Molecular evolution of tropinone-reductase-like and tau GST genes duplicated in tandem in Brassicaceae

Gene duplication is an opportunity for evolving new functions from
the newer gene, but also has a disadvantage due to local
gene-rearrangement effects and, if duplications are numerous,
through alterations of genome size. Therefore, selection is playing
a central role in determining the fate of a duplicate gene. Plants
are known to harbor numerous gene families, and are thus an ideal
system to test the fate of gene duplicates. This thesis tackles the
tropinone-reductase like enzymes (further TRL) and the tau GSTs
located upstream from this gene family. TRL enzymes are short-chain
dehydrogenases that are involved in a reduction step downstream in
the synthesis of tropane alkaloids in Solanaceae, important defense
compounds of plants. The function of TRLs in Brassicaceae is not
clear, since most of the plants in this family do not produce
tropane alkaloids, but some have been associated with the
oxidative-stress response. This gene family contains 80\% of its
members duplicated in tandem in Arabidopsis thaliana. We profited
from this fact to isolate 12 TRL (+ pseudogenes) from this species,
further six species of Brassicaceae (A. thaliana, A. lyrata, A.
cebennensis, Capsella rubella, Boechera divaricarpa and Brassica
rapa), and one species from a closely related plant family, Cleome
spinosa. We tested the role that selection plays in maintaining
large numbers of this gene family. We used phylogenetic methods to
analyze non-coding sequence evolution and identified regulatory
motifs. We analyzed non-coding sequence evolution. Microarray
expression data from A. thaliana and qPCR for A. thaliana and A.
lyrata were analyzed to detect divergence in the expression
patterns of orthologs and paralogs. TRL genes follow a gene birth
and death dynamics. More probable, they originated from non-equal
recombination of tandem duplicated genes. Positive selection at the
origin of the duplicated genes allowed these to acquire
differential expression patterns, leading to the preservation of
numerous TRLs. The analysis of coding and non-coding sequences
shows them to display correlated evolution, particularly in species
recently separated by speciation. We further tested for selection
on the tau glutathione-S-transferases (GST) enzymes, adjacent 3' in
the genome to TRLs. Tau GSTs are unique to plants and are involved
in detoxification. Multiple copies of these enzymes will allow
flexibility in substrate specificity, which is important for the
detoxification function. We detected positive selection among
paralogs of tau GSTs supporting their potential of functional
diversity, but we also detected negative selection among paralogs
and groups of orthologs, indicating that more often their functions
are conserved.