TABLE 1.
Group II introns in Methanosarcina acetivorans
| Introna | GenBank acc. no.b | RNA domainsc | ORF domainsd | Intron classe | Upstream flankf | Downstream flankf | Identity to M.a.I1-1g | Identity to M.a.I5-1h | Mi | Cj | Nk |
|---|---|---|---|---|---|---|---|---|---|---|---|
| aIntron names are consistent with earlier names of bacterial introns (Dai and Zimmerly 2002) and are based on the species abbreviation and a number. “F” indicates a fragment. I1-1, I1-2, and so forth denote closely related copies of the same intron. M.a.F1, M.a.F2, M.a.F3, and M.a.F4 are fragments that do not belong to the other six divisions and may be derived from other intron species. | |||||||||||
| bGenBank entry with the outer boundaries of the intron indicated (see Fig. 1 for internal structures). | |||||||||||
| cThe presence of ribozyme structural domains 1–6. “—” indicates an ORF fragment without RNA structure domains. | |||||||||||
| dORF domains include RT subdomains 0–7 and domain X. “—” indicates the absence of ORF domains. | |||||||||||
| eCL1, chloroplast-like class 1; Bact D, bacterial class D. Intron classes are based on ORF phylogenetic groupings, and each class also has a distinct RNA secondary structure (Zimmerly et al. 2001; Toor et al. 2001). | |||||||||||
| fSequence immediately upstream or downstream of an intron: PQG H.S., homing site that includes the PQG motif; YADD H.S., homing site that includes YADD or FADD motif (see Fig. 1F). “—” indicates the absence or an ORF and lack of conserved sequence in the exons. | |||||||||||
| g% identity to M.a.I1-1 based on RNA domains 1–6 and excluding the ORF. | |||||||||||
| h% identity to M.a.I5-1 based on RNA domains 1–6 and excluding the ORF. | |||||||||||
| iThe number of sequence differences that cause mispairing (M) of the secondary structure relative to either M.a.I1-1 or M.a.I5-1 (e.g., A-U to A-A). | |||||||||||
| jThe number of sequence differences that cause a compensatory (C) variation in the secondary structure (e.g., A-U to G-C, would count as one event in the table). | |||||||||||
| kThe number of sequence differences that are neutral (N) and retain base pairing (e.g., A-U to G-U). | |||||||||||
| lThe sequence flanking the intron is a conserved hypothetical protein rather than a group II intron ORF. However the insertion site is somewhat conserved in sequence and an alternative reading frame includes a PQG sequence (see Fig. 1F). | |||||||||||
| mM.a.F4 may be the downstream half of M.a.I3-F1 because its RNA domain 4 pairs with that of M.a.I3-F1, and because their ORFs both have 50% identities to the M.a.I1-1 ORF, and together would produce a continuous ORF. | |||||||||||
| M.a.I1-1 | AE010073 (4279–6431) | 1–6 | RT(0–7), X | CL1 | Conserved hypothetical proteinl | Conserved hypothetical proteinl | 100% | 0 | 0 | 0 | |
| M.a.I1-2 | AE011185 (1722–5744) | 1–6 | RT(0–7), X | CL1 | PQG H.S. | — | 90.8% | 1 | 9 | 7 | |
| M.a.I1-3 | AE011130 (2228–6247) | 1–6 | RT(0–7), X | CL1 | RQG H.S. | — | 93.5% | 0 | 14 | 14 | |
| M.a.I1-F1 | AE011130 (6428–7525) | 1–3 | RT(0–4) | CL1 | Transposase | — | 87.5% | 3 | 6 | 8 | |
| M.a.I1-F2 | AE010979 (6611–7239) | 5–6 | RT(7), X | CL1 | Transposase | PQG H.S. | 96.1% | 0 | 1 | 0 | |
| M.a.I2-F1 | AE011130 (7526–9438) | 1–3 | RT(0–4) | CL1 | — | — | 61.6% | 3 | 73 | 13 | |
| M.a.I3-F1 | AE011185 (5745–7226) | 1–3 | RT(0–4) | CL1 | — | — | 61.2% | 2 | 77 | 19 | |
| M.a.I4-1 | AE010882 (4828–5781) | 1–6 | — | CL1 | — | — | 61.9% | 8 | 70 | 15 | |
| M.a.I4-2 | AE011106 (4446–5200) | 1–6 | — | CL1 | — | — | 61.9% | 8 | 70 | 16 | |
| M.a.I4-3 | AE010996 (801–1555) | 1–6 | — | CL1 | — | — | 61.9% | 8 | 70 | 15 | |
| M.a.I5-1 | AE011130 (2949–4823) | 1–6 | RT(0–7),X | Bact D | YADD H.S. | YADD H.S. | 100% | 0 | 0 | 0 | |
| M.a.I5-2 | AE010979 (4618–6492) | 1–6 | RT(0–7),X | Bact D | YADD H.S. | YADD H.S. | 100% | 0 | 0 | 0 | |
| M.a.I5-3 | AE011185 (2451–4325) | 1–6 | RT(0–7),X | Bact D | YADD H.S. | YADD H.S. | 99.9% | 1 | 1 | 1 | |
| M.a.I6-1 | AE011030 (5879–6500) | 1–6 | — | Bact D | — | — | 82% | 6 | 14 | 14 | |
| M.a.I6-2 | AE010851 (441–1059) | 1–6 | — | Bact D | — | — | 83% | 6 | 17 | 13 | |
| M.a.I6-3 | AE011040/1 (10510/497) | 1–6 | — | Bact D | — | — | 83% | 6 | 16 | 10 | |
| M.a.I6-F1 | AE010902 (10030–10335) | 2–6 | — | Bact D | — | — | 82% | 1 | 0 | 0 | |
| M.a.F1 | AE010964 (6933–8146) | 5–6 | RT(4–7), X | CL1 | — | Conserved hypothetical proteinl | 55.3% | 0 | 12 | 1 | |
| M.a.F2 | AE010848 (4041–4124) | 5–6 | — | CL1 | — | — | 55.3% | 4 | 5 | 4 | |
| M.a.F3 | AE011134 (6345–7286) | — | RT(0–4) | CL1 | — | — | |||||
| M.a.F4m | AE010979 (3887–6610) | 5–6 | RT(4–7), X | CL1 | — | — | 71.1% | 0 | 6 | 3 | |
