Abstract
Previous studies have shown that the eukaryotic microbe Euglena gracilis contains an unusually large assortment of small nucleolar RNAs (snoRNAs) and ribosomal RNA (rRNA) modification sites. However, little is known about the evolutionary mechanisms contributing to this situation. In this study, we have examined the organization and evolution of snoRNA genes in Euglena with the additional objective of determining how these properties relate to the rRNA modification pattern in this protist. We have identified and extensively characterized a clustered pattern of genes encoding previously biochemically isolated snoRNA sequences in E. gracilis. We show that polycistronic transcription is a prevalent snoRNA gene expression strategy in this organism. Further, we have identified 121 new snoRNA coding regions through sequence analysis of these clusters. We have identified an E. gracilis U14 snoRNA homolog clustered with modification-guide snoRNA genes. The U14 snoRNAs in other eukaryotic organisms examined to date typically contain both a modification and a processing domain. E. gracilis U14 lacks the modification domain but retains the processing domain. Our analysis of U14 structure and evolution in Euglena and other eukaryotes allows us to propose a model for its evolution and suggest its processing role may be its more important function, explaining its conservation in many eukaryotes. The preponderance of apparent small and larger-scale duplication events in the genomic regions we have characterized in Euglena provides a mechanism for the generation of the unusually diverse collection and abundance of snoRNAs and modified rRNA sites. Our findings provide the framework for more extensive whole genome analysis to elucidate whether these snoRNA gene clusters are spread across multiple chromosomes and/or form dense “arrays” at a limited number of chromosomal loci.
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Notes
Variable annealing temperature was altered for different primer combinations.
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Acknowledgments
This work was supported by Discovery Grant funding to AGR from the Natural Sciences and Engineering Research Council of Canada (NSERC). ANM was supported by an NSERC CGS-M Graduate Fellowship. We would like to thank Michael Gray (Dalhousie University) in whose lab this project was initiated and Murray Schnare (Dalhousie University) for his assistance in initially identifying the Euglena U14 snoRNA and sharing his rRNA nucleotide modification mapping data before publication.
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Communicated by C. Dieckmann.
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Moore, A.N., Russell, A.G. Clustered organization, polycistronic transcription, and evolution of modification-guide snoRNA genes in Euglena gracilis . Mol Genet Genomics 287, 55–66 (2012). https://doi.org/10.1007/s00438-011-0662-8
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DOI: https://doi.org/10.1007/s00438-011-0662-8