Unresolved orthology and peculiar coding sequence properties of lamprey genes: the KCNA gene family as test case.

BACKGROUND: In understanding the evolutionary process of vertebrates, cyclostomes (hagfishes and lamprey) occupy crucial positions. Resolving molecular phylogenetic relationships of cyclostome genes with gnathostomes (jawed vertebrates) genes is indispensable in deciphering both the species tree and gene trees. However, molecular phylogenetic analyses, especially those including lamprey genes, have produced highly discordant results between gene families. To efficiently scrutinize this problem using partial genome assemblies of early vertebrates, we focused on the potassium voltage-gated channel, shaker-related (KCNA) family, whose members are mostly single-exon. RESULTS: Seven sea lamprey KCNA genes as well as six elephant shark genes were identified, and their orthologies to bony vertebrate subgroups were assessed. In contrast to robustly supported orthology of the elephant shark genes to gnathostome subgroups, clear orthology of any sea lamprey gene could not be established. Notably, sea lamprey KCNA sequences displayed unique codon usage pattern and amino acid composition, probably associated with exceptionally high GC-content in their coding regions. This lamprey-specific property of coding sequences was also observed generally for genes outside this gene family. CONCLUSIONS: Our results suggest that secondary modifications of sequence properties unique to the lamprey lineage may be one of the factors preventing robust orthology assessments of lamprey genes, which deserves further genome-wide validation. The lamprey lineage-specific alteration of protein-coding sequence properties needs to be taken into consideration in tackling the key questions about early vertebrate evolution.

A grapevine Shaker inward K(+) channel activated by the calcineurin B-like calcium sensor 1-protein kinase CIPK23 network is expressed in grape berries under drought stress conditions.

Grapevine (Vitis vinifera), the genome sequence of which has recently been reported, is considered as a model species to study fleshy fruit development and acid fruit physiology. Grape berry acidity is quantitatively and qualitatively affected upon increased K(+) accumulation, resulting in deleterious effects on fruit (and wine) quality. Aiming at identifying molecular determinants of K(+) transport in grapevine, we have identified a K(+) channel, named VvK1.1, from the Shaker family. In silico analyses indicated that VvK1.1 is the grapevine counterpart of the Arabidopsis AKT1 channel, known to dominate the plasma membrane inward conductance to K(+) in root periphery cells, and to play a major role in K(+) uptake from the soil solution. VvK1.1 shares common functional properties with AKT1, such as inward rectification (resulting from voltage sensitivity) or regulation by calcineurin B-like (CBL)-interacting protein kinase (CIPK) and Ca(2+)-sensing CBL partners (shown upon heterologous expression in Xenopus oocytes). It also displays distinctive features such as activation at much more negative membrane voltages or expression strongly sensitive to drought stress and ABA (upregulation in aerial parts, downregulation in roots). In roots, VvK1.1 is mainly expressed in cortical cells, like AKT1. In aerial parts, VvK1.1 transcripts were detected in most organs, with expression levels being the highest in the berries. VvK1.1 expression in the berry is localized in the phloem vasculature and pip teguments, and displays strong upregulation upon drought stress, by about 10-fold.VvK1.1 could thus play a major role in K(+) loading into berry tissues, especially upon drought stress.

Seizure activity affects neuroglial Kv1 channel immunoreactivities in the gerbil hippocampus.

In order to confirm the species-specific distribution of voltage-gated K(+) (Kv) channels and the definitive relationship between their immunoreactivities and seizure activity, we investigated Kv1 channel immunoreactivities in the hippocampus of seizure resistant (SR) and seizure sensitive (SS) gerbils. There was distinct difference of the Kv1 channel subtypes immunoreactivity in the hippocampi in both SR and SS gerbils. Kv1.1, Kv1.2, Kv1.3, Kv1.4, and Kv1.6 immunoreactivities in the SS gerbil hippocampus were lower than that in the SR gerbil hippocampus. However, Kv1 immunoreactivities were obviously presented in astrocyte within the stratum radiatum of the CA1 region of pre-seizure SS gerbil hippocampus. Following seizure-onset, Kv1 immunoreactivities (except Kv1.5) were markedly elevated, whereas their immunoreactivites in astrocytes were down-regulated. Therefore, the present study demonstrates that seizure activity may distinctly affect neuroglial Kv1 immunoreactivities in the gerbil hippocampus.

4-aminopyridine prevents the conformational changes associated with p/c-type inactivation in shaker channels.

The effect of 4-aminopyridine (4-AP) on Kv channel activation has been extensively investigated, but its interaction with inactivation is less well understood. Voltage-clamp fluorimetry was used to directly monitor the action of 4-AP on conformational changes associated with slow inactivation of Shaker channels. Tetramethylrhodamine-5-maleimide was used to fluorescently label substituted cysteine residues in the S3-S4 linker (A359C) and pore (S424C). Activation- and inactivation-induced changes in fluorophore microenvironment produced fast and slow phases of fluorescence that were modified by 4-AP. In Shaker A359C, 4-AP block reduced the slow-phase contribution from 61 +/- 3 to 28 +/- 5%, suggesting that binding inhibits the conformational changes associated with slow inactivation and increased the fast phase that reports channel activation from 39 +/- 3 to 72 +/- 5%. In addition, 4-AP enhanced both fast and slow phases of fluorescence return upon repolarization (tau reduced from 87 +/- 15 to 40 +/- 1 ms and from 739 +/- 83 to 291 +/- 21 ms, respectively), suggesting that deactivation and recovery from inactivation were enhanced. In addition, the effect of 4-AP on the slow phase of fluorescence was dramatically reduced in channels with either reduced (T449V) or permanent P-type (W434F) inactivation. Interestingly, the slow phase of fluorescence return of W434F channels was enhanced by 4-AP, suggesting that 4-AP prevents the transition to C-type inactivation in these channels. These data directly demonstrate that 4-AP prevents slow inactivation of Kv channels and that 4-AP can bind to P-type-inactivated channels and selectively inhibit the onset of C-type inactivation.