Ion Channel Regulatory Proteins Research Articles

Whole-Genome Sequencing of KMR3 and Oryza rufipogon-Derived Introgression Line IL50-13 (Chinsurah Nona 2/Gosaba 6) Identifies Candidate Genes for High Yield and Salinity Tolerance in Rice.

The genomes of an elite rice restorer line KMR3 (salinity-sensitive) and its salinity-tolerant introgression line IL50-13, a popular variety of coastal West Bengal, India, were sequenced. High-quality paired-end reads were obtained for KMR3 (147.6 million) and IL50-13 (131.4 million) with a sequencing coverage of 30X-39X. Scaffolds generated from the pre-assembled contigs of each sequenced genome were mapped separately onto the reference genome of Oryza sativa ssp. japonica cultivar Nipponbare to identify genomic variants in terms of SNPs and InDels. The SNPs and InDels identified for KMR3 and IL50-13 were then compared with each other to identify polymorphic SNPs and InDels unique and common to both the genomes. Functional enrichment analysis of the protein-coding genes with unique InDels identified GO terms involved in protein modification, ubiquitination, deubiquitination, peroxidase activity, and antioxidant activity in IL50-13. Linoleic acid metabolism, circadian rhythm, and alpha-linolenic acid metabolism pathways were enriched in IL50-13. These GO terms and pathways are involved in reducing oxidative damage, thus suggesting their role in stress responses. Sequence analysis of QTL markers or genes known to be associated with grain yield and salinity tolerance showed polymorphism in 20 genes, out of which nine were not previously reported. These candidate genes encoded Nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4 (NB-ARC) domain-containing protein, cyclase, receptor-like kinase, topoisomerase II-associated protein PAT1 domain-containing protein, ion channel regulatory protein, UNC-93 domain-containing protein, subunit A of the heteromeric ATP-citrate lyase, and three conserved hypothetical genes. Polymorphism was observed in the coding, intron, and untranslated regions of the genes on chromosomes 1, 2, 4, 7, 11, and 12. Genes showing polymorphism between the two genomes were considered as sequence-based new candidates derived from Oryza rufipogon for conferring high yield and salinity tolerance in IL50-13 for further functional studies.

Personalized medicine for long QT syndrome: Restoration of ion channel function with RNA interference technology

With a prevalence of 1/2500, long QT Syndrome (LQTS) is one of the leading causes of sudden cardiac death in young and otherwise healthy individuals. LQTS is a proarrhythmic disorder hallmarked by prolongation of cardiac repolarization due to underlying ion channelopathies. This translates to the typical electrocardiographic (ECG) findings of prolonged QT interval, notched or biphasic T waves, and T wave alternans, and puts individuals at high risk of developing ventricular tachyarrhythmias and sudden cardiac death. To date, there are 13 subtypes of LQTS classified according to the 13 identified genetic defects, all encoding subunits of cardiac ion channels (Kþ , Naþ , Ca2þ) or ion channel regulatory proteins. Current treatment options for LQTS including beta-blockers, left cardiac sympathetic denervation, and implantable cardioverter-defibrillators are largely palliative [1]. Each of these existing modalities is associated with limitations such as adverse effects related to drug and surgical therapies and the limited lifespan of implantable devices. In the age of molecular genetics, a molecular diagnosis of the underlying ion channel defect not only establishes the disease state but paves the way for personalized medicine. Recently, Lu et al. adopted the use of RNA interference technology to target and rescue the channelopathy phenotype observed in LQTS type 2 due to KCNH2 mutation [2]. RNA interference therapy is based on the concept derived from the natural cellular mechanism where sequence-specific gene silencing can be achieved by creation of double-stranded RNA [3]. A synthetic effector small

Kinetic Considerations on the Development of Binding Assays in Single-Addition Mode: Application to the Search for α2δ1 Modulators

The development of assays in single-addition mode is of great interest for screening purposes given the multiple advantages of minimizing the number of intervention steps. Binding assays seem to be more prone to this attractive format because no functional biological activity is taking place but instead a biophysical process, whose dynamics seem easier to control without introducing significant alterations, is happening. Therefore, single-addition assays based on the displacement of prebound labeled ligands can be conceived, but careful kinetic considerations must still be taken to maximize the sensitivity of the assay and to avoid jeopardizing the identification of compounds with slow-binding kinetics. This article shows the development of a single-addition, displacement-based binding assay intended to identify modulators that act by binding to the gabapentin site of the ion channel regulatory protein α2δ1. After studying the kinetics of gabapentin binding and the influence they might have on the assay sensitivity, the best conditions were identified, and the sensitivity was compared with that of the more classical two-additions competition-based assay. Although the present study focuses on α2δ1 and its interaction with gabapentin, the rationale and the methodology followed are of broad purpose and can be applied to virtually every binding assay.

Prevalence of Significant Genetic Variants in Congenital Long QT Syndrome is Largely Underestimated

Congenital long QT syndrome (LQTS) is clinically characterized by the occurrence of syncope due to polymorphic ventricular tachycardia (torsades de pointes), associated to delayed cardiac repolarization that is reflected by a prolongation of the QT interval on the ECG (Webster and Berul, 2008). Thus far, 13 genes coding for ion channel subunits and ion channel regulatory proteins have been found mutated in patients and families with LQTS (Schwartz et al., 2009). The estimated prevalence of LQTS in the general population is reported to be in the range of 1:7000–1:2000 (0.01–0.05%), without any significant ethnical disparity (Roden and Spooner, 1999; Tester et al., 2006; Schwartz et al., 2009). Different research groups from many countries have reported similar data or cited the same sources (Roden and Spooner, 1999; Tester et al., 2006; Schwartz et al., 2009). Recently, two original studies reported a high prevalence of LQTS founder mutations in the Finnish and Norwegian population (Berge et al., 2008; Marjamaa et al., 2009). In Finland, it was concluded that 1 out of 250 individuals (0.4%) carry a LQTS founder mutation (Marjamaa et al., 2009). In Norway, the prevalence of LQTS mutation carriers was estimated to be close to 1%, which is a prevalence that is the highest documented worldwide (Berge et al., 2008). These findings are of clear interest to researchers and clinicians since they may not be only relevant for the Finnish and Norwegian populations, but may also give some important clues about the actual worldwide distribution of genetic variants predisposing to cardiac arrhythmias. In a study looking at variants in KCNQ1 in a subgroup with the longest QTc interval (403–443 ms) from French general population of 100 non-related and non-treated individuals from the DESIR cohort, two new mutations in KCNQ1 were found (Gouas et al., 2004). This study suggests that such low-penetrant variants might be found with 2% frequency within one “healthy” cohort after screening of one only one gene of interest. As it can be seen, there are clear discrepancies in estimations of LQTS mutation prevalence depending on the sources. Long QT syndrome is considered as a Mendelian arrhythmic disorder which is transmitted mainly in an autosomal dominant mode of inheritance (Priori et al., 2008). Thus, one should be able to apply the basic concepts of genetics such as Mendel’s law for families and Hardy–Weinberg equation for population in equilibrium. Hereafter, we analyze and interpret published data and our own results to estimate the prevalence of LQTS using different approaches.

Channelopathies and drug discovery in the postgenomic era

Ion channels are a diverse group of pore-forming proteins that provide selective pathways for the movement of ions (Na+, K+, Ca2+, Cl−, etc) across the lipid membrane barrier. Aquaporins facilitate water movement across cell membranes in response to osmotic gradients. There is an increasing body of information on the molecular structure and functional roles of ion and water channels in health and disease, linking channel function at the molecular level to organ physiology. Because ion channels play essential roles in all cells, defects in ion channels are associated with a wide variety of pathophysiological conditions and human diseases. Diseases caused by disturbed function of ion channel subunits or regulatory proteins have been defined as “channelopathies”1, 2. In the postgenomic era the rapid progress in the molecular identification of genes for new ion channels and elucidation of their transport properties, physiological functions, and disease relevant mutations has significantly advanced the knowledge of channelopathies and potential new therapies3, 4, 5, 6, 7, 8, 9. For examples, the discovery of aquaporin water channels, a family of integral membrane proteins that selectively transport water, has led to the identification of water channelopathies including autosomal dominant and recessive forms of hereditary nepherogenic diabetes insipidus caused by aquaporin-2 mutations10, congenital cataracts incurred by aquaporin-0 mutations11 and aquired neuronal inflammatory disease neuromyelitis optica in which pathogenic autoantibodies target aquaporin-412. Impaired Cl− transport caused by mutations in genes belonging to distinct Cl− channel families has been found to cause diverse diseases such as cystic fibrosis, myotonia, epilepsy, hyperekplexia, lysosomal storage disease, deafness, renal salt loss, kidney stones, osteopetrosis, and cardiovascular diseases7, 13, 14. In addition, the studies on the role of ion channel regulatory proteins, including the sub-membrane adapter ankyrins and alpha-1 syntrophin, membrane coat protein caveolin-3, signaling platform yotiao, and lamins, have also provided novel insights into understanding of human diseases15.

Lipid Raft in Cardiac Health and Disease

Lipid rafts are sphingolipid and cholesterol rich micro-domains of the plasma membrane that coordinate and regulate varieties of signaling processes. Lipid rafts are also present in cardiac myocytes and are enriched in signaling molecules and ion channel regulatory proteins. Lipid rafts are receiving increasing attention as cellular organelles contributing to the pathogenesis of several structural and functional processes including cardiac hypertrophy and heart failure. At present, very little is known about the role of lipid rafts in cardiac function and dysfunction. This review will discuss the possible role of lipid rafts in cardiac health and disease.

Sup-9, sup-10, andunc-93May Encode Components of a Two-Pore K+Channel that Coordinates Muscle Contraction inCaenorhabditis elegans

Genetic studies of sup-9, unc-93, and sup-10 strongly suggest that these genes encode components of a multi-subunit protein complex that coordinates muscle contraction in Caenorhabditis elegans. We cloned sup-9 and sup-10 and found that they encode a two-pore K+ channel and a novel transmembrane protein, respectively. We also found that UNC-93 and SUP-10 colocalize with SUP-9 within muscle cells, and that UNC-93 is a member of a novel multigene family that is conserved among C. elegans, Drosophila, and humans. Our results indicate that SUP-9 and perhaps other two-pore K+ channels function as multiprotein complexes, and that UNC-93 and SUP-10 likely define new classes of ion channel regulatory proteins.