1,721,032 research outputs found
Plasma-membrane calcium pumps and hereditary deafness
No full textIn mammals, four different genes encode four PMCA (plasma-membrane Ca(2+)-ATPase) isoforms. PMCA1 and 4 are expressed ubiquitously, and PMCA2 and 3 are expressed predominantly in the central nervous system. More than 30 variants are generated by mechanisms of alternative splicing. The physiological meaning of the existence of so many isoforms is not clear, but evidently it must be related to the cell-specific demands of Ca(2+) homoeostasis. Recent studies suggest that the alternatively spliced regions in PMCA are responsible for specific targeting to plasma membrane domains, and proteins that bind specifically to the pumps could contribute to further regulation of Ca(2+) control. In addition, the combination of proteins obtained by alternative splicing occurring at two different sites could be responsible for different functional characteristics of the pumps
Structural Insight into the Binding Mode of FXR and GPBAR1 Modulators
No full textIn this chapter we provide an exhaustive overview of the binding modes of bile acid (BA) and non-BA ligands to the nuclear farnesoid X receptor (FXR) and the G-protein bile acid receptor 1 (GPBAR1). These two receptors play a key role in many diseases related to lipid and glucose disorders, thus representing promising pharmacological targets. We pay particular attention to the chemical and structural features of the ligand-receptor interaction, providing guidelines to achieve ligands endowed with selective or dual activity towards the receptor and paving the way to future drug design studies
Calcium pumps
No full textThree P-type Ca2+-transporting ATPases have been recognized
in animal cells. Other cell types, such as yeast and plant, contain additional P-type Ca2+ pumps. This succinct
chapter will concentrate on the animal pumps privileging
recent developments, rather than established aspects that are adequately covered in a number of comprehensive reviews which can be consulted for details [1–5]. Two pumps have been known for over 40 years; one has been identified only recently. They share the essential properties of the catalytic cycle (Figure 118.1), and are sensitive to the classical inhibitors lanthanum and vanadate. They are essential to normal cell life: genetic dysfunctions of each one of the three pumps are associated with various disease processes.
In discussing the three pumps, few specific references will be given: most of the information will come from the five general reviews quoted
Comparative analysis of Oxford Nanopore Technologies error-rate during direct-RNA and DNA sequencing
Full text linkGene expression studies and transcriptome analyses are essential tools of molecular biology although, until a few years ago, the respective protocols suffered from two limitations, namely Polymerase Chain Reaction (PCR) amplification and read length. All the gene expression study-protocols included at least one step of PCR preventing, de facto, the possibility of measuring the “real amount” of a transcript. Transcript characterization, instead, is limited by the maximal read length achievable by the sequencing technology, especially in species with high heterozygosity or with a high degree of genomic duplications. Oxford Nanopore Technology (ONT) direct RNA sequencing, is a peculiar solution to the complementary DNA conversion needed for other platforms. Besides, direct RNA can potentially sequence entire transcripts and also resolve the complexity due to isoforms and to the alternative splicing process. Since the error rate in ONT (flowcells R9.4.1) is quite high (5-15%), the investigation of the errors, especially in DNA sequencing, has been widely done to understand the main sources of insertion, deletion, and substitution other than natural biological variation. However, very few studies are present in the literature investigating the errors occurring in direct RNA sequencing. In this work we present a comparison between the overall error occurrence together with a more detailed investigation on each source of error (insertion, deletion, substitution), in human transcriptome reads obtained with direct RNA sequencing and the classical rates known for the DNA sequencing. Error-rate assessments are performed by parsing transcripts alignment files in search of single errors category that are then summarized in the complete error-rate. Insertion, deletion, and substitution-rates showed a similar pattern for both direct RNA and DNA sequencing indicating that all the software and pipelines developed for ONT cDNA protocols can be also used for the analysis of data obtained from direct-RNA experiments
Functional specificity of PMCA isoforms?
No full textIn mammals, four different genes encode four PMCA isoforms. PMCA1 and PMCA4 are expressed ubiquitously. PMCA2 and PMCA3 are expressed prevalently in the central nervous systems. More than 30 variants are generated by mechanisms of alternative splicing. The physiological meaning of the existence of such elevated number of isoforms is not clear, but it would be plausible to relate it to the cell-specific demands of Ca2+ homeostasis. To characterize functional specificity of PMCA variants we have investigated two aspects: the effects of the overexpression of the different PMCA variants on cellular Ca2+ handling and the existence of possible isoform-specific interactions with partner proteins using a yeast two-hybrid technique. The four basic PMCA isoforms were coexpressed in CHO cells together with the Ca2+-sensitive recombinant photoprotein aequorin. The effects of their overexpression on Ca2+ homeostasis were monitored in the living cells. They had revealed that the ubiquitous isoforms 1 and 4 are less effective in reducing the Ca2+ peaks generated by cell stimulation as compared to the neuron-specific isoforms 2 and 3. To establish whether these differences were related to different and new physiological regulators of the pump, the 90 N-terminal residues of PMCA2 and PMCA4 have been used as baits for the search of molecular partners. Screening of a human brain cDNA library with the PMCA4 bait specified the epsilon-isoform of protein 14-3-3, whereas no 14-3-3 epsilon clone was obtained with the PMCA2 bait. Overexpression of PMCA4/14-3-3 epsilon (but not of PMCA2/14-3-3 epsilon) in HeLa cells together with targeted aequorins showed that the ability of the cells to export Ca2+ was impaired. Thus, the interaction with 14-3-3 epsilon inhibited PMCA4 but not PMCA2. The role of PMCA2 has been further characterized by Ca2+ measurements in cells overexpressing different splicing variants. The results indicated that the combination of alternative splicing at two different sites in the pump structure was responsible for different functional characteristics of the pumps
Inhibitory interaction of the 14-3-3 proteins with ubiquitous (PMCA1) and tissue-specific (PMCA3) isoforms of the plasma membrane Ca2+ pump
No full textA previous study has demonstrated that the ubiquitous plasma membrane Ca(2+) pump PMCA4 interacted with isoform epsilon of the 14-3-3 protein, whereas the nervous tissue-specific PMCA2 did not. The 14-3-3 proteins are widely expressed small acidic proteins, which modulate cell signaling, intracellular trafficking, transcription and apoptosis. The investigation has been extended to the other tissue-restricted pump (PMCA3) and to the other ubiquitous pump (PMCA1). At variance with PMCA2, PMCA3 interacted with the 14-3-3epsilon protein in a two-hybrid system assay, which could not be used for PMCA1. The 14-3-3epsilon protein immunoprecipitated with both PMCA3 and PMCA1 when expressed in HeLa cells. Pull-down experiments using GST-PMCA1 and GST-PMCA3 fusion products confirmed the interaction of both pumps with the 14-3-3epsilon protein. The binding was phosphorylation-independent with both PMCA3 and PMCA1. The 14-3-3zeta isoform also interacted with PMCA3; however, it did not interact with PMCA1. The effect of the interaction on the activity of the two pumps, and thus on the homeostasis of Ca(2+), was investigated by co-expressing the 14-3-3epsilon protein and PMCA3 or PMCA1 in CHO cells together with the recombinant Ca(2+) indicator aequorin: the ability of cells to re-establish the basal Ca(2+) concentration following a Ca(2+) transient induced by an InsP(3)-producing agonist was substantially decreased with both pumps, indicating that the interaction with the 14-3-3 protein inhibited the activity of both PMCA3 and PMCA1
Plasma-membrane calcium pumps and hereditary deafness
No full textIn mammals, four different genes encode four PMCA (plasma-membrane Ca 2+-ATPase) isoforms. PMCA1 and 4 are expressed ubiquitously, and PMCA2 and 3 are expressed predominantly in the central nervous system. More than 30 variants are generated by mechanisms of alternative splicing. The physiological meaning of the existence of so many isoforms is not clear, but evidently it must be related to the cell-specific demands of Ca2+ homoeostasis. Recent studies suggest that the alternatively spliced regions in PMCA are responsible for specific targeting to plasma membrane domains, and proteins that bind specifically to the pumps could contribute to further regulation of Ca2+ control. In addition, the combination of proteins obtained by alternative splicing occurring at two different sites could be responsible for different functional characteristics of the pumps. ©The Authors
Functional specificity of PMCA isoforms?
No full textIn mammals, four different genes encode four PMCA isoforms. PMCA1 and PMCA4 are expressed ubiquitously. PMCA2 and PMCA3 are expressed prevalently in the central nervous systems. More than 30 variants are generated by mechanisms of alternative splicing. The physiological meaning of the existence of such elevated number of isoforms is not clear, but it would be plausible to relate it to the cell-specific demands of Ca2+ homeostasis. To characterize functional specificity of PMCA variants we have investigated two aspects: the effects of the overexpression of the different PMCA variants on cellular Ca2+ handling and the existence of possible isoform-specific interactions with partner proteins using a yeast two-hybrid technique. The four basic PMCA isoforms were coexpressed in CHO cells together with the Ca2+-sensitive recombinant photoprotein aequorin. The effects of their overexpression on Ca2+ homeostasis were monitored in the living cells. They had revealed that the ubiquitous isoforms 1 and 4 are less effective in reducing the Ca2+ peaks generated by cell stimulation as compared to the neuron-specific isoforms 2 and 3. To establish whether these differences were related to different and new physiological regulators of the pump, the 90 N-terminal residues of PMCA2 and PMCA4 have been used as baits for the search of molecular partners. Screening of a human brain cDNA library with the PMCA4 bait specified the epsilon-isoform of protein 14-3-3, whereas no 14-3-3 epsilon clone was obtained with the PMCA2 bait. Overexpression of PMCA4/14-3-3 epsilon (but not of PMCA2/14-3-3 epsilon) in HeLa cells together with targeted aequorins showed that the ability of the cells to export Ca2+ was impaired. Thus, the interaction with 14-3-3 epsilon inhibited PMCA4 but not PMCA2. The role of PMCA2 has been further characterized by Ca2+ measurements in cells overexpressing different splicing variants. The results indicated that the combination of alternative splicing at two different sites in the pump structure was responsible for different functional characteristics of the pumps
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