RNase P


RNase P

Ribonuclease P (RNase P) is a type of Ribonuclease that is currently under heavy research. 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 on tRNA molecules cite journal |author=Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S |title=The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme |journal=Cell |volume=35 |issue=3 Pt 2 |pages=849–57 |year=1983 |pmid=6197186 |doi=] . Further RNase P is one of two known multiple turnover ribozymes in nature (the other being the ribosome), the discovery of which earned Professor Sidney Altman the Nobel Prize in Chemistry in 1989. In fact, Sidney 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 back in the 70's. Recent findings also reveal that RNase P has a new function cite journal |author=Jarrous N, Reiner R |title=Human RNase P: a tRNA-processing enzyme and transcription factor |journal=Nucleic Acids Res. |volume=35 |issue=11 |pages=3519–24 |year=2007 |pmid=17483522 |doi=10.1093/nar/gkm071] . 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 cite journal |author=Reiner R, Ben-Asouli Y, Krilovetzky I, Jarrous N |title=A role for the catalytic ribonucleoprotein RNase P in RNA polymerase III transcription |journal=Genes Dev. |volume=20 |issue=12 |pages=1621–35 |year=2006 |pmid=16778078 |doi=10.1101/gad.386706] , which are transcribed by RNA polymerase III, one of three major nuclear RNA polymerases in human cells.

In bacteria

In bacteria, such as "E. coli", RNase P has two components: an RNA chain, called M1 RNA, and a polypeptide chain, or protein, called C5 protein cite journal |author=Evans D, Marquez SM, Pace NR |title=RNase P: interface of the RNA and protein worlds |journal=Trends Biochem. Sci. |volume=31 |issue=6 |pages=333–41 |year=2006 |pmid=16679018 |doi=10.1016/j.tibs.2006.04.007] , cite journal |author=Tsai HY, Masquida B, Biswas R, Westhof E, Gopalan V |title=Molecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme |journal=J. Mol. Biol. |volume=325 |issue=4 |pages=661–75 |year=2003 |pmid=12507471 |doi=] . In vivo, both components are necessary for the ribozyme to function properly, but in vitro, the M1 RNA can act alone as a catalyst cite journal |author=Guerrier-Takada C, Gardiner K, Marsh T, Pace N, Altman S |title=The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme |journal=Cell |volume=35 |issue=3 Pt 2 |pages=849–57 |year=1983 |pmid=6197186 |doi=] . 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 bacterial RNase P RNA has been recently resolved, revealing its flat surface that is generated by a number of coaxially stacked helical domains connected by local and long-range contacts. This flat surface facilitates binding and cleavage of precursor tRNA substrates. For review see cite journal |author=Evans D, Marquez SM, Pace NR |title=RNase P: interface of the RNA and protein worlds |journal=Trends Biochem. Sci. |volume=31 |issue=6 |pages=333–41 |year=2006 |pmid=16679018 |doi=10.1016/j.tibs.2006.04.007] .

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 are ribonucleoproteins. 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 holoenzyme s have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous -- helices 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.

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 cite journal |author=Hall TA, Brown JW |title=Archaeal RNase P has multiple protein subunits homologous to eukaryotic nuclear RNase P proteins |journal=RNA |volume=8 |issue=3 |pages=296–306 |year=2002 |pmid=12003490 |doi=] , cite journal |author=Fukuhara H, Kifusa M, Watanabe M, Terada A, Honda T, Numata T, Kakuta Y, Kimura M |title=A fifth protein subunit Ph1496p elevates the optimum temperature for the ribonuclease P activity from Pyrococcus horikoshii OT3 |journal=Biochem. Biophys. Res. Commun. |volume=343 |issue=3 |pages=956–64 |year=2006 |pmid=16574071 |doi=10.1016/j.bbrc.2006.02.192] , cite journal |author=Tsai HY, Pulukkunat DK, Woznick WK, Gopalan V |title=Functional reconstitution and characterization of Pyrococcus furiosus RNase P |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=103 |issue=44 |pages=16147–52 |year=2006 |pmid=17053064 |doi=10.1073/pnas.0608000103] . 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 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 homologous -- helices 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.

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.cite journal |author=Randau L, Schröder I, Söll D |title=Life without RNase P |journal=Nature |volume=453 |issue=7191 |pages=120–3 |year=2008 |month=May |pmid=18451863 |doi=10.1038/nature06833 |url=]

In eukaryotes

In eukaryotes, such as humans and yeast, RNase P consists of an RNA chain that is structurally similar to that found in bacteria cite journal |author=Marquez SM, Chen JL, Evans D, Pace NR |title=Structure and function of eukaryotic Ribonuclease P RNA |journal=Mol. Cell |volume=24 |issue=3 |pages=445–56 |year=2006 |pmid=17081993 |doi=10.1016/j.molcel.2006.09.011] as well as nine to ten associated proteins (as opposed to the single bacterial RNase P protein, C5) cite journal |author=Jarrous N, Reiner R |title=Human RNase P: a tRNA-processing enzyme and transcription factor |journal=Nucleic Acids Res. |volume=35 |issue=11 |pages=3519–24 |year=2007 |pmid=17483522 |doi=10.1093/nar/gkm071] , cite journal |author=Chamberlain JR, Lee Y, Lane WS, Engelke DR |title=Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP |journal=Genes Dev. |volume=12 |issue=11 |pages=1678–90 |year=1998 |pmid=9620854 |doi=] . Five of these protein subunits exhibit homology to archaeal counterparts. These protein subunits of RNase P are shared with RNase MRP cite journal |author=Chamberlain JR, Lee Y, Lane WS, Engelke DR |title=Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP |journal=Genes Dev. |volume=12 |issue=11 |pages=1678–90 |year=1998 |pmid=9620854 |doi=] , cite journal |author=Salinas K, Wierzbicki S, Zhou L, Schmitt ME |title=Characterization and purification of Saccharomyces cerevisiae RNase MRP reveals a new unique protein component |journal=J. Biol. Chem. |volume=280 |issue=12 |pages=11352–60 |year=2005 |pmid=15637077 |doi=10.1074/jbc.M409568200] , cite journal |author=Welting TJ, Kikkert BJ, van Venrooij WJ, Pruijn GJ |title=Differential association of protein subunits with the human RNase MRP and RNase P complexes |journal=RNA |volume=12 |issue=7 |pages=1373–82 |year=2006 |pmid=16723659 |doi=10.1261/rna.2293906] , a catalytic ribonucleoprotein involved in processing of ribosomal RNA in the nucleolus cite journal |author=Clayton DA |title=A big development for a small RNA |journal=Nature |volume=410 |issue=6824 |pages=29, 31 |year=2001 |pmid=11242026 |doi=10.1038/35065191] . RNase P RNA from eukaryotes was only recently demonstrated to be a ribozyme cite journal |author=Kikovska E, Svärd SG, Kirsebom LA |title=Eukaryotic RNase P RNA mediates cleavage in the absence of protein |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=104 |issue=7 |pages=2062–7 |year=2007 |pmid=17284611 |doi=10.1073/pnas.0607326104] . Accordingly, the numerous protein subunits of eucaryal RNase P have a minor contribution to tRNA processing per se cite journal |author=Willkomm DK, Hartmann RK |title=An important piece of the RNase P jigsaw solved |journal=Trends Biochem. Sci. |volume=32 |issue=6 |pages=247–50 |year=2007 |pmid=17485211 |doi=10.1016/j.tibs.2007.04.005] , 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 cite journal |author=Reiner R, Ben-Asouli Y, Krilovetzky I, Jarrous N |title=A role for the catalytic ribonucleoprotein RNase P in RNA polymerase III transcription |journal=Genes Dev. |volume=20 |issue=12 |pages=1621–35 |year=2006 |pmid=16778078 |doi=10.1101/gad.386706] , cite journal |author=Gill T, Cai T, Aulds J, Wierzbicki S, Schmitt ME |title=RNase MRP cleaves the CLB2 mRNA to promote cell cycle progression: novel method of mRNA degradation |journal=Mol. Cell. Biol. |volume=24 |issue=3 |pages=945–53 |year=2004 |pmid=14729943 |doi=] .

References

*cite journal | last = Frank | first = DN | coauthors = Pace NR | year = 1998 | title = Ribonuclease P: unity and diversity in a tRNA processing ribozyme | journal = Annu Rev Biochem | volume = 67 | pages = 153–180 | pmid = 9759486 | doi = 10.1146/annurev.biochem.67.1.153
*cite journal | last = Brown | first = JW | year = 1999 | title = The Ribonuclease P Database | journal = Nucleic Acids Res | volume = 27 | pages = 314– | pmid = 9847214 | doi = 10.1093/nar/27.1.314

External links

* [http://www.mbio.ncsu.edu/RNaseP/threed.html RNase P Database] at ncsu.edu
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