J. L. Ingraham

M. Schaechter

Schaechter, M.

Ingraham, J. L.

Hemeroteca Cientifica Catalana

EDITORIALM. Schaechter Æ J.L. IngrahamWhat limits genomics, proteomics, transcriptomics?Published online: 29 May 2002 Springer-Verlag and SEM 2002Studies on gene expression at a global scale are beingcarried out with breathtaking speed. Entire genome se-quences, levels of mRNAs and catalogues of all thedetectable proteins in a cell are subjects of almost dailypublications. As with other extraordinary methodolog-ical breakthroughs, the current ones promise nothingshort of a paradigm shift. Biology, accordingly, maybecome largely a computational science, an opinionviewed by some with mixed emotions. Perhaps mostreaders of this journal agree that work along more tra-ditional lines must continue to receive its fair share ofemphasis and that the computer and the bench mustdwell under the same tent.Here, we would like to pose some questions that maynot be answered by global studies alone and that mightrequire both traditional and novel approaches. Formany of these questions, the answers will be slow tocome, a delay that may test the patience of investigators.That is the way of science.Here are some examples of questions that appear tous to surpass the power of present-day global studies:Protein activityHow many of the protein molecules in a cell are active?What are the ‘‘real times’’ of biochemical reactions inliving cells? Does the law of mass action alone determinethe frequency of collision of small numbers of moleculeswith their target ? Analogous questions can be posed formRNAs. The answers are compounded greatly by dif-ferences in the stability between individual molecularspecies. Thus, we are reminded, measuring the totalnumber of molecules present in a cell does not tell ushow many are actually made, leave alone how many areactive.Cellular locationsWhere in the cell are biochemical transactions carriedout? Increasingly, the application of ﬂuorescence andother kinds of microscopy tell us the location of speciﬁcproteins and DNA sequences in cells. However, are thefoci of localized macromolecules revealed by thesemethods the actual site of macromolecular activity orare these aggregates molecular reservoirs? Answeringsuch questions requires quantitation of molecularactivity and discrimination between molecular species,both of which are diﬃcult to achieve. Progress in single-molecule chemistry may well help here. In addition,there is much to learn about the internal milieu of thecell. In the apt words of Mahadevan and Matsudaira‘‘In this soft, wet, and dynamic world, structural featuresare dominated by ﬁlamentous and membranous objects,a constant reminder that all events at this level are me-diated by interfacial interactions’’ [Mahadevan L, Mat-sudaira P (2000) Motility powered by supermolecularsprings and ratchets. Science 288:95–100].Gene expressionThe aim of many global studies is to determine the ef-fects of speciﬁc imposed conditions on gene expressionor protein levels. A grand example is the work done ongene expression in yeast (see http://genome-www.stan-ford.edu/Saccharomyces/). The level of signiﬁcance ofchanges is often set arbitrarily, typically a factor of 2between two conditions. Yet, one can imagine situationsin which a two-fold change in a protein or an mRNAmay have little physiological consequence, and otherswhere a 20% change may be critical. The trouble here isInt Microbiol (2002) 5: 51–52DOI 10.1007/s10123-002-0065-0M. Schaechter (&)Department of Biology, San Diego State University,California, USAE-mail: mschaech@sunstroke.sdsu.eduJ.L. IngrahamDepartment of Microbiology.University of California-Davies, USAthat bioinformatics, in its raw versions, demands a ‘‘onesize ﬁt all’’ criterion of signiﬁcance. With increased so-phistication and a measure of diﬃdence, this problemmay become tractable. Of course, a change is compre-hensible and reproducible only if the starting point isclearly deﬁned. Tragically, many global studies are doneon cultures grown in complex media for an unspeciﬁedperiod. Under such conditions, the composition of themedium and therefore, the physiological state of the cellsis unknown at the starting point. Is it too much to askfor standard experimental conditions?The basis of changes in gene expressionSome of the changes in gene expression or protein levelsdetermined en masse are speciﬁc to the conditions understudy, others not. Some are due to global responses;others are speciﬁcally elicited by the condition imposed.Collecting vast amounts of data may well help sort outwhich is which. Furthermore, why are there so manycircuits to regulate gene expression? In bacteria, therepertoire of control mechanisms is formidable, but thereal life importance of each is elusive. Why so many, andwhen and where do they function?AnnotationFor many reasons, annotation, the attribution of func-tion to genes is a complicated and vexing business. Forexample, many, perhaps most proteins are multifunc-tional and participate in more than one biochemicalactivity, often as part of protein complexes. Moreover,sequential metabolic steps catalyzed by a single multi-functional enzyme in one organism are often catalyzedby several unifunctional enzymes in others. The trypto-phan biosynthesis pathway in bacteria is a worthy ex-ample. Sequence similarity between enzymes withdiﬀerent function is an added complication. Programssettle for a close ﬁt without searching for a closer one.The startlingly excess of malic over lactic dehydrogenaseresulting from computational annotation illustrates thepoint. In addition, backups and redundancies commonlyoccur. Which of the functionally cognate moleculesworks under what circumstances? Annotation (as withthe blind men and the elephant) is giving a single nameto an entity that has several.The morphomeMorphome, the complete structure of the cell, an evermore popular word in computational biology, is be-coming its Holy Grail. But will we, as the word’s cur-rency implies, ever be able to deduce a cell’s totalityfrom its genome sequence? Franklin Harold (and wetoo) think not [Harold FM (2001) The way of the cell:molecules, organisms and the order of life. Oxford Uni-versity Press, Oxford] One problem is the genome’s de-pendence on the cell. A simple example is the synthesisof ATP. Even knowing all gene products and theirfunction, the cleverest computer program would con-sider ATP synthesis impossible unless it was told ADPwas already present in the cell. Many of these questionswill have solutions, some to arise sooner, some later.What lies beyond? In narrow terms, global studies arethe ‘‘what,’’ not the ‘‘where’’ or ‘‘when.’’ Currently,global studies, however sophisticated, are essentiallyenumerative. But, coupled with ‘‘one-gene-at-a-time’’experimentation, global studies will paint for us a grandpicture of when genes are turned on and oﬀ. Let usanticipate the day when coupled studies will have beencarried out as extensively as is reasonable and with astaggering degree of sophistication. We will be able tomake predictions about the structure of proteins andﬁgure out the rules that govern their work. We will thenknow a lot about phenomena such as the cell cycle,developmental processes, responses to mild and not somild environmental stresses, and probably others. Andthat’s not all. Although the horizon of our questions islikely to recede, the acquisition of knowledge is incre-mental and breakthrough feeds on breakthrough.Beyond these considerations, however, remain theoverarching questions of ecology and evolution. Hap-pily, the study of microbes in natural environments isbecoming quite popular. There is increased realizationthat these are not isolated ﬁelds but that they are centralto gaining an understanding of how the pieces of thepuzzle ﬁt together. With novel approaches, we will beable to ask deeper and deeper questions about what it isthat organisms actually do in The Real World.Moselio Schaechter is Distinguished Professor ofMolecular Biology and Microbiology, Emeritus, TuftsUniversity School of Medicine, Boston, Massachusetts,and past president of the American Society for Micro-biology (1986). He lives now in San Diego, California.He coauthored Mechanisms of Microbial Disease,Physiology of the Bacterial Cell, and Escherichia coli andSalmonella. Cellular and Molecular Biology, amongother books.John L. Ingraham is Emeritus Professor, Section ofMicrobiology, University of California, Davis, and pastpresident of the American Society for Microbiology(1993). He has coauthored The Microbial World (sinceits 4th edition), The Growth of the Bacterial Cell, ThePhysiology of the Bacterial Cell and Introduction toMicrobiology (the latter with his daughter CatherineIngraham Vigran). He was Associate Editor of AnnualReview of Microbiology, North American editor ofArchives of Microbiology, and Editor-in-Chief ofMicrobiological Reviews (formerly BacteriologicalReviews and now Microbiological and MolecularBiological Reviews).52

What limits genomics, proteomics, transcriptomics?

http://revistes.iec.cat/revistes/index.php/IM/article/view/5992

What limits genomics, proteomics, transcriptomics?

Abstract

Similar works

Full text

Available Versions

Hemeroteca Cientifica Catalana