SPRINT Home UMBER Home Contents Standard Search Advanced Search Relation Search

==SPRINT==> PRINTS View



  selected as


PR01120

Identifier
CLCHANNELPLT  [View Relations]  [View Alignment]  
Accession
PR01120
No. of Motifs
5
Creation Date
06-MAY-1999
Title
Plant CLC chloride channel signature
Database References
PRINTS; PR00762 CLCHANNEL
PRODOM; PD009582; PD008462; PD008463
INTERPRO; IPR002251
Literature References
1. JENTSCH, T.J. AND GUNTHER, W.
Chloride channels: an emerging molecular picture.
BIOESSAYS 19 117-126 (1997).
 
2. JENTSCH, T.J., STEINMEYER, K. AND SCHWARZ, G.
Primary structure of Torpedo marmorata chloride channel isolated by
expression cloning in Xenopus oocytes.
NATURE 348 510-514 (1990).
 
3. SCHMIDT-ROSE, T. AND JENTSCH, T.J.
Transmembrane topology of a CLC chloride channel.
PROC.NATL.ACAD.SCI.U.S.A. 94 7633-7638 (1997).
 
4. LEHMANN-HORN, F., MAILANDER, V., HEINE, R. AND GEORGE, A.L.
Myotonia levior is a chloride channel disorder.
HUM.MOL.GENET. 4 1397-1402 (1995).
 
5. LLOYD, S.E., PEARCE, S.H.S., FISHER, S.E., STEINMEYER, K.,
SCHWAPPACH, B., SCHEINMAN, S.J., HARDING, B., BOLINO, A., DEVOTO, M.,
GOODYER, P., RIGDEN, S.P.A., WRONG, O., JENTSCH, T.J., CRAIG, I.W. AND
THAKKER, R.V.
A common molecular basis for three inherited kidney stone diseases.
NATURE 379 445-449 (1996).
 
6. HECHENBERGER, M., SCHWAPPACH, B., FISCHER, W.N., FROMMER, W.B.,
JENTSCH, T.J. AND STEINMAYER, K.
A family of putative chloride channels from Arabidopsis and functional
complementation of a yeast strain with a CLC gene disruption.
J.BIOL.CHEM. 271 33632-33638 (1996).
 
7. LURIN, C., GEELEN, D., BARBIER-BRYGOO, H., GUERN, J. AND MAUREL, C.
Cloning and functional expression of a plant voltage-dependent chloride
channel.
PLANT CELL 8 701-711 (1996).

Documentation
Chloride channels (CLCs) constitute an evolutionarily well-conserved family
of voltage-gated channels that are structurally unrelated to the other known
voltage-gated channels. They are found in organisms ranging from bacteria to
yeasts and plants, and also to animals. Their functions in higher animals
likely include the regulation of cell volume, control of electrical 
excitability and trans-epithelial transport [1].
 
The first member of the family (CLC-0) was expression-cloned from the
electric organ of Torpedo marmorata [2], and subsequently nine CLC-like
proteins have been cloned from mammals. They are thought to function as
multimers of two or more identical or homologous subunits, and they have
varying tissue distributions and functional properties. To date, CLC-0, 
CLC-1, CLC-2, CLC-4 and CLC-5 have been demonstrated to form functional Cl-
channels; whether the remaining isoforms do so is either contested or 
unproven. One possible explanation for the difficulty in expressing 
activatable Cl- channels is that some of the isoforms may function as Cl- 
channels of intracellular compartments, rather than of the plasma membrane.
However, they are all thought to have a similar transmembrane (TM) topology,
initial hydropathy analysis suggesting 13 hydrophobic stretches long enough
to form putative TM domains [2]. Recently, the postulated TM topology has
been revised, and it now seems likely that the CLCs have 10 (or possibly 12)
TM domains, with both N- and C-termini residing in the cytoplasm [3].
 
A number of human disease-causing mutations have been identified in the
genes encoding CLCs. Mutations in CLCN1, the gene encoding CLC-1, the major
skeletal muscle Cl- channel, lead to both recessively and dominantly-
inherited forms of muscle stiffness or myotonia [4]. Similarly, mutations
in CLCN5, which encodes CLC-5, a renal Cl- channel, lead to several forms 
of inherited kidney stone disease [5]. These mutations have been
demonstrated to reduce or abolish CLC function.
 
In plants, chloride channels contribute to a number of plant-specific
functions, such as regulation of turgor, stomatal movement, nutrient
transport and metal tolerance. By contrast with Cl- channels in animal
cells, they are also responsible for the generation of action potentials.
The best documented examples are the chloride channels of guard cells,
which control opening and closing of stomata. Recently, four homologous
proteins that belong to the CLC family have been cloned from Arabidopsis
thaliana (mouse ear-cress) [6]. Hydropathy analysis suggests that they have
a similar membrane topology to other CLC proteins, with up to 12 TM domains.
Expression in Xenopus oocytes failed to generate measurable Cl- currents, 
although protein analysis suggested they had been synthesised and inserted
into cell membranes. However, similar CLC proteins have since been cloned 
from other plants, and one, CIC-Nt1 (from tobacco), has been demonstrated to
form funtional Cl- channels, suggesting that at least some of these proteins
do function as Cl- channels in plants (7).
 
CLCHANNELPLT is a 5-element fingerprint that provides a signature for plant
CLC voltage-gated Cl- channels. The fingerprint was derived from an initial
alignment of 3 sequences: the motifs were drawn from conserved regions from 
the N-terminal two thirds of the alignment, focusing on those sections that 
characterise the plant CLC Cl- channels but distinguish them from others -
motif 1 resides within the putative cytoplasmic N-terminus; motif 2 lies
within the sixth hydrophilic domain; motif 3 resides within the sixth
hydrophobic domain; motif 4 encodes the C-terminus of the sixth hydrophobic
domain, and leads into the subsequent hydrophilic region; and motif 5 lies
within the ninth hydrophilic domain. Two iterations on SPTR37_9f were 
required to reach convergence, at which point a true set comprising 9
sequences was identified.
Summary Information
9 codes involving  5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
599999
400000
300000
200000
12345
True Positives
O64990        O81491        P92941        P92942        
P92943 P93567 Q40485 Q96282
Q96325
Sequence Titles
O64990      ANION CHANNEL PROTEIN - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS). 
O81491 F9D12.10 PROTEIN - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
P92941 CLC-A CHLORIDE CHANNEL PROTEIN - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
P92942 CLC-B CHLORIDE CHANNEL PROTEIN - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
P92943 CLC-D CHLORIDE CHANNEL PROTEIN - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
P93567 CHLORIDE CHANNEL STCLC1 - SOLANUM TUBEROSUM (POTATO).
Q40485 VOLTAGE-DEPENDENT CHLORIDE CHANNEL - NICOTIANA TABACUM (COMMON TOBACCO).
Q96282 CHLORIDE CHANNEL - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
Q96325 VOLTAGE-GATED CHLORIDE CHANNEL - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
Scan History
SPTR37_9f  2  300  NSINGLE    
Initial Motifs
Motif 1  width=9
Element Seqn Id St Int Rpt
EINENDLFK O64990 60 60 -
EINENDLFK P92941 60 60 -
EINENDLFK Q96325 60 60 -

Motif 2 width=9
Element Seqn Id St Int Rpt
VATWWRSAL O64990 271 202 -
VATWWRSAL P92941 271 202 -
VATWWRSAL Q96325 271 202 -

Motif 3 width=11
Element Seqn Id St Int Rpt
FSTAVVVVVLR O64990 285 5 -
FSTAVVVVVLR P92941 285 5 -
FSTAVVVVVLR Q96325 285 5 -

Motif 4 width=8
Element Seqn Id St Int Rpt
SGKCGLFG O64990 303 7 -
SGKCGLFG P92941 303 7 -
SGKCGLFG Q96325 303 7 -

Motif 5 width=17
Element Seqn Id St Int Rpt
LSTLLLTTNDDAVRNIF O64990 427 116 -
LSTLLLTTNDDAVRNIF P92941 427 116 -
LSTLLLTTNDDAVRKHF Q96325 425 114 -
Final Motifs
Motif 1  width=9
Element Seqn Id St Int Rpt
EINENDLFK P92942 59 59 -
EINENDLFK O64990 60 60 -
EINENDLFK P92941 60 60 -
EINENDLFK Q96325 60 60 -
EIIENDLFK Q40485 70 70 -
EIFENDFFK Q96282 69 69 -
DIVENDLFK P93567 55 55 -
EVIENYAYR O81491 50 50 -
EVIENYAYR P92943 50 50 -

Motif 2 width=9
Element Seqn Id St Int Rpt
VATWWRSAL P92942 270 202 -
VATWWRSAL O64990 271 202 -
VATWWRSAL P92941 271 202 -
VATWWRSAL Q96325 271 202 -
VASWWRSAL Q40485 281 202 -
AASWWRNAL Q96282 280 202 -
IASWWRSAL P93567 266 202 -
VTSWWRSQL O81491 273 214 -
VTSWWRSQL P92943 260 201 -

Motif 3 width=11
Element Seqn Id St Int Rpt
FSTAVVVVVLR P92942 284 5 -
FSTAVVVVVLR O64990 285 5 -
FSTAVVVVVLR P92941 285 5 -
FSTAVVVVVLR Q96325 285 5 -
FSTAVVAMVLR Q40485 295 5 -
FTTAVVAVVLR Q96282 294 5 -
FTTAIVAMVLR P93567 280 5 -
FTSAIVAVVVR O81491 287 5 -
FTSAIVAVVVR P92943 274 5 -

Motif 4 width=8
Element Seqn Id St Int Rpt
SGKCGLFG P92942 302 7 -
SGKCGLFG O64990 303 7 -
SGKCGLFG P92941 303 7 -
SGKCGLFG Q96325 303 7 -
SGKCGLFG Q40485 313 7 -
SGRCGLFG Q96282 312 7 -
GGNCGLFG P93567 298 7 -
SGICGHFG O81491 305 7 -
SGICGHFG P92943 292 7 -

Motif 5 width=17
Element Seqn Id St Int Rpt
LATLLLTTNDDAVRNLF P92942 426 116 -
LSTLLLTTNDDAVRNIF O64990 427 116 -
LSTLLLTTNDDAVRNIF P92941 427 116 -
LSTLLLTTNDDAVRKHF Q96325 425 114 -
LASLFMNTNDDAIRNLF Q40485 437 116 -
LSSLLLNTNDDAIRNLF Q96282 437 117 -
LASLFLNTNDDAIRNLF P93567 422 116 -
LATIFFNTQDDAIRNLF O81491 435 122 -
LATIFFNTQDDAIRNLF P92943 422 122 -