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Evolution of Nuclear Ribosomal Rnas in Kinetoplastid Protozoa

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Evolution of Nuclear Ribosomal Rnas in Kinetoplastid Protozoa Proc. Natl. Acad. Sci. USA Vol. 90, pp. 11608-11612, December 1993 Evolution Evolution of nuclear ribosomal RNAs in kinetoplastid protozoa: Perspectives on the age and origins of parasitism (RNA editing/mitochondrial rRNA/Bodo caudaus/Trypanosomatldae) ANA PAULA FERNANDES, KIMBERLYN NELSON*, AND STEPHEN M. BEVERLEYt Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 Communicated by Walter Gilbert, September 7, 1993 (receivedfor review July 16, 1993) ABSTRACT Molecular evolutionary relationships within number ofindependent origins ofdigenetic parasitism has been the protozoan order Kinetoplastida were deduced from com- estimated variously as from 1 to 5 (6-9). An alternative model parisons of the nuclear smail and large subunit ribosomal RNA suggests that digenetic parasites originated from free-living (rRNA) gene sequences. These studies show that relationships invaders and secondarily gave rise to monogenetic parasites among the trypanosomatid protozoans differ from those previ- (10). Thus, an unambiguous view ofboth parasite relationships ously proposed from studies of organismal characteristics or and the origins of vertebrate parasitism has not emerged. mitochondrial rRNAs. The genera Leishmania, Endotrypanum, Recently molecular evolutionary methods have been ap- Leptomonas, and Crithidia form a closely related group, which plied to the study of trypanosomatid relationships. Compar- shows progressively more distant relationships to Phytomonas isons of mitochondrial (kinetoplast) rRNAs suggested that and Blastocrithidia, Trypanosoma cruzi, and lastly Trypanosoma the genera Crithidia, Leptomonas, Leishmania, and Trypano- brucei. The rooting ofthe trypanosomatid tree was accomplished soma diverged successively, with the digenetic life-style by using Bodo caudatus (family Bodonidae) as an outgroup, a originating once before the separation of Leishmania (11). status conflrmed by molecular comparisons with other eukary- However, analysis of nuclear small subunit ribosomal RNAs otes. The nuclear rRNA tree agrees weil with data obtained from (SSU rRNAs) suggested a different evolutionary tree, in comparisons of other nuclear genes. Differences with the pro- which Trypanosoma brucei and Trypanosoma cruzi diverge posed mitochondrial rRNA tree probably reflect the lack of a before the lineage leading to Crithidia and Leishmania, which suitable outgroup for this tree, as the topologies are otherwise are closely related (Figs. 1-4; refs. 12-14). The implications similar. Smail subunit rRNA divergences within the trypanoso- of these various topologies to models concerning the age and matids are large, approaching those among plants and animals, origins of parasitism are profound. Significantly, the mito- which underscores the evolutionary antiquity of the group. chondrial tree lacked an independent outgroup required to Analysis of the distribution of different parasitic life-styles of root the tree, which cast doubts about the direction of these species in conjunction with a probable timing of evolu- evolution. Were the root placed on the T. brucei lineage, the tionary divergences suggests that vertebrate parasitism arose topologies of the mitochondrial and nuclear trees would be multiple times in the trypanosomatids. quite similar. In this study we report on the sequence of the SSU and large subunit (LSU) rRNAs from a close outgroup The protist order Kinetoplastida is a cosmopolitan group of relative of trypanosomatids, Bodo caudatus of the Kineto- flagellates containing prominent groups that parasitize virtu- plastid family Bodonidae (15), as well as additional sequences ally every major group of eukaryotic organisms, including for monogenetic (Leptomonas, Blastocrithidia) and digenetic other protozoans (1, 2). Kinetoplastids are distinguishable (Endotrypanum, Leishmania, Phytomonas) trypanosoma- from other protozoa by the presence of kinetoplast DNA, a tids. These data permit an unambiguous rooting of the different type of mitochondrial DNA consisting of maxi- and nuclear evolutionary tree, which confirms the view that T. mini-circle DNAs located in the single mitochondrion near brucei represents the most ancient divergence within the the basal body of the flagellum (1, 3). In addition, these trypanosomatids. We consider this tree to accurately depict organisms exhibit unusual molecular phenomena such as phylogenetic relationships within the Trypanosomatidae and antigenic variation, trans-splicing, and RNA editing (3-5). use this perspective to view the age and origins of vertebrate Kinetoplastids exhibit three different life-styles: free-living, parasitism in this important group. monogenetic parasitism involving a single host (usually an AND METHODS invertebrate), and digenetic parasitism alternating between MATERIALS invertebrate and vertebrate or plant hosts. The family Parasite Strains and DNAs. The strains were as follows: B. Bodonidae contains both free-living and monogenetic taxa, caudatus (a clonal derivative obtained from S. Hajduk, whereas the family Trypanosomatidae is a diverse group of University of Alabama, Birmingham; ref. 16), T. cruzi (Peru monogenetic and digenetic taxa (1, 2). In humans and animals strain; from D. McMahon-Pratt, Yale University Medical Trypanosoma and Leishmania cause severe diseases, includ- School), Endotrypanum monterogei (strain LV88; from M. ing sleeping sickness, Chagas disease, and kala-azar, while Chance, Liverpool School of Tropical Medicine), Leptomo- Phytomonas are pathogens of plants. nas sp. (from L. Simpson, University of California, Los Previous studies of evolutionary relationships within the Angeles; ref. 11), Leishmania major and L. donovani (strains Trypanosomatidae emphasized traits derived from morphology LT252 and HU-3, this laboratory), Phytomonas sp. (isolated or consideration of the parasitic life-style. Many workers fa- from Euphorbia hyssopifolia; from I. Roitman, Universidade vored a model where the digenetic genera such as Endo- de Brasilia, ref. 17) and Blastocrithidia culicis (ATCC 30268, trypanum, Leishmania, and Trypanosoma originated from monogenetic, Leptomonas-like ancestors (6, 7). However, the Abbreviations: SSU rRNA, small subunit ribosomal RNA; LSU rRNA, large subunit ribosomal RNA. *Present address: Institute of Molecular Evolutionary Genetics, The publication costs of this article were defrayed in part by page charge Department of Biology, Pennsylvania State University, University payment. This article must therefore be hereby marked "advertisement" Park, PA 16802. in accordance with 18 U.S.C. §1734 solely to indicate this fact. tTo whom reprint requests should be addressed. 11608 Downloaded by guest on September 30, 2021 Evolution: Femandes et al. Proc. Natl. Acad. Sci. USA 90 (1993) 11609 from L. Landweber, Harvard University). Bodo cells were quences. If the minimum match obtained in these pairwise separated from the feeder bacteria by velocity and density- comparisons were at least A, all N positions were considered gradient centrifugation (16). DNAs were isolated by prepa- to be sufficiently related for retention. Then, the pairwise ration of chromosomes in agarose plugs (Blastocrithidia, comparisons were repeated successively with windows be- Endotrypanum, and Leishmania; ref. 18), banding in CsCl ginning at aligned position 2, 3, . (Y - N + 1) to give the gradients (Bodo, Leptomonas; ref. 19), or phenol-chloroform final filtered data set. Empirical evaluation suggested that a extraction (T. cruzi, Phytomonas; ref. 20). filter (A/N) of4/7 yielded satisfactory data sets (as shown by PCR Amplification and DNA Sequencing. Nuclear rRNA the results obtained above with alignment 1). genes were amplified with oligonucleotide primers chosen from conserved sequences evident in published sequences of RESULTS AND DISCUSSION T. brucei, Leishmania donovani, and Crithidia fasciculata Sequences and Methodology. We used PCR amplification (21-25). The entire SSU rRNA gene was amplified by using the followed by molecular cloning to sequence the entire 2.2-kb primers situated at the extreme 5' and 3' termini of the rRNA SSU rRNA gene and a 1-kb segment of the LSU rRNA gene coding region. Primers for a 1-kb segment of the LSU rRNA from B. caudatus, T. cruzi (Peru strain), E. monterogei, were xba-CLS378 (5'-GGGTCTAGAGTAGGAAGAC- Leptomonas sp. (11), and L. donovani (LSU rRNA only); the CGATAGC) and kpn-CLS1373 (5'-GTGGTACCGGTGGAT- LSU and SSU rRNA sequences ofC.fasciculata and T. brucei TCGGTTGGTGAG). PCR amplification (26) was performed have been reported, as have the SSU rRNA sequences forfive by 30 cycles, consisting of 1 min at 94°C, 2 min at 55°C, and species of Leishmania (14, 21-25, 31). LSU sequences were 3 min at 72°C. Amplified DNAs were digested with appropriate additionally obtained for isolates of Phytomonas and B. culi- enzymes, purified on low-melting-temperature agarose gels, cus. Multiple independent PCR clones were sequenced from and cloned into appropriately digested M13mpl8 and each species, and some variation was evident. For example, M13mpl9 vectors (27). Single-stranded DNAs were prepared within a species variation of 0.02% was seen among different for several clones from each orientation and sequenced indi- PCR-generated recombinants of the SSU rRNA gene. This vidually or after pooling. Both strands were sequenced by the heterogeneity arose from both nucleotide substitutions and dideoxynucleotide chain-termination method by using either single-base insertions and deletions and, presumably,
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