Transcription in archaea

Abstract

Using the sequences of all the known transcription-associated proteins from Bacteria and Eucarya (a total of 4,147), we have identified their homologous counterparts in the four complete archaeal genomes. Through extensive sequence comparisons, we establish the presence of 280 predicted transcription factors or transcription-associated proteins in the four archaeal genomes, of which 168 have homologs only in Bacteria, 51 have homologs only in Eucarya, and the remaining 61 have homologs in both phylogenetic domains. Although bacterial and eukaryotic transcription have very few factors in common, each exclusively shares a significantly greater number with the Archaea, especially the Bacteria. This last fact contrasts with the obvious close relationship between the archaeal and eukaryotic transcription mechanisms per se, and in particular, basic transcription initiation. We interpret these results to mean that the archaeal transcription system has retained more ancestral characteristics than have the transcription mechanisms in either of the other two domains.

Figure 1

Distribution of bacterial-, eukaryotic-, and universal transcription-associated homologs in the four complete archaeal genomes of M. jannaschii (blue), A. fulgidus (green), M. thermoautotrophicum (red), and P. horikoshii (yellow). A two-way ANOVA 3 (domain) × 4 (species) (df = 12–1 = 11) for normalized genome compositions (data not shown) of the transcription-associated homologs listed here, suggests that the variance arises mainly from the domain differences (F^d_2,11 = 7.76 > F_2,11 = 7.21) and not the species differences (F^s_3,11 = 0.73 < F_3,11 = 6.22) at 99% significance level. The inset represents the distribution of transcription-associated protein families. For ORF identifiers and species distribution of particular families, see Tables 1–3.

Figure 2

Distribution of universal (ABE), bacterial/eukaryotic (BE), archaeal/bacterial (AB), and archaeal/eukaryotic (AE) families of transcription-associated proteins.