Identification and removal of proteins that co-purify with infectious prion protein improves the analysis of its secondary structure

Site-specific analysis of N-glycans from different sheep prion strains

Prion diseases are a group of neurodegenerative diseases affecting a wide range of mammalian species, including humans. During the course of the disease, the abnormally folded scrapie prion protein (PrP^Sc) accumulates in the central nervous system where it causes neurodegeneration. In prion disorders, the diverse spectrum of illnesses exists because of the presence of different isoforms of PrP^Sc where they occupy distinct conformational states called strains. Strains are biochemically distinguished by a characteristic three-band immunoblot pattern, defined by differences in the occupancy of two glycosylation sites on the prion protein (PrP). Characterization of the exact N-glycan structures attached on either PrP^C or PrP^Sc is lacking. Here we report the characterization and comparison of N-glycans from two different sheep prion strains. PrP^Sc from both strains was isolated from brain tissue and enzymatically digested with trypsin. By using liquid chromatography coupled to electrospray mass spectrometry, a site-specific analysis was performed. A total of 100 structures were detected on both glycosylation sites. The N-glycan profile was shown to be similar to the one on mouse PrP, however, with additional 40 structures reported. The results presented here show no major differences in glycan composition, suggesting that glycans may not be responsible for the differences in the two analyzed prion strains.

To date, prion diseases remain a controversy amongst scientists. Although we know now it is the abnormal form of the prion protein (PrP^Sc) that causes the disease, many questions are still left unanswered. To understand the cellular mechanism of these diseases, we should first and foremost try to fully understand the prion protein itself. Even though many findings have been made regarding the structure of the protein, a large part of it is still unknown. Since the prion protein is actually a glycoprotein, to resolve its structure we need to put our focus not only on the protein part of the glycoprotein but also on the glycan structures as well. Here we compared two different sheep prion strains and although no major differences have been found between the glycan structures, this analysis may help the understanding of the role glycans have in prion diseases.

Prion Efficiently Replicates in α-Synuclein Knockout Mice

Prion diseases are a group of neurodegenerative disorders associated with the conformational conversion of the cellular prion protein (PrP^C) into an abnormal misfolded form named PrP^Sc. Other than accumulating in the brain, PrP^Sc can bind PrP^C and force it to change conformation to PrP^Sc. The exact mechanism which underlies the process of PrP^C/PrP^Sc conversion still needs to be defined and many molecules or cofactors might be involved. Several studies have documented an important role of PrP^C to act as receptor for abnormally folded forms of α-synuclein which are responsible of a group of diseases known as synucleinopathies. The presence of PrP^C was required to promote efficient internalization and spreading of abnormal α-synuclein between cells. In this work, we have assessed whether α-synuclein exerts any role in PrP^Sc conversion and propagation either in vitro or in vivo. Indeed, understanding the mechanism of PrP^C/PrP^Sc conversion and the identification of cofactors involved in this process is crucial for developing new therapeutic strategies. Our results showed that PrP^Sc was able to efficiently propagate in the brain of animals even in the absence of α-synuclein thus suggesting that this protein did not act as key modulator of prion propagation. Thus, α-synuclein might take part in this process but is not specifically required for sustaining prion conversion and propagation.

Independent amplification of co-infected long incubation period low conversion efficiency prion strains

Prion diseases are caused by a misfolded isoform of the prion protein, PrP^Sc. Prion strains are hypothesized to be encoded by strain-specific conformations of PrP^Sc and prions can interfere with each other when a long-incubation period strain (i.e. blocking strain) inhibits the conversion of a short-incubation period strain (i.e. non-blocking). Prion strain interference influences prion strain dynamics and the emergence of a strain from a mixture; however, it is unknown if two long-incubation period strains can interfere with each other. Here, we show that co-infection of animals with combinations of long-incubation period strains failed to identify evidence of strain interference. To exclude the possibility that this inability of strains to interfere in vivo was due to a failure to infect common populations of neurons we used protein misfolding cyclic amplification strain interference (PMCAsi). Consistent with the animal bioassay studies, PMCAsi indicated that both co-infecting strains were amplifying independently, suggesting that the lack of strain interference is not due to a failure to target the same cells but is an inherent property of the strains involved. Importantly PMCA reactions seeded with long incubation-period strains contained relatively higher levels of remaining PrP^C compared to reactions seeded with a short-incubation period strain. Mechanistically, we hypothesize the abundance of PrP^C is not limiting in vivo or in vitro resulting in prion strains with relatively low prion conversion efficiency to amplify independently. Overall, this observation changes the paradigm of the interactions of prion strains and has implications for interspecies transmission and emergence of prion strains from a mixture.

This is the first example of prion strains that replicate independently in vitro and in vivo. This observation changes the paradigm of the interactions of prion strains and provides further evidence that strains are a dynamic mixture of substrains. Strain interference is influenced by the abundance of PrP^C that is convertible by the strains involved. These observations have implications for interspecies transmission and emergence of prion strains from a mixture.

Experimental models of human prion diseases and prion strains

Prion strains occur in natural prion diseases, including prion diseases of humans. Prion strains can correspond with differences in the clinical signs and symptoms of disease and the distribution of prion infectivity in the host and are hypothesized to be encoded by strain-specific differences in the conformation of the disease-specific isoform of the host-encoded prion protein, PrP^TSE. Prion strains can differ in biochemical properties of PrP^TSE that can include the relative sensitivity to digestion with proteinase K and conformational stability in denaturants. These strain-specific biochemical properties of field isolates are maintained upon transmission to experimental animal models of prion disease. Experimental human models of prion disease include traditional and gene-targeted mice that express endogenous PrP^C. Transgenic mice that express different polymorphs of human PrP^C or mutations in human PrP^C that correspond with familial forms of human prion disease have been generated that can recapitulate the clinical, pathologic, and biochemical features of disease. These models aid in understanding disease pathogenesis, evaluating zoonotic potential of animal prion diseases, and assessing human-to-human transmission of disease. Models of sporadic or familial forms of disease offer an opportunity to define mechanisms of disease, identify key neurodegenerative pathways, and assess therapeutic interventions.

Cellular prion protein is present in mitochondria of healthy mice

Cellular prion protein (PrP^C) is a mammalian glycoprotein which is usually found anchored to the plasma membrane via a glycophosphatidylinositol (GPI) anchor. PrP^C misfolds to a pathogenic isoform PrP^Sc, the causative agent of neurodegenerative prion diseases. The precise function of PrP^C remains elusive but may depend upon its cellular localization. Here we show that PrP^C is present in brain mitochondria from 6–12 week old wild-type and transgenic mice in the absence of disease. Mitochondrial PrP^C was fully processed with mature N-linked glycans and did not require the GPI anchor for localization. Protease treatment of purified mitochondria suggested that mitochondrial PrP^C exists as a transmembrane isoform with the C-terminus facing the mitochondrial matrix and the N-terminus facing the intermembrane space. Taken together, our data suggest that PrP^C can be found in mitochondria in the absence of disease, old age, mutation, or overexpression and that PrP^C may affect mitochondrial function.

Prion Strain Diversity

Prion diseases affect a wide range of mammal species and are caused by a misfolded self-propagating isoform (PrPSc) of the normal prion protein (PrPC). Distinct strains of prions exist and are operationally defined by differences in a heritable phenotype under controlled experimental transmission conditions. Prion strains can differ in incubation period, clinical signs of disease, tissue tropism, and host range. The mechanism by which a protein-only pathogen can encode strain diversity is only beginning to be understood. The prevailing hypothesis is that prion strain diversity is encoded by strain-specific conformations of PrPSc; however, strain-specific cellular cofactors have been identified in vitro that may also contribute to prion strain diversity. Although much progress has been made on understanding the etiological agent of prion disease, the relationship between the strain-specific properties of PrPSc and the resulting phenotype of disease in animals is poorly understood.

Incongruity between Prion Conversion and Incubation Period following Coinfection

When multiple prion strains are inoculated into the same host, they can interfere with each other. Strains with long incubation periods can suppress conversion of strains with short incubation periods; however, nothing is known about the conversion of the long-incubation-period strain during strain interference. To investigate this, we inoculated hamsters in the sciatic nerve with long-incubation-period strain 139H prior to superinfection with the short-incubation-period hyper (HY) strain of transmissible mink encephalopathy (TME). First, we found that 139H is transported along the same neuroanatomical tracks as HY TME, adding to the growing body of evidence indicating that PrP(Sc) favors retrograde transneuronal transport. In contrast to a previous report, we found that 139H interferes with HY TME infection, which is likely due to both strains targeting the same population of neurons following sciatic nerve inoculation. Under conditions where 139H blocked HY TME from causing disease, the strain-specific properties of PrP(Sc) corresponded with the strain that caused disease, consistent with our previous findings. In the groups of animals where incubation periods were not altered, we found that the animals contained a mixture of 139H and HY TME PrP(Sc) This finding expands the definition of strain interference to include conditions where PrP(Sc) formation is altered yet disease outcome is unaltered. Overall, these results contradict the premise that prion strains are static entities and instead suggest that strain mixtures are dynamic regardless of incubation period or clinical outcome of disease.

IMPORTANCE

Prions can exist as a mixture of strains in naturally infected animals, where they are able to interfere with the conversion of each other and to extend incubation periods. Little is known, however, about the dynamics of strain conversion under conditions where incubation periods are not affected. We found that inoculation of the same animal with two strains can result in the alteration of conversion of both strains under conditions where the resulting disease was consistent with infection with only a single strain. These data challenge the idea that prion strains are static and suggests that strain mixtures are more dynamic than previously appreciated. This observation has significant implications for prion adaptation.

The Distribution of Prion Protein Allotypes Differs Between Sporadic and Iatrogenic Creutzfeldt-Jakob Disease Patients

Sporadic Creutzfeldt-Jakob disease (sCJD) is the most prevalent of the human prion diseases, which are fatal and transmissible neurodegenerative diseases caused by the infectious prion protein (PrP^Sc). The origin of sCJD is unknown, although the initiating event is thought to be the stochastic misfolding of endogenous prion protein (PrP^C) into infectious PrP^Sc. By contrast, human growth hormone-associated cases of iatrogenic CJD (iCJD) in the United Kingdom (UK) are associated with exposure to an exogenous source of PrP^Sc. In both forms of CJD, heterozygosity at residue 129 for methionine (M) or valine (V) in the prion protein gene may affect disease phenotype, onset and progression. However, the relative contribution of each PrP^C allotype to PrP^Sc in heterozygous cases of CJD is unknown. Using mass spectrometry, we determined that the relative abundance of PrP^Sc with M or V at residue 129 in brain specimens from MV cases of sCJD was highly variable. This result is consistent with PrP^C containing an M or V at residue 129 having a similar propensity to misfold into PrP^Sc thus causing sCJD. By contrast, PrP^Sc with V at residue 129 predominated in the majority of the UK human growth hormone associated iCJD cases, consistent with exposure to infectious PrP^Sc containing V at residue 129. In both types of CJD, the PrP^Sc allotype ratio had no correlation with CJD type, age at clinical onset, or disease duration. Therefore, factors other than PrP^Sc allotype abundance must influence the clinical progression and phenotype of heterozygous cases of CJD.

In Creutzfeldt-Jakob disease (CJD), heterozygosity at residue 129 for methionine or valine in normal prion protein may affect disease phenotype, onset and progression. However, the relative contribution of each prion protein allotype to the infectious, disease associated form of prion protein (PrP^Sc) is unknown. Here we report the novel observation that in heterozygous cases of sporadic CJD the PrP^Sc allotype ratio is highly variable. This case-by-case variability is consistent with the origin of sporadic CJD being the spontaneous, but random, misfolding of either host prion protein allotype into infectious PrP^Sc. By contrast, in heterozygous cases of iatrogenic CJD in the United Kingdom resulting from exposure to contaminated human growth hormone, the PrP^Sc allotype ratio is much more homogeneous and consistent with exposure to infectious PrP^Sc containing valine at residue 129. Surprisingly, the PrP^Sc allotype ratio did not correlate with disease onset or duration in either disease type. Thus, factors other than PrP^Sc allotype ratio likely influence the clinical progression of heterozygous cases of CJD. Moreover, our results suggest that the ratio of methionine to valine in PrP^Sc may be a means of determining the origin of prion infection.

Proteomics applications in prion biology and structure

Prion diseases are a heterogeneous class of fatal neurodegenerative disorders associated with misfolding of host cellular prion protein (PrP(C)) into a pathological isoform, termed PrP(Sc). Prion diseases affect various mammals, including humans, and effective treatments are not available. Prion diseases are distinguished from other protein misfolding disorders - such as Alzheimer's or Parkinson's disease - in that they are infectious. Prion diseases occur sporadically without any known exposure to infected material, and hereditary cases resulting from rare mutations in the prion protein have also been documented. The mechanistic underpinnings of prion and other neurodegenerative disorders remain poorly understood. Various proteomics techniques have been instrumental in early PrP(Sc) detection, biomarker discovery, elucidation of PrP(Sc) structure and mapping of biochemical pathways affected by pathogenesis. Moving forward, proteomics approaches will likely become more integrated into the clinical and research settings for the rapid diagnosis and characterization of prion pathogenesis.

Techniques to elucidate the conformation of prions

Proteinaceous infectious particles (prions) are unique pathogens as they are devoid of any coding nucleic acid. Whilst it is assumed that prion disease is transmitted by a misfolded isoform of the cellular prion protein, the structural insight of prions is still vague and research for high resolution structural information of prions is still ongoing. In this review, techniques that may contribute to the clarification of the conformation of prions are presented and discussed.

A novel and rapid method for obtaining high titre intact prion strains from mammalian brain

Mammalian prions exist as multiple strains which produce characteristic and highly reproducible phenotypes in defined hosts. How this strain diversity is encoded by a protein-only agent remains one of the most interesting and challenging questions in biology with wide relevance to understanding other diseases involving the aggregation or polymerisation of misfolded host proteins. Progress in understanding mammalian prion strains has however been severely limited by the complexity and variability of the methods used for their isolation from infected tissue and no high resolution structures have yet been reported. Using high-throughput cell-based prion bioassay to re-examine prion purification from first principles we now report the isolation of prion strains to exceptional levels of purity from small quantities of infected brain and demonstrate faithful retention of biological and biochemical strain properties. The method's effectiveness and simplicity should facilitate its wide application and expedite structural studies of prions.

Applying the tools of chemistry (mass spectrometry and covalent modification by small molecule reagents) to the detection of prions and the study of their structure

Prions are molecular pathogens, able to convert a normal cellular prion protein (PrP(C)) into a prion (PrP(Sc)). The information necessary for this conversion is contained in the conformation of PrP(Sc). Mass spectrometry (MS) and small-molecule covalent reactions have been used to study prions. Mass spectrometry has been used to detect and quantitate prions in the attomole range (10⁻¹⁸ mole). MS-based analysis showed that both possess identical amino acid sequences, one disulfide bond, a GPI anchor, asparagine-linked sugar antennae, and unoxidized methionines. Mass spectrometry has been used to define elements of the secondary and tertiary structure of wild-type PrP(Sc) and GPI-anchorless PrP(Sc). It has also been used to study the quaternary structure of the PrP(Sc) multimer. Small molecule reagents react differently with the same lysine in the PrP(C) conformation than in the PrP(Sc) conformation. Such differences can be detected by Western blot using mAbs with lysine-containing epitopes, such as 3F4 and 6D11. This permits the detection of PrP(Sc) without the need for proteinase K pretreatment and can be used to distinguish among prion strains. These results illustrate how two important chemical tools, mass spectrometry and covalent modification by small molecules, are being applied to the detection and structural study of prions. Furthermore these tools are or can be applied to the study of the other protein misfolding diseases such as Alzheimer Disease, Parkinson Disease, or ALS.

Proteomics analysis of amyloid and nonamyloid prion disease phenotypes reveals both common and divergent mechanisms of neuropathogenesis

Prion diseases are a heterogeneous group of neurodegenerative disorders affecting various mammals including humans. Prion diseases are characterized by a misfolding of the host-encoded prion protein (PrP^C) into a pathological isoform termed PrP^Sc. In wild-type mice, PrP^C is attached to the plasma membrane by a glycosylphosphatidylinositol (GPI) anchor and PrP^Sc typically accumulates in diffuse nonamyloid deposits with gray matter spongiosis. By contrast, when mice lacking the GPI anchor are infected with the same prion inoculum, PrP^Sc accumulates in dense perivascular amyloid plaques with little or no gray matter spongiosis. In order to evaluate whether different host biochemical pathways were implicated in these two phenotypically distinct prion disease models, we utilized a proteomics approach. In both models, infected mice displayed evidence of a neuroinflammatory response and complement activation. Proteins involved in cell death and calcium homeostasis were also identified in both phenotypes. However, mitochondrial pathways of apoptosis were implicated only in the nonamyloid form, whereas metal binding and synaptic vesicle transport were more disrupted in the amyloid phenotype. Thus, following infection with a single prion strain, PrP^C anchoring to the plasma membrane correlated not only with the type of PrP^Sc deposition but also with unique biochemical pathways associated with pathogenesis.

Cofactor molecules induce structural transformation during infectious prion formation

The spread of misfolded proteins may occur in many neurodegenerative diseases. Mammalian prions are currently the only misfolded proteins in which high specific biological infectivity can be produced in vitro. Using a system that generates infectious prions de novo from purified recombinant PrP and conversion cofactors palmitoyl-oleoyl-phosphatidylglycerol (POPG) and RNA, we examined by deuterium exchange mass spectrometry (DXMS) the stepwise protein conformational changes that occur during prion formation. We found that initial incubation with POPG causes major structural changes in PrP involving all three α helices and one β strand, with subsequent addition of RNA rendering the N terminus highly exposed. Final conversion into the infectious PrP(Sc) form was accompanied by globally decreased solvent exposure, with persistence of the major cofactor-induced conformational features. Thus, we report that cofactor molecules appear to induce major structural rearrangements during prion formation, initiating a dynamic sequence of conformational changes resulting in biologically active prions.

Role of proteomics in understanding prion infection

Transmissible spongiform encephalopathies or prion diseases are fatal neurodegenerative pathologies characterized by the autocatalytic misfolding and polymerization of a cellular glycoprotein (cellular prion protein [PrP(C)]) that accumulates in the CNS and leads to neurodegeneration. The detailed mechanics of PrP(C) conversion to its pathological isoform (PrP(TSE)) are unclear but one or more exogenous factors are likely involved in the process of PrP misfolding. In the last 20 years, proteomic investigations have identified several endogenous proteins that interact with PrP(C), PrP(TSE) or both, which are possibly involved in the prion pathogenetic process. However, current approaches have not yet produced convincing conclusions on the biological value of such PrP interactors. Future advancements in the comprehension of the molecular pathogenesis of prion diseases, in experimental techniques and in data analysis procedures, together with a boost in more productive international collaborations, are therefore needed to improve the understanding on the role of PrP interactors. Finally, the advancement of 'omics' techniques in prion diseases will contribute to the development of novel diagnostic tests and effective drugs.