Direct evidence for redundant segmental replacement between multiple 18S rRNA genes in a single Prototheca strain

Abstract

Informational genes such as those encoding rRNAs are related to transcription and translation, and are thus considered to be rarely subject to lateral gene transfer (LGT) between different organisms, compared to operational genes having metabolic functions. However, several lines of evidence have suggested or confirmed the occurrence of LGT of DNA segments encoding evolutionarily variable regions of rRNA genes between different organisms. In the present paper, we show, for the first time to our knowledge, that variable regions of the 18S rRNA gene are segmentally replaced by multiple copies of different sequences in a single strain of the green microalga Prototheca wickerhamii, resulting in at least 17 genotypes, nine of which were actually transcribed. Recombination between different 18S rRNA genes occurred in seven out of eight variable regions (V1-V5 and V7-V9) of eukaryotic small subunit (SSU) rRNAs. While no recombination was observed in V1, one to three different recombination loci were demonstrated for the other regions. Such segmental replacement was also implicated for helix H37, which is defined as V6 of prokaryotic SSU rRNAs. Our observations provide direct evidence for redundant recombination of an informational gene, which encodes a component of mature ribosomes, in a single strain of one organism.

Ribosomal Internal Transcribed Spacer of Prototheca wickerhamii Has Characteristic Structure Useful for Identification and Genotyping

“…This may be due to the inter-copy heterogeneity revealed in this study. The heterogeneity of the D1/D2 sequneces found in this study is also comparable with the previous report that the SSU rDNA sequences of a single strain of P. wickerhamii are variable [23]. Heterogeneity between different copies of rDNA has previously been documented for other eukaryotic microorganisms, such as Plasmodium spp., with its functional significance [24].…”

“…P. zopfii has been classified to genotypes 1 and 2 based on the difference in the SSU rDNA sequences [4]. However, SSU-based intraspecies genotyping of P. wickerhamii would be difficult because SSU rDNA of P. wickerhamii are very variable, resulting in at least 17 different groups in a single strain [23]. Our results suggest that sequence determination of a few ITS clones derived from a strain of P. wickerhamii combined with the phylogenetic analysis of the obtained data by using the ITS sequences determined in this study might be able to decide genotype of the strain.…”

Detection of Helicosporidium spp. in metagenomic DNA

“…Homology searches (BLAST) and phylogenetic analyses confirmed the nature and taxonomic origin of all sequences. The generation of several 18S rDNA sequences from a single P. wickerhamii strain is consistent with a recent report (Ueno et al, 2007) and explains initial sequencing difficulties. However, this phenomenon seems restricted to P. wickerhamii and was not found for other Prototheca or Helicosporidium spp.…”

Ribosomal Gene Polymorphism in Small Genomes: Analysis of Different 16S rRNA Sequences Expressed in the Honeybee Parasite Nosema ceranae (Microsporidia)

“…Moreover, as stated by Ueno et al. (), the changes are systematically located in specific regions that tend to be more variable and do not alter the overall secondary structure; in vitro errors were expected to be randomly distributed, irrespective of the in vivo relevance of a given region.…”