ABSTRACT
Influenza viruses encode a viral RNA-dependent RNA polymerase (FluPol), which is responsible for transcribing and replicating the negative-sense viral RNA (vRNA) genome. FluPol transcribes vRNA using a host-capped mRNA primer and replicates it by synthesizing a positive-sense cRNA intermediate, which is copied back into vRNA. To carry out these functions, FluPol interacts with vRNA and cRNA using conserved promoter elements at the 5' and 3' termini. Recent structural studies have identified a new surface binding site for the 3' vRNA and cRNA promoters on FluPol, referred to as the mode B site. However, the role of this binding site in FluPol function is unknown. In this study, we used a combination of cell-based and biochemical assays to show that the mode B site is important for both viral genome transcription and replication in influenza A virus. Furthermore, we show that the mode B site is not needed for initiating transcription in vitro but is required to synthesize a full-length product. This is consistent with a model in which the 3' terminus of the vRNA template binds in the mode B site during elongation. Our data provide the first functional insights into the role of the mode B site on FluPol, which advances our understanding of FluPol function and influenza virus replication.IMPORTANCE Influenza viruses are responsible for up to 650,000 deaths per year through seasonal epidemics, and pandemics have caused tens of millions of deaths in the past. Most current therapeutics suffer from widespread resistance, creating a need for new drug targets against influenza virus. The virus encodes an RNA-dependent RNA polymerase, which replicates and transcribes the vRNA genome. The polymerase interacts with vRNA and the complementary replicative intermediate cRNA using several specific binding sites; however, the functions associated with these binding sites remain unknown. Here, we functionally characterize a binding site for the 3' vRNA and cRNA promoters. Our data offer insight into the mechanism of viral genome transcription by the influenza virus polymerase and may be applicable to other related viruses.
Subject(s)
Influenza A virus/genetics , Promoter Regions, Genetic/genetics , RNA-Dependent RNA Polymerase/genetics , 3' Untranslated Regions/genetics , Binding Sites/genetics , Genome, Viral/genetics , HEK293 Cells , Humans , Influenza A virus/metabolism , Influenza A virus/pathogenicity , Mutation/genetics , Orthomyxoviridae/genetics , RNA Recognition Motif Proteins , RNA, Complementary/genetics , RNA, Complementary/metabolism , RNA, Messenger/metabolism , RNA, Viral/genetics , RNA-Dependent RNA Polymerase/metabolism , Transcription, Genetic/genetics , Virus Replication/geneticsABSTRACT
Eight-segmented, negative-sense, single-stranded genomic RNAs of influenza A virus are terminated with 5' and 3' untranslated regions (UTRs). All segments have highly conserved extremities of 13 and 12 nucleotides at the 5' and 3' UTRs, respectively, constructing the viral RNA (vRNA) promoter. Adjacent to the duplex stem of 3 base pairs (bps) between the two conserved strands, additional 1-4 bps are existing in a segment-specific manner. We investigated the roles of the matrix (M) segment-specific base pair between the 14th nucleotide uridine (U14') of the 5' UTR and the 13th nucleotide adenosine (A13) of the 3' UTR by preparing possible vRNA promoters, named vXY, as well as cRNA promoters, named cYX. We analysed their RNA-dependent RNA replication efficiency using the minigenome replicon system and an enzyme assay system in vitro with synthetic RNA promoters. Notably, in contrast to vAC(s) that is a synthetic vRNA promoter with A14' and C13, base-pair disruption at the complementary RNA (cRNA) promoter in cAC(s), which has A13' and C14, not only reduced viral RNA replication in cells but also impaired de novo initiation of unprimed vRNA synthesis. Reverse genetics experiments confirmatively exhibited that this breakage in the cRNA promoter affected the rescue of infectious virus. The present study suggests that the first segment-specific base pair plays an essential role in generating infectious viruses by regulating the promoter activity of cRNA rather than vRNA. It could provide insights into the role of the segment-specific nucleotides in viral genome replication for sustainable infection.
Subject(s)
Influenza A virus/genetics , RNA, Complementary/genetics , RNA, Viral/genetics , 3' Untranslated Regions/genetics , Animals , Dogs , Gene Expression Regulation, Viral , HEK293 Cells , Humans , Madin Darby Canine Kidney Cells , Nucleic Acid Conformation , Nucleotides/chemistry , Nucleotides/genetics , Promoter Regions, Genetic/genetics , Transcription, GeneticABSTRACT
Argonaute proteins use small RNAs to guide the silencing of complementary target RNAs in many eukaryotes. Although small RNA biogenesis pathways are well studied, mechanisms for removal of guide RNAs from Argonaute are poorly understood. Here we show that the Argonaute2 (Ago2) guide RNA complex is extremely stable, with a half-life on the order of days. However, highly complementary target RNAs destabilize the complex and significantly accelerate release of the guide RNA from Ago2. This "unloading" activity can be enhanced by mismatches between the target and the guide 5' end and attenuated by mismatches to the guide 3' end. The introduction of 3' mismatches leads to more potent silencing of abundant mRNAs in mammalian cells. These findings help to explain why the 3' ends of mammalian microRNAs (miRNAs) rarely match their targets, suggest a mechanism for sequence-specific small RNA turnover, and offer insights for controlling small RNAs in mammalian cells.
Subject(s)
Argonaute Proteins/genetics , RNA, Complementary/genetics , Base Pair Mismatch , Cell Line , Gene Silencing , HEK293 Cells , Half-Life , Humans , MicroRNAs/genetics , RNA-Induced Silencing Complex/genetics , RNA, Small UntranslatedABSTRACT
BACKGROUND: Vast amounts of next generation sequencing RNA data has been deposited in archives, accompanying very diverse original studies. The data is readily available also for other purposes such as genome annotation or transcriptome assembly. However, selecting a subset of available experiments, sequencing runs and reads for this purpose is a nontrivial task and complicated by the inhomogeneity of the data. RESULTS: This article presents the software VARUS that selects, downloads and aligns reads from NCBI's Sequence Read Archive, given only the species' binomial name and genome. VARUS automatically chooses runs from among all archived runs to randomly select subsets of reads. The objective of its online algorithm is to cover a large number of transcripts adequately when network bandwidth and computing resources are limited. For most tested species VARUS achieved both a higher sensitivity and specificity with a lower number of downloaded reads than when runs were manually selected. At the example of twelve eukaryotic genomes, we show that RNA-Seq that was sampled with VARUS is well-suited for fully-automatic genome annotation with BRAKER. CONCLUSIONS: With VARUS, genome annotation can be automatized to the extent that not even the selection and quality control of RNA-Seq has to be done manually. This introduces the possibility to have fully automatized genome annotation loops over potentially many species without incurring a loss of accuracy over a manually supervised annotation process.
Subject(s)
Databases, Genetic , RNA, Complementary/genetics , Sequence Analysis, RNA/methods , Software , Algorithms , Animals , Drosophila melanogaster/genetics , Eukaryota/genetics , High-Throughput Nucleotide Sequencing , Introns/genetics , Molecular Sequence Annotation , Transcriptome/geneticsABSTRACT
SmartFlare technology allows detection of mRNA in single living cells. We studied the possibility of using SmartFlare nanoprobes for detection of small subsets of CD4+ lymphocytes. It was found that SmartFlare allows detection of transcriptional master regulators of major CD4+T helper subsets in living human lymphocytes. Nanoprobes labeled with Cy5 fluorophore were better detected by flow cytometry than nanoprobes labeled with Cy3. Appropriate time of lymphocyte incubation with SmartFlare probes was 24 h.
Subject(s)
Flow Cytometry/methods , Fluorescent Dyes/chemistry , RNA, Complementary/genetics , RNA, Messenger/genetics , T-Lymphocyte Subsets/cytology , T-Lymphocytes, Helper-Inducer/cytology , Carbocyanines/chemistry , Gold/chemistry , Humans , Metal Nanoparticles/chemistryABSTRACT
l-Cysteine is an endogenous sulfur-containing amino acid with multiple and varied roles in the central nervous system, including neuroprotection and the maintenance of the redox balance. However, it was also suggested as an excitotoxic agent implicated in the pathogenesis of neurological disorders such as Parkinson's and Alzheimer's disease. l-Cysteine can modulate the activity of ionic channels, including voltage-gated calcium channels and glutamatergic NMDA receptors, whereas its effects on GABAergic neurotransmission had not been studied before. In the present work, we analyzed the effects of l-cysteine on responses mediated by homomeric GABAA ρ1 receptors, which are known for mediating tonic γ-aminobutyric acid (GABA) responses in retinal neurons. GABAA ρ1 receptors were expressed in Xenopus laevis oocytes and GABA-evoked chloride currents recorded by two-electrode voltage-clamp in the presence or absence of l-cysteine. l-Cysteine antagonized GABAA ρ1 receptor-mediated responses; inhibition was dose-dependent, reversible, voltage independent, and susceptible to GABA concentration. Concentration-response curves for GABA were shifted to the right in the presence of l-cysteine without a substantial change in the maximal response. l-Cysteine inhibition was insensitive to chemical protection of the sulfhydryl groups of the ρ1 subunits by the irreversible alkylating agent N-ethyl maleimide. Our results suggest that redox modulation is not involved during l-cysteine actions and that l-cysteine might be acting as a competitive antagonist of the GABAA ρ1 receptors.
Subject(s)
Cysteine/pharmacology , GABA-A Receptor Antagonists/pharmacology , Receptors, GABA-A/drug effects , Animals , Binding, Competitive , Chlorides/metabolism , Cystine/pharmacology , Dose-Response Relationship, Drug , Ethylmaleimide/pharmacology , Homocysteine/pharmacology , Humans , Ion Transport/drug effects , Oocytes , Patch-Clamp Techniques , RNA, Complementary/genetics , Receptors, GABA-A/physiology , Recombinant Proteins/metabolism , Xenopus laevis , gamma-Aminobutyric Acid/pharmacologyABSTRACT
Sperm-specific phospholipase C zeta (PLCζ) is widely considered to be the physiological stimulus that evokes intracellular calcium (Ca2+) oscillations that are essential for the initiation of egg activation during mammalian fertilisation. A recent genetic study reported a male infertility case that was directly associated with a point mutation in the PLCζ C2 domain, where an isoleucine residue had been substituted with a phenylalanine (I489F). Here, we have analysed the effect of this mutation on the in vivo Ca2+ oscillation-inducing activity and the in vitro biochemical properties of human PLCζ. Microinjection of cRNA or recombinant protein corresponding to PLCζI489F mutant at physiological concentrations completely failed to cause Ca2+ oscillations and trigger development. However, this infertile phenotype could be effectively rescued by microinjection of relatively high (non-physiological) amounts of recombinant mutant PLCζI489F protein, leading to Ca2+ oscillations and egg activation. Our in vitro biochemical analysis suggested that the PLCζI489F mutant displayed similar enzymatic properties, but dramatically reduced binding to PI(3)P and PI(5)P-containing liposomes compared with wild-type PLCζ. Our findings highlight the importance of PLCζ at fertilisation and the vital role of the C2 domain in PLCζ function, possibly due to its novel binding characteristics.
Subject(s)
C2 Domains , Calcium/metabolism , Infertility, Male/genetics , Phosphoinositide Phospholipase C/chemistry , Point Mutation , Amino Acid Substitution , Animals , Calcium Signaling , Cattle , Female , Fertilization , Gene Expression , Humans , Isoleucine/chemistry , Isoleucine/metabolism , Liposomes/chemistry , Liposomes/metabolism , Male , Mice , Microinjections , Oocytes/cytology , Oocytes/metabolism , Phenylalanine/chemistry , Phenylalanine/metabolism , Phosphatidylinositol Phosphates/chemistry , Phosphatidylinositol Phosphates/metabolism , Phosphoinositide Phospholipase C/genetics , Phosphoinositide Phospholipase C/metabolism , Protein Binding , RNA, Complementary/administration & dosage , RNA, Complementary/genetics , RNA, Complementary/metabolism , Recombinant Proteins/administration & dosage , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Spermatozoa/metabolism , Spermatozoa/pathologyABSTRACT
MicroRNAs (miRNAs) guide RNA-induced silencing complexes to target RNAs based on miRNA-target complementarity. Using a dual-luciferase based sensor system in Nicotiana benthamiana, we quantitatively assessed the relationship between miRNA-target complementarity and silencing efficacy measured at both the RNA and protein levels, using several conserved miRNAs and their known target sites from Arabidopsis thaliana. We found that naturally occurring sites have variable efficacies attributable to their complementarity patterns. We also observed that sites with a few mismatches to the miRNA 3' regions, which are common in plants, are often equally effective and sometimes more effective than perfectly matched sites. By contrast, mismatches to the miRNA 5' regions strongly reduce or eliminate repression efficacy but are nonetheless present in several natural sites, suggesting that in some cases, suboptimal miRNA efficacies are either tolerated or perhaps selected for. Central mismatches fully abolished repression efficacy in our system, but such sites then became effective miRNA target mimics. Complementarity patterns that are functional in animals (seed sites, 3'-supplementary sites, and centered sites) did not reliably confer repression, regardless of context (3'-untranslated region or open reading frame) or measurement type (RNA or protein levels). Overall, these data provide a robust and empirical foundation for understanding, predicting, and designing functional miRNA target sites in plants.
Subject(s)
Genetic Techniques , MicroRNAs/metabolism , Nicotiana/genetics , RNA, Complementary/genetics , 3' Untranslated Regions/genetics , Animals , Base Sequence , Gene Expression Regulation, Plant , MicroRNAs/chemistry , MicroRNAs/genetics , Molecular Sequence Data , Nucleic Acid Conformation , Open Reading Frames/genetics , Plant Proteins/genetics , Plant Proteins/metabolism , RNA, Complementary/chemistry , Repressor Proteins/metabolismABSTRACT
In this study, we demonstrate the upregulation in the expression of caspases 1 and 11 by SJL/J mouse brain astrocytes infected with the BeAn strain of Theiler's murine encephalomyelitis virus (TMEV). The upregulation of both proteases hints at protection of astrocytic cells from apoptotic death. We therefore looked for the reason of the demonstrated absence of programmed cell death in BeAn-infected SJL/J astrocytes. Complementary RNA (cRNA) from mock- and TMEV-infected cells was hybridized to the whole murine genome U74v2 DNA microarray from Affymetrix. Those experiments demonstrated the upregulation of gene expression for caspases 1 and 11 in infected cells. We further confirmed and validated their messenger RNA (mRNA) increase by reverse transcriptase quantitative real-time PCR (qPCR). The presence of both enzymatically active caspases 1 and 11 was demonstrated in cell lysates using a colorimetric and fluorymetric assay, respectively. We also show that overexpressed caspase 11 activated caspase 1 after preincubation of cytosol in vitro following a time-dependent process. This induction was neutralized by an anti-caspase 11 polyclonal antibody. These results demonstrate the activation of the caspase 1 precursor by caspase 11 and suggest a new mechanism of protection of BeAn-infected astrocytes from apoptosis. The direct experimental evidence that the protection effect demonstrated in this article was mediated by caspase 1, is provided by the fact that its specific inhibitor Z-WEHD-FMK induced de novo apoptotic death.
Subject(s)
Astrocytes/virology , Cardiovirus Infections/virology , Caspase 1/genetics , Caspases/genetics , Host-Pathogen Interactions , Theilovirus/genetics , Amino Acid Chloromethyl Ketones/pharmacology , Animals , Animals, Newborn , Antibodies/pharmacology , Apoptosis/drug effects , Astrocytes/drug effects , Astrocytes/metabolism , Cardiovirus Infections/pathology , Caspase 1/metabolism , Caspase Inhibitors/pharmacology , Caspases/metabolism , Caspases, Initiator , Gene Expression Regulation , Mice , Primary Cell Culture , RNA, Complementary/genetics , RNA, Complementary/metabolism , RNA, Messenger/antagonists & inhibitors , RNA, Messenger/genetics , RNA, Messenger/metabolism , Theilovirus/drug effects , Theilovirus/metabolismABSTRACT
Negative-strand RNA viruses represent a significant class of important pathogens that cause substantial morbidity and mortality in human and animal hosts worldwide. A defining feature of these viruses is that their single-stranded RNA genomes are of opposite polarity to messenger RNA and are replicated through a positive-sense intermediate. The replicative intermediate is thought to exist as a complementary ribonucleoprotein (cRNP) complex. However, isolation of such complexes from infected cells has never been accomplished. Here we report the development of an RNA-based affinity-purification strategy for the isolation of cRNPs of influenza A virus from infected cells. This technological advance enabled the structural and functional characterization of this elusive but essential component of the viral RNA replication machine. The cRNP exhibits a filamentous double-helical organization with defined termini, containing the viral RNA-dependent RNA polymerase (RdRp) at one end and a loop structure at the other end. In vitro characterization of cRNP activity yielded mechanistic insights into the workings of this RNA synthesis machine. In particular, we found that cRNPs show activity in vitro only in the presence of added RdRp. Intriguingly, a replication-inactive RdRp mutant was also able to activate cRNP-templated viral RNA synthesis. We propose a model of influenza virus genome replication that relies on the trans-activation of the cRNP-associated RdRp. The described purification strategy should be applicable to other negative-strand RNA viruses and will promote studies into their replication mechanisms.
Subject(s)
Genome, Viral/genetics , Influenza A virus/genetics , Models, Genetic , RNA, Complementary/genetics , RNA, Viral/biosynthesis , Virus Replication/genetics , Animals , Blotting, Western , Cattle , HEK293 Cells , Humans , Influenza A virus/ultrastructure , Microscopy, Electron, Transmission , Oligonucleotides/geneticsABSTRACT
Soluble cytosolic carbonic anhydrases (CAs) are well known to participate in pH regulation of the cytoplasm of mammalian cells. Membrane-bound CA isoforms--such as isoforms IV, IX, XII, XIV, and XV--also catalyze the reversible conversion of carbon dioxide to protons and bicarbonate, but at the extracellular face of the cell membrane. When human CA isoform IV was heterologously expressed in Xenopus oocytes, we observed, by measuring H(+) at the outer face of the cell membrane and in the cytosol with ion-selective microelectrodes, not only extracellular catalytic CA activity but also robust intracellular activity. CA IV expression in oocytes was confirmed by immunocytochemistry, and CA IV activity measured by mass spectrometry. Extra- and intracellular catalytic activity of CA IV could be pharmacologically dissected using benzolamide, the CA inhibitor, which is relatively slowly membrane-permeable. In acute cerebellar slices of mutant mice lacking CA IV, cytosolic H(+) shifts of granule cells following CO(2) removal/addition were significantly slower than in wild-type mice. Our results suggest that membrane-associated CA IV contributes robust catalytic activity intracellularly, and that this activity participates in regulating H(+) dynamics in the cytosol, both in injected oocytes and in mouse neurons.
Subject(s)
Carbonic Anhydrase IV/metabolism , Animals , Benzolamide/pharmacology , Carbonic Anhydrase II/antagonists & inhibitors , Carbonic Anhydrase II/genetics , Carbonic Anhydrase II/metabolism , Carbonic Anhydrase IV/antagonists & inhibitors , Carbonic Anhydrase IV/deficiency , Carbonic Anhydrase IV/genetics , Carbonic Anhydrase Inhibitors/pharmacology , Cerebellum/cytology , Cerebellum/enzymology , Cytosol/enzymology , Extracellular Fluid/enzymology , Female , GPI-Linked Proteins/genetics , GPI-Linked Proteins/metabolism , Humans , Hydrogen-Ion Concentration , Intracellular Fluid/enzymology , Mice , Mice, Knockout , Neurons/enzymology , Oocytes/enzymology , RNA, Complementary/genetics , Recombinant Proteins/antagonists & inhibitors , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Xenopus laevisABSTRACT
Calcium/voltage-gated, large conductance potassium (BK) channels control numerous physiological processes, including myogenic tone. BK channel regulation by direct interaction between lipid and channel protein sites has received increasing attention. Leukotrienes (LTA4, LTB4, LTC4, LTD4, and LTE4) are inflammatory lipid mediators. We performed patch clamp studies in Xenopus oocytes that co-expressed BK channel-forming (cbv1) and accessory ß1 subunits cloned from rat cerebral artery myocytes. Leukotrienes were applied at 0.1 nm-10 µm to either leaflet of cell-free membranes at a wide range of [Ca(2+)]i and voltages. Only LTB4 reversibly increased BK steady-state activity (EC50 = 1 nm; Emax reached at 10 nm), with physiological [Ca(2+)]i and voltages favoring this activation. Homomeric cbv1 or cbv1-ß2 channels were LTB4-resistant. Computational modeling predicted that LTB4 docked onto the cholane steroid-sensing site in the BK ß1 transmembrane domain 2 (TM2). Co-application of LTB4 and cholane steroid did not further increase LTB4-induced activation. LTB4 failed to activate ß1 subunit-containing channels when ß1 carried T169A, A176S, or K179I within the docking site. Co-application of LTB4 with LTA4, LTC4, LTD4, or LTE4 suppressed LTB4-induced activation. Inactive leukotrienes docked onto a portion of the site, probably preventing tight docking of LTB4. In summary, we document the ability of two endogenous lipids from different chemical families to share their site of action on a channel accessory subunit. Thus, cross-talk between leukotrienes and cholane steroids might converge on regulation of smooth muscle contractility via BK ß1. Moreover, the identification of LTB4 as a highly potent ligand for BK channels is critical for the future development of ß1-specific BK channel activators.
Subject(s)
Ion Channel Gating/physiology , Large-Conductance Calcium-Activated Potassium Channel alpha Subunits/metabolism , Large-Conductance Calcium-Activated Potassium Channel beta Subunits/metabolism , Leukotriene B4/metabolism , Animals , Calcium/metabolism , Cerebral Arteries/cytology , Female , Ion Channel Gating/drug effects , Ion Channel Gating/genetics , Large-Conductance Calcium-Activated Potassium Channel alpha Subunits/chemistry , Large-Conductance Calcium-Activated Potassium Channel alpha Subunits/genetics , Large-Conductance Calcium-Activated Potassium Channel beta Subunits/chemistry , Large-Conductance Calcium-Activated Potassium Channel beta Subunits/genetics , Leukotriene A4/chemistry , Leukotriene A4/metabolism , Leukotriene A4/pharmacology , Leukotriene B4/chemistry , Leukotriene B4/pharmacology , Leukotriene C4/chemistry , Leukotriene C4/metabolism , Leukotriene C4/pharmacology , Leukotriene D4/chemistry , Leukotriene D4/metabolism , Leukotriene D4/pharmacology , Leukotriene E4/chemistry , Leukotriene E4/metabolism , Leukotriene E4/pharmacology , Membrane Potentials/drug effects , Microinjections , Models, Molecular , Molecular Structure , Muscle Cells/cytology , Muscle Cells/metabolism , Oocytes/drug effects , Oocytes/metabolism , Oocytes/physiology , Patch-Clamp Techniques , Protein Binding , Protein Structure, Tertiary , RNA, Complementary/administration & dosage , RNA, Complementary/genetics , Rats , Xenopus laevisABSTRACT
Homologous chromosome segregation errors during meiosis I are common and generate aneuploid embryos. Here, we provide a reason for this susceptibility to mis-segregation by live cell imaging of mouse oocytes. Our results show that stable kinetochore-microtubule attachments form in mid-prometaphase, 3-4 hours before anaphase. This coincided with the loss of Mad2 from kinetochores and with the start of anaphase-promoting complex/cyclosome (APC/C)-mediated cyclin B1 destruction. Therefore, the spindle assembly checkpoint (SAC) ceased to inhibit the APC/C from mid-prometaphase. This timing did not coincide with bivalent congression in one-third of all oocytes examined. Non-aligned bivalents were weakly positive for Mad2, under less tension than congressed bivalents and, by live-cell imaging, appeared to be in the process of establishing correct bi-orientation. The time from when the APC/C became active until anaphase onset was affected by the rate of loss of CDK1 activity, rather than by these non-aligned bivalents, which occasionally persisted until anaphase, resulting in homolog non-disjunction. We conclude that, in oocytes, a few erroneous attachments of bivalent kinetochores to microtubules do not generate a sufficient SAC 'wait anaphase' signal to inhibit the APC/C.
Subject(s)
Chromosome Segregation/physiology , Kinetochores/metabolism , Microtubules/metabolism , Oocytes/physiology , Prometaphase/physiology , Ubiquitin-Protein Ligase Complexes/metabolism , Anaphase-Promoting Complex-Cyclosome , Animals , Cell Cycle Proteins/metabolism , Cyclin B1/metabolism , Fluorescent Antibody Technique , Image Processing, Computer-Assisted , Immunoblotting , Mad2 Proteins , Mice , Microscopy, Confocal , Microscopy, Fluorescence , Oocytes/metabolism , RNA, Complementary/genetics , Time FactorsABSTRACT
Small interfering RNAs (siRNAs) direct Argonaute proteins, the core components of the RNA-induced silencing complex (RISC), to cleave complementary target RNAs. Here, we describe a method to purify active RISC containing a single, unique small RNA guide sequence. We begin by capturing RISC using a complementary 2'-O-methyl oligonucleotide tethered to beads. Unlike other methods that capture RISC but do not allow its recovery, our strategy purifies active, soluble RISC in good yield. The method takes advantage of the finding that RISC partially paired to a target through its siRNA guide dissociates more than 300 times faster than a fully paired siRNA in RISC. We use this strategy to purify fly Ago1- and Ago2-RISC, as well as mouse AGO2-RISC. The method can discriminate among RISCs programmed with different guide strands, making it possible to deplete and recover specific RISC populations. Endogenous microRNA:Argonaute complexes can also be purified from cell lysates. Our method scales readily and takes less than a day to complete.
Subject(s)
Argonaute Proteins/isolation & purification , Drosophila/enzymology , MicroRNAs/isolation & purification , RNA, Complementary/genetics , RNA, Small Interfering/isolation & purification , RNA-Induced Silencing Complex/isolation & purification , Animals , Argonaute Proteins/metabolism , Base Pairing , Blotting, Northern , Drosophila/genetics , Drosophila/metabolism , Drosophila Proteins/isolation & purification , Drosophila Proteins/metabolism , Mass Spectrometry , Mice , MicroRNAs/genetics , MicroRNAs/metabolism , RNA Interference , RNA, Small Interfering/genetics , RNA, Small Interfering/metabolism , RNA-Induced Silencing Complex/genetics , RNA-Induced Silencing Complex/metabolism , Sensitivity and Specificity , Time Factors , RNA, Small UntranslatedABSTRACT
The endometrium is a dynamic tissue, demonstrating cyclical growth/remodelling in preparation for implantation. In mice, seminal constituents trigger mechanisms to prepare the endometrium, a process dubbed 'seminal priming' that modifies immune system components and mediates endometrial remodelling in preparation for pregnancy. An array of cytokines has been reported to mediate this interaction, although much of the literature relates to in vitro studies on isolated endometrial epithelial cells. This study measured changes in immune-related gene expression in endometrial epithelial and stromal cells in vivo following natural mating. CD1 mice were naturally mated and sacrificed over the first 4 days post-coitum (n=3 each day). Endometrial epithelial and stromal compartments were isolated by laser capture microdissection. Labelled cRNA was generated and hybridised to genome-wide expression microarrays. Pathway analysis identified several immune-related pathways active within epithelial and stromal compartments, in particular relating to cytokine networks, matrix metalloproteinases and prostaglandin synthesis. Cluster analysis demonstrated that the expression of factors involved in immunomodulation/endometrial remodelling differed between the epithelial and stromal compartments in a temporal fashion. This study is the first to examine the disparate responses of the endometrial epithelial and stromal compartments to seminal plasma in vivo in mice, and demonstrates the complexity of the interactions between these two compartments needed to create a permissive environment for implantation.
Subject(s)
Endometrium/immunology , Epithelium/immunology , Immunity/physiology , Stromal Cells/immunology , Animals , Cytokines/biosynthesis , Cytokines/genetics , Embryo Implantation/physiology , Endometrium/cytology , Female , Gene Expression/immunology , Genome-Wide Association Study , Immunity/genetics , Male , Matrix Metalloproteinases/biosynthesis , Matrix Metalloproteinases/genetics , Mice , Microarray Analysis , Microdissection , Pregnancy , Prostaglandins/biosynthesis , RNA, Complementary/biosynthesis , RNA, Complementary/genetics , Semen/metabolism , Signal Transduction/genetics , Signal Transduction/immunology , Uterus/cytology , Uterus/metabolismABSTRACT
UNLABELLED: Natural oestrogens, which are degraded but not completely removed in wastewater treatment plants, are suspected of causing the endocrine disruption of aquatic organisms in the receiving water body. While several bacterial isolates were reported to be oestrogen-degrading bacteria, our previous study implied that only the unidentified rod-shaped Betaproteobacteria in chains were responsible for estrone (E1) degradation by activated sludge especially at the sub-milligram per litre level. The Betaproteobacteria were suspected to be related to genera Sphaerotilus and Leptothrix according to morphological observations. Probe Spha823 was newly developed to target 16S rRNA gene clones obtained from activated sludge and closely related to the above genera. [(3) H]E1-incubated sludge samples showed that most of the (3) H-labelled cells hybridized with probe Spha823 by microautoradiography (MAR) fluorescent in situ hybridization. Spha823-defined cells were present in all three activated sludge samples tested, where they accounted for up to 3% of the total microbial biomass. Spha823-defined cells comprised 59·5-80·1% of the total MAR-positive cells, which suggested that the Sphaerotilus-Leptothrix-related bacteria were the most abundant micro-organisms involved in E1 degradation (at 200 µg l(-1) ) in the activated sludge samples. SIGNIFICANCE AND IMPACT OF THE STUDY: Estrone (E1) is one of the natural estrogens, which can be degraded but is not always completely removed in wastewater treatment plants. E1 is suspected of causing the endocrine disruption of aquatic organisms in the receiving water body. We identified dominant E1-incorporating bacteria, which should include E1-degrading bacteria, in activated sludge treating domestic wastewater. Sphaerotilus-Leptothrix-related bacteria, which had never been reported in the previous attempts based on culture-dependent approach, occupied 60-80% of the E1-incorporating bacteria. This study demonstrates the identification of functionally active bacteria to degrade micro-pollutants at sub-milligram per litre level.
Subject(s)
Autoradiography/methods , Betaproteobacteria/isolation & purification , Estrone/metabolism , Sewage/microbiology , Water Purification/methods , Betaproteobacteria/genetics , Betaproteobacteria/metabolism , In Situ Hybridization, Fluorescence , Molecular Sequence Data , Oligonucleotide Probes/genetics , RNA, Complementary/genetics , RNA, Ribosomal, 16S/geneticsABSTRACT
Previous studies have identified two salt bridges in human CFTR chloride ion channels, Arg(352)-Asp(993) and Arg(347)-Asp(924), that are required for normal channel function. In the present study, we determined how the two salt bridges cooperate to maintain the open pore architecture of CFTR. Our data suggest that Arg(347) not only interacts with Asp(924) but also interacts with Asp(993). The tripartite interaction Arg(347)-Asp(924)-Asp(993) mainly contributes to maintaining a stable s2 open subconductance state. The Arg(352)-Asp(993) salt bridge, in contrast, is involved in stabilizing both the s2 and full (f) open conductance states, with the main contribution being to the f state. The s1 subconductance state does not require either salt bridge. In confirmation of the role of Arg(352) and Asp(993), channels bearing cysteines at these sites could be latched into a full open state using the bifunctional cross-linker 1,2-ethanediyl bismethanethiosulfonate, but only when applied in the open state. Channels remained latched open even after washout of ATP. The results suggest that these interacting residues contribute differently to stabilizing the open pore in different phases of the gating cycle.
Subject(s)
Arginine/metabolism , Aspartic Acid/metabolism , Cystic Fibrosis Transmembrane Conductance Regulator/metabolism , Ion Channel Gating , Adenosine Triphosphate/pharmacology , Algorithms , Amino Acid Sequence , Animals , Arginine/genetics , Aspartic Acid/genetics , Binding Sites/genetics , Chlorides/pharmacology , Cystic Fibrosis Transmembrane Conductance Regulator/genetics , Female , Humans , Kinetics , Membrane Potentials/drug effects , Membrane Potentials/physiology , Mutation , Oocytes/metabolism , Oocytes/physiology , Patch-Clamp Techniques , RNA, Complementary/genetics , Xenopus laevisABSTRACT
Mature mammalian oocytes undergo a prolonged series of cytoplasmic calcium (Ca(2+)) oscillations at fertilization that are the cause of oocyte activation. The Ca(2+) oscillations in mammalian oocytes are driven via inositol 1,4,5-trisphosphate (IP3) generation. Microinjection of the sperm-derived phospholipase C-zeta (PLCζ), which generates IP3, causes the same pattern of Ca(2+) oscillations as observed at mammalian fertilization and it is thought to be the physiological agent that triggers oocyte activation. However, another sperm-specific protein, 'post-acrosomal WW-domain binding protein' (PAWP), has also been reported to elicit activation when injected into mammalian oocytes, and to produce a Ca(2+) increase in frog oocytes. Here we have investigated whether PAWP can induce fertilization-like Ca(2+) oscillations in mouse oocytes. Recombinant mouse PAWP protein was found to be unable to hydrolyse phosphatidylinositol 4,5-bisphosphate in vitro and did not cause any detectable Ca(2+) release when microinjected into mouse oocytes. Microinjection with cRNA encoding either the untagged PAWP, or yellow fluorescent protein (YFP)-PAWP, or luciferase-PAWP fusion proteins all failed to trigger Ca(2+) increases in mouse oocytes. The lack of response in mouse oocytes was despite PAWP being robustly expressed at similar or higher concentrations than PLCζ, which successfully initiated Ca(2+) oscillations in every parallel control experiment. These data suggest that sperm-derived PAWP is not involved in triggering Ca(2+) oscillations at fertilization in mammalian oocytes.
Subject(s)
Calcium/metabolism , Carrier Proteins/metabolism , Oocytes/metabolism , Phosphoinositide Phospholipase C/metabolism , Seminal Plasma Proteins/metabolism , Spermatozoa/metabolism , Animals , Bacterial Proteins , Calcium Signaling , Carrier Proteins/administration & dosage , Female , Inositol 1,4,5-Trisphosphate/biosynthesis , Luminescent Proteins , Male , Mice , Microinjections , Phosphatidylinositol 4,5-Diphosphate/metabolism , Phosphoinositide Phospholipase C/administration & dosage , RNA, Complementary/administration & dosage , RNA, Complementary/genetics , Recombinant Fusion Proteins/administration & dosage , Recombinant Fusion Proteins/metabolism , Seminal Plasma Proteins/administration & dosage , Sperm-Ovum InteractionsABSTRACT
PURPOSE: We examined the effect of a single apple juice intake on the pharmacokinetics of fexofenadine enantiomers in healthy Japanese subjects. METHODS: In a randomized two phase, open-label crossover study, 14 subjects received 60 mg of racemic fexofenadine simultaneously with water or apple juice. For the uptake studies, oocytes expressing organic anion-transporting polypeptide 2B1 (OATP2B1) were incubated with 100 µM (R)- and (S)-fexofenadine in the presence or absence of 10 % apple juice. RESULTS: One-time ingestion of apple juice significantly decreased the area under the plasma concentration-time curve (AUC0-24) for (R)- and (S)-fexofenadine by 49 and 59 %, respectively, and prolonged the time to reach the maximum plasma concentration (t max) of both enantiomers (P < 0.001). Although apple juice greatly reduced the amount of (R)- and (S)-fexofenadine excretion into urine (Ae0-24) by 54 and 58 %, respectively, the renal clearances of both enantiomers were unchanged between the control and apple juice phases. For in vitro uptake studies, the uptake of both fexofenadine enantiomers into OATP2B1 complementary RNA (cRNA)-injected oocytes was significantly higher than that into water-injected oocytes, and this effect was greater for (R)-fexofenadine. In addition, apple juice significantly decreased the uptake of both enantiomers into OATP2B1 cRNA-injected oocytes. CONCLUSIONS: These results suggest that OATP2B1 plays an important role in the stereoselective pharmacokinetics of fexofenadine and that one-time apple juice ingestion probably inhibits intestinal OATP2B1-mediated transport of both enantiomers. In addition, this study demonstrates that the OATP2B1 inhibition effect does not require repeated ingestion or a large volume of apple juice.
Subject(s)
Beverages , Food-Drug Interactions , Fruit , Malus , Organic Anion Transporters/metabolism , Terfenadine/analogs & derivatives , Adult , Animals , Anti-Allergic Agents/blood , Anti-Allergic Agents/chemistry , Anti-Allergic Agents/pharmacokinetics , Anti-Allergic Agents/urine , Area Under Curve , Cross-Over Studies , Eating , Female , Histamine H1 Antagonists, Non-Sedating/blood , Histamine H1 Antagonists, Non-Sedating/chemistry , Histamine H1 Antagonists, Non-Sedating/pharmacokinetics , Histamine H1 Antagonists, Non-Sedating/urine , Humans , Intestinal Absorption , Male , Oocytes/metabolism , Organic Anion Transporters/genetics , RNA, Complementary/genetics , Stereoisomerism , Terfenadine/blood , Terfenadine/chemistry , Terfenadine/pharmacokinetics , Terfenadine/urine , Xenopus laevis , Young AdultABSTRACT
BACKGROUND/AIMS: The transmembrane Klotho protein contributes to inhibition of 1,25(OH)2D3 formation. The extracellular domain of Klotho protein could function as an enzyme with e.g. ß-glucuronidase activity, be cleaved off and be released into blood and cerebrospinal fluid. Klotho regulates several cellular transporters. Klotho protein deficiency accelerates the appearance of age related disorders including neurodegeneration and muscle wasting and eventually leads to premature death. The main site of Klotho protein expression is the kidney. Klotho protein is also appreciably expressed in other tissues including chorioid plexus. The present study explored the effect of Klotho protein on the creatine transporter CreaT (Slc6A8), which participates in the maintenance of neuronal function and survival. METHODS: To this end cRNA encoding Slc6A8 was injected into Xenopus oocytes with and without additional injection of cRNA encoding Klotho protein. Creatine transporter CreaT (Slc6A8) activity was estimated from creatine induced current determined by two-electrode voltage-clamp. RESULTS: Coexpression of Klotho protein significantly increased creatine-induced current in Slc6A8 expressing Xenopus oocytes. Coexpression of Klotho protein delayed the decline of creatine induced current following inhibition of carrier insertion into the cell membrane by brefeldin A (5 µM). The increase of creatine induced current by coexpression of Klotho protein in Slc6A8 expressing Xenopus oocytes was reversed by ß-glucuronidase inhibitor (DSAL). Similarly, treatment of Slc6A8 expressing Xenopus oocytes with recombinant human alpha Klotho protein significantly increased creatine induced current. CONCLUSION: Klotho protein up-regulates the activity of creatine transporter CreaT (Slc6A8) by stabilizing the carrier protein in the cell membrane, an effect requiring ß-glucuronidase activity of Klotho protein.