Transcript Folie 1 - uni

Fabian Birzele
Ludwig-Maximilians-University Munich
Alternative Splicing and Protein Structure Evolution
Fabian Birzele, Gergely Csaba and Ralf Zimmer,
Nucleic Acids Research, 36 (2008), 550-558
Alternative splicing and protein structure evolution
Introduction - Protein Structure Analysis
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Many more known structures than
distinct protein structure topologies
 cluster proteins on different levels
of similarity (Topology, homology…)
 SCOP and CATH
Structure alignments reveal the
insertions, deletions and mutations
which have been tolerated by a
structure family in evolution
 “evolutionary isoforms”
SCOP family d.9.1.1, Interleukin 8-like chemokines
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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Alternative splicing and protein structure evolution
Introduction –Alternative splicing
Introduction – Alternative splicing
Protein1
Protein2
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Function 1
?
Function 2
Alternative splicing assembles the exons of a gene in different ways
74% of all human genes are alternatively spliced (Johnson et al, Science 2003)
Many examples where splicing isoforms carry out different functions
Splicing increases the functional diversity of the proteome
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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Alternative splicing and protein structure evolution
Alternative Splicing in the light of protein structures
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Very few experimental protein structures of splicing
isoforms.
Splicing changes structures only moderately:
– Exposed, non-core elements (Wang et al., PNAS
2005)
– Disordered (Romero et al., PNAS, 2006)
– complete domains (e.g. Resch et al. J.Prot.Res.
2004)
Splicing is deleterious for most protein
structures
– Often alters the hydrophobic core (Tress et al,
PNAS, 2007 and Yura et al., Gene, 2006)
Garcia et al., Nat. Struct. Biol., 2003
 Tress et al: “… it seems unlikely that the spectrum of … enzymatic
or structural function can be substantially extended through
alternative splicing”
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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Alternative splicing and protein structure evolution
Hypotheses
• Splicing is a major main contributor for functional diversity
– Non-trivial splicing events can lead to proteins with well defined functions
– Structures may tolerate large structural changes
• Tolerance against changes is linked to the evolutionary history of a
protein fold
– Evolutionary isoforms are a useful tool to understand splicing events
– Alternative splicing is a useful tool to study protein structure evolution
• Alternative Splicing is a genetic mechanism to explore the protein fold space
– Splice isoforms may adopt different folds in the protein fold space
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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Alternative splicing and protein structure evolution
OK
Methods and Data
Nontrivial
Varsplic isoforms
Swissprot entry
PDB structure
SCOP
superfamily
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Splicing events annotated in Swissprot (high quality, manual annotations)
Structures have been modeled very conservatively, 60% id, 75% coverage
Multiple structure alignments of SCOP superfamilies  variable and conserved regions
Results in 367 proteins and 488 additional isoforms
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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Alternative splicing and protein structure evolution
Distribution of splicing events
OK
(228)
Nontrivial
(260)
Many splicing events are very complex on the structure level.
 Are they functional?
 What is their structure?
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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Alternative splicing and protein structure evolution
Evolutionary isoforms help to understand splice isoforms
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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Alternative splicing and protein structure evolution
Evolutionary isoforms
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MHC antigen recognition domain
1de4G, SCOP: d.19.1.1
HFE_HUMAN, Isoform 2
Evolutionary isoform, same family
Dimer (chain G and H)
1aqdH
Evolutionary isoforms can help to understand the structure of splicing isoforms
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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Alternative splicing and protein structure evolution
Non-trivial isoforms can have well defined functions
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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Alternative splicing and protein structure evolution
Functional evidence for non-trivial isoforms
CC3 metastasis suppressor inducing
apoptosis
• Splice variant TC3, 107 aa removed
and 21 aa replaced, large scale event
• has anti-apoptotic function
• Reference: Whitman et al (1992)
Mol. Cell. Biol. 20, 583-93
remove
replace
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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Alternative splicing and protein structure evolution
Functional evidence for non-trivial isoforms
LMPTP tyrosine phosphatase
• Removal of peripheral αβ-motif
from β-sheet
• no phosphatase activity (active
center removed)
• antogonist of native isoform
– still binds substrates and
regulators
– But cannot dephosphorylate
its targets
• Alter signaling pathways
through non-trivial splicing
events
• Reference: Tailor et al (1999)
Eur. J. Biochem. 262, 277-82
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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Alternative splicing and protein structure evolution
Functional evidence for non-trivial isoforms
• Comprehensive analysis of biological literature for all 260 non-trivial isoforms
• Only few studies analyzed isoforms on the protein and / or the function, but nevertheless:
– 17% (43) isoforms confirmed on the protein level
– 10% (26) isoforms with a well defined function
– Often we find antagonistic functions  activator vs. repressor
• Those isoforms are interesting starting points for experimental structure determination
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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Alternative splicing and protein structure evolution
Alternative Splicing and Fold Evolution
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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Alternative splicing and protein structure evolution
Evolution of beta-propellers
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Beta-Propellers with different number of blades
are known (4-8) but very low sequence identity
and diverse functions
 different folds in SCOP and CATH
 Are they evolutionary related?
Beta-propellers from different folds in SCOP
are related on the sequence level (Chaudhuri,
Söding and Lupas., Proteins 2008)
Many known splicing events (60 in Swissprot,
50 in Human) where beta-propellers with
different number of blades are generated from
one gene
 Different beta-propeller folds are
explored from one gene
 Connection between different propeller
folds suggested by splicing
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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Alternative splicing and protein structure evolution
Can splicing “tunnel” between folds?
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Different folds are not thought to be evolutionary related (or at least
the signals are very weak)
Many splicing events can not be explained within the own fold
Can they be explained by structures from different folds?
 Are those isoform structures more similar to proteins from a different
fold than to their own fold?
X
Splicing?
X
c.2
c.30
Splicing?
X
c.1
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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Alternative splicing and protein structure evolution
Fold changing splicing event: c.2.1.2  c.30.1.1
apoptotic
anti-apoptotic
SCOP
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=
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c.2
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splicing isoform
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Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
c.30
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Alternative splicing and protein structure evolution
Can splicing “tunnel” between folds?
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In those cases we propose that the structure of the isoform adopts a
fold different from the native one  traceable link between
different folds
Alternative splicing data provides evidence that it is possible to jump
from one fold to the other
 Splicing may be a genetic mechanism to explore the fold space
Splicing!
Splicing?
c.2
c.30
Splicing?
X
c.1
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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Alternative splicing and protein structure evolution
The ProSAS Database
• http://www.bio.ifi.lmu.de/ProSAS
• Comprehensive resource to analyze
known splicing events in the context
of protein structures.
• Events annotated in Swissprot and
Ensembl (Human, Chimp, Mouse
and Rat)
• ProSAS also allows for a structurebased analysis of experimental
data like Affymetrix Exon Chips or
Deep Sequencing
– Those have the potential to verify
or falsify our hypotheses
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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Alternative splicing and protein structure evolution
Conclusion and Discussion
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Splicing is a major contributor to functional diversity, although the effects on the structure level are complex
– Evolution makes use of the large plasticity of protein structures to generate functional and structural diversity
via alternative splicing
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A structure‘s tolerance against changes is linked to its evolutionary history
– Use evolutionary isoforms to understand alternative splicing
– Use alternative splicing to understand structure evolution
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Isoforms may adopt folds different from the fold of the native isoform
– Splicing may reveal novel links between protein folds
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Need for experimental structures and protein-level confirmations of isoforms
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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Alternative splicing and protein structure evolution
Acknowledgements
• The U.S.Department of Energy (DOE) for the travel
fellowship award: “Participant travel costs to present the project
described was partly supported by Grant Number DE-FG02-06ER64270
from the U.S Department of Energy. The content is solely the responsibility
of the author(s) and does not necessarily represent the official views of the
Department of Energy.”
• My colleagues Gergely Csaba and Ralf Zimmer for their
contribution to the paper and the talk
• The ProSAS-Team: Eva Hoffmann, Robert Küffner, Franziska
Meier, Florian Oefinger, Christian Potthast
• You: for your attention
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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Alternative splicing and protein structure evolution
Publications
•
Fabian Birzele, Gergely Csaba and Ralf Zimmer, Alternative Splicing and Protein Structure Evolution, Nucleic Acids
Research, 36 (2008), 550-558
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Fabian Birzele, Robert Küffner, Franziska Meier, Florian Oefinger, Christian Potthast and Ralf Zimmer, ProSAS: a
database for analyzing alternative splicing in the context of protein structures, Nucleic Acids Research, 36 (2008),
D63-D68
•
http://www.bio.ifi.lmu.de/ProSAS
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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Alternative splicing and protein structure evolution
AUHM: Do events tunnel between different folds?
SCOP
c.13.2.1
c.14.1.3
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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Alternative splicing and protein structure evolution
Do events tunnel between different folds?
SCOP
c.2.1.2
c.30.1.1
• Are there any connections between distinct folds in SCOP explored by
alternative splicing?
• Search for “isoform structures” in a different fold based on structure
similarity (TM-score), secondary structure fit and topology
Splicing reveals possible links (“tunnels”) between different folds
in SCOP for several examples
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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Alternative splicing and protein structure evolution
Superfamily b.62.1
2ok3_A, b.62.1.1, CYP10_CAAEL
1x7f_A, b.62.1.2
Fabian Birzele, LMU Institut für Informatik, Lehrstuhl für Praktische Informatik und Bioinformatik, ISMB 2008
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