Table 1.
A-to-I editing in the transcriptome of S. pyogenes SF370
| Mean editing level in % | |||||||
|---|---|---|---|---|---|---|---|
| Genomic position | Locus tag | Gene | Function | Amino acid | EL | ML | ES |
| Synonymous editing | |||||||
| 12573 | SPy_0014 | hpt | hypoxanthine phosphoribosyltransferase | L111 | 7.3 | 3.4 | 6.1 |
| 87875 | SPy_0093 | adcC | ATP-binding protein (zinc transporter) | L72 | 15.0 | 19.1 | 20.9 |
| 450742 | SPy_0558 | hypothetical (Fic family member) | L35 | 1.4 | 1.8 | 0.0 | |
| 476075 | SPy_0591 | trhP1 | tRNA-U34 hydroxylase | L40 | 4.9 | 2.9 | 5.2 |
| 490385 | SPy_0608 | ppc | phosphoenolpyruvate carboxylase | L916 | 4.3 | 3.2 | 3.3 |
| 819206 | SPy_1007 | speI | streptococcal pyrogenic exotoxin I | L43 | 8.9 | 2.4 | 1.4 |
| 1004058 | SPy_1219 | putative NAD(P)H dehydrogenase | L296 | 16.7 | 19.8 | 18.2 | |
| 1022344 | SPy_1239 | pepN | aminopeptidase N | L179 | 21.3 | 19.9 | 27.8 |
| 1302726 | SPy_1584 | aroE | shikimate dehydrogenase | L165 | 22.9 | 14.0 | 29.9 |
| Recoding / non-synonymous editing | |||||||
| 365684 | SPy_0442 | glpT | glycerol-3-phosphate permease | T14A | 3.6 | 2.2 | 1.8 |
| 375257 | SPy_0458 | ftsK | DNA segregation ATPase | K13E | 30.4 | 25.8 | 27.0 |
| 390540 | SPy_0477 | putative Nudix hydrolase | Y103C | 3.4 | 3.1 | 2.6 | |
| 569196 | SPy_0711 | speC | streptococcal pyrogenic exotoxin C | K30E | 9.1 | 8.4 | 14.0 |
| 895755 | SPy_1094 | pplD | cell wall deacetylase | K208E | 0.0 | 2.1 | 3.1 |
| 928775 | SPy_1134 | egtUBC | ergothioneine permease/substrate-binding protein | K317E | 5.0 | (0.0) | 10.0 |
| 962967 | SPy_1173 | gid | tRNA-U54 methyltransferase | K6E | 6.1 | 4.3 | 4.5 |
| 1079794 | SPy_1302 | amyA | cyclodextrin glycosyltransferase | K644E | 13.6 | 7.5 | 10.2 |
| 1117210 | SPy_1351 | aroK | shikimate kinase | K124E | 14.9 | 13.6 | 19.4 |
| 1224618 | SPy_1493 | fakB2 | fatty acid kinase binding protein | T210A | 31.5 | 40.6 | 33.5 |
| 1271565 | SPy_1543 | arcD | putative arginine/ornithine antiporter | K41E | 1.8 | — | 7.7 |
| 1416155 | SPy_1708 | lacA.1 | galactose-6-phosphate isomerase | Y64C | 14.1 | — | (16.7) |
| 1532359 | SPy_1846 | dinP | DNA polymerase IV | K73E | (38.5) | (30.7) | (34.7) |
| 1576103 | SPy_1900 | thiD | hydroxy-/phosphomethylpyrimidine kinase | T67A | 0.0 | 0.8 | 2.2 |
| 1615713 | SPy_1941 | cysS | cysteinyl-tRNA synthetase | Y135C | 4.9 | 0.8 | 9.0 |
| 1634340 | SPy_1962 | proS | prolyl-tRNA synthetase | Y181C | 7.4 | 5.0 | 8.8 |
| 1712462 | SPy_2055 | pflA | putative pyruvate formate-lyase activating enzyme | Y81C | 4.8 | (5.6) | — |
| 1769509 | SPy_2118 | tag | DNA-3-methyladenine glycosylase I | K9E | (4.4) | (0.0) | 3.0 |
Identified A-to-I editing sites were grouped according to their potential effect on the coding sequence (synonymous versus non-synonymous). For each genomic position, locus tag, name (if available) and function of the affected gene and the encoded amino acid are indicated along with the mean editing level (in %) for each growth phase (EL: early logarithmic, ML: mid-logarithmic, ES: early stationary). If the editing levels could not be determined in all three replicates, the values are shown in brackets. The ‘—’ sign indicates that editing levels could not be determined in any of the replicates.