, and PLK are all substantially expanded, perhaps reflecting the additional signaling

, and PLK are all substantially expanded, perhaps reflecting the additional signaling complexity required by two nuclei that simultaneously engage in very different processes within the same cell cytoplasm. Also expanded are multiple kinases that interact with the microtubule network , possibly reflecting PF-562271 supplier diversification of cytoskeletal systems. Of the kinase families with known functions, PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19861667 the most striking expansion is the presence of 83 histidine protein kinases, which are generally involved in transducing signals from the external environment. HPKs are found predominantly in two-component regulatory systems of bacteria, archaea, protists, and plants and are absent from metazoans. Most of the T. thermophila HPKs have substrate receiver domains, and many are predicted to be transmembrane receptors. The full meaning of the kinome diversity in T. thermophila is hard to predict as a great deal of the diversification has occurred in classes for which the functions are poorly understood. For example, in many of the known kinase families, the T. thermophila PR 619 price proteins are highly diverse in sequence, both relative to those in other species as well as to each other. The scope of the diversification in T. thermophila is perhaps best seen in the fact that 630 of the kinases could not be assigned to any known family or subfamily. Overall, 37 novel classes of kinases and hundreds of unique proteins were identified in this genome. The presence of so many novel kinases and expansions in many known classes of kinases is both an indication of the versatility of the eukaryotic protein kinase domain seen in other lineages and suggestive of a great elaboration of ciliate-specific functions. Diversification of membrane transport systems. Many of the most greatly expanded T. thermophila gene families encode proteins predicted to be involved in membrane transport. Most of these are channel-type transporters and cation-transporting P-type ATPases. Interestingly, despite the apparent massive amplification of cation transporters, T. thermophila has a very limited repertoire of transporters for inorganic anions: only one member each for sulfate, phosphate, arsenite, and chromate ion were identified, and there are no predicted anion channels. The reason for the difference in the amplification of cation versus anion transporters is unclear. As with kinases, some of the most interesting properties are revealed by examination of the lineage-specific duplications of transporters. The recent clusters include K channel proteins, ABC transporters, cation-transporting ATPases, K channel beta subunit proteins, oxalate:formate antiporters, sugar transporters, and phospholipid-transporting ATPases. The expansion of the K channel proteins, which are VIC-type transporters, was particularly large and was pursued further. In total, 308 VIC-type K-selective channels have been predicted, many more than in any other sequenced species and over three times as many as identified in humans. A multigene family of potassium ion channels has also been identified in P. tetraurelia and thus may be a general characteristic of some ciliates. Some lines of evidence suggest that this expansion in ciliates could be adaptive. First, K channels control the passive permeation of K across the membrane, which is essential for ciliary motility. Second, a novel adenylyl cyclase with a putative N-terminal K ion channel regulates the formation of the universal second messenger cAMP in ciliates and apico., and PLK are all substantially expanded, perhaps reflecting the additional signaling complexity required by two nuclei that simultaneously engage in very different processes within the same cell cytoplasm. Also expanded are multiple kinases that interact with the microtubule network , possibly reflecting diversification of cytoskeletal systems. Of the kinase families with known functions, PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/19861667 the most striking expansion is the presence of 83 histidine protein kinases, which are generally involved in transducing signals from the external environment. HPKs are found predominantly in two-component regulatory systems of bacteria, archaea, protists, and plants and are absent from metazoans. Most of the T. thermophila HPKs have substrate receiver domains, and many are predicted to be transmembrane receptors. The full meaning of the kinome diversity in T. thermophila is hard to predict as a great deal of the diversification has occurred in classes for which the functions are poorly understood. For example, in many of the known kinase families, the T. thermophila proteins are highly diverse in sequence, both relative to those in other species as well as to each other. The scope of the diversification in T. thermophila is perhaps best seen in the fact that 630 of the kinases could not be assigned to any known family or subfamily. Overall, 37 novel classes of kinases and hundreds of unique proteins were identified in this genome. The presence of so many novel kinases and expansions in many known classes of kinases is both an indication of the versatility of the eukaryotic protein kinase domain seen in other lineages and suggestive of a great elaboration of ciliate-specific functions. Diversification of membrane transport systems. Many of the most greatly expanded T. thermophila gene families encode proteins predicted to be involved in membrane transport. Most of these are channel-type transporters and cation-transporting P-type ATPases. Interestingly, despite the apparent massive amplification of cation transporters, T. thermophila has a very limited repertoire of transporters for inorganic anions: only one member each for sulfate, phosphate, arsenite, and chromate ion were identified, and there are no predicted anion channels. The reason for the difference in the amplification of cation versus anion transporters is unclear. As with kinases, some of the most interesting properties are revealed by examination of the lineage-specific duplications of transporters. The recent clusters include K channel proteins, ABC transporters, cation-transporting ATPases, K channel beta subunit proteins, oxalate:formate antiporters, sugar transporters, and phospholipid-transporting ATPases. The expansion of the K channel proteins, which are VIC-type transporters, was particularly large and was pursued further. In total, 308 VIC-type K-selective channels have been predicted, many more than in any other sequenced species and over three times as many as identified in humans. A multigene family of potassium ion channels has also been identified in P. tetraurelia and thus may be a general characteristic of some ciliates. Some lines of evidence suggest that this expansion in ciliates could be adaptive. First, K channels control the passive permeation of K across the membrane, which is essential for ciliary motility. Second, a novel adenylyl cyclase with a putative N-terminal K ion channel regulates the formation of the universal second messenger cAMP in ciliates and apico.