Comparison of Chargaff Differences of Thermophilic and Nonthermophilic Bacteria
| Bacterium | Chargaff difference (%) | Base composition of average 1-kb window | Purine-loading index | |||||||||||
| Genome segment | transcriptional orientation | leftward-transcribed | rightward-transcribed | |||||||||||
| (C + G)% | length(kb) | leftward | rightward | A | C | G | T | A | C | G | T | |||
| Thermophilic | ||||||||||||||
| M. thermoauto | 49.5 | 245 | (A − T)/W | T > A −9.44 ± 0.25 | A > T 7.96 ± 0.27 | 229 | 268 | 227 | 276 | 273 | 235 | 260 | 232 | 153 |
| trophicum | (C − G)/S | C > G 8.16 ± 0.21 | G > C −4.91 ± 0.21 | A − T = −47 | C − G = 41 | A − T = 40 | C − G = −25 | |||||||
| A. aeolicus | 43.4 | 248 | (A − T)/W | T > A −12.75 ± 0.36 | A > T 9.86 ± 0.36 | 247 | 239 | 195 | 319 | 311 | 199 | 235 | 255 | 208 |
| (C − G)/S | C > G 10.21 ± 0.29 | G > C −8.30 ± 0.24 | A − T = −72 | C − G = 44 | A − T = 56 | C − G = −36 | ||||||||
| M. jannaschii | 31.4 | genome | (A − T)/W | T > A −9.78 ± 0.09 | A > T 9.92 ± 0.09 | 309 | 195 | 119 | 377 | 377 | 119 | 195 | 309 | 288 |
| (C − G)/S | C > G 24.06 ± 0.15 | G > C −24.16 ± 0.14 | A − T = −68 | C − G = 76 | A − T = 68 | C − G = −76 | ||||||||
| Nonthermophilic | ||||||||||||||
| E. coli | 50.7 | 200 | (A − T)/W | T > A −1.5 ± 0.3 | T > A −1.3 ± 0.3 | 243 | 255 | 252 | 250 | 243 | 234 | 273 | 250 | 42 |
| (C − G)/S | C > G 0.5 ± 0.2 | G > C −7.6 ± 0.1 | A − T = −7 | C − G = 3 | A − T = −7 | C − G = −39 | ||||||||
| M. pneumoniae | 40 | genome | (A − T)/W | T > A −5.49 ± 0.20 | A > T 3.08 ± 0.28 | 284 | 204 | 196 | 316 | 309 | 197 | 203 | 291 | 64 |
| (C − G)/S | C > G 1.87 ± 0.16 | G > C −1.52 ± 0.21 | A − T = −32 | C − G = 8 | A − T = 18 | C − G = −6 | ||||||||
| H. influenzae | 38.1 | 350 | (A − T)/W | A > T 0.3 ± 0.2 | A > T 2.1 ± 0.2 | 310 | 210 | 171 | 309 | 316 | 184 | 197 | 303 | 64 |
| (C − G)/S | C > G 10.2 ± 0.2 | G > C −3.6 ± 0.2 | A − T = 1 | C − G = 39 | A − T = 13 | C − G = −13 | ||||||||
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↵Analysis involved either entire genomes (Methanococcus jannaschii, 1665 kb; Mycoplasma pneumoniae, 816 kb) or large segments (Methanobacterium thermoautotrophicum, 374431–619430; Aquifex aeolicus,871431–1119930; Escherichia coli, 1–200000; Haemophilus influenzae, 1–350000).
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↵Base composition for an average window in each category (leftward-transcribed or rightward transcribed), with Chargaff differences (A − T and C − G) expressed as base excesses. The mean pyrimidine excess in leftward-transcribed ORFs of the three thermophiles [(88 + 116 + 144)/(3)], is greater (P= 0.012; paired t-test with 2 df) than that of the three nonthermophiles [(10 + 40 + 38)/(3)]. The mean purine excess in rightward-transcribed ORFs of the three thermophiles [(65 + 92 + 144)/(3)] is greater (P = 0.10) than that of the three non-thermophiles [(32 + 24 + 26)/(3)].
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↵The purine-loading index is the sum of the four absolute Chargaff difference values (base excesses) when they relate positively to purine-loading (i.e., excess pyrimidines when transcription to the left; excess purines when transcription is to the right). All three thermophilic bacteria fulfill this criterion (mean value 216.3 ± 39.2 bases/kb). The absolute values are subtracted from the sum when Chargaff differences relate negatively to purine-loading (e.g., T > A for rightward-transcribed ORFs inE. coli). Thus, for the three nonthermophilic bacteria the mean value is 56.7 ± 7.7 bases/kb.
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↵Each Chargaff difference value (%) is presented ± the s.e. of the mean.
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↵These data are from Bell et al. (1998).
