Further studies of ion channels in the electroreceptor of the skate through deep sequencing, cloning and cross species comparisons

• Published in: Gene Vol. 718; p. 143989
• Main Authors: Clusin, William T., Wu, Ting-Hsuan, Shi, Ling-Fang, Kao, Peter N.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 15.11.2019
• Subjects: amino acids; Ampulla of Lorenzini; BK channels; calcium; calcium channels; comparative study; Deep sequencing; electric potential difference; genes; high-throughput nucleotide sequencing; humans; Kv1.1; Kv1.5; messenger RNA; Petromyzontiformes; phylogeny; Potassium channels; reverse transcriptase polymerase chain reaction; Rhincodon typus; Scyliorhinidae; seawater; sharks; synaptic transmission; Ampulla of Lorenzini; nBlast; Deep sequencing; BK; Potassium channels; BK channels; TEA; Hz; NIP; SNP; RT-PCR; SK; Kv1.5; PCR; Kv1.1; B(K) channels
• ISSN: 0378-1119; 1879-0038; 1879-0038
• DOI: 10.1016/j.gene.2019.143989

Our comparative studies seek to understand the structure and function of ion channels in cartilaginous fish that can detect very low voltage gradients in seawater. The principal channels of the electroreceptor include a calcium activated K channel whose α subunit is Kcnma1, and a voltage-dependent calcium channel, Cacna1d. It has also been suggested based on physiological and pharmacological evidence that a voltage-gated K channel is present in the basal membranes of the receptor cells which modulates synaptic transmitter release. Large conductance calcium-activated K channels (BK) are comprised of four α subunits, encoded by Kcnma1 and modulatory β subunits of the Kcnmb class. We recently cloned and published the skate Kcnma1 gene and most of Kcnmb4 using purified mRNA of homogenized electroreceptors. Bellono et al. have recently performed RNA sequencing (RNA-seq) on purified mRNA from skate electroreceptors and found several ion channels including Kcnma1. We searched the Bellono et al. RNA-seq repository for additional channels and subunits. Our most significant findings are the presence of two Shaker type voltage dependent K channel sequences which are grouped together as isoforms in the data repository. The larger of these is a skate ortholog of the voltage dependent fast potassium channel Kv1.1, which is expressed at appreciable levels. The second ortholog is similar to Kv1.5 but has fewer N-terminal amino acids than other species. The sequence for Kv1.5 in the skate is very strongly aligned with the recently reported sequence for potassium channels in the electroreceptors of the cat shark, S. retifer, which also modulate synaptic transmission. The latter channel was designated as Kv1.3 in the initial report, but we suggest that these channels are actually orthologs of each other, and that Kv1.5 is the prevailing designation. We also found a beta subunit sequence (Kcnab2) which may co-assemble with one or both of the voltage gated channels. The new channels and subunits were verified by RT-PCR and the Kv1.1 sequence was confirmed by cloning. We also searched the RNA-seq repository for accessory subunits of Kcnma1, and found a computer-generated assembly that contained a complete sequence of its β subunit, Kcnmb2. Skate Kcnmb2 has a total of 279 amino acids, with 51 novel amino acids at the N-terminus which may play a specific physiological role. This sequence was confirmed by PCR and cloning. However, skate Kcnmb2 is expressed at low levels in the electroreceptor compared to Kcnma1 and skate Kcnmb1 is absent. The evolutionary origin of the newly described K channels and their subunits was studied by alignments with mammalian sequences, including human, and also those in related fish: the whale shark (R. typus), the ghost shark (C.milii), and (S. retifer). There are also orthologous K channels of the lamprey, which has electroreceptors. Tree building and bootstrap programs were used to confirm phylogenetic inferences. Further research should focus on the subcellular locations of these channels, their gating behavior, and the effects of accessory subunits on gating. •We searched deep sequencing files for K channels in skate electroreceptor.•We found two voltage gated Shaker type channels, Kv1.1, Kv1.5, and their β subunit.•We also found a β subunit of the BK channel with 51 novel N-terminal amino acids.•Based on earlier studies Kv1.1 and Kv1.5 probably mediate oscillations that explain sensitivity.•We computed a phylogenetic tree of the Shaker type potassium channels and we review the physiological correlates in selected species.