discovery of additional pathways to perpetuate geneticinformation,
i.e.
, from RNA to DNA (Baltimore, 1970;Temin and Mizutani, 1970) and to conformationalchanges induced by proteinaceous infectious agents(Prusiner
et al.
, 1982). The production of RNA, termedtranscription, is a highly coordinated process mediatedby RNA polymerase, whose enzymatic activity wasfirst discovered by Weiss and Gladstone in 1959from rat liver nuclei. This enzyme could synthesizeRNA in a DNA-dependent manner, as evidencedby the observation that, upon addition of DNase,incorporation of [
α
-
32
P]CTP into RNA was drasticallyreduced (Weiss and Gladstone, 1959). A similar RNA-synthesizing activity was later identified from
Escherichia coli
(Hurwitz
et al
., 1960; Stevens, 1960;Chamberlin and Berg, 1962), thereby establishing auniversal role of RNA polymerases in transcribingDNA in both eukaryotes and prokaryotes. To date,four different RNA polymerases have been identifiedin higher eukaryotes. In contrast, only one RNApolymerase is found in prokaryotes and archaea.Three eukaryotic RNA polymerases (I, II, and III,or named A, B, and C, respectively) were first iden-tified by Roeder and Rutter, based on the chromato-graphic fractionation of sea urchin embryo nuclei ona DEAE-Sephadex column. RNA polymerase I cameoff the column first at the lowest salt concentration,whereas RNA polymerase III eluted at the highest saltconcentration (Roeder and Rutter, 1969). Although theexistence of three eukaryotic RNA polymerases wasestablished in 1969, their functions remained elusiveuntil Chambon’s and Roeder’s groups found that thespecific activity of each RNA polymerase could beresolved based upon their differential sensitivities to
α
-amanitin (Gniazdowski
et al.
, 1970; Kedinger
et al.
,1970; Weinmann and Roeder, 1974; Weinmann
et al.
,1974), a drug isolated from the death cap fungus,
Amanita phalloides
, that inhibits 50% activity of RNApolymerase II at low concentrations (0.02
µ
g/mL) andthat of RNA polymerase III at high concentrations(20
µ
g/mL; Weinmann
et al.
, 1974). Using
α
-amanitinsensitivity assay with endogenous RNA polymerasespresent in isolated nuclei, Roeder and Rutter (1970) dis-covered that RNA polymerase I is primarily involvedin transcribing 18S and 28S ribosomal RNAs, whileRNApolymeraseIItranscribesmRNAs,andRNApoly-merase III is responsible for synthesis of cellular 5SrRNA, tRNAs, and adenovirus VA RNAs. These resultswereconsistentwiththefindingthatRNApolymeraseIis localized within nucleoli, the sites for rRNA synthe-sis, whereas RNA polymerase II and III are normallypresent in the nucleoplasm (Roeder and Rutter, 1970;Zylber and Penman, 1971; Weil and Blatti, 1976).The fourth RNA polymerase, recently identified inplants to facilitate the production of small interferingRNA (siRNA) involved in RNA-directed DNA methy-lation and transcriptional silencing and formation of heterochromatin, is also present in the nucleus andis resistant to
α
-amanitin (Herr
et al.
, 2005; Kanno
et al.
, 2005; Onodera
et al.
, 2005). Although this plant-specific RNA polymerase IV appears to be nonessentialfor viability, it exhibits unique properties not sharedby other nuclear RNA polymerases. Interestingly, an
α
-amanitin-resistant single-polypeptide nuclear RNApolymerase (spRNAP-IV), structurally unrelated to themultisubunit plant RNA polymerase IV, has been ad-ditionally found in human HeLa cells (Kravchenko
et al.
, 2005). This spRNAP-IV enzyme, encoded by analternative transcript derived from the mitochondrialRNA polymerase gene (
POLRMT
) that also encodesthe single-polypeptide mitochondrial RNA polymerase(mtRNAP), lacks the N-terminal 262-amino acids en-compassing the mitochondrial targeting sequence butcontains the same C-terminal 968 amino acid cat-alytic region of mtRNAP. While spRNAP-IV appears tobe structurally distinct from
α
-amanitin-sensitive RNApolymerase II, it represents a second RNA polymeraseable to transcribe a subset of mRNA-encoding genesthat do not contain the core promoter elements andregulatory sequences commonly found in RNA poly-merase II-transcribed genes.Clearly, the findings that each of these eukaryoticRNA polymerases has unique biochemical properties,as exhibited by their distinct chromatographic elutionprofile, nuclear localization, and differential sensitivityto
α
-amanitin, and that RNA polymerase I has 14 sub-units, while RNA polymerase II and III possess 12 and17 subunits, respectively, suggest that these three clas-sical eukaryotic RNA polymerases and the newly iden-tified plant RNA polymerase IV and human spRNAP-IV are unlikely to play a functionally redundant rolein the cell. However, these enzymes do share a com-mon property in transcribing a diverse set of DNA se-quences, although they lack sequence-specific recogni-tion ability to correctly specify the transcription startsite unique to each gene. For site-specific initiation, ad-ditional proteins are necessary to form an initiation-competent RNA polymerase complex. Here, we review
106
M. C. Thomas and C.-M. Chiang
D o w nl o ad ed A t : 03 :14 19 J a n u a r y 2009
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