Influenza virus RNA polymerase with the subunit composition PB1-PB2-PA is a multifunctional enzyme with the activities of both synthesis and cleavage of RNA and is involved in both transcription and replication of the viral genome. In order to produce large amounts of the functional viral RNA polymerase sufficient for analysis of its structure-function relationships, the cDNAs for RNA segments 1, 2, and 3 of influenza virus A/PR/8, each under independent control of the alcohol oxidase gene promoter, were integrated into the chromosome of the methylotrophic yeast Pichia pastoris. Simultaneous expression of all three P proteins in the yeast P. pastoris was achieved by the addition of methanol. To purify the P protein complexes, a sequence coding for a histidine tag was added to the PB2 protein gene at its N terminus. Starting from the induced P. pastoris cell lysate, we partially purified a 3P complex by Ni 2؉ -agarose affinity column chromatography. The 3P complex showed influenza virus model RNA-directed and ApG-primed RNA synthesis in vitro but was virtually inactive without addition of template or primer. The kinetic properties of model template-directed RNA synthesis and the requirements for template sequence were analyzed using the 3P complex. Furthermore, the 3P complex showed capped RNA-primed RNA synthesis. Thus, we conclude that functional influenza virus RNA polymerase with the catalytic properties of a transcriptase is formed in the methylotrophic yeast P. pastoris. Influenza A virus contains eight different RNA segments of negative polarity in its genome, each encoding one or two unique viral proteins. The viral RNA polymerase is associated with each RNA segment as a viral component and in infected cells, responsible for both transcription and replication of the viral genome (for reviews, see references 7, 13, and 21). The pathway for the synthesis of viral mRNA involves multiple-step reactions, consisting of endonucleolytic cleavage of host cell mRNA, capped oligonucleotide-primed transcription of viral RNA (vRNA), and the addition of a poly(A) tail to the nascent mRNA. On the other hand, replication takes place in two steps, vRNA-directed synthesis of full-length complementary RNA (cRNA) without any modification at both the 5Ј and 3Ј termini and cRNA-directed reproduction of vRNA.Starting from the viral ribonucleoprotein (RNP), we isolated an RNA-3P (PB1, PB2, and PA) protein complex without NP by equilibrium centrifugation in cesium sulfate or cesium chloride (15, 16). The RNA-3P complex is enzymatically active in the in vitro synthesis of short attenuated RNA chains (but NP is needed for RNA chain elongation [12]), indicating that the three P proteins participate in the catalytic function of RNA polymerization. The vRNA-free 3P complex, consisting of one molecule each of the three P proteins, was isolated from the RNA-3P complex by centrifugation in cesium chloride or cesium trifluoroacetate (11). The 3P complexes exhibited RNA synthesis only when a model vRNA template with 5Ј-and 3Ј-terminal cons...