Studies on the structure, expression, genome organization, and evolution of U3 snoRNA genes in Euglena gracilis.
Date
2007
Authors
Charette, Joseph Michael Claude.
Journal Title
Journal ISSN
Volume Title
Publisher
Dalhousie University
Abstract
Description
Small nucleolar RNAs (snoRNAs) are small RNA molecules present in eukaryotic nucleoli. They guide nucleoside modification (formation of O2'-methylribose and pseudouridine) and endonucleolytic cleavage events necessary in the processing, folding, and assembly of the pre-rRNA transcript into mature rRNAs. In all known cases, the site of modification or cleavage in the pre-rRNA/rRNA is specified by short nucleotide sequences present in the snoRNA, complementary to the target rRNA sequence. This specificity, provided by the snoRNA through base pairing interactions with the target rRNA, localizes a specific snoRNP to the rRNA target where the relevant protein-catalyzed modification or cleavage reaction occurs. U3 snoRNA plays an essential role in many of the endonucleolytic processing events that produce the mature 18S rRNA.
This thesis examines the organization of U3 snoRNA genes in the genome of Euglena gracilis. Southern analysis revealed at least 13 U3-hybridizing bands. Both PCR and genomic lambda library screening were used to isolate U3 sequences. Analysis of the recovered sequences identified 14 U3 gene variants. Sequence heterogeneities identified in the U3 gene variants were located in the 3'-stem-loop domain. An examination of the genomic neighborhood of Euglena U3 snoRNA genes revealed the presence of at least three different genomic organizations: (i) stand-alone, (ii) linked to tRNAArgUCG genes, and (iii) linked to a U5 snRNA gene. In the U3 snoRNA-tRN Arg linkage, the U3 snoRNA gene is linked to two identical, downstream, convergently oriented (relative to the U3 gene) tRNAArg genes. This scenario is reminiscent of, but different in a number of key ways from, the U3 snoRNA-tRNA gene linkage in trypanosomatids. Twelve different U3 snoRNA-U5 snRNA gene linkages were identified. In each case, the U3 gene is linked to a downstream and convergently oriented U5 snRNA gene. The multiple U3 snoRNA-U5 snRNA gene linkages cluster into distinct families based on sequence similarities within the intergenic spacer. The multiple Euglena U3 gene copies may have arisen by genome, chromosome, and/or locus duplications. Finally, the unexpected variability in the signal intensities of the multiple Southern hybridizing bands raises the possibility that Euglena might contain a naturally aneuploid chromosome complement.
Thesis (Ph.D.)--Dalhousie University (Canada), 2007.
This thesis examines the organization of U3 snoRNA genes in the genome of Euglena gracilis. Southern analysis revealed at least 13 U3-hybridizing bands. Both PCR and genomic lambda library screening were used to isolate U3 sequences. Analysis of the recovered sequences identified 14 U3 gene variants. Sequence heterogeneities identified in the U3 gene variants were located in the 3'-stem-loop domain. An examination of the genomic neighborhood of Euglena U3 snoRNA genes revealed the presence of at least three different genomic organizations: (i) stand-alone, (ii) linked to tRNAArgUCG genes, and (iii) linked to a U5 snRNA gene. In the U3 snoRNA-tRN Arg linkage, the U3 snoRNA gene is linked to two identical, downstream, convergently oriented (relative to the U3 gene) tRNAArg genes. This scenario is reminiscent of, but different in a number of key ways from, the U3 snoRNA-tRNA gene linkage in trypanosomatids. Twelve different U3 snoRNA-U5 snRNA gene linkages were identified. In each case, the U3 gene is linked to a downstream and convergently oriented U5 snRNA gene. The multiple U3 snoRNA-U5 snRNA gene linkages cluster into distinct families based on sequence similarities within the intergenic spacer. The multiple Euglena U3 gene copies may have arisen by genome, chromosome, and/or locus duplications. Finally, the unexpected variability in the signal intensities of the multiple Southern hybridizing bands raises the possibility that Euglena might contain a naturally aneuploid chromosome complement.
Thesis (Ph.D.)--Dalhousie University (Canada), 2007.
Keywords
Chemistry, Biochemistry.