Short-term sequence evolution and vertical inheritance of the Naegleria twin-ribozyme group I intron
© Wikmark et al; licensee BioMed Central Ltd. 2006
Received: 28 December 2005
Accepted: 02 May 2006
Published: 02 May 2006
Ribosomal DNA of several species of the free-living Naegleria amoeba harbors an optional group I intron within the nuclear small subunit ribosomal RNA gene. The intron (Nae.S516) has a complex organization of two ribozyme domains (NaGIR1 and NaGIR2) and a homing endonuclease gene (NaHEG). NaGIR2 is responsible for intron excision, exon ligation, and full-length intron RNA circularization, reactions typical for nuclear group I intron ribozymes. NaGIR1, however, is essential for NaHEG expression by generating the 5' end of the homing endonuclease messenger RNA. Interestingly, this unusual class of ribozyme adds a lariat-cap at the mRNA.
To elucidate the evolutionary history of the Nae.S516 twin-ribozyme introns we have analyzed 13 natural variants present in distinct Naegleria isolates. Structural variabilities were noted within both the ribozyme domains and provide strong comparative support to the intron secondary structure. One of the introns, present in N. martinezi NG872, contains hallmarks of a degenerated NaHEG. Phylogenetic analyses performed on separate data sets representing NaGIR1, NaGIR2, NaHEG, and ITS1-5.8S-ITS2 ribosomal DNA are consistent with an overall vertical inheritance pattern of the intron within the Naegleria genus.
The Nae.S516 twin-ribozyme intron was gained early in the Naegleria evolution with subsequent vertical inheritance. The intron was lost in the majority of isolates (70%), leaving a widespread but scattered distribution pattern. Why the apparent asexual Naegleria amoebae harbors active intron homing endonucleases, dependent on sexual reproduction for its function, remains a puzzle.
Naegleria is a common genus of soil and freshwater free-living amoeba of the vahlkampfiid family . Naegleria apparently lack a sexual reproduction cycle since meiosis never has been observed or proven experimentally. Subsequently, a number of genetically-defined variants have been isolated in nature and proposed as distinct species [1, 2]. A typical Naegleria amoeba cell contains a distinct nucleus with a large and predominant nucleolus containing as much as 3000–5000 copies of an approximately 14-kb ribosomal DNA (rDNA) plasmid [3, 4]. Each rDNA molecule carries a single transcription unit for the ribosomal RNA (rRNA) genes. Some Naegleria isolates have been reported to contain group I intron insertions at conserved sequence sites, both within the small subunit (SSU) and large subunit (LSU) rRNA genes . Introns have been noted at position 516 in SSU rDNA (i.e. a position that is homologous to corresponding position in the E. coli rRNA gene) and at positions 1921, 1926, 1949, and 2563 in LSU rDNA [5–11].
Group I introns are autocatalytic genetic elements carrying a ribozyme domain responsible for the intron self-splicing reaction, and occasionally a homing endonuclease gene (HEG) encoding an endonuclease protein directly involved in intron mobility at the DNA level [12, 13]. A group I splicing ribozyme possess a well-defined three-dimensional structure organized into three functional domains (catalytic domain, folding domain, and substrate domain) by approximately ten paired RNA segments named P1–P10 [14, 15]. The most common and best characterized of the Naegleria rDNA introns is Nae.S516. Group I introns at position 516 in SSU rDNA are relatively common among eukaryotic microorganisms with more than 250 cases reported so far [16, 17], and with both lateral and vertical inheritance patterns compared to that of host rDNA. A widespread distribution and structural diversity among the S516 group I introns have been noted, including several complex introns carrying HEGs [16, 18].
A typical Naegleria S516 intron has a twin-ribozyme organization and represents the most complex class of all group I introns known . Nae.S516 consists of a small group I-like mRNA capping ribozyme (NaGIR1) and a HEG domain, both inserted into the P6b segment of a regular group IC1 splicing ribozyme (NaGIR2). Expression and functional aspects of the Naegleria S516 intron have been reported. The splicing ribozyme (NaGIR2) is responsible for the autocatalytic activity that generates intron excision and exon ligation, as well as full-length intron RNA circle formations . The ability to form full-length intron RNA circles is a general property of nuclear group I introns and could be important in RNA mobility at the RNA level, or even as an intermediate in the expression of the homing endonuclease [11, 20, 21]. The Naegleria HEG (NaHEG) encodes a 245 amino acid protein that belongs to the His-Cys box family of homing endonucleases [22, 23]. The intron endonuclease recognizes and binds to a 19-bp DNA sequence flanking the S516 rDNA site and cleaves the DNA generating a five-nucleotide 3' staggered end [24, 25]. In general, group I intron endonucleases promote intron homing at the DNA-level by generating a double-stranded break in the intron-less target DNA, followed by invasion of the donor intron-containing allele and DNA repair using the intron-containing allele as template . However, sexual mating is the biological framework for nuclear group I intron homing [26, 27] and it is unclear why the apparently asexual Naegleria contains and maintains homing introns.
The expression of the NaHEG is dependent on a functional NaGIR1 ribozyme, which defines the 5' end of the homing endonuclease mRNA by internal processing and modification of the excised Nae.S516 intron [7, 28, 29]. Primer extension analyses of both cellular RNA from Naegleria and in vitro transcribed intron RNA [7, 28] are consistent with the formation of a tiny lariat cap structure between nucleotide 1 and 3 of the messenger, as recently reported in the related DiGIR1 ribozyme . Thus, the NaGIR1 capping ribozyme represents a novel class of ribozymes possessing a new catalytic function, which is reflected in its unique RNA architecture [29, 31].
The complex and unique structural organization of the Naegleria twin-ribozyme intron makes it interesting to investigate the evolutionary origin of the different intron domains, as well as the inheritance pattern within the Naegleria genus. Here we report several new intron variants and have performed sequence and phylogenetic analyses providing new insight into fundamental questions such as intron structure, intron-host biology, and the origin and evolution of intron HEG and ribozyme domains. The Naegleria twin-ribozyme intron serves as an attractive model system in the characterization of evolutionary processes behind a recently gained, but vertically inherited, selfish genetic element.
Results and discussion
Widespread but sporadic distribution of Nae.S516 introns within the Naegleria genus
Structural features and sequence variability of intron domains
NaGIR1 is a group I-like ribozyme with an evolved biological role in intron NaHEG expression [29, 30], likely to generate a lariat cap-structure at the 5' end of the Naegleria homing endonuclease messenger . The three-dimensional architecture of NaGIR1 is related to that of bacterial tRNA group I intron ribozymes [18, 29, 33], but with a unique catalytic core organization that contains the novel pseudoknot segment P15 [7, 29, 31, 34]. As seen from Figure 2, most of the core nucleotides are highly conserved among the various Naegleria capping ribozymes. Variable regions are almost exclusively located in the terminal loops of P6 and P8, the internal loop junction J5/4, and sequences flanking NaGIR1 and NaHEG.
The splicing ribozyme of Nae.S516 intron is vertically inherited in Naegleria
The capping ribozyme NaGIR1 and its downstream NaHEG are evolutionary linked
A Naegleria S516 group I intron with only NaHEG or only NaGIR1 insertions has never been observed, suggesting a strong linkage between the domains. Both structural and functional data give further support to a close linkage between the NaGIR1 and NaHEG domains. Jabri and Cech  showed that the RNA structure essential for NaGIR1 catalysis includes nucleotide residues within the NaHEG coding region. Functional experiments in yeast conclude that expression of NaHEG, and subsequent endonuclease activity in yeast extracts, is completely dependent on a functional NaGIR1 ribozyme . Thus, the NaGIR1 and NaHEG domains have to be considered as one functional unit within the Nae.S516 intron.
Gain of a L5b GNRA tetraloop in NaGIR2 during Naegleria evolution
One of the best-studied tetraloop receptor interaction is the L5b-P6a tertiary structure in the Tetrahymena group I intron ribozyme . Here, the GAAA loop in L5b specifically binds to the 11-nt receptor motif CCUAAG-UAUGG within the helical stem of P6a by docking into the shallow groove. The L5b-P6a interaction in Tetrahymena is essential for an efficient folding of the P4–P6 domain, and subsequently the folding and activity of the splicing ribozyme.
The primary function of GNRA tetraloops is to participate in long-range RNA-RNA interactions by specific binding to a receptor motif. A variety of receptor motifs, ranging from 4 to 12 nt, have been recognized experimentally [41–43]. Figure 6B presents secondary structure diagrams of the various NaGIR2 P6a regions and their corresponding L5b loops. A prominent difference in the P6a structure is noted among introns possessing L5b GNRA tetraloops compared to those with penta- or hexaloops. Introns with GNRA loops contain a less tightly base-paired P6a stem with several proposed exposed residues (see Figure 6B) compared to the P5b penta- or hexaloop containing introns (compare N. clarki RU30 and N. carteri NG055). We speculate that the exposed residues in P6a could be involved in RNA-RNA interactions as GNRA receptors. However, these sequences do not fit any known consensus motifs, suggesting that new motifs are yet to be experimentally identified.
Evolutionary aspects on the structural organization of Naegleria twin-ribozyme group I introns have been reported previously . Whereas the NaGIR2 splicing ribozyme appears related to other eukaryote rDNA group IC1 intron , the NaGIR1 capping ribozyme has recently evolved from a bacterial tRNA group I introns . Here we present phylogenetic evidence of a vertical inheritance pattern of the Nae.S516 intron in Naegleria that includes each of the domains NaGIR1, NaGIR2, and NaHEG, and corroborates a previous study based on 5 intron sequences . Based on the reported distribution pattern and phylogeny, we propose the following vertical inheritance scenario for the Nae.S516 evolution. 1) A pre-organized twin-ribozyme group I intron was gained in the rDNA early in evolution of the Naegleria genus, but after the Cluster 6 branching (see Figure 1). 2) Once established, the Naegleria intron co-evolved along with its host rDNA by maintaining intron activities including intron splicing, endonuclease mRNA capping, and homing endonuclease DNA cleavage. 3) The intron was subsequently lost (see Figure 1) by sporadic deletions in most isolates (70 %). 4) Degradation of the NaHEG is initiated due to loss of biological function, and subsequent selection pressure (e.g. N. martinezi NG872), resulting in complete deletion of the NaHEG as well as its regulatory NaGIR1 capping ribozyme (e.g. N. byersi NG597) . 5) The remaining introns have to improve and adjust their functions by continuous sequence evolution in order to be maintained within rDNA. Here, a recent gain of a GNRA tetraloop receptor in the P4–P6 domain would facilitate folding of the splicing ribozyme (Figure 6).
What is the biological role of a functional NaHEG in Naegleria S516 introns? There are only two reported examples addressing the biological role of nuclear group I intron HEGs in experimental settings. In sexual matings between intron-containing and intron-lacking strains of either the myxomycetes Physarum polycephalum or Didymium iridis, group I introns were shown to be mobile due to the double-strand-break-repair pathway induced by intron-encoded homing endonucleases [26, 27]. In both cases the homing endonucleases were found to cleave the group I intron lacing alleles in a highly sequence specific manner, resulting in unidirectional transfers of introns into the intron-lacking strains. This process is dependent on a sexual reproduction of the host organism, which is apparently absent in Naegleria. However, the Naegleria intron endonucleases possess hallmarks linked to a function in intron homing. First, sequence comparisons show that the Naegleria enzymes belong to the same His-Cys homing endonuclease family as the known homing endonucleases I-Ppo I and I-Dir I encoded by the mobile Physarum and Didymium group I introns [10, 11, 25]. Second, the Naegleria endonucleases cleave only intron lacking alleles flanking the intron insertion site at the SSU rRNA gene [24, 25]. Finally, artificial expression of the Naegleria endonuclease and its intron in yeast generate intron homing intermediates consistent with a homing endonuclease function . Interestingly, Naegleria may occasionally perform sexual reproduction in nature since Pernin and co-workers [44, 45] reported evidence for genetic exchange in N. lovaniensis, including chromosomal recombination. Both haploid and diploid strains of the N. gruberi NEG isolate have been described based on both amoeba DNA content and UV-sensitivity [46, 47]. Perhaps the observed recombination-like feature of NaGIR1 in N. carteri NG055 (see Figure 5) is a result of rare sexual mating. This possibility remains to be experimentally explored.
Naegleria strains, DNA amplification, plasmid cloning, and DNA sequencing
The following Naegleria isolates were DNA sequenced at ITS-rDNA and Nae.S516 intron regions in this study: N. clarki RU30 (ITS-rDNA and Nae.S516); N. clarki RU42 (ITS-rDNA and Nae.S516); N. pringsheimi 1D (ITS-rDNA and Nae.S516); N. philippinensis RJTM (ITS-rDNA and Nae.S516); N. carteri NG055 (ITS-rDNA and Nae.S516); Naegleria sp. NG647 (ITS-rDNA and Nae.S516); Naegleria sp. NG358 (ITS-rDNA and Nae.S516); Naegleria sp. NG393 (ITS-rDNA and Nae.S516); Naegleria sp. NG498 (ITS-rDNA and Nae.S516); Naegleria sp. NG169 (ITS-rDNA);Naegleria sp. NG336 (ITS-rDNA); Naegleria sp. NG491 (ITS-rDNA); Naegleria sp. NG492 (ITS-rDNA). The strains without designation are under revision and will be proposed proper species names based on phylogenetic analyses of ITS1-5.8S-ITS2 sequences (De Jonckheere et al. in preparation). A complete list of all 70 Naegleria isolates included in this study is presented in Table 1. DNA samples of Naegleria strains were prepared as described previously , dissolved in water, and applied as template in 50 μl standard PCR reactions. Amplified product of interest were plasmid cloned into the pGEM®-T Easy Vector System I (Promega). Individual clones where DNA purified and sequenced with the ABI PRISM BigDyeTerminator Cycle Sequencing Ready Reaction Kit (Perkin-Elmer), running on an ABI Prism 377 system (Perkin-Elmer), or using the sequencing service from MWG Biotech . Two or more individual clones were sequenced from all introns and ITS-rDNA regions analysed. The following oligoprimers were used in Nae.S516 PCR amplifications and DNA sequencing analyses: OP 25 (5'-CTC GAA TTC GCT CTT GGA GCT GGA ATT A-3'), OP 26 (5'-ACG AAG CTT ATT TCT AAG CCT-3'), OP 28 (5'-CAG AGG AGT TTC TTA CCT ATC-3'), OP 131 (5'-AAA CGA ATT CTA TTG ATT AGT AGT-3'), OP 946 (5'-GAA TTG AAA AAG CTT GAT-3'), OP 1200 (5'-AAA CAA ATG CTA TTG ATC A-3'), OP 1201 (5'-GAA CGT CTA GAG ACT ACA CGG-3'), OP 1042 (5'-CGA TTT TCC ATG ATT TGG G-3'), OP 1043 (5'-ATA CCT CAA CAG AGG TCC-3'), OP 1044 (5'-GGA CGT CTA GAG ACT ACA CGG-3'), OP 1045 (5'-TGA TGC ACG TAC GAA TCG GAG C-3'), OP 276 (5'-GGT AAA CAA ATC CCT GTT-3'), OP 823 (5'-TAA CCA TTT TGT ATG GGA-3'). Heteroplasmic rDNA alleles (intron-containing/intron lacing) were not observed. The following oligoprimers were used in ITS-rDNA PCR amplifications and DNA sequencing analyses: OP 918 (5'-AAC CTG CGT AGG GAT CAT TT-3'), OP 919 (5'-TTT CCT CCC CTT ATT AAT AT-3').
Sequence alignment and phylogenetic analysis
Multiple alignment of sequences were performed by using Megalign (Version 5.06) included in the Lasergene package from DNASTAR, Inc , Bioedit (Version 22.214.171.124; ), manuel refinements. Phylogenetic analyses and non-synonymous to synonymous substitution rates  were conducted using MEGA version 2.1 , PAUP* (Version 4.0 Beta) , and MrBayes (version 3.1) [54, 55]. Trees were built with the methods of neighbor-joining (NJ) using different distance matrixes, maximum parsimony (MP) with the branch and bound search method, as well as Bayesian analyses (BAY) and maximum likelihood (ML) using different evolutionary models. The reliabilities of the tree topologies were evaluated by bootstrapping (NJ, MP, and ML), and posterior probability (BAY).
ITS and intron sequence analyses
Two different data sets of the internal transcribed rDNA spacer region (ITS-rDNA: ITS1-5.8S-ITS2) were used. In analysis with all the 70 Naegleria isolates, only 287 nucleotide positions could unambiguously be aligned due to high sequence variation in ITS2. However, when the analysis was restricted to the 14 intron-containing Naegleria isolates we extended the ITS-rDNA region to 415 nucleotide positions. Based on the multiple sequence alignment a NJ tree was constructed with the Kimura-2 evolutionary model of substitution (K2), with pair wise deletion of gaps and bootstrapped with 2000 replications with a cut-off value of 50%. Similarly, intron trees are constructed with NJ-K2 parameters. The robustness of the tree topologies were tested by the NJ-K2 parameter (first value), MP branch and bound search criteria (second value), and ML with the HKY+G model of substitution selected by Modeltest 3.7 , all from 1000 replicates. The last values where constructed by running 1000000 generations of Metropolis-coupled Markov chain Monte Carlo, and trees were sampled every 100 generations (average standard deviation of split frequencies below 0.01). A consensus tree was generated from the 75% last trees to find posterior probabilities (Burn-in value = 2500).
We thank Peik Haugen and Dag H. Coucheron for discussions. This work was supported by grants to SDJ from the Norwegian Research Council, The Norwegian Cancer Society, and The Aakre Foundation for Cancer Research.
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