Abstract
The complete small subunit rRNA (SSU rRNA) gene sequences of five microsporidia including Nosema heliothidis, and four novel microsporidia isolated from Pieris rapae, Phyllobrotica armta, Hemerophila atrilineata, and Bombyx mori, respectively, were obtained by PCR amplification, cloning, and sequencing. Two phylogenetic trees based on SSU rRNA sequences had been constructed by using Neighbor-Joining of Phylip software and UPGMA of MEGA4.0 software. The taxonomic status of four novel microsporidia was determined by analysis of phylogenetic relationship, length, G+C content, identity, and divergence of the SSU rRNA sequences. The results showed that the microsporidia isolated from Pieris rapae, Phyllobrotica armta, and Hemerophila atrilineata have close phylogenetic relationship with the Nosema, while another microsporidium isolated from Bombyx mori is closely related to the Endoreticulatus. So, we temporarily classify three novel species of microsporidia to genus Nosema, as Nosema sp. PR, Nosema sp. PA, Nosema sp. HA. Another is temporarily classified into genus Endoreticulatus, as Endoreticulatus sp. Zhenjiang. The result indicated as well that it is feasible and valuable to elucidate phylogenetic relationships and taxonomic status of microsporidian species by analyzing information from SSU rRNA sequences of microsporidia.
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Introduction
Microsporidia are obligate intracellular parasites that infect a broad range of invertebrates and humans, they were recognized as a causative agent for many hosts including insects, fishes, rodents, and primates. In 1857, the first microsporidian species—N. bombycis was described by Nageli [1]. Until now, more than 1,200 microsporidia species belonging to ~150 genera have been reported [2, 3].
The adaptation of microsporidia to a parasitic lifestyle precipitates a number of profound changes which lead to a seemingly paradoxical mixture of characteristics [4]: on one hand, parasites may evolve extremely complex and sophisticated mechanisms to invade their host and evade its defenses, while on the other hand, they may also appear more “simple” by dispensing with characteristics they no longer need as they increasingly depend on host metabolism for nutrients and energy. Although microsporidia were considered to be eukaryotes, they lack some typical eukaryotic characteristics including mitochondria, peroxisomes, classical stacked Golgi apparatus, and 80S ribosomes. The microsporidia contain 70S ribosomes, ribosomal subunits (30S and 50S), and rRNAs (16S and 23S) with prokaryotic size, and they have no separate 5.8S rRNA. They also lack flagella, pilus and 9 + 2 microtubular structure [5]. Up to now, the genome size has been determined for numerous microsporidian species, and they range from 19.5 Mbp in Glugea atherinae to just 2.3 Mbp in Encephalitozoon intestinalis [6].
For a long time, microsporidia were generally regarded as primitively simple eukaryotes and classified as an early branch from prokaryotes to eukaryotes [7], and they were universally thought to be classified as Protista, Protozoa, Microspora in five kingdom system. This conclusion was supported by early molecular phylogenic evidence, but more and more recent trees constructed from the conserved protein genes provide further evidence for the argument that microsporidia should properly be classified as fungi. Thus, in 1998 Cavalier-Smith [8] classified the microsporidia into the kingdom Fungi. And in 2002 NCBI concluded a description of microsporidia as Cellular Organisms, Eukaryote, Fungi/Metazoa group, Fungi, Microsporidia. For the Society of Classification has not approved the description of microsporidia, there is not universal agreement on the evolution and classification of microsporidia.
There has been increasing interest in studying large subunit rRNA (LSU rRNA), SSU rRNA, internal transcribed spacers (ITS), translation elongation factors (EF), heat shock protein (HSP), and beta-tubulin of microsporidium at the molecular level, which provided important evidence for the phylogenic analysis of microsporidia. As a conserved gene, the SSU rRNA universally existed in eukaryotic and prokaryotic organisms, varied with constant rate, and can be used as the molecular clock of evolution. For its relatively highly variable regions provides important information for the relationship among species, the SSU rRNA gene also can be used as the biological identification label. And the molecular characterization of different microsporidia has widely relied on sequencing and analyzing of SSU rRNA genes [9], which also can be used as a molecular marker for estimating relationships among microsporidia [10]. Therefore, the SSU rRNA gene plays an important role in the phylogenetic research.
Traditional taxonomic studies and species classification of the microsporidia are mainly based on biological characters such as morphology and development of spore, microsporidium–host relationships, life cycle, parasitic site as well as transmission way. However, for some basic biological problems, taxonomic determinations based on these criteria alone can sometimes be problematic. With the development of molecular biotechnology, many Nosema species were proven to be distant from N. bombycis in molecular phylogeny, and divided into other genus [11, 12]. So, phylogenetic analysis of SSU rRNA gene is an important tool for the classification of microsporidian species, which helps to construct more valuable classification system for the microsporidia.
In this paper, we cloned the complete SSU rRNA sequences of five microsporidia, compared them with the corresponding sequences of other 94 microsporidia for which data were available, and have preliminarily determined the taxonomic status of the four novel microsporidian isolates by constructing and analyzing of phylogenetic tree, and comparing the length and G+C content of SSU rRNA sequences.
Materials and Methods
The Origin of Microsporidia
The five species of microsporidia studied in this paper were isolated from diverse geographic regions and different hosts. The names of isolates, host insects, geographic regions, and accession number for them are described in Table 1. The five microsporidian species were isolated by Professor Shen ZhongYuan in 2006–2007 and kept in Pathology Department of Sericulture Research Institute of Chinese Academy of Agricultural Sciences. Additionally, the four novel microsporidian isolates which were separately isolated from Pieris rapae, Phyllobrotica armta, Hemerophila atrilineata, and Bombyx mori were unclassified.
Preparation of Genomic DNA of Microsporidia
To prepare the genomic DNA of microsporidia, 400 μl suspension of purified spores (1010 spores/ml) was mixed with 40 μl KOH (2 mol/l) in a 1.5 ml Eppendorf tube and incubated at 27°C for 1 h, TEK buffer (1 mmol/l Tris–HCl, 10 mmol/l EDTA, 0.17 mol/l KCl, pH 8.0) was added and continued incubating at 27°C for 1 h. Adjusted pH to 8.0 with 1 mol/l HCl, added 10% SDS in order to attain 0.5% in the mixture and kept it in ice-bath for 15 min. 20 mg/ml proteinase K (TaKaRa Biotechnology Co. LTD) was added in order to attain 200 μg/ml in the mixture and incubated at 50°C for 4 h. Subsequently, isovolumetric tris–phenol extraction was performed twice, and washed with chloroform: isoamyl alcohol (24:1 v/v). 10% NaOAC was added to the recovered aqueous phase after centrifuging (10,000 r/min, 5 min), and then the DNA was precipitated by 2.5 times volume of cold ethanol at −20°C for 40 min before centrifuging (12,000 r/min, 10 min). In addition, the precipitated DNA was rinsed twice with 500 μl cold 70% ethanol before drying at 37°C for 5–10 min. Then, the extracted DNA was stored at −20°C after dissolution in 50 μl TE buffer at 65°C for 10 min.
Amplification, Cloning and Sequencing of SSU rRNA Gene
To amplify the SSU rRNA genes, primer sets were designed as Huang et al. [13] described, forward primer: 5′-CACCAGGTTGATTCTGCC-3′; reverse primer: 5′-TTATGATCCTGCTAATGGTTC-3′. The amplification was performed with following condition: after initial denaturation of DNA at 94°C for 8 min, 28 cycles were run—94°C for 1 min, 43°C for 1 min 40 s, and 72°C for 1 min 40 s—with a 10 min 72°C extension.
The PCR amplified products were cloned into pGEM-T vector and then sequenced. All the sequences were submitted to GenBank, and the accession number were shown in Table 1.
Construction of Phylogenetic Tree and Analysis of SSU rRNA Gene Sequences
The SSU rRNA gene sequences were aligned using the “ClustalX 1.83” program. Phylogenetic trees based on the resultant alignments were, respectively, constructed using the Neighbor-Joining algorithm (NJ) of Phylip software with Kimura-2 parameter and UPGMA algorithm of MEGA 4.0 software with Maximum Composite Likelihood, and one thousand replications were generated to test the robustness of the tree. Subsequently, the length and GC content of the complete SSU rRNA sequences of 22 microsporidia were analyzed with the Editseq program of DNAStar software, and the identity and divergence of the sequences of 26 microsporidia were analyzed with the MegAlign program of DNAStar software.
Results
Analysis of Phylogenetic Tree of Microsporidia
The complete SSU rRNA gene sequences of the five microsporidia were aligned with the homologs from other 94 species of various microsporidian genera, such as Nosema, Amblyospora, Endoreticulatus, Vairimorpha, Pleistophora, Encephalitozoon, and Glugea, available in public databases (Table 2). And Beauveria bassiana was used as an out-group (Table 2).
Both the two phylogenetic trees of SSU rRNA genes (Figs. 1, 2) constructed by Neighbor-Joining and UPGMA revealed that, besides Nosema microsporidia, the microsporidia of other genera such as Amblyospora, Endoreticulatus, Vairimorpha, Pleistophora, Encephalitozoon, Glugea clustered in each clades, which is consistent to early published classifications of microsporidia. Consequently, the phylogenetic tree we constructed is valuable.
Three novel microsporidian isolates isolated from Pieris rapae, Phyllobrotica armta, and Hemerophila atrilineata separately, were grouped in the Nosema clade, indicating that this three novel microsporidian isolates belong to the genus Nosema. Therefore, we temporarily name them as Nosema sp. PA, Nosema sp. PR and Nosema sp. HA, respectively. Another novel microsporidium isolated from Bombyx mori got clustered with the Endoreticulatus clade. So, we propose to classify it into the genus Endoreticulatus, with temporary designation Endoreticulatus sp. Zhenjiang. These two phylogenetic trees based on the SSU rRNA sequences suggest that Nosema sp. PR is closely related to N. bombycis, while Nosema sp. PA, Nosema sp. PR, and Nosema sp. HA have close relationship with each other.
Further analysis of two SSU rRNA phylogenetic trees manifests that Vairimorpha lymantriae, Vairimopha necatrix, Oligosporidium occidentalis, and 20 Nosema species form a large cluster which can be classified into two parts. Part one is composed of four Nosema species cloned in this experiment and other nine Nosema species, while part two is composed of Vairimorpha lymantriae, Vairimopha necatrix, Oligosporidium occidentalis, and seven Nosema species. Consequently, we divide 20 Nosema species into two groups for further analysis. Group I comprise 13 Nosema species and group II comprise other seven Nosema species.
Analysis of Length and GC Content of SSU rRNA Gene of Microsporidia
We analyzed the complete SSU rRNA sequences of 22 microsporidia and found that the lengths of complete SSU rRNA gene sequences of Nosema species ranged from 1231 to 1393 bp, and that of Endoreticulatus species ranged from 1252 to 1254 bp (Table 3). For the four Nosema species cloned in this experiment, the lengths of complete SSU rRNA gene sequences of Nosema heliothidis, Nosema sp. PA, Nosema sp. PR, and Nosema sp. HA are 1232 and 1233 bp, respectively, and that of Endoreticulatus sp. Zhenjiang is 1254 bp. These results provide further molecular information for the four novel microsporidian species in our study.
It is found as well that the GC content of the Nosema sp. PR, Nosema sp. PA, N. heliothidis, and Nosema sp. HA varied from 33.98 to 34.25%, and the GC content of Endoreticulatus sp. Zhenjiang is 50.96% (Table 3). The GC content of the SSU rRNA gene in Nosema species ranged from 33.93 to 38.73%, and that of Endoreticulatus species ranged from 50.96 to 51.12% (Table 3), which is significantly higher than that Nosema species. Based on the GC content, the nucleotide acid length and phylogenetic analysis for the SSU rRNA gene, we suggested that the four novel microsporidian species, Nosema sp. PA, Nosema sp. PR and Nosema sp. HA, belong to genus Nosema, while Endoreticulatus sp. Zhenjiang belongs to the genus Endoreticulatus.
Additionally, we analyzed the lengths and GC content of the two Nosema groups. Nosema group I, which contains 1231–1237 bp with GC content of 33.93–34.93%, is shorter and lower than that of Nosema group II, which contains 1242–1393 bp with GC content of 35.75–38.73%.
Analysis of Identity and Divergence of the SSU rRNA Sequences of Microsporidia
The identities and divergence of SSU rRNA gene among 20 Nosema species varied from 83 to 100%, and 0–0.193, while that among six Endoreticulatus species varied from 98.3 to 99.7%, and 0.003–0.017, respectively. The identities and divergence of SSU rRNA gene between Nosema and six Endoreticulatus varied from 66.0 to 71.0%, and 0.369–0.457. Consequently, the genus Endoreticulatus is markedly different from the genus Nosema, and the relationship among Endoreticulatus species is closer than that of Nosema species. Additionally, the identities and divergence of SSU rRNA gene among Nosema species in group I varied from 96.3 to 100% and 0–0.038, while that among Nosema species in group II varied from 94.8 to 99.8%, and 0.002–0.054, indicating that there was higher degree of similarity of SSU rRNA gene sequence among the group I species than that among group II species in Nosema.
It is clear that the SSU rRNA genes of microsporidia have high identities and less divergence among species in same genus and have lower identities and higher divergence between different genera. Consequently, it is limited to measure the close phylogenetic relationships between various species in the genus based on the identities and divergence of the SSU rRNA gene, while the identities and divergence of the SSU rRNA gene are more suitable for the analysis of phylogenetic relationships between different genera and the determination of taxonomical status on the genus level.
Discussion
Ribosomal gene sequences of microsporidia are frequently used for diagnostic tests, phylogenetic studies, epidemiological investigations of the host range, and the geographic distribution and pathogenetic studies of fish pathogens [14]. Baker et al. [15] analyzed a short fragment of LSU rRNA gene of eight Nosema species, and found the N. bombycis shared high homologies with other Nosema species isolated from Lepidoptera insects, low homologies with Vairimorpha species, and very low homologies with Amblyospora species. Slamovits [11] proposed transferring N. locustae to the genus Antonospora, as Antonospora locustae n. comb. by constructing a phylogenetic tree based on the SSU rRNA gene and with the ultrastructure of mature N. locustae spores.
In this study, three novel microsporidia, isolated from Pieris rapae, Phyllobrotica armta, and Hemerophila atrilineata, were classified into genus Nosema, as Nosema sp. PR, Nosema sp. PA, Nosema sp. HA, respectively. And the novel microsporidium isolated from the silkworm in countryside in Zhenjiang, Jiangsu Province, China, was temporarily classified into genus Endoreticulatus, as Endoreticulatus sp. Zhenjiang. The first report of Endoreticulatus species which infected Bombyx mori was in Mianyang Silkworm Eggs Production Farm and Santai Silkworm Eggs Production Farm in Sichuan Province, China. Subsequently, the Endoreticulatus species were successively found in silkworm eggs production in China. For their rather small size, they were usually called “mini-spore”. In 1995, Wan Yongji classified a “mini-spore” isolated from the silkworm in Sichuan Province into genus Endoreticulatus by studying its morphological character, ultrastructure, and life cycle [16].
Further analysis of two SSU rRNA phylogenetic trees manifests that the 20 Nosema species can be divided into two groups. Group I comprise 13 Nosema species, while group II comprise other seven Nosema species. The comparison of the SSU rRNA genes revealed that the phylogenetic relationship among 13 Nosema species in group I is closer than that of seven Nosema species in group II. For the significant differences between Nosema group I and Nosema group II, the phylogenetic trees based on SSU rRNA gene also provide further evidence for the argument that the genus Nosema should properly be separated into two groups [10, 15, 17, 18]. And SSU rRNA gene can be used to explore the differences among Nosema species, study the microsporidian phylogenetic relationship, and provide more evidence for the classification of microsporidia.
The complete SSU rRNA gene sequence of the N. heliothidis had 100% identity with the previously reported homologous sequences of Nosema sp. PX1 (isolated from Plutella xylostella) and N. spodopterae (isolated from Spodoptera litura). But the other ribosomal RNA sequences of these three microsporidian species, such as LSU, ITS, IGS and 5S sequences, did not have such high identity (data not shown). So the SSU rRNA sequence may not be a suitable marker for identifying closely related microsporidia [18, 19]. In 2007, Ku [20] constructed phylogenetic trees of the LSU rRNA, SSU rRNA, alpha-tubulin, beta-tubulin, and RPB1 (DNA dependent RNA polymerase II largest subunit) sequences of Nosema sp. PX1, Nosema sp. PX2, N. spodopterae and N. bombycis with four kinds of algorithm, found that PX2 was a novel species of microsporidia, and PX1 was closer to N. bombycis and probably a sub-species of N. bombycis. Recently, the ITS gene of ribosome was frequently used for the identification of parasite species and strain, and the molecular diagnosis for its inter-specific divergence. Consequently, SSU rRNA gene is suitable for the phylogenetic relationship analysis between genera and can be used as the taxonomical status at the genus level, while ITS gene of ribosome is better than SSU rRNA gene in the analysis of phylogenetic relationship between different species in the same genus and can be used for the classification of microsporidium at the species level. Therefore, phylogenetic analysis based on the combination of SSU rRNA gene and ITS gene of ribosome will provide more molecular evidence for the classification and evolution study of microsporidia.
Microsporidia are obligate intracellular parasites. They are different from independent organisms, and they live in the environments controlled by the genomes of the hosts with coevolution [21]. Since many microsporidia are considered to have a wide host range [22], the cross infection of microsporidia often occurs between hosts, sometimes, microsporidia can infect new hosts through the transition of intermediate host, generate and evolve in this procedure. So, the gene sequences of microsporidia have some variations through the long evolutionary process. Phylogenetic trees constructed from the SSU rRNA sequences of microsporidia indicated that microsporidia formed complicated phylogenetic relationship with each other in the evolutionary process. Therefore, the research of phylogenetic relationship based on microsporidian SSU rRNA gene and the epidemiological investigation of the host range have practical value on the prevention of microsporidiosis.
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We thanked all partners and lab members for kindly help and criticism, especially for Professor XingJia Shen and ShunMing Tang.
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Open Access This is an open access article distributed under the terms of the Creative Commons Attribution Noncommercial License (https://creativecommons.org/licenses/by-nc/2.0), which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.
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Dong, S., Shen, Z., Xu, L. et al. Sequence and Phylogenetic Analysis of SSU rRNA Gene of Five Microsporidia. Curr Microbiol 60, 30–37 (2010). https://doi.org/10.1007/s00284-009-9495-7
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DOI: https://doi.org/10.1007/s00284-009-9495-7