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Upcoming Articles of interest in JBC
Prion gene intron alleles and diagnosis of sporadic CJD
Repeat diseases: repeat not involved in oligomerization

Upcoming Articles of interest

Nature 386: 242 March 20
 Typing prion isoforms (Scientific Correspondence)  P Parchi, ...  H Kretzschmar  Nature 386, 284 (1997)

Homer: a protein that selectively binds metabotropic glutamate receptors 
                  Spatial localization and clustering of membrane proteins is critical to neuronal development
                  and synaptic plasticity. Recent studies have identified a family of proteins, the PDZ proteins,
                  that contain modular PDZ domains and interact with synaptic ionotropic glutamate receptors
                  and ion channels. PDZ proteins are thought to have a role in defining the cellular distribution
                  of the proteins that interact with them. Here the authors report a novel dendritic protein,
                  Homer, that contains a single, PDZ-like domain and binds specifically to the carboxy terminus
                  of phosphoinositide-linked metabotropic glutamate receptors.

 Homer is highly divergent from
                  known PDZ proteins and seems to represent a novel family. The Homer gene is also distinct
                  from members of the PDZ family in that its expression is regulated as an immediate early gene
                  and is dynamically responsive to physiological synaptic activity, particularly during cortical
                  development. This dynamic transcriptional control suggests that Homer mediates a novel
                  cellular mechanism that regulates metabotropic glutamate signalling. 
                  P R Brakeman, A A Lanahan, R O'Brien, K Roche, C A Barnes, R L Huganir & P F Worley 
                  Homer: a protein that selectively binds metabotropic glutamate receptors

 Nature  20 March 1997  Vol. 386, No.6622:

Errors: Transmission dynamics and epidemiology of BSE in British cattle (Nature  382, 779-788; 1996)
 In Table 2 of this Letter, the reported number of cases saved for policy 9 was erroneously  given for 1996 to 2001 rather than for 1997 to 2001. The number should be 584 rather  than 797. Thus the number of cases saved in policies 11-14 should be reduced by 213. Also, the culling policy description for policy 6 should begin 'As 5)' rather than 'As 15)'.  An error caused Figs 1d and e in this article to be
transposed. The legends are correct.  On page 783, in the first column in th e sixth line of text 'F and G are two operators' should  have been 'G and F are two operators'. Finally, the manuscript on maternal transmission of the BSE agent in cows by J. W. Wilesmith et al. described in the paper as ref. 6, under consideration by Nature, has been withdrawn.

Natural scrapie in a goat.

 J Am Vet Med Assoc 154: 538-539 (1969) 
Hourrigan JL, Klingsporn AL, McDaniel HA, Riemenschneider MN
J. Biol. Chem. 1997 Mar 28 A. O. Gramolini, C. L. Dennis, J. M. Tinsley, ...and B. J. Jasmin. Local transcriptional control of utrophin expression at the neuromuscular synapse. J. Biol. Chem. 1997 Mar 28; 272 (13): 8117. Y. F. Liu, R. C. Deth and D. Devys. SH3 domain-dependent association of huntingtin with epidermal growth factor receptor signaling complexes. J. Biol. Chem. 1997 Mar 28; 272 (13): 8121. H. Saito, J. Papaconstantinou, H. Sato and S. Goldstein. Regulation of a novel gene encoding a lysyl oxidase-related protein in cellular adhesion and senescence. J. Biol. Chem. 1997 Mar 28; 272 (13): 8157. M. A. Gacad, H. Chen, J. E. Arbelle, T. LeBon and J. S. Adams. Functional characterization and purification of an intracellular vitamin D-binding protein in vitamin D-resistant new world primate cells. Amino acid sequence homology with proteins in the HSP-70 family. J. Biol. Chem. 1997 Mar 28; 272 (13): 8433. E. de Heuvel, A. W. Bell, A. R. Ramjaun, K. Wong, W. S. Sossin and P. S. McPherson. Identification of the major synaptojanin-binding proteins in brain. J. Biol. Chem. 1997 Mar 28; 272 (13): 8710. Z. Zhou, J. L. Corden and T. R. Brown. Identification and characterization of a novel androgen response element composed of a direct repeat. J. Biol. Chem. 1997 Mar 28; 272 (13): 8227. D. H. Kim, K. Magoori, T. R. Inoue, C. C. Mao, H. J. Kim, H. Suzuki, T. Fujita, Y. Endo, S. Saeki and T. T. Yamamoto. Exon/intron organization, chromosome localization, alternative splicing, and transcription units of the human apolipoprotein E receptor 2 gene. J. Biol. Chem. 1997 Mar 28; 272 (13): 8498. A. Oulmouden, A. Wierinckx, J. M. Petit, M. Costache, M. M. Palcic, R. Mollicone, R. Oriol and R. Julien. Molecular cloning and expression of a bovine {alpha}(1,3)-fucosyltransferase gene homologous to a putative ancestor gene of the human FUT3-FUT5-FUT6 cluster. J. Biol. Chem. 1997 Mar 28; 272 (13): 8764. N. Benaroudj, B. Fouchaq and M. M. Ladjimi. The COOH-terminal peptide binding domain is essential for self-association of the molecular chaperone HSC70. J. Biol. Chem. 1997 Mar 28; 272 (13): 8744. 1997 Apr 4; 272 (14) JBC J. P. Fawcett, R. Aloyz, J. H. McLean, S. Pareek, F. D. Miller, P. S. McPherson and R. A. Murphy. Detection of brain-derived neurotrophic factor in a vesicular fraction of brain synaptosomes. J. Biol. Chem. 1997 Apr 4; 272 (14): 8837. M. N. Weitzmann, K. J. Woodford and K. Usdin. DNA secondary structures and the evolution of hypervariable tandem arrays. J. Biol. Chem. 1997 Apr 4; 272 (14): 9517. S. Saito, K. Goto, A. Tonosaki and H. Kondo. Gene cloning and characterization of CDP-diacylglycerol synthase from rat brain. J. Biol. Chem. 1997 Apr 4; 272 (14): 9503. E. M. Kramer, T. Koch, A. Niehaus and J. Trotter. Oligodendrocytes direct glycosyl phosphatidylinositol-anchored proteins to the myelin sheath in glycosphingolipid-rich complexes. J. Biol. Chem. 1997 Apr 4; 272 (14): 8937.

Sequence variation of intron of prion protein gene, crucial for complete diagnostic strategies

Human Mutation 1996; 7(N3): 280-1
Palmer,M.S.; Vanleeven,R.H.; Mahal,S.P.; Campbell,T.A.; Humphreys,C.B.; Collinge,J

We have isolated a 450 bp PvuII fragment from the prion protein gene, which includes 95 bp of intron sequence flanking the 5' end of exon 2. This fragment contains four differences from the flanking region previously published (Hsiao et al., 1989), including an A-G transition at position -21 (Fig.1). An oligonucleotide (PDG-106 5' CTATGCACTCATTCATTATGC 3') from the 5' end of this fragment was used to amplify the flanking intron and open reading frame from two related patients with a valine 117 mutation. The mutant valine 117 allele of both patients was associated with the sequence present in oligo-45 (an A at -21), whereas the normal wild-type allele contained the variant found in the new intron sequence at this point (a G at -21) (Fig.1). Both alleles from each sample were identical to the new intron sequence at all positions outside the oligo-45 region.

We determined the frequency of this variation by amplifying DNA from 62 normal control samples and using allele-specific oligonucleotide hybridisation against the two variant sequences. All samples contained the G variant, whereas seven also contained the A variant. Therefore, the previously published intron sequence containing an A at - 21 is present in just 5.6% of alleles. All of the normal control samples with an A-variant had previously been shown to contain a noncoding polymorphism at codon 117 (alanine PvuII negative). The original patient from which the previously published intron sequence was derived also had a codon 117 polymorphism. This intron variant is thus associated with both polymorphisms and mutations at codon 117 of the open reading frame, both of which also occur on alleles carrying the codon 129 valine polymorphism.

The significance of this intron variant lies in its proximity to the open reading frame containing exon 2. Because of this, oligonucleotides similar to PDG-45 containing the rarer A-variant have been used by numerous groups in amplifying this gene for diagnostic purposes and clinical decisions are being made based on the results (Gabizon et al., 1993, Hsiao et al., 1992, Kitamoto et al., 1993, Kretzschmar et al., 1992, Nicholl et al., 1995, Gwen et al., 1992, Ripoll et al., 1993). We recommend that amplifications that require inclusion of the intron exon boundary should use oligonucleotide PDG-106 or primers from the region of oligo PDG-106.

                 -80                 -60                 -40
                   I                   I                   I
            106 ------------------>  *                *
B                           cattatgca-gaaacatttagtaatt-caacat
                    -20                 -1
                      I                  I
            *        *                    I
B   aaatatggaactctgacattctcctcttcattttgcagIagcagtcattatggcg
               45 -------------------->
FIGURE 1. Comparison of sequence of prion protein gene intron-exon boundary obtained in this study (A) with that previously published (Hsiao et al., 1989) (B). The sequence to the left of the vertical bar is intron and to the right is exon 2. The open reading frame commences with the ATG shown underlined and the bold letters represent untranslated sequence.

The positions of oligonucleotides PDG-45 and PDG-106 are indicated. Differences between the two sequences are indicated by an asterisk; 94.4% of alleles were found to have the G variant at -21 of sequence A. The frequency of the three other variants was not determined; none were present in any of the alleles sequenced here.


Gabizon R, Rosenmann H, Meiner Z, Kahana I, Kahana E, Shugart Y, Ott J, Prusiner SB (1993) Mutation and polymorphism of the prion protein gene in Libyan Jews with Creutzfeldt-Jakob disease (CJD). Am J Hum Genet 53:828-835
Hsiao K, Baker HF, Crow TJ, Poulter M, Owen F, Terwilliger JD, Westaway D, Ott J, Prusiner SB (1989) Linkage of a prion protein missense variant to Gerstmann-Str”ussler syndrome. Nature 338:342-345.
Hsiao K, Dlouhy SR, Fatlow MR, Cass C, Da Costa M, Conneally PM, Hodes ME, Chetti B, Prusiner SB (1992) Mutant prion proteins in Gerstmann-Str”ussler-Scheinker disease with neurofibrillary tangles. Nature Genet 1:68-71.
Kitamoto T, Ohta M, Dohura K, Hitoshi S, Terao Y, Tateishi J (1993) Novel missense variants of prion protein in Creutzfeldt Jakob disease or Gerstmann-Str”ussler syndrome. Biochem Biophys Res Comm 191:709-714.
Kretzschmar HA, Kufer P, Riethmuller G, DeArmond S, Prusiner SB, Schiffer D (1992) Prion protein mutation at codon-102 in an Italian family with Gerstmann-Str”ussler-Scheinker syndrome. Neurology 42:809-810.
Nicholl D, Windl 0, de Silva R, Sawcer S, Dempster M, Ironside JW, Estibeiro JP, Yuill GM, Lathe R, Will RG (1995) Inherited Creutzfeldt-Jakob disease in a British family associated with a novel 144 base pair insertion of the prion protein gene. J Neurol Neurosurg Psych 58:65-69.
Owen F, Poulter M, Collinge J, Leach M. Lofthouse R, Crow TJ, Harding AE (1992) A dementing illness associated with a novel insertion in the prion protein gene. Molec Brain Res 13:155-157.
Ripoll L, Laplanche J-L, Salzmann M, Jouvet A, Planques B, Dussaucy M, Chatelain J, Beardty P, Launay J-M (1993) A new point mutation in the prion protein gene at codon 210 in Creutzfeldt-Jakob disease. Neurology 43:1934-1938.

Should prion disease be analyzed as an "infection?"

Should prion disease be analyzed as an "infection?"

19 Mar 1997 Listserve 19.03.97

Phylogenetic predictions of the species barrier to infection don't work very well for parasites, bacteria or viruses, why should we expect them to work for prions? To use the term "infection" when referring to TSEs is making an analogy (like computer "viruses"), rather than referring to infection in the classical meaning of the word. The proposed mechanism of prion propagation (conformational change of pre-formed prions by rogue prions) is more a physical than a biological process. We are thus misled into thinking of TSEs as just another class of infection, when a better analogy might be to a seed crystal causing enhanced crystalization in a saturated solution. Think of the species barrier to protein conformational change rather than infection.

Response: it was astonishing to see Nature accepting a recent nvCJD modeling paper based on malarial epidemics and what not. No particlular reason for that modeling math to be applicable here.

One of the many complexities of this set of diseases is that there is not just one rogue conformer, but hundreds. I don't mean by this just the various dynamic population states of a single protein molecule, but rather rogue conformers of different amino acid sequence. Two proteins of different primary sequence cannot possibly have the same tertiary structure, though certain features and capabilities might carry over (eg, beta sheet and ability to recruit normal in hetero-oligomers). Humans alone produce some 13 different and distinct rogue conformers -- that is how many rogue alleles have been found. (There could be fewer due to endopeptidase convergence, but many more due to different post-translational modifications). Now, following Gibbs, multiply this by the number of species of mammals.

I would say this aspect of TSEs falls not so much within physics as within a classical area within protein biochemistry that concerns itself with quaternary structure and oligomericity. This sounds esoteric, but in fact there have been tens of thousands of scientific publications concerning this subject (because it is applicable to perhaps half of all known proteins).

Seed crystallization (or the ice IX story of Kurt Vonnegut from 1950's) is a good enough metaphor but here the rogue conformer _catalyzes_ recruitment of normal. And I would not omit the role of heat shock protein 60. Things in biology are nowhere near thermodynamic equilibrium because of potential barriers. It is can really be more a case of the law of mass action, overproduction of normal pushing the equilibrium towards more rogue.

Identification of a self-association region within the SCA1 gene product, ataxin-1

Eric N. Burright , Jennifer D. Davidson , Lisa A. Duvick , Beena Koshy , Huda Y. Zoghbi and Harry T. Orr

Spinocerebellar ataxia type 1 (SCA1) is an autosomal dominant neurodegenerative disorder caused by the expansion of a polyglutamine tract within the SCA1 gene product, ataxin-1. Expansion of this tract is believed to result in a gain of function by the mutant protein, perhaps through altered self-associations or interactions with other cellular proteins. We have used the yeast two hybrid system to determine if ataxin-1 is capable of multimerization. This analysis revealed that ataxin-1 does have the ability to self-associate, however, this association does not appear to be influenced by expansion of the polyglutamine tract.

Consistent with this finding, deletion analysis excluded the involvement of the polyglutamine tract in ataxin-1 self-association, and instead localized the multimerization region to amino acids 495-605 of the wild type protein. These results, while identifying an ataxin-1 self-interaction region, fail to support a proposed model of polar-zipper mediated multimerization involving the ataxin-1 polyglutamine tract.

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