Methanogens transcription

The sequences immediately upstream from the open reading frames of both the sulfo-thermophiles and the thermophilic methanogens are presented in Table 7. Stretches of purines located 3-9 nucleotides upstream from the start codon which could interact with the polypyrimidine sequence present at the 3 terminus of each archaeal 16S rRNA (Shine Dalgamo interaction) are underlined. For the thermophilic methanogen transcripts, as for those of the methanogen and extreme halophiles [1], a purine-rich sequence, of varying length, is present at the appropriate position. However, for the sulfothermophiles... 

It is also unclear whether archaeal mRNAs can be cotranscriptionally or post-transcriptionally modified. Polyadenylated RNAs have been identified in several archaea [21-23], the poIy(A) tails being quite short in methanogens [22] and rather long in the halophiles and the crenarchaeota [21-23]. However, evidence that they are indeed mRNAs is lacking. In any event Poly(A)+ RNAs are not capped in Methanococcus vannielii [22]. 

Analysis of the sequences located upstream of archaeal rRNA genes has shown that archaeal rRNA promoters consist of the sequence TTTA(A/T)A located 20-30 nucleotides upstream of the transcription initiation site and a weakly conserved sequence, (A/T)TG(A/C) around the transcription initiation site [40]. Transcription of the rRNA genes terminates within pyrimidine-rich regions in the extreme thermophiles [30,41], in pyrimidine-rich regions followed by a short hairpin loop in the methanogens [27,34] and in AT-rich regions preceded by a GC-rich region in the extreme... 

Transcription usually ends within or after pyrimidine-rich regions [120,141,145,150]. Among the methanogens, inverted repeats that might form stem-loop structures, reminiscent of the rho-independent terminators of bacteria, have been identified close to the termination sites [100]. Usually, there are multiple transcription stops in the archaea. 

Transcripts of 5S rRNAs and tRNAs generally start just before and terminate immediately after single genes amongst sulfothermophiles, while these stable RNA genes are often clustered in transcriptional units in the thermophilic methanogens and other archaea. 

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