polyQ and other homorepeats Miguel Andrade Faculty of Biology, Johannes Gutenberg University Institute of Molecular Biology Mainz, Germany andrade@uni-mainz.de
Schaefer et al (2012) Nucleic Acids Res. Function of polyQ Martin Schaefer polyQ in Huntingtin Human Dog Mouse Opossum Chicken Frog Zebrafish Trout Fugu Stickleback Lancelet Capitella Limpet Nematostella Trichoplax Ciona intestinalis Ciona savignyi D. melanogaster D. mojavensis D. sechellia D. erecta D. yakuba D. grimshawi D. pseudoobscura D. persimilis D. ananassae D. willistoni D. virilis Schaefer et al (2012) Nucleic Acids Res.
Human Dog Mouse Opossum Chicken Frog Zebrafish Trout Fugu Stickleback Lancelet Capitella Limpet Nematostella Trichoplax Ciona intestinalis Ciona savignyi D. melanogaster D. mojavensis D. sechellia D. erecta D. yakuba D. grimshawi D. pseudoobscura D. persimilis D. ananassae D. willistoni D. virilis 14 families: Human polyQ, fly polyQ, fish no polyQ. P-value < 0.05 75/4759 4293/4759 354/4759 14 trios P-val < 0.05
human partners polyQ TFs long non polyQ 1 5 10 50 100 500 1000 partners polyQ TFs long non polyQ
polyQ non polyQ TFs long yeast human partners polyQ TFs long non polyQ 1 5 10 50 100 500 1000 human 1 5 10 50 100 500 1000 partners polyQ TFs long non polyQ Systems Biology no polyQ polyQ >14 polyQ 4-14 partners 1 2 5 10 20 50 100 200 500 1 5 10 50 100 500 1000
proteins with near polyP 86 human polyQ proteins polyP polyQ 13 polyQ proteins with near polyP 12 C-term polyQ coiled coil 109 polyQ regions 54 overlap/near N-terminal polyQ Run of P>=3 max dist 3. C-terminal
40 human polyQ/coiled-coil proteins (no polyP) 86 human polyQ proteins polyP polyQ 13 polyQ proteins with near polyP 12 C-term polyQ coiled coil N-terminal 36 N-term polyQ Run of P>=3 max dist 3. C-terminal
86 human polyQ proteins interacting proteins polyP coiled coil polyP coiled coil 49 interactions with another polyQ protein (p-value = 0.0023)
Non-polyQ interacting proteins 86 human polyQ proteins Non-polyQ interacting proteins polyP coiled coil coiled coil Enrichment (p-value < 2.2e-16)
polyQ protein N-terminal C-terminal polyP polyQ coiled coil unbound polyP polyQ disordered coiled coil
polyQ protein polyQ protein protein X N-terminal coiled coil C-terminal unbound polyP polyQ disordered coiled coil polyQ protein protein X polyP coiled coil polyQ
polyQ protein polyQ protein protein X N-terminal coiled coil C-terminal unbound polyP polyQ disordered coiled coil polyQ protein bound protein X coiled coil polyQ polyP
ATXN1Q82NT is toxic ATXN1Q82NT aggregates Spyros Petrakis Erich Wanker Toxicity: transfection into COS-1 cells (monkey fibroblasts), caspase activity assay Production of aggregates: filter retardation assay Erich Wanker Petrakis et al. (2012) PLoS Genetics
interactors that change ATXN1Q82NT toxicity
MED15 PUM1
MED15 GST PUM1
GST
Normal polyQ protein CC polyQ disordered CC partner
Normal polyQ protein CC polyQ disordered CC partner
Toxic polyQ protein Normal polyQ protein CC polyQ disordered CC partner polyQ alpha-helix
Toxic polyQ protein Normal polyQ protein beta-aggregates Normal polyQ protein CC polyQ disordered CC partner polyQ alpha-helix
Toxic polyQ protein Normal polyQ protein beta-aggregates Normal polyQ protein CC polyQ disordered CC partner polyQ alpha-helix polyQ beta-aggregates
Normal polyQ protein Toxic polyQ protein CC polyQ polyQ disordered beta-aggregates CC partner polyQ alpha-helix polyQ beta-aggregates
increased beta-aggregates Normal polyQ protein Toxic polyQ protein CC polyQ polyQ disordered beta-aggregates CC partner polyQ alpha-helix polyQ increased beta-aggregates non-CC partner
increased beta-aggregates Toxic polyQ protein polyQ beta-aggregates Normal polyQ protein CC polyQ disordered CC partner polyQ increased beta-aggregates polyQ alpha-helix non-CC partner
increased beta-aggregates Toxic polyQ protein polyQ beta-aggregates Normal polyQ protein CC polyQ disordered CC partner polyQ increased beta-aggregates polyQ alpha-helix non-CC partner
increased beta-aggregates Normal polyQ protein Toxic polyQ protein CC polyQ polyQ disordered beta-aggregates polyQ increased beta-aggregates CC partner polyQ alpha-helix non-CC partner
increased beta-aggregates Normal polyQ protein Toxic polyQ protein CC polyQ polyQ disordered beta-aggregates polyQ increased beta-aggregates CC partner polyQ alpha-helix non-CC partner
increased beta-aggregates Normal polyQ protein Toxic polyQ protein CC polyQ polyQ disordered beta-aggregates polyQ increased beta-aggregates CC partner polyQ alpha-helix non-CC partner
Caudate nucleus network 66 proteins 84 interactions HTT network 509 proteins 1319 interactions Erich Wanker Brain network 88 proteins 113 interactions Caudate nucleus network 66 proteins 84 interactions Matthias Futschik HD dysreg 14 proteins 13 interactions David Fournier Stroedicke et al. (2015) Genome Research
CRMP1 MED15 CRMP is the drosophila protein
Exercise 1/2. Search for a polyQ insertion in the MR family Open in jalview the alignment of the mineralocorticoid receptor: MR1_fasta.txt Find a polyQ insertion. Do you see any other biased region nearby?
Clustering proteins FastaHerder2 Pablo Mier Mier and Andrade-Navarro (2016) J. Comp. Biol.
Clustering proteins polyQ Escherichia Pablo Mier Mier and Andrade-Navarro (2016) J. Comp. Biol.
Context of polyX Pablo Mier Mier et al. In revision
polyQ followed by polyP dependency Context of polyX Pablo Mier polyQ followed by polyP dependency Mier et al. In revision
Species specific differences Context of polyX Pablo Mier Species specific differences Mier et al. In revision
Composition of linkers Daniel Brüne Pablo Mier Brüne et al. In preparation
Composition of linkers Daniel Brüne Pablo Mier 38 species: 9 Bacteria 12 Archaea 17 Eukaryota Brüne et al. In preparation
Composition of linkers Daniel Brüne Pablo Mier DNA binding domain Brüne et al. In preparation
3D context of polyQ 3D 3D Franziska Totzeck Pablo Mier polyQ Totzek et al. Submitted
3D context of polyQ Franziska Totzeck Pablo Mier Totzek et al. Submitted
3D context of polyQ Franziska Totzeck Pablo Mier Totzek et al. Submitted
3D context of polyQ Franziska Totzeck Pablo Mier Totzek et al. Submitted
3D context of polyQ Franziska Totzeck Pablo Mier Totzek et al. Submitted
polyQ variability Felix Korda (Joachim Burger)
Exercise 2/2. Find a 3D of a polyQ ortholog Go to FASTAHERDER2: http://cbdm-01.zdv.uni-mainz.de/~munoz/fh2/ Find a cluster containing polyQ and a PDB using mode 4 Find the structure surrounding the place of polyQ insertion Any problems?
Exercise 2/2. Find a 3D of a polyQ ortholog Go to FASTAHERDER2: http://cbdm-01.zdv.uni-mainz.de/~munoz/fh2/ Find a cluster containing polyQ and a PDB using mode 4 Find the structure surrounding the place of polyQ insertion Any problems? If yes, then use this example: Species: “Escherichia coli”, PDB “yes”, and polyQ “yes” Get the E. coli sequence and the one with polyQ and align them. Can you see the polyQ insertions? Compare to PDB:4JNF (from DNAK_ECOLI P0A6Y8)
Exercise 2/2. Find a 3D of a polyQ ortholog FH2 mode 3 with C4YKT4 / Candida albicans 288 aa with two polyQ Align and compare to P01123 S. cerevisiae 206 alpha-helix and polyQ inserts after. See PDB 2BCG chain Y = YPT1