Gene Structure, Organization, And Expression In Archaebacteria

Abstract

Major advances have recently been made in understanding the molecular biology of the archaebacteria. In this review, we compare the structure of protein and stable RNA-encoding genes cloned and sequenced from each of the major classes of archaebacteria: the methanogens, extreme halophiles, and acid thermophiles. Protein-encoding genes, including some encoding proteins directly involved in methanogenesis and photoautotrophy, are analyzed on the basis of gene organization and structure, transcriptional control signals, codon usage, and evolutionary conservation. Stable RNA-encoding genes are compared for gene organization and structure, transcriptional signals, and processing events involved in RNA maturation, including intron removal. Comparisons of archaebacterial structures and regulatory systems are made with their eubacterial and eukaryotic homologs.

Transcription in vitro and in vivo of the 7S RNA gene associated with the ribosomal RNA operon in the hyperthermophilic archaeon Methanothermus fervidus

“…2B and 2C). This is exactly the site predicted from the consensus to be the initiator sequence [10,12,15] and also the site calculated from the run-off transcription experiments using fragments fl and f2 (Fig. 1).…”

“…This sequence conforms well to the consensus for initiator sequences established for methanogen Promoters of tRNA and protein genes [10][11][12] and transcription initiates, as mandated by the consensus, at a pyrimidine/ purine dinucleotide. The consensus methanogen Promoter contains a TATA-box located 21-25 bp upstream of the site of transcription initiation [10][11][12]. The sequence 5'TTTAAATA, located 24 bp upstream of the site of 7S RNA initiation, conforms precisely to the consensus for methanogen TATA-boxes.…”

“…If so, this promoter with a G residue at position no. 4 of the TATA-box [10][11][12] would be very unusual and, as observed (Fig. 1B), would not be expected to function in vitro with the M. thermolithotrophicus derived System [10,11].…”

“…It appears therefore that the M. fervidus 7S RNA gene is transcribed from a 'typical' methanogen promoter. The sequences initially proposed as the consensus for promoter elements in methanogens on the basis of their conservation upstream of many genes [12,15,18], and subsequently shown to function in vitro as Promoters for tRNA and protein genes [10,11], have now therefore been extended to include a promoter for a 7S RNA gene.…”

Cloning of a potential cytochrome P450 from the Archaeon Sulfolobus solfataricus

“…The first of the two potential N-terminal methionines, Met I and Met s, was assigned as the initiator methionine based on two factors. First, the codon for Met 1 is located adjacent to a strong potential ribosome binding sequence, AAGGTAATTCC, as is typically the case for many archaeal genes [8]. Second, the sequence between Met 1 and Met s contains several amino acid residues conserved in other cytochrome P450s, most notably Phe 5, but also including Asp 3, Trp 4, and Glu 7 (Fig.…”