Ribosomes Cannot Interact Simultaneously with Elongation Factors EF Tu and EF G

Prior binding of EF G and GDP to 70S ribosomes from Escherichia coli prevents the subsequent binding of aminoacyl-tRNA, mediated by EF Tu. However, the interaction of EF Tu.GTP.aminoacyl-tRNA with the 30S subunit, which results in aminoacyl-tRNA binding without GTP hydrolysis, appears to be unaffected by EF G, GDP, and fusidic acid. We conclude that elongation factors Tu and G cannot interact simultaneously with the ribosome. The simplest interpretation of these and earlier data is that EF G and EF Tu interact with the same, or overlapping, 50S ribosomal sites in the course of GTP hydrolysis associated with translocation and aminoacyl-tRNA binding, respectively. In any event, these factors must alternate in binding to the ribosome in the course of each elongation cycle.     

Elongation Factors EF Tu and EF G Interact at Related Sites on Ribosomes

The binding of elongation factor EF G to ribosomes inhibits the subsequent reaction of the ribosomes with the ternary complex aminoacyl-tRNA·EF Tu·GTP. Both the hydrolysis of GTP and the binding of aminoacyl-tRNA to ribosomes are nearly abolished by the previous binding of factor EF G to ribosomes in the presence of either fusidic acid plus either GTP or a nonhydrolyzable analog of GTP. The results suggest that each elongation factor binds to the same region on the ribosome. The GTPase activities of both factors EF G and EF Tu may be activated by interaction at the same ribosomal site, as has been previously suggested by others.     

Translation of Bacteriophage Qβ RNA by Cytoplasmic Extracts of Mammalian Cells

Cytoplasmic extracts from Krebs II mouse ascites cells and from L cells translate messenger RNA from coliphage Qbeta with fidelity to produce products that migrate on polyacrylamide gels with those products directed by Qbeta RNA in an Escherichia coli cell-free system. The mammalian cell extracts correctly initiate and terminate Qbeta coat protein synthesis, as shown by: (i) [(3)H]lysine-and [(3)H]arginine-labeled tryptic peptides derived from the coat-sized product resemble these from authentic Qbeta coat protein, (ii) Qbeta coat (which contains methionine only at the N-terminal end) can be radioactively labeled with methionine only if the methionine is formylated, and (iii) L cell extracts directed by Qbeta am(-)11 (an amber mutant in the coat protein) RNA make no completed coat-sized material, but do make a peptide the size of the authentic amber coat fragment.     

Location of the Coat Cistron on the RNA of Phage Qβ

A new approach for the localization of a cistron on a phage RNA has been developed. The coat protein cistron of phage Qbeta was found to begin between the 1100th and 1400th nucleotide from the 5' terminus of Qbeta RNA and therefore lies in the middle of the genome.     

Structural Assembly of Qβ Virion and Its Diverse Forms of Virus-like Particles

The coat proteins (CPs) of single-stranded RNA bacteriophages (ssRNA phages) directly assemble around the genomic RNA (gRNA) to form a near-icosahedral capsid with a single maturation protein (Mat) that binds the gRNA and interacts with the retractile pilus during infection of the host. Understanding the assembly of ssRNA phages is essential for their use in biotechnology, such as RNA protection and delivery. Here, we present the complete gRNA model of the ssRNA phage Qβ, revealing that the 3′ untranslated region binds to the Mat and the 4127 nucleotides fold domain-by-domain, and is connected through long-range RNA–RNA interactions, such as kissing loops. Thirty-three operator-like RNA stem-loops are located and primarily interact with the asymmetric A/B CP-dimers, suggesting a pathway for the assembly of the virions. Additionally, we have discovered various forms of the virus-like particles (VLPs), including the canonical T = 3 icosahedral, larger T = 4 icosahedral, prolate, oblate forms, and a small prolate form elongated along the 3-fold axis. These particles are all produced during a normal infection, as well as when overexpressing the CPs. When overexpressing the shorter RNA fragments encoding only the CPs, we observed an increased percentage of the smaller VLPs, which may be sufficient to encapsidate a shorter RNA.     

Uniqueness of RNA Coliphage Qβ Display System in Directed Evolutionary Biotechnology

Phage display technology involves the surface genetic engineering of phages to expose desirable proteins or peptides whose gene sequences are packaged within phage genomes, thereby rendering direct linkage between genotype with phenotype feasible. This has resulted in phage display systems becoming invaluable components of directed evolutionary biotechnology. The M13 is a DNA phage display system which dominates this technology and usually involves selected proteins or peptides being displayed through surface engineering of its minor coat proteins. The displayed protein or peptide’s functionality is often highly reduced due to harsh treatment of M13 variants. Recently, we developed a novel phage display system using the coliphage Qβ as a nano-biotechnology platform. The coliphage Qβ is an RNA phage belonging to the family of Leviviridae, a long investigated virus. Qβ phages exist as a quasispecies and possess features making them comparatively more suitable and unique for directed evolutionary biotechnology. As a quasispecies, Qβ benefits from the promiscuity of its RNA dependent RNA polymerase replicase, which lacks proofreading activity, and thereby permits rapid variant generation, mutation, and adaptation. The minor coat protein of Qβ is the readthrough protein, A₁. It shares the same initiation codon with the major coat protein and is produced each time the ribosome translates the UGA stop codon of the major coat protein with the of misincorporation of tryptophan. This misincorporation occurs at a low level (1/15). Per convention and definition, A₁ is the target for display technology, as this minor coat protein does not play a role in initiating the life cycle of Qβ phage like the pIII of M13. The maturation protein A₂ of Qβ initiates the life cycle by binding to the pilus of the F⁺ host bacteria. The extension of the A₁ protein with a foreign peptide probe recognizes and binds to the target freely, while the A₂ initiates the infection. This avoids any disturbance of the complex and the necessity for acidic elution and neutralization prior to infection. The combined use of both the A₁ and A₂ proteins of Qβ in this display system allows for novel bio-panning, in vitro maturation, and evolution. Additionally, methods for large library size construction have been improved with our directed evolutionary phage display system. This novel phage display technology allows 12 copies of a specific desired peptide to be displayed on the exterior surface of Qβ in uniform distribution at the corners of the phage icosahedron. Through the recently optimized subtractive bio-panning strategy, fusion probes containing up to 80 amino acids altogether with linkers, can be displayed for target selection. Thus, combined uniqueness of its genome, structure, and proteins make the Qβ phage a desirable suitable innovation applicable in affinity maturation and directed evolutionary biotechnology. The evolutionary adaptability of the Qβ phage display strategy is still in its infancy. However, it has the potential to evolve functional domains of the desirable proteins, glycoproteins, and lipoproteins, rendering them superior to their natural counterparts.     

The Nucleotide Sequence at the 5′-Terminus of the Qβ RNA Minus Strand

The sequence of the first 52 nucleotides at the 5'-end of the Qbeta minus strand has been determined and found to be complementary in an antiparallel fashion to the 3'-terminal region of the Qbeta plus strand. There are few similarities between the corresponding sequences of Qbeta plus and minus strands; however, both have a hydrogen-bonded loop close to the 5'-end. The sequence of the 3'-terminal region of the plus strand was deduced: there are no termination signals within the last 32 nucleotides. A notable homology exists between the 3'-ends of Qbeta and R17 RNA.     

Interferon α2–Thymosin α1 Fusion Protein (IFNα2–Tα1): A Genetically Engineered Fusion Protein with Enhanced Anticancer and Antiviral Effect

Human interferon α2 (IFNα2) and thymosin α1 (Tα1) are therapeutic proteins used for the treatment of viral infections and different types of cancer. Both IFNα2 and Tα1 show a synergic effect in their activities when used in combination. Furthermore, the therapeutic fusion proteins produced through the genetic fusion of two genes can exhibit several therapeutic functions in one molecule. In this study, we determined the anticancer and antiviral effect of human interferon α2–thymosin α1 fusion protein (IFNα2–Tα1) produced in our laboratory for the first time. The cytotoxic and genotoxic effect of IFNα2–Tα1 was evaluated in HepG2 and MDA-MB-231 cells. The in vitro assays confirmed that IFNα2–Tα1 inhibited the growth of cells more effectively than IFNα2 alone and showed an elevated genotoxic effect. The expression of proapoptotic genes was also significantly enhanced in IFNα2–Tα1-treated cells compared to IFNα2-treated cells. Furthermore, the HCV RNA level was significantly reduced in IFNα2–Tα1-treated HCV-infected Huh7 cells compared to IFNα2-treated cells. The quantitative PCR analysis showed that the expression of various genes, the products of which inhibit HCV replication, was significantly enhanced in IFNα2–Tα1-treated cells compared to IFNα2-treated cells. Our findings demonstrate that IFNα2–Tα1 is more effective than single IFNα2 as an anticancer and antiviral agent.     

Influence of TiO2 and ZnO Nanoparticles on α-Synuclein and β-Amyloid Aggregation and Formation of Protein Fibrils

The most common neurological disorders, i.e., Parkinson’s disease (PD) and Alzheimer’s disease (AD), are characterized by degeneration of cognitive functions due to the loss of neurons in the central nervous system. The aggregation of amyloid proteins is an important pathological feature of neurological disorders.The aggregation process involves a series of complex structural transitions from monomeric to the formation of fibrils. Despite its potential importance in understanding the pathobiology of PD and AD diseases, the details of the aggregation process are still unclear. Nanoparticles (NPs) absorbed by the human circulatory system can interact with amyloid proteins in the human brain and cause PD. In this work, we report the study of the interaction between TiO₂ nanoparticles (TiO₂-NPs) and ZnO nanoparticles (ZnO-NPs) on the aggregation kinetics of β-amyloid fragment 1-40 (βA) and α-synuclein protein using surface-enhanced Raman spectroscopy (SERS) and tip-enhanced Raman spectroscopy (TERS). The characterizations of ZnO-NPs and TiO₂-NPs were evaluated by X-ray diffraction (XRD) spectrum, atomic force microscopy (AFM), and UV-Vis spectroscopy. The interaction of nanoparticles with amyloid proteins was investigated by SERS. Our study showed that exposure of amyloid protein molecules to TiO₂-NPs and ZnO-NPs after incubation at 37 °C caused morphological changes and stimulated aggregation and fibrillation. In addition, significant differences in the intensity and location of active Raman frequencies in the amide I domain were found. The principal component analysis (PCA) results show that the effect of NPs after incubation at 4 °C does not cause changes in βA structure.     

Reciprocal regulation of Gsα by palmitate and the βγ subunit

Hormonal activation of G_s, the stimulatory regulator of adenylyl cyclase, promotes dissociation of α_s from Gβγ, accelerates removal of covalently attached palmitate from the Gα subunit, and triggers release of a fraction of α_s from the plasma membrane into the cytosol. To elucidate relations among these three events, we assessed biochemical effects in vitro of attached palmitate on recombinant α_s prepared from Sf9 cells. In comparison to the unpalmitoylated protein (obtained from cytosol of Sf9 cells, treated with a palmitoyl esterase, or expressed as a mutant protein lacking the site for palmitoylation), palmitoylated α_s (from Sf9 membranes, 50% palmitoylated) was more hydrophobic, as indicated by partitioning into TX-114, and bound βγ with 5-fold higher affinity. βγ protected GDP-bound α_s, but not α_s· GTP[γS], from depalmitoylation by a recombinant esterase. We conclude that βγ binding and palmitoylation reciprocally potentiate each other in promoting membrane attachment of α_s and that dissociation of α_s·GTP from βγ is likely to mediate receptor-induced α_s depalmitoylation and translocation of the protein to cytosol in intact cells.     

Crosstalk between Gαi- and Gαq-coupled receptors is mediated by Gβγ exchange

Activation of Galpha(i)-coupled receptors often causes enhancement of the inositol phosphate signal triggered by Galpha(q)-coupled receptors. To investigate the mechanism of this synergistic receptor crosstalk, we studied the Galpha(i)-coupled adenosine A(1) and alpha(2C) adrenergic receptors and the Galpha(q)-coupled bradykinin B(2) and a UTP-preferring P2Y receptor. Stimulation of either Galpha(i)-coupled receptor expressed in COS cells increased the potency and the efficacy of inositol phosphate production by bradykinin or UTP. Likewise, overexpression of Gbeta(1)gamma(2) resulted in a similar increase in potency and efficacy of bradykinin or UTP. In contrast, these stimuli did not affect the potency of direct activators of Galpha(q); a truncated Gbeta(3) mutant had no effect on the receptor-generated signals whereas signals generated at the G-protein level were still enhanced. This suggests that the Gbetagamma-mediated signal enhancement occurs at the receptor level. Almost all possible combinations of Gbeta(1-3) with Ggamma(2-7) were equally effective in enhancing the signals of the B(2) and a UTP-preferring P2Y receptor, indicating a very broad specificity of this synergism. The enhancement of the bradykinin signal by (i) Galpha(i)-activating receptor ligands or (ii) cotransfection of Gbetagamma was suppressed when the B(2) receptor was replaced by a B(2)Gbeta(2) fusion protein. Gbetagamma enhanced the B(2) receptor-stimulated activation of G-proteins as determined by GTPgammaS-induced decrease in high affinity agonist binding and by B(2) receptor-enhanced [(35)S]GTPgammaS binding. These findings support the concept that Gbetagamma exchange between Galpha(i)- and Galpha(q)-coupled receptors mediates this type of receptor crosstalk.     

Anti-β2 glycoprotein I (β2GPI) autoantibodies recognize an epitope on the first domain of β2GPI

Anticardiolipin (aCL) autoantibodies are associated with thrombosis, recurrent fetal loss, and thrombocytopenia. Only aCL found in autoimmune disease require the participation of the phospholipid binding plasma protein β2 glycoprotein I (β2GPI) for antibody binding and now are called anti-β2GPI. The antigenic specificity of aCL affinity purified from 11 patients with high titers was evaluated in an effort to better understand the pathophysiology associated with aCL. Seven different recombinant domain-deleted mutants of human β2GPI, and full length human β2GPI (wild-type), were used in competition assays to inhibit the autoantibodies from binding to immobilized wild-type β2GPI. Only those domain-deleted mutants that contained domain 1 inhibited the binding to immobilized wild-type β2GPI from all of the patients. The domain-deleted mutants that contained domain 1 inhibited all aCL in a similar but not identical pattern, suggesting that these aCL recognize a similar, but distinguishable, epitope(s) present on domain 1.     

SARS-CoV-2 Nucleocapsid Protein Interacts with RIG-I and Represses RIG-Mediated IFN-β Production

SARS-CoV-2 is highly pathogenic in humans and poses a great threat to public health worldwide. Clinical data shows a disturbed type I interferon (IFN) response during the virus infection. In this study, we discovered that the nucleocapsid (N) protein of SARS-CoV-2 plays an important role in the inhibition of interferon beta (IFN-β) production. N protein repressed IFN-β production induced by poly(I:C) or upon Sendai virus (SeV) infection. We noted that N protein also suppressed IFN-β production, induced by several signaling molecules downstream of the retinoic acid-inducible gene I (RIG-I) pathway, which is the crucial pattern recognition receptor (PRR) responsible for identifying RNA viruses. Moreover, our data demonstrated that N protein interacted with the RIG-I protein through the DExD/H domain, which has ATPase activity and plays an important role in the binding of immunostimulatory RNAs. These results suggested that SARS-CoV-2 N protein suppresses the IFN-β response through targeting the initial step, potentially the cellular PRR–RNA-recognition step in the innate immune pathway. Therefore, we propose that the SARS-CoV-2 N protein represses IFN-β production by interfering with RIG-I.     

Angiogenesis promoted by vascular endothelial growth factor: Regulation through α1β1 and α2β1 integrins

Vascular endothelial growth factor (VEGF), also known as vascular permeability factor, is a cytokine of central importance for the angiogenesis associated with cancers and other pathologies. Because angiogenesis often involves endothelial cell (EC) migration and proliferation within a collagen-rich extracellular matrix, we investigated the possibility that VEGF promotes neovascularization through regulation of collagen receptor expression. VEGF induced a 5- to 7-fold increase in dermal microvascular EC surface protein expression of two collagen receptors—the α₁β₁ and α₂β₁ integrins—through induction of mRNAs encoding the α₁ and α₂ subunits. In contrast, VEGF did not induce increased expression of the α₃β₁ integrin, which also has been implicated in collagen binding. Integrin α₁-blocking and α₂-blocking antibodies (Ab) each partially inhibited attachment of microvascular EC to collagen I, and α₁-blocking Ab also inhibited attachment to collagen IV and laminin-1. Induction of α₁β₁ and α₂β₁ expression by VEGF promoted cell spreading on collagen I gels which was abolished by a combination of α₁-blocking and α₂-blocking Abs. In vivo, a combination of α₁-blocking and α₂-blocking Abs markedly inhibited VEGF-driven angiogenesis; average cross-sectional area of individual new blood vessels was reduced 90% and average total new vascular area was reduced 82% without detectable effects on the pre-existing vasculature. These data indicate that induction of α₁β₁ and α₂β₁ expression by EC is an important mechanism by which VEGF promotes angiogenesis and that α₁β₁ and α₂β₁ antagonists may prove effective in inhibiting VEGF-driven angiogenesis in cancers and other important pathologies.     

Minimal requirements for template recognition by bacteriophage Qβ replicase: Approach to general RNA-dependent RNA synthesis

Any oligo- or polynucleotide able to offer a C-C-C-sequence at the 3′-terminus and a second C-C-C-sequence in a defined steric position to Qβ replicase is an efficient template. Corresponding chemical modifications convert non-template RNAs to template RNAs.     

β-Trcp couples β-catenin phosphorylation-degradation and regulates Xenopus axis formation

Regulation of beta-catenin stability is essential for Wnt signal transduction during development and tumorigenesis. It is well known that serine-phosphorylation of beta-catenin by the Axin-glycogen synthase kinase (GSK)-3beta complex targets beta-catenin for ubiquitination-degradation, and mutations at critical phosphoserine residues stabilize beta-catenin and cause human cancers. How beta-catenin phosphorylation results in its degradation is undefined. Here we show that phosphorylated beta-catenin is specifically recognized by beta-Trcp, an F-box/WD40-repeat protein that also associates with Skp1, an essential component of the ubiquitination apparatus. beta-catenin harboring mutations at the critical phosphoserine residues escapes recognition by beta-Trcp, thus providing a molecular explanation for why these mutations cause beta-catenin accumulation that leads to cancer. Inhibition of endogenous beta-Trcp function by a dominant negative mutant stabilizes beta-catenin, activates Wnt/beta-catenin signaling, and induces axis formation in Xenopus embryos. Therefore, beta-Trcp plays a central role in recruiting phosphorylated beta-catenin for degradation and in dorsoventral patterning of the Xenopus embryo.     

RGS4 and GAIP are GTPase-activating proteins for Gqα and block activation of phospholipase Cβ by γ-thio-GTP-Gqα

RGS proteins constitute a newly appreciated and large group of negative regulators of G protein signaling. Four members of the RGS family act as GTPase-activating proteins (GAPs) with apparent specificity for members of the G_iα subfamily of G protein subunits. We demonstrate here that two RGS proteins, RGS4 and GAIP, also act as GAPs for G_qα, the G_α protein responsible for activation of phospholipase Cβ. Furthermore, these RGS proteins block activation of phospholipase Cβ by guanosine 5′-(3-O-thio)triphosphate-G_qα. GAP activity does not explain this effect, which apparently results from occlusion of the binding site on G_α for effector. Inhibitory effects of RGS proteins on G protein-mediated signaling pathways can be demonstrated by simple mixture of RGS4 or GAIP with plasma membranes.     

α2-macroglobulin associates with β-amyloid peptide and prevents fibril formation

We have used the yeast two-hybrid system to isolate cDNAs encoding proteins that specifically interact with the 42-aa β-amyloid peptide (Aβ), a major constituent of senile plaques in Alzheimer’s disease. The carboxy terminus of α₂-macroglobulin (α2M), a proteinase inhibitor released in response to inflammatory stimuli, was identified as a strong and specific interactor of Aβ, utilizing this system. Direct evidence for this interaction was obtained by co-immunoprecipitation of α2M with Aβ from the yeast cell, and by formation of SDS-resistant Aβ complexes in polyacrylamide gels by using synthetic Aβ and purified α2M. The association of Aβ with α2M and various purified amyloid binding proteins was assessed by employing a method measuring protein–protein interactions in liquid phase. The dissociation constant by this technique for the α2M–Aβ association using labeled purified proteins was measured (K_d = 350 nM). Electron microscopy showed that a 1:8 ratio of α2M to Aβ prevented fibril formation in solution; the same ratio to Aβ of another acute phase protein, α₁-antichymotrypsin, was not active in preventing fibril formation in vitro. These results were corroborated by data obtained from an in vitro aggregation assay employing Thioflavine T. The interaction of α2M with Aβ suggests new pathway(s) for the clearance of the soluble amyloid peptide.