DM: no longer alone

MEETING REPORTS

Computer science and meta-evolution

BOX 1. Web links Bibliography on DNA, molecular computation and splicing systems http://www.wi.leidenuniv.nl/~jdassen/dna.html

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

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

The Molecular Sciences Institute at Berkeley http://www.molsci.org

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

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

Further reading 1 Vogel, G. (1998) Tracking the history of the genetic code. Science 281, 329–331 2 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

circuits. They described how to represent different levels of digital signals – which in conventional computers are composed of electrical currents to form the on/off logic gates – as concentrations of DNA-binding proteins. By acting as promoters or repressors, these control the rate of production of other DNA-binding proteins, triggering biochemical switches in a biological ‘computer’. Taken as a whole, these experiments offer fertile ground for new developments and theoretical insight in multiple fields. Not only do biological and computational sciences stand to benefit, but continued work in this area might even provide engineers with new avenues for technological innovation inspired by nature. As one speaker reminded us, ‘There are more things in heaven and earth, Horatio, than are dreamt of in your philosophy.’ (Hamlet, Act I, Scene V.)

origin of the standard genetic code. J. Mol. Evol. 47, 1–13 4 Freeland, S.J. and Hurst, L.D. (1998) The genetic code is one in a million. J. Mol. Evol. 47, 238–248 5 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 of internal 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

JOURNAL CLUB

Ancient molecular parasites Eukaryotic genomes are riddled with various kinds of short and long repetitive elements, called SINEs and LINEs. Many of these are the products of retroposition and thus ultimately depend on active retroviruses. Prokaryotic cells are also continually attacked by viruses that can leave their signatures as prophages in the genome. It has been estimated that for every prokaryotic cell in natural isolates, there are ten phage particles, making them the most abundant organismal entity in the world. Compared to this, only about 40 phage and prophage genomes have been sequenced so far, which would suggest that only a tiny fraction of the whole diversity has been sampled. But intriguingly, Hendrix et al.1 show that at least those with double-stranded DNA

genomes are all interrelated, implying an ancient origin. But the relationships are patchy and complex, suggesting that continuous horizontal exchange of parts of their genomes has played a significant role in their evolutionary history. In fact, Hendrix et al. suggest that these exchange processes might have even occurred in multiple steps across huge phylogenetic distances, making the authors speculate on ‘...random walks through phylogenetic space’. In a similar vein, Gilbert and Labuda2 show that a certain class of SINE elements harbours a common, short, core sequence that can be identified in vertebrate and invertebrate genomes. Again this suggests an ancient origin and the authors speculate that this core has served as an assembly structure during the evolu-

DM: no longer alone Up until now, myotonic dystrophy (DM) has been an oddball among repeat-expansion disorders, because it has been the only disease associated with an expansion

Outlook

of a non-coding DNA repeat that exhibits dominant inheritance. This lonely status can now be consigned to history, because it appears that one form of spinocerebellar

Outlook

tion of the elements onto which different 59- and 39-blocks became added. Although horizontal transfer of blocks is not specifically suggested in this case, the data would probably not rule out this possibility either. Thus both papers show that prokaryotes and eukaryotes have lived with ancient classes of molecular parasites from the beginning of their evolution, testifying that the molecular war against such infections cannot ultimately be won.

1 Hendrix, R.W. et al. (1999) Evolutionary relationships among diverse bacteriophages and 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 retroposing elements with common sequence motifs. Proc. Natl. Acad. Sci. U. S. A. 96, 2869–2874

ataxia (SCA8) has very similar properties1. Spinocerebellar ataxia is a heterogeneous, dominant disorder, caused by triplet-repeat expansions at any one of a number of different loci. Hitherto, all cases have been shown to be CAG (polyglutamine) expansions within coding DNA, as for a number of other dominant

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Diethard Tautz [email protected]

Howy Jacobs [email protected] 221

Outlook

JOURNAL CLUB

disorders of this type, such as Huntington or Kennedy diseases. SCA8 appears to differ from this pattern. As in the case of DM, the repeat-expansion associated with SCA8 lies within an untranslated portion of a transcript in which the expanded triplet is CUG. No transcript from the other strand, which would contain the repeated sequence CAG, was detected, nor is there any open reading frame in which the CAG run or, for that matter the CUG repeat on the transcribed strand is embedded. The expansion co-segregates with the disorder in affected families, and shows an unusual maternal penetrance bias, apparently associated with a sex-specific repeat-length mutational process in the germ line. These findings strengthen the idea that the dominant inheritance

pattern of DM, and now SCA8 as well, results from inappropriate expression of a CUG-repeat-containing RNA (Ref. 2). In both DM and SCA8, the CUG repeat expansion is found near the 39 end of the affected transcript. One difference in the two cases, however, concerns the normal function of the RNA molecule in which the repeat is found. In DM, the repeat is found in the 39 UTR of a conventional mRNA, encoding the DMPK protein kinase. In SCA8, the RNA molecule containing the CUG repeat, although spliced, appears to be entirely non-coding, at least no convincing open reading frame was found in any detectable splice variant. The simplest explanation is that the normal function of the RNA is not relevant to the disease process in either case. Transgenic

From p53 to p63 and p73

Frank Conlon [email protected]

The cellular response to the local environment has been shown to be mediated through the p53 (TP53 human gene; Trp53, mouse gene) tumour suppresser, which controls both cell-cycle arrest and apoptosis. Consistent with proposed functions for p53, mice that lack p53 undergo normal embryogenesis but show a susceptibility to a wide range of cancers. However, the p53 phenotype appears to be in conflict with that observed for its direct downstream target Cdkn1a (p21WAF); homozygous Cdkn1a mice have defects in cell-cycle control but show no propensity for spontaneous tumours. These and other observations led to the cloning of two p53-related genes, p73 and p63. In contrast to the ubiquitous expression of p53, p63 is expressed in the epidermis and regions of the embryo that

undergo epidermal–mesencyhymal interactions. Now two independent studies1,2 have shown that p63 further differs from p53 in being required for normal embryogenesis: mice lacking p63 have numerous defects, including dramatic limb truncations, craniofacial abnormalities, and a complete absence of epidermis. Both groups have characterized the limb and skin defects in greater detail and have reached similar conclusions. In the limb, the most striking feature of p63 –/– mice is a complete absence of the AER, which probably results from defects with in the ectoderm as shown by the absence of Msx1 expression. Interestingly, these defects show a striking resemblance to the limbless phenotype in chickens raising the interesting possibility that limbless might arise due to a defect in p63 or another

Polyglutamine diseases

Majid Hafezparast Elizabeth Fisher m.hafezparast@ ic.ac.uk e.fisher@ ic.ac.uk 222

Polyglutamine tract expansion has been shown to cause at least eight inherited neurodegenerative disorders, including spinocerebellar ataxia type 3 (SCA3/ MJD) which is caused by repeat expansion in the ataxin-3 protein. It is known that mutant proteins with expanded polyglutamine tracts aggregate and lead to the formation of nuclear inclusions (NI). Paulson’s group1 have shown, by immunohistochemical staining on brainstem sections from a SCA3/MJD affected individual, that the NI immunostained positively for the 26S proteasome complex. In vitro studies on several cell lines, and a primary neuronal culture transfected with two path-

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ogenic forms of ataxin-3 and an unrelated fusion protein with an expanded polyglutamine tract, confirmed the recruitment of proteasome complex into the polyglutamine aggregates. Moreover, inhibition of proteasome with lactacystin increased the formation of aggregates in a manner dependent on the repeat length, dose of lactacystin and time. Intriguingly, lactacystin caused not only intranuclear but also cytoplasmic aggregation of full-length mutant ataxin-3 that was tagged with a nuclear localization signal (NLS), suggesting that lactacystin promoted aggregation of NLS-ataxin-3 before it could be transported into the nucleus. Data

models suggest strongly, for example, that abnormal expression of DMPK is not the cause of myotonic dystrophy. The phenotypes of the two diseases are, nevertheless, clearly distinct. Therefore, if this idea of a toxic, CUG repeat-containing RNA is correct, its different effects in the two cases would be attributable to the different tissue-patterns of its expression.

1 Koob, M.D. et al. (1999) An untranslated CTG expansion causes a novel form of spinocerebellar ataxia. Nat. Genet. 21, 379–384 2 Singer, R.H. (1998) Triplet-repeat transcripts: a role for DNA in disease. Science 280, 696–697

member of the p63 signalling pathway. In the skin, the p63 –/– mice appear to lack all stratified epidermis and their derivatives. Although the basal or progenitor cells do appear to be present these cells fail to differentiate1,2 and subsequently undergo apoptosis2. Although these initial studies define an essential role for p63 in epidermal cell types we await answers to the following most interesting questions. Does p63 function directly in cell-cycle control and/or apoptosis in vivo? Does it function as a tumour suppresser gene? And, if so, does it share direct downstream targets, such as CDKN1A, with p53?

1 Mills, A. et al. (1999) p63 is a p53 homoloque required for limb and epidermial morphogenesis. Nature 398, 708–713 2 Yang, A. et al. (1999) p63is essential for regenerative proliferation in limb, craniofacial and epithelial development. Nature 398, 714–718

presented in this paper, and an earlier report indicating co-localization of proteasome to NI formed by the SCA1 disease protein (ataxin-1), support the hypothesis that polyglutamine expansion leads to misfolding of the disease protein, which in turn results in its aggregation. Also proteasome function might be the key towards development of new therapeutic approaches for the treatment of at least some of the polyglutamine diseases.

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