Hypothesized behavioral host manipulation by SARS-CoV2/COVID-19 infection

Although not widely studied, behavioral host manipulation by various pathogens has been documented. Host manipulation is the process by which a pathogen evolves adaptations to manipulate the behavior of the host to maximize reproduction (Ro) of the pathogen. The most notable example is rabies. When a host is infected with the rabies virus it gets into the host's central nervous system and triggers hyper aggression. The virus is also present in the rabid animal's saliva so being bitten transmits the infection to a new host and the old host is left to eventually die if untreated. Toxoplasmosis is another example. When mice are infected they demonstrate a fearlessness toward cats, thus increasing their chances of being eaten. Toxoplasmosis needs the digestive tract of the feline to survive. Recent studies have shown that exposure to toxoplasmosis in humans (e.g., through cat feces) has also been associated with behavioral changes that are predicted to enhance the spread of the pathogen. Even the common influenza virus has been shown to selectively increase in-person sociality during the 48-hour incubation period, thus producing an obvious vector for transmission. Here we hypothesize that the novel coronavirus, SARS-CoV2, which produces the COVID-19 disease may produce similar host manipulations that maximize its transmission between humans.

Caspase cleavage of the APC tumor suppressor and release of an amino-terminal domain is required for the transcription-independent function of APC in apoptosis

The adenomatous polyposis coli (APC) tumor suppressor is inactivated by mutation in most colorectal tumors. APC is a component of the Wnt signaling pathway and is best known for its ability to downregulate beta-catenin and consequent effects on transcriptional regulation. Previous work demonstrated that APC accelerates apoptosis-associated caspase activity independently of transcription, and suggested novel tumor suppressor functions of APC. In this work, we have mapped the APC apoptosis-accelerating region to amino acids (aa) 1-760 by testing a series of non-overlapping APC segments. Interestingly, this segment corresponds to a stable group II caspase cleavage product of APC released during apoptosis that includes the amino-terminal aa1-777. Mutation of the APC aspartic acid residue at position 777 to an alanine completely abolished in vitro cleavage of APC by a recombinant group II caspase and rendered the full-length protein unable to accelerate apoptosis in vitro. A truncated APC protein associated with familial and sporadic colorectal cancer, also unable to accelerate apoptosis in vitro and in vivo, is resistant to group II caspase cleavage. These results demonstrate that cleavage of APC and the subsequent release of an amino-terminal segment are necessary for the transcription-independent mechanism of APC-mediated apoptosis.

p53 targets chromatin structure alteration to repress alpha-fetoprotein gene expression

Many of the functions ascribed to p53 tumor suppressor protein are mediated through transcription regulation. We have shown that p53 represses hepatic-specific alpha-fetoprotein (AFP) gene expression by direct interaction with a composite HNF-3/p53 DNA binding element. Using solid-phase, chromatin-assembled AFP DNA templates and analysis of chromatin structure and transcription in vitro, we find that p53 binds DNA and alters chromatin structure at the AFP core promoter to regulate transcription. Chromatin assembled in the presence of hepatoma extracts is activated for AFP transcription with an open, accessible core promoter structure. Distal (-850) binding of p53 during chromatin assembly, but not post-assembly, reverses transcription activation concomitant with promoter inaccessibility to restriction enzyme digestion. Inhibition of histone deacetylase activity by trichostatin-A (TSA) addition, prior to and during chromatin assembly, activated chromatin transcription in parallel with increased core promoter accessibility. Chromatin immunoprecipitation analyses showed increased H3 and H4 acetylated histones at the core promoter in the presence of TSA, while histone acetylation remained unchanged at the site of distal p53 binding. Our data reveal that p53 targets chromatin structure alteration at the core promoter, independently of effects on histone acetylation, to establish repressed AFP gene expression.

Chromatin alteration, transcription and replication: What's the opening line to the story?

Polymerase accessibility to chromatin is a limiting step in both RNA and DNA synthesis. Unwinding DNA and nucleosomes during polymerase complex binding and processing likely requires priming by chromatin restructuring. The initiating step in these processes remains an area of speculation. This review focuses on the physical handling of chromatin during transcription and replication, the fate of nucleosomes assembled on DNA during unwinding and processing the chromatin substrate, and how these alterations in chromatin structure may affect gene expression. Transcription or replication may alter chromatin structure during synthesis, enabling regulatory factor binding and, potentially, future rounds of transcription. As chromatin remodeling and transcription factor binding augment transcription and replication, and are themselves increased by these processes, a temporal model of structural alterations and gene activation is built that may be more circular than linear.

UV-induced inhibition of transcription involves repression of transcription initiation and phosphorylation of RNA polymerase II

Cells from patients with Cockayne syndrome (CS) are hypersensitive to DNA-damaging agents and are unable to restore damage-inhibited RNA synthesis. On the basis of repair kinetics of different types of lesions in transcriptionally active genes, we hypothesized previously that impaired transcription in CS cells is a consequence of defective transcription initiation after DNA damage induction. Here, we investigated the effect of UV irradiation on transcription by using an in vitro transcription system that allowed uncoupling of initiation from elongation events. Nuclear extracts prepared from UV-irradiated or mock-treated normal human and CS cells were assayed for transcription activity on an undamaged beta-globin template. Transcription activity in nuclear extracts closely mimicked kinetics of transcription in intact cells: extracts from normal cells prepared 1 h after UV exposure showed a strongly reduced activity, whereas transcription activity was fully restored in extracts prepared 6 h after treatment. Extracts from CS cells exhibited reduced transcription activity at any time after UV exposure. Reduced transcription activity in extracts coincided with a strong reduction of RNA polymerase II (RNAPII) containing hypophosphorylated C-terminal domain, the form of RNAPII known to be recruited to the initiation complex. These results suggest that inhibition of transcription after UV irradiation is at least partially caused by repression of transcription initiation and not solely by blocked elongation at sites of lesions. Generation of hypophosphorylated RNAPII after DNA damage appears to play a crucial role in restoration of transcription. CS proteins may be required for this process in a yet unknown way.

Hepatitis B viral transactivator HBx alleviates p53-mediated repression of alpha-fetoprotein gene expression

Chronic infection with hepatitis B virus (HBV) is associated with development of hepatocellular carcinoma (HCC). The exact mechanism by which chronic infection with HBV contributes to onset of HCC is unknown. However, previous studies have implicated the HBV transactivator protein, HBx, in progression of HCC through its ability to bind the human tumor suppressor protein, p53. In this study, we have examined the ability of HBx to modify p53 regulation of the HCC tumor marker gene, alpha-fetoprotein (AFP). By utilizing in vitro chromatin assembly of DNA templates prior to transcription analysis, we have demonstrated that HBx functionally disrupts p53-mediated repression of AFP transcription through protein-protein interaction. HBx modification of p53 gene regulation is both tissue-specific and dependent upon the p53 binding element. Our data suggest that the mechanism by which HBx alleviates p53 repression of AFP transcription is through an association with DNA-bound p53, resulting in a loss of p53 interaction with liver-specific transcriptional co-repressors.

S-Phase progression mediates activation of a silenced gene in synthetic nuclei

Aberrant expression of developmentally silenced genes, characteristic of tumor cells and regenerating tissue, is highly correlated with increased cell proliferation. By modeling this process in vitro in synthetic nuclei, we find that DNA replication leads to deregulation of established developmental expression patterns. Chromatin assembly in the presence of adult mouse liver nuclear extract mediates developmental stage-specific silencing of the tumor marker gene alpha-fetoprotein (AFP). Replication of silenced AFP chromatin in synthetic nuclei depletes sequence-specific transcription repressors, thereby disrupting developmentally regulated repression. Hepatoma-derived factors can target partial derepression of AFP, but full transcription activation requires DNA replication. Thus, unscheduled entry into S phase directly mediates activation of a developmentally silenced gene by (i) depleting developmental stage-specific transcription repressors and (ii) facilitating binding of transactivators.

von Hippel-Lindau protein induces hypoxia-regulated arrest of tyrosine hydroxylase transcript elongation in pheochromocytoma cells

Rat pheochromocytoma (PC12) cells were stably transfected with either wild type or mutated human von Hippel-Lindau tumor suppressor protein (hpVHL). These proteins have opposing effects on regulating expression of the gene encoding tyrosine hydroxylase (TH), the rate-limiting enzyme in catecholamine synthesis. Whereas wild type hpVHL represses levels of TH mRNA and protein 5-fold, a truncated pVHL mutant, pVHL(1-115), induces accumulation of TH mRNA and protein 3-fold. hpVHL-induced inhibition of TH gene expression does not involve either a decrease in TH mRNA stability or repression of TH promoter activity. However, repression results from inhibition of RNA elongation at a downstream region of the TH gene. This elongation pause is accompanied by hpVHL sequestration in the nuclear extracts of elongins B and C, regulatory components of the transcription elongation heterotrimer SIII (elongin A/B/C). Hypoxia, a physiological stimulus for TH gene expression, alleviates the elongation block. A truncated pVHL mutant, pVHL(1-115), stimulates TH gene expression by increasing the efficiency of TH transcript elongation. This is the first report showing pVHL-dependent regulation of specific transcript elongation in vivo, as well as dominant negative activity of pVHL mutants in pheochromocytoma cells.

Hepatocyte nuclear factor 3 relieves chromatin-mediated repression of the alpha-fetoprotein gene

The alpha-fetoprotein gene (AFP) is tightly regulated at the tissue-specific level, with expression confined to endoderm-derived cells. We have reconstituted AFP transcription on chromatin-assembled DNA templates in vitro. Our studies show that chromatin assembly is essential for hepatic-specific expression of the AFP gene. While nucleosome-free AFP DNA is robustly transcribed in vitro by both cervical (HeLa) and hepatocellular (HepG2) carcinoma extracts, the general transcription factors and transactivators present in HeLa extract cannot relieve chromatin-mediated repression of AFP. In contrast, preincubation with either HepG2 extract or HeLa extract supplemented with recombinant hepatocyte nuclear factor 3 alpha (HNF3alpha), a hepatic-enriched factor expressed very early during liver development, is sufficient to confer transcriptional activation on a chromatin-repressed AFP template. Transient transfection studies illustrate that HNF3alpha can activate AFP expression in a non-liver cellular environment, confirming a pivotal role for HNF3alpha in establishing hepatic-specific gene expression. Restriction enzyme accessibility assays reveal that HNF3alpha promotes the assembly of an open chromatin structure at the AFP promoter. Combined, these functional and structural data suggest that chromatin assembly establishes a barrier to block inappropriate expression of AFP in non-hepatic tissues and that tissue-specific factors, such as HNF3alpha, are required to alleviate the chromatin-mediated repression.

Functional analysis of chromatin assembled in synthetic nuclei

Numerous regulatory mechanisms contribute to the control of eukaryotic transcription. These controls are manifested through higher-order protein-DNA structure within the nucleus. In vitro assays have proven extremely useful in deciphering the potential regulatory roles of chromatin and nuclear structure in transcription. Embryonic egg extracts of Xenopus with their vast maternal stores and rapid cell-cycle oscillations can be exploited to recapitulate multiple layers of nuclear regulation. Incubation of cloned DNA templates in Xenopus egg extracts promotes a self-ordered assembly of physiologically spaced nucleosomes and synthetic nuclei structure formation. Interaction of membrane vesicles with chromatin leads to formation of a bilayer nuclear envelope encapsulating the DNA. These synthetic nuclei are functional organelles capable of active protein transport and a single round of semiconservative DNA synthesis. This system can be used to directly test the mechanisms by which trans-acting factors promote transcription on nucleosomal DNA, either during chromatin assembly or postassembly or in conjunction with remodeling machinery and/or DNA replication. The functional consequences of trans-acting factor interaction within synthetic nuclei are determined by a coupled in vitro transcription analysis. Immobilizing biotin end-labeled DNA templates on paramagnetic streptavidin beads greatly improves the flexibility of the system. The ease of chromatin-assembled template recovery allows the introduction of wash steps, buffer changes, and specific reaction optimization. These methods for reconstituting gene regulatory mechanisms in vitro are an attempt to strike a balance between biochemical accessibility and physiological relevance.

p53-mediated repression of alpha-fetoprotein gene expression by specific DNA binding

Aberrant expression of the alpha-fetoprotein (AFP) gene is characteristic of a majority of hepatocellular carcinoma cases and serves as a diagnostic tumor-specific marker. By dissecting regulatory mechanisms through electromobility gel shift, transient-transfection, Western blot, and in vitro transcription analyses, we find that AFP gene expression is controlled in part by mutually exclusive binding of two trans-acting factors, p53 and hepatic nuclear factor 3 (HNF-3). HNF-3 protein activates while p53 represses AFP transcription through sequence-specific binding within the previously identified AFP developmental repressor domain. A single mutation within the DNA binding domain of p53 protein or a mutation of the p53 DNA binding element within the AFP developmental repressor eliminates p53-repressive effects in both transient-transfection and cell-free expression systems. Coexpression of p300 histone acetyltransferase, which has been shown to acetylate p53 and increase specific DNA binding, amplifies the p53-mediated repression. Western blot analysis of proteins present in developmentally staged, liver nuclear extracts reveal a one-to-one correlation between activation of p53 protein and repression of AFP during hepatic development. Induction of p53 in response to actinomycin D or hypoxic stress decreases AFP expression. Studies in fibroblast cells lacking HNF-3 further support a model for p53-mediated repression that is both passive through displacement of a tissue-specific activating factor and active in the presence of tissue-specific corepressors. This mechanism for p53-mediated repression of AFP gene expression may be active during hepatic differentiation and lost in the process of tumorigenesis.

Distal enhancer regulation by promoter derepression in topologically constrained DNA in vitro

Long-range promoter-enhancer interactions are a crucial regulatory feature of many eukaryotic genes yet little is known about the mechanisms involved. Using cloned chicken betaA-globin genes, either individually or within the natural chromosomal locus, enhancer-dependent transcription is achieved in vitro at a distance of 2 kb with developmentally staged erythroid extracts. This occurs by promoter derepression and is critically dependent upon DNA topology. In the presence of the enhancer, genes must exist in a supercoiled conformation to be actively transcribed, whereas relaxed or linear templates are inactive. Distal protein-protein interactions in vitro may be favored on supercoiled DNA because of topological constraints. In this system, enhancers act primarily to increase the probability of rapid and efficient transcription complex formation and initiation. Repressor and activator proteins binding within the promoter, including erythroid-specific GATA-1, mediate this process.

Regulated expression of the beta-globin gene locus in synthetic nuclei

Regulated gene expression within a complex chromosomal locus requires multiple nuclear processes. We have analyzed the transcriptional properties of the cloned chick beta-globin gene family when assembled into synthetic nuclei made by use of Xenopus egg extracts. Assembly in an erythroid protein environment correctly recapitulates tissue-specific chromatin structure and long-range promoter-enhancer interaction within the chromosomal locus, resulting in beta-globin gene activation. Nucleosome-repressed beta-globin templates can be transcriptionally activated by double-stranded DNA replication in the presence of staged erythroid proteins by remodeling of the chromatin structure within the promoter region and establishment of distal promoter-enhancer communication. The programmed transcriptional state of a gene, as encoded by its chromatin structure and long-range promoter-enhancer interactions, is stable to nuclear decondensation and DNA replication unless active remodeling occurs in the presence of specific DNA-binding proteins.

The erythroid protein cGATA-1 functions with a stage-specific factor to activate transcription of chromatin-assembled beta-globin genes

The chick beta-globin gene is regulated developmentally within erythroid cells by the interaction of multiple proteins with the promoter and the 3' enhancer. These interactions are correlated with changes in chromatin structure, which are characteristic of the actively expressed gene. Using in vitro chromatin assembly and transcription with staged erythroid extracts, we have determined the critical proteins required to activate expression of nucleosome-reconstituted beta-globin genes. These genes contain a specialized TATA box at -30 (GATA) through which the erythroid-restricted protein cGATA-1 and TFIID both function to regulate different steps in beta-globin expression. We find that TBP (TATA-binding protein) alone can activate transcription of beta-globin chromatin templates from promoters mutated to a canonical TATA box but is ineffective on those containing the normal -30 GATA site. The occupancy of this site by cGATA-1 also fails to generate efficient expression of beta-globin chromatin unless combined with a stage-specific protein, NF-E4, that binds to an adjacent site. However, NF-E4 does not function with TBP to derepress nucleosome-assembled beta-globin genes. We propose that the developmental regulation of beta-globin expression is achieved, in part, by the requirement of an erythroid protein and a stage-specific factor, rather than TBP, to activate chromatin through a specialized TATA box.

Site-directed, recombination-mediated mutagenesis of a complex gene locus

We have generated a site-specific 17 bp insertion within a 38 kb chick globin gene cluster by employing the recombination abilities of Saccharomyces cerevisiae. This gene cluster contains four beta-type globin genes which share a high degree of sequence homology. In this procedure, a small fragment of beta A-globin DNA containing a 17 bp insertion is subcloned into a URA3-based yeast integrating vector (YIp). This mutated globin subclone is introduced into cells that carry the 38 kb globin cluster clone on a single-copy, circular vector derived from a yeast artificial chromosome (YAC). Insertion of the 17 bp oligomer is achieved by targeted integration of the Ylp subclone. The recombinant contains the normal beta A-globin gene, the mutant gene and Ylp vector sequences between the two copies. Excision of the vector sequences and one copy of the duplicated globin sequences by homologous recombination is required for cell survival when exposed to the selective agent 5-fluoroorotic acid, which is toxic to ura+ yeast cells. Depending upon the point of the cross-over, a ura- yeast cell bearing either a wild-type globin gene or a 17 bp insertion mutation will result. By restriction mapping and in vitro transcription analysis, the beta A-globin gene containing the 17 bp insert has no nonspecific mutations generated during the recombination and selection procedures. Specific mutations of regulatory regions, including protein-DNA binding sites, can be accurately targeted within extensive DNA clones by this method.

Transient administration of estradiol-17 beta establishes an autoregulatory loop permanently inducing estrogen receptor mRNA

A single transient dose of estradiol-17 beta is sufficient to elicit the permanent induction of hepatic estrogen receptor mRNA, which is induced 18-fold (from 0.13 to 2.4 molecules per cell) and then remains fully induced for at least 125 days. In primary liver cultures, extremely low concentrations of estradiol-17 beta, which are below the Kd of the Xenopus laevis estrogen receptor, maintain persistent induction of estrogen receptor mRNA but not of estrogen-inducible vitellogenin mRNA. These data and the ability of the antiestrogen, hydroxytamoxifen, to reverse persistent induction of estrogen receptor mRNA, support a model in which transient doses of estradiol-17 beta induce the estrogen receptor and thereby establish an autoregulatory loop. The low levels of estradiol-17 beta normally circulating in male X. laevis and the elevated level of receptor provide sufficient hormone-receptor complex to permanently maintain the induced level of expression of the estrogen receptor gene. The permanent induction of the estrogen receptor may be the regulatory switch that results in the persistent expression of a recently identified class of proteins that exhibit long-term responses to estrogen.

Estrogen induces transcription of the Xenopus laevis serum retinol-binding protein gene

We have isolated and sequenced a full-length cDNA cloned tentatively identified as encoding Xenopus laevis serum retinol-binding protein (RBP) mRNA. The derived amino acid sequence of the Xenopus protein is 63% homologous to the sequence of the human RBP. 17 of 19 amino acids identified as critical in the retinol-binding pocket of human RBP are identical or conservative replacements in the Xenopus protein. The RBP cDNA clone has been used as a hybridization probe to demonstrate that administration of estradiol-17 beta to male X. laevis induces hepatic RBP mRNA 10-fold from its constitutive in vivo level of 1,800 molecules/cell to approximately 18,000 molecules/cell. Using a simplified method for determining relative rates of gene transcription, we demonstrate an estrogen-mediated increase in the rate of RBP gene transcription. These quantitative data provide the first demonstration that a steroid hormone regulates the levels of vertebrate retinol-binding protein mRNA.

Coordinate estrogen induction of vitellogenin and a small serum protein mRNA in Xenopus laevis liver

We have used plus-minus hybridization to identify Xenopus liver cDNA clones of mRNAs whose levels are regulated by estrogen. One clone identified in this way was shown to be a nearly full-length cDNA clone of the mRNA coding for a small 22 000 dalton estrogen-inducible serum protein (EISP). Quantitation of EISP mRNA levels by in vitro translation and by hybridization to the cloned DNA demonstrated a 7-12-fold estrogen induction of EISP mRNA, both in vivo and in primary Xenopus liver cultures. The kinetics of induction of EISP mRNA closely parallel those of the mRNA coding for the abundant estrogen-inducible serum protein, vitellogenin. In contrast, the massive, and toxic, estrogen-mediated accumulation of vitellogenin in serum of male Xenopus laevis is accompanied by a sharp decline in the levels of albumin mRNA and in the levels of the mRNAs coding for several other serum proteins.

3-Hydroxy-3-methylglutaryl-coenzyme A reductase is present in peroxisomes in normal rat liver cells

The location inside rat liver parenchymal cells of 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMG-CoA reductase; EC 1.1.1.34), the key regulatory enzyme in cholesterol biosynthesis, has been examined by immunoelectron microscopy and by subcellular fractionation. Although HMG-CoA reductase is generally thought to be exclusively a microsomal enzyme, we find that a substantial portion of cellular HMG-CoA reductase is localized in peroxisomes. Immunoelectron microscopic labeling of ultrathin frozen sections of normal rat liver, using two monoclonal antibodies to purified HMG-CoA reductase, showed that the enzyme is present in the peroxisomes at a higher concentration than at any other site inside the hepatocytes. Subcellular fractionation studies using Percoll and metrizamide gradients demonstrated a close correspondence of peaks of HMG-CoA reductase activity and of catalase activity, again revealing the presence of the reductase enzyme in peroxisomes. HMG-CoA reductase is therefore localized in peroxisomes in addition to being in the microsomal fraction.

Production and characterization of monoclonal antibodies to rat liver microsomal 3-hydroxy-3-methylglutaryl-coenzyme A reductase

Rat liver microsomal 3-hydroxy-3-methylglutaryl-CoA reductase [HMG-CoA reductase; mevalonate:NADP+ oxidoreductase (CoA-acylating), EC 1.1.1.34], the key regulatory enzyme in cholesterol biosynthesis, has been purified to apparent homogeneity. Purified HMG-CoA reductase yields a single diffuse band when NaDodSO4/polyacrylamide gels are stained with Coomassie blue and yields two adjacent bands when gels are stained with silver. Purified reductase was used to elicit the production of monoclonal antibodies. Spleen cells from BALB/c mice immunized with purified HMG-CoA reductase were fused with Sp-2/0 myeloma cells. Clones producing monoclonal antibodies to HMG-CoA reductase were identified by using a solid-phase radioimmunoassay and were subcloned in soft agar. The three relatively stable hybridoma lines isolated secrete different Igs as judged by their antibody subclasses and differing abilities to inhibit HMG-CoA reductase in solution. Efficient precipitation of solubilized HMG-CoA reductase was achieved with the two IgG antibodies but not with the IgM. A mixture of all three monoclonal antibodies immunoprecipitates more than 90% of the HMG-CoA reductase activity in solubilized rat liver extracts. These monoclonal antibodies should be useful probes for investigation of the regulation of HMG-CoA reductase and cholesterol synthesis.