Use of 16S rRNA and rpoB Genes as Molecular Markers for Microbial Ecology Studies

This study examined some of the first uses of the rpoB (RNA polymerase B subunit) gene as a molecular marker for phylogenetic sorting in microbes, comparing its efficiency with previously used markers. The 16S rRNA gene, a part of the small subunit in prokaryotic ribosomes, is what was commonly used previously due to the fact that is essential for protein production and therefore is common in cells. However, this also means that in a given microbe there are several copies of this gene, but often with slight differences in sequence—which could affect its use for phylogenetic sorting. Gene sequences of the 16S rRNA gene and the rpoB gene were compared—if heterogeneity was found in a specific region of the 16S rRNA gene, it was also examined in the rpoB gene. rpoB was discovered to help define small differences at the subspecies level between organisms that were closely related by providing better resolutions at both nucleotide and amino acid levels. rpoB is being used increasingly more today to help differentiate between organisms with identical 16S rRNA sequences.

Case, Rebecca J., Yan Boucher, Ingela Dahllöf, Carola Holmström, Ford W. Dolittle, and Staffan Kjelleberg. 2007. Use of 16S RRNA and RpoB Genes as Molecular Markers for Microbial Ecology Studies. Applied and Environmental Microbiology 1st ser. 73: 278-88.American Society for Microbiology. Web. <http://aem.asm.org/cgi/reprint/73/1/278&gt;.

*Citation edited on 4/21/11