Now we'll use clustalw (through its EMBOSS frontend emma)
to make some multiple alignments of ribosomal RNA. We will look at the
small ribosomal subunit (16S) rRNA from a group of bacterial species.
Ribosomal RNAs have
had a large impact on our views concerning evolution. Based on
rRNA, Carl Woese and collaborators introduced the term
'domain' and named the major three groups Bacteria, Archaea and
Eucarya (Fig2). This could be done because 16S rRNA is a
very ancient molecule, which was already present before the
divergence of the tree domains of life. It is thus present in all
living species and organelles. The molecule is conserved in structure
and function over this wide range of species (Fig1). The conservation
in secondary structure can help in providing a basis for an accurate
alignment. The high degree of conservation across species also makes
it a useful target for amplification of DNA from previously
uncharacterized species such as uncultured bacteria, and is often
used to decide the phylogenetic placement of an unknown bacterial or
archaeal species.
The major divisions within the bacteria and archaea have also
been established mainly based on 16S
rRNA.
Fig
1. Structure of the 16S rRNA molecule
Fig2. The tree of life based on 16S
rRNA
2. Align the file
16SrRNA.fas using emma trying a few different values for gap
opening and gap extension penalties. See how to set these by doing
% emma -help
Try just changing the multiple
alignment gap parameters.
Compare your results with the manually aligned
sequences. You can look at your alignments using Seaview. What
gap penalties are working best for this dataset?
