ribonuclease p ( rnase p ) was originally described as an endoribonuclease that processes the 5 leader sequence of precursor trna ( 1 ) . in bacteria , rnase p is a small ribonucleoprotein complex ( 2 ) , consisting of a catalytic rna and a protein cofactor ( 3,4 ) . the crystal structures of bacterial rnase p rnas have recently been resolved , revealing the locations of the substrate - binding domains and the active sites in these rna enzymes ( 57 ) . by contrast , when compared with their bacterial counterparts , nuclear forms of eukaryal rnase p are large ribonucleoprotein complexes ( 810 ) . biochemical purification analyses have shown that a highly purified nuclear rnase p from hela cells has at least 10 distinct protein subunits associated with a single rna species , h1 rna ( 8,10 ) . these protein subunits are termed rpp14 , rpp20 , rpp21 , rpp25 , rpp29 , rpp30 , rpp38 , rpp40 , hpop1 and hpop5 ( table 1 ) ( 8,1013 ) . since this purified hela rnase p has been enzymatically defined by virtue of its ability to cleave precursor trna in vitro ( 8,10 ) , the potential existence of other forms of rnase p complexes with different subunit compositions is not excluded . similarly , saccharomyces cerevisiae nuclear rnase p possesses nine protein subunits , designated pop1p , pop3p , pop4p , pop5p , pop6p , pop7p / rpp2p , pop8p , rpp1p and rpr2p ( 14 ) , most of which are homologous to protein subunits of human rnase p ( table 1 ) ( 14,15 ) . in addition , these protein subunits are shared with rnase mrp ( 1417 ) , a mitochondrial and ribosomal rna - processing ribonucleoprotein ( 18 ) . however , it is not known if these protein subunits are shared with the mitochondrial form of human rnase p , a ribonucleoprotein particle shown to have an rna moiety that is identical to h1 rna ( 19 ) . table 1.subunits of human rnase p , functions and evolutionary conservationsubunitfunction / interaction ( in trna processing)chromatin binding / pol iii transcriptionhomolog yeast / archaearpp14rna binding+/+pop8prpp20atpase , helicase / hsp27 , smn , rpp25+/+pop7p , rpp2prpp21rna binding , activity / rpp29+/+rpr2p / arpp21rpp25rna binding / rpp20+/ndpop6prpp29trna binding , activity / rpp21+/+pop4p / arpp29rpp30rna binding , activity / pop5+/+rpp1p / arpp30rpp38rna binding , activity+/+pop3p / arpp38rpp40+/+hpop1nd / ndpop1phpop5rna binding , activity / rpp30nd/+pop5p / apop5h1 rnaactivity / rpp21 , rpp29 , rpp30 , rpp38nd/+rpr1/rpr rnajarrous and altman ( 8).binding to chromatin of trna and 5s rrna genes ( 33).required for pol iii transcription in whole hela extracts and/or in cells ( 33).walker and engelke ( 14).hall and brown ( 20).rosenblad et al . subunits of human rnase p , functions and evolutionary conservation jarrous and altman ( 8) . binding to chromatin of trna and 5s rrna genes ( 33 ) . required for pol iii transcription in whole hela extracts and/or in cells ( 33 ) . rpp21 , rpp29 , rpp30 , rpp38 and hpop5 are highly conserved proteins that have homologs in archaea ( table 1 ) ( 2023 ) . rpp21 , rpp29 and h1 rna are sufficient for reconstitution of rnase p activity in trna processing in vitro ( 24 ) . the archaeal rpp21 , rpp29 , pop5 , rpp30 and rpp38 proteins are required for efficient reconstitution of thermostable rnase p ribonucleoprotein ( 23,2527 ) . nonetheless , recent findings reveal that protein subunits of pyrococcus horikoshii ot3 rnase p are individually dispensable for enzyme activity in vitro ( 26 ) . in the case of the p. furiosus rnase p , it has been shown that pairs of its protein subunits are sufficient for reconstitution of enzyme activity ( 27 ) . thus , archaeal rpp21 with rpp29 or pop5 with rpp30 are sufficient for rnase p rna - based catalysis ( 27 ) . these pairs of archaeal proteins interact with each other in two - hybrid system ( 28 ) . the reconstitution studies described above underline the conserved role of archaeal and eukaryal rnase p rnas in substrate recognition and cleavage . recent progress in modeling the tertiary folding of eukaryal rnase p rna uncovers that it has a conserved core structure similar to that of its bacterial counterpart ( 29 ) . mutations that disrupt the predicted tertiary folding of h1 rna abolish catalysis in vitro ( 24 ) . remarkably , kikovska et al . , has shown that h1 rna is active in trna processing in vitro in the absence of any protein ( 30 ) , a finding that is consistent with previous observation that h1 rna alone binds to precursor trnas in vitro and has a conserved catalytic core ( 24,29 ) . since most of the protein subunits of nuclear rnase p are shared with rnase mrp , including those responsible for reconstitution of rnase p activity in vitro , it seems that the rna subunits alone may be sufficient for diversification of function of these catalytic ribonucleoproteins as trna and rrna endoribonucleases ( 24,2931 ) . hence , the precise role of the protein subunits of rnase p and rnase mrp in hydrolyzing the phosphodiester bond in different rna substrates remains unknown . apparently , protein subunits may allow substrate recognition and catalysis by facilitating the proper folding of the rna subunits of rnase p and rnase mrp . for instance , rpp20 and rpp25 transiently associate with 12s monoparticles of rnase mrp , but these subunits dissociate from subsets of rnase mrp bound to 6080s pre - ribosomal complexes ( 32 ) . additionally , protein subunits may permit the recognition of yet unknown rna substrates for rnase p and rnase mrp or implicate these complexes in other biological settings , such as chromatin binding and transcription ( 33 ; see below ) , cell cycle progression ( 34 ) and rna metabolism ( 35 ) . accordingly , studying the protein subunits of rnase p and rnase mrp could be useful in elucidating the diversification of functions of these two evolution - related ribonucleoprotein complexes ( 36 ) . studies in cell biology reveal that h1 rna and protein subunits of human rnase p are differentially concentrated in distinct intracellular compartments , including the nucleoplasm , nucleolus , cajal bodies , perinucleolar compartment and cytoplasm ( 17,3742 ) . rpp21 and rpp29 , two protein subunits that are sufficient for reconstitution of rnase p activity ( 24 ) , localize mainly in the nucleoplasm and nucleolus , though the latter subunit rapidly shuttles between these compartments ( 43 ) . cajal bodies are sites of assembly of transcription and processing machines ( 44,45 ) , while the nucleolus specializes in transcription and processing of rrna and ribosome biogenesis ( 46 ) . the nucleoplasm , which defines the interchromatin compartment , hosts transcription factories for pol ii and pol iii ( 4749 ) . the lack of a specific locale for the h1 rna and protein subunits of human rnase p and the differential distribution of these subunits in intranuclear compartments specialized in gene transcription suggested the possibility that the assembly of rnase p is dynamic and linked to active gene transcription ( 50 ) . a recent study has shown that human nuclear rnase p is required for transcription of trna and other small noncoding rna genes by pol iii in whole hela cells and cell extracts ( 33 ) . rnase p exerts its role on transcription through association with chromatin of trna and 5s rrna genes as determined by chromatin immunoprecipitation analysis ( 33 ) . all the protein subunits of rnase p tested so far , i.e. rpp14 , rpp20 , rpp21 , rpp29 , rpp30 , rpp38 and rpp40 , can be found associated with chromatin of trna and 5s rrna genes in rapidly dividing cells ( figure 1 ) ( 33 ; also unpublished data ) , an indication that a multi - protein rnase p complex binds to the chromatin of these genes . binding of these protein subunits to chromatin is dynamic , in the sense that they associate with trna and 5s rrna genes in dividing hela cells and dissociate from these genes when cells cease proliferating . furthermore , chromatin occupancy by rnase p associates with active gene transcription in extracts and in cells , and coincides with that of pol iii , which could be brought down with active rnase p ribonucleoprotein in coimmunoprecipitation experiments ( 33 ) . 
 figure 1.rnase p subunits bind to chromatin of active trna genes . many protein subunits of human rnase p associate with chromatin of trna genes , as determined by chromatin immunoprecipitation ( 33 ) . subunits that their binding to chromatin was not verified are shown with a question mark . based on knockdown analysis ( 33 ) , rnase p subunits seem not to be required for the recruitment of pol iii subunits and hence its transcription factors tfiiib and tfiiic ( 51,52 ) to the trna gene . many protein subunits of human rnase p associate with chromatin of trna genes , as determined by chromatin immunoprecipitation ( 33 ) . subunits that their binding to chromatin was not verified are shown with a question mark . based on knockdown analysis ( 33 ) , rnase p subunits seem not to be required for the recruitment of pol iii subunits and hence its transcription factors tfiiib and tfiiic ( 51,52 ) to the trna gene . knockdown of the essential protein rpp29 of human rnase p by rna interference did not affect the binding of rpb8 ( a core component of pol iii ) to trna and 5s rrna genes , even though this knockdown results in severe inhibition of rnase p activity and pol iii transcription ( 33 ) . additionally , rpp29 disengaged from target genes independently of rpb8 in cells that ceased proliferating ( 33 ) . hence , the possibility exits that recruitment of pol iii to trna and 5s rrna genes is independent of that of rnase p ( or at least rpp29 ) . the association of rnase p with chromatin of trna genes could be explained in terms of coordination of trna gene expression at transcription and processing steps . however , rnase p is also critical for transcription of 5s rrna , 7sl rna and u6 snrna genes ( 33 ) , whose precursor transcripts are not recognized as substrates for rnase p. hence , rnase p acts solely as a transcription factor for pol iii in transcribing these latter small rna genes . screening of a genomic library identified rpr1 rna , the rna subunit of s. cerevisiae rnase p , as the specific overexpression suppressor of very slow growth at 37c due to a small deletion of bdp1 , a subunit of the transcription factor tfiiib complex ( 53 ) . processing of the 5 leader sequence of precursor trna is defective in cells producing this mutant bdp1p , called bdp1253269 . transcription of the rpr1 rna gene is selectively diminished when recombinant bdp1253269 replaced wild - type bdp1p in an in vitro pol iii transcription system . the physical interaction of rnase p with bdp1p was demonstrated by coimmunoprecipitation and pull - down assays , implying a role for tfiiib in 5 end processing of precursor trna ( 53 ) . in s. cerevisiae , early processing of precursor trnas occurs in the nucleolus , which is enriched with rnase p rna ( 54 ) . additionally , trna gene families , which are dispersed in various chromosomes , colocalize with 5s rdna genes at the nucleolus ( 55,56 ) . this nucleolar clustering of yeast trna genes depends on transcription - complex formation and the existence of proficient promoters . clustering of trna and 5s rrna genes in the nucleolus forms pol iii transcription sites containing concentrations of pol iii and its general transcription factors , tfiiib , tfiiic and tfiiia . such nucleolar sites may also initiate nucleolar organization of the trna - processing pathway that includes 5 end processing by rnase p ( 55,56 ) . it should be noted that in contrast to the localization of pol iii and rnase p in the nucleolus in s. cerevisiae , confocal immunofluorescence microscopy analyses of hela cells reveal that specific protein subunits of human pol iii and rnase p primarily colocalize in the nucleoplasm , even though fluorescent signals are also visible in defined spots in large nucleoli ( r.r . and j.n . one possibility could be that rnase p as a whole particle is recruited to these target genes . nonetheless , protein subunits of human rnase p have been shown to exhibit differential patterns of binding to chromatin of trna and 5s rrna genes ( 33 ) . moreover , sirna knockdown of rpp29 , a key core component for the assembly of active rnase p , does not affect chromatin binding by other subunits , including rpp20 and rpp21 ( 33 ; r.r . and n.j . , unpublished data ) . hence , chromatin occupancy by rpp29 is not a prerequisite for binding by other subunits . stepwise assembly of catalytic ribonucleoproteins , including the spliceosome and h / aca small nucleolar ribonucleoprotein , at transcriptionally active genes has been proposed ( 45,5759 ) . archaeal and eukaryal rnase p are ensembles of structurally and functionally related rnas with highly conserved protein subunits ( 810,14,17,20,50 ) . reconstitution experiments of archaeal and eukaryal rnase p activities reveal that two protein subunits , e.g. rpp21 and rpp29 , with their corresponding rna moieties are sufficient for having endonucleolytic cleavage of trna substrates neutral ph7 and 5 - 30 mm divalent ion ( 24,27 ) . notably , rpp29 but not rpp21 can activate a bacterial rnase p rna ( 24,60 ) . in addition , p. furiosus pop5 has an  sandwich structure that bears structural similarity to the bacterial rnase p protein ( 25 ) . since archaeal and eucaryal rnase p rnas are active under unphysiological conditions of high ion concentrations ( 30,61 ) , it would be interesting to check if a single protein cofactor ( rpp29 , pop5 or other ) can reconstitute some activity under physiological reaction conditions . previous studies which revealed ambiguous properties related to rnase p or its subunits that were not consistent with its activity as a trna - processing enzyme could be reexamined from the perspective of its transcriptional activity . for instance , rpp20 that exhibits atpase activity ( 62 ) and chromatin - binding capability ( 33 ) may enable rnase p ( and/or rnase mrp ) to use atp as a cofactor for binding and modulating chromatin structure and function . rpp20 , as well as rpp25 , belong to the alba superfamily of proteins which seem to have originated as rna - binding proteins , attaching to a variety of ribonucleoprotein complexes , including rnase p and rnase mrp ( 13,17 ) and then being recruited as chromatin - binding proteins ( 63 ) . a dual role for rpm2p , a component of yeast mitochondrial rnase p , in trna processing and transcription has also been described ( 64 ) . the molecular mechanisms by which human rnase p binds to chromatin of noncoding rna genes and controls transcription by pol iii are not known . future work will reveal if rnase p acts at initiation , elongation and/or termination of transcription . in addition , the physical and functional links between pol iii and rnase p during the cell cycle remains to be studied . future studies will also unveil the significance of the effect of binding of rnase p ( or its subunits ) to hundreds of small noncoding rna genes and others ( r.r . and n.j . , unpublished data ) on chromatin structure , organization and function of the human genome . whatever the outcome of these studies , the discovery that human rnase p is a chromatin - binding complex which is critical for normal gene transcription ( 33 ) expands the definition of this entity as an enzyme that hydrolyzes a phosphodiester bond in precursor trna .
ribonuclease p ( rnase p ) has been hitherto well known as a catalytic ribonucleoprotein that processes the 5 leader sequence of precursor trna . 
 recent studies , however , reveal a new role for nuclear forms of rnase p in the transcription of trna genes by rna polymerase ( pol ) iii , thus linking transcription with processing in the regulation of trna gene expression . 
 however , rnase p is also essential for the transcription of other small noncoding rna genes , whose precursor transcripts are not recognized as substrates for this holoenzyme . accordingly , rnase p can act solely as a transcription factor for pol iii , a role that seems to be conserved in eukarya .