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Turning Yeast Sequence Into Protein Function in Vivo Veritas: Live Phage

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Turning Yeast Sequence Into Protein Function in Vivo Veritas: Live Phage © 1996 Nature Publishing Group http://www.nature.com/naturebiotechnology • RESEARCH NEWS Turning yeast sequence into protein function Gunnar von Heijne By the beginning of April, the full DNA A particularly interesting example is bridge, UK) pointed out, about 15% of all sequence of the Saccharomyces cerevisiae PDRS, a protein that has all the hallmarks of the yeast proteins are sufficiently similar to genome should have been completed. As the so-called ATP binding cassette (ABC) pro­ proteins of known 3D structure to allow reported at the recent "Perspectives in Pro­ teins, but with the ATP-binding domains automatic generation of 3D models. Such tein Engineering" meeting (March 3-6, 1996, attached on the N-terminal rather than the C­ models are expected to be very accurate Montpellier, France), a mere 1% or so of the terminal side of the membrane-embedded around the active site, fairly accurate within 12.5 million base yeast genome remained to domains. As is usually the case for membrane the central core of the protein, and unreliable be sequenced as of March 1. The question in the exterior loop regions. They would be now is not "When will the data be available?" useful in, for instance, guiding site-directed but ''What will we do with it?': mutagenesis studies. Of the 6200-6300 potential open reading IMAGE Program packages such as GeneQuiz frames (ORFs) in the genome, around 25% UNAVAILABLE (http://www.embl-heidelberg.de/-casari/­ have been sequenced and functionally char- _gi genequiz.html) or the software developed at acterized before: 30% encode proteins with } FOR COPYRIGHT the Institute for Genomic Research (Gaithers­ significant similarity to proteins of known ~ REASONS burg, MD) use a battery of sequence analysis function from other organisms, and the 15 routines to scan entire genomes. Results for ~ remaining 40% represent completely novel ~ 5000 yeast open ready frames (ORFs), as well proteins. Work is now underway (partly © as for the fully sequenced Haemophilus influen­ within the European Commission-funded proteins, overproduction of this protein zae, Staphylococcus aureus, and Mycoplasma EUROFAN project) to make a rapid assess- turned out to be difficult. However, a muta­ genitalium genomes are already out (Nature ment of the functions of these new genes by tion in the PDRl transcription factor was iso­ Biotechnology 14: 255-256, 1996) and more are gene disruption, and, for some genes, by lated that not only led to a I 00-fold increase in coming. more detailed phenotypic studies. synthesis of active PDRS, but also allowed effi- Since analysis is dependent upon the quali­ The yeast data has already led to the iden- cient sorting to the plasma membrane. ty of the databanks, the latest release of the tification of a number of proteins that had Whether this or similar mutant strains will be widely used SWISS-PROT protein sequence previously not been suspected to be part of a general panacea for membrane protein over­ database attempts to strike a new balance the S. cerevisiae genetic repertoire. As Andre production in yeast remains to be seen; the between quantity and quality, Rolf Apweiler of Goffeau (University of Louvain, Belgium) success with the PDRS/PDRI system certainly EBI-EMBL told the meeting. The SWISS­ described in Montpellier, a large number of suggests that genetic selection of overproduc­ PROT database is now supplemented with a plasma membrane proteins with different ing strains may aid the assignment of protein new, automatically annotated database transport functions have been identified by function. (TREMEL) including all ORFs from the EMBL sifting through about half of the genome The rapid accumulation of fully nucleotide sequence database that are not with hydrophobicity analysis and sequence sequenced prokaryotic and eukaryotic already present in SWISS-PROT. Some 20,000 alignment methods. Some of these are clearly genomes puts new demands on bioinformat­ entries from TREMBL will eventually make it homologous to the multidrug resistance pro- ics. If, for instance, the sensitivity of into SWISS-PROT, while other sequences will teins of bacteria and higher eukaryotes. sequence similarity searches can be increased be transferred to specialized databases. by even a few percent, hundreds of new Between the large-scale sequencing pro­ genes may be functionally and even struc­ jects and the World Wide Web, the long Gunnar von Heijne is at the department of turally classified with minimal requirement awaited unification of experimental and biochemistry, Arrhenius Laboratory, Stockholm for tedious experimental investigations. computational biology is finally happening. University, S-106 91 Stockholm, Sweden Thus, as Chris Sander of the European Where this will eventually take us is any­ ( [email protected]). Bioinformatics Institute (EBI-EMBL, Cam- body's guess. In vivo veritas: Live phage display panning AnnaM. Wu Phage display of antibody fragments or pep­ libraries of filamentous phage displaying Ruoslahti from the La Jolla Cancer Research tides has provided a powerful method for diverse antibody or peptide sequences are Foundation (La Jolla, CA), have extended generating molecules with novel binding "panned" on purified antigen or whole phage display further, reporting successful characteristics 1• Bypassing immunization, cells2,3 in order to select for molecules that "panning in vivo" to yield phage that home bind appropriately. Subsequent elution and to specific organs. amplification of the bound phage allows the It has been known for some time that Anna M. Wu is an associate research scientist recovery of proteins that can interact with lymphocyte and tumor cells can home to in the department of molecular biology, targets previously inaccessible to convention­ various organs by virtue of selective Beckman Research Institute of the City of al hybridoma technology; for instance, toxic "address" molecules on endothelial surfaces 6• Hope, 1450 East Duarte Road, Duarte, CA substances or self-antigens4• Now, in the As a more general approach to investigating 91010 ([email protected],g). March 28 issue of Nature5, Pasqualini and the presence of such endothelial markers, NATURE BIOTECHNOLOGY VOLUME 14 APRIL 1996 429 .
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