Diversity of 5S rRNA genes within individual prokaryotic genomes

• Published in: FEMS microbiology letters Vol. 335; no. 1; pp. 11 - 18
• Main Authors: Pei, Anna, Li, Hongru, Oberdorf, William E., Alekseyenko, Alexander V., Parsons, Tamasha, Yang, Liying, Gerz, Erika A., Lee, Peng, Xiang, Charlie, Nossa, Carlos W., Pei, Zhiheng
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01.10.2012; Wiley-Blackwell; Oxford University Press
• Subjects: 5S rRNA; Amino acid sequence; Bacteria - chemistry; Bacteria - classification; Bacteria - genetics; Biological and medical sciences; Databases, Nucleic Acid; Divergence; DNA, Ribosomal - chemistry; DNA, Ribosomal - genetics; Fundamental and applied biological sciences. Psychology; Genes; Genetic Variation; Genome, Bacterial; Genomes; Microbiology; Nucleic Acid Conformation; Protein structure; ribosomal constraints; RNA, Ribosomal, 5S - chemistry; RNA, Ribosomal, 5S - genetics; rRNA 5S; rRNA diversity; Secondary structure; Spacer; Species; Species diversity; 5S rRNA; ribosomal constraints; rRNA diversity; Ribosomal RNA; Ribosomal DNA; Genome; 5S-RNA
• ISSN: 0378-1097; 1574-6968
• DOI: 10.1111/j.1574-6968.2012.02632.x

Abstract We examined intragenomic variation of paralogous 5S rRNA genes to evaluate the concept of ribosomal constraints. In a dataset containing 1161 genomes from 779 unique species, 96 species exhibited > 3% diversity. Twenty-seven species with > 10% diversity contained a total of 421 mismatches between all pairs of the most dissimilar copies of 5S rRNA genes. The large majority (401 of 421) of the diversified positions were conserved at the secondary structure level. The high diversity was associated with partial rRNA operon, split operon, or spacer length–related divergence. In total, these findings indicated that there are tight ribosomal constraints on paralogous 5S rRNA genes in a genome despite of the high degree of diversity at the primary structure level.