This paper examines whether the in vivo behavior of yeast glycolysis can be understood in terms of the in vitro kinetic properties of the constituent enzymes. In nongrowing, anaerobic, compressed Saccharomyces cerevisiae the values of the kinetic parameters of most glycolytic enzymes were determined. For the other enzymes appropriate literature values were collected. By inserting these values into a kinetic model for glycolysis, fluxes and metabolites were calculated. Under the same conditions fluxes and metabolite levels were measured.In our first model, branch reactions were ignored. This model failed to reach the stable steady state that was observed in the experimental flux measurements. Introduction of branches towards trehalose, glycogen, glycerol and succinate did allow such a steady state. The predictions of this branched model were compared with the empirical behavior. Half of the enzymes matched their predicted flux in vivo within a factor of 2. For the other enzymes it was calculated what deviation between in vivo and in vitro kinetic characteristics could explain the discrepancy between in vitro rate and in vivo flux.

In Escherichia coli, a signal recognition particle (SRP) has been identified which binds specifically to the signal sequence of presecretory proteins and which appears to be essential for efficient translocation of a subset of proteins. In this study we have investigated the function of E. coli FtsY which shares sequence similarity with the alpha‐subunit of the eukaryotic SRP receptor (‘docking protein’) in the membrane of the endoplasmic reticulum. A strain was constructed which allows the conditional expression of FtsY. Depletion of FtsY is shown to cause the accumulation of the precursor form of beta‐lactamase, OmpF and ribose binding protein in vivo, whereas the processing of various other presecretory proteins is unaffected. Furthermore, FtsY‐depleted inverted cytoplasmic membrane vesicles are shown to be defective in the translocation of pre‐beta‐lactamase using an in vitro import assay. Subcellular localization studies revealed that FtsY is located in part at the cytoplasmic membrane with which it seems peripherally associated. These observations suggest that FtsY is the functional E. coli homolog of the mammalian SRP receptor.

An important question is to what extent metabolic fluxes are regulated by gene expression or by metabolic regulation. There are two distinct aspects to this question: (i) the local regulation of the fluxes through the individual steps in the pathway and (ii) the influence of such local regulation on the pathway's flux. We developed regulation analysis so as to address the former aspect for all steps in a pathway. We demonstrate the method for the issue of how Saccharomyces cerevisiae regulates the fluxes through its individual glycolytic and fermentative enzymes when confronted with nutrient starvation. Regulation was dissected quantitatively into (i) changes in maximum enzyme activity (V max, called hierarchical regulation) and (ii) changes in the interaction of the enzyme with the rest of metabolism (called metabolic regulation). Within a single pathway, the regulation of the fluxes through individual steps varied from fully hierarchical to exclusively metabolic. Existing paradigms of flux regulation (such as single-and multisite modulation and exclusively metabolic regulation) were tested for a complete pathway and falsified for a major pathway in an important model organism. We propose a subtler mechanism of flux regulation, with different roles for different enzymes, i.e., ''leader,'' ''follower,'' or ''conservative,'' the latter attempting to hold back the change in flux. This study makes this subtlety, so typical for biological systems, tractable experimentally and invites reformulation of the questions concerning the drives and constraints governing metabolic flux regulation.gene expression and metabolic regulation ͉ glycolysis ͉ regulation analysis ͉ metabolic control analysis T he flux through a metabolic pathway is determined by the activities of its enzymes and by their interactions with other enzymes. Metabolic-flux changes have often been observed in response to environmental or genetic changes. In the yeast Saccharomyces cerevisiae, for example, changes in glycolytic flux have frequently been found to be accompanied by a myriad of changes in glycolytic enzyme activities (e.g., 1, 2, this work) or amounts (3), which varied in magnitude and direction. The complexity of interactions between enzymes translates into a vast possibility space of combinations of enzyme-activity modulations leading to the same flux change. We wondered how the cell actually regulates its fluxes.Among the proposed mechanisms for metabolic-flux changes, the two clearest hypotheses are (i) modulation of single ratelimiting enzymes and (ii) multisite modulation, i.e., simultaneous and proportional modulation of all enzymes in the pathway, thus causing a change in flux while leaving metabolite concentrations unchanged (4). Although single rate-limiting enzymes exist, control of flux is quite often distributed over several enzymes (5). In the latter case, modulation of a single enzyme is likely to be an ineffective mechanism for changing a pathway's flux. Indeed, attempts to correlate flux changes with changes in single enzyme ac...

An effector strain has been constructed for use in the replacement therapy of dental caries. Recombinant DNA methods were used to make the Streptococcus mutans supercolonizing strain, JH1140, lactate dehydrogenase deficient by deleting virtually all of the ldh open reading frame (ORF). To compensate for the resulting metabolic imbalance, a supplemental alcohol dehydrogenase activity was introduced by substituting the adhB ORF from Zymomonas mobilis in place of the deleted ldh ORF. The resulting clone, BCS3-L1, was found to produce no detectable lactic acid during growth on a variety of carbon sources, and it produced significantly less total acid due to its increased production of ethanol and acetoin. BCS3-L1 was significantly less cariogenic than JH1140 in both gnotobiotic-and conventional-rodent models. It colonized the teeth of conventional rats as well as JH1140 in both aggressive-displacement and preemptive-colonization models. No gross or microscopic abnormalities of major organs were associated with oral colonization of rats with BCS3-L1 for 6 months. Acid-producing revertants of BCS3-L1 were not observed in samples taken from infected animals (reversion frequency, <10 ؊3 ) or by screening cultures grown in vitro, where no revertants were observed among 10 5 colonies examined on pH indicator medium. The reduced pathogenic potential of BCS3-L1, its strong colonization potential, and its genetic stability suggest that this strain is well suited to serve as an effector strain in the replacement therapy of dental caries in humans.

DNA of prokaryotes is in a nonequilibrium structural state, characterized as ÔactiveÕ DNA supercoiling. Alterations in this state a ect many life processes and a homeostatic control of DNA supercoiling has been suggested [Menzel, R. & Gellert, M. (1983) Cell 34, 105±113]. We here report on a new method for quantifying homeostatic control of the high-energy state of in vivo DNA. The method involves making small perturbation in the expression of topoisomerase I, and measuring the e ect on DNA supercoiling of a reporter plasmid and on the expression of DNA gyrase. In a separate set of experiments the expression of DNA gyrase was manipulated and the control on DNA supercoiling and topoisomerase I expression was measured [part of these latter experiments has been published in Jensen, P.R., van der Weijden, C.C., Jensen, L.B., Westerho , H.V. & Snoep, J.L. (1999) Eur. J. Biochem. 266, 865±877]. Of the two regulatory mechanisms via which homeostasis is conferred, regulation of enzyme activity or regulation of enzyme expression, we quanti®ed the ®rst to be responsible for 72% and the latter for 28%. The gene expression regulation could be dissected to DNA gyrase (21%) and to topoisomerase I (7%). On a scale from 0 (no homeostatic control) to 1 (full homeostatic control) we quanti®ed the homeostatic control of DNA supercoiling at 0.87. A 10% manipulation of either topoisomerase I or DNA gyrase activity results in a 1.3% change of DNA supercoiling only. We conclude that the homeostatic regulation of the nonequilibrium DNA structure in wild-type Escherichia coli is almost complete and subtle (i.e. involving at least three regulatory mechanisms).Keywords: metabolic control analysis (MCA); hierarchical control analysis (HCA); homeostasis coe cient.DNA in the bacterial nucleoid is negatively supercoiled and it has been estimated that roughly 50% of the supercoiling is constrained by proteins binding to the DNA [1]. This constraint does not depend on the continuous expenditure of ATP. The remaining supercoils are maintained actively at the cost of ATP hydrolysis, via topoisomerase activities. Four topoisomerases have been identi®ed in Escherichia coli (reviewed in [2]). Topoisomerase I [3,4] and DNA gyrase (topoisomerase II) are mostly held responsible for maintaining the supercoiled state of the DNA while topoisomerase III and IV manage the decatenation reactions. A recent publication suggested that topoisomerase IV may also be important for the relaxation of DNA supercoiling [5].The importance of DNA gyrase and topoisomerase I for supercoiling has been shown in studies involving mutants with activities differing greatly from the wild-type activity. Such studies cannot be used to assess the homeostasis of supercoiling in the physiological situation, where the response to smaller challenges is important. When challenged suf®ciently, all systems will respond in drastic manners, or fail. It may well be that a system is robust with respect to small challenges, whilst it fails to deal with the same but larger challenges, or vice v...

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A novel method dissecting the regulation of a cellular function into direct metabolic regulation and hierarchical (e.g., gene-expression) regulation is applied to yeast starved for nitrogen or carbon. Upon nitrogen starvation glucose influx is down-regulated hierarchically. Upon carbon starvation it is down-regulated both metabolically and hierarchically. The method is expounded in terms of its implications for diverse types of regulation. It is also fine-tuned for cases where isoenzymes catalyze the flux through a single metabolic step.

tbstract In this study, we have established that FtsY, the E. coil homolog of the mammalian signal recognition particle (SRP) receptor, is a GTP-binding protein which displays intrinsic GTPase activity. GTP was found to influence the protease sensil ivity of FtsY indicative of a conformational change. FtsY mutated in the 4th GTP-binding consensus element displayed reduced GTP-binding and -hydrolysis which correlated with a reduced ability to interact with SRP. Overexpression of the mutant proteins had a stronger inhibitory effect on protein translocation than overexpression of wild-type FtsY. These observations sugzest that in E. coli GTP is important for proper functioning of ~tsY in protein-targeting.