Table 3. Protein coding genes whose TSS showed a more than threefold increase in the number of reads.
| Protein in Nodularia CCY9414 | Absolute read counts (control) | FC HL+O2/control | ASC DE probability O2+HL/control | FC HL/control | ASC DE probability HL/control | Annotation | ORF in 6803 (e-value) |
|---|---|---|---|---|---|---|---|
| NSP_50790 | 1 | 1334 | 1.0 | 1 | 0.0 | Glycosyl transferase, group 1 | Sll0045 (e−30) |
| NSP_43710 | 20 | 50.3 | 1.0 | 0.1 | 0.0 | LSU ribosomal protein L5p (L11e) | Sll1808 (e−108) |
| NSP_41430 | 96 | 18.9 | 1.0 | 0.9 | 0.0 | 4Fe–4S ferredoxin, nitrogenase-associated | Sll0741 (2e−08) |
| NSP_16900 | 109 | 13.3 | 1.0 | 0.9 | 0.0 | Hypothetical protein | None |
| NSP_24490 | 89 | 13.1 | 1.0 | 1.1 | 0.0 | Phytoene synthase | Slr1255 (2e−135) |
| NSP_14160 | 338 | 12.7 | 1.0 | 0.6 | 0.0 | Cytochrome b559 α-Chain (PsbE) | Ssr3451 (2e−45) |
| NSP_3790 | 142 | 10.2 | 1.0 | 2 | 0.61 | Photosystem I subunit IX (PsaJ) | Sml0008 (2e−04) |
| NSP_6400 | 149 | 9.8 | 1.0 | 2.9 | 1.0 | NifU-like protein | Ssl2667 (e−43) |
| NSP_18580 | 409 | 9.3 | 1.0 | 0.5 | 0.0 | General secretion pathway protein H, Type IV pilin PilA | Sll1694HL (e−32) |
| NSP_2690 | 384 | 8.8 | 1.0 | 0.2 | 0.0 | Hypothetical protein | Slr1900 (e−49) |
| NSP_22750 | 299 | 7.9 | 1.0 | 0 | 0.0 | WD repeat-containing protein | Slr8038 (3e−39) |
| NSP_47150 | 203 | 7.4 | 1.0 | 1 | 0.0 | Hypothetical protein | None |
| NSP_6930 | 206 | 7.3 | 1.0 | 1.2 | 0.0 | Hypothetical protein | None |
| NSP_9450 | 1264 | 6.9 | 1.0 | 2.9 | 1.0 | RND efflux membrane fusion protein | Sll0141 (e−83) |
| NSP_45100 | 200 | 6.8 | 1.0 | 1.3 | 0.0 | Phycoerythrin linker protein CpeS homolog | Slr2049 (e−59) |
| NSP_38040 | 217 | 6.6 | 1.0 | 2.4 | 1.0 | Hypothetical protein | None |
| NSP_48690 | 450 | 6.3 | 1.0 | 1.5 | 0.0 | Protein CP12, regulation of Calvin cycle | Ssl3364 (2e−21) |
| NSP_49270 | 178 | 6.1 | 1.0 | 2.6 | 1.0 | WD40 repeat | Sll0877 (2e−77) |
| NSP_19890 | 226 | 5.9 | 1.0 | 1.1 | 0.0 | Ferric uptake regulation protein | Sll1937 (2e−06) |
| NSP_33730 | 341 | 5.6 | 1.0 | 2.1 | 0.94 | Dihydroxy-acid dehydratase | Slr0452 (0.0) |
| NSP_14650 | 306 | 5.5 | 1.0 | 0.1 | 0.0 | Major facilitator family transporter | Sll1154 (e−112) |
| NSP_10860 | 578 | 5.4 | 1.0 | 0.7 | 0.0 | Carbohydrate-selective porin. OprB family | Sll0772 (e−98) |
| NSP_36640 | 195 | 5.4 | 1.0 | 0.4 | 0.0 | Hypothetical protein | None |
| NSP_31680 | 704 | 5.4 | 1.0 | 2.5 | 1.0 | PHP family metal-dependent phosphoesterase | Sll0549 (e−73) |
| NSP_34350 | 677 | 5.3 | 1.0 | 1.1 | 0.0 | Hypothetical protein | Slr2073 (3e−49) |
| NSP_19030 | 308 | 5.3 | 1.0 | 2.5 | 1.0 | Hypothetical protein | Slr1391 (e−16) |
| NSP_15460 | 1702 | 5.3 | 1.0 | 0.6 | 0.0 | ATPase involved in DNA repair | None |
| NSP_700 | 368 | 5.1 | 1.0 | 0.7 | 0.0 | Uracil–DNA glycosylase, family 4 | None |
| NSP_42260 | 614 | 5 | 1.0 | 1.6 | 0.0 | Chorismate synthase | Sll1747 (0.0) |
| NSP_48530 | 992 | 4.9 | 1.0 | 1.1 | 0.0 | Cell division trigger factor (EC 5.2.1.8) | Sll0533HL (e−125) |
| NSP_52140 | 387 | 4.8 | 1.0 | 0.5 | 0.0 | Sigma54 homolog | Ssr0657 (3e−32) |
| NSP_33420 | 320 | 4.8 | 1.0 | 0.9 | 0.0 | Hypothetical protein | Slr0975 (6e−117) |
| NSP_24390 | 434 | 4.7 | 1.0 | 1.1 | 0.0 | NADH dehydrogenase I subunit 4, PS1 cyclic electron flow | Slr1291HL (0.0) |
| NSP_50790 | 1 | 4.7 | 1.0 | 2.4 | NA | Glycosyl transferase, group 1 | Sll0045 (2e−30) |
| NSP_40430 | 248 | 4.6 | 1.0 | 0.7 | 0.0 | Protein of unknown function DUF820 | Slr1613 (3e−44) |
| NSP_42360 | 322 | 4.6 | 1.0 | 0.6 | 0.0 | Nucleoside triphosphate pyrophosphohydrolase MazG | Sll1005HL (e−121) |
| NSP_15410 | 281 | 4.5 | 1.0 | 0.7 | 0.0 | ATPase associated with various activities or gas vesicle protein GvpN | Slr1416 (e−05) |
| NSP_35650 | 417 | 4.5 | 1.0 | 0.9 | 0.0 | Hypothetical protein | None |
| NSP_14220 | 4891 | 4.4 | 1.0 | 1.1 | 0.0 | Transposase. IS605 OrfB | None |
| NSP_25450 | 638 | 4.4 | 1.0 | 1 | 0.0 | Hypothetical protein | None |
| NSP_48520 | 453 | 4.3 | 1.0 | 1.2 | 0.0 | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | Sll0534 (e−125) |
| NSP_1470 | 356 | 4.3 | 1.0 | 2.2 | 0.99 | Hypothetical protein | None |
| NSP_27850 | 1945 | 4.2 | 1.0 | 0.3 | 0.0 | TldD protein, part of proposed TldE/TldD proteolytic complex | Slr1322 (0.0) |
| NSP_35830 | 777 | 4.2 | 1.0 | 1.5 | 0.0 | Hemolysin-like | Slr0483 (e−38) |
| NSP_42990 | 333 | 4.2 | 1.0 | 2.6 | 1.0 | Nuclease subunit of the excinuclease complex | Slr1035 (e−12) |
| NSP_10200 | 1257 | 4.1 | 1.0 | 1.1 | 0.0 | Hypothetical protein | Slr0575 (e−78) |
| NSP_47200 | 6886 | 4.1 | 1.0 | 0.5 | 0.0 | Hypothetical protein | Sll0749 (e−38) |
| NSP_39370 | 265 | 4 | 1.0 | 1.2 | 0.0 | Dihydrolipoamide dehydrogenase | Slr1096 (0.0) |
| NSP_10630 | 444 | 4 | 1.0 | 2.2 | 1.0 | ATP-dependent peptidase S16 | Sll0195 (e−117) |
| NSP_17370 | 303 | 4 | 1.0 | 2 | 0.92 | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | Slr0164 (e−99) |
| NSP_15490 | 549 | 3.9 | 1.0 | 1 | 0.0 | Cell division control protein FtsH | Slr0228HL (e−58) |
| NSP_17490 | 2512 | 3.9 | 1.0 | 2.1 | 1.0 | Hypothetical protein | Sll1483HL (e−43) |
| NSP_48980 | 1335 | 3.9 | 1.0 | 0.8 | 0.0 | Hypothetical protein | None |
| NSP_46280 | 1582 | 3.9 | 1.0 | 1.2 | 0.0 | 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100) | Sll0330 (e−17) |
| NSP_16440 | 414 | 3.9 | 1.0 | 1.8 | 0.13 | Hypothetical protein | None |
| NSP_33860 | 721 | 3.9 | 1.0 | 1.1 | 0.0 | Putative protein | Slr1378 (e−75) |
| NSP_830 | 283 | 3.8 | 1.0 | 0.9 | 0.0 | Octaprenyl-diphosphate synthase (EC 2.5.1.-)/Geranylgeranyl pyrophosphate synthetase | Slr0739 (e−156) |
| NSP_51180 | 279 | 3.8 | 1.0 | 0.7 | 0.0 | Hypothetical protein | None |
| NSP_4850 | 268 | 3.8 | 1.0 | 0.2 | 0.0 | EsV-1-176 | Slr0645 (2e−94) |
| NSP_53130 | 640 | 3.7 | 1.0 | 0.5 | 0.0 | Translation IF3 | Slr0974 (e−26) |
| NSP_50960 | 510 | 3.7 | 1.0 | 1.4 | 0.0 | Hypothetical protein | None |
| NSP_1350 | 1083 | 3.7 | 1.0 | 0.7 | 0.0 | Hypothetical Protein | Slr0476HL (9e−15) |
| NSP_38540 | 1663 | 3.7 | 1.0 | 0.4 | 0.0 | Photosystem II protein PsbK | Sml0005 (e−13) |
| NSP_3140 | 1342 | 3.7 | 1.0 | 0.5 | 0.0 | Hypothetical protein | None |
| NSP_50680 | 446 | 3.6 | 1.0 | 1.5 | 0.0 | Glycogen phosphorylase (EC 2.4.1.1) | Slr1367 (e−18) |
| NSP_25450 | 638 | 3.6 | 1.0 | 2.2 | 0.0 | Hypothetical protein | None |
| NSP_51790 | 945 | 3.6 | 1.0 | 1.4 | 0.0 | Cytochrome b6-f complex iron-sulfur subunit PetC1 (Rieske) | Sll1316 (e−98) |
| NSP_36900 | 814 | 3.6 | 1.0 | 1 | 0.0 | Peptidoglycan-binding domain 1 | None |
| NSP_30660 | 517 | 3.6 | 1.0 | 1.9 | 0.59 | Hypothetical protein | None |
| NSP_51310 | 1074 | 3.6 | 1.0 | 1.4 | 0.0 | Ton-B like periplasmic protein | None |
| NSP_19230 | 4411 | 3.5 | 1.0 | 1.1 | 0.0 | Hypothetical protein | Slr2070 (e−61) |
| NSP_51330 | 368 | 3.5 | 1.0 | 0.2 | 0.0 | Phage shock protein A | Sll0617 (e−85) |
| NSP_46110 | 555 | 3.5 | 1.0 | 1.2 | 0.0 | NADH dehydrogenase (EC 1.6.99.3), NdhD | Slr1743 (e−170) |
| NSP_52960 | 1906 | 3.5 | 1.0 | 0.9 | 0.0 | Shikimate kinase I (EC 2.7.1.71) | Sll1660 (e−70) |
| NSP_30840 | 381 | 3.5 | 1.0 | 1.5 | 0.0 | NAD (P) transhydrogenase alpha subunit (EC 1.6.1.2) | Slr1239 (e−107) |
| NSP_52090 | 313 | 3.5 | 1.0 | 0.9 | 0.0 | Two-component response regulator | Slr1909 (e−109) |
| NSP_25460 | 964 | 3.5 | 1.0 | 1.7 | 0.0 | Oxidoreductase, Gfo/Idh/MocA family | Slr0338 (0.0) |
| NSP_15680 | 3773 | 3.4 | 1.0 | 1.1 | 0.0 | Hypothetical protein | Slr2025 (e−37) |
| NSP_51030 | 335 | 3.4 | 1.0 | 2 | 0.71 | Hypothetical protein | None |
| NSP_43620 | 299 | 3.4 | 1.0 | 0.5 | 0.0 | Large SU ribosomal protein L36p | Sml0006 (e−17) |
| NSP_41520 | 335 | 3.3 | 1.0 | 2.1 | 0.96 | Photosystem I P700 chlorophyll a apoprotein subunit Ia (PsaA) | Slr1834HL (0.0) |
| NSP_16880 | 962 | 3.3 | 1.0 | 1.8 | 0.11 | Sorbitol dehydrogenase (EC 1.1.1.14) | Sll0990 (e−13) |
| NSP_40730 | 1758 | 3.3 | 1.0 | 1.7 | 0.0 | DNA methylase N-4/N-6 | None |
| NSP_26680 | 734 | 3.3 | 1.0 | 2.2 | 1.0 | Phage integrase | None |
| NSP_33380 | 1633 | 3.3 | 1.0 | 1.7 | 0.0 | Chaperone protein DnaK | Sll1932 (0.0) |
| NSP_7750 | 464 | 3.3 | 1.0 | 0.3 | 0.0 | Iron (III)-traNSP_ort ATP-binding protein SfuC | Slr0354 (e−101) |
| NSP_9910 | 2965 | 3.3 | 1.0 | 1.3 | 0.0 | Hypothetical protein | None |
| NSP_38190 | 375 | 3.3 | 1.0 | 2 | 0.88 | Similar to Ymc | None |
| NSP_19230 | 4411 | 3.2 | 1.0 | 1 | 0.0 | Hypothetical protein | Slr2070 (2e−67) |
| NSP_22130 | 7582 | 3.2 | 1.0 | 1.1 | 0.0 | Hypothetical protein | None |
| NSP_300 | 403 | 3.2 | 1.0 | 2.1 | 0.98 | 3-Polyprenyl-4-hydroxybenzoate carboxy-lyase | Sll0936 (0.0) |
| NSP_19990 | 736 | 3.2 | 1.0 | 1.6 | 0.0 | ADP-heptose–lipooligosaccharide heptosyltransferase II (EC 2.4.1.-) | Slr0606 (e−101) |
| NSP_24440 | 328 | 3.2 | 1.0 | 2.3 | 1.0 | Hypothetical protein | None |
| NSP_37380 | 514 | 3.1 | 1.0 | 0.1 | 0.0 | ATP synthase β-chain (EC 3.6.3.14) | Slr1329HL (0.0) |
| NSP_45180 | 2481 | 3.1 | 1.0 | 2.7 | 1.0 | Carboxyl-terminal processing protease | Slr0008 (e−171) |
| NSP_1410 | 1125 | 3.1 | 1.0 | 1.2 | 0.93 | Ribulose-phosphate 3-epimerase (EC 5.1.3.1) | Sll0807 (e−144) |
| NSP_12600 | 483 | 3.1 | 1.0 | 0.6 | 0.0 | Hypothetical protein | Sll1381 (3e−53) |
| NSP_50770 | 1649 | 3.1 | 1.0 | 0.8 | 0.0 | RNA-binding protein | Slr0193 (e−48) |
| NSP_890 | 591 | 3.1 | 1.0 | 1.5 | 0.0 | Flavodoxin reductases (ferredoxin–NADPH reductases) family 1 | Sll0765 (e−110) |
| NSP_50880 | 1046 | 3 | 1.0 | 0.6 | 0.0 | Phage integrase | None |
| NSP_42140 | 351 | 3 | 1.0 | 0.3 | 0.0 | Amino acid adenylation protein NdaA involved in nodularin synthesis | None |
| NSP_6650 | 927 | 3 | 1.0 | 0.9 | 0.0 | Serine/threonine kinase | Sll1380 (e−23) |
| NSP_29410 | 734 | 3 | 1.0 | 0.7 | 0.0 | Hypothetical protein | Sll1142 (e−82) |
| NSP_1450 | 1317 | 3 | 1.0 | 0.3 | 0.0 | Acetolactate synthase large subunit (EC 2.2.1.6) | Slr2088 (0.0) |
| NSP_2440 | 424 | 3 | 1.0 | 0.8 | 0.0 | Hypothetical protein | Sll1022 (e−82) |
Abbreviations: ASC, analysis of sequence counts; DE, differentially expressed; ELIP, early light induced protein; FC, fold change; HL, high light; IF3, initiation factor 3; LSU, large subunit; ORF, open reading frame; RND, resistance-nodulation-cell division; WD, Trp-Asp.
Protein coding genes whose TSS showed a more than threefold increase in the number of reads specifically under combined HL and oxygen (HL+O2) stress (minimum number of 620 reads at combined HL+O2 stress).
For comparison, the expression levels after HL stress in Nodularia CCY9414 as well as the orthologs in Synechocystis are given. Genes were indicated by the suffix HL, when they were HL-induced in Synechocystis according to microarray data sets (CyanoEXpress 1.2 database; Hernandez-Prieto and Futschik, 2012). For the complete list of TSSs see Supplementary Table S3.