Trichinella pseudospiralis vs. T. spiralis thymidylate synthase gene structure and T. pseudospiralis thymidylate synthase retrogene sequence
© Jagielska et al.; licensee BioMed Central Ltd. 2014
Received: 16 January 2014
Accepted: 27 March 2014
Published: 9 April 2014
Thymidylate synthase is a housekeeping gene, designated ancient due to its role in DNA synthesis and ubiquitous phyletic distribution. The genomic sequences were characterized coding for thymidylate synthase in two species of the genus Trichinella, an encapsulating T. spiralis and a non-encapsulating T. pseudospiralis.
Based on the sequence of parasitic nematode Trichinella spiralis thymidylate synthase cDNA, PCR techniques were employed.
Each of the respective gene structures encompassed 6 exons and 5 introns located in conserved sites. Comparison with the corresponding gene structures of other eukaryotic species revealed lack of common introns that would be shared among selected fungi, nematodes, mammals and plants. The two deduced amino acid sequences were 96% identical. In addition to the thymidylate synthase gene, the intron-less retrocopy, i.e. a processed pseudogene, with sequence identical to the T. spiralis gene coding region, was found to be present within the T. pseudospiralis genome. This pseudogene, instead of the gene, was confirmed by RT-PCR to be expressed in the parasite muscle larvae.
Intron load, as well as distribution of exon and intron phases in thymidylate synthase genes from various sources, point against the theory of gene assembly by the primordial exon shuffling and support the theory of evolutionary late intron insertion into spliceosomal genes. Thymidylate synthase pseudogene expressed in T. pseudospiralis muscle larvae is designated a retrogene.
Trichinella spiralis and Trichinella pseudospiralis are two parasitic nematode species colonizing mammalian striated muscles. Transmission of Trichinella spp. to the next host occurs by ingestion of meat contaminated with the parasite muscle larvae. In the intestine, after mating, adult female worms give birth to the newborn larvae which migrate to the muscles to become the muscle larvae. T. spiralis is an encapsulating species whose muscle larvae reside in discrete structures called nurse cells, separated from myofibers by collagen capsules[2, 3]. Instead, muscle larvae of T. pseudospiralis, migrate freely throughout the muscle tissue. Our previous studies documented high thymidylate synthase activity persisting in developmentally arrested muscle larvae of both species, as well as in T. spiralis adult forms[4, 5]. Thymidylate synthase (EC 220.127.116.11), catalyzing deoxyuridylate methylation to yield a DNA precursor, thymidylate, is the only cellular source of de novo synthesis of the latter. High enzyme activity is known to accompany proliferation, as well as to persist in certain growth-arrested systems where it is not associated with cell division cf.. Consequently, while the enzyme expressed in embryos developing in the T. spiralis adult uterus may be considered a marker of proliferation, its localization to excretory-secretory organ, i.e. stichosome, of T. spiralis adult forms, as well as to gonads and stichosome primordial cells of non-growing muscle larvae, appears to reflect the state of cell cycle arrest. Of note is that high thymidylate synthase activity found in T. spiralis and T. pseudospiralis muscle larvae does not appear to vary in connection with the difference in the intracellular niche occupied by two species.
Thymidylate synthase belongs to the proteins most highly conserved in evolution. It is encoded by a housekeeping gene, considered ancient by virtue of the enzyme’s role in DNA synthesis and its ubiquitous phylogenetic distribution. This implies that the gene was likely to play a role in the transition from an RNA to a DNA world and to exist in the common ancestor of modern organisms before kingdoms diverged. Analyses of evolutionary pathways of thymidylate synthase and other ancient genes may serve delineation of the origin of modern DNA sequences and the molecular basis of their evolutionary dynamics. Those genes are also used as models for studying spliceosomal intron distribution among phylogenetic lineages, as the issue of intron loss or gain during evolution of eukaryotic protein-coding genes remains unsettled. Since the discovery of introns, two concepts of their origin have been considered: (i) the introns-early theory or exon theory of genes assumes gene assembly by primordial exon shuffling in a common ancestor of bacteria and eukaryotes, and subsequent massive intron loss over evolution, and (ii) the introns-late theory or insertional theory assumes considerable intron gain during recent times. Of note is that the two theories are also viewed as unlinked rather than incompatible, since introns present in the primordial genes might have been removed and new ones rapidly inserted in different positions. It is also commonly agreed that the last eukaryotic common ancestor had a high intron density[14, 15].
T. spiralis thymidylate synthase cDNA has been cloned, allowing determination of the nucleotide and deduced amino acid sequences that turned out to be identical with the gene coding sequence inferred from the recently published draft version of the T. spiralis genome. Phylogenetic analysis of amino acid sequences corresponding to the enzymes of different specific origin showed T. spiralis thymidylate synthase to branch off before other nematode species and display higher overall similarity with mammalian than other nematode enzymes. Early divergence of the genus Trichinella in the evolution of the phylum Nematoda, as well as differences in the genome characteristics of Trichinella in relation to other nematode lineages were also documented by others[18, 19].
The goal of the present study was to characterize the T. pseudospiralis thymidylate synthase cDNA and genomic sequences, in order to perform analysis of introns distribution and compare it with that of the corresponding T. spiralis gene determined previously. Considering previously suggested evolutionary distinctness of the genus Trichinella in the evolution of the phylum Nematoda (see above), of interest was also to compare both Trichinella thymidylate synthase genes with the corresponding genes of various eukaryotic species.
IVTF: 5′ GGGTCTAGACTTGAATGTTATAGATATTTATACAATG 3′, IVTR: 5′ GGGAAGCTTCCATGAAATTTTATTTC 3′, RGENP: 5′ GAGAGCGGCCGCCAATGACAGAAACTGTTCACAAATTAG 3′, RGENK: 5′ AAAGCGGCCGCGATCACACAGCCATAGGCATTG 3′, RGEN5′1: 5′ AAAAGCGGCCGCACGTAATCATCCTGAGATG 3′, RGEN5′2: 5′ AAAAGCGGCCGCAGCTTTCAGAGAAGAATGTC 3′, RGEN3′1: 5′ GAGAGCGGCCGCCTATGGCTGTGTGATCAATTG 3′, RGEN3′2: 5′ GAGAGCGGCCGCCCAAATCACCTTCTTCATAATTG, SYNEX1: 5′ GGGGATCCATATGACAGAAACTGTTCACAAATTAG 3′, SYNEX2: 5′ AAAAGCTTACACAGCCATAGGCATTGATA 3′.
T. spiralis (ISS 569 155 569) and T. pseudospiralis muscle larvae were maintained and isolated, as previously described.
Nucleic acids isolation
Total RNA was isolated from T. pseudospiralis muscle larvae using TRIZOL reagent (Life Technologies) and genomic DNA from muscle larvae of both species was extracted using Wizard Genomic DNA Purification Kit (Promega), with the manufacturer’s protocols applied in each case.
This was performed on total RNA prepared from T. pseudospiralis muscle larvae with SYNEX2 primer, in two rounds of 1 h incubation at 42°C, using MMLV reverse transcriptase (Promega).
Polymerase Chain Reaction (PCR)
In order to amplify T. pseudospiralis thymidylate synthase ds cDNA, as well as T. spiralis and T. pseudospiralis thymidylate synthase genes, standard PCR on ss cDNA or genomic DNA was performed, using Taq DNA polymerase (Promega), as recommended by the enzyme manufacturer. The following primer combinations and cycling conditions were applied: (i) in the case of T. pseudospiralis thymidylate synthase cDNA, SYNEX1 and SYNEX2 primers were used, with initial 3 min at 95°C and the hot start steps, followed by 35 cycles of 30 sec at 95°C, 30 sec at 57°C and 1 min at 72°C, (ii) in the case of T. spiralis gene, RGENP and RGENK primers were used, with initial 2 min at 95°C and the hot start steps, followed by 3 cycles of 15 sec at 95°C, 15 sec at 60°C and 2 min at 72°C, and subsequent 29 cycles of 15 sec at 95°C, 1 min at 68°C and 2 min at 72°C, (iii) in the case of T. pseudospiralis gene, IVTF and IVTR primers were used, with cycling conditions as in (ii), but for the annealing step being performed at 40°C in the initial 3 cycles and at 58°C in the subsequent 29 cycles. For each amplification a negative control was included. Amplification products were analyzed by electrophoresis in Tris-acetate-EDTA buffered 0.8% agarose gels.
In order to determine T. spiralis thymidylate synthase gene 5′ and 3′ flanking regions, inverse PCR was used. Genomic DNA extracted from T. spiralis muscle larvae was digested for 1 h at 37°C with Eco RI (Life Technologies), then ligated overnight at 16°C using phage T4 DNA ligase (Promega). A 1/100 dilution of the ligation mixture served as a template for PCR with Taq DNA polymerase (Promega), applied as recommended by the enzyme manufacturer. In the case of the 5′ region amplification, RGEN5′1/RGEN5′2 primers and the following cycling steps were applied: (i) 2 min at 95°C, followed by the hot start step, (ii) 3 cycles of 15 sec at 95°C, 15 sec at 50°C and 2 min at 72°C, (iii) 29 cycles of 15 sec at 95°C, 1 min at 68°C and 2 min at 72°C. In the case of the 3′ region amplification, RGEN3′1/RGEN3′2 primers were used and cycling conditions as described above, but for the annealing step during the initial 3 cycles performed at 60.5°C. For each amplification a negative control was included. Amplification products were analyzed by electrophoresis in Tris-acetate-EDTA buffered 0.8% agarose gels.
Cloning and sequencing
cDNA corresponding to T. pseudospiralis thymidylate synthase coding sequence was cloned into Bam HI and Hind III sites of pBluescript SK (+) phagemid (Agilent Technologies) propagated in E. coli DH5αF’ strain. DNA amplicons corresponding to T. spiralis thymidylate synthase gene and gene flanking regions were cloned into Not I site of the same vector. DNA corresponding to T. pseudospiralis thymidylate synthase gene was cloned into Xba I and Hind III sites also into pBluescript SK (+) vector. Sequencing of cloned T. spiralis genomic DNA fragments was performed using Sequenase Version 2.0 DNA Sequencing kit (Affymetrix) and sequencing of T. pseudospiralis thymidylate synthase cDNA and genomic DNA was done by DNA Sequencing and Oligonucleotide Synthesis core facility at the Institute of Biochemistry and Biophysics (Warsaw, Poland).
T. spiralis and T. pseudospiralis thymidylate synthase gene sequences were deposited in the GenBank and are available under accessions [GenBank:AF406808] and [GenBank:KF186231], respectively.
Protein secondary structure analysis
Crystal structures of thymidylate synthase protein monomers complexed with enzyme substrate deoxyuridylate, dUMP, were obtained from Protein Data Bank (http://www.rcsb.org), under the accession codes [PDB:4G9U] for T. spiralis, [PDB:4E5O] for M. musculus and [PDB:3HB8] for H. sapiens R163K mutated enzyme. Secondary structure element assignment for subunit A of each model, was determined by PDB managing system. Graphical structure representation was obtained using VMD 1.8.7 software, implemented with “vmd_use_pdb_ss” script enabling reading of secondary structure elements from PDB files athttp://www.ks.uiuc.edu/Research/vmd/.
Ethical approval was granted by the First Warsaw Local Ethics Committee for Animal Experimentation at the Nencki Institute.
T. spiralis and T. pseudospiralis thymidylate synthase genes share the same structure and show 11 substitutions at the deduced amino acid sequence level
Two conserved introns and one homologous are present in Trichinella and mammalian thymidylate synthase genes
Lack of correlation among location of conserved and homologous introns and the protein secondary structure entities
Thymidylate synthase retrogene is expressed instead of the gene in T. pseudospiralis muscle larvae
In the present study T. spiralis and T. pseudospiralis thymidylate synthase genes were found to share exon-intron structure. Comparison with the gene structures of other eukaryotes, including animal, fungal and plant species, revealed lack of a common intron. However, a conserved intron is found in the vicinity of the region encoding the enzyme active center in nematode (with the exception of C. elegans), fungal and mammalian genes. In T. pseudospiralis genomic DNA, apart from the gene, thymidylate synthase retrogene was identified, of the sequence identical to T. spiralis thymidylate synthase ORF. This retrogene was found to be expressed, instead of the gene, in the parasite muscle larvae.
Comparison of intron distribution among Trichinella and other eukaryotic thymidylate synthase genes shows lack of a conserved or even slid intron that would be shared by the organisms included in the analysis, representing animal, plant and fungal crown groups. The intron sliding, termed also intron slippage or drifting, indicates either preexisting intron relocation to a nearby position or its replacement by a new intron at a nearby position. This phenomenon is proposed to be associated with alternative splicing, proceeding by reverse splicing mechanism, i.e. insertion of a spliced-out intron into gene transcript, followed by reverse transcription and homologous recombination. Intron slippage is considered to reflect intron gain events rather than indicate location of an ancient intron, i.e. being remnant from the eukaryotic common ancestor[11, 15, 25]. Among the species studied, the most highly conserved is the intron corresponding to Trichinella intron 3, present also in other nematodes (with the exception of C. elegans), fungal and mammalian genes. As absent from plant genes, it cannot be considered ancient but rather constituting a relic from the common ancestor of fungi and animal evolutionary lineages. Commonality of intron load within animal lineage only is further evident, based on the presence in all nematodes and mammals of an intron homologous to Trichinella intron 2 and conservation of two other introns, one corresponding to Trichinella intron 5 and present in all other species, and the other, absent from Trichinella and C. elegans genes but present in B. malayi, L. loa and mammalian genes as intron 5. An overall lower intron number in C. elegans than in other nematode thymidylate synthase genes (2 vs. 5/6), remains in agreement with a notion that C. elegans phylogeny, unlike with other nematodes, is characterized by extensive intron loss and restricted intron gain[14, 27]. Thus excluding C. elegans, which does not seem to be a representative model for spliceosomal intron studies, it can be inferred that thymidylate synthase genes of all animal species included in the analysis represent a similar intron location pattern. Also plant thymidylate synthase genes show apparently kingdom-specific intron distribution. Therefore, it can be hypothesized that locations of introns in thymidylate synthase genes represent new insertional events, occurring independently in animal and plant kingdoms, with fungi sharing possibly a common thymidylate synthase gene origin with animals. The aforementioned conservation of Trichinella intron 3 in nematodes (with the exception of C. elegans), fungal and mammalian genes may be associated with the downstream proximity of the enzyme active center-coding region. Also in plant A. thaliana and D. carota genes, there is an intron located proximally, but downstream from that region highly conserved among various species. The distance (44 nt) between locations of fungal/animal and plant introns, on the opposite sites of the active center coding-sequence, is too long to result from intron sliding (up to 15 nt are allowed for a slide), and rather too short for coding a functional peptide, considering an assumed minimum evolutionary exon length of 45 base pairs. Therefore, it is not likely that both introns were present in the last common eukaryotic ancestor. Their locations seem to point rather to late insertional events, occurring in the vicinity of 21 base pairs-long region coding the enzyme active center, which remained uninterrupted due to selection pressure. Additionally, only in Trichinella and plant genes the active center-containing exon is symmetric, unlike in other nematode, fungal and mammalian genes, where it is asymmetric. Exon symmetry is claimed to be required for maintenance of the reading frame in the case of exon shuffling. Thus in the majority of thymidylate synthase genes analyzed, the active center-coding exon does not conform to this criterion. According to the exon shuffling theory, not only symmetric exons but also phase 0 introns are believed to be favored. Such intron positions are not predominant in Trichinella, C. elegans, fungal and mammalian genes, except in that of B. Taurus, but in B. malayi, L. leo, B. taurus and plant genes phase 0 introns prevail. However, a high number of phase 0 introns occurs in intron-rich regions and appears correlated with higher overall intron load. Also, in animal and plant thymidylate synthase genes, short exons, associated with phase 0 intron-rich regions, tend to be symmetric. Thus, based on the distribution of intron and exon phases within thymidylate synthase genes, and in light of the lack of an ancient intron, the rules apparently governing the evolutionary exon shuffling seem to apply to introns late insertional events. A positive correlation between high intron density and species developmental complexity has been established and an overall high intron complement, evident for mammalian and plant thymidylate synthase genes, conforms to that rule. However, the intron load, similarly high in nematodes, with the exception of C. elegans, and mammalian genes, casts doubt on this statement. Interestingly, while the two Trichinella species display thymidylate synthase gene structure similar to other nematodes (with the exception of C. elegans), the enzyme sequence similarity analysis implicates early evolutionary divergence of the genus Trichinella from the phylum Nematoda. This observation indicates that sequence and gene structure evolution may not be closely linked phenomena. In summary, analysis of gene structures of various thymidylate synthase genes provides support for the introns-late theory, pointing to a recent acquisition of the introns in the course of eukaryotic spliceosomal gene evolution. This conclusion is also supported by an apparent lack of correlation between conserved or homologous intron locations and the positions of the edge amino acid residues of thymidylate synthase protein secondary structure entities. In respect to the latter, intron insertion seems to proceed rather as a stochastic event. Analogous conclusions were inferred also from the intron load pattern in other ancient housekeeping genes, including actin, glyceraldehyde-3-phosphate dehydrogenase, triose-phosphate isomerase[12, 26, 30] and tubulin.
The present paper reports on thymidylate synthase retrogene identified in T. pseudospiralis muscle larvae. Pseudogenes are defective copies of functional genes that accumulated in the genomes of many modern organisms, especially mammals. They tended to be considered as molecular relics, accumulating numerous mutations due to release from selection pressure. Pseudogenes may arise either by duplication of genomic DNA or by retroposition, i.e. reverse transcription primed at poly A tails of an intron-less transcript, followed by insertion of a transposable element into another genomic location. Pseudogenes arising by the second mechanism, called processed pseudogenes or retropseudogenes, display a low survival rate[33, 34]. Only 10% of protein coding genes of the human genome have been estimated to have at least one processed pseudogene. Processed pseudogenes of highly expressed housekeeping genes, including those coding for ribosomal proteins, keratin, glyceraldehyde-3-phosphate dehydrogenase and actin, account for the majority of the total number of ~8000 human processed pseudogenes. Mouse genome was estimated to contain ~5000 processed pseudogenes. Thymidylate synthase processed pseudogene incapable of encoding functional enzyme was reported for a mouse fibroblast cell line. Among human and mouse genes, those having multiple copies of processed pseudogenes are predominantly housekeeping genes highly expressed in the germ lines or embryonic cells. Although the vast majority of pseudogenes remain functionally inactive, the evidence is accumulating on the abundance of functional processed pseudogenes, called retrogenes, especially in mammals and insects. In particular, 20% of human genome processed pseudogenes are believed to be expressed.
To our best knowledge, it is not only the first retrogene of a housekeeping gene, but also the first pseudogene in general, described for genus Trichinella. C. elegans genome was estimated to contain ~2000 pseudogenes. However, this number may not be meaningful for Trichinella whose thymidylate synthase protein sequence, as well as gene structure (vide supra), are apparently divergent from those of C. elegans. Understanding the mode of thymidylate synthase retrogene insertion into T. pseudospiralis genome and its transcriptional regulation require further investigation. However, as the muscle larvae of this species move freely within the muscle tissue, in contrast to T. spiralis muscle larvae being confined to a capsule, a possibility appears that the retrogene expression accounts for the life style adaptation (cf.). In the absence of the capsule, overall transcription regulation may require hypertranscription of thymidylate synthase gene, in order to maintain high enzyme activity, and consequently high levels of its product. This type of regulation is known to take place for retrogenes of broadly expressed housekeeping genes, located to the autosomal chromosomes during and after male meiosis. This reasoning corresponds with a notion that the energy demands of transcription and splicing may favor selection for compactness in the case of highly expressed and/or rapidly regulated genes[40, 41], and thymidylate synthase was identified as highly expressed in Trichinella muscle larvae.
The mechanisms of both phenomena discussed in this paper in regard to Trichinella thymidylate synthase genomic sequences, i.e. relatively high intron load and retroposition, are underlain by reverse transcriptase activity. Thus, high levels of reverse transcription seems to shape genome evolution of this lineage. Analysis of other processed pseudogenes and their flanking sequences is required, in order to identify a putative general mode of retroposition specific for this genus. In mammals, involvement of the L1 LINE retrotransposon has been established[42, 43].
Intron load and distribution within thymidylate synthase genes of various species display kingdom-specific patterns with no conserved or homologous introns shared among fungi, animals and plant genes. Locations of conserved and homologous introns within animal genes do not show correlation with the enzyme protein structural motifs borders. This allows us to conclude that intron insertion into thymidylate synthase genes depicts evolutionary late gain events, being rather stochastic in regard to the enzyme structure. Identification of thymidylate synthase retrogene in T. pseudospiralis muscle larvae points to a possibility that compactness of genomic sequence coding for this enzyme may reflect larval adaptation to existence within the muscle tissue in a non-encapsulated form.
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