Lineage-specific partitions in archaeal transcription

Abstract

The phylogenetic distribution of the components comprising the transcriptional machinery in the crenarchaeal and euryarchaeal lineages of the Archaea was analyzed in a systematic manner by genome-wide profiling of transcription complements in fifteen complete archaeal genome sequences. Initially, a reference set of transcription-associated proteins (TAPs) consisting of sequences functioning in all aspects of the transcriptional process, and originating from the three domains of life, was used to query the genomes. TAP-families were detected by sequence clustering of the TAPs and their archaeal homologues, and through extensive database searching, these families were assigned a function. The phylogenetic origins of archaeal genes matching hidden Markov model profiles of protein domains associated with transcription, and those encoding the TAP-homologues, showed there is extensive lineage-specificity of proteins that function as regulators of transcription: most of these sequences are present solely in the Euryarchaeota, with nearly all of them homologous to bacterial DNA-binding proteins. Strikingly, the hidden Markov model profile searches revealed that archaeal chromatin and histone-modifying enzymes also display extensive taxon-restrictedness, both across and within the two phyla.

Figure 1.

Transcription-associated protein abundance in archaeal lineages. The genome sizes of the Crenarchaeota (orange) and Euryarchaeota (green) species are displayed as bar graphs, with the percentage of TAPs present in each of the genomes superimposed as blue line plots.

Figure 2.

Phylogenetic distribution of genes matching protein domains associated with transcription. The Pfam accession numbers of the TA-HMMs that match archaeal sequences are shown on the left, with the next column indicating the total number of sequences matched in all the fifteen archaeal genomes. The matches in individual genomes are shown as bar graphs, and grouped into the two lineages (orange representing the Crenarchaeota, and green the Euryarchaeota), with the number of matching sequences normalised by genome size and expressed as number of sequences per 10,000 genes. Beneath each bar graph, in square brackets, is shown the actual number of matching genes. The two numbers above one another and immediately to the right of the two groupings of bar graphs show the maximum and minimum number of matches for the phylum, and the column next to these values shows the mean number of matches with the standard deviation. The letter in the circle indicates which transcriptional functional class the TA-HMM is a member of: basal, elongation and termination factors (B); nucleosomes and HDACs (N); transcriptional regulators (R); unclassified (u). The Pfam description of the TA-HMM is shown at the right. Species codes: P. aerophilum (P_a); A. pernix (A_p); S. tokodaii (S_t); S. solfataricus (S_s); T. acidophilum (T_a); T. volcanium (T_v); M. kandleri (M_k); P. abyssi (P_a); M. jannaschii (M_j); M. thermoautotrophicum (M_t); P. horikoshii (P_h); A. fulgidus (A_f); Halobacterium sp. (H_a); M. mazei (M_m); and M. acetivorans (M_a).