5) | Garza de Leon et al., 2017 |
| DNA polymerase 1 (PolA) | DNA repair/replication | 128 (monomer) | 500 | 1.04 (1.02–1.07) | 6.6 (6.5–6.7) | 4 (3–4) | 58 (56–64) | 37 (33–41) | Uphoff et al., 2013 |
| DNA ligase (LigA) | DNA repair/replication | 102 (monomer) | 100 | 1.18 (1.11–1.23) | 6.9 (6.5–7.1) | 7 (4–9) | 56 (52–59) | 37 (35–41) | Uphoff et al., 2013 |
| Histone-like nucleoid structuring protein (H-NS) | nucleoid associated protein/gene regulation | 87 (dimer) | 20,000 | 0.41 (0.40–0.42) | 8.0b (5.8–10.0) | 73 (71–75) | 27b (25–29) | 0.1b (0–1) | Katayama et al., 1996 |
| Heat-unstable protein (HU) | nucleoid associated protein/gene regulation | 48 (heterodimer) | 30,000 | 0.33 (0.32–0.34) | 12.6b (7.9–17.4) | 23 (21–24) | 77b (76–79) | 0.4b (0–1) | Gruber, 2014 |
Brackets indicate 95% confidence bounds.
a
In some cases, the functional complex contains more than one copy of the subunit that was labeled, and the complex therefore contains more than one PAmCherry protein.
b
Predicted values based on extrapolation of Dfree values shown in Figure 6.