The cost of enzyme synthesis in the genetics of energy balance and physiological performance

The genotype-phenotype relationship and evolutionary genetics in the light of the Metabolic Control Analysis

Metabolic control analysis has long been used as a systemic model of the genotype-phenotype (GP) relationship. By considering kinetic parameters and enzyme concentrations as reflecting the genotype level and metabolic fluxes or pools as phenotypes related to fitness, MCA has given a biological basis to the relationship between these two levels. The non-linear and concave relationship between enzymes and fluxes can account for common genetic effects that reductionist approaches have been powerless to explain, such as the dominance of active alleles over less active alleles, the various types of epistasis and heterosis, and reveals the structural links between these genetic effects. The summation property of the flux control coefficients accounts for the L-shaped distribution of Quantitative Trait Locus (QTL) effects, irrespective of other possible causes. Metabolic models of response to selection results in evolutionary scenarios that are markedly different from those derived from the classical infinitesimal model of quantitative genetics. In particular, evolution towards selective neutrality appears to be a consequence of the diminishing return of the flux-enzyme relationship. In this paper, we survey the historical and recent achievements of MCA in genetics, quantitative genetics and evolution, focusing on epistasis and the evolution of flux in relation to enzyme concentrations.

Evolution of enzyme levels in metabolic pathways: A theoretical approach. Part 2

Metabolism is essential for cell function and adaptation. Because of their central role in metabolism, kinetic parameters and enzyme concentrations are under constant selective pressure to adapt the fluxes of the metabolic networks to the needs of the organism. In line with various studies dealing with enzyme evolution, we recently developed a model of the evolution of enzyme concentrations under selection for increased flux, considered as a proxy for fitness (Coton et al., 2022). With this model, taking into account two realistic cellular constraints, competition for resources and co-regulation, we determined the evolutionary equilibria and range of neutral variations of enzyme concentrations. In this article, we expanded this model by considering that the enzymes in a pathway can belong to different co-regulation groups. We determined the equilibria and showed that the constraints modify the adaptive landscape by limiting the number of independent dimensions. We also showed that any trade-off between enzyme concentrations is sufficient to limit the flux and relax selection for increasing the concentration of other enzymes. Even though this model is based on simplifying assumptions, the complexity of the relationship between enzyme concentrations prevents the formal analysis of the range of neutral variation of enzyme concentrations. However, we could show that selection for maximizing the flux results in selective neutrality for all enzymes regardless the constraints applied, giving generality to the prediction of Hartl et al. (1985).

Tryptophan-96 in cytochrome P450 BM3 plays a key role in enzyme survival

Flavocytochrome P450 from Bacillus megaterium (P450BM3 ) is a natural fusion protein containing reductase and heme domains. In the presence of NADPH and dioxygen the enzyme catalyses the hydroxylation of long-chain fatty acids. Analysis of the P450BM3 structure reveals chains of closely spaced tryptophan and tyrosine residues that might serve as pathways for high-potential oxidizing equivalents to escape from the heme active site when substrate oxidation is not possible. Our investigations of the total number of enzyme turnovers before deactivation have revealed that replacement of selected tryptophan and tyrosine residues with redox inactive groups leads to a twofold reduction in enzyme survival time. Tryptophan-96 is critical for prolonging enzyme activity, suggesting a key protective role for this residue.

Evolution of enzyme levels in metabolic pathways: A theoretical approach

The central role of metabolism in cell functioning and adaptation has given rise to countless studies on the evolution of enzyme-coding genes and network topology. However, very few studies have addressed the question of how enzyme concentrations change in response to positive selective pressure on the flux, considered a proxy of fitness. In particular, the way cellular constraints, such as resource limitations and co-regulation, affect the adaptive landscape of a pathway under selection has never been analyzed theoretically. To fill this gap, we developed a model of the evolution of enzyme concentrations that combines metabolic control theory and an adaptive dynamics approach, and integrates possible dependencies between enzyme concentrations. We determined the evolutionary equilibria of enzyme concentrations and their range of neutral variation, and showed that they differ with the properties of the enzymes, the constraints applied to the system and the initial enzyme concentrations. Simulations of long-term evolution confirmed all analytical and numerical predictions, even though we relaxed the simplifying assumptions used in the analytical treatment.

Energy expenses on prey processing are comparable, but paid at a higher metabolic scope and for a longer time in ambush vs active predators: a multispecies study on snakes

Snakes are characterized by distinct foraging strategies, from ambush to active hunting, which can be predicted to substantially affect the energy budget as a result of differential activity rates and feeding frequencies. Intense foraging activity and continuously upregulated viscera as a result of frequent feeding leads to a higher standard metabolic rate (SMR) in active than in ambush predators. Conversely, the costs of digestion (Specific Dynamic Action—SDA) are expected to be higher in ambush predators following the substantial remodelling of the gut upon ingestion of a meal after a long fasting period. This prediction was tested on an interspecific scale using a large multispecies dataset (> 40 species) obtained from published sources. I found that the metabolic scope and duration of SDA tended to reach higher values in ambush than in active predators, which probably reflects the greater magnitude of postprandial physiological upregulation in the former. In contrast, the SDA energy expenditure appeared to be unrelated to the foraging mode. The costs of visceral activation conceivably are not negligible, but represent a minor part of the total costs of digestion, possibly not large enough to elicit a foraging-mode driven variation in SDA energy expenditure. Non-mutually exclusive is that the higher costs of structural upregulation in ambush predators are balanced by the improved, thus potentially less expensive, functional performance of the more efficient intestines. I finally suggest that ambush predators may be less susceptible than active predators to the metabolic ‘meltdown effect’ driven by climate change.

The number of catalytic cycles in an enzyme's lifetime and why it matters to metabolic engineering

The continuous replacement of enzymes and other proteins appropriates up to half the maintenance energy budget in microorganisms and plants. High enzyme replacement rates therefore cut the productivity of biosystems ranging from microbial fermentations to crops. However, yardsticks to assess what drives enzyme protein replacement and guidelines on how to reduce it are lacking. Accordingly, we compared enzymes’ life spans across kingdoms using a new yardstick (catalytic cycles until replacement [CCR]) and related CCR to enzyme reaction chemistry. We concluded that 1) many enzymes fail due to collateral damage from the reaction they catalyze, and 2) such damage and its attendant enzyme replacement costs are mitigable by engineering and are therefore promising targets for synthetic biology.

Metabolic engineering uses enzymes as parts to build biosystems for specified tasks. Although a part’s working life and failure modes are key engineering performance indicators, this is not yet so in metabolic engineering because it is not known how long enzymes remain functional in vivo or whether cumulative deterioration (wear-out), sudden random failure, or other causes drive replacement. Consequently, enzymes cannot be engineered to extend life and cut the high energy costs of replacement. Guided by catalyst engineering, we adopted catalytic cycles until replacement (CCR) as a metric for enzyme functional life span in vivo. CCR is the number of catalytic cycles that an enzyme mediates in vivo before failure or replacement, i.e., metabolic flux rate/protein turnover rate. We used estimated fluxes and measured protein turnover rates to calculate CCRs for ∼100–200 enzymes each from Lactococcus lactis, yeast, and Arabidopsis. CCRs in these organisms had similar ranges (<10³ to >10⁷) but different median values (3–4 × 10⁴ in L. lactis and yeast versus 4 × 10⁵ in Arabidopsis). In all organisms, enzymes whose substrates, products, or mechanisms can attack reactive amino acid residues had significantly lower median CCR values than other enzymes. Taken with literature on mechanism-based inactivation, the latter finding supports the proposal that 1) random active-site damage by reaction chemistry is an important cause of enzyme failure, and 2) reactive noncatalytic residues in the active-site region are likely contributors to damage susceptibility. Enzyme engineering to raise CCRs and lower replacement costs may thus be both beneficial and feasible.

Linking post-translational modifications and variation of phenotypic traits

Enzymes can be post-translationally modified, leading to isoforms with different properties. The phenotypic consequences of the quantitative variability of isoforms have never been studied. We used quantitative proteomics to dissect the relationships between the abundances of the enzymes and isoforms of alcoholic fermentation, metabolic traits, and growth-related traits in Saccharomyces cerevisiae. Although the enzymatic pool allocated to the fermentation proteome was constant over the culture media and the strains considered, there was variation in abundance of individual enzymes and sometimes much more of their isoforms, which suggests the existence of selective constraints on total protein abundance and trade-offs between isoforms. Variations in abundance of some isoforms were significantly associated to metabolic traits and growth-related traits. In particular, cell size and maximum population size were highly correlated to the degree of N-terminal acetylation of the alcohol dehydrogenase. The fermentation proteome was found to be shaped by human selection, through the differential targeting of a few isoforms for each food-processing origin of strains. These results highlight the importance of post-translational modifications in the diversity of metabolic and life-history traits.

A novel approach for determining environment-specific protein costs: the case of Arabidopsis thaliana

Motivation: Comprehensive understanding of cellular processes requires development of approaches which consider the energetic balances in the cell. The existing approaches that address this problem are based on defining energy-equivalent costs which do not include the effects of a changing environment. By incorporating these effects, one could provide a framework for integrating ‘omics’ data from various levels of the system in order to provide interpretations with respect to the energy state and to elicit conclusions about putative global energy-related response mechanisms in the cell.

Results: Here we define a cost measure for amino acid synthesis based on flux balance analysis of a genome-scale metabolic network, and develop methods for its integration with proteomics and metabolomics data. This is a first measure which accounts for the effect of different environmental conditions. We applied this approach to a genome-scale network of Arabidopsis thaliana and calculated the costs for all amino acids and proteins present in the network under light and dark conditions. Integration of function and process ontology terms in the analysis of protein abundances and their costs indicates that, during the night, the cell favors cheaper proteins compared with the light environment. However, this does not imply that there is squandering of resources during the day. The results from the association analysis between the costs, levels and well-defined expenses of amino acid synthesis, indicate that our approach not only captures the adjustment made at the switch of conditions, but also could explain the anticipation of resource usage via a global energy-related regulatory mechanism of amino acid and protein synthesis.

Contact:nikoloski@mpimp-golm.mpg.de

Supplementary information:Supplementary data are available at Bioinformatics online.

Systemic properties of metabolic networks lead to an epistasis-based model for heterosis

The genetic and molecular approaches to heterosis usually do not rely on any model of the genotype-phenotype relationship. From the generalization of Kacser and Burns' biochemical model for dominance and epistasis to networks with several variable enzymes, we hypothesized that metabolic heterosis could be observed because the response of the flux towards enzyme activities and/or concentrations follows a multi-dimensional hyperbolic-like relationship. To corroborate this, we used the values of systemic parameters accounting for the kinetic behaviour of four enzymes of the upstream part of glycolysis, and simulated genetic variability by varying in silico enzyme concentrations. Then we "crossed" virtual parents to get 1,000 hybrids, and showed that best-parent heterosis was frequently observed. The decomposition of the flux value into genetic effects, with the help of a novel multilocus epistasis index, revealed that antagonistic additive-by-additive epistasis effects play the major role in this framework of the genotype-phenotype relationship. This result is consistent with various observations in quantitative and evolutionary genetics, and provides a model unifying the genetic effects underlying heterosis.

Lipid remodeling in wild and selectively bred hard clams at low temperatures in relation to genetic and physiological parameters

A temperature decrease usually induces an ordering effect in membrane phospholipids, which can lead to membrane dysfunction. Poikilotherms inhabiting eurythermal environments typically counteract this temperature effect by remodeling membrane lipids as stipulated in the homeoviscous adaptation theory (HVA). Hard clams, Mercenaria mercenaria, can suffer high overwintering mortalities in the Gulf of St Lawrence, Canada. The selectively bred M. mercenaria var. notata can have higher overwintering mortalities than the wild species, thus suggesting that the two varieties have different degrees of adaptation to low temperatures. The objective of this study was to investigate the changes in lipid composition of soft tissues in wild and selected hard clams in relation to their metabolic and genetic characteristics. Clams were placed at the northern limit of their distribution from August 2003 to May 2004; they were exposed to a gradual temperature decrease and then maintained at <0 degrees C for 3.5 months. This study is the first to report a major remodeling of lipids in this species as predicted by HVA; this remodeling involved a sequential response of the phospholipid to sterol ratio as well as in levels of 22:6n-3 and non-methylene interrupted dienoic fatty acids. Hard clams showed an increase in 20:5n-3 as temperature decreased, but this was not maintained during overwintering, which suggests that 20:5n-3 may have been used for eicosanoid biosynthesis as a stress response to environmental conditions. Selectively bred hard clams were characterized by a higher metabolic demand and a deviation from Hardy-Weinberg equilibrium at several genetic loci due to a deficit in heterozygote frequency compared with wild clams, which is believed to impose additional stress and render these animals more vulnerable to overwintering mortality. Finally, an intriguing finding is that the lower metabolic requirements of wild animals coincide with a lower unsaturation index of their lipids, as predicted by Hulbert's theory of membranes as pacemakers of metabolism.

An extension to the metabolic control theory taking into account correlations between enzyme concentrations

The classical metabolic control theory [Kacser, H. & Burns, J.A. (1973) Symp. Soc. Exp. Biol.27, 65-104; Heinrich, R. & Rapoport, T. (1974) Eur. J. Biochem.42, 89-95.] does not take into account experimental evidence for correlations between enzyme concentrations in the cell. We investigated the implications of two causes of linear correlations: competition between enzymes, which is a mere physical adaptation of the cell to the limitation of resources and space, and regulatory correlations, which result from the existence of regulatory networks. These correlations generate redistribution of enzyme concentrations when the concentration of an enzyme varies; this may dramatically alter the flux and metabolite concentration curves. In particular, negative correlations cause the flux to have a maximum value for a defined distribution of enzyme concentrations. Redistribution coefficients of enzyme concentrations allowed us to calculate the 'combined response coefficient' that quantifies the response of flux or metabolite concentration to a perturbation of enzyme concentration.

Resting metabolic expenditure as a potential source of variation in growth rates of the sagebrush lizard

Along an elevational gradient on SW Utah, sagebrush lizards (Sceloporus graciosus) exhibit an unexpected pattern of growth. Lizards from a high elevation population grow faster than lizards from two populations at lower elevations despite shorter daily and seasonal activity. Results from a common environment study of growth suggest that the differences in growth are not due to adaptation to local environmental conditions. In this study, I test the hypothesis that higher growth rates in lizards from high elevation may be attributable to reduced resting metabolic expenditure compared to that of lizards from populations at two lower elevations. Resting metabolic rates were measured for individuals from each of the study populations across different times of day and over a broad range of temperatures. Under the same laboratory conditions, field-caught lizards from the high elevation population exhibited lower metabolic rates when compared to lizards from lower elevations. Daily resting metabolic expenditures were calculated using the observed metabolic rates coupled with estimates of daily activity. Daily resting metabolic expenditure was 50% greater for individuals from the two lower elevation populations, which could result in 12.5% more energy that could be potentially allocated to growth for lizards from high elevation. Such energetic savings may be able to explain differences in the patterns of growth observed in nature.

Relations between variable rates of growth, metabolic costs and growth efficiencies in individual Sydney rock oysters (Saccostrea commercialis)

Rock oysters from a mass selection trial were compared with wild-caught (control) oysters of the same age to determine the physiological basis for faster growth rates amongst the selected individuals, and to describe the associated flexibility in phenotypic traits of feeding, metabolism and growth. In confirmation of earlier studies, fast growth was associated with faster rates of feeding, reduced metabolic rates and lower metabolic costs of growth. Selected individuals deposited more protein, at a lower metabolic cost, than the controls. Control oysters, however, deposited more lipid than the selected oysters, though the unit costs of lipid deposition did not differ between categories. The results indicated a wide plasticity of physiological rates and efficiencies and demonstrated how, by selection, interactions between physiological traits can serve to enhance growth. If differences in lipid deposition observed here were indicative of different rates of gametogenesis, then the results also suggest that selection alters the balance between growth and reproduction. Whether these differences can be termed compensatory with respect to the life history of the species remains to be determined, but the results indicate some of the ways in which physiological flexibility may be expressed to effect different patterns of energy allocation.

Effects of 5-fluorouracil on macromolecular synthesis during secondary palate development in quail

A study was undertaken to examine the growth of normal and 5-fluorouracil-treated quail secondary palate during embryogenesis. The rates of DNA, RNA, and protein synthesis were measured in the developing quail palate by liquid scintillation counting of radiolabelled thymidine, uridine, or leucine. In addition, shelf volume was determined morphometrically. The results showed that in control palates the shelf volume increased rapidly between days 5 and 7 of incubation. Drug treatment on day 4 did not alter the shelf volume until day 9 of incubation, at which time the treated shelves were smaller than controls. In control palates, the rate of DNA synthesis decreased steadily between days 5 and 9 of incubation. A burst in RNA synthesis on day 7 of incubation was followed by an increase in protein synthesis. Administration of FU seems to exert its effect via disturbing the synthesis of RNA and protein, instead of disruption of DNA synthesis, to ultimately affect the shelf area, and thus palate morphogenesis in quail. Comparison of avian and mammalian data indicated that differences in their palate morphogenesis are also reflected in the different temporal patterns of various macromolecular synthesis.

Cost of growth in cells and organisms: general rules and comparative aspects

In a crude fashion it can be said that metabolizable energy (M) is partitioned into metabolic work, paid for by 'oxidations' (R), and 'assimilation', i.e. production (P), so that M = R+P. However, a fraction of R is required to meet the expenses of production and if these expenses represent, Joule for Joule, a constant proportion of the amount produced, then Rt = Rm+cP, where Rt = total metabolic expenditures, Rm = metabolic expenditures for maintaining the non-producing organism, and cP = Rp = metabolic expenditures connected with the processes of production. The partitioning of metabolizable energy into R and P as well as into Rm and Rp may vary depending on the phylogeny and life-history of the species concerned and on ecological circumstances. Thus selection is expected to act on both ratios, R/P and Rm/Rp. By comparing the ratios P/(P+Rp) (the apparent efficiency of production) and Rp/P (the apparent metabolic cost of production) in different types of organisms, one finds that a value of P/(P+Rp) = 0.75, equal to 75% efficiency, 10 mgdbm/mmol ATP, and 16 mumolO2/mg dbm (when I mg identical to 22 J), can be used as a 'consensus value' for the average efficiency, or cost, of the transformation of metabolizable energy into production in a wide range of organisms, from bacteria to mammals. This value corresponds to about three times the theoretical cost of synthesizing the same amount of tissue on the basis of known biochemical principles. The reasons why the empirical costs of production are higher than the theoretical costs of synthesis by what appears to be a common factor may be quite different in bacteria, small ectothermic and large endothermic organisms. Deviations from the consensus value may be due to differences in energy density of the nutrients assimilated and the tissues synthesized. Further complications arise because of interactions between P, Rp, and Rm. In microorganisms the existence of a constant and a variable component of maintenance metabolism has been postulated, the latter decreasing with increasing rate of production. In small ectothermic metazoans, on the other hand, the nonlinear relationship between growth metabolism and growth rate has led to the speculation that above a critical value of Pg certain energy consuming functions of maintenance are suppressed and the energy thus gained used for fuelling growth processes. There is some evidence that, at least in ectothermic metazoans, the apparent cost of growth decreases with the rate of growth, reaching a low plateau of about 10 mumolO2/mgdbm at growth rates exceeding about 8 mgdbm/g/h.(ABSTRACT TRUNCATED AT 400 WORDS)

The population genetics of alleles affecting enzyme activity

It is possible to predict the population genetics of allozymes by assuming that fitness is proportional to flux through a biochemical pathway. The model presented here extends previous work by incorporating two additional features of biological realism. Firstly, that more than one biochemical route may exist between any two metabolites. The major routes have been identified as the classical biochemical pathways but in the event of a mutation blocking a major route, minor routes become significant. These minor routes are named "bypass fluxes" and have profound effects on the population genetics of allozymes. Secondly, recent work has suggested that a metabolic cost is associated with enzyme synthesis; this will constitute an additional selective pressure on alleles which affect the amount of enzyme synthesized. The model generates a fitness curve which predicts the fitness associated with any level of enzyme activity. It can utilize data on null or near-null, structural or regulatory, mutations in the presence or absence of bypass fluxes. When data from natural populations of Drosophila are investigated, it is concluded that selection pressures acting on enzyme variants may be much higher than previously thought.