Download AMPK and apoptosis

AMPK and Apoptosis
Emeline Van Goethem
José Manuel López
Apoptosis or programmed cell death is an important part of the
development of all multicellular organisms and controls
homeostasis and tissue modeling. In the cell there are mitochondrial
dependent and independent pathways to induce apoptosis.
Mitochondria
Cytochrome c
Caspase activation
AMPK: Energy Homeostasis and Apoptosis
AMPK is conserved between different species
(Blast & ClustalW analysis)
Rat
Mouse
Human
Xenopus
Drosophila
C.elegans
-----------MAEKQKHDG-RVKIGHYILGDTLGVGTFGKVKVGKHELTGHKVAVKILN
MRRLSSWRKMATAEKQKHDG-RVKIGHYILGDTLGVGTFGKVKVGKHELTGHKVAVKILN
MRRLSSWRKMATAEKQKHDG-RVKIGHYILGDTLGVGTFGKVKVGKHELTGHKVAVKILN
MRRLSSLMKMAADKQKHHDG-RVKIGHYILGDTLGVGTFGKVKVGKHELTGHKVAVKILN
MPQMRAAAAEAVAAGSANGQPLVKIGHYLLGATLGTGTFGKVKIGEHQITRVKVAVKILN
---MPPSGRFDRTIALAGTG-HLKIGNFVIKETIGKGAFGAVKRGTHIQTGYDVAIKILN
:***:::: *:* *:** ** * * * .**:****
Rat
Mouse
Human
Xenopus
Drosophila
C.elegans
RQKIRSLDVVGKIRREIQNLKLFRHPHIIKLYQVISTPSDIFMVMEYVSGGELFDYICKN
RQKIRSLDVVGKIRREIQNLKLFRHPHIIKLYQVISTPSDIFMVMEYVSGGELFDYICKN
RQKIRSLDVVGKIRREIQNLKLFRHPHIIKLYQVISTPSDIFMVMEYVSGGELFDYICKN
RQKIRSLDVVGKIRREIQNLKLFRHPHIIKLYQVISTPTDIFMVMEYVAGGELFDYICKN
RQKIKSLDVVGKIRREIQNLKLFRHPHIIKLYQVISTPSDIFMIMEYVSGGELFDYIVKH
RGRMKGLGTVNKTRNEIDNLQKLTHPHITRLFRVISTPSDIFLVMELVSGGELFSYITRK
* :::.*..*.* *.**:**: : **** :*::*****:***::** *:*****.** ::
Rat
Mouse
Human
Xenopus
Drosophila
C.elegans
GRLDEKESRRLFQQILSGVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGE
GRLDEKESRRLFQQILSGVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGE
GRLDEKESRRLFQQILSGVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGE
GKLDEKESRRLFQQILSGVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMADGE
GKLQEHQARRFFQQIISGVDYCHRHMIVHRDLKPENLLLDHNMHVKIADFGLSNMMLDGE
GALPIRESRRYFQQIISGVSYCHNHMIVHRDLKPENLLLDANKNIKIADFGLSNYMTDGD
* * :::** ****:***.***.**:*********:*** : : ********* * **:
Rat
Mouse
Human
Xenopus
Drosophila
C.elegans
FLRTSCGSPNYAAPEVISGRLYAGPEVDIWSSGVILYALLCGTLPFDDDHVPTLFKKICD
FLRTSCGSPNYAAPEVISGRLYAGPEVDIWSSGVILYALLCGTLPFDDDHVPTLFKKICD
FLRTSCGSPNYAAPEVISGRLYAGPEVDIWSSGVILYALLCGTLPFDDDHVPTLFKKICD
FLRTSCGSPNYAAPEVISGRLYAGPEVDIWSCGVILYALLCGTLPFDDDHVPTLFKKICD
FLRTSCGSPNYAAPEVISGKLYAGPEVDIWSCGVILYALLCGTLPFDDEHVPTLFRKIKS
LLSTACGSPNYAAPELISNKLYVGPEVDLWSCGVILYAMLCGTLPFDDQNVPTLFAKIKS
:* *:**********:**.:**.*****:**.******:*********::***** ** .
Rat
Mouse
Human
Xenopus
Drosophila
C.elegans
GIFYTPQYLNPSVISLLKHMLQVDPMKRATIKDIREHEWFKQDLPKYLFPEDPSYSSTMI
GIFYTPQYLNPSVISLLKHMLQVDPMKRAAIKDIREHEWFKQDLPKYLFPEDPSYSSTMI
GIFYTPQYLNPSVISLLKHMLQVDPMKRATIKDIREHEWFKQDLPKYLFPEDPSYSSTMI
GIFYTPQYLNPPVISLLKHMLLVDPMKRATIKDIREHEWFKQDLPKYLFPEDPSYSTNMI
GIFPIPEYLNKQVVNLVCQMLQVDPLKRANIEEIKKHEWFQKDLPAYLFPSSIEQDSNVI
GRYTVPYSMEKQAADLISTMLQVDPVKRADVKRIVNHSWFRIDLPYYLFPECEN-ESSIV
* : * :: . .*: ** ***:*** :: * :*.**: *** ****. . .:.::
Rat
Mouse
Human
Xenopus
Drosophila
C.elegans
DDEALKEVCEKFECSEEEVLSCLYNRNHQDPLAVAYHLIIDNRRIMNEAK-------DFY
DDEALKEVCEKFECSEEEVLSCLYNRNHQDPLAVAYHLIIDNRRIMNEAK-------DFY
DDEALKEVCEKFECSEEEVLSCLYNRNHQDPLAVAYHLIIDNRRIMNEAK-------DFY
DDEALKEVCDKCECTEEEVLSCLYSRNHQDPLAVAYHLIIDNRRIMNEAK-------DFY
DTYAVAEVCTKFGVKETEVHNSLLSGDPHDQLAIAYHLIIDNKRFADDAANQINEINNFF
DIDVVQSVAEKFDVKEEDVTGALLAEDHHHFLCIAYRLEVNHKRNADESS---------* .: .*. *
.* :* ..*
: :. *.:**:* ::::* :::
Rat
Mouse
Human
Xenopus
Drosophila
C.elegans
LATSPP--------DSFLDDHH---------------------------------LTRPH
LATSPP--------DSFLDDHH---------------------------------LTRPH
LATSPP--------DSFLDDHH---------------------------------LTRPH
LATSPP--------DSFMEEPP---------------------------------ISRPH
VAGSPPPPPPPPVPQSSMDHQAPLATVTVGGGTSASSGTATPVPPVAGGTPSSTIPIRPH
--------------QKAMEDFW--------------------------------EIGKTM
:. ::.
:.
Rat
Mouse
Human
Xenopus
Drosophila
C.elegans
PERVPFLVAE--TPRARHTLDELNPQKSKHQG--VRKAKWHLGIRSQSRPNDIMAEVCRA
PERVPFLVAE--TPRARHTLDELNPQKSKHQG--VRKAKWHLGIRSQSRPNDIMAEVCRA
PERVPFLVAE--TPRARHTLDELNPQKSKHQG--VRKAKWHLGIRSQSRPNDIMAEVCRA
PERVPFLIAE--SPRQRHTLDELNPQKTKHQVG-VRRAKWHLGIRSQSRPNDIMAEVCRA
PERIAPMRDRQLAMSVQTSGGGAFPEKTARGGTPIKRAKWHLGIRSQSKPNDIMLEVYRA
KMGSTSLPVG---ATTKTNVGRKILEGLKKEQ---KKLTWNLGIRACLDPVETMKHVFLS
. :
: . .
:
:
:: .*:****:
* : * .* :
AIM
Looking for an
Apoptotic
protein
Regulated by
AMPK
Consensus sequence
(X,)XXS/TXXX
FEBS Letters 361 (1995) 191-195
Dale S., et al.
: MVLIF
: R>K>H
Expasy Tools
Scan Prosite
[MVLIF]x(0,1)[RKH]xx[ST]xxx[MVLIF]
Target proteins for AMPK
Homo sapiens
>1000
Xenopus laevis
678
Xenopus laevis + mitochondria
17
VDAC2 (Voltage dependent anion channel 2)
Regulates cytochrome c release / apoptosis
Xenopus VDAC isoforms
(Blast Search)
VDAC2
-AVPPSYADLGKSARDIFNKGYGFGLVKLDVKTKSATGVEFTTSGTSNTDSGKVNGSLET
VDAC1
MAIPPAYVDLGKSARDIFTKGYGFGFIKLDLKTKSENGLEFTSSGSANAETSKVSGNLET
MGC81430
MAVPPTYADLGKSARDVFNKGYGFGLVKLEVKTKSSSGVEFTSSGSSNTDTGKASGNLET
VDAC2
KYKWGEYGLTFTEKWNTDNTLGTEIAIEDQIAKGLKLTFDTTFSPNTGKKSGKVKAAYKQ
VDAC1
KYKWAEYGLTFTEKWNTDNTLGTEITVEDQLAKGLKLTFDSSFSPNTGKKNAKVKSAYKR
MGC81430
KYKMKETGLTFTQKWNTDNTLGTEVALEDKLAKGLKLSLDTTFVPNTGKKSAKLKTSYKR
VDAC2
EYVNLGCDVDFDFAGPAIHGSAVVGYEGWLAGYQMTFDSAKSKLTKNNFAVGYKTGDFQL
VDAC1
EHLNVGCDMDFDIAGPSVRGAVVFGYEGWLAGYQMTFESSKSRVSQSNFAVGYKTDEFQL
MGC81430
DYANLGIDIDLDLAGPTIYGWGVLGYQGWLAGYQMAFDTAKSRLAQNNFALGYTAGDFQL
VDAC2
HTNVNDGSEFAGSIYQKVSDKMETAVNLAWTSGNNSTRFGIAAKYQLDSHAAISAKVNNS
VDAC1
HTNVNDGTDFGGSVYQKVNDKLETAINLAWTAGNSNTRFGIAAKYQIDSDASFSAKVNNS
MGC81430
HTNVNDGTEFGGSVYQKVSKDVETSVSLAWSAGSNNTRFGIGAKYQLDSNTTISAKVNNA
VDAC2
SLVGVGYTQTLRPGVKLTLSALVDGKNINAGGHKLGLGLELEA
VDAC1
SLIGLGYTQTLKPGIKLTLSTLVDGKNINAGGHKLGLGLEFEA
MGC81430
SLIGVGYTQTLRPGVKLTLSALVNGKNFSAGGHKVGLGFELEA
AMPK consensus sequence is preserved in Xenopus VDAC 1,2,3 isoforms
Checking for a transmembrane domain in VDAC2
Kdoolite hydrophobicity result
Query Statistics:
Window Size = 19
Start Position = 1
End Position = 282
Query Length = 282
Effective Length = 264
When the window size is 19, peaks with scores greater than 1.8 (red line ) indicate
possible transmembrane regions. The score at window position 1 is the average
hydropathy of the 19 amino acids from position 1 to position 19 in the input
sequence.
Tyrosine kinase group (Y_kin)
Gene Card FGR
Fgr Kinase
Site
Score
Percentile
Sequence
SA
Y121
0.4203
0.502 %
KAAYKQEYVNLGCDV 1.101
Other Protein Kinases
can phosphorylate VDAC2?
Src homology 2 group (SH2)
Gene Card LCK
Lck SH2
Site
Score
Percentile
Sequence
SA
Y194
0.4264
0.824 %
SEFAGSIYQKVSDKM
0.867
Gene Card GRB2
Grb2 SH2
Site
Score
Percentile
Sequence
SA
Y121
0.5194
0.732 %
KAAYKQEYVNLGCDV 1.101
Scan Site
Motif Scan
Basophilic serine/threonine kinase group (Baso_ST_kin)
Gene Card CAMK2G
Calmodulin dependent Kinase 2
Site
Score
Percentile
Sequence
SA
T155
0.4492
0.219 %
WLAGYQMTFDSAKSK 1.098
Gene Card PRKCA
PKC alpha/beta/gamma
Site
Score
Percentile
Sequence
SA
T106
0.4755
0.973 %
DTTFSPNTGKKSGKV
3.380
Gene Card PRKCM
PKC mu
Site
Score
Percentile
Sequence
SA
S240
0.4821
0.801 %
SAKVNNSSLVGVGYT 0.416
Kinase binding site group (Kin_bind)
Gene Card PDPK1
PDK1 Binding
Site
Score
Percentile
Sequence
E65
0.6102
0.800 %
ETKYKWGEYGLTFTE 0.528
Site
Erk D-domain
Score
Percentile
Sequence
L258
0.5631
RPGVKLTLSALVDGK 0.251
0.135 %
SA
Gene Card MAPK1
SA
PKC
Conclusions
AMPK is conserved in different species
VDAC isoforms (1,2,3) are present in Xenopus
VDAC could be a target of Xenopus AMPK
Open Questions...
Why VDAC does not show hydrophobic domain with Kdoolite program?
How accesible is the AMPK phosphorylation site in VDAC?