Table 1.
GsI-IIC introns in G. stearothermophilus strain 10 (accession number: CP008934). In-trons are numbered 1 to 45 in order of their genomic location. GsI-IIC3, which has the most common intron RNA sequence, was set as a standard for comparison of other introns. Length indicates the length of the intron in nt, with type A and B referring to introns containing the longer (type B) or shorter (type A) form of the DIIb stem-loop (see Fig. 1). Mutations indicate changes in the intron relative to GsI-IIC3, including base substitutions, insertions (+), and deletions (Δ). Accession numbers are listed for each RT, along with any changes compared to the RT encoded by GsI-IIC3. GsI-IIC41 has a 3,130-nt transposon inserted after amino acid residue 133 of the intron ORF. The final columns indicate the protein-coding gene upstream of the intron and the distance between its termination codon and the intron insertion site. Introns that are inserted within genes are indicated as being “Inside” with * indicating insertion in the sense (spliceable) orientation, and ** indicating insertion in the antisense (non-spliceable) orientation.
| Intron | Genomic location | Length (nt) |
Type | Mutations | RT Accession | RT Mutation (aa) |
Upstream gene | Distance (nt) |
|
|---|---|---|---|---|---|---|---|---|---|
| 5′ end | 3′ end | ||||||||
|
| |||||||||
| 1 | 90362 | 88479 | 1884 | A | C347A | WP_053413520, ALA68829 | 105 | DUF1320 domain-containing protein | 72 |
| 2 | 113253 | 111370 | 1884 | A | WP_053413546, ALA68851 | Acetoacetyl-CoA ligase | 64 | ||
| 3 | 130439 | 128546 | 1894 | B | WP_053413546, ALA68868 | Nucleotidyltransferase | In-side* | ||
| 4 | 310616 | 312509 | 1894 | B | G33A | WP_053413546, ALA69020 | Bifunctional diguanylate cyclase/phosphodiesterase | 41 | |
| 5 | 316517 | 318410 | 1894 | B | WP_053413546, ALA69026 | Cold-shock protein CspB | 73 | ||
| 6 | 362250 | 360367 | 1884 | A | G213A | WP_053413546, ALA69069 | RNA-binding protein Hfq | 62 | |
| 7 | 386691 | 384808 | 1884 | A | WP_053413546, ALA69087 | Recombinase RecA | 42 | ||
| 8 | 569299 | 567406 | 1894 | B | WP_053413546, ALA69261 | RNA polymerase sporulation sigma factor SigE | 34 | ||
| 9 | 667580 | 665697 | 1884 | A | WP_053413768, ALA69363 | 49,105,66 | YqzE family protein | 36 | |
| 10 | 834441 | 832548 | 1894 | B | WP_053413546, ALA69535 | Prephenate dehydratase | 45 | ||
| 11 | 882716 | 880833 | 1884 | A | WP_053413546, ALA69582 | YihA family ribosome biogenesis GTP-binding protein EngB | 37 | ||
| 12 | 1035372 | 1033488 | 1885 | A | +1 nt after 257 | WP_053413546, ALA69722 | Thiol peroxidase | 33 | |
| 13 | 1041637 | 1039754 | 1884 | A | A165G, U288C | WP_053413910, ALA69729 | 137 | Acyl-CoA ligase | 98 |
| 14 | 1098849 | 1096956 | 1894 | B | WP_053413546, ALA69777 | Rhodanese-like domain-containing protein | 250 | ||
| 15 | 1107091 | 1108974 | 1884 | A | A165G | WP_013522881, ALA69786 | 49,105 | Gamma carbonic anhydrase family protein | 21 |
| 16 | 1216594 | 1214701 | 1894 | B | WP_053413546, ALA69883 | Hypothetical protein | 75 | ||
| 17 | 1225036 | 1223153 | 1884 | A | WP_053413546, ALA69891 | TIGR01457 family HAD-type hydrolase | 38 | ||
| 18 | 1250285 | 1248392 | 1894 | B | WP_053413546, ALA69919 | Fe-S cluster assembly protein SufB | 201 | ||
| 19 | 1332211 | 1334094 | 1884 | A | WP_053413546, ALA69995 | ATP-dependent Clp protease proteolytic subunit | 94 | ||
| 20 | 1562077 | 1560188 | 1890 | A | +6 nt after 552 | WP_053413768, ALA70188 | 49,105,66 | DUF1861 domain-containing protein | 146 |
| 21 | 1591714 | 1589834 | 1881 | A | C430U, A1887G, Δ366-368 | WP_053414153, ALA70217 | 49,105,40,41,379 | Hypothetical protein | 32 |
| 22 | 1644550 | 1642667 | 1884 | A | WP_053413546, ALA70276 | Fructose-1,6-bisphosphate aldolase, class II | 40 | ||
| 23 | 1722290 | 1720407 | 1884 | A | WP_053413546, ALA70344 | RNA methyltransferase | Inside* | ||
| 24 | 1784959 | 1786842 | 1884 | A | WP_053413546, ALA70396 | Seryl-tRNA synthetase | 219 | ||
| 25 | 1892784 | 1894677 | 1894 | B | WP_053413546, ALA70492 | Elongation factor Tu | 48 | ||
| 26 | 1979108 | 1981001 | 1894 | B | WP_053413546, ALA70581 | Spore coat protein | 41 | ||
| 27 | 1992453 | 1994346 | 1894 | B | WP_053413546, ALA70591 | ATP-dependent helicase srmB | 13 | ||
| 28 | 2012352 | 2014245 | 1894 | B | WP_013522881, ALA70605 | 49,105 | tRNA (A(37)-N6)-threonylcarbamoyltransferase subunit TsaD | 65 | |
| 29 | 2027255 | 2029148 | 1894 | B | WP_013522881, ALA70620 | 49,105 | Class II fumarate hydratase | 41 | |
| 30 | 2142821 | 2144714 | 1894 | B | WP_053413546, ALA70707 | MFS transporter | 223 | ||
| 31 | 2230026 | 2231909 | 1884 | A | WP_053413546, ALA70779 | L-lactate permease | 182 | ||
| 32 | 2313797 | 2315690 | 1894 | B | WP_053413546, ALA70861 | Fur transcriptional repressor | 36 | ||
| 33 | 2375555 | 2377438 | 1884 | A | WP_053413546, ALA70914 | HlyC/CorC family transporter | 56 | ||
| 34 | 2532418 | 2530525 | 1894 | B | WP_053413768, ALA71042 | 49,105,66 | Metal-sulfur cluster assembly factor PaaD | 60 | |
| 35 | 2702663 | 2700780 | 1884 | A | WP_053413546, ALA71201 | RNA polymerase subunit sigma peudogene | 24 | ||
| 36 | 2735871 | 2737764 | 1894 | B | WP_013522881, ALA71232 | 49,105 | Phosphate propanoyltransferase | 60 | |
| 37 | 2752726 | 2754609 | 1884 | A | WP_053413546, ALA71246 | Hypothetical protein | 33 | ||
| 38 | 2789544 | 2791427 | 1884 | A | WP_013522881, ALA71278 | 49,105 | Hypothetical protein | 24 | |
| 39 | 2848575 | 2850468 | 1894 | B | WP_053413546, ALA71335 | Two-component sensor histidine kinase | Inside* | ||
| 40 | 2989610 | 2991503 | 1894 | B | WP_053413546, ALA71452 | HAMP domain-containing protein | 45 | ||
| 41 | 3399882 | 3404880 | 4999 | A | WP_053414828, WP_053414829 | Hypothetical protein | 20 | ||
| 42 | 3458333 | 3456444 | 1890 | A | +6 nt after 552 | WP_053413768, ALA71876 | 49,105,66 | Nicotinate phosphoribosyltransferase | 145 |
| 43 | 3492554 | 3490671 | 1884 | A | WP_013522881, ALA71896 | 49,105 | Nitrate reductase subunit beta | In-side** | |
| 44 | 3553833 | 3551940 | 1894 | B | WP_053413546, ALA71946 | Methylmalonate-semialdehyde dehydrogen-ase (CoA acylating) | 49 | ||
| 45 | 3600422 | 3598529 | 1894 | B | WP_053413546, ALA71984 | Alanyl-tRNA editing protein | In-side** | ||