Analyses of the Ribosomal DNA Region in Nosema bombycis NIS 001

Abstract

Ribosomal DNA (rDNA) containing small subunit (SSU) rDNA and both flanking regions in the entomopathogenic microsporidian Nosema bombycis NIS 001 was amplified from genomic DNA with a primer set based on the sequence of an inverse polymerase chain reaction (PCR)-derived fragment. In this fragment, SSU rDNA was divided by a 618-bp insert at nt 599, and 5S rDNA was located downstream of the SSU rDNA, fragmented by 284-bp intergenic spacer. In addition, the 48-bp 3'-end of large subunit (LSU) rDNA was located 118 bp upstream of the fragmented SSU rDNA. In the amplicon, the region upstream of the LSU rDNA was a homologue of the C-terminal CHARLIE8 transposon-like element of human GTF2IRD2. In this organism, another fragmented SSU rDNA, which was divided by a 231-bp insert at nt 50, was also detected. Both the intact (insertless) and fragmented SSU rDNAs clustered with LSU rDNA and 5S rDNA and the intergenic sequences between SSU rDNA and 5S rDNA were divergent in an organism. Reverse transcription (RT)-PCR assay indicated that not only the intact SSU rDNA but also the fragmened SSU rDNA were transcribed in N. bombycis.

Multiple rDNA units distributed on all chromosomes of Nosema bombycis

“…We also found fragmented SSU rDNAs, which were interrupted by insertion sequences ( Fig. 1B), a result that has been previously documented (Iiyama et al, 2004).…”

“…This arrangement is the reverse to that of Nosema ceranae and eukaryotes in general (Huang et al, 2008). Also the SSU rRNA gene was found to contain insertion sequences (Iiyama et al, 2004), which indicates that rRNA genes can be interrupted by some repeat elements.…”

Multiple losses of sex within a single genus of Microsporidia

“…The Nosema / Vairimorpha rRNA repeat unit occurs as multiple copies [15,31] and there is evidence for intragenomic variation in the sequence of the rRNA genes, indicating relatively low levels of concerted evolution [15,41]. It is therefore possible that rRNA repeat units with both gene orders coexisted in the Nosema / Vairimorpha genome for some time.…”

“…The unusual ribosomal subunit gene order demonstrated by N. bombycis also occurs in N. spodopterae [39], N. plutellae (direct submission to Genbank: AY960987) and N. antheraeae [40], which, like N. bombycis , are parasites of Lepidoptera and which fall close to N. bombycis in phylogenetic trees based on the 16S rRNA gene sequence [29]. Nosema / Vairimorpha species possess multiple copies of the ribosomal RNA repeat unit which can show intragenomic variation in sequence [15,31] and some isolates of N. bombycis also possess fragmented copies of rRNA genes (Figure 3d, e) [41] which are transcriptionally active and coexist with intact rRNA copies within the same genome. The fact that, within Nosema / Vairimorpha , the rRNA repeat unit exists in multiple copies with intragenomic variation in gene order, integrity and sequence is a potential source of confusion in phylogenies based entirely upon 16S rRNA gene sequences.…”

Diversity and Recombination of Dispersed Ribosomal DNA and Protein Coding Genes in Microsporidia

“…Furthermore, within isolates of Nosema bombycis from the host Bombyx mori , rDNA units are highly variable, differing with regard to nucleotide sequence, subunit organisation and the presence of transposable elements [22]. This suggests that, in Nosema , the evolution of rDNA units may occur through a birth-and-death process rather than through concerted evolution.…”