Prediction of transcription regulatory sites in Archaea by a comparative genomic approach

Abstract

Intragenomic and intergenomic comparisons of upstream nucleotide sequences of archaeal genes were performed with the goal of predicting transcription regulatory sites (operators) and identifying likely regulons. Learning sets for the detection of regulatory sites were constructed using the available experimental data on archaeal transcription regulation or by analogy with known bacterial regulons, and further analysis was performed using iterative profile searches. The information content of the candidate signals detected by this method is insufficient for reliable predictions to be made. Therefore, this approach has to be complemented by examination of evolutionary conservation in different archaeal genomes. This combined strategy resulted in the prediction of a conserved heat shock regulon in all euryarchaea, a nitrogen fixation regulon in the methanogens Methanococcus jannaschii and Methanobacterium thermoautotrophicum and an aromatic amino acid regulon in M.thermoautotrophicum. Unexpectedly, the heat shock regulatory site was detected not only for genes that encode known chaperone proteins but also for archaeal histone genes. This suggests a possible function for archaeal histones in stress-related changes in DNA condensation. In addition, comparative analysis of the genomes of three Pyrococcus species resulted in the prediction of their purine metabolism and transport regulon. The results demonstrate the feasibility of prediction of at least some transcription regulatory sites by comparing poorly characterized prokaryotic genomes, particularly when several closely related genome sequences are available.

Figure 1

Possible operon structure of some candidate members of the heat shock regulon in the archaea. Blue, helix–turn–helix DNA-binding protein; green, A1 family ATPase; red, chaperone hsp20; yellow, grpE–dnaK–dnaJ gene string; black, candidate heat shock regulatory site; grey, weak heat shock site; white circles, delimiters. If there are several paralogs, only one is shown (see Table 1 for details).

Figure 2

Organization of archaeal nitrogen fixation loci. Yellow, nif operon (nifH–glnBa–glnBb–nifK–nifE–nifN); red, glnA; green, glnB; blue, amtB (ammonium transporter); white, genes that are not members of the NIF regulon; black, NIF boxes. See Table 2 for details.

Figure 3

A phylogenetic tree of archaeal nitrogenases. Italic, regulated nifH genes from nif operons (as opposed to stand-alone, apparently unregulated genes); bold, nifH genes with upstream candidate signals. SwissProt or GenBank ‘gi’ identifiers are given. The numbers indicate the number of bootstrap replications, out of 1000, that support each node. MJ, Methanococcus jannaschii (complete genome); MCtl, Methanococcus thermolithotrophus; MCma, Methanococcus maripaludis; MCvo, Methanococcus voltae; MTH, Methanobacterium thermoautotrophicum strain delta (complete genome); MBth, M.thermoautotrophicum strain Marburg; MBiv, Methanobacterium ivanovii; MSba, Methanosarcina barkeri.

Figure 4

Candidate regulatory sites upstream of glnA genes. Red, HSP (heat shock promoter); blue, NIF (nitrogen fixation) box; numbers, distance to the start codon. Abbreviations are as in Figure 3.

Figure 5

TRP boxes upstream of archaeal aromatic amino acid operons. Blue, candidate TRP boxes; red, a position mutated in a deregulated strain of M.thermoautotrophicum Marburg (an upstream site with a mutation that has the same effect is not shown); bold, protein-coding regions; italic, transcribed regions (when known); underlined, TATA box; numbers, distance to start codon. MTH, M.thermoautotrophicum delta; MBth, M.thermoautotrophicum Marburg; Hvu, Haloferax volcanii.

Figure 6

The predicted purine regulons in Pyrococcus spp. Shades of red and yellow, purine metabolism genes; shades of blue, candidate members of the purine regulon; shades of green, genes that are apparently unrelated to purine biosynthesis; black, cooperative PUR signal (two boxes); grey, cooperative signal or strong non-cooperative signal; white circle, delimiter.

Figure 6

The predicted purine regulons in Pyrococcus spp. Shades of red and yellow, purine metabolism genes; shades of blue, candidate members of the purine regulon; shades of green, genes that are apparently unrelated to purine biosynthesis; black, cooperative PUR signal (two boxes); grey, cooperative signal or strong non-cooperative signal; white circle, delimiter.