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.

Comparative Genomics of the Vitamin B12 Metabolism and Regulation in Prokaryotes

“…Then we scanned nearly 100 genomic sequences using the RNA-PATTERN program and the pattern of a novel, B 12 -specific RNA element (30) and found approximately 200 B12 elements unevenly distributed in 66 eubacterial genomes ( In attempt to analyze potential cobalamin regulons in archaea, a large phylogenetic group without B12 elements, we collected upstream regions of all CBL genes and applied the signal detection procedure to each archaeal genome (31). The same strongest signal, a 15-bp palindrome with consensus 5Ј-TGGATAantTATCCA-3Ј, was observed in candidate cobalamin regulons in three Pyrococcus genomes (Table I).…”

Comparative Genomics and Experimental Characterization of N-Acetylglucosamine Utilization Pathway of Shewanella oneidensis

“…Regulatory Signals and Regulons-An iterative motif detection procedure implemented in the program SignalX was used to identify common regulatory DNA motifs in a set of upstream gene fragments and to construct the motif recognition profiles as described previously (28). For the NagC regulon, we started from a training set of the upstream regions of known NagC targets in E. coli and their orthologs in other NagC-encoding genomes (15,29,30).…”

Regulation of the aerobic respiratory chain in the facultatively aerobic and hyperthermophilic archaeon Pyrobaculum oguniense

“…5(a) shows the gene structure of the cloned genomic region with poxC and surrounding oxidase genes. The genes of the oxidase complex, poxA, poxB, poxC, poxK and poxL, are present in an operon-like arrangement and each gene is preceded by putative TATA box elements (Bell et al, 1999;Gelfand et al, 2000;Soppa, 1999a, b). PoxA, containing 79 amino acid residues, is a hypothetical membrane-binding protein which is a homologue of SoxI of Sulfolobus acidocaldarius, whose function is unknown (Castresana et al, 1995).…”