Structure of the UHRF1 Tandem Tudor Domain Bound to a Methylated Non-histone Protein,LIG1, Reveals Rules for Binding and Regulation

1. Download : Download high-res image (275KB)
2. Download : Download full-size image

     

Arabidopsis Synaptotagmin SYT1, a Type I Signal-anchor Protein,Requires Tandem C2 Domains for Delivery to the Plasma Membrane

The correct localization of integral membrane proteins to subcellular compartments is important for their functions. Synaptotagmin contains a single transmembrane domain that functions as a type I signal-anchor sequence in its N terminus and two calcium-binding domains (C₂A and C₂B) in its C terminus. Here, we demonstrate that the localization of an Arabidopsis synaptotagmin homolog, SYT1, to the plasma membrane (PM) is modulated by tandem C2 domains. An analysis of the roots of a transformant-expressing green fluorescent protein-tagged SYT1 driven by native SYT1 promoter suggested that SYT1 is synthesized in the endoplasmic reticulum, and then delivered to the PM via the exocytotic pathway. We transiently expressed a series of truncated proteins in protoplasts, and determined that tandem C₂A-C₂B domains were necessary for the localization of SYT1 to the PM. The PM localization of SYT1 was greatly reduced following mutation of the calcium-binding motifs of the C₂B domain, based on sequence comparisons with other homologs, such as endomembrane-localized SYT5. The localization of SYT1 to the PM may have been required for the functional divergence that occurred in the molecular evolution of plant synaptotagmins.     

Activation of Distinct α5β1-mediated Signaling Pathways by Fibronectin's Cell Adhesion and Matrix Assembly Domains

The interaction of cells with fibronectin generates a series of complex signaling events that serve to regulate several aspects of cell behavior, including growth, differentiation, adhesion, and motility. The formation of a fibronectin matrix is a dynamic, cell-mediated process that involves both ligation of the α₅β₁ integrin with the Arg-Gly-Asp (RGD) sequence in fibronectin and binding of the amino terminus of fibronectin to cell surface receptors, termed “matrix assembly sites,” which mediate the assembly of soluble fibronectin into insoluble fibrils. Our data demonstrate that the amino-terminal type I repeats of fibronectin bind to the α₅β₁ integrin and support cell adhesion. Furthermore, the amino terminus of fibronectin modulates actin assembly, focal contact formation, tyrosine kinase activity, and cell migration. Amino-terminal fibronectin fragments and RGD peptides were able to cross-compete for binding to the α₅β₁ integrin, suggesting that these two domains of fibronectin cannot bind to the α₅β₁ integrin simultaneously. Cell adhesion to the amino-terminal domain of fibronectin was enhanced by cytochalasin D, suggesting that the ligand specificity of the α₅β₁ integrin is regulated by the cytoskeleton. These data suggest a new paradigm for integrin-mediated signaling, where distinct regions within one ligand can modulate outside-in signaling through the same integrin.     

ABCA1, ABCG1, and ABCG4 Are Distributed to Distinct Membrane Meso-Domains and Disturb Detergent-Resistant Domains on the Plasma Membrane

ATP-binding cassette A1 (ABCA1), ABCG1, and ABCG4 are lipid transporters that mediate the efflux of cholesterol from cells. To analyze the characteristics of these lipid transporters, we examined and compared their distributions and lipid efflux activity on the plasma membrane. The efflux of cholesterol mediated by ABCA1 and ABCG1, but not ABCG4, was affected by a reduction of cellular sphingomyelin levels. Detergent solubility and gradient density ultracentrifugation assays indicated that ABCA1, ABCG1, and ABCG4 were distributed to domains that were solubilized by Triton X-100 and Brij 96, resistant to Triton X-100 and Brij 96, and solubilized by Triton X-100 but resistant to Brij 96, respectively. Furthermore, ABCG1, but not ABCG4, was colocalized with flotillin-1 on the plasma membrane. The amounts of cholesterol extracted by methyl-β-cyclodextrin were increased by ABCA1, ABCG1, or ABCG4, suggesting that cholesterol in non-raft domains was increased. Furthermore, ABCG1 and ABCG4 disturbed the localization of caveolin-1 to the detergent-resistant domains and the binding of cholera toxin subunit B to the plasma membrane. These results suggest that ABCA1, ABCG1, and ABCG4 are localized to distinct membrane meso-domains and disturb the meso-domain structures by reorganizing lipids on the plasma membrane; collectively, these observations may explain the different substrate profiles and lipid efflux roles of these transporters.     

miR-146a Enhances the Oncogenicity of Oral Carcinoma by Concomitant Targeting of the IRAK1, TRAF6 and NUMB Genes

MicroRNAs are short non-coding RNAs that regulate gene expression and are crucial to tumorigenesis. Oral squamous cell carcinoma (OSCC) is a prevalent malignancy worldwide. Up-regulation of miR-146 has been identified in OSCC tissues. However, the roles of miR-146 in carcinogenesis are controversial as it is suppressive in many other malignancies. The present study investigated the pathogenic implications of miR-146a in oral carcinogenesis. Microdissected OSCC exhibits higher levels of miR-146a expression than matched adjacent mucosal cells. The plasma miR-146a levels of patients are significantly higher than those of control subjects; these levels decrease drastically after tumor resection. miR-146a levels in tumors and in patients’ plasma can be used to classify OSCC and non-disease status (sensitivity: >0.72). Exogenous miR-146a expression is significantly increased in vitro oncogenic phenotypes as well as during xenograft tumorigenesis and OSCC metastasis. The plasma miR-146a levels of these mice parallel the xenograft tumor burdens of the mice. A miR-146a blocker abrogates the growth of xenograft tumors. miR-146a oncogenic activity is associated with down-regulation of IRAK1, TRAF6 and NUMB expression. Furthermore, miR-146a directly targets the 3′UTR of NUMB and a region within the NUMB coding sequence when suppressing NUMB expression. Exogenous NUMB expression attenuates OSCC oncogenicity. Double knockdown of IRAK1 and TRAF6, and of TRAF6 and NUMB, enhance the oncogenic phenotypes of OSCC cells. Oncogenic enhancement modulated by miR-146a expression is attenuated by exogenous IRAK1 or NUMB expression. This study shows that miR-146a expression contributes to oral carcinogenesis by targeting the IRAK1, TRAF6 and NUMB genes.     

Focus: Vaccines: Sufficient Sleep,Time of Vaccination,and Vaccine Efficacy: A Systematic Review of the Current Evidence and a Proposal for COVID-19 Vaccination

Introduction: The emergence of the novel Coronavirus Disease 2019 (COVID-19) sparked an unprecedented effort to develop effective vaccines against the disease. Some factors may boost the vaccine efficacy, including sufficient sleep and morning vaccination. We aimed to conduct a rapid systematic review to summarize data regarding the association between sleep and time of vaccination with immunity after vaccination. Materials and Methods: The systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) protocol, and three databases (PubMed, Web of Science, and Scopus) were searched up to March 12, 2022. Results: Eight studies were included regarding the sleep and immune response after vaccination, of them, five studies were on influenza, two studies on hepatitis A (HAV), and one study on hepatitis B. Accordingly, six out of eight studies found a positive correlation between sleep and immune response after vaccination. Regarding the time of vaccination, seven studies were eligible to be included (two studies on influenza, one study on HAV and influenza, one study on BCG, one study on hexavalent vaccine, and two studies on SARS-CoV-2 vaccine). Among them, four out of seven studies (including a study on SARS-CoV-2 inactivated vaccine) reported the priorities of morning versus afternoon vaccination regarding antibody production and immune response after vaccination. Conclusion: Taken together, cumulative evidence suggests that sufficient sleep and vaccination in the morning could enhance the immune response after vaccination. Hence, modulating the time of vaccination and sufficient sleep could a be simple and applicable strategy for increasing vaccine efficacy. Future studies could be performed with SARS-CoV-2 vaccines to investigate the effects of time of vaccination and sufficient sleep on COVID-19 vaccine efficacy.     

C1q/TNF-related Protein 4 (CTRP4) Is a Unique Secreted Protein with Two Tandem C1q Domains That Functions in the Hypothalamus to Modulate Food Intake and Body Weight

CTRP4 is a unique member of the C1q family, possessing two tandem globular C1q domains. Its physiological function is poorly defined. Here, we show that CTRP4 is an evolutionarily conserved, ∼34-kDa secretory protein expressed in the brain. In human, mouse, and zebrafish brain, CTRP4 expression begins early in development and is widespread in the central nervous system. Neurons, but not astrocytes, express and secrete CTRP4, and secreted proteins form higher-order oligomeric complexes. CTRP4 is also produced by peripheral tissues and circulates in blood. Its serum levels are increased in leptin-deficient obese (ob/ob) mice. Functional studies suggest that CTRP4 acts centrally to modulate energy metabolism. Refeeding following an overnight fast induced the expression of CTRP4 in the hypothalamus. Central administration of recombinant protein suppressed food intake and altered the whole-body energy balance in both chow-fed and high-fat diet-fed mice. Suppression of food intake by CTRP4 is correlated with a decreased expression of orexigenic neuropeptide (Npy and Agrp) genes in the hypothalamus. These results establish CTRP4 as a novel nutrient-responsive central regulator of food intake and energy balance.     

Histone Deacetylase-1 (HDAC1) Is a Molecular Switch between Neuronal Survival and Death

Both neuroprotective and neurotoxic roles have previously been described for histone deacetylase-1 (HDAC1). Here we report that HDAC1 expression is elevated in vulnerable brain regions of two mouse models of neurodegeneration, the R6/2 model of Huntington disease and the Ca²⁺/calmodulin-dependent protein kinase (CaMK)/p25 double-transgenic model of tauopathic degeneration, suggesting a role in promoting neuronal death. Indeed, elevating HDAC1 expression by ectopic expression promotes the death of otherwise healthy cerebellar granule neurons and cortical neurons in culture. The neurotoxic effect of HDAC1 requires interaction and cooperation with HDAC3, which has previously been shown to selectively induce the death of neurons. HDAC1-HDAC3 interaction is greatly elevated under conditions of neurodegeneration both in vitro and in vivo. Furthermore, the knockdown of HDAC3 suppresses HDAC1-induced neurotoxicity, and the knockdown of HDAC1 suppresses HDAC3 neurotoxicity. As described previously for HDAC3, the neurotoxic effect of HDAC1 is inhibited by treatment with IGF-1, the expression of Akt, or the inhibition of glycogen synthase kinase 3β (GSK3β). In addition to HDAC3, HDAC1 has been shown to interact with histone deacetylase-related protein (HDRP), a truncated form of HDAC9, whose expression is down-regulated during neuronal death. In contrast to HDAC3, the interaction between HDRP and HDAC1 protects neurons from death, an effect involving acquisition of the deacetylase activity of HDAC1 by HDRP. We find that elevated HDRP inhibits HDAC1-HDAC3 interaction and prevents the neurotoxic effect of either of these two proteins. Together, our results suggest that HDAC1 is a molecular switch between neuronal survival and death. Its interaction with HDRP promotes neuronal survival, whereas interaction with HDAC3 results in neuronal death.     

Distinct Mechanisms of Regulation by Ca2+/Calmodulin of Type 1 and 8 Adenylyl Cyclases Support Their Different Physiological Roles

Nine membrane-bound mammalian adenylyl cyclases (ACs) have been identified. Type 1 and 8 ACs (AC1 and AC8), which are both expressed in the brain and are stimulated by Ca²⁺/calmodulin (CaM), have discrete neuronal functions. Although the Ca²⁺ sensitivity of AC1 is higher than that of AC8, precisely how these two ACs are regulated by Ca²⁺/CaM remains elusive, and the basis for their diverse physiological roles is quite unknown. Distinct localization of the CaM binding domains within the two enzymes may be essential to differential regulation of the ACs by Ca²⁺/CaM. In this study we compare in detail the regulation of AC1 and AC8 by Ca²⁺/CaM both in vivo and in vitro and explore the different role of each Ca²⁺-binding lobe of CaM in regulating the two enzymes. We also assess the relative dependence of AC1 and AC8 on capacitative Ca²⁺ entry. Finally, in real-time fluorescence resonance energy transfer-based imaging experiments, we examine the effects of dynamic Ca²⁺ events on the production of cAMP in cells expressing AC1 and AC8. Our data demonstrate distinct patterns of regulation and Ca²⁺ dependence of AC1 and AC8, which seems to emanate from their mode of regulation by CaM. Such distinctive properties may contribute significantly to the divergent physiological roles in which these ACs have been implicated.Nine membrane-bound mammalian adenylyl cyclases (ACs),² AC1–AC9, have been identified (1). They possess a common predicted structure (2)³ and are stimulated by forskolin (FSK; except AC9) and G_sα, although they are distributed and regulated differently (1, 3, 4). Four ACs are regulated by physiological concentrations of Ca²⁺ and thereby provide a critical link between the Ca²⁺- and cAMP-signaling pathways (3, 5); AC5 and AC6 are directly inhibited by Ca²⁺, whereas AC1 and AC8 are stimulated by Ca²⁺ in a calmodulin (CaM)-dependent manner (5). AC3 is also regulated by CaM in vitro, although this requires supramicromolar concentration of Ca²⁺ (6), and in vivo AC3 is inhibited by Ca²⁺ via CaM kinase II (7), unlike AC1 and AC8.AC1 is closely related in sequence to the Ca²⁺/CaM-stimulable rutabaga AC from Drosophila, which is important in Drosophila learning tasks (8–10). AC1 and the other Ca²⁺/CaM-stimulable mammalian AC, AC8, have also been implicated in learning and memory (11). As a means of establishing their proposed roles, single and/or double AC1 and AC8 knockout mice have been generated. Mouse models have demonstrated that Ca²⁺/CaM-stimulable ACs are involved in long-term potentiation and long-term memory (12). However, despite the general view that AC1 and AC8 can behave similarly, discrete physiological actions of each isoform are becoming apparent. Recent studies by Zhuo''s group demonstrated that AC1 specifically participates in N-methyl-d-aspartic acid receptor-induced neuronal excitotoxicity (13) and an increase in GluR1 synthesis induced by blocking AMPA receptors (14). Furthermore, Nicol and colleagues (15, 16) showed a contribution of AC1, but not AC8, in axon terminal refinement in the retina. On the other hand, AC8 specifically was seen to be responsible for retrieval from adaptive presynaptic silencing (17) and the acquiring of new spatial information (18). These differences in physiological roles must reflect not only differences in their distributions but also presumably in their regulatory properties. Both enzymes are expressed in brain; AC1 is neuro-specific, whereas the expression of AC8 is more widespread (1, 12). Within the central nervous system, AC1 is abundant in the hippocampus, the cerebral cortex, and the granule cells of the cerebellum, whereas AC8 has a high expression level in the thalamus and the cerebral cortex (19). Studies of mouse brain revealed that AC1 is distributed pre-synaptically and AC8 post-synaptically (18, 20).Although physiological differences in the roles of these two enzymes are suggested from the studies outlined above, the regulatory mechanisms that might underlie these differences are not. AC1 is more sensitive to Ca²⁺ than is AC8 in vitro (21, 22), yet details on how these two enzymes are regulated by Ca²⁺/CaM are sparse. In non-excitable cells, a Ca²⁺ elevation caused by capacitative Ca²⁺ entry (CCE), the mode of Ca²⁺ entry triggered by emptying Ca²⁺ from internal stores (23), preferentially stimulates AC1 and AC8 (21). Although stimulation of AC8 by CCE has been shown to be at least partially dependent on its localization at lipid rafts (24), whether AC1 is also targeted to this region of plasma membranes has never been addressed. In addition, CaM regulation of AC1 and AC8 has not been compared in detail, although CaM appears to bind to different domains of the two enzymes. AC8 utilizes two CaM binding domains: a classic amphipathic “1-5-8-14” motif at the N terminus and an IQ-like motif in the C2b domain (25). A recent study indicates that CaM pre-associates with the N terminus of AC8, where it becomes fully saturated upon a Ca²⁺ rise, and activates the enzyme via a C-terminally mediated relief of auto-inhibitory mechanisms (26). By contrast, only residues 495–522 of the C1b region of AC1 have been shown to bind CaM in a Ca²⁺-dependent manner (27, 28). With the presence of only one CaM binding domain in AC1, a simpler mechanism of CaM regulation might be expected.CaM mediates the regulation of numerous Ca²⁺-dependent processes in eukaryotic cells (29). The protein possesses N- and C-terminal lobes, both of which contain two Ca²⁺ binding EF hands (EF1 and EF2 in the N lobe, and EF3 and EF4 in the C lobe (30)). Mutations in the EF hands have been valuable for investigating the interaction of CaM with its targets. Alanine substitutions in the EF12 pair or EF34 pair have generated CaM₁₂ and CaM₃₄ to investigate the independent function of the C and N lobes of CaM, respectively (31, 32).Against the background of the distinct physiological roles carried out by AC1 and AC8, we performed a detailed comparison of the two enzymes expressed in HEK 293 cells. Their sensitivity to Ca²⁺/CaM was compared both in vitro and in vivo; the possibility that they might be expressed in different domains of the plasma membrane was addressed; and putative lobe-specific CaM regulation was assessed using Ca²⁺-binding mutants of CaM. Single cell measurements using a FRET-based cAMP sensor were performed to compare the kinetic responses of the enzymes to physiological elevations of [Ca²⁺]_i. The results demonstrate superficial similarities in the regulation of AC1 and AC8 but critical disparities in their mechanism of activation by the lobes of CaM and in the speed and pattern of their responsiveness to [Ca²⁺]_i. These discrete behaviors provide a physiological opportunity for different outcomes to elevation of [Ca²⁺]_i, depending on the AC that is expressed in particular contexts.     

Evaluation of the Use of the Polyubiquitin Genes,Ubi4 and Ubi10 as Reference Genes for Expression Studies in Brachypodium distachyon

Background

Brachypodium distachyon is emerging as the model plant for temperate grass research and the genome of the community line Bd21 has been sequenced. Additionally, techniques have been developed for Agrobacterium-mediated transformation for the generation of T-DNA insertional lines. Recently, it was reported that expression of the polyubiquitin genes, Ubi4 and Ubi10 are stable in different tissues and growth hormone-treated plant samples, leading to the conclusion that both Ubi4 and Ubi10 are good reference genes for normalization of gene expression data using real-time, quantitative PCR (qPCR).

Principal Findings

Mining of the Joint Genome Institute (JGI) 8X Brachypodium distachyon genome assembly showed that Ubi4 and Ubi10 share a high level of sequence identity (89%), and in silico analyses of the sequences of Ubi4 (Bradi3g04730) and Ubi10 (Bradi1g32860) showed that the primers used previously exhibit multiple binding sites within the coding sequences arising from the presence of tandem repeats of the coding regions. This can potentially result in over-estimation of steady-state levels of Ubi4 and Ubi10. Additionally, due to the high level of sequence identity between both genes, primers used previously for amplification of Ubi4 can bind to Ubi10 and vice versa, resulting in the formation of non-specific amplification products.

Conclusions

The results from this study indicate that the primers used previously were not sufficiently robust and specific. Additionally, their use would result in over-estimation of the steady-state expression levels of Ubi4. Our results question the validity of using the previously proposed primer sets for qPCR amplification of Ubi4 and Ubi10. We demonstrate that primers designed to target the 3′-UTRs of Ubi4 and Ubi10 are better suited for real-time normalization of steady-state expression levels in Brachypodium distachyon.     

Identification of Genes Upregulated by the Transcription Factor Bcr1 That Are Involved in Impermeability,Impenetrability, and Drug Resistance of Candida albicans a/α Biofilms

Candida albicans forms two types of biofilm, depending upon the configuration of the mating type locus. Although architecturally similar, a/α biofilms are impermeable, impenetrable, and drug resistant, whereas a/a and α/α biofilms lack these traits. The difference appears to be the result of an alternative matrix. Overexpression in a/a cells of BCR1, a master regulator of the a/α matrix, conferred impermeability, impenetrability, and drug resistance to a/a biofilms. Deletion of BCR1 in a/α cells resulted in the loss of these a/α-specific biofilm traits. Using BCR1 overexpression in a/a cells, we screened 107 genes of interest and identified 8 that were upregulated by Bcr1. When each was overexpressed in a/a biofilms, the three a/α traits were partially conferred, and when each was deleted in a/α cells, the traits were partially lost. Five of the eight genes have been implicated in iron homeostasis, and six encode proteins that are either in the wall or plasma membrane or secreted. All six possess sites for O-linked and N-linked glycosylation that, like glycosylphosphatidylinositol (GPI) anchors, can cross-link to the wall and matrix, suggesting that they may exert a structural role in conferring impermeability, impenetrability, and drug resistance, in addition to their physiological functions. The fact that in a screen of 107 genes, all 8 of the Bcr1-upregulated genes identified play a role in impermeability, impenetrability, and drug resistance suggests that the formation of the a/α matrix is highly complex and involves a larger number of genes than the initial ones identified here.