TABLE 1.
List of archaeal genomes analyzed
| tDNAs | tRNAs | Introns located at 37/38 | Introns located at other positions | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BHB type | BHB type | ||||||||||||
| tDNAs | tRNAs | Nr | Min size | hBHBh′ | hBH | Nr | Min size | hBHBh′ | HBh′ | Double introns | Endo type | References | |
| The first column lists the archaeon names and strains for which the genomes have been fully sequenced (the corresponding references are listed in the last column). For each of these genomes, under headings “tDNAs” and “tRNAs” are listed the total number of tRNA genes (tDNA redundancy) and the corresponding number of isoacceptor tRNAs with different anticodons able to read the 61 sense codons (anticodon choice pattern; Marck and Grosjean 2002). The total number of introns located at position 37/38 or at other positions of the tRNA molecules, the size (in nucleotides) of the shortest intron identified in each family of intron-containing pre-tRNAs, and the number of splicing motifs harboring either the canonical or relaxed splicing motif as defined in the text are listed under the headings “Nr” and “Min size” and splicing motif (“BHB type”), respectively. Few archaeons contain tDNAs with two introns within the same pre-tRNA molecule; their numbers are listed under “Double introns.” Under the heading “Endo type”, “4×” means that the endonuclease is a homotetramer (α4), and “2×” means it is a homodimer (β2; see Materials and Methods). | |||||||||||||
| atDNA-Glu (TTC) of M. kandleri (two introns located at positions 37/38 and 21/22) is present in two nearly identical copies in the genome (C or T at position 17). | |||||||||||||
| bThe sequence data for P. abyssi were obtained from Genoscope at http://www.genoscope.cns.fr/Pab/Pabyssi_complete_genome.fasta. | |||||||||||||
| cThe missing tDNA-Cys of F. acidarmanus (Marck and Grosjean 2002) was identified using tRNAScan-SE (Lowe and Eddy 1997) with lowest constraints (it contains an unusual A18-C55 base pair). | |||||||||||||
| dPreliminary sequence data for F. acidarmanus and M. barkeri were obtained from The DOE Joint Genome Institute (JGI) at http://genome.ornl.gov/microbial/faci/ and http://genome.ornl.gov/microbial/mbar/. Large and small contigs files were concatenated (1,932,066 bp and 5,133,054 bp, respectively). | |||||||||||||
| Crenarchaeota | |||||||||||||
| Pyrobaculum aerophilum IM2 | 46 | 46 | 7 | 13 | 2 | 5 | 19 | 13 | 8 | 11 | 3 | 4× | Fitz-Gibbon et al. 2002 |
| Aeropyrum pernix K1 | 46 | 46 | 9 | 18 | 8 | 1 | 5 | 19 | 3 | 2 | 0 | 4× | Kawarabayasi et al. 1999 |
| Sulfolobus solfataricus P2 | 46 | 46 | 17 | 12 | 4 | 13 | 3 | 15 | 0 | 3 | 1 | 4× | She et al. 2001 |
| Sulfolobus tokodaii 7 | 46 | 46 | 20 | 11 | 8 | 12 | 4 | 16 | 1 | 3 | 0 | 4× | Kawarabayasi et al. 2001 |
| Euryarchaeota | |||||||||||||
| Methanopyrus kandleri AV19 | 34 | 33 | 8 | 15 | 8 | 0 | 1a | 33 | 0 | 1 | 1 | 4× | Slesarev et al. 2002 |
| Methanobacterium thermoautotrophicum delta H | 39 | 37 | 3 | 16 | 3 | 0 | 1 | 32 | 1 | 0 | 1 | 4× | Smith et al. 1997 |
| Methanococcus jannaschii DSM2661 | 36 | 34 | 2 | 33 | 2 | 0 | – | – | – | – | – | 4× | Bult et al. 1996 |
| Pyrococcus abyssi GE5 | 46 | 46 | 2 | 31 | 2 | 0 | – | – | – | – | – | 4× | Cohen et al. 2003b |
| Pyrococcus horikoshii (shinkai) OT3 | 46 | 46 | 2 | 31 | 2 | 0 | – | – | – | – | – | 4× | Kawarabayasi et al. 1998 |
| Pyrococcus furiosus | 46 | 46 | 2 | 32 | 2 | 0 | – | – | – | – | – | 4× | Robb et al. 2001 |
| Archaeoglobus fulgidus DSM4304 | 46 | 46 | 5 | 15 | 4 | 1 | – | – | – | – | – | 2× | Klenk et al. 1997 |
| Halobacterium sp. NRC-1 | 47 | 46 | 3 | 33 | 3 | 0 | – | – | – | – | – | 2× | Ng et al. 2000 |
| Thermoplasma acidophilum DSM1728 | 46 | 46 | 4 | 12 | 2 | 2 | – | – | – | – | – | 2× | Ruepp et al. 2000 |
| Thermoplasma volcanium GSS1 | 46 | 46 | 4 | 14 | 3 | 1 | – | – | – | – | – | 2× | Kawashima et al. 2000 |
| Ferroplasma acidarmanus | 46 | 46c | 3 | 16 | 3 | 0 | – | – | – | – | – | 2× | d |
| Methanosarcina barkeri | 46 | 46 | 4 | 20 | 3 | 1 | – | – | – | – | – | 2× | d |
| Methanosarcina mazei Go1 (DSMW 3647) | 46 | 46 | 4 | 20 | 4 | 0 | – | – | – | – | – | 2× | Deppenmeier et al. 2002 |
| Methanosarcina acetivorans C2A | 46 | 46 | 4 | 20 | 4 | 0 | – | – | – | – | – | 2× | Galagan et al. 2002 |
| Total:18 genomes | 800 | 794 | 103 | 67 | 36 | 33 | 13 | 20 | 6 | ||||
