Table V. Genes whose expression was affected by ndhR mutation in Synechocystis 6803.
Values are given as log2 fold changes and were regarded as significant (asterisks) if the log2 value was −1 or less or 1 or more and the P value was 0.05 or less. Fold changes between the wild type and ∆ndhR were calculated for each time point by subtracting the corresponding wild-type value. Categories were defined based on the regulatory pattern observed after Ci downshift (for explanations, see text). For comparison reasons, the log2 fold changes of ∆ndhR observed by Wang et al. (2004; only HC conditions were considered there [n.c. = no change]) were compared with the changes observed in this study. The transcriptional organization (operon structure and presence of TSSs) was extracted from Kopf et al. (2014a). NA, Not available.
| Identifier | Gene Name | Protein Name | Wang et al. (2004) at HC | ∆ndhR-Wild Type |
Category Type | Operon | First Gene of Cluster | Motif Upstream | ||
|---|---|---|---|---|---|---|---|---|---|---|
| HC | 3 h of LC | 24 h of LC | ||||||||
| slr2006 | NA | Hypothetical protein | 5.84 | 4.30* | 3.19* | 3.32* | I | a | + | + |
| slr2007 | ndhD5 | NADH dehydrogenase subunit 4 | 4.42 | 3.29* | 2.34* | 2.58* | I | a | − | − |
| slr2008 | NA | Hypothetical protein | 3.20 | 2.71* | 1.57* | 1.76* | I | b | + | − |
| slr2009 | ndhD6 | NADH dehydrogenase subunit 4 | 2.42 | 2.21* | 1.21* | 1.32* | I | b | − | − |
| slr2010 | NA | Hypothetical protein | 3.16 | 2.34* | 1.27* | 1.36* | I | b | − | − |
| slr2011 | NA | Hypothetical protein | 2.19 | 2.21* | 1.10* | 1.29* | I | b | − | − |
| slr2012 | NA | Hypothetical protein | 1.80 | 2.22* | 1.11* | 1.38* | I | b | − | − |
| slr2013 | NA | Hypothetical protein | 1.69 | 1.74* | 0.69 | 0.86 | I | b | − | − |
| ssr3409 | NA | Hypothetical protein | 1.61 | 2.41* | 1.31* | 1.53* | I | b | − | − |
| ssr3410 | NA | Hypothetical protein | 3.15 | 2.50* | 1.47* | 1.59* | I | b | − | − |
| sll1732 | ndhF3 | NADH dehydrogenase subunit 5 (involved in low CO2-inducible, high-affinity CO2 uptake) | 4.22 | 2.78* | −0.92 | 0.90 | II | c | + | + |
| sll1733 | ndhD3 | NADH dehydrogenase subunit 4 (involved in low CO2-inducible, high-affinity CO2 uptake) | 4.25 | 2.63* | −0.86 | 0.94 | II | c | − | − |
| sll1734 | cupA | Protein involved in low CO2-inducible, high-affinity CO2 uptake | 3.88 | 2.28* | −0.87 | 0.91 | II | c | − | − |
| sll1735 | NA | Hypothetical protein | 2.47 | 1.77* | −0.75 | 1.01* | II | c | − | − |
| slr1512 | sbtA | Sodium-dependent bicarbonate transporter | 3.31 | 1.76* | −0.95 | 1.55* | II | d | + | + |
| slr1513 | NA | Periplasmic protein, function unknown | 1.43 | 1.15 | −0.77 | 1.55* | II | d | − | − |
| sll0529 | NA | Hypothetical protein | 1.66 | 1.01* | 0.94 | 0.57 | III | No | + | + |
| sll0834 | bicA | Low-affinity bicarbonate transporter | n.c. | 2.85* | 2.55* | 1.04* | III | No | + | + |
| slr1592 | NA | Probable pseudouridine synthase | 2.10 | 1.98* | 1.62* | 1.23* | III | No | + | + |
| slr0907 | NA | Unknown protein | n.c. | −1.24* | −1.73* | −1.04* | IV | e | + | − |
| sll1862 | NA | Unknown protein | n.c. | −0.89 | −0.78 | −1.02* | IV | No | + | In coding sequence |
| slr1259 | NA | Hypothetical protein | n.c. | −0.20 | 1.39* | 1.87* | V | f | + | − |
| slr1261 | NA | Hypothetical protein | n.c. | −0.18 | 0.96 | 1.29* | V | f | − | − |
| slr1260 | NA | Hypothetical protein | n.c. | −0.13 | 0.81 | 1.22* | V | f | − | − |
| slr1302 | cupB | Protein involved in constitutive low-affinity CO2 uptake | n.c. | 0.07 | 0.93 | 1.13* | V | No | + | In coding sequence |
| slr1535 | NA | Hypothetical protein | 1.20 | 0.15 | 1.47* | 0.99 | V | No | + | + |
| ssl3769 | NA | Unknown protein | n.c. | −0.02 | 0.40 | 1.52* | V | No | + | + |