Transcription in chloroplasts and mitochondria: A tale of two polymerases

Abstract

D espite their eubacterial origin’, chloroplasts and mitochondria employ different strategies for expressing the genetic information they contain (Fig. 1). Chloroplast genomes encode a multicomponent, Eubacteria-like (aJ@‘) core RNA polymerasez. In contrast, mitochondria use a singlepolypeptide, bacteriophage T3/T7like RNA polymerase encoded in the nucleus’. Recently, clues to the evolution of these distinct transcriptional modes have surfaced. Although the plastid-encoded RNA polymerase (PEP)“ has an essential role in transcription in the chloroplast, a second, nucleusencoded, RNA polymerase (NEP)4 has been implicated in chloroplast gene expression (reviewed in Ref. 5). Early work suggested that the NEP (which must be imported into the chloroplast) might be a singlepolypeptide, phage-like RNA polymerase6. Distinct promoter classes for PEP and NEP have been identified in chloroplast DNA (Refs 4,7), with each polymerase functioning to transcribe a subset of chloroplast genes. A candidate NEP gene has now emerged with the recent report8 of two different but related phage-type RNA polymerase genes in the nuclear genome of the dicotyledonous angiosperm Arabidopsis thaliana. These genes, RpoY and RpoZ, encode proteins that share substantial sequence similarity with both fungal (Saccharomyces cerevisiae and Neuvospora cvassa) mitochondrial and bacteriophage (T3, T7 and SP6) RNA polymerases. In experiments in which the recombinant proteins (RPOY and RPOZ, respectively) were incubated with isolated organelles in vitro, RPOY was found to be specifically targeted to and imported into mitochondria, whereas RPOZ was taken up by chloroplasts but not mitochondria. These data strongly suggest that RPOY represents the mitochondrial RNA polymerase, whereas RPOZ represents the previously described nucleus-encoded, chloroplast-localized enzyme (NEP). Further biochemical analysis will be necessary to show definitively that RPOZ functions in chloroplasts; however, the signs are good that this is indeed the case. The degree of sequence conservation between RPOY and RPOZ is not exceptionally high (63% nucleotide identity, 55% amino acid identity); nevertheless, phylogenetic analysis shows that these genes are more closely related to one another than to the homologous fungal mitochondrial RNA polymerase genes*. Moreover, RpoY and RpoZ share the same organization of 19 exons (16 of which are identical in length), with all 18 intron insertion sites precisely conserved with respect to the amino acid sequences. This implies that the two genes are the products of a relatively recent gene duplication (Fig. Id-e). Phage-type (putative mitochondrial) RNA polymerase genes are widely distributed within the eukaryotic lineage9, having been found in eukaryotes that both do and do not contain chloroplasts (Fig. 2). Thus, it is reasonable to postulate that a gene encoding the mitochondrial RNA polymerase was duplicated at some