Table 2.
Type II TA systems of Synechocystis 6803 according to the TADB [16], Makarova et al. 2009 [3], more specific studies, or newly defined according to this work (TW). Systems investigated in the course of this work biochemically are labeled “BC”. The respective gene loci, protein domains, the distance between the start codon and the start site of transcription (TSS) are given. Moreover, the replicon (chr, chromosome or plasmid name pSYS A, G, M or X) and the respective arrangement of toxin (T) and antitoxin (AT) component (Ord.) are indicated. Symbols and domain names: N/K, not known; COG, Cluster of Orthologous Genes; DUF, Domain of Unknown Function; TSS, Transcriptional Start Site (R, reverse strand; F, forward strand); TU, Transcriptional Unit; asRNA, antisense RNA; PIN, PIN domain (homologues of the ”pilT N“-terminal domain); Hic, Hic domain (hif-contiguous); YcfA, YcfA like domain; GNAT, GCN5-related .-acetyltransferases; RelE, RelE domain (relaxed response); YhaV, YhaV domain; YoeB, YoeB domain; PemK, PemK domain (plasmid emergency maintenance); MNT, MNT domain (minimal nucleotidyl transferase); HigB, HigB domain (Host Inhibition of Growth); cas, CRISPR-associated; HEPN; HEPN domain (higher eukaryotes and prokaryotes nucleotide-binding); PhdYeFM-antitox, prevent-host-death protein Phd/YefM antitoxin; HTH, helix-turn-helix; VagC, VagC domain (virulence associated gene); MazE, MazE domain; AbrB, AidB regulator domain; ChpI, chromosomal homolog of pem; Xre, xenobiotic response element. Information on TSSs was taken from published studies targeting the primary transcriptome of Synechocystis 6803 [28,29].
| Toxin | Type | A.toxin | Type | TSS | Dis. | Repl. | Ord. | Reference | Comment |
|---|---|---|---|---|---|---|---|---|---|
| sll0205 | PIN | ssl0385 | COG5559/DUF2281 | 2516776 R | 27 | Chr | AT-T | TW | - |
| ssl0258 | HicA (YcfA) | ssl0259 | HicB (COG1598) | 2193884 R | 72 | Chr | T-AT | TW | only second component exhibits TSS |
| sll0286 | GNAT | sll0284 | HEPN (DUF86) | 3024345 R | 74 | Chr | AT-T | TW | - |
| ssr0335 | HicA (YcfA) | ssr0336 | HicB (COG1598) | 2754240 F | 401 | Chr | T-AT | TW | - |
| ssl0350a | HicA (YcfA) | ssl0350 | HicB (COG1598) | 2740742 R | 1609 | Chr | AT-T | TW | TSS of TU |
| sll0406 | PIN | sll0405 | hypothetical | 2552996 R | 34 | Chr | AT-T | TW | potential asRNA regulation |
| sll0525 | PIN | ssl1004 | PhdYeFM_antitox | 3262737 | 30 | Chr | AT-T | [3,16] | see Figure 3 |
| sll0624 | PIN3 | sll0624a | HicB (COG1598) | 3342723 R | 281 | Chr | T-AT | TW | both components exhibit TSS |
| sll0658 | PIN | ssl1255 | HTH (COG2886) | 3121956 R | 3 | Chr | AT-T | [3,16] | - |
| slr0664 | RelE (DUF1044) | ssr1114 | hypothetical | 3347861 F | 80 | Chr | AT-T | [16,18] | - |
| sll0690 | PIN | ssl1300 | VagC | 2632007 R | 139 | Chr | AT-T | [3,16] | alternative TSS (2631867 R) |
| slr0725 | YhaV | slr0724 | MazE (AbrB) | 110366 F | 26 | Chr | AT-T | [3,16] | - |
| ssl0739 | HicA (YcfA) | ssl0738 | HicB (COG1598) | N/K | N/K | Chr | AT-T | TW | - |
| ssr0756 | PIN | ssr0755 | hypothetical | 2084115 F | 28 | Chr | AT-T | TW | - |
| ssr0757 | DUF497/COG2929 | ssr0757a | DUF4415/COG3514 | 2084877 F | 45 | Chr | T-AT | TW | - |
| ssr0761a | YoeB | ssr0761 | PhdYeFM_antitox | 2085833 F | 27 | Chr | AT-T | TW | - |
| slr0771 | PIN | slr0770 | COG2442/Duf433 | 2393421 F | 811 | Chr | AT-T | [3,16] | joint tricistronic TU2489 with slr0769 |
| slr1062 | PemK | slr1062a | hypothetical | 357724 | 7353 | Chr | AT-T | TW | TSS of TU |
| sll1092 | PIN | ssl2138 | COG5559/DUF2281 | N/K | N/K | Chr | AT-T | [16,19] | see Figure 3 |
| sll1130 | PemK | ssl2245 | hypothetical | 1049139 R | 123 | Chr | AT-T | [16,21] | potential asRNA regulation; involved in the heat shock response |
| slr1210 | PIN | slr1209 | COG2442/Duf433 | 891086 F | 2175 | Chr | AT-T | [3,16] | TSS of TU; potential asRNA regulation |
| sll1225 | PIN | ssl2420 | hypothetical | 1678733 R | 4435 | Chr | AT-T | [16] | - |
| slr1241 | MNT | slr1240 | hypothetical | 1053924 F | 1650 | Chr | AT-T | TW | TSS of TU |
| ssr1260 | HicA (YcfA) | ssr1258 | HicB (COG1598) | 3428302 F | 660 | Chr | AT-T | TW | TSS of TU |
| slr1327 | PIN3 | ssr2201 | hypothetical | 1660041 F | 28 | Chr | AT-T | [16] | - |
| ssl1377 | HicA (YcfA) | ssl1376 | HicB (COG1598) | 3427318 R | 115 | Chr | AT-T | TW | - |
| slr1383 | PIN | ssr2317 | hypothetical | 679231 F | 459 | Chr | T-AT | TW | - |
| sll1400 | PIN | ssl2733 | COG2442/Duf433 | 50262 R | 1627 | Chr | AT-T | [3,16] | TSS of TU |
| slr1421 | DUF4258 | ssr2377 | HicB (COG1598) | 3273485 F | 24 | Chr | AT-T | TW | - |
| ssl1493a | PIN | ssl1493 | PhdYeFM_antitox | 3044721 R | 66 | Chr | AT-T | TW | - |
| sll1504 | MNT | sll1505 | HEPN (DUF86) | 477658 R | 1915 | Chr | T-AT | [3,16] | TSS of TU |
| sll1543 | PIN | ssl2999 | hypothetical | 3475237 R | 53 | Chr | T-AT | TW | both components exhibit TSS |
| sll1651 | DUF497/COG2929 | sll1652 | DUF3680/COG5304 | 282821 R | 0 | Chr | T-AT | TW | leader-less |
| sll1715 | PIN | sll1714 | hypothetical | 969538 R | 244 | Chr | AT-T | [16] | - |
| ssr1766 | HicA (YcfA) | ssr1765 | HicB (COG1598) | 382338 F | 54 | Chr | AT-T | [3,16] | - |
| slr1767 | PIN | ssr2962 | COG2442/Duf433 | 544995 F | 34 | Chr | AT-T | [3,16,20] | alternative TSS (2085834 F); excludon-like arrangement |
| slr1906 | GNAT | slr1907 | hypothetical | 609442 F | 27 | Chr | T-AT | TW | - |
| sll1912 | PIN | ssl3615 | hypothetical | 776369 R | 27 | Chr | AT-T | [16] | - |
| sll1965 | DUF497/COG2929 | ssl3719 | DUF4415/COG3514 | 915052 R | 0 | Chr | T-AT | TW | leader-less |
| slr1999 | HicA (YcfA) | slr1999 | HicB (COG1598) | 1444698 | 727 | Chr | AT/T | TW | both domains in one protein |
| ssr2066 | HicA (YcfA) | ssr2067 | HicB (COG1598) | 1053924 F | 2563 | Chr | T-AT | TW | TSS of TU |
| ssl2749 | MNT | sll1411 | HEPN (DUF86) | 1619636 R | 1540 | Chr | T-AT | [3,16] | TSS of TU |
| ssr2755 | YoeB | ssr2754 | PhdYeFM_antitox | 2074673 F | 21 | Chr | AT-T | TW | - |
| N/K | N/K | ssr2784 | hypothetical (ChpI homolog) | 3474436 F | 26 | Chr | AT | TW | stand-alone |
| N/K | N/K | ssr2784a | COG2442/Duf433 | N/K | N/K | Chr | AT | TW | stand-alone; potential asRNA regulation |
| ssl2921 | HigB | ssl2920 | hypothetical | N/K | N/K | Chr | AT-T | TW | TSS of TU |
| ssl2923 | PIN | ssl2922 | VagC | N/K | N/K | Chr | AT-T | [3,16] | see Figure 3 |
| N/K | N/K | ssr3154 | HTH (COG2886) | 1211302 F | 99 | Chr | AT | TW | stand-alone; potential asRNA regulation |
| ssr3572 | YoeB | ssr3571 | PhdYeFM_antitox | 1620247 F | 29 | Chr | AT-T | TW | - |
| ssr3589 | PIN | ssr3588 | hypothetical | 1644850 F | 3314 | Chr | AT-T | TW | TSS of TU |
| sll5003 | PIN | sll5004 | COG2442/Duf433 | 1846 R | 20 | pSYSM | AT-T | [3,16] | - |
| slr5017 | MNT | slr5018 | HEPN (DUF86) | 23222 F | 33 | pSYSM | T-AT | [3,16] | - |
| ssr5020 | HigB | slr5021 | HTH-Xre | 24162 F | 19 | pSYSM | T-AT | [3,16] | - |
| N/K | N/K | ssl5025 | COG2442/Duf433 | 28079 R | 26 | pSYSM | AT | TW | stand-alone |
| sll5094 | PIN | ssl5095 | PhdYeFM_antitox | 93540 F | 20 | pSYSM | AT-T | [3,16] | - |
| slr5102 | DUF1814 | slr5101 | hypothetical | 96110 F | 14 | pSYSM | AT-T | TW | - |
| slr5116 | PIN3 | ssr5117 | HicB | 106534 F | 571 | pSYSM | T-AT | [3,16] | - |
| slr6049 | PIN | ssr6048 | hypothetical | 47161 F | 21 | pSYSX | AT-T | TW | - |
| slr6057 | COG2856/Duf955 | slr6056 | HTH-Xre | 54326 F | 17 | pSYSX | AT-T | [3,16] | potential asRNA regulation; linked to possible bacterial multiubiquitin system; see Figure 4 |
| slr6100 | RelE (DUF2136) | slr6101 | HTH-Xre | 93754 F | 66 | pSYSX | T-AT | [3,16,22] | - |
| sll7003 | PIN | ssl7004 | plasmid stability | 2074 R | 42 | pSYSA | AT-T | [3,16,23] | - |
| ssl7007 | PIN | sll7006 | HicB | 3798 R | 207 | pSYSA | T-AT | [3,16,23] | - |
| ssr7017 | cas2 | slr7016 | cas1 | N/K | N/K | pSYSA | T-AT | [33] | potential asRNA regulation |
| sll7030 | GNAT | sll7031 | COG4453/DUF1778 | 29663 R (27264 R) | 24 | pSYSA | AT-T | [3,16] | - |
| N/K | N/K | slr7032 | HEPN (DUF86) | 30317 F (27918 F) | 35 | pSYSA | AT | TW | stand-alone |
| sll7033 | PIN | sll7034 | COG2442/Duf433 | 31387 R (28988 R) | 18 | pSYSA | AT-T | [3,16,23] | - |
| ssl7039 | RelE | ssl7038 | HTH-Xre | 36479 R (34080 R) | 0 | pSYSA | T-AT | [3,16,23] | leader-less; see Figure 5 and Figure 6 |
| slr7041 | MazF | ssr7040 | MazE | 36567 F (34168 F) | 28 | pSYSA | AT-T | [3,16,23] | - |
| ssl7046 | PIN3 | N/K | N/K | 40539 R (38140 R) | 25 | pSYSA | T | TW | stand-alone |
| N/K | N/K | ssl7048 | MazE (AbrB) | N/K | N/K | pSYSA | AT | TW | stand-alone |
| ssr7072 | cas2 | slr7071 | cas1 | 64765 F (62366 F) | 57 | pSYSA | AT-T | [33] | - |
| ssr7093 | cas2 | slr7092 | cas1 | 88315 F | 312 | pSYSA | AT-T | [33] | - |
| sll8007 | PIN | ssl8008 | COG2442/Duf433 | 6626 R | 25 | pSYSG | AT-T | [3,16] | - |
| sll8011 | PIN | sll8012 | hypothetical | 9650 R | 29 | pSYSG | AT-T | [3,16] | - |
| slr8014 | PIN3 | ssr8013 | DUF2281 | 8658 F | 1055 | pSYSG | AT-T | [3,16] | see Figure 3 and Figure 7 |
| sll8027 | PIN3 | ssl8028 | MazE (AbrB) | 24116 R | 39 | pSYSG | AT-T | [3,16] | - |