An unusual recent expansion of the C-terminal domain of RNA polymerase II in primate malaria parasites features a motif otherwise found only in mammalian polymerases

Abstract

The tail of the enzyme RNA polymerase II is responsible for integrating the diverse events of gene expression in eukaryotes and is indispensable for life in yeast, fruit flies, and mice. The tail features a C-terminal domain (CTD), which is comprised of tandemly repeated Y(1)-S(2)-P(3)-T(4)-S(5)-P(6)-S(7) amino acid heptads that are highly conserved across evolutionary lineages, with all mammalian polymerases featuring 52 identical heptad repeats. However, the composition and function of protozoan CTDs remain less well understood. We find that malaria parasites (genus Plasmodium) display an unprecedented plasticity within the length and composition of their CTDs. The CTD in malaria parasites which infect human and nonhuman primates has expanded compared to closely related species that infect rodents or birds. In addition, this variability extends to different isolates within a single species, such as isolates of the human malaria parasite, Plasmodium falciparum. Our results indicate that expanded CTD heptads in malaria parasites correlates with parasitism of primates and provide the first demonstration of polymorphism of the RNA polymerase II CTD within a single species. The expanded set of CTD heptads feature lysine in the seventh position (Y(1)-S(2)-P(3)-T(4)-S(5)-P(6)-K(7)), a sequence only seen otherwise in the distal portion of mammalian polymerases. These observations raise new questions for the radiation of malaria parasites into diverse hosts and for the molecular evolution of RNA polymerase II.

Figure 1. Plasticity of the heptads in the RNA polymerase II CTD across the Plasmodium genus

Schematic depiction of the CTD heptads from eight species of Plasmodium. The species names are listed at the left of each line along with a tree indicating their evolutionary relationships, constructed using sequences from the three mitochondrial protein-coding genes of the parasites as described in Perkins (2008). R1 is the linker domain, R2 is the heptad-bearing region and R3 is the acidic tail region following the last repeat of the CTD. Diamonds and hexagons symbolize individual heptads, with the amino acid in the 7^th position indicated. The plasticity of the CTD is restricted to heptad-containing region, R2. Rodent malaria parasites (P. yoelii and P. berghei) and the bird parasite (P. gallinaceum) exhibit eight repeats with a common stalk (Q,V,K,A,V). Primate malaria parasites feature an expanded set of tandemly arrayed heptads all containing lysine in position 7 of heptads immediately preceding this stalk. Two separate, independent expansions are proposed to have occurred (indicated by asterisks). Sequences of the CTDs drawn from PlasmoDB (www.plasmodb.org) and contigs at the Sanger Institute: P. berghei: ANK,PB000038.00.0; P. yoelii17xNL: PY03187; P. vivax Sal-1: PV095320; P. knowlesi Strain H: PKH_082310; P. falciparum 3D7: Pfc0805w. P. gallinaceum: EU840284 and P. reichinowi: EU850397, P. fragile: EU840282 and P. ovale: EU887536.

Figure 2. Plasticity of the heptads in the RNA polymerase II CTD across Plasmodium species

A. Amino acid sequences of the R2 domain of 2 isolates of P. berghei, 5 isolates of P. yoelii and 4 isolates of P. vinckei (all rodent parasites), 3 isolates of P. cynomolgi, 5 isolates of P. vivax and 12 geographical isolates of P. falciparum. The lysine in the 7^th position of each heptad repeat is shown in red. Numbers of total heptads and diheptads are tabulated at the right. B. Phylogenetic tree of various P. falciparum isolates based on 137 SNPs and arranged according to geographical origin. The number of heptad repeats found in the CTD of each isolate is shown in red. Adapted from (Volkman, Sabeti, DeCaprio, Neafsey, Schaffner, Milner, Jr., Daily, Sarr, Ndiaye, Ndir, Mboup, Duraisingh, Lukens, Derr, Stange-Thomann, Waggoner, Onofrio, Ziaugra, Mauceli, Gnerre, Jaffe, Zainoun, Wiegand, Birren, Hartl, Galagan, Lander, and Wirth 2007).

Figure 2. Plasticity of the heptads in the RNA polymerase II CTD across Plasmodium species

A. Amino acid sequences of the R2 domain of 2 isolates of P. berghei, 5 isolates of P. yoelii and 4 isolates of P. vinckei (all rodent parasites), 3 isolates of P. cynomolgi, 5 isolates of P. vivax and 12 geographical isolates of P. falciparum. The lysine in the 7^th position of each heptad repeat is shown in red. Numbers of total heptads and diheptads are tabulated at the right. B. Phylogenetic tree of various P. falciparum isolates based on 137 SNPs and arranged according to geographical origin. The number of heptad repeats found in the CTD of each isolate is shown in red. Adapted from (Volkman, Sabeti, DeCaprio, Neafsey, Schaffner, Milner, Jr., Daily, Sarr, Ndiaye, Ndir, Mboup, Duraisingh, Lukens, Derr, Stange-Thomann, Waggoner, Onofrio, Ziaugra, Mauceli, Gnerre, Jaffe, Zainoun, Wiegand, Birren, Hartl, Galagan, Lander, and Wirth 2007).

Figure 3. Enrichment of “SP” motifs in the tails of RNA Pol II from eight different protozoan species

Serine-proline (SP) motifs that represent potential phosphorylation sites are marked with vertical lines (|). Sequence accession numbers are: Stylonchia mytilus: AAK00313.1; Paramecium tetraurelia: CAI39063.1; Tetrahymena thermophila: GI accession: 118348890; Trypanasoma brucei: P17545; Trypanasoma cruzi: XP_812569; Trichomonas vaginalis: TVU20501; Giardia lamblia: XP_001704218