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Protein
Sequencing
Protein
sequencing was a technique developed relatively early on in molecular
phylogenetics. As the primary structures of proteins are genetically
determined, the degree of similarity in the amino acid sequences of
the proteins reflects the genealogy between two species. For example,
one of the most studied amino-acid sequences was that of cytochrome
c, an ancient protein common to all aerobic organisms. The more differences
in the sequence of the protein, the more distantly related the species.
The amino acid sequence of human cytochrome c is identical to that
of the chimpanzee, but differs from the dog's by 13 amino acids, and
from the tuna by 31 amino acids (Campbell 1999).
The
actual process of sequencing the proteins is achieved using gel electrophoresis,
a technique first developed in the mid-1960's. Gel electrophoresis separates
protein molecules by size and charge, and consequently allows small
changes in their amino acid sequences to be detected. Once the sequence
of amino acids that make up a particular protein is known, it can be
compared with sequences of the protein from other species. From the
degree of similarity between species, phylogenetic trees can be hypothesized,
as Miyamoto and Goodman did for the orders of Eutheria in 1986. By translating
the amino acid data for a- and b-haemoglobins, myoglobin, lens a-crystallin
A, fibrinopeptides A and B, cytochrome c and ribonuclease into mRNA
sequences, following the genetic code, the sequence data was arranged
in an extended tandem alignment and then analysed as if each species
was represented by a singlegigantic polypeptide. The species were then
directly compared and trees were constructed which minimised the total
number of nucleotide replacements (NR). This method of tree construction
was developed by Goodman and Moore in the 1970's (Goodman et al 1979),
and in this study produced several most-parsimonious
trees.
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