novel vertebrate homologues detected for two families of mechanosensitive channels
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1. 4. A Genomic Landscape of Ion Channels. Phylogenetic Trees with Evolutionary Distance combined. Novel vertebrate homologues detected for two families of mechanosensitive channels. HYUN JI KIM and MARK S. P. SANSOM - PowerPoint PPT PresentationTRANSCRIPT
Novel vertebrate homologues detected for two families of mechanosensitive channels.
HYUN JI KIM and MARK S. P. SANSOMStructural Bioinfomatics and Computational Biochemistry Unit, Department of Biochemistry, University of
Oxford, South Parks Road, Oxford, OX1 3QU, UK
*For further information, contact Hyunji Kim Email: [email protected] and Mark Sansom Email: [email protected]
1. Genomic scanning of mechanosensitive channels revealed unprecedented vertebrate homologues of Large and Small conductance MS channels.2. It is speculated that Gly and Aln may serve key residues accounting for mechanosensation observed in families of 2 pore potassium channels, Transient Receptor Potential channels and Large/Small mechanosensitive channels.
Phylogenetic Trees with Evolutionary Distance combined.
4A Vertebrate Homologue of Large-conductance MechanoSensitive Channel
2
A Mammalian Homologue of Small-conductance MechanoSensitive Channel
3 3-D Mapping of Sequence Conservation5
(1)Biggin PC, Sansom MSP (2003) Mechanosensitive Channels: Stress Relief. Current Biology 13(5): R183-R185.
(2) Honore E (2007) The neuronal background K2P channels: focus on TREK1. Nature Reviews Neuroscience 8:251- 261
SBCB website, http://sbcb.bioch.ox.ac.uk.
ReferencesConclusions7
6 Mechanosensitivity is traced down to Gly & Aln.
MscL MscS
.
A) b)
C)
A)Sequence alignment of MscL family, colour-coded for two conserved residues, Gly and Aln.B) Pairwise comparison of profile Hidden Markov Models: Font in proportion to emission
probabilities, whilst letters shown per column correspond to symbols emitted from each state.
Chick4_results
Chim
p4_resultsH
uman4_results
Mouse4_results
Zebra1_resultsC
and_gl_pep_resultsEnce_cu_pep_resultsPara_te_pep_resultsYeast_pep_resultsB
aci_su_pep_resultsC
hla_tr_pep_resultsC
ory_gl_pep_resultsH
alo_sa_pep_resultsM
eth_ja_pep_resultsM
eth_th_pep_resultsM
yco_pn_pep_resultsN
ano_eq_pep_resultsPire_sp_pep_resultsPyro_ho_pep_resultsShig_fl1_pep_resultsStap_au3_pep_resultsStre_co_pep_resultsSulf_to_pep_resultsVibr_ch_pep_results
KvAP;S1-S4Bacteriorhodopsin
MscLMscS
Na+_alphaTRP
ChakKvB2
clcAKcsA;S5-S6
nAChR;LBDCa2+_beta1
Ca2+_beta4Kv1.2;S1-S4
ENaC7TM_class1
NBD1SUR1
0
100
200
300
400
500
600
Genomic landscape of ion channels & related proteins
Num
ber of homologues
80 genomes in total, were screened for homologues of 17 ion channels and related proteins. ‘WU-BLAST’ was employed as search-engine, and ‘blastp’ was executed with 6 various amino acid substitution matrices, for enhanced sensitivity, whereas ‘MSPcrunch’ was plugged in our automation-script for removing spurious hits, thus higher specificity.
A Genomic Landscape of Ion Channels1
TMH1
TMH3
A) Sequence alignment of MscS family, Gly (yellow) and Aln (sky blue), as in MscL-TMH1. B) Pairwise comparison of two profile Hidden Markov Models, each representing MscS-TMH3 (upper) and a consensus mechanosensitive TM helix (lower). The latter was co-extracted from two additional protein families, which are two pore potassium channels (K2P) and transient receptor potential (TRP) channels.
A)
A)
B)
B)The vertebrate homologues, detected for MscL and MscS, are predicted to encode three TM helices (Pongo and Dr. Cuthbertson’s). Sequence conservation was measured and mapped onto correspondingcrystal structures, 2oau (MscL) and 2oar (MscS), in Chimera. Degree of conservation is expressed by the thickness of worm-shaped presentation and also by the strength of blue shades.
A)A consensus mechanosensitive motif, detected from 4 protein families, which are MscL, MscS, two pore potassium channel (K2P) and TRP channels. One transmembrane helix (TMH) was extracted from each family, such as TMH1 of MscL, TMH3 of MscS, TMH2 of pore 1 and pore 2 of K2P, and TMH4 of TRP channels.
B) Principal Component Analysis showing co-relationship amongst the above 4 protein families.C) A profile Hidden Markov Model was constructed from the assembled alignment on the left, which was
subsequently visualised by HMM Logos. Notable are strong signals detected for conserved Gly and Aln, despite a very low overall sequence identity across those ion channel families.
MscL
TRPV4NOMPC
K2P
MscS
MscSmouse
MscLchick
MscL MscS
MscL_HAEIN
MscL_PSEFL
MscL_BACSU
MscL_CLOPE
MscL_CHICK
MscL_STAAW
2oar
MscL_MYCTU
MscL_SYNY3
MscL_ECOLI
MscS_ECO57
2oau
MscS_mouse
Q51409_BOR
Q55882_SYN
Q34897_BAC
Q05781_MYC
MscS_EDWIC
MscS_SHIFL
Evolutionary distances were calculated from pairwise sequencecomparison (using PHYLIP), based on the two alignments presented for MscL and MscS. Identical pairs are lined in the central diagonal direction.Each shade of blue increments 0.5 in the range of 0 to 3.5.