Adaptation of Oxford Nanopore technology for hepatitis C whole genome sequencing and identification of within-host viral variants

Background

Hepatitis C (HCV) and many other RNA viruses exist as rapidly mutating quasi-species populations in a single infected host. High throughput characterization of full genome, within-host variants is still not possible despite advances in next generation sequencing. This limitation constrains viral genomic studies that depend on accurate identification of hemi-genome or whole genome, within-host variants, especially those occurring at low frequencies. With the advent of third generation long read sequencing technologies, including Oxford Nanopore Technology (ONT) and PacBio platforms, this problem is potentially surmountable. ONT is particularly attractive in this regard due to the portable nature of the MinION sequencer, which makes real-time sequencing in remote and resource-limited locations possible. However, this technology (termed here ‘nanopore sequencing’) has a comparatively high technical error rate. The present study aimed to assess the utility, accuracy and cost-effectiveness of nanopore sequencing for HCV genomes. We also introduce a new bioinformatics tool (Nano-Q) to differentiate within-host variants from nanopore sequencing.

Results

The Nanopore platform, when the coverage exceeded 300 reads, generated comparable consensus sequences to Illumina sequencing. Using HCV Envelope plasmids (~ 1800 nt) mixed in known proportions, the capacity of nanopore sequencing to reliably identify variants with an abundance as low as 0.1% was demonstrated, provided the autologous reference sequence was available to identify the matching reads. Successful pooling and nanopore sequencing of 52 samples from patients with HCV infection demonstrated its cost effectiveness (AUD$ 43 per sample with nanopore sequencing versus $100 with paired-end short read technology). The Nano-Q tool successfully separated between-host sequences, including those from the same subtype, by bulk sorting and phylogenetic clustering without an autologous reference sequence (using only a subtype-specific generic reference). The pipeline also identified within-host viral variants and their abundance when the parameters were appropriately adjusted.

Conclusion

Cost effective HCV whole genome sequencing and within-host variant identification without haplotype reconstruction are potential advantages of nanopore sequencing.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07460-1.

Intronic ATTTC repeat expansions in STARD7 in familial adult myoclonic epilepsy linked to chromosome 2

Familial Adult Myoclonic Epilepsy (FAME) is characterised by cortical myoclonic tremor usually from the second decade of life and overt myoclonic or generalised tonic-clonic seizures. Four independent loci have been implicated in FAME on chromosomes (chr) 2, 3, 5 and 8. Using whole genome sequencing and repeat primed PCR, we provide evidence that chr2-linked FAME (FAME2) is caused by an expansion of an ATTTC pentamer within the first intron of STARD7. The ATTTC expansions segregate in 158/158 individuals typically affected by FAME from 22 pedigrees including 16 previously reported families recruited worldwide. RNA sequencing from patient derived fibroblasts shows no accumulation of the AUUUU or AUUUC repeat sequences and STARD7 gene expression is not affected. These data, in combination with other genes bearing similar mutations that have been implicated in FAME, suggest ATTTC expansions may cause this disorder, irrespective of the genomic locus involved.

High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes

High-throughput single-cell RNA sequencing is a powerful technique but only generates short reads from one end of a cDNA template, limiting the reconstruction of highly diverse sequences such as antigen receptors. To overcome this limitation, we combined targeted capture and long-read sequencing of T-cell-receptor (TCR) and B-cell-receptor (BCR) mRNA transcripts with short-read transcriptome profiling of barcoded single-cell libraries generated by droplet-based partitioning. We show that Repertoire and Gene Expression by Sequencing (RAGE-Seq) can generate accurate full-length antigen receptor sequences at nucleotide resolution, infer B-cell clonal evolution and identify alternatively spliced BCR transcripts. We apply RAGE-Seq to 7138 cells sampled from the primary tumor and draining lymph node of a breast cancer patient to track transcriptome profiles of expanded lymphocyte clones across tissues. Our results demonstrate that RAGE-Seq is a powerful method for tracking the clonal evolution from large numbers of lymphocytes applicable to the study of immunity, autoimmunity and cancer.

Single cell RNA sequencing generates short reads from one end of a template, providing incomplete transcript coverage and limiting identification of diverse sequences such as antigen receptors. Here the authors combine long read nanopore sequencing with short read profiling of barcoded libraries to generate full-length antigen receptor sequences.

Numerical simulation of optical Stark effect saturable absorbers in mode-locked femtosecond VECSELs using a modified two-level atom model

The interaction of an optical pulse with a quantum well saturable absorber is simulated using a semi-classical two-level-atom model which has been modified to approximate spectral hole burning in the carrier distribution. Saturable absorption behaviour is examined in the limit where pulse duration approaches the carrier-carrier scattering time. For long pulses bleaching dominates the absorber response but as the pulse duration approaches the carrier-carrier scattering timescale an additional pulse shaping mechanism becomes active, allowing the absorber to continue to shorten pulses beyond the limit set by bleaching. Examination of the spectral and temporal absorption profiles suggests that intense pulses experience additional pulse shortening from the optical Stark effect.

Monitoring the biological activity of micropollutants during advanced wastewater treatment with ozonation and activated carbon filtration

A bioanalytical test battery was used to monitor the removal efficiency of organic micropollutants during advanced wastewater treatment in the South Caboolture Water Reclamation Plant, Queensland, Australia. This plant treats effluent from a conventional sewage treatment plant for industrial water reuse. The aqueous samples were enriched using solid-phase extraction to separate some organic micropollutants of interest from metals, nutrients and matrix components. The bioassays were chosen to provide information on groups of chemicals with a common mode of toxic action. Therefore they can be considered as sum indicators to detect certain relevant groups of chemicals, not as the most ecologically or human health relevant endpoints. The baseline toxicity was quantified with the bioluminescence inhibition test using the marine bacterium Vibrio fischeri. The specific modes of toxic action that were targeted with five additional bioassays included aspects of estrogenicity, dioxin-like activity, genotoxicity, neurotoxicity, and phytotoxicity. While the accompanying publication discusses the treatment steps in more detail by drawing from the results of chemical analysis as well as the bioanalytical results, here we focus on the applicability and limitations of using bioassays for the purpose of determining the treatment efficacy of advanced water treatment and for water quality assessment in general. Results are reported in toxic equivalent concentrations (TEQ), that is, the concentration of a reference compound required to elicit the same response as the unknown and unidentified mixture of micropollutants actually present. TEQ proved to be useful and easily communicable despite some limitations and uncertainties in their derivation based on the mixture toxicity theory. The results obtained were reproducible, robust and sensitive. The TEQ in the influent ranged in the same order of magnitude as typically seen in effluents of conventional sewage treatment plants. In the initial steps of the treatment chain, no significant degradation of micropollutants was observed, and the high levels of dissolved organic carbon probably affected the outcome of the bioassays. The steps of coagulation/flocculation/dissolved air flotation/sand filtration and ozonation decreased the effect-based micropollutant burden significantly.

Removal of micropollutants and reduction of biological activity in a full scale reclamation plant using ozonation and activated carbon filtration

Pharmaceutical compounds are found in secondary treated effluents up to microg L(-1) levels and therefore discharged into surface waters. Since the long term effects of these compounds on the environment and human health are, to date, largely unknown, implementation of advanced treatment of wastewaters is envisaged to reduce their discharge. This is of particular relevance where surface waters are used as drinking water sources and when considering indirect potable reuse. This study aimed at assessing the removal of organic micropollutants and the concurrent reduction of their biological activity in a full scale reclamation plant treating secondary effluent. The treatment consists of 6 stages: denitrification, pre-ozonation, coagulation/flocculation/dissolved air flotation and filtration (DAFF), main ozonation, activated carbon filtration and final ozonation for disinfection. For that purpose, representative 24-hour composite samples were collected after each stage. The occurrence of 85 compounds was monitored by LC/MS-MS. A battery of 6 bioassays was also used as a complementary tool to evaluate non-specific toxicity and 5 specific toxic modes of action. Results show that, among the 54 micropollutants quantified in the influent water, 50 were removed to below their limit of quantification representing more than 90% of concentration reduction. Biological activity was reduced, depending on the specific response that was assessed, from a minimum of 62% (AhR response) to more than 99% (estrogenicity). The key processes responsible for the plant's performances were the coagulation/flocculation/DAFF, main ozonation and activated carbon filtration. The effect of these 3 processes varied from one compound or bioassay to another but their combination was almost totally responsible for the overall observed reduction. Bioassays yielded complementary information, e.g. estrogenic compounds were not detected in the secondary effluent by chemical analysis, but the samples had an estrogenic effect. The main ozonation formed oxidation by-products of the organic micropollutants but decreased the level of non-specific toxicity and other specific toxic modes of action, demonstrating that the mixture of oxidation by-products was less potent than the mixture of the parent compounds for the considered effects.

CEP-1347/KT-7515, an inhibitor of c-jun N-terminal kinase activation, attenuates the 1-methyl-4-phenyl tetrahydropyridine-mediated loss of nigrostriatal dopaminergic neurons In vivo

We have identified a bis-ethylthiomethyl analog of K-252a, CEP-1347/KT-7515, that promotes neuronal survival in culture and in vivo. The neuronal survival properties of CEP-1347/KT-7515 may be related to its ability to inhibit the activation of c-jun N-terminal kinase, a key kinase in some forms of stress-induced neuronal death and perhaps apoptosis. There is evidence that the selective nigrostriatal dopaminergic neurotoxin, MPTP, produces neuronal apoptosis in culture and in adult mice. Thus, our studies were designed to determine if CEP-1347/KT-7515 could protect dopaminergic neurons from MPTP-mediated neurotoxicity. CEP-1347/KT-7515 was assessed for neuroprotective activity in a low dose MPTP model (20 mg/kg) where there was a 50% loss of striatal dopaminergic terminals in the absence of substantia nigra neuronal loss, and a high dose (40 mg/kg) MPTP model where there was a complete loss of dopaminergic terminals and 80% loss of dopaminergic cell bodies. In the low dose MPTP model, CEP-1347/KT-7515 (0.3 mg/kg/day) attenuated the MPTP-mediated loss of striatal dopaminergic terminals by 50%. In the high dose model, CEP-1347/KT-7515 ameliorated the loss of dopaminergic cell bodies by 50% and partially preserved striatal dopaminergic terminals. CEP-1347/KT-7515 did not inhibit monoamine oxidase B or the dopamine transporter, suggesting that the neuroprotective effects of CEP-1347/KT-7515 occur downstream of the metabolic conversion of MPTP to MPP+ and accumulation of MPP+ into dopaminergic neurons. These data implicate a c-jun N-terminal kinase signaling system in MPTP-mediated dopaminergic degeneration and suggest that CEP-1347/KT-7515 may have potential as a treatment for Parkinson's disease.

Preservation of cholinergic activity and prevention of neuron death by CEP-1347/KT-7515 following excitotoxic injury of the nucleus basalis magnocellularis

We have identified a class of small organic molecules, derived from the indolocarbazole K-252a, that promote the survival of cultured neurons. However, many of these indolocarbazoles inhibit protein kinase C and neurotrophin-activated tyrosine kinase receptors. These kinase inhibitory activities may limit the utility of these compounds for neurological disorders. A bis-ethyl-thiomethyl analogue of K-252a, CEP-1347/KT-7515, has been identified that lacks protein kinase C and tyrosine kinase receptor inhibitory activities, yet retains the ability to promote survival of cultured neurons, including cholinergic neurons derived from the basal forebrain. In the present studies, CEP-1347/KT-7515 was assessed for neurotrophic activity on basal forebrain neurons of in vivo rats following excitotoxic insult. Ibotenate infusion into the nucleus basalis magnocellularis reduced levels of choline acetyltransferase activity in the cortex, as well as reduced numbers of choline acetyltransferase-immunoreactive and retrogradely (FluoroGold)-labelled cortically-projecting neurons in the nucleus basalis. Systemically administered CEP-1347/KT-7515 attenuated the loss of cortical choline acetyltransferase activity and the loss of the number of choline acetyltransferase-immunoreactive and retrogradely-labelled FluoroGold neurons in the nucleus basalis. Moreover, CEP-1347/KT-7515 ameliorated the loss of cortical choline acetyltransferase if administration was initiated one day, but not seven days post-lesion. Together, these results demonstrate that CEP-1347/KT-7515 protects damaged cortically-projecting basal forebrain neurons from degeneration. Thus, CEP-1347/KT-7515 may have therapeutic potential in neurodegenerative diseases, such as Alzheimer's disease, in which basal forebrain cholinergic neurons degenerate.

Chronic sparing of delayed alternation performance and choline acetyltransferase activity by CEP-1347/KT-7515 in rats with lesions of nucleus basalis magnocellularis

Peripheral injection of the indolocarbazole CEP-1347/KT-7515 into rats that have sustained ibotenic acid lesions of the nucleus basalis magnocellularis has been shown to prevent the loss of cortically-projecting neurons in that basal forebrain region. The present study tested whether this neuroprotective activity would lead to chronic sparing of a behaviour known to be impaired by that lesion, as well as to chronic maintenance of cholinergic activity in cortical target regions of the nucleus basalis. CEP-1347/KT-7515 was injected into adult rats that had sustained bilateral ibotenic acid lesions of the nucleus basalis magnocellularis; the first injection occurred 18-24 h after lesioning, with subsequent injections of CEP-1347/KT-7515 occurring every other day over 12 days. One day following the last injection the animals were tested for retention of a previously-learned delayed alternation task. Animals that received CEP-1347/KT-7515 committed significantly fewer errors than lesioned animals receiving vehicle. These same animals were tested again eight to 10 weeks later (which was 10-12 weeks post-dosing), without receiving further drug or behaviour training during the test-retest interval. The animals that had received CEP-1347/KT-7515 continued to commit significantly fewer errors than vehicle animals. Furthermore their performance at this time point was indistinguishable from normal controls. Analysis of errors showed that CEP-1347/KT-7515 prevented a lesion-induced increase in perseverative errors, suggesting the drug improved attention in the lesioned animals. Choline acetyltransferase activity in the frontal cortex of the behaviourally tested animals that received CEP-1347/KT-7515 three months previously showed a significant 40% recovery of the lesion-induced loss seen in the vehicle animals. These results demonstrate that treatment with CEP-1347/KT-7515 over 12 days following excitotoxic damage to the nucleus basalis magnocellularis produces long-term sparing of an attention-demanding behaviour.

1Alpha, 25 dihydroxyvitamin D3-dependent up-regulation of calcium-binding proteins in motoneuron cells

Our understanding of selective neuronal vulnerability as well as etiopathogenesis of sporadic neurodegenerative diseases is extremely limited. In ALS, altered calcium homeostasis appears to contribute significantly to selective neuronal injury. Further in ALS, the absence of calcium binding proteins (calbindin-D28K, parvalbumin, and calretinin) correlates with selective vulnerability and cell loss. In motoneuron cell culture models an ALS IgG-triggered and calcium-mediated destruction can be reversed by increased expression of calbindin-D28K following retroviral infection with calbindin-D28K cDNA. To increase calcium binding protein expression in motoneurons in vitro and in vivo, we have employed vitamin D3. Forty-eight hr treatment of differentiated VSC 4.1 cells with 0.1-30 nM 1,25 dihydroxyvitamin D3 induced a two-fold increase in the immunoreactivity for calbindin-D28K and parvalbumin. Injection of 80-120 ng, 1,25 dihydroxyvitamin D3 in the cerebral ventricles of adult rats also induced positive immunoreactivity for calcium binding proteins in ventral motoneurons which are completely devoid of such reactivity in the adult stage. These data suggest that analogs of 1,25 dihydroxyvitamin D3 may be useful tools in enhancing the expression of calcium binding proteins in the motor system and may have possible therapeutic value in neurodegenerative disease.

High levels of synthesis and local effects of nerve growth factor in the septal region of the adult rat brain

NGF found in the basal forebrain is believed to be localized to NGF-dependent cholinergic neurons and derived via retrograde axonal transport from NGF-synthesizing target hippocampal and cortical neurons. The basis for this concept of target-derived NGF is the detection of only limited amounts of NGF mRNA in the basal forebrain, despite relatively high NGF levels there. Our work, using a more sensitive and quantitative RNase protection method for detecting relative NGF mRNA levels, suggested, instead, relatively high levels of NGF mRNA synthesis in the septal region of the basal forebrain (BF-S), a region which contained primarily cells that project to the hippocampus. Similar results were obtained in analyses of a larger portion of the basal forebrain, designated "BF," that encompassed cholinergic neurons that project to both the hippocampus and the cortex. The level of NGF mRNA measured in both BF-S and BF was equivalent to approximately 50% of the amount observed in the hippocampus. Furthermore, relative NGF mRNA levels detected in the BF-S, cortex, and hippocampus were shown to be proportional to NGF protein levels quantitated in each region. The detection of relatively high amounts of NGF synthesis in the BF-S was supported in studies demonstrating rapid NGF receptor (Trk) activation in the basal forebrain by exogenous NGF and in experiments showing that NGF mRNA was inducible in the BF-S by 1,25 dihydroxyvitamin D3. The extent of NGF mRNA induction was similar (approximately twofold) in the BF-S, hippocampus, and cortex, suggesting similar regulatory mechanisms.(ABSTRACT TRUNCATED AT 250 WORDS)

Systemic dexamethasone administration increases septal Trk autophosphorylation in adult rats via an induction of nerve growth factor

Nerve growth factor (NGF) maintains cholinergic neurons in various animals models of neurodegeneration and is thus a potential treatment for certain neurodegenerative disorders such as Alzheimer's disease. Because NGF does not cross the blood-brain barrier, we have proposed elevating endogenous levels of NGF in the central nervous system with small molecules that induce NGF expression, as an alternative strategy. The present studies were conducted to determine whether pharmacologically elevated levels of NGF are sufficient to cause subsequent stimulation of its high affinity receptor, as measured by increased levels of Trk phosphorylation. Dexamethasone (0.5-20 mg/kg, intraperitoneally) caused a time- and dose-dependent increase in NGF mRNA and NGF protein in the hippocampus and septum of adult male Sprague-Dawley rats. Exogenously administered NGF (1 microgram, intracerebroventricularly) led to a rapid (30 min) and transient increase in Trk phosphorylation in the septum, which has high levels of NGF-specific TrkA. Similarly, dexamethasone led to an increase in Trk phosphorylation only within the septum. Dexamethasone-mediated Trk phosphorylation was dose and time dependent, with peak increases being observed 12 hr after injection, concurrently with peak increases in NGF protein. These data demonstrate an increase in activation of the high affinity NGF receptor with a compound that elevates levels of NGF in the central nervous system, and they support the strategy of discovering a pharmacological agent that induces NGF as a method for treating neurodegenerative disorders.

Chronic 1,25-dihydroxyvitamin D3-mediated induction of nerve growth factor mRNA and protein in L929 fibroblasts and in adult rat brain

We have proposed that elevating levels of nerve growth factor (NGF) in the CNS is a rational strategy for treating certain neurodegenerative disorders. The present studies were conducted to determine: (1) if pharmacologically induced levels of NGF could be sustained for an extended time, and (2) if correlations exist between increases in NGF mRNA and NGF protein in L929 cells and in vivo. Short-term treatment of L929 cells with 1,25-dihydroxyvitamin D3 resulted in a two-fold increase in both NGF mRNA and NGF protein. These increases were sustained for up to 48 h with continuous exposure to 1,25-dihydroxyvitamin D3. In rats, 1,25-dihydroxyvitamin D3 (2.5 nmol; i.c.v.) induced NGF mRNA transiently, with peak two-fold increases observed 4 h post-injection. In contrast to L929 cells, 1,25-dihydroxyvitamin D3 did not elicit an increase in NGF protein after a single administration in vivo. However, consistent with long-term exposure in L929 cells, chronic 6 day infusion of 1,25-dihydroxyvitamin D3 resulted in induction of both NGF mRNA and NGF protein in the brain. These results indicate that 1,25-dihydroxyvitamin D3-mediated NGF induction in cultured L929 cells may predict of NGF induction in vivo, suggesting that L929 cells may have utility in studying underlying mechanisms of NGF induction by 1,25-dihydroxyvitamin D3. On the basis of NGF's ability to increase cholinergic function in animal models of cholinergic degeneration, these results are supportive of a role for NGF inducers as potential drugs for neurodegenerative disorders.

Pharmacological induction of nerve growth factor mRNA in adult rat brain

Three structurally unrelated compounds, all of which induce nerve growth factor (NGF) in cell culture systems, were assessed for their ability to induce NGF mRNA in adult rat brain using a highly sensitive RNAse protection assay. Interleukin-1 beta (0.5-1 pmol) and 1,25-dihydroxyvitamin D3 (25-25,000 pmol) were extremely potent inducers of NGF mRNA, being respectively at least 50,000 and 4000 times more potent than 4-methylcatechol. These compounds elicited an approximate twofold increase in NGF mRNA in both the hippocampus and cortex, without altering beta-actin mRNA levels after a single intracerebroventricular injection. The duration of NGF induction was dependent on the compound administered. For example, the elevation of NGF mRNA elicited by interleukin-1 beta peaked at 8 h and lasted for at least 24 h. In contrast, the induction of NGF after 1,25-dihydroxyvitamin D3 and 4-methylcatechol administration peaked between 4 and 8 h and was not apparent 24 h after injection. These results demonstrate induction of NGF mRNA in vivo by administration of physiological or pharmacological agents and differentiate these agents by potency and duration of action. Further, these findings indicate that pharmacological induction of NGF may be a viable strategy for the treatment of neurodegenerative disorders such as Alzheimer's disease.

Distribution of [125I]nerve growth factor in the rat brain following a single intraventricular injection: correlation with the topographical distribution of trkA messenger RNA-expressing cells

The present study determined the topographical distribution of [125I] nerve growth factor in rat brain at various time points following an intraventricular injection. In addition, we quantified the tissue content of nerve growth factor in various brain tissues following the injection. Autoradiographic analysis of the distribution of [125] nerve growth factor indicated that the neurotrophin is rapidly distributed within the entire ventricular system. However, penetration of nerve growth factor into the brain parenchyma was very limited. At early time points following an injection of nerve growth factor, there was an accumulation of label in the immediate vicinity of the lateral ventricle and third ventricle with predominant labeling around the septum, hypothalamus and cerebellum. By 24 h following nerve growth factor administration, there was discreet labeling of the lateral septum, medial septum, diagonal band, hypothalamus, olfactory tubercle and nucleus of the olfactory tract, and some label was present in the hippocampus and subiculum. Quantitative ELISA of nerve growth factor in brain tissues 1 h following the injection indicated a 446% and 133% increase over basal levels of nerve growth factor in the basal forebrain and hippocampus, respectively. At 24 h nerve growth factor levels measured in brain were not significantly different from endogenous basal levels as determined by ELISA, whereas there were high quantities of 125I present in the thyroid gland, suggesting that the administered [125I] nerve growth factor was rapidly degraded following the intraventricular injection. We observed a similar labeling pattern of the medial septum/diagonal band cholinergic cell body group 24 h following either an intraventricular or intrahippocampal injection of [125I] nerve growth factor. There was a good correlation between the [125I] nerve growth factor labeling pattern and the presence of trkA messenger RNA. This suggested that, at least in the septohippocampal pathway, nerve growth factor accumulated in a region which contained trkA nerve growth factor receptors. Thus, this study shows that after a single unilateral intraventricular injection of nerve growth factor into rat brain there is effective uptake by diagonal band/septal cells on both sides of the brain, and by cells whose positions correlate with the locations of cholinergic and trk A messenger RNA-expressing cells. Significant uptake was also observed in the hypothalamus and cerebellum. The very limited penetration and rapid degradation of intraventricularly administered nerve growth factor suggests that tissue penetration may be a limiting factor when attempting to influence brain neurons by exogenous neurotropic factors.

Induction of NGF by isoproterenol, 4-methylcatechol and serum occurs by three distinct mechanisms

Evidence is provided that isoproterenol, 4-methylcatechol and serum induce NGF by three separate mechanisms. Isoproterenol and 4-methylcatechol induced NGF and NGF mRNA in mouse fibroblast L929 cells in either the presence or absence of serum. Propranolol prevented NGF induction by isoproterenol, but not by 4-methylcatechol or serum. All possible combinations of these inducers resulted in additive increases in the levels of NGF and NGF mRNA.

The human immunodeficiency virus type 1 polyadenylylation signal: a 3' long terminal repeat element upstream of the AAUAAA necessary for efficient polyadenylylation

Several polyadenylylation (PA) signals containing elements upstream of the AAUAAA have recently been characterized. Similar to PA elements found downstream of the AAUAAA, the upstream elements function to increase efficiency of AAUAAA use as a signal for cleavage and PA. Using deletion and linker scanning mutations we show that the PA signal of human immunodeficiency virus type 1 contains upstream elements transcribed from the U3 region of the 3' long terminal repeat. The element that has the greatest effect on PA site use lies 77 to 94 nucleotides upstream of the AAUAAA, between the TATA element and the transcriptional initiation site. Mutations in the adjacent region, between 59 and 76 nucleotides upstream of the AAUAAA, have a smaller effect on PA efficiency. Mutations in a region further upstream, between 141 and 176 nucleotides upstream of the AAUAAA, also affected PA modestly. Functional similarity between upstream elements was indicated by the ability of the human immunodeficiency virus upstream region to replace the upstream region of the simian virus 40 late PA signal. The sequence of the major upstream element of human immunodeficiency virus is uracil-rich, analogous to many defined downstream PA elements. This fact may imply that upstream and downstream elements have similar mechanisms of action.

The growth of simian virus 40 (SV40) host range/adenovirus helper function mutants in an African green monkey cell line that constitutively expresses the SV40 agnoprotein

The simian virus 40 T-antigen carboxy-terminal mutants, dlA2459 and dlA2475, are cell line and temperature dependent for growth and plaque formation in monkey kidney cells. Although these mutants did form plaques on BSC-1 cells at 37 degrees C, they were about fivefold less efficient for plaque formation than wild-type simian virus 40. These mutants did not grow in CV-1 cells and did not synthesize agnoprotein in those cells. CV-1 cells which constitutively express the agnoprotein were permissive for mutant plaque formation. However, late mRNAs, virion proteins, and progeny virion yields did not accumulate to wild-type levels during mutant infection of the agnoprotein-producing cells.

Infection of CV1 cells expressing the polyoma virus middle T antigen or the SV40 agnogene product with simian virus 40 host-range mutants

SV40 viruses bearing mutations at the carboxy-terminus of large T antigen exhibit a host-range phenotype: such viruses are able to grow in BSC monkey kidney cells at 37 degrees C, but give at least 10,000-fold lower yields than wild type virus in BSC cells at 32 degrees C or in CV1 monkey kidney cells at either temperature. The block to infection in the nonpermissive cell type occurs after the onset of viral DNA replication. Infectious progeny virions are produced at very low efficiency. Although capsid proteins are synthesized at decreased levels, this does not account for the magnitude of the defect. Presumably some step of virion assembly or maturation is affected in these mutants. We have previously reported that the viral agnogene product, a protein thought to be involved in viral assembly or release, fails to accumulate in CV1 cells infected with host-range mutants. In polyoma virus the middle T antigen plays a role in virion maturation by influencing the phosphorylation of capsid proteins. In this communication we show that host-range mutants fail to undergo productive infection of CV1 cells expressing middle T antigen. These mutants do form plaques on an agnoprotein-expressing cell line. However, the agnoprotein does not seem to act by correcting the mutational block but rather increases the efficiency of plaque formation.

Efficiency of utilization of the simian virus 40 late polyadenylation site: effects of upstream sequences

The late polyadenylation signal of simian virus 40 functions with greater efficiency than the early polyadenylation signal, in turn affecting steady-state mRNA levels. Two chloramphenicol acetyltransferase (CAT) transient expression vectors, pL-EPA and pL-LPA, that differ only in their polyadenylation signals were constructed by using the early and late polyadenylation signals, respectively. In transfections of Cos, CV-1P, or HeLa cells and subsequent Northern blot analysis of CAT-specific RNA, approximately five times more steady-state CAT mRNA was produced in transfections with pL-LPA than with pL-EPA. The basis for this difference was not related to the specific promoter used or to RNA stability. Overall, the difference in steady-state mRNA levels derived from the two plasmids appeared to be attributable to intrinsic properties of the two polyadenylation signals, resulting in distinctly different cleavage and polyadenylation efficiencies. Additionally, we found that the utilization of the late polyadenylation site was dramatically reduced by deletion of sequences between 48 and 29 nucleotides 5' of the AAUAAA hexanucleotide. This reduction of mRNA levels was shown not to be caused by altered stability of mutant precursor RNAs or mRNAs, suggesting that these upstream sequences constitute an element of the late polyadenylation signal and may cause, at least to some extent, the greater efficiency of utilization of the late polyadenylation site.

Simian virus 40 agnoprotein facilitates perinuclear-nuclear localization of VP1, the major capsid protein

The agnoprotein of simian virus 40 (SV40) is a 61-amino-acid protein encoded in the leader of some late mRNAs. In indirect immunofluorescence studies with antisera against SV40 capsid proteins, we show that mutants which make no agnoprotein display abnormal perinuclear-nuclear localization of VP1, the major capsid protein, but not VP2 or VP3, the minor capsid proteins. In wild-type (WT) SV40-infected CV-1P cells, VP1 was found predominantly in the cytoplasm until 36 h postinfection (p.i.), approximately the time that high levels of agnoprotein became detectable under our infection conditions. Thereafter, VP1 localized rapidly to the perinuclear region and to the nucleus. In contrast, in agnoprotein-minus mutant-infected CV-1P cells, perinuclear-nuclear accumulation of VP1 occurred much less efficiently; a significantly greater fraction of cells with predominantly cytoplasmic fluorescence was observed up to 48 h p.i. At 48 and 60 h p.i., more cells with largely perinuclear and little nuclear staining were seen than in WT-infected controls. In similar analyses with stably transfected cell lines constitutively expressing the agnoprotein, VP1 localized to the nucleus before 30 h p.i., regardless of the infecting virus. Delayed nuclear entry of VP1 in a mutant which makes no agnoprotein was also overcome in a revertant which has a second site point mutation in VP1. This suggests that an alteration of VP1 can partially overcome the defect of the agnogene mutation by enhancement of the rate of its own nuclear localization. Taken together, these results indicate that at least one function of the agnoprotein is to enhance the efficiency of perinuclear-nuclear localization of VP1.

Construction and characterization of CV-1P cell lines which constitutively express the simian virus 40 agnoprotein: alteration of plaquing phenotype of viral agnogene mutants

The simian virus 40 (SV40) agnoprotein is a 61-amino-acid polypeptide encoded in the leader region of some late viral mRNAs. Its function is unclear, although previous investigations suggest that the agnoprotein may function in late transcriptional regulation and virus assembly. To define the specific role(s) of agnoprotein in the SV40 lytic cycle, CV-1P cell lines were constructed in which the agnogene was stably integrated and constitutively expressed under the control of a retroviral long terminal repeat. Two types of cell lines were isolated. One group, typified by the cell line Ag18, produced low levels of agnogene-specific mRNA and agnoprotein. The other type, represented by a single isolate named Ag8, produced high levels of agnogene-specific mRNA and correspondingly high levels of agnoprotein. By indirect immunofluorescence, the agnoprotein was located predominantly in the cytoplasmic and perinuclear region of both cell lines; this is its site of localization in wild-type (WT)-infected CV-1P cells. Viruses that were agnoprotein-minus formed small plaques on normal CV-1P cells, but produced nearly WT-sized plaques on Ag18 cells. Conversely, the plaques formed on Ag8 cells infected with agnoprotein-minus mutants of WT SV40 were markedly smaller than the plaques formed by these viruses when they were grown on control cells. Overall, our results suggest that the agnoprotein is a trans-effector of virus production. The opposite effects on plaquing that were observed with Ag8 and Ag18 cells correlated with the very different levels of agnogene expression in the two cell lines. This suggests that the nature of the effect of the agnoprotein on virus production may vary depending on its intracellular concentration.