DM: no longer alone

Up until now, myotonic dystrophy (DM)has been an oddball among repeat-expan-sion disorders, because it has been theonly disease associated with an expansion

of a non-coding DNA repeat that exhibitsdominant inheritance. This lonely statuscan now be consigned to history, becauseit appears that one form of spinocerebellar

ataxia (SCA8) has very similar prop-erties1. Spinocerebellar ataxia is a hetero-geneous, dominant disorder, caused bytriplet-repeat expansions at any one of anumber of different loci. Hitherto, allcases have been shown to be CAG (poly-glutamine) expansions within codingDNA, as for a number of other dominant

DM: no longer alone

circuits. They described how to represent different levelsof digital signals – which in conventional computers arecomposed of electrical currents to form the on/off logicgates – as concentrations of DNA-binding proteins. Byacting as promoters or repressors, these control the rate of production of other DNA-binding proteins, triggeringbiochemical switches in a biological ‘computer’.

Taken as a whole, these experiments offer fertileground for new developments and theoretical insight inmultiple fields. Not only do biological and computationalsciences stand to benefit, but continued work in this areamight even provide engineers with new avenues for tech-nological innovation inspired by nature. As one speakerreminded us, ‘There are more things in heaven and earth,Horatio, than are dreamt of in your philosophy.’ (Hamlet,Act I, Scene V.)

OutlookMEETING REPORTSComputer science and meta-evolution

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BOX 1. Web links

Bibliography on DNA, molecular computation and splicing systemshttp://www.wi.leidenuniv.nl/~jdassen/dna.html

Sites related to microbial engineeringhttp://www.ai.mit.edu/people/tk/ce/microbial-engineering.html

Site on amorphous computinghttp://www-swiss.ai.mit.edu/~swiss/amorphous/index.html

The Molecular Sciences Institute at Berkeleyhttp://www.molsci.org

Laura F. Landweber’s homepagehttp://www.princeton.edu/~lfl

Erik Winfree’s DNA computing pagehttp://hope.caltech.edu/winfree/DNA.html

Further reading1 Vogel, G. (1998) Tracking the history of the genetic code.

Science 281, 329–3312 Knight, R.D. and Landweber, L.F. (1998) Rhyme or reason:

RNA–arginine interactions and the genetic code. Chem. Biol.5, R215–R220

3 Ardell, D.H. (1998) On error minimization in a sequential

origin of the standard genetic code. J. Mol. Evol. 47, 1–134 Freeland, S.J. and Hurst, L.D. (1998) The genetic code is one in

a million. J. Mol. Evol. 47, 238–2485 Freeland, S.J. and Hurst, L.D. (1998) Load minimization of the

genetic code: history does not explain the pattern. Proc. R.Soc. London Ser. B 265, 2111–2119

6 Endy, D. et al. (1997) Intracellular kinetics of a growing virus:

a genetically structured simulation for bacteriophage T7.Biotech. Bioeng. 55, 375–389

7 Prescott, D.M. (1997) Origin, evolution, and excision ofinternal elimination segments in germline genes of ciliates.Curr. Opin. Genet. Dev. 7, 807–813

8 Pennisi, E. (1998) How the genome readies itself for evolution.Science 281, 1131–1133

Howy Jacobs

howy.jacobs@uta.fi

Eukaryotic genomes are riddled with vari-ous kinds of short and long repetitive ele-ments, called SINEs and LINEs. Many ofthese are the products of retroposition andthus ultimately depend on active retro-viruses. Prokaryotic cells are also continu-ally attacked by viruses that can leavetheir signatures as prophages in thegenome. It has been estimated that forevery prokaryotic cell in natural isolates,there are ten phage particles, making themthe most abundant organismal entity inthe world. Compared to this, only about40 phage and prophage genomes havebeen sequenced so far, which would sug-gest that only a tiny fraction of the wholediversity has been sampled. But intrigu-ingly, Hendrix et al.1 show that at leastthose with double-stranded DNA

genomes are all interrelated, implying anancient origin. But the relationships arepatchy and complex, suggesting that con-tinuous horizontal exchange of parts oftheir genomes has played a significant rolein their evolutionary history. In fact,Hendrix et al. suggest that these exchangeprocesses might have even occurred inmultiple steps across huge phylogeneticdistances, making the authors speculateon ‘...random walks through phylogeneticspace’. In a similar vein, Gilbert andLabuda2 show that a certain class of SINEelements harbours a common, short, coresequence that can be identified in verte-brate and invertebrate genomes. Againthis suggests an ancient origin and theauthors speculate that this core has servedas an assembly structure during the evolu-

tion of the elements onto which different59- and 39-blocks became added.Although horizontal transfer of blocks isnot specifically suggested in this case, thedata would probably not rule out this pos-sibility either. Thus both papers show thatprokaryotes and eukaryotes have livedwith ancient classes of molecular parasitesfrom the beginning of their evolution, tes-tifying that the molecular war againstsuch infections cannot ultimately be won.

Ancient molecular parasites

1 Hendrix, R.W. et al. (1999) Evolutionaryrelationships among diverse bacteriophagesand prophages: all the world’s a phage. Proc.Natl. Acad. Sci. U. S. A. 96, 2192–2197

2 Gilbert, N. and Labuda, D. (1999) CORE-SINEs:eukaryotic short interspersed retroposingelements with common sequence motifs. Proc.Natl. Acad. Sci. U. S. A. 96, 2869–2874

Diethard Tautz

tautz@uni-koeln.de

The cellular response to the local environ-ment has been shown to be mediatedthrough the p53 (TP53 human gene;Trp53, mouse gene) tumour suppresser,which controls both cell-cycle arrest andapoptosis. Consistent with proposed func-tions for p53, mice that lack p53 undergonormal embryogenesis but show a suscep-tibility to a wide range of cancers.However, the p53 phenotype appears tobe in conflict with that observed for itsdirect downstream target Cdkn1a(p21WAF); homozygous Cdkn1a mice havedefects in cell-cycle control but show nopropensity for spontaneous tumours.These and other observations led to thecloning of two p53-related genes, p73 andp63. In contrast to the ubiquitous expres-sion of p53, p63 is expressed in the epider-mis and regions of the embryo that

undergo epidermal–mesencyhymal inter-actions. Now two independent studies1,2

have shown that p63 further differs fromp53 in being required for normal embryo-genesis: mice lacking p63 have numerousdefects, including dramatic limb trunca-tions, craniofacial abnormalities, and acomplete absence of epidermis. Bothgroups have characterized the limb andskin defects in greater detail and havereached similar conclusions. In the limb,the most striking feature of p63 –/– mice isa complete absence of the AER, whichprobably results from defects with in theectoderm as shown by the absence ofMsx1 expression. Interestingly, thesedefects show a striking resemblance to thelimbless phenotype in chickens raising theinteresting possibility that limbless mightarise due to a defect in p63 or another

member of the p63 signalling pathway. Inthe skin, the p63 –/– mice appear to lackall stratified epidermis and their deriva-tives. Although the basal or progenitorcells do appear to be present these cells fail to differentiate1,2 and subsequentlyundergo apoptosis2. Although these initialstudies define an essential role for p63 inepidermal cell types we await answers tothe following most interesting questions.Does p63 function directly in cell-cyclecontrol and/or apoptosis in vivo? Does itfunction as a tumour suppresser gene?And, if so, does it share direct downstreamtargets, such as CDKN1A, with p53?

From p53 to p63 and p73

1 Mills, A. et al. (1999) p63 is a p53 homoloquerequired for limb and epidermialmorphogenesis. Nature 398, 708–713

2 Yang, A. et al. (1999) p63is essential forregenerative proliferation in limb, craniofacialand epithelial development. Nature 398, 714–718

Frank Conlon

fconlon@nimr.mrc.ac.uk

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TIG June 1999, volume 15, No. 6222

disorders of this type, such as Huntingtonor Kennedy diseases. SCA8 appears to dif-fer from this pattern. As in the case ofDM, the repeat-expansion associated withSCA8 lies within an untranslated portionof a transcript in which the expandedtriplet is CUG. No transcript from theother strand, which would contain therepeated sequence CAG, was detected,nor is there any open reading frame inwhich the CAG run or, for that matter theCUG repeat on the transcribed strand isembedded. The expansion co-segregateswith the disorder in affected families, andshows an unusual maternal penetrancebias, apparently associated with a sex-spe-cific repeat-length mutational process inthe germ line. These findings strengthenthe idea that the dominant inheritance

pattern of DM, and now SCA8 as well,results from inappropriate expression of aCUG-repeat-containing RNA (Ref. 2). Inboth DM and SCA8, the CUG repeatexpansion is found near the 39 end of theaffected transcript. One difference in thetwo cases, however, concerns the normalfunction of the RNA molecule in whichthe repeat is found. In DM, the repeat isfound in the 39 UTR of a conventionalmRNA, encoding the DMPK proteinkinase. In SCA8, the RNA molecule con-taining the CUG repeat, although spliced,appears to be entirely non-coding, at leastno convincing open reading frame wasfound in any detectable splice variant. Thesimplest explanation is that the normalfunction of the RNA is not relevant to thedisease process in either case. Transgenic

models suggest strongly, for example, thatabnormal expression of DMPK is not thecause of myotonic dystrophy. The pheno-types of the two diseases are, nevertheless,clearly distinct. Therefore, if this idea of atoxic, CUG repeat-containing RNA is cor-rect, its different effects in the two caseswould be attributable to the different tis-sue-patterns of its expression.

1 Koob, M.D. et al. (1999) An untranslated CTGexpansion causes a novel form ofspinocerebellar ataxia. Nat. Genet. 21, 379–384

2 Singer, R.H. (1998) Triplet-repeat transcripts: arole for DNA in disease. Science 280, 696–697

Polyglutamine tract expansion has beenshown to cause at least eight inheritedneurodegenerative disorders, includingspinocerebellar ataxia type 3 (SCA3/MJD) which is caused by repeat expan-sion in the ataxin-3 protein. It is knownthat mutant proteins with expandedpolyglutamine tracts aggregate and leadto the formation of nuclear inclusions(NI). Paulson’s group1 have shown, byimmunohistochemical staining onbrainstem sections from a SCA3/MJDaffected individual, that the NIimmunostained positively for the 26Sproteasome complex. In vitro studies onseveral cell lines, and a primary neu-ronal culture transfected with two path-

ogenic forms of ataxin-3 and an unre-lated fusion protein with an expandedpolyglutamine tract, confirmed therecruitment of proteasome complex intothe polyglutamine aggregates. More-over, inhibition of proteasome with lactacystin increased the formation ofaggregates in a manner dependent onthe repeat length, dose of lactacystinand time. Intriguingly, lactacystincaused not only intranuclear but alsocytoplasmic aggregation of full-lengthmutant ataxin-3 that was tagged with anuclear localization signal (NLS), sug-gesting that lactacystin promoted aggre-gation of NLS-ataxin-3 before it couldbe transported into the nucleus. Data

presented in this paper, and an earlierreport indicating co-localization of proteasome to NI formed by the SCA1disease protein (ataxin-1), support the hypothesis that polyglutamineexpansion leads to misfolding of the dis-ease protein, which in turn results in itsaggregation. Also proteasome functionmight be the key towards developmentof new therapeutic approaches for the treatment of at least some of thepolyglutamine diseases.

Polyglutamine diseases

1 Chai, Y. et al. (1999) Evidence for proteasomeinvolvement in polyglutamine disease:localization to nuclear inclusions in SCA3/MJDand suppression of polyglutamine aggregationin vitro. Hum. Mol. Genet. 8, 673–682

Majid Hafezparast Elizabeth Fisher

m.hafezparast@ ic.ac.uke.fisher@ ic.ac.uk