Looking forward, looking backward
2
TIBS 25 – OCTOBER 2000 487 MEETING REPORT The 18th IUBMB Congress of Biochemistry (now Biochemistry and Molecular Biology)* was the first return of this triennial series to the UK since the 1st Congress held in Cambridge in 1949. That first meeting had been planned in response to the reluctance of the organizers of the International Congresses of Physiology to give greater prominence to biochemistry and, per- haps, took place at a moment when, four years after the end of WWII, the world seemed ripe for renewal. Fifty-one years on, the move from Cambridge 1949 to Birmingham 2000 represented, as one chair remarked, ‘progress of a kind’. Mid-20th century biochemistry, then still struggling for its independence from classical physiology, has now itself been pre-empted by the as yet incom- pletely formalized disciplines of molecu- lar biology – genomics and proteomics. Genomics The opening plenary lecture by J. Craig Venter (Rockville, USA), founder of the private genome sequencing and patent- ing company Celera, set the scene. The dramatic increase in rate and efficiency of genetic sequencing over the past decade will culminate in the listing of a human (five-person, three female, two male, mixed ethnicity) genome by December of this year. Thirteen years since the se- quencing of the 48-kbp l phage genome by Sanger and co-workers, we now have ~20 complete genomes for both prokary- otes and eukaryotes, the latter including the recent completion 1 of the sequences for the chromosomes of T.H. Morgan’s favourite Drosophila. The genes include the ‘known’, the ‘unknown’ and the ‘hypothetical’ (the transition from ‘hypothetical’ to ‘unknown’ depends upon assurance of expression). Fifty per cent of the Drosophila genes are unknown, many predictably membrane associated. The 120 Mbp of the fly took hardly more personnel and much less time than the 1.8 Mbp of the first prokary- ote, Haemophilus influenzae. Craig Venter’s iconic slide showing his sequencing laboratory resembled the NASA space command centre in Houston, containing no visible human beings (see Fig. 1). Evidently, it is only a matter of time before large genomes can be sequenced and the results recorded by machines alone. However, there was a striking contrast between Venter’s tri- umphant talk and his diffidence at ques- tion time (the only such time allotted after a plenary). He then said that he will soon need to become a biochemist again to relearn the necessities of pro- teomics as well as genomics. But it will not be the old kind of biochemist, who spent, as Venter once did, nearly ten years isolating and partially purifying a single adrenergic receptor protein. Proteomics As the rest of the meeting showed, the old biochemistry is a thing of the past, evoking nostalgia in some more than others. Will the Krebs cycle still be taught at the end of this new century? The meeting agenda showed that small- molecule metabolism had disappeared, except for a few exotic outliers. Classical enzymology had gone long before. David Hilbert said in the late 1920s that ‘physics has become too hard for the physicists’. Equally, enzyme behaviour became too hard for enzymologists at some point in the late 1950s. Semi-auto- mated screening of protein–protein in- teractions in two-dimensional gel sys- tems (a kind of generalized Western blot), ‘hybrigenics’, are now being done, in a pseudo-ecological world of ‘preda- tor’, ‘prey’ and ‘bait’ proteins, as de- scribed by Simon Whiteside (Paris, France) and elaborated on by Matthias Mann (Odense, Denmark). Such global analyses of multi-protein systems are an essential part of the proteomic approach to full analysis of cell function. How are we to analyse and understand protein–protein interactions? David Eisenberg (Los Angeles, USA) spoke in Birmingham’s magnificent Symphony Hall. He introduced two ideas in developing a ‘Rosetta Stone’ method of determining protein func- tional relationships. The first idea is that of domain swapping. Many func- tional monomers with multiple do- mains can be induced to form stable dimers by partial (‘soft’) denaturations in which domain 2 of monomer A binds to domain 1 of monomer B and vice versa. Such creation of dimers, both homo- and heterodimers, might also have been an evolutionary event in the formation of protein complexes. The second idea is therefore that of analysing protein function by compar- ing genomes. Comparative biochem- istry, the importance of which used to be emphasized by my supervisor David Keilin (who would probably not have discovered cytochromes had he re- stricted himself to haemoglobin-con- taining organisms), might thus be re- turning in the guise of comparative genomics. Linkage of two protein genes in one genome can indicate linked functions in their genetically unlinked relatives in other genomes. Prions Proteins ain’t what they used to be. Their native structures in vivo were once thought of as shallowly balanced, thermodynamically unstable versions of their ‘dead’ denatured forms. Following the triumph of the linear genome and mRNA models of protein synthesis, they became molecules existing in low-en- ergy sinks containing only very few, rapidly fluctuating, possible conforma- tions. They are now becoming unstable again, often vulnerable to autocatalytic conformational changes between a- helix and b-sheet states, reminiscent of Eisenberg’s domain-swapping monomers, but with the catch that the final species remains transformed as the monomer. Such, apparently, are prions, as discov- ered by Stanley Prusiner. By lucky chance I was in the bar at Cold Spring Harbor in 1997, moments after the radio announcement of his Nobel prize. Of course, Jim Watson must have known al- ready, and his only comment was ‘ah, Prusiner’. But the prion model has de- veloped into a major exception to the spirit of the central dogma and to the Weismannian ‘DNA alone’ theory of in- heritance. As Prusiner (San Francisco, USA) explained, prions are a complex group of proteins with their own genet- ics and examples throughout the living world. Their probable involvement in scrapie, BSE and hence new-variant CJD has made them newsworthy. But neither physicochemical understanding at the one end nor therapy at the other seems yet to be available. 0968 – 0004/00/$ – See front matter © 2000, Elsevier Science Ltd. All rights reserved. PII: S0968-0004(00)01673-X Looking forward, looking backward *18th International Congress of Biochemistry and Molecular Biology ‘Beyond the Genome’, Birmingham, UK, 16–20 July 2000.
-
Upload
peter-nicholls -
Category
Documents
-
view
226 -
download
7
Transcript of Looking forward, looking backward
TIBS 25 – OCTOBER 2000
487
MEETING REPORT
The 18th IUBMB Congress ofBiochemistry (now Biochemistry andMolecular Biology)* was the first returnof this triennial series to the UK sincethe 1st Congress held in Cambridge in1949. That first meeting had beenplanned in response to the reluctance ofthe organizers of the InternationalCongresses of Physiology to give greaterprominence to biochemistry and, per-haps, took place at a moment when, fouryears after the end of WWII, the worldseemed ripe for renewal. Fifty-one yearson, the move from Cambridge 1949 toBirmingham 2000 represented, as onechair remarked, ‘progress of a kind’.Mid-20th century biochemistry, thenstill struggling for its independencefrom classical physiology, has now itselfbeen pre-empted by the as yet incom-pletely formalized disciplines of molecu-lar biology – genomics and proteomics.
GenomicsThe opening plenary lecture by J. Craig
Venter (Rockville, USA), founder of theprivate genome sequencing and patent-ing company Celera, set the scene. Thedramatic increase in rate and efficiency ofgenetic sequencing over the past decadewill culminate in the listing of a human(five-person, three female, two male,mixed ethnicity) genome by December ofthis year. Thirteen years since the se-quencing of the 48-kbp l phage genomeby Sanger and co-workers, we now have~20 complete genomes for both prokary-otes and eukaryotes, the latter includingthe recent completion1 of the sequencesfor the chromosomes of T.H. Morgan’sfavourite Drosophila. The genes includethe ‘known’, the ‘unknown’ and the ‘hypothetical’ (the transition from ‘hypothetical’ to ‘unknown’ dependsupon assurance of expression). Fifty percent of the Drosophila genes are unknown, many predictably membraneassociated. The 120 Mbp of the fly tookhardly more personnel and much lesstime than the 1.8 Mbp of the first prokary-ote, Haemophilus influenzae.
Craig Venter’s iconic slide showinghis sequencing laboratory resembledthe NASA space command centre inHouston, containing no visible humanbeings (see Fig. 1). Evidently, it is only amatter of time before large genomes canbe sequenced and the results recordedby machines alone. However, there wasa striking contrast between Venter’s tri-umphant talk and his diffidence at ques-tion time (the only such time allottedafter a plenary). He then said that hewill soon need to become a biochemistagain to relearn the necessities of pro-teomics as well as genomics. But it willnot be the old kind of biochemist, whospent, as Venter once did, nearly tenyears isolating and partially purifying asingle adrenergic receptor protein.
ProteomicsAs the rest of the meeting showed,
the old biochemistry is a thing of thepast, evoking nostalgia in some morethan others. Will the Krebs cycle still betaught at the end of this new century?The meeting agenda showed that small-molecule metabolism had disappeared,except for a few exotic outliers. Classicalenzymology had gone long before. DavidHilbert said in the late 1920s that‘physics has become too hard for thephysicists’. Equally, enzyme behaviourbecame too hard for enzymologists atsome point in the late 1950s. Semi-auto-mated screening of protein–protein in-teractions in two-dimensional gel sys-tems (a kind of generalized Westernblot), ‘hybrigenics’, are now being done,in a pseudo-ecological world of ‘preda-tor’, ‘prey’ and ‘bait’ proteins, as de-scribed by Simon Whiteside (Paris,France) and elaborated on by MatthiasMann (Odense, Denmark). Such globalanalyses of multi-protein systems are anessential part of the proteomic approachto full analysis of cell function. How are we to analyse and understand protein–protein interactions?
David Eisenberg (Los Angeles, USA)spoke in Birmingham’s magnificentSymphony Hall. He introduced twoideas in developing a ‘Rosetta Stone’method of determining protein func-tional relationships. The first idea is
that of domain swapping. Many func-tional monomers with multiple do-mains can be induced to form stabledimers by partial (‘soft’) denaturationsin which domain 2 of monomer A bindsto domain 1 of monomer B and viceversa. Such creation of dimers, bothhomo- and heterodimers, might alsohave been an evolutionary event in theformation of protein complexes. Thesecond idea is therefore that ofanalysing protein function by compar-ing genomes. Comparative biochem-istry, the importance of which used tobe emphasized by my supervisor DavidKeilin (who would probably not havediscovered cytochromes had he re-stricted himself to haemoglobin-con-taining organisms), might thus be re-turning in the guise of comparativegenomics. Linkage of two protein genesin one genome can indicate linked functions in their genetically unlinkedrelatives in other genomes.
PrionsProteins ain’t what they used to be.
Their native structures in vivo wereonce thought of as shallowly balanced,thermodynamically unstable versions oftheir ‘dead’ denatured forms. Followingthe triumph of the linear genome andmRNA models of protein synthesis, theybecame molecules existing in low-en-ergy sinks containing only very few,rapidly fluctuating, possible conforma-tions. They are now becoming unstableagain, often vulnerable to autocatalyticconformational changes between a-helix and b-sheet states, reminiscent ofEisenberg’s domain-swapping monomers,but with the catch that the final speciesremains transformed as the monomer.Such, apparently, are prions, as discov-ered by Stanley Prusiner. By luckychance I was in the bar at Cold SpringHarbor in 1997, moments after the radioannouncement of his Nobel prize. Ofcourse, Jim Watson must have known al-ready, and his only comment was ‘ah,Prusiner’. But the prion model has de-veloped into a major exception to thespirit of the central dogma and to theWeismannian ‘DNA alone’ theory of in-heritance. As Prusiner (San Francisco,USA) explained, prions are a complexgroup of proteins with their own genet-ics and examples throughout the livingworld. Their probable involvement inscrapie, BSE and hence new-variant CJDhas made them newsworthy. But neitherphysicochemical understanding at theone end nor therapy at the other seemsyet to be available.
0968 – 0004/00/$ – See front matter © 2000, Elsevier Science Ltd. All rights reserved. PII: S0968-0004(00)01673-X
Looking forward, looking backward
*18th International Congress of Biochemistry andMolecular Biology ‘Beyond the Genome’,Birmingham, UK, 16–20 July 2000.
TIBS 25 – OCTOBER 2000
488
Differentiation and apoptosis‘Meta-metabolism’ – the changes of
DNA function and protein function cre-ated by other proteins – was a centraltheme. Anne Ephrussi (Heidelberg,Germany) returned to the fruit fly andthe molecular biology of its develop-ment, which involves new proteins withfey names and their DNA targets, by uti-lizing both genomics and proteomics.Suzanne Cory (Melbourne, Australia),in one of the best presentations of theweek, dealt with apoptosis. Classicalmetabolism told us ‘how a cell lives’,whereas proteomics is needed to tell‘how a cell dies’. The latter seems muchmore complex than the former. Only thefinal elements of the cascades play a familiar role as the aspartate residue-specific proteolytic caspases. Their ac-tivation and inhibition are a function ofnumerous other proteins, including thedeath promoter Bax, the inhibitor Bcland the Bcl-binding Bim. There is theextra unexpected role of mitochondriain releasing cytochrome c to activatethe caspase complex2. This symbioti-cally acquired organelle seems to playconflicting cellular functions. The major energy generator of the nonphoto-synthetic aerobic cell, it is also themajor producer of reactive oxygenspecies (ROS). The latter are both phys-iological, as discussed by Toren Finkel(Bethesda, USA), and pathophysiologi-cal. A major target is the mitochondrialDNA, as it is less well protected than nu-clear DNA. Is cell suicide therefore anevolutionary result of the mitochon-drion’s own suicidal needs?
Pumps and channelsSometimes, the basics still escape us,
even with proteins whose functionswere known before their structures.Although soluble proteins were notmuch in evidence, proteins as channelsand pumps were, with Peter Mitchell’s‘vectorial chemistry’3 increasingly im-portant for understanding membraneproteins. But despite the beauty of thestructural and dynamic knowledge ofthe mitochondrial and prokaryoticmembrane H1-pumping ATPase (H1-utilizing ATP synthase)4, whose most recent developments were discussed by John Walker (Cambridge, UK), keyfunctional and even stoichiometric in-formation still eludes us. For example,the number of protons translocated forevery ATP synthesized is still uncertain.And so is the relationship between thatratio and the several ratios of proteinsubunits. Sometimes, old certainties
are not only sidelined but lost forever.Walker now thinks that the keyhydrophobic ‘c’ subunits in the mem-branous F0 component are present as aring of ten copies for every F1, the lattera trimer of ab subunits that rotates by120° for every ATP formed or hydro-lysed. If this be translated most simplyinto a H1:ATP ratio, the number be-comes the nonintegral 10/3 5 3.333.Different H1ATPases might have differ-ent ratios. The same ATPase might varyits ratio under different conditions. A fixed H1:ATP ratio and the tradi-tional textbook arguments for overall ATP:glucose ratios in respiration, whichstudents demand to be able to learnand then reproduce under exam condi-tions, might not exist as meaningfulconcepts. This also would be a kind ofbiochemistry that Krebs might havehad difficulty incorporating into hisworld view5.
Pasts and futures‘Jonathan, do not put up the poster.
Call the laboratory.’ – Cyril.(names changed to protect the innocent)This somewhat too public announce-
ment was posted on the message boardby a tactless official for all to see on thesecond day. It was only possible in a cul-ture ‘on the cusp’ between the old era ofindividual responsibility and the futureglobal village of continuous intra-research group communication by cellphone – in which case we shall not evensee such messages. I cannot conceiveKeilin telling me at the last minute not topresent my 10-minute talk at the earliestsuch Congress I attended (the 4th,Vienna, 1958), although I suspect that he might have thought even less of itsscientific usefulness than did Cyril ofJonathan’s poster. Even had he, in a mo-ment of weakness, considered sending
such a message, he certainly would nothave signed it ‘David’.
Did biochemistry, and does molecu-lar biology, provide substantial socialbenefits? Three speakers alluded to dif-ferent levels of societal influence. BillWhelan (Miami, USA), in boldest mil-lenarian mode, spoke of ‘transformingsociety for its betterment’. Julio Celis(Århus, Denmark) merely referred to‘applications that are good for society’,whereas Brian Clark (Århus, Denmark)further narrowed this to ‘transforma-tion of health diagnosis and treatment’.Proteomics, said Venter, might give uscancer vaccines. Greenpeace had notbeen invited, although their position onmedical genomics is more positive thanthat on nutritional and agricultural as-pects. George Poste (Harlow, UK), theconcluding plenary speaker, is a leadingadvocate of the transformation ofmedicine to emphasize preventionbased upon diagnostic knowledge instead of treatment of expressed dis-ease. We can expect a transition ofmedicine from art to technology6. This,he believes, will be economically asmuch as knowledge driven. We nowknow too much, but our resources aretoo modest to treat all the desperatelysick at a level modern medicine wouldregard as adequate. We must thereforeall become medically informed and re-sponsible for our own health, or, as cur-rent feel-good convention would haveit, ‘wellness’. A brave new world.
There was all this and, pace Nabokov,‘much much more’7 at this meeting.More than 2500 took part. I met severalold friends. Others may comment onwhat I have omitted.
References1 Adams, M. D. et al. (2000) The genome sequence of
Drosophila melanogaster. Science 287, 2185–21952 Brown, G.C., Nicholls, D.G. and Cooper, C.E., eds
(1999) Mitochondria and cell death. Biochem. Soc.Symp. 66, Portland Press, London
3 Mitchell, P. (1991) Foundations of vectorial metabolismand osmochemistry. Bioscience Reports 11, 297–346
4 Abrahams, J.P. et al. (1994) Structure at 2.8 Åresolution of F1-ATPase. Nature 370, 621–628
5 Krebs, H.A. and Kornberg, H. L. (1957) EnergyTransformations in Living Matter. Springer-Verlag,Berlin
6 Barnaby, W. and Poste, G. (1999) Shaping the agendafor health-care. In Science, technology and socialresponsibility, pp. 71–73 (Wolpert, L., ed.) The RoyalSociety, London
7 Nabokov, V. (1969) Ada, or Ardor. McGraw-Hill, NewYork
PETER NICHOLLS
Dept of Biological Sciences, University of Essex, Colchester, UK CO4 3SQ.Email: [email protected]
MEETING REPORT
Figure 1The Celera sequencing lab. There are300 automated DNA sequencers in thisroom (ABI 3700). Photograph courtesy ofCelera.
