Mehdi Layeghifard

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Transcript Mehdi Layeghifard

Evolutionary Mechanisms Underlying the
Functional Divergence of Vertebrates’ Circadian
Rhythm Genes
Mehdi Layeghifard
Gene duplication
• is one of the most important mechanisms in the
evolution of gene diversity
• is any duplication of a region of DNA that
contains a gene; it may occur as an error in
homologous recombination, a retrotransposition
event, or duplication of an entire chromosome
Gene duplication
Duplications arise from
an event termed unequal
crossing-over that
occurs during meiosis
between misaligned
homologous
chromosomes
Gene duplication
Evolutionary Mechanisms
• What is the evolutionary fate of duplicates?
• How duplicate genes are retained in a genome?
Natural Selection
• If reproductive success is impeded by a mutation,
then selection of organisms with the mutation is
Negative
• If reproductive success is promoted then the
selection is Positive
• In the middle is Neutral selection, that may lead
to either weak positive or weak negative selection
Natural Selection
Concerted Evolution
• The extra amount of a gene product is sometimes
beneficial (dosage effect)
• Daughter genes may become fixed through strong
Purifying Selection
• Duplicate genes will have very similar sequences
and functions and will be prevented from being
diverged
Concerted Evolution
Neofunctionalization
• Genetic redundancy after duplication
• Gain of a new function by one of the duplicates
• Includes two scenarios
Neofunctionalization
First scenario:
Functional redundancy leads to the fixation of
random mutations in one duplicate under Relaxed
Functional Constraint
Later, when the environment or genetic
background is altered, the fixed mutations may
induce a change in gene function (Dykhuizen–
Hartl effect)
Neofunctionalization
Second scenario:
After duplication, a new but weak function maybe
created by a few neutral or nearly neutral
mutations
Positive Darwinian selection then, accelerates the
fixation of advantageous mutations that enhance
the activity of novel function
Subfunctionalization
• Genetic redundancy after duplication
• Both duplicates undergo Relaxed Functional
Constraint
• Includes two scenarios
Subfunctionalization
Division of Expression scenario:
Random fixations of complementary degenerate
mutations under Relaxed Functional Constraint
are the main causes of duplicates fixation in the
genome
Subfunctionalization
Functional Specialization scenario:
Ancestral gene already has dual functions and the
duplication provides the opportunity for each
duplicate to adopt one ancestral function and
further substitutions under positive Darwinian
selection can refine the function
Evolutionary Mechanisms
Evolutionary Mechanisms
Circadian Rhythms
• Important in determining the sleeping and feeding
patterns of all animals
• Have been described in many eukaryotic and prokaryotic
species
• Living organisms use this endogenous circadian clock,
which can be synchronized to daily and seasonal
changes in light and temperature, to anticipate
environmental transitions, perform activities at
biologically advantageous times during the day, and
undergo characteristic seasonal responses
Circadian Genes
Circadian rhythm pathway of vertebrates is
consisted of seven groups of genes:
Per, Clock, Bmal, NR1D, DEC, Cry, and CKI
The circadian system, like many other multigene
families, has undergone gene duplication, and so
circadian genes that are found in single copies in
insects are duplicated in vertebrates
Circadian Genes
Material & Methods
1)
2)
3)
4)
5)
Data sets and phylogenetic analysis
Protein domain analysis
Analysis of functional divergence
Analysis of positive selection
Analysis of recombination
Material & Methods
1) Data sets and phylogenetic analysis
a) Retrieving gene sequences
164 sequences from 7 groups
b) Constructing phylogenies
Material & Methods
2) Protein domain analysis
The Simple Modular Architecture Research Tool
(SMART) is an online resource used for protein
domain identification and the analysis of protein
domain architectures
We used this tool to identify the potential domains of
circadian proteins in order to better predict the
functional properties of these single domains and also
to depict their role in the functional divergence of
circadian proteins
Material & Methods
3) Analysis of functional divergence
Gene family evolution reflects a balance between
homogenization by unequal crossing over and gene
conversion and diversification by mutation
Among these mechanisms, only mutation followed by
positive Darwinian selection or relaxation of functional
constraints can account for the evolution of new
functions, although the two other factors play an
important role in the evolutionary fate of duplicated
genes
Material & Methods
3) Analysis of functional divergence
DIVERGE
Type I functional divergence refers to the
evolutionary process that results in altered selective
constraints (different evolutionary rates) between two
duplicate genes, regardless of the underlying
evolutionary mechanisms, developed by Gu (1999)
SHIFT-FINDER
Uses the same approach used by DIVERGE but with
more sensitivity
Material & Methods
4) Analysis of positive selection
Site-based methods
Using several codon models of molecular evolution that allow
for heterogeneous dN/dS ratios at sites
SLAC method
Conservative tests of positive selection based on Suzuki and
Gojobori (1999) method
Branch-site method
Using branch-site test 2 (also called the branch-site test of
positive selection) developed by Zhang et al. (2005)
Material & Methods
5) Analysis of recombination
Recombination can play a dominant role in the
generation of novel patterns of genetic variation through
the rearrangement of existing genetic variation generated
through mutation. These patterns of genetic variation can
closely resemble the effects of positive selection
GENECONV
MaxChi
Bootscan
Results & Discussion
• Phylogeny
The phylogenetic analysis indicated that members of
each group of circadian genes were generated by a gene
duplication event in the early stages of vertebrates'
evolution
The duplication events of Cry and Bmal groups were
seemingly occurred in teleosts and those of other groups
were occurred before the evolution of teleosts
Results & Discussion
• Functional divergence
Site-specific altered selective constraint after
the gene duplications was statistically significant
for all groups
Functionally important sites were mapped on
the sequences
Results & Discussion
• Positive selection
The SLAC method, like codon models of PAML,
predicted no positively selected site in circadian genes
with probabilities above 95%
Periods of positive Darwinian selection following the
duplication events were found in Clock, NPAS2,
PER1,2,3, and NR1D1 lineages by branch-site method
Results & Discussion
• Recombination
Those events that were detected by at least two of the
three implemented methods were only considered
Zero to three recombination events for gene groups
Low levels of recombination (fewer than three events
in a dataset of about ten sequences) have no significant
effect on positive selection analysis
Results & Discussion
• Molecular evolutionary history of duplicates
The data obtained from all the molecular
evolutionary analyses were used to provide a
clearer picture of mechanisms behind the
functional divergence of circadian genes
Results & Discussion
• Molecular evolutionary history of duplicates
a) NR1Ds
1) Significant functional divergence was mainly
because of amino acid changes occurred in HOLI
domain
2) HOLI is a highly conserved DNA-binding
domain
3) Functional divergence between these proteins may
due to recognizing different DNA sequences
Results & Discussion
• Molecular evolutionary history of duplicates
a) NR1Ds
4) Two positively selected sites with P < 0.05 in
NR1D1
5) 1% of NR1D2 amino acids have experienced
positive selection
6) Functional Specification is probably the most suitable model
for describing the evolutionary fates of these duplicates
Results & Discussion
•
Molecular evolutionary history of duplicates
b) CKIs
1) Only three functionally important sites
between CKIδ and CKIε
2) None of the detected sites was mapped to Pkinase
domain
3) Majority of negative sites were located in Pkinase
domain
Results & Discussion
•
Molecular evolutionary history of duplicates
b) CKIs
4) Pkinase domain is highly conserved
5) Might have only experienced the purifying selection
6) Occurrence of functional divergence without the
operation of positive selection Dykhuizen–Hartl effect
Results & Discussion
• Molecular evolutionary history of duplicates
c) DECs
1) Detection of functional divergence between
DEC proteins without signatures of positive selection
2) Dykhuizen–Hartl effect as the most suitable model
Results & Discussion
• Molecular evolutionary history of duplicates
d) CLOCK and NPAS2
1) Positive selection and significant functional divergence were
found
2) Neofunctionalization with positive selection or Functional
Specification
3) Experimental studies have shown that both genes play almost
the same role in circadian rhythm pathway, but in different tissues
Results & Discussion
• Molecular evolutionary history of duplicates
d) CLOCK and NPAS2
4) Ancestral gene might have been active in all tissues
5) Duplicates underwent Functional Specification
6) CLOCK is active in central circadian clock in suprachiasmatic
nuclei, while NPAS2 is active in peripheral oscillator within other
tissues like liver
Results & Discussion
• Molecular evolutionary history of duplicates
e) BMALs
1) Significant functional divergence and
positive Darwinian selection
2) Neofunctionalization with positive selection
model suggested as the most suitable explanation
Results & Discussion
• Molecular evolutionary history of duplicates
f) CRYs
1) No signatures of positive selection
2) Experimental and computational evidence of
functionally divergence
3) Dykhuizen–Hartl effect as the most suitable model
Results & Discussion
• Molecular evolutionary history of duplicates
g) PERs
1) PER family members acquired their new functions
through mutations followed by positive selection after
gene duplication
2) Neofunctionalization with positive selection
model suggested as the most suitable explanation
Final Words
• We showed that the evolution of circadian genes have depended on
gene duplication and functional divergence and that each group of
genes involved in circadian rhythm pathway (which are duplicates
of one-copy ancestral genes) has experienced an independent
evolutionary fate following duplication, i.e., there have been
different forces behind the functional divergence detected between
circadian rhythms gene
• This research also showed the importance of molecular evolution
approaches in finding supporting evidence for experimental results
as well as proposing new hypotheses to be tested by experimental
research