Prediction of the archaeal exosome and its connections with the proteasomeand the translation and transcription machineries by a comparative-genomicapproach
Ev. Koonin et al., Prediction of the archaeal exosome and its connections with the proteasomeand the translation and transcription machineries by a comparative-genomicapproach, GENOME RES, 11(2), 2001, pp. 240-252
By comparing the gene order in the completely sequenced archaeal genomes co
mplemented by sequence profile analysis, we predict the existence and prote
in composition of the archaeal counterpart of the eukaryotic exosome, a com
plex of RNAses, RNA-binding proteins, and helicases that mediates processin
g and 3'->5' degradation of a variety of RNA species. The majority of the p
redicted archaeal exosome subunits are encoded in what appears to be a prev
iously undetected superoperon. In Methanobacterium thermoautotrophicum, thi
s predicted superoperon consists of 15 genes; in the Crenarchaea, Sulfolobu
s solfataricus and Aeropyrum pernix, one and two of the genes From the supe
roperon, respectively, are relocated ill the genome, whereas in other Eurya
rchaeota, the superoperon is split into a variable number of predicted oper
ons and solitary genes. Methanococcus jannaschii partially retains the supe
roperon, but lacks the three core exosome subunits, and in Halobacterium sp
., the superoperon is divided into two predicted operons, with the same thr
ee exosome subunits missing. This suggests concerted gene loss and an alter
ation of the structure and function of the predicted exosome in the Methano
coccus and Halobacterium lineages. Additional potential components of the e
xosome are encoded by partially conserved predicted small operons. Along wi
th the orthologs of eukaryotic exosome subunits, namely an RNase PH and two
RNA-binding proteins, the predicted archaeal exosomal superoperon also enc
odes orthologs of two protein subunits of RNase P. This suggests a function
al and possibly a physical interaction between RNase P and the postulated a
rchaeal exosome, a connection that has not been reported in eukaryotes. In
a pattern of apparent gene loss complementary to that seen in Methanococcus
and Halobacterium, Thermoplasma acidophilum lacks the RNase P subunits. Un
expectedly, the identified exosomal superoperon, in addition to the predict
ed exosome components, encodes the catalytic subunits of the archaeal prote
asome, two ribosomal proteins and a DNA-directed RNA polymerase subunit. Th
ese observations suggest that in archaea, a tight Functional coupling exist
s between translation, RNA processing and degradation, (apparently mediated
by the predicted exosome) and protein degradation (mediated by the proteas
ome], and may have implications for cross-talk between these processes in e
ukaryotes.