Archaebacterial genomics: The complete genome sequence of Methanococcus jannaschii

Abstract

SummaryThe first complete sequence of an archaebacterial genome, that of Methanococcus jannaschii, has recently been published('). Less than half of the open reading frames (ORFs) can be assigned a function based on similarity to known sequences in databases. These assignable ORFs fall into two general classes; those involved in transcription, translation and replication are more similar to eukaryotic homologs, while those determining metabolic processes are more similar to eubacterial versions. The immense but very rewarding task of making biological and evolutionary sense of all this information has only just begun. What are the archaebacteria and why is it important to sequence an archaebacterial genome?The archaebacteria (Archaea) are a diverse collection of organisms first 'discovered' by Carl Woese and colleagues on the basis of comparisons of 16s ribosomal RNA (rRNA) in the late 1 97Os(*a3). Although prokaryote-like in cellular structure and appearance, 16s rRNA showed that they were as distinct from eubacteria (then, the only known prokaryotic group) as these were from eukaryotes. Since their discovery, much effort has been directed towards understanding the molecular biology and biochemistry of archaebacteria, and to determining the deep structure of the tree of life (that is, the order of the earliest branchings). The current consensus, based on universal trees for gene families that derive from duplications occurring before any branchings (translation elongation factors, aminoacyl-tRNA synthetases), is that archaebacteria and eukaryotes are 'sister groups', sharing a more recent common ancestor with each other than either did with e~b a c t e r i a (~-~) .This consensus has been challenged. Foremost are arguments which claim that the rooting is based on a limited number of protein coding genes involved in translation and transcription, 'core' cellular functions -and that these do not tell the whole I ) . Phylogenies of protein-coding genes not involved in transcription or translation often do not support the sisterhood of eukaryotes and archaebacteria. Depending on which protein dataset is used, molecular phylogenies show various relationships between archaebacteria, eubacteria and eukaryotes, in some cases disrupting the monophyly (phylogenetic integrity) of the three domains (see for example refs 9 and 12-14). A number of fusion hypotheses, different from each other and each dependent on a particular molecular phylogeny, have been proposed in an attempt to reconcile these phylogenies with those based on transcription/translation prot e i n~(~~~~~~~~~~) .Several authors have argued that the best way to sort this out will be the comparison of complete genomic sequences from representatives of the eubacteria, archaebacteria and e~karyotes('~). Instead of one or two protein phylogenies, there would be hundreds of phylogenies on which to base the rooting of the universal tree of life.Of course, there are other reasons to sequence the genome of an archaebacterium, especially a thermophilic, autotrophic one...

Two Family B DNA Polymerases from Aeropyrum pernix , an Aerobic Hyperthermophilic Crenarchaeote

“…In the complete genome sequences of Methanococcus jannaschii and Pyrococcus horikoshii in Euryarchaeota, one DNA polymerase gene each was predicted from the similarity of the deduced amino acid sequences to family B DNA polymerases, and no more pol-like genes were found (4,16). The fact that these euryarchaeotes may survive with just a single DNA polymerase was very perplexing (8,11,19). Recently, however, a novel two-subunit DNA polymerase whose sequence has no similarity to that of any DNA polymerase family was identified in Pyrococcus furiosus (28), in addition to a family B DNA polymerase isolated earlier from this organism (30).…”

A Novel DNA Polymerase Family Found inArchaea

“…Surprisingly, it was found that this genome includes only one open reading frame with a sequence homologous to ␣-like DNA polymerases and lacks other DNA polymerase sequences. One of the most controversial issues from the first complete genome sequence from Archaea is whether this organism indeed possesses only one DNA polymerase (3,4,6,11). More definitely, it would be very surprising if the life of this archaeon were dominated by only a single DNA polymerase with a unique mechanism, since it is well established that both eucaryotic and eubacterial cells contain several DNA polymerases involved in replication and repair.…”

The euryarchaeotes, a subdomain of Archaea, survive on a single DNA polymerase: Fact or farce?

“…However, our knowledge on the DNA polymerases and DNA replication in Archaea at that time was so fragmentary. The complete genome sequence of the hyperthermophilic euryarchaeote, Methanococcus jannaschii (Bult et al, 1996), complicated the issue by suggesting that this organism depends on a single DNA polymerase for its DNA metabolic functions (Edgell and Doolittle, 1996;Gray, 1996;Morell, 1996). Three complete genome reports of other members of this subdomain (Kawarabayasi et al, 1998;Klenk et al, 1997;Smith et al, 1997) seem to substantiate this puzzling observation.…”