Protein Modularity and Evolution: An examination of organism complexity via protein domain structure

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Protein Modularity and EvolutionAn examination
of organism complexity via protein domain
structure

• Presented by
• Jennelle Heyer and Jonathan Ebbers
• December 7, 2004

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Presentation Outline

• Background Material
• - Protein Evolution, Theory of Domains,
  
• Gene Number
• Hypothesis
• - Using a model protein family
• Procedure/Methods
• - DPIP Program, Phylogenic Analysis
• Results
• Discussion/Conclusions

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Theories of Protein Evolution
A long time ago, in the primodial soup of life,
small polypeptides began to form
HDLC or TCP or. HDLC TCP HCLCTCP HCICTCP
TCP Functional proteins
HDLC or TCP or. HDLC TCP HCLCTCP HCICTCP
QZX Functional proteins
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Concept of Modularity

• Proteins consist of one or more domains that were
  pieced together over time
• Domain ? building blocks of proteins
• Defined as spatially distinct structures that
  could conceivably fold and function in isolation
  (Pontig and Russell, 2002)
• Dictate the function of the protein
• Evolutionary pressure to conserve (sequence
  and/or structure)

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Organismal Complexity

• The nematode, C. elegans, has 19,500 genes in its
  genome

• Humans have between 20,000 and 25,000 genes in
  their genome
• HOW CAN THAT BE?

• Alternate splicing, multi-functional/network
  proteins

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Hypothesis

• Gene products, proteins, can be multi-functional
  with the introduction of domains
• evolution does not produce innovation from
  scratch. It works on what already exists, either
  transforming a system to give it a new function
  or combining several systems to produce a more
  complex one (Jacob, 1946)
• More complex or phylogenetically derived
  organisms produce proteins with greater domain
  complexity

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Hypothesis Part II

• Create a protein domain tool
• Position
• Partner domain
• General organization
• Protein evolution
• Using a variety of sequenced genomes
• Allow investigators to learn about domain of
  interest and apply to research

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Kinesins A model protein family

• Motor proteins found in eukaryotic organisms
• Contain a conserved motor domain
• Bind and walk along microtubules
• Can carry a variety of cargo
• May contain multiple domains

http//www.mb.tn.tudelft.nl/projects/
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Kinesins A model protein family
From Reddy and Day, 2001

• Arabidopsis thaliana, a model plant species,
  contains 61 kinesins
• S. pombe 10, C. elegans 22, Drosophlia 25,
• Human and mouse 45

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Programming Approach

• Two programs used, BLAST and InterProScan, held
  together with perl scripts
• Give a domain sequence to PSI-BLAST, which will
  identify proteins that have that domain.
• One by one, give those protein sequences to IPR,
  which identifies domains in the protein.
• Create a listing of proteins and map the data
  into a phylogeny.
• Create a tree based on the phylogeny and domains

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Program Flowchart
Domain Sequence
BLAST
List of proteins with similar domains
InterProScan
Maketree
List of domains in every protein
Tree (includes domains)
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Program Details

• Database selection
• BLAST Refseq over nr
• InterProScan SMART database, only
• Threshold values
• BLAST Option to change, improve resolution
• InterProScan E-value at 0.99, up from 0.01
• Used Arabidopsis sequences as a control
• Name DPIP (Domain Placement in Proteins)

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Results

• A Quick Look at the Data
• Phylogenetic Approach
• Hypothesis I
• Qualitative Approach
• Hypothesis II

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A Quick L k
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Phylogenetic Approach

• More complex or phylogenically derived organisms
  produce proteins with greater domain complexity
• Trace domain characteristics on a preset tree
• Use MacClade tree drawing software
• Uses input data to create most parsimonious trace
• Characteristics Maximum domains
  
• Unique domains

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Maximum of Domains per Protein
Green 1 Black 3
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Number of Unique Domains per Organism
Blue 1 Pink 2 Dk. Blue 3 Yellow 5 Black
6 Dash - ???
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Phylogenetic Conclusions

• Inconclusive or null hypothesis supported
• Possible explanations
• Kinesins may have limited domain complexity due
  to function or folding
• Inherent bias in DPIP (refseq database)
• Future Work
• Testing other domains through same process
• Updating database
• Include measure for position (N/I/C)

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Qualitative Approach

• Create a protein domain tool
• Position
• Partner domain
• General organization
• Protein evolution
• Using a variety of sequenced genomes
• Compile data into a more informative table

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- Can I trace domain or protein evolution??
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Presence of FHA/PH domain in kinesins
Yellow Absent Blue - Present
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Conclusions

• DPIP program was created to answer two questions
• Does organismal complexity correspond with
  protein complexity?
• Can we create a tool for researched to better
  understand domain in protein families?
• For kinesins motor domains No and Yes
• For other domains????

Thanks to Webb Miller, Richard Cyr Claude
DePamphillis, Alexander Richter, Plant
Physiology, Biology, and Bioinformatics Depts.