Abstract:
RNA is necessary for protein synthesis and for
gene regulation in all living organisms. Most
RNA molecules are transcribed as precursors
which are then maturated by ribonucleases
(RNases) and RNA modification enzymes.
Often large multiprotein complexes are
responsible for the maturation and for the
degradation of various RNA molecules in the
cell. The general mechanisms of RNA
processing and degradation are highly
conserved and include endonucleolytic
cleavages, posttranscriptional modification at
the 3'-end (RNA tailing) and exoribonucleolytic
degradation or trimming in 3'-5' direction or in
5'-3' direction (for recent reviews see Refs (1-3).
Controlled RNA degradation as a part of the
posttranscriptional gene regulation is especially
important for u nic ellular, prokaryotic
microorganisms, which are exposed to changing
environmental conditions. Prokaryotes are a
highly heterogeneous group which include
b a c te ria and Archaea. Archaea show
morphological similarities to bacteria, but are
closely related phylogenetically to eukarya than
to bacteria (4). They also show a strong
similarity to eukarya at the molecular level, for
example in the mechanisms of replication,
transcription and translation. Archaeal mRNA,
however, is more similar to bacterial mRNA: it
is generally intron-less and lacks a long
stabilising poly (A)-tail at the 3'-end as well as a
methylguanosine cap at the 5'-end. In
accordance with this, the mechanisms of RNA
degradation in Archaea show strong similarities
to those operating in bacteria (2). For example,
the archaeal protein complex named exosome is
structurally and functionally similar to the
bacterial polynucleotide phosphorylase
(PNPase) (5-8). The bacterial PNPase and the
archaeal exosome show structural similarities to the eukaryotic nine-subunit exosome (9), but
there are important functional differences
between the eukaryotic and prokaryotic
exosome-like machineries. The activity of the
eukaryotic nine subunit exosome is due to a
tenth subunit with similarity to the bacterial
RNase R, while its PNPase-like, nine-subunit
core is catalytically inactive (10). The
eukaryotic ten-subunit exosome that functions
as a hydrolytic 3'-5' exoribonuclease and an
endoribonuclease (11,12) is essential and
participates in various RNA processing and
RNA degrading pathways both in the nucleus
and in the cytoplasm (13,14). Eukaryotic RNAs
are intended for exoribonucleolytic 3'-5'
degradation by the addition of short poly (A)
tails. This destabilizing polyadenylation is
performed by specialized protein complexes
that are different from the eukaryotic exosome
(15,16). In contrast, both the bacterial PNPase
and the archaeal nine subunit exosome are
phosphorolytic 3'-5' exoribonucleases, which
also can use NDPs to synthesize destabilizing,
heteropolymeric RNA tails, which are used
as loading platforms for exo-ribonucleases
(6,17,19). In Archaea lacking the exosome,
RNA is not post-transcriptionally modified at
the 3'-end (19). In these exosome-less Archaea,
RNA is either exoribonucleolytically degraded
in 3'-5' direction by a homologue of bacterial
RNase R (in halophiles) or seems to be
exclusively degraded in 5’-3’ direction by a
homologue of the bacterial RNase J (in some
methanogenic Archaea) (20,21). Like in
Bacteria, in Archaea degradation in 5’-3’
direction is inhibited by a 5 ’ - triphosphate and is
performed by RNase J homologues (22,23). The
endoribonucleolytic mechanisms, which are of
central importance for RNA degradation in
Bacteria (3,24) are still not explored in Archaea.
The recently described, endonucleolytically active RNase J homologues in methanogens
are good c a n d id a te s fo r p r in c ip le
endoribonucleases in the third domain of life
(21). The existence of the archaeal exosome was
proposed by bioinformatic analyses based on its
similarity to the eukaryotic exosome (25) and
was verified by co-immunoprecipitation from
the thermoacidophilic archaeon Sulfolobus
solfataricus (26). Later, its existence in vivo was
verified for two further archaeal species,
Methanotermobacter thermoautotrophicus and
Thermococcus kodakarensis (27,28). Major
components of the archaeal exosome are the
orthologs of the eukaryotic exosomal subunits
Rrp41, Rrp42, Rrp4 and Csl4 forming the ninesubunit
form of the archaeal complex, and the
archaeal DnaG protein, the function of which in
respect to RNA is still unknown. The structure
and the catalytic mechanism of the reconstituted
archaeal nine-subunit exosome are well
understood. It is built of a phosphorolytically
active hexametric ring containing the subunits
Rrp41 (harbouring the active centre) and Rrp42,
to which a trimeric cap of the RNA-binding
proteins Rrp4 and/or Csl4 is bound. It performs
metal-dependent phosphorolysis of RNA in the
presence of inorganic phosphate (Pi) and Mg2Cl,
and synthesizes RNA using NDPs without a
template (5-8,29-31).