RNase P

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Crystal structure of a bacterial ribonuclease P holoenzyme in complex with tRNA (yellow), showing metal ions involved in
catalysis (pink spheres), PDB 3Q1R
Bacterial RNase P class A

Predicted secondary structure and sequence conservation of
RNaseP_bact_a
Identifiers
Symbol RNaseP_bact_a
Rfam RF00010
Other data
RNA type Gene; ribozyme
Domain(s) Bacteria
GO 0008033 00045260030680
SO 0000386
Bacterial RNase P class B

Predicted secondary structure and sequence conservation of
RNaseP_bact_b
Identifiers
Symbol RNaseP_bact_b
Rfam RF00011
Other data
RNA type Gene; ribozyme
Domain(s) Bacteria
GO 0008033 00045260030680
SO 0000386
Archaeal RNase P

Predicted secondary structure and sequence conservation of Archaeal
RNase P
Identifiers
Symbol RNaseP_arch
Rfam RF00373
Other data
RNA type Gene; ribozyme
Domain(s) Archaea
GO 0008033 00045260030680
SO 0000386
Archaeal RNase P class T
220px
Predicted secondary structure and sequence conservation of the small form
of Archaeal RNase P found in the Thermoproteaceae
Identifiers
Symbol RNaseP_arch_t
Rfam TBD
Other data
RNA type Gene; ribozyme
Domain(s) Archaea
GO 0008033 00045260030680
SO 0000386
Ribonuclease P (RNase P) is a type of ribonuclease which cleaves RNA. RNase P is unique from other
RNases in that it is a ribozyme a ribonucleic acid that acts as a catalyst in the same way that a protein based
enzyme would. Its function is to cleave off an extra, or precursor, sequence of RNA
ontRNA molecules.
[1]
Further RNase P is one of two known multiple turnover ribozymes in nature (the other
being the ribosome), the discovery of which earned Sidney Altman and Thomas Cech the Nobel Prize in
Chemistry in 1989: in the 1970s, Altman discovered the existence of precursor tRNA with flanking sequences
and was the first to characterize RNase P and its activity in processing of the 5' leader sequence of precursor
tRNA. Recent findings also reveal that RNase P has a new function.
[2]
It has been shown that human nuclear
RNase P is required for the normal and efficient transcription of various small noncoding RNA genes, such as
tRNA, 5S rRNA, SRP RNA and U6 snRNA genes,
[3]
which are transcribed by RNA polymerase III, one of three
major nuclear RNA polymerases in human cells.
Contents
[hide]
1 In bacteria
o 1.1 Bacterial RNase P class A and B
2 In archaea
3 In eukaryotes
4 References
5 Further reading
6 External links
[edit]In bacteria
Bacterial RNase P has two components: an RNA chain, called M1 RNA, and a polypeptide chain, or protein,
called C5 protein.
[4][5]
In vivo, both components are necessary for the ribozyme to function properly, but in vitro,
the M1 RNA can act alone as a catalyst.
[1]
The primary role of the C5 protein is to enhance the substrate
binding affinity and the catalytic rate of the M1 RNA enzyme probably by increasing the metal ion affinity in the
active site. The crystal structure of a bacterial RNase P holoenzyme with tRNA has been recently resolved,
showing how the large, coaxially stacked helical domains of the RNase P RNA engage in shape selective
recognition of the pre-tRNA target. This crystal structure confirms earlier models of substrate recognition and
catalysis, identifies the location of the active site, and shows how the protein component increases RNase P
functionality.
[6][7]

[edit]Bacterial RNase P class A and B
Ribonuclease P (RNase P) is a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well
as chloroplasts and mitochondria. Its best characterised activity is the generation of mature 5'-ends of tRNAs
by cleaving the 5'-leader elements of precursor-tRNAs. Cellular RNase Ps areribonucleoproteins (RNP). RNA
from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme.
Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still
essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a
much greater protein content than the bacterial ones, the RNA cores from all the three lineages are
homologoushelices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs.
Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs.
[edit]In archaea
In archaea, RNase P ribonucleoproteins consist of 4-5 protein subunits that are associated with RNA. As
revealed by in vitro reconstitution experiments these protein subunits are individually dispensable for tRNA
processing that is essentially mediated by the RNA component.
[8][9][10]
The structures of protein subunits of
archaeal RNase P have been resolved by x-ray crystallography and NMR, thus revealing new protein domains
and folding fundamental for function.
Isolated eukaryotic RNase P RNA has not been shown to retain its catalytic function, but is still essential for the
catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater
protein content than the bacterial ones, the RNA cores from all the three lineages are homologoushelices
corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is
considerable sequence variation, particularly among the eukaryotic RNAs.
Using comparative genomics and improved computational methods, a radically minimized form of the RNase P
RNA, dubbed "Type T", has been found in all complete genomes in the crenarchaeal phylogenetic family
Thermoproteaceae, including species in the genera Pyrobaculum, Caldivirga and Vulcanisaeta
[11]
. All retain a
conventional catalytic domain, but lack a recognizable specificity domain. 5 tRNA processing activity of the
RNA alone was experimentally confirmed. The Pyrobaculum and Caldivirga RNase P RNAs are the smallest
naturally occurring form yet discovered to function as trans-acting ribozymes.
[11]
Loss of the specificity domain
in these RNAs suggests potential altered substrate specificity.
It has recently been argued that the archaebacteriium Nanoarchaeum equitans does not possess RNase P.
Computational and experimental studies failed to find evidence for its existence. In this organism the tRNA
promoter is close to the tRNA gene and it is thought that transcription starts at the first base of the tRNA thus
removing the requirement for RNase P.
[12]

[edit]In eukaryotes
Further information: Nuclear RNase P
In eukaryotes, such as humans and yeast, most RNase P consists of an RNA chain that is structurally similar to
that found in bacteria
[13]
as well as nine to ten associated proteins (as opposed to the single bacterial RNase P
protein, C5).
[2][14]
Five of these protein subunits exhibit homology to archaeal counterparts. These protein
subunits of RNase P are shared with RNase MRP,
[14][15][16]
a catalytic ribonucleoprotein involved in processing
of ribosomal RNA in the nucleolus.
[17]
RNase P from eukaryotes was only recently demonstrated to be a
ribozyme.
[18]
Accordingly, the numerous protein subunits of eucaryal RNase P have a minor contribution to
tRNA processing per se,
[19]
while they seem to be essential for the function of RNase P and RNase MRP in
other biological settings, such as gene transcription and the cell cycle.
[3][20]
It has recently been discovered that
human mitochondrial RNase P is a protein and does not contain RNA.
[21]