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Shiri FreilichJanet Thornton’s group, EBICambridge University
Relating the evolution of gene content to tissue specialization
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“...And when he was 93, Grandpa decided that the time had come for a man-to-man conversation.
(I was 36 at the time, I have been married for 15 years).
‘All my life I am all the time looking at woman, looking and learning. Nu, and what I learned, I want to learn to you now also.’
‘Woman, in some ways is just like us exactly the same. But in some other ways a woman is entirely different.’
‘But you know what? In which ways a woman is just like us and in which ways she is very different –
nu, on this I am still working’.”
(Amos Oz, A Tale of Love and Darkness)
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The full genome sequence from various species can highlight the common versus unique
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What’s new?
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The transition from unicellularity to multicellularity as an interior
design challenge
- gene
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Overview
• Part 1: Expression pattern of ‘old’ and ‘new’ proteins in mouse tissues
• Part 2: Expression pattern of singleton and duplicate proteins in mouse tissues
• Part 3: The evolution of tissue-specific metabolic pathways in mammals
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Part 1:
Relating age and function of a protein to its expression pattern in mouse tissues
A collaboration with Tom Freeman’s group
(MRC RFCGR)Freilich et al, Genome Biol. 2005;6(7):R56.
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Processing mouse expression and sequence data
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Classification of mouse proteins into phylogenetic groups
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Tissues have a similar composition of functional classes
Tissue type
Frac
tion
enzymes
transcription regul.signal transductiontransporters
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Tissues have a similar composition of phylogenetic classes
Tissue type
Frac
tion
universaleukaryote sp.metazoan sp.mammalian sp.
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Expression distribution of proteins from different
categories• Tissues have almost identical functional/
phylogenetic composition• Tissue diversity must be achieved through
differences in the protein composition within each category
• Do proteins from different categories duffer in their expression pattern?
Number of tissues where protein is expressed
Frac
tion
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Regulatory proteins are more specifically expressed
Number of tissues where is expressed
Frac
tion
~1/3
~1/10
Mouse proteinsclassified into functional groupsRegulatory
proteins
Metabolic proteins
enzymes
transcription regul.signal transductiontransporters
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Metazoan-specific proteins are more specifically expressed
Present in a unicellular ancestor of metazoa
Number of tissues where protein is expressed
Frac
tion
universaleukaryote sp.metazoan sp.mammalian sp.
Mouse proteinsclassified into phyletic groupsSpecific to
metzoa
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Functional categories overlap with phylogenetic categories
• Most of the pre-metazoan proteins are metabolic proteins (transporters and enzymes)
• Most of the metazoan-specific proteins are regulatory proteins (signal transduction and transcription regulation)
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Identifying the dominant influence: function or age
• Obvious differences between ‘old’ and ‘new’ proteins, within the metabolic functional group
• Yet, less than 1/3 of the pre-metazoa proteins are expressed in all tissues
Number of tissues where protein is expressed
Frac
tion
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Still, some of the pre-metazoa proteins are tissue specific
• Functions occurring in the unicellular cell become tissue-specific in multicellular species (Ldh example)
• Universal genes that have been duplicated become specific to a tissue whilst a second copy maintains its original expression pattern (Pgk-2 example)
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Part 2:
Relating duplication events to expression pattern in mouse tissuesFreilich et al, Genome Biol. 2006;7.
“…duplication events had contributed greatly to the attainment of the complex body organisation in metazoa, where cells having identical genetic material can differentiate … due to the presence of duplicated genes in their genomes” Ohno S. (1970). Evolution by gene duplication.
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The subfunctionalization model
Lynch M & Force A, Genetics. 154 (2000):The division of expression of an ancestor gene between its daughter duplicates promotes the retention of a gene in the genome
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Microarray expression data provide support to the
subfunctionalization model• Gu et al: expression divergence between
duplicate genes increases with evolutionary time (differentiation modes in yeast). Trends Genet. 2002;18: 609-13.
• Makova et al: spatial expression divergence between duplicate genes increases with evolutionary time (human tissues). Genome Res. 2003;13:1638-45 .
• Huminiecki and Wolfe: a general trend for increased tissue-specificity of expression as family size increase was observed for mammalian genes. Genome Res. 2004;14:1870-79 .
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Project Overview:The relationship between gene
duplication and breadth of expression
Protein’s perspective: 1. Does duplication event lead to an increase in tissue
specificity?
Time of duplication perspective:2. Does the date of duplication event matters? (i.e., do
duplication events occurring in the ancestral unicellular lead to an increase in tissue specificity)
Protein-family perspective: 3. does a protein family maintain a non-specific expression
pattern? (i.e., is a specific expression of proteins from big families complementary)
(Freilich et al, Genome Biol. 2006;7(10):R89)
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Singleton proteins are more globally expressed
Number of tissues in which protein is expressed
Frac
tion
Singletons (570) Duplicate proteins (1886) Proteins with many close homologues (417)
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Negative correlation between expression breadth and number
of homologues
Groups of proteins, ordered by their number of homologues
Mea
n nu
mbe
r of
ti
ssue
s
SingletonsDuplicate proteins
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Large variation
Number of homologues proteins
Num
ber
of t
issu
es
Correlation -0.20P-value 1.5e-55
SingletonsDuplicate proteins
Mean number of expressed tissues
Correlation -0.20 P-value 1.5e-55
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Does the date of duplication event matter?
(i.e., do duplication events occurring in the ancestral unicellular lead to an increase in tissue specificity)
?
Increase in tissue specificity
Global expression
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Identifying ‘old’ and ‘new’ duplications
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Only post-multicelullarity duplication events lead to
expression specificity
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The protein-family perspective: Is the specific expression of
family members complementary?
Proteins from big families tend to be more specifically expressed.
Does a protein family maintain a non specific expression pattern?
?
Complementary expression
Overlapping expression
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Calculating the cumulative tissue distribution of protein
families
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Cumulative tissue distribution of protein families is not
correlated with family size
Complementary expression pattern in protein families:
While a duplication event leads to a tissue specialisation of one or
both copy, the total tissue-distribution of the protein family remains
constant.
Protein families, ordered by size
Aver
age
tiss
ue-
cove
rage
of
prot
ein
fam
ilies
Singletons
Families with any expression information
Families with >=75%expression information
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The findings support the subfunctionalization model
Protein’s perspective: 1. Does duplication event lead to an increase in
tissue specificity? YesTime of duplication perspective:2. Does the date of duplication event maters?
only duplication events that that place in a multicellular species lead to a specific expression-> suggests that expression divergence, following gene duplication, promotes the retention of a gene in the genome
Protein-family perspective: 3. Does a protein family maintain a non-specific
expression pattern? Yes-> suggests the division of expression between family members
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Part 3:The evolution of the mammalian
metabolic pathways
Some of the tissue-specific pathways are specific to mammals.
Can we understand how tissue-differentiation of animals’ metabolism reflects their evolution?
Freilich et al, BMC evolutionary biology 2008, 8:247.
STEROID HORMONE METABOLISM
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Why studying metabolic networks?
• Metabolic networks’ structure and composition are well defined
• Available metabolic databases
• Genotype is highly related to phenotype
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The structure of the KEGG database
STEROID HORMONE METABOLISM
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The reactions within a pathway can be absent/present in a
species
Arabidopsis Thaliana
Homo Sapiens
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Project overview:
• Identification of pathways absent/present in a species
• Classification of human pathways according to their phyletic origin
• Characterization of lineage-specific metabolic pathways
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Phylogenetic classification of human pathways
All pathways in human (metabolic)Universal pathways
Eukaryota-specific pathways
Metazoan-specificpathways
Mammalian-specific pathways
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Components of theEukaryotic membrane(sphingolipids, glycosaminoglycan)
Phylogenetic classification of human pathways
33 Universal pathways
8 Eukaryota-specific pathways
10 Metazoan-specific pathways
14 Mammalian-spc. pathways
Metabolic skeleton: sugars, nucleotides, some amino-acids, energy
Tissue specific activities:Neuronal guidance, hormonal activity, digestion Tissue specific activities and intracellular signaling(blood cell recognition)
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The pathways can be linked to form a network
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The network structure of the metabolic pathways
Universal pathwaysEukaryota-spc. pathwaysMetazoan-spc. pathwaysMammalian-spc. pathways
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The integration of the steroid biosynthesis pathway into the sterol biosynthesis pathway
sterol
cholesterol
steroid hormonebile acid
UniversalEukaryotaHuman
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From manually selected examples to a computational approach
Creating a list of adjacent reactions:
2.7.4.2 -> 4.1.1.334.1.1.33->2.5.1.1..2.5.1.1->2.5.1.212.5.1.21-
>1.14.99.7
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Using the adjacency list for a large-scale characterization
of the metabolic network
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What’s new (metabolic pathways)?
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Summary
• ‘New’ genes tend to be more tissue-specific, ‘ancient’ genes tend to be globally expressed
• Despite this trend, many metazoan genes are ubiquitous and many universal proteins are tissue specific
• ‘New’ duplications of ‘old’ and ‘new’ proteins lead to a more specific expression, and therefore can facilitate the evolution of new, tissue-specific, functions
• The core of metabolic-pathways, inherited from a uniclellular ancestor, provides a platform for the evolution of mammalian-specific, tissue-specific pathways
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Thanks
Thornton GroupJanet ThorntonTim MassinghamEric BlancExpression data:Tom Freeman
Sumit Bhattacharyya