The Genom of Homo sapiens.pdf

350 WESTON ET AL.ures prominently in the activity of any given repressor oractivator. The absence of Gal80 alone, for instance, is sufficientfor high-level transcription of the GAL genes(Ideker et al. 2001), and this cofactor has been shown toblock recruitment of SAGA specifically at Gal4-occupiedpromoters (Carrozza et al. 2002). In another example, thetranscription factor Ste12 binds to distinct program-specifictarget genes depending on the developmental condition(i.e., filamentation versus mating). This selectivebinding is dictated by the status of Tec1, a binding partnerfor Ste12 during filamentation but not under conditionsthat induce mating (Zeitlinger et al. 2003). Thus, signaltransduction pathways, controlling the status of a transcriptionfactor partner, can infer program-specific distributionof Ste12 binding (Zeitlinger et al. 2003). In additionto transcription factor partners, cofactors, which aretethered to DNA indirectly through DNA-binding proteins,often serve as adapters to switch transcription on oroff, or to facilitate either process. At the GAL1 promoter,for example, the global Cyc8–Tup1 co-repressor has beenshown to convert from a repressor complex to an activatorcomplex upon binding to the novel protein Cti6 (Papamichos-Chronakiset al. 2002). Cti6 recruits SAGA to theGAL1 promoter, in turn recruiting the basal transcriptionmachinery. Whether Cti6 affects other genes outside ofthe galactose pathway is not yet known. If this factor isspecific for the GAL genes, however, it may infer somelevel of specificity with respect to repression by theCyc8–Tup1 global repressor. To understand the role offactors like Cti6 will require genome-wide binding analysisand protein–protein interaction studies.FUTURE CHALLENGES FORCHARACTERIZING GENE REGULATORYNETWORKSWith ongoing improvements in technologies aimed atstudying gene regulatory networks, we anticipate enormousprogress in the near future toward characterizingthese networks on a global scale. Genome-wide analysishas already been employed on a large scale to identify theDNA targets of most transcription factors in yeast. Althoughthese studies, combined with mounting microarraydata for gene expression changes, provide an excellentbasis for studying regulatory networks, a number ofchallenges remain to fully understand gene regulation.For instance, characterizing protein–DNA interactionsunder different conditions will be critical for understandingany given cellular response. This is emphasized bythe condition-specific binding distributions for Ste12(Zeitlinger et al. 2003). Since most transcriptional eventstake place in response to some environmental change,this is critical. In addition, many transcriptional switchesmay be of a transient nature, necessitating kinetic studiesthat can capture transient interactions. Similarly, profilinggene expression changes, both mRNA and protein,over time will be much more useful for extracting causeand-effectrelationships within gene responses. Despiteall these future challenges, we have clearly demonstratedthe power of systems biology over conventional approachesfor characterizing biological systems. Afteryears of intense research on the galactose system, a systemsapproach revealed new insights and demonstrated amuch more global effect to what has traditionally beenconsidered a simple system.HALOBACTERIUM SP.Halobacterium sp. is an extreme halophile that thrivesin saturated brine environments such as those associatedwith the Dead Sea and solar salterns. It offers a versatileand easily assayed system for an array of well-coordinatedphysiologies that give it an edge for survival in these harshenvironments (DasSarma and Fleischmann 1995; Das-Sarma and Arora 1999; Oren 1999). It has robust DNA repairsystems that can efficiently reverse the damagescaused by a variety of mutagens, including UV radiationand cycles of desiccation and rehydration (McCreadyand Marcello 2003; N.S. Baliga and J. Diruggeiro, unpubl.).Halobacterium sp. responds to anaerobic conditionswith the synthesis of a purple membrane whosemajor component, bacteriorhodopsin, facilitates the conversionof light into ATP (energy). The completely sequencedgenome of Halobacterium sp. has also providedinsights into much of its physiological capabilities; however,nearly two-thirds of all genes encoded in thehalobacterial genome have no known function (Ng et al.1998, 2000).Halobacterium sp. can adapt to both aerobic and anaerobicenvironments in the presence or the absence of lightand, therefore, is an ideal model system for decipheringthe regulatory circuits that coordinate various metabolicpathways in response to frequent changes in oxygen concentrationand light intensity (Fig. 3). In an aerobic environment,Halobacterium sp. flourishes as a chemoheterotrophsurviving on organic remnants of deceased lesserhalophiles incapable of living in extreme 4.5 M salt concentrations.It produces energy predominantly throughrespiration utilizing oxygen as the terminal electron acceptor(Ng et al. 2000). During the aerobic phase, the regulatorycircuits operate through a two-component signaltransduction system comprising the retinal-bound sensoryrhodopsin II (SRII) and its interacting transducerHtrII. When SRII is activated by blue-green light, it transmitsa signal to HtrII exposing methylation sites on thetransducer and transiently alters autophosphorylation activityof a bound histidine kinase (CheA). The consequenceof the resulting phosphorylation–dephosphorylationcascade is the movement of the organism away frombright light to distance itself from damaging UV radiation(Perazzona and Spudich 1999; Luecke et al. 2001; Spudichand Luecke 2002).A drop in oxygen tension results in dramatic changes inHalobacterium sp. physiology, including repression ofthe SRII/HtrII complex and induction of an opposingSRI/HtrI complex (Fig. 3). SRI, unlike SRII, translatesorange light into an attractant stimulus by communicatingwith the flagellar motor through the transducer HtrI. Thelow oxygen tension also induces synthesis of gas vesicles,which are flotation devices that work in conjunctionwith SRI/HtrI to mediate net upward mobility towardsunlight. SRI, upon absorbing orange light, shifts to a