Table 3 Comparison of expression level and regulatory pattern for RNA-seq results [36] and Ypet fluorescence for native Synechococcus sp. PCC 7002 promoters
From: Genetic tools for advancement of Synechococcus sp. PCC 7002 as a cyanobacterial chassis
Promoter gene locus | Native gene locus function | Expression level | Regulatory pattern | Correlation coefficient (Ypet vs RNA-seq) | ||
|---|---|---|---|---|---|---|
Average RNA-seq (counts/total counts) | Average Ypet fluorescence (normalized to 7002) | RNA-seq (slope of counts/total counts vs. OD730) | Ypet fluorescence (slope of fluorescence vs. OD730) | |||
Synpcc7002_A0047 | Hypothetical protein | 2.17E−04 | 1.322 ± 0.116* | Stationary phase (9.68E−04) | Constitutive (−0.0192) | 0.0967 |
Synpcc7002_A0255 | UDP-N-acetyl-D-mannosaminuronic acid transferase | 5.09E−05 | 1.073 ± 0.133 | Stationary phase (1.63E−05) | Constitutive (−0.0265) | −0.722 |
Synpcc7002_A0304 | Hypothetical protein | 5.55E−05 | 1.038 ± 0.158 | Linear phase (−1.77E−05) | Constitutive (−0.107) | 0.715 |
Synpcc7002_A0318 | Hypothetical protein | 8.72E−04 | 1.137 ± 0.135* | Constitutive (5.75E−06) | Constitutive (0.196) | 0.212 |
Synpcc7002_A0670 | Hypothetical protein | 2.16E−05 | 1.239 ± 0.442 | Constitutive (5.72E−07) | Constitutive (0.178) | 0.678 |
Synpcc7002_A0740 | ATP synthase subunit I | 1.04E−03 | 1.186 ± 0.0919* | Linear phase (−2.73E−04) | Constitutive (3.83E−04) | −0.628 |
Synpcc7002_A1173 | Polyketide synthase | 1.22E−03 | 1.087 ± 0.0914* | Constitutive (1.62E−05) | Constitutive (0.172) | 0.252 |
Synpcc7002_A1181 | ATPase AAA | 2.58E−03 | 1.074 ± 0.0937 | Stationary phase (9.41E−04) | Constitutive (−0.0108) | −0.0121 |
Synpcc7002_A1731 | Hypothetical protein | 6.03E−05 | 1.075 ± 0.0967 | Constitutive (−8.49E−07) | Constitutive (0.0640) | 0.181 |
Synpcc7002_A1798 (rbc) | Ribulose bisophosphate carboxylase, large subunit | 4.77E−03 | 4.153 ± 2.17* | Linear phase (−6.24E−04) | Stationary phase (2.88) | −0.335 |
Synpcc7002_A1929 | Allophycocyanin subunit beta | 1.29E−02 | 1.046 ± 0.0866 | Linear phase (−2.75E−03) | Constitutive (−0.0547) | 0.800 |
Synpcc7002_A1930 | Allophycocyanin subunit alpha | 7.46E−03 | 2.338 ± 0.197* | Linear phase (−1.51E−03) | Constitutive (−0.107) | 0.249 |
Synpcc7002_A1961 | Photosystem I P700 chlorophyll-a apoprotein A1 | 1.95E−02 | 2.076 ± 0.237* | Constitutive (6.59E−04) | Stationary phase (0.744) | 0.348 |
Synpcc7002_A1962 | Photosystem I P700 chlorophyll-a apoprotein A2 | 2.61E−02 | 1.059 ± 0.126 | Stationary phase (2.42E−03) | Constitutive (−0.0533) | 0.256 |
Synpcc7002_A2062 | Elongation factor G | 5.33E−03 | 1.038 ± 0.00945* | Constitutive (3.95E−06) | Constitutive (0.0392) | −0.0315 |
Synpcc7002_A2127 | Acetyl-CoA carboxylase biotin carboxylase subunit | 3.62E−04 | 1.073 ± 0.0576* | Constitutive (1.64E−06) | Constitutive (0.0583) | 0.457 |
Synpcc7002_A2165 | Hypothetical protein | 9.95E−05 | 1.205 ± 0.129* | Stationary phase (3.20E−05) | Constitutive (0.148) | 0.960 |
Synpcc7002_A2210 | C-phycocyanin subunit alpha | 2.91E−02 | 1.129 ± 0.191 | Linear phase (−4.85E−03) | Constitutive (0.163) | −0.907 |
Synpcc7002_A2520 | Hypothetical protein | 7.27E−05 | 31.88 ± 4.61* | Linear phase (−2.78E−05) | Stationary phase (35.4) | −0.954 |
Synpcc7002_A2531 | Hypothetical protein | 1.24E−02 | 2.340 ± 0.199* | Constitutive (−7.74E−04) | Constitutive (0.105) | −0.638 |
Synpcc7002_A2579 | Hypothetical protein | 6.80E−03 | 33.51 ± 6.28* | Linear phase (−2.79E−03) | Stationary phase (30.2) | −0.968 |
Synpcc7002_A2595 | Hypothetical protein | 9.20E−04 | 1.061 ± 0.107 | Stationary phase (3.90E−04) | Constitutive (−0.0697) | −0.972 |
Synpcc7002_A2596 | Hypothetical protein | 2.77E−04 | 1.108 ± 0.0762* | Stationary phase (9.99E−05) | Constitutive (−0.0649) | −0.895 |
Synpcc7002_A2663 | Bacterioferritin | 2.87E−04 | 1.490 ± 0.169* | Linear phase (−6.99E05) | Constitutive (0.0140) | −0.116 |
Synpcc7002_A2813 | S-layer protein | 2.47E−02 | 3.486 ± 0.791* | Stationary phase (2.26E−03) | Constitutive (0.108) | −0.213 |