# How many RNA polymerases do eukaryotes have? > Eukaryotes have three nuclear RNA polymerases: Pol I makes ribosomal RNA, Pol II makes mRNA and Pol III makes tRNA and 5S rRNA. Land plants add Pol IV and Pol V, and mitochondria and chloroplasts carry their own enzymes. Eukaryotes have **three nuclear RNA polymerases**, named Pol I, Pol II and Pol III. Pol I makes the large ribosomal RNAs, Pol II makes messenger RNA and many regulatory RNAs, and Pol III makes transfer RNAs, 5S ribosomal RNA and other short RNAs. Every eukaryote studied, from yeast to humans, uses this three-way division. The answer grows when the count reaches beyond the nucleus. Land plants have two more nuclear enzymes, Pol IV and Pol V, for a total of five. Mitochondria use a separate single-subunit polymerase, and plant chloroplasts use both a bacterial-type enzyme and phage-type enzymes. A human cell therefore relies on four distinct DNA-dependent RNA polymerases, while bacteria and archaea each manage with one. ## What each nuclear RNA polymerase makes Eukaryotes have three different RNA polymerases that divide nuclear genes between them by the [type of RNA](/guides/how-many-types-of-rna-are-there) produced. Each copies a DNA template into RNA by the same base-pairing rule a [DNA-to-RNA](/app/dna-to-rna) conversion applies; what differs is which genes each enzyme reads and how it is recruited to them. Pol I works in the nucleolus, the dense region of the nucleus where [ribosomes](/guides/how-many-ribosomes-are-in-a-cell) are assembled. It transcribes a single long precursor, 7 to 14 kilobases long, that is cut into the 18S, 5.8S and 25S or 28S ribosomal RNAs. That one job is enormous: in a rapidly growing yeast cell, 60% of all transcription goes to ribosomal RNA, and rRNA makes up 80 to 90% of the RNA mass in mammalian cells. Pol II transcribes every protein-coding gene into messenger RNA. It also makes most small nuclear RNAs of the spliceosome, small nucleolar RNAs, long non-coding RNAs and the primary transcripts of microRNAs. Lee and colleagues showed that primary microRNA transcripts carry a cap and a poly(A) tail, the hallmarks of a Pol II product, and that they disappear at α-amanitin doses that block only Pol II. Pol III makes the entire pool of transfer RNAs, the 5S ribosomal RNA precursor and U6 spliceosomal RNA. Its other products include 7SL RNA, the scaffold of the signal recognition particle that steers secreted proteins to the endoplasmic reticulum. These RNAs are short and fold into compact structures such as the [tRNA cloverleaf](/guides/rna-secondary-structure), the kind of secondary structure [RNAfold](/app/rnafold) predicts from sequence. Table 1. The three nuclear RNA polymerases of eukaryotes. Subunit counts are for the complete enzyme in budding yeast (Saccharomyces cerevisiae) and humans; bovine Pol II, used as the mammalian model, differs from the human enzyme by seven amino acids. α-amanitin sensitivity is for mouse enzymes; yeast Pol I and Pol III show the reverse pattern. Sources: Misiaszek et al. (2021), Yang et al. (2023), Ramsay et al. (2020), Lindell et al. (1970), Carter and Drouin (2010), Bernecky et al. (2016), Weinmann and Roeder (1974). Polymerase Main products Location Subunits in yeast Subunits in humans α-amanitin Pol I 18S, 5.8S and 28S rRNA (one precursor) Nucleolus 14 13 Resistant Pol II mRNA, most snRNAs, snoRNAs, miRNA precursors, lncRNAs Nucleoplasm 12 12 Inhibited at low concentrations Pol III tRNA, 5S rRNA, U6 snRNA, 7SL RNA Nucleoplasm 17 17 Inhibited only at high concentrations The subunit counts describe three enzyme complexes, not 43 separate polymerases. Yeast Pol I, II and III contain 14, 12 and 17 subunits. Human Pol I has 13 because humans lack a homolog of the small yeast stalk subunit A14, while human Pol III keeps all 17. The extra subunits of Pol I and Pol III are not random additions. They resemble the general transcription factors TFIIE and TFIIF that Pol II recruits separately, built permanently into the enzyme. ## How α-amanitin told the polymerases apart The three enzymes were first told apart around 1970 by their behavior on ion-exchange columns and their response to α-amanitin, the toxin of the death cap mushroom. In sea urchin, rat and calf, α-amanitin blocked the nucleoplasmic Pol II and left the nucleolar Pol I untouched. Pol III took higher doses to reveal itself. In mouse myeloma cells it ignored the low concentrations that fully inhibit Pol II but was blocked at higher ones, and the synthesis of tRNA precursors and 5S RNA followed exactly the same inhibition curve. That match is how Pol III was assigned its products, and the same dose ladder later showed that microRNA genes belong to Pol II. The ladder is not universal. Schultz and Hall numbered the yeast enzymes in the order they eluted from an ion-exchange column and found that Pol II was again the most sensitive, half inhibited at 1 µg/mL. Yeast Pol I, however, was half inhibited at 600 µg/mL, and yeast Pol III resisted until concentrations exceeded 1 mg/mL: the reverse of the vertebrate order for Pol I and Pol III. ## Why plants have five nuclear RNA polymerases Land plants are the main exception to the answer of three. Their nuclei also contain Pol IV and Pol V, which evolved from Pol II and are present in every land plant from liverworts to flowering plants but not in the green alga _Chlamydomonas_. Neither enzyme makes messenger RNA. Pol IV produces the precursors of almost all 24-nucleotide small interfering RNAs, most of them from transposable elements and repeats. Pol V makes long non-coding RNAs that act as landing pads for those small RNAs, which then guide DNA methylation to silence the same transposons. In _Arabidopsis_ both enzymes have 12 subunits, sharing seven with Pol II. The count of five refers to DNA-dependent RNA polymerases, which read DNA. Pol IV works in a tight partnership with RDR2, an RNA-dependent RNA polymerase that copies Pol IV transcripts into double-stranded RNA. RNA-dependent enzymes of that kind are a separate family and are not part of the usual count. ## RNA polymerases in mitochondria and chloroplasts Mitochondria carry their own small genome and their own polymerase. Human mitochondrial RNA polymerase (POLRMT) is a single protein chain related to the RNA polymerase of bacteriophage T7, not to the nuclear enzymes. Unlike T7 polymerase, it needs two helper factors, TFAM and TFB2M, to bind and open its promoters. This one enzyme transcribes the whole mitochondrial genome, including all [37 genes of human mitochondrial DNA](/guides/how-many-genes-in-mitochondrial-dna). Chloroplasts use two kinds of polymerase at once. The plastid-encoded polymerase (PEP) is a multisubunit enzyme of the bacterial type, with core subunits encoded by the chloroplast's own rpoA, rpoB, rpoC1 and rpoC2 genes and six nuclear-encoded sigma factors in _Arabidopsis_. Alongside it work one or two nuclear-encoded, phage-type single-subunit polymerases (NEP). PEP dominates the transcription of photosynthesis genes. These organelle enzymes, together with Pol IV and Pol V, are why some sources give a number other than three, and why the precise answer depends on scope. Counting only the nucleus gives three for animals and fungi and five for plants. Adding mitochondria gives four for humans, and a flowering plant cell adds several more. ## How many RNA polymerases do prokaryotes have? Bacteria and archaea each use a single RNA polymerase to transcribe all of their genes, which is why eukaryotes are often described as having divided the work of one ancestral enzyme between three or five. ![Bar chart: bacteria and archaea each have one cellular RNA polymerase, animals and fungi have three nuclear RNA polymerases and land plants have five](/images/charts/rna-polymerase-types-across-life.webp '**Figure 1. RNA polymerase types across cellular life.** Cellular or nuclear DNA-dependent RNA polymerases only; organelle polymerases and RNA-dependent RNA polymerases are excluded. Sources: [Carter and Drouin (2009)](https://doi.org/10.1016/j.ygeno.2009.08.011), [Yang et al. (2023)](https://pmc.ncbi.nlm.nih.gov/articles/PMC10533338/), [Fouqueau et al. (2018)](https://pmc.ncbi.nlm.nih.gov/articles/PMC7289017/).') The two single enzymes are not alike. Most bacterial RNA polymerases have five subunits, two α subunits plus β, β′ and ω. Different sigma factors attach to that core to direct it to different sets of promoters, but they do not create additional polymerases. Archaeal RNA polymerase is closer to eukaryotic Pol II in its subunits, architecture, promoters and transcription factors. It has about 12 subunits, with the exact number depending on whether the large catalytic subunits are split into separate genes and whether a species carries lineage-specific subunits. A core of five subunits is shared by every cellular RNA polymerase and predates the split between bacteria, archaea and eukaryotes. ## How many DNA polymerases do eukaryotes have? DNA polymerases are counted differently from RNA polymerases. There is no single eukaryotic number: human cells have 16 DNA polymerases, while budding yeast has eight. Only three of the human enzymes do most [nuclear genome](/guides/human-genome-size) replication. Pol α makes and extends the initial primer, Pol ε copies most of the leading strand and Pol δ copies the lagging strand as short Okazaki fragments. The rest have specialized roles in DNA repair, copying past damaged bases, immune-cell DNA rearrangement or mitochondrial DNA replication. Older textbook lists of three or five eukaryotic DNA polymerases cover the main replication enzymes known at the time, not every DNA-template-dependent polymerase identified since. A human cell copies its [nuclear DNA](/guides/how-long-does-dna-replication-take) in about eight hours because many replication forks work at once, not because all 16 polymerases copy chromosomes in parallel. ![Bar chart: E. coli has five recognized DNA polymerases, budding yeast has eight and humans have 16](/images/charts/dna-polymerase-counts-by-species.webp '**Figure 2. DNA polymerase counts in three model species.** Identified DNA-template-dependent DNA polymerases in each species. Sources: [Machacova et al. (2024)](https://www.nature.com/articles/s41467-024-51667-1), [Fijalkowska et al. (2012)](https://pmc.ncbi.nlm.nih.gov/articles/PMC3391330/).') ## How many DNA polymerases do bacteria have? Bacteria do not share one DNA polymerase count either. _E. coli_ has five, Pol I to Pol V, while _Helicobacter pylori_ has been reported to have only two. In _E. coli_, Pol III is the main chromosome-replicating enzyme. Pol I removes and replaces the RNA primers left between Okazaki fragments, while Pol II, IV and V mainly support repair or tolerance of DNA damage. Five is the right number for [_E. coli_](/guides/e-coli-statistics), not a rule for every bacterium. Archaea differ again. Most archaeal groups replicate their chromosomes with a two-subunit enzyme called PolD, often alongside a B-family polymerase with an ancillary role. Crenarchaea such as _Sulfolobus_ lack PolD entirely and rely on B-family enzymes. The two counts answer different questions. RNA polymerase counts track how a lineage divides transcription: one enzyme in prokaryotes, three specialized nuclear enzymes in eukaryotes, two more in plants for genome defense, and separate enzymes in each organelle. DNA polymerase counts instead track how many specialized jobs, from repair to damage bypass, a genome has accumulated around its few replicative enzymes.