Potassium channels

From Purdue Genomics Database Facility

Contents 1 Potassium channels in Selaginella 2 Large conductance calcium-activated K+ channels 3 Tandem Pore K+ Channels 4 References 5 More Information

Potassium channels in Selaginella

The genomes of Selaginella were screened for the occurance of charactistic fingerprints known from plant potassium channels. In total in each of the two sequenced genomes 6 loci coding for potassium channel subunits could be identified. Four of the identified polypeptides belong to the class of "Tandem Pore K⁺ Channels" (TPK). The other two (SmKC1 and SmKC2) have homologs in Physcomitrella and share similarities (up to 20% identities in larger core regions) to large conductance calcium-activated K⁺ channels from human and rat.

Large conductance calcium-activated K⁺ channels

Channels of this type are built of 4 alpha subunits whereby each subunit contributes equally to the permeation pathway for potassium ions. In animals large conductance calcium-activated K⁺ channels are characterized by the fact that they can be independently activated by either membrane depolarization or intracellular calcium ions, or synergistically by both signals. It remains to be elucidated whether large conductance calcium-activated K⁺ channels from mosses and spikemosses are voltage-activated.

In comparison with Aribidopsis two observations are worth to be noted:

1. similar proteins were not found in Arabidopsis
2. Shaker-like voltage-gated potassium channels cound not be identified in Selaginella

In Arabidopsis there are nine genes coding for Shaker-like voltage-gated potassium channel subunits. Channels of this class are important for the uptake of K⁺ from the soil (besides high-affinity K⁺ transporters, e.g. H⁺/K⁺-symporters), but mainly for the redistribution of K⁺ within the plant (Véry and Sentenac, 2003; Lebaudy et al., 2007).

Tandem Pore K⁺ Channels

The central permeation pathway of Tandem Pore K⁺ Channels is built by the assembly of two channel subunits. Each subunit contains two P-regions that both contribute to the forming of the selectivity filter of the channel. In Selaginella four TPKs (SmTPK1, SmTPK2, SmTPK3, SmTPK4) could be identified.

Phylogenic relationship between TPK proteins from Arabidopsis thaliana and Selaginella moellendorffii. Minimum Evolution (ME) consensus tree under the JTT + Gamma evolutionary model (chosen by ProtTest (Abascal et al., 2005)). Gamma distribution was split into 8 categories to model rate heterogeneity among sites. Bootstrap analysis were done with 1000 replicates for TPKs. Gamma distribution and protein distances were computed with TREE-PUZZLE and PUZZLEBOOT (Schmidt et al., 2002). ME trees were computed with "fitch" from the Software package PHYLIP (Felsenstein, 2005).

Phylogenetic analyses revealed that the group of TPKs clearly subdivides into two subclasses. One comprises the channels AtTPK1, SmTPK1, and SmTPK4. The other is built of the channels AtTPK2, AtTPK3, AtTPK4, AtTPK5, SmTPK2, and SmTPK3. This separation was not uncovered without the Selaginella data.

Experimental analyses allowed also to subdivide the class of TPKs in Arabidopsis into two sub-groups: Sub-group I comprises the channels AtTPK1, AtTPK2, AtTPK3, and AtTPK5; sub-group II comprises the channel AtTPK4 (displayed in red in the tree above). All TPKs of sub-group I were found to be targeted to the vacuolar membrane and to comprise Ca²⁺-binding EF-hands in the cytosolic C-terminal region (Voelker et al., 2006). In contrast, AtTPK4 was targeted to the plasma membrane and does not comprise EF-hands (Becker et al., 2004). Because SmTPK1, SmTPK2, SmTPK3, and SmTPK4 comprise EF-hands all TPKs identified in Selaginella might belong to the sub-group I. Thus, the working hypothesis is that also the Selaginella TPKs are vacuolar, Ca²⁺-regulated K⁺ channels. Very likely, the specialization of AtTPK4-like channels occured only in angiosperms. The phylogenetic analysis suggests that the specialization of AtTPK4-like channels occured later in plant evolution. This is also supported by the fact that AtTPK4 has a restricted expression pattern that is mainly limited to pollen (Becker et al., 2004) which is a seed plant specific structure.

Table 1: TPKs in Selaginella moellendorffii and Arabidopsis thaliana

Selaginella moellendorffii	Arabidopsis thaliana
Name (Protein ID)	Name (locus)
SmTPK1 (450200) SmTPK2 (450196) SmTPK3 (105305) SmTPK4 (450202)	AtTPK1 (AT5G55630) AtTPK2 (AT5G46370) AtTPK3 (AT4G18160) AtTPK4 (AT1G02510) AtTPK5 (AT4G01840)

References

• Abascal F, Zardoya R, Posada D (2005) ProtTest: Selection of best-fit models of protein evolution. Bioinformatics 21:2104-2105.

• Becker D, Geiger D, Dunkel M, Roller A, Bertl A, Latz A, Carpaneto A, Dietrich P, Roelfsema MR, Voelker C, Schmidt D, Mueller-Roeber B, Czempinski K, Hedrich R. (2004) AtTPK4, an Arabidopsis tandem-pore K⁺ channel, poised to control the pollen membrane voltage in a pH- and Ca²⁺-dependent manner. Proc Natl Acad Sci U S A. 101(44):15621-15626.

• Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.

• Lebaudy A, Véry AA, Sentenac H (2007) K⁺ channel activity in plants: genes, regulations and functions. FEBS Lett. 581(12):2357-2366.

• Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504.

• Véry AA, Sentenac H. (2003) Molecular mechanisms and regulation of K⁺ transport in higher plants. Annu Rev Plant Biol. 54:575-603.

• Voelker C, Schmidt D, Mueller-Roeber B, Czempinski K. (2006) Members of the Arabidopsis AtTPK/KCO family form homomeric vacuolar channels in planta. Plant J. 48(2):296-306.

More Information

For further information and questions please contact:

Ingo Dreyer <dreyer at uni-potsdam.de>

Luiz Gustavo Guedes Correa <correa at uni-potsdam.de>

Diego Mauricio Riaño-Pachón <diriano at uni-potsdam.de>