Molecular cloning of single-stranded DNA purified from scrapie-infected hamster brain

RNA as a component of scrapie fibrils

Recently, electron cryo-microscopy (cryo-EM) maps of fibrils from the brains of mice and hamsters with five infectious scrapie strains have been published and deposited in the electron microscopy data bank (EMDB). As noted by the primary authors, the fibrils contain a second component other than protein. The aim of the present study was to identify the nature of this second component in the published maps using an in silico approach. Extra densities (EDs) containing this component were continuous, straight, axial, at right angles to protein rungs and within hydrogen-bonding distance of protein, consistent with a structural role. EDs co-located with strips of basic residues, notably lysines, and formed a conspicuous cladding over parts of the N-terminal lobe of the protein. A Y-shaped polymer consistent with RNA was found, in places forming a single chain and at one location forming a duplex, comprising two antiparallel chains, and raising the intriguing possibility of replicative behaviour. To reflect the monotonous nature of the protein interface, it is suggested that the RNA may be a short tandem repeat. Fibrils from brains of patients with Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and other neurodegenerations also contain EDs and may be of a similar aetiology.

Replicating RNA as a component of scrapie fibrils

Recently, electron cryo-microscopy (cryo-EM) maps of fibrils from the brains of mice and hamsters with five infectious scrapie strains have been published1-5 and deposited in the electron microscopy data bank (EMDB)6. This represents long-awaited near-atomic level structural evidence, widely expected to confirm the protein-only prion hypothesis7,8. Instead, the maps reveal a second component, other than protein. The aim of the present study was to identify the nature of this second component, in the published maps1-5, using an in silico approach. Extra densities (EDs) containing this component were continuous, straight, axial, at right angles to protein rungs and within hydrogen-bonding distance of protein, consistent with a role as guide and support in fibril construction. EDs co-located with strips of basic residues, notably lysines, and formed a conspicuous cladding over parts of the N-terminal lobe of the protein. In one ED, there was evidence of a Y-shaped polymer forming two antiparallel chains, consistent with replicating RNA. Although the protein-only prion hypothesis7 is still popular, convincing counter-evidence for an essential role of RNA as a cofactor has amassed in the last 20 years8. The present findings go beyond this in providing evidence for RNA as the genetic element of scrapie. To reflect the monotonous nature of the protein interface, it is suggested that the RNA may be a tandem repeat. This is against the protein-only prion hypothesis and in favour of a more orthodox agent, more akin to a virus. Fibrils from brains of patients with Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS) and other neurodegenerations also contain EDs9 and may be of a similar aetiology.

A critical review of the nature of the spongiform encephalopathy agent: protein theory versus virus theory

All spongiform encephalopathies (SEs) result in brain disorders brought about by a slow virus. Since the origin of bovine SE (BSE), the infectious nature of the disease has been firmly established. Tubulofilamentous particles/scrapie termed nemavirus (NVP) and scrapie-associated fibrils (SAF) are ultrastructural markers, whereas protease-resistant protein (PrP(sc)) is a protein marker. The PrP molecules aggregate to form SAF. Each NVP consists of three layers: an outer protein coat, an intermediate ssDNA layer, and inner PrP/SAF. Therefore, ssDNA and PrP/SAF are physically associated with each other. The existence of at least 20 stable strains of SEs implies that a nucleic acid molecule serves as the information molecule. Animals inoculated with PrP(sc) do not develop the clinical disease, however, ssDNA purified from scrapie-hamster brains by alkaline gel electrophoresis mixed with binding proteins before inoculation developed the clinical disease. It appears that an "accessory protein" coded by the ssDNA of the NVP interacts with normal PrP(c) molecules, resulting in their conversion to PrP(sc)/SAF. The pathogenesis process in the infected animal, with increasing incubation periods, reveals that larger amounts of normal PrP molecules are modified to form SAF. This interferes with the normal supply of PrP to cell membranes, which become disrupted and eventually fragment, resulting in the vacuoles typical of those found in the SEs. Critical review of scientific literature has demonstrated that the agent contains a DNA genome.

Lingering doubts about spongiform encephalopathy and Creutzfeldt-Jakob disease

Bovine spongiform encephalopathy (BSE) is an infectious disease and has been transmitted orally to many other animals, including humans. There is clear evidence of maternal transmission, although disagreement on the source of the BSE agent remains. The current theories link the origin of BSE to common scrapie in sheep. Twenty different strains of the scrapie agent have been isolated from sheep. A search of the literature indicates two distinct clinical syndromes in sheep, both of which have been called scrapie. I have designated these Type I (the common type), which exhibits itchiness and lose their wool, and Type II, which exhibits trembling and ataxia. Sheep inoculated with BSE develop Type II scrapie and they exhibit trembling. When cattle or mink are injected with the Type I strain, only a few will develop a clinical disease. By contrast, no clinical disease has so far been shown in cattle or mink by feeding them with Type I-infected sheep brains. However, either by injecting or feeding with the BSE strain, 100% of calves and mink develop the clinical disease. Evidence suggests that Type II is the cause of BSE. Identical clinical signs of Type II trembling are found in kuru and many of the recent cases of Creutzfeldt-Jakob disease. The BSE agent has caused spongiform encephalopathies (SEs) in domestic cats, tigers, and in some species of ruminants in zoos. The nature of the BSE agent remains unchanged when passaged through a range of species, irrespective of their genetic make up, demonstrating that variations in the host PrP gene are not a major factor in the susceptibility to the BSE agent. Since more than 85 zoo animals of many species have been diagnosed with SEs, from these studies it seems reasonable to conclude that the BSE agent can infect almost all mammalian species, including humans. For eradication of BSE and to reduce the risk of infection to humans, the development of a vaccine against BSE is suggested. Such a possibility should be fully explored.

Evidence that single-stranded DNA wrapped around the tubulofilamentous particles termed "nemaviruses" is the genome of the scrapie agent

Homogenized brain tissue from scrapie-infected hamsters and uninfected hamsters was subjected to subcellular fractionation to isolate unique tubulofilamentous particles termed "nemaviruses". Nucleic acid was purified from the concentrate by the phenol/chloroform extraction procedure and by alkaline gel electrophoresis; a single band of ssDNA corresponding to about 1.2 kb was visualized. The gel-purified ssDNA was mixed before inoculation with (a) MgCl2, (b) lipofectin, (c) ssDNA-binding protein and (d) normal brain homogenate. Hamsters in group b, c and d injected with a mixture of ssDNA developed the clinical disease. Brain pathology revealed generalized vacuolation, while animals injected with ssDNA mixed with MgCl2 and controls remained healthy. These results suggest that ssDNA is the genome of the scrapie agent.

Evidence that homologous ssDNA is present in scrapie, Creutzfeldt-Jakob disease, and bovine spongiform encephalopathy

Homogenized brain tissue from scrapie-infected hamsters and uninfected hamsters was subjected to sub-cellular fractionation to isolate nemavirus. Nucleic acid was extracted from these fractions, which also contained mitochondria. Agarose-gel electrophoresis revealed a band corresponding to the size of circular hamster mtDNA in both infected and uninfected samples, but slower migrating bands were observed only in samples from scrapie-infected brain. A single band of ssDNA corresponding to about 1.2 kb was purified by alkaline gel electrophoresis from the nucleic acid content of the enriched preparations of nemavirus. The ssDNA was synthesized into double-stranded DNA, cloned and sequenced. An unusual palindromic six base TACGTA repeat sequence was observed suggesting that 1.2 kb molecules consist of multiple copies of (TACGTA)n spaced along the length of the ssDNA with a preceding sequence TATATA. The comparison of the nucleotide sequence of the inserted DNA to the GenBank nucleotide database revealed no significant homology to other sequences. A probe prepared from the Nar 50 clone was hybridized against DNA prepared from scrapie, CJD, BSE and normal brains under various salt and temperature conditions. The probe reacted with a band of about 1.2 kb in scrapie, CJD and BSE but not with control normal DNA specimens, thereby confirming the presence of ssDNA in these SEs. The results suggest an intimate association between the presence of nemavirus particles and scrapie, CJD and BSE.