For a project within the iGEM competition, we are willing to construct a new biological biomarker detection system. For a read-out, we are considering an electric readout. Therefore, we want to stimulate the opening of ion channels upon a secondary messenger signal. Most bacterial ion channels we have found so far are uniquely stimulated by an extracellular ligand.
We are happy for all suggestions upon this topic and the expertise in the field.
They are proteins characterised by the domain PF02932/IPR006029. Check PFAM/InterPro or Superfamily, they have info about protein families, diversity, species where is found... not sure is cytosol activated though
In the link below there is a list of bacterial genomes with those domains/proteins. They only have 1 sequence per genome compared to the multiple copies in some animals. There is also one copy from one Archaea, Candidatus Nitrosoarchaeum limnia.
http://supfam.cs.bris.ac.uk/SUPERFAMILY/cgi-bin/genome.cgi?sf=90112&listtype=sf&cgi_bacd=yes
Maybe a bacterial CNG channel, like CNG from Mesorhizobium loti (MLCNG) ? I don't know much about it, but it's probably worth having a look...
See Clayton et al., Structural Basis of Ligand Activation in a Cyclic Nucleotide Regulated Potassium Channel, Cell, 2004
doi:10.1016/j.cell.2004.10.030
The best known (as far as I know) is the GLIC receptor (bacterial (Gloeobacter) Ligand-gated Ion Channel, homolog to the nicotinic acetylcholine receptors), activated by intracellular protons
http://www.nature.com/nsmb/journal/v19/n6/abs/nsmb.2307.html
GLIC activation has essentially been shown to occur from extracellular application of protons - although a modulation by intracellular pH may still be possible.
Although the nature of activation is not well understood in prokaryotes, eukaryotic Kir channels are activated by cytosolic PIP2. In contrast, PIP2 inhibits the bacterial KirBac1.1 channel, however, PIP2 is not typically found in bacterial membranes. Here is an interesting article about how lipids could potentially drive the evolution of ion channels:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3241986/
You may refer the below mentioned article in Nature:
Marie S Prevost, Ludovic Sauguet, Hugues Nury, Catherine Van Renterghem, Christèle Huon, Frederic Poitevin, Marc Baaden, Marc Delarue & Pierre-Jean Corringer, 2012, A locally closed conformation of a bacterial pentameric proton-gated ion channel, Nature Structural & Molecular Biology 19, 642–649 (2012).
I think it will helpful for you:
Phylogenetic conservation of protein–lipid motifs in pentameric ligand-gated ion channels, Francisco J. Barrantes, Biochimica et Biophysica Acta (BBA) - Biomembranes, Available online 31 March 2015
The bCNG channel family has members found in over 180 different genomes, we predict that these gate in response to cyclic nucleotides in the cytosol. These channels are a part of the MscS Superfamily of ion channels, of which some members are predicted to have different binding domains. Here is the first paper on bCNG channels.
http://www.sciencedirect.com/science/article/pii/S0005273610001859
GluR0 from Nostoc punctiforme (NpGluR0) or from Synechocystis are bacterial homologues of the ionotropic glutamate receptor (iGluR).
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