Structural Phylogenomics Reveals Gradual Evolutionary Replacement of Abiotic Chemistries by Protein Enzymes in Purine Metabolism

The origin of metabolism has been linked to abiotic chemistries that existed in our planet at the beginning of life. While plausible chemical pathways have been proposed, including the synthesis of nucleobases, ribose and ribonucleotides, the cooption of these reactions by modern enzymes remains shrouded in mystery. Here we study the emergence of purine metabolism. The ages of protein domains derived from a census of fold family structure in hundreds of genomes were mapped onto enzymes in metabolic diagrams. We find that the origin of the nucleotide interconversion pathway benefited most parsimoniously from the prebiotic formation of adenine nucleosides. In turn, pathways of nucleotide biosynthesis, catabolism and salvage originated ∼300 million years later by concerted enzymatic recruitments and gradual replacement of abiotic chemistries. Remarkably, this process led to the emergence of the fully enzymatic biosynthetic pathway ∼3 billion years ago, concurrently with the appearance of a functional ribosome. The simultaneous appearance of purine biosynthesis and the ribosome probably fulfilled the expanding matter-energy and processing needs of genomic information.     

The DNA damage response: making it safe to play with knives

Damage to our genetic material is an ongoing threat to both our ability to faithfully transmit genetic information to our offspring as well as our own survival. To respond to these threats, eukaryotes have evolved the DNA damage response (DDR). The DDR is a complex signal transduction pathway that has the ability to sense DNA damage and transduce this information to the cell to influence cellular responses to DNA damage. Cells possess an arsenal of enzymatic tools capable of remodeling and repairing DNA; however, their activities must be tightly regulated in a temporal, spatial, and DNA lesion-appropriate fashion to optimize repair and prevent unnecessary and potentially deleterious alterations in the structure of DNA during normal cellular processes. This review will focus on how the DDR controls DNA repair and the phenotypic consequences of defects in these critical regulatory functions in mammals.     

Mitochondrial enzymatic adaptation of skeletal muscle to endurance training.

Some mitochondrial enzymatic activities (succinate dehydrogenase, NADH cytochrome reductase, cytochrome oxidase) were studied in the gastrocnemius and soleus muscle of the rat. The modifications of the enzyme activity, induced by endurance training, were found to be functions of 1) daily work load and 2) total training time. The treatment with an effective dose of vasodilating substances (papaverine, nicergoline, dipyridamole, and bamethan) showed that 1) nicergoline, bamethan, and dipyridamole were differently able to shorten the time of appearance of the increase in the enzymatic activities; 2) however, long-term treatments with these drugs did not prove able to modify the plateau level of the enzymatic activity increase, for a given amount of endurance training; 3) the pharmacodynamic effect on enzymatic activities was in no way related to the vasodilating effect of these drugs, since the effect was not observed with papaverine. The transition from a given level of endurance training to a lower one led to a proportional decrease of the mitochondrial enzymatic activities, thus pointing out the relation between amount of training and enzymatic activity. The drugs studied were unable to modify the decrease of enzymatic activity induced by lower work load.     

Reconstructing a missing link in the evolution of a recently diverged phosphotriesterase by active-site loop remodeling

Only decades after the introduction of organophosphate pesticides, bacterial phosphotriesterases (PTEs) have evolved to catalyze their degradation with remarkable efficiency. Their closest known relatives, lactonases, with promiscuous phosphotriasterase activity, dubbed PTE-like lactonases (PLLs), share only 30% sequence identity and also differ in the configuration of their active-site loops. PTE was therefore presumed to have evolved from a yet unknown PLL whose primary activity was the hydrolysis of quorum sensing homoserine lactones (HSLs) (Afriat et al. (2006) Biochemistry45, 13677-13686). However, how PTEs diverged from this presumed PLL remains a mystery. In this study we investigated loop remodeling as a means of reconstructing a homoserine lactonase ancestor that relates to PTE by few mutational steps. Although, in nature, loop remodeling is a common mechanism of divergence of enzymatic functions, reproducing this process in the laboratory is a challenge. Structural and phylogenetic analyses enabled us to remodel one of PTE's active-site loops into a PLL-like configuration. A deletion in loop 7, combined with an adjacent, highly epistatic, point mutation led to the emergence of an HSLase activity that is undetectable in PTE (k(cat)/K(M) values of up to 2 × 10(4)). The appearance of the HSLase activity was accompanied by only a minor decrease in PTE's paraoxonase activity. This specificity change demonstrates the potential role of bifunctional intermediates in the divergence of new enzymatic functions and highlights the critical contribution of loop remodeling to the rapid divergence of new enzyme functions.     

Oxidation of the flavonoid eriodictyol by tyrosinase.

A pathway is proposed for the oxidation of the flavonoid eriodictyol by mushroom tyrosinase. In it, the enzymatic oxidation of eriodictyol leads to the formation of eriodictyol-o-quinone, which undergoes the nucleophilic attack of another eriodictyol unit to yield a dimer. This dimer is then oxidized by the eriodictyol-o-quinone. The reaction was followed by recording the time course of formation of this second o-quinone at 475 nm. Progress curves at this wavelength showed the appearance of a lag, the length of which varied with enzyme and substrate concentrations, and which must have been caused by the chemical reactions taking place after the enzymatic reaction. When eriodictyol oxidation was studied in the presence of 3-methyl-2-benzothiazolinone hydrazone hydrochloride (MBTH), which competes with the substrate in the reaction with eriodictyol-o-quinone, the lag disappeared. The kinetic parameters were similar with and without MBTH. Eriodictyol oxidation was inhibited by tropolone, which behaved as a slow-binding inhibitor.     

Reverse-engineering of biochemical reaction networks from spatio-temporal correlations of fluorescence fluctuations

Recent developments of fluorescence labeling and highly advanced microscopy techniques have enabled observations of activities of biosignaling molecules in living cells. The high spatial and temporal resolutions of these video microscopy experiments allow detection of fluorescence fluctuations at the timescales approaching those of enzymatic reactions. Such fluorescence fluctuation patterns may contain information about the complex reaction-diffusion system driving the dynamics of the labeled molecule. Here, we have developed a method of identifying the reaction-diffusion system of fluorescently labeled signaling molecules in the cell, by combining spatio-temporal correlation function analysis of fluctuating fluorescent patterns, stochastic reaction-diffusion simulations, and an iterative system identification technique using a simulated annealing algorithm. In this report, we discuss the validity and usability of spatio-temporal correlation functions in characterizing the reaction-diffusion dynamics of biomolecules, and demonstrate application of our reaction-diffusion system identification method to a simple conceptual model for small GTPase activation.     

Cyclic nucleotide phosphodiesterase in vertebrates

The cellular concentration of cyclic nucleotides is largely dependent upon the activity of the enzymatic system responsible for their degradation: cyclic nucleotide phosphodiesterase. This enzymatic system thus plays a crucial role in the regulation of the multiple functions which are modulated by cyclic nucleotides in the organism. Many methodological problems, as well as the complexity of the phosphodiesterase system have long maintained a confusion in this field. Recent progresses (purification to homogeneity of some enzymatic forms, discovery of regulatory mechanisms, particularly) have brought a considerable evolution in the knowledge of the system. It is now well established that cyclic nucleotide phosphodiesterase exists under several isoenzymatic forms, the properties and distribution of which largely differ from a tissue to another. Some of these forms are relatively well characterized, while the representativity of others is still discussed. The significance of this multiplicity of isoenzymes, and their interrelationships are presently under study. A very interesting aspect in the study of this enzymatic system is that it is submitted to several physiological regulatory processes. Recent studies on this point suggest that phosphodiesterase might play a major role in the response of the organism to several hormones. These fundamental studies of phosphodiesterase system find a most interesting application in the pharmacological field. Indeed, numerous synthetic compounds which inhibit the enzyme present a strong pharmacological interest.     

Characterization of cysteine thiol modifications based on protein microenvironments and local secondary structures

We have demonstrated earlier that protein microenvironments were conserved around disulfide‐bridged cystine motifs with similar functions, irrespective of diversity in protein sequences. Here, cysteine thiol modifications were characterized based on protein microenvironments, secondary structures and specific protein functions. Protein microenvironment around an amino acid was defined as the summation of hydrophobic contributions from the surrounding protein fragments and the solvent molecules present within its first contact shell. Cysteine functions (modifications) were grouped into enzymatic and non‐enzymatic classes. Modifications studied were—disulfide formation, thio‐ether formation, metal‐binding, nitrosylation, acylation, selenylation, glutathionylation, sulfenylation, and ribosylation. 1079 enzymatic proteins were reported from high‐resolution crystal structures. Protein microenvironments around cysteine thiol, derived from above crystal structures, were clustered into 3 groups—buried‐hydrophobic, intermediate and exposed‐hydrophilic clusters. Characterization of cysteine functions were statistically meaningful for 4 modifications (disulfide formation, thioether formation, sulfenylation, and iron/zinc binding) those have sufficient amount of data in the current dataset. Results showed that protein microenvironment, secondary structure and protein functions were conserved for enzymatic cysteine functions, in contrast to the same function from non‐enzymatic cysteines. Disulfide forming enzymatic cysteines were tightly packed within intermediate protein microenvironment cluster, have alpha‐helical conformation and mostly belonged to CxxC motif of electron transport proteins. Disulfide forming non‐enzymatic cysteines did not belong to conserved motif and have variable secondary structures. Similarly, enzymatic thioether forming cysteines have conserved microenvironment compared to non‐enzymatic cystienes. Based on the compatibility between protein microenvironment and cysteine modifications, more efficient drug molecules could be designed against cysteine‐related diseases.     

Physiological Adaptations in the Gastrointestinal Tract of Crayfish

SYNOPSIS. Crayfish are the dominant macrocrustacean in manyaquatic ecosystems and are the largest crustacean aquaculturalindustry in the United States, yet we know relatively littleabout their preferred and nutritionally important foods, aswell as their ability to utilize those foods. This review focuseson the ability of crayfish to detect foods, reduce food particlesize, digest macronutrients and the control of those functions.Of particular interest are the enzymatic capabilities of crayfish,especially trypsin, an alkaline protease, cellulase, muramidase,and possibly chitinase and chitobiase. The coordinated neuralcontrol of crayfish food location, ingestion and movement hasbeen well documented, while hormonal control mechanisms havenot. The conclusion we must draw from our current state of knowledgeis that crayfish have ample abilities to taste and locate potentialfoods and enzymatic adaptations developed in crayfish that allowuse of many of the foods they encounter in a benthic aquaticenvironment; other adaptations are lacking or have not beenelucidated.     

Quantitative analysis of the effective functional structure in yeast glycolysis

The understanding of the effective functionality that governs the enzymatic self-organized processes in cellular conditions is a crucial topic in the post-genomic era. In recent studies, Transfer Entropy has been proposed as a rigorous, robust and self-consistent method for the causal quantification of the functional information flow among nonlinear processes. Here, in order to quantify the functional connectivity for the glycolytic enzymes in dissipative conditions we have analyzed different catalytic patterns using the technique of Transfer Entropy. The data were obtained by means of a yeast glycolytic model formed by three delay differential equations where the enzymatic rate equations of the irreversible stages have been explicitly considered. These enzymatic activity functions were previously modeled and tested experimentally by other different groups. The results show the emergence of a new kind of dynamical functional structure, characterized by changing connectivity flows and a metabolic invariant that constrains the activity of the irreversible enzymes. In addition to the classical topological structure characterized by the specific location of enzymes, substrates, products and feedback-regulatory metabolites, an effective functional structure emerges in the modeled glycolytic system, which is dynamical and characterized by notable variations of the functional interactions. The dynamical structure also exhibits a metabolic invariant which constrains the functional attributes of the enzymes. Finally, in accordance with the classical biochemical studies, our numerical analysis reveals in a quantitative manner that the enzyme phosphofructokinase is the key-core of the metabolic system, behaving for all conditions as the main source of the effective causal flows in yeast glycolysis.     

Peroxide processing in photosynthesis: antioxidant coupling and redox signalling

Photosynthesis has a high capacity for production of hydrogen peroxide (H2O2), but the intracellular levels of this relatively weak oxidant are controlled by the antioxidant system, comprising a network of enzymatic and non-enzymatic components that notably includes reactions linked to the intracellular ascorbate and glutathione pools. Mutants and transformed plants with specific decreases in key components offer the opp ortunity to dissect the complex system that maintains redox homeostasis. Since H2O2 is a signal-transducing molecule relaying information on intracellular redox state, the pool size must be rigorously controlled within each compartment of the cell. This review focuses on compartment-specific differences in the stringency of redox coupling between ascorbate and glutathione, and the significance this may have for the flexibility of the control of gene expression that is linked to photosynthetic H2O2 production.     

Characterization and production of multifunctional cationic peptides derived from rice proteins

Food proteins have been identified as a source of bioactive peptides. These peptides are inactive within the sequence of the parent protein and must be released during gastrointestinal digestion, fermentation, or food processing. Of bioactive peptides, multifunctional cationic peptides are more useful than other peptides that have specific activity in promotion of health and/or the treatment of diseases. We have identified and characterized cationic peptides from rice enzymes and proteins that possess multiple functions, including antimicrobial, endotoxin-neutralizing, arginine gingipain-inhibitory, and/or angiogenic activities. In particular, we have elucidated the contribution of cationic amino acids (arginine and lysine) in the peptides to their bioactivities. Further, we have discussed the critical parameters, particularly proteinase preparations and fractionation or purification, in the enzymatic hydrolysis process for producing bioactive peptides from food proteins. Using an ampholyte-free isoelectric focusing (autofocusing) technique as a tool for fractionation, we successfully prepared fractions containing cationic peptides with multiple functions.     

Acid ceramidase and human disease

Acid ceramidase (N-acylsphingosine deacylase, EC 3.5.1.23; AC) is the lipid hydrolase responsible for the degradation of ceramide into sphingosine and free fatty acids within lysosomes. The enzymatic activity was first identified over four decades ago, and is deficient in the inherited lipid storage disorder, Farber Lipogranulomatosis (Farber disease). Importantly, AC not only hydrolyzes ceramide into sphingosine, but also can synthesize ceramide from sphingosine and free fatty acids in vitro and in situ. This "reverse" enzymatic activity occurs at a distinct pH from the hydrolysis ("forward") reaction (6.0 vs. 4.5, respectively), suggesting that the enzyme may have diverse functions within cells dependent on its subcellular location and the local pH. Most information concerning the role of AC in human disease stems from work on Farber disease. This lipid storage disease is caused by mutations in the gene encoding AC, leading to a profound reduction in enzymatic activity. Recent studies have also shown that AC activity is aberrantly expressed in several human cancers, and that the enzyme may be a useful cancer drug target. For example, AC inhibitors have been used to slow the growth of cancer cells, alone or in combination with other established, anti-oncogenic treatments. Aberrant AC activity also has been described in Alzheimer's disease, and overexpression of AC may prevent insulin resistant (Type II) diabetes induced by free fatty acids. Current information concerning the biology of this enzyme and its role in human disease is reviewed within.     

Nitroglycerin metabolism by Phanerochaete chrysosporium: evidence for nitric oxide and nitrite formation.

We have demonstrated that a filamentous fungus Phanerochaete chrysosporium converts glyceryl trinitrate (GTN) into its di- and mononitrate derivatives concurrently with the formation of nitric oxide detected by electron paramagnetic resonance (EPR), and the formation of nitrite. The metabolisms of nitrite and nitrate by the fungus are evaluated and taken into account when considering GTN degradation. Lack of evidence for nitrate formation from GTN suggests that an esterase-type activity is not involved. Furthermore, the kinetics of appearance of the hemoprotein-NO and non-heme protein-NO (FeS-NO) complexes indicate that an enzymatic process producing NO directly from GTN may be involved concurrently with a glutathione transferase-like system.     

Absence of cue-recruitment for extrinsic signals: sounds, spots, and swirling dots fail to influence perceived 3D rotation direction after training

The visual system can learn to use information in new ways to construct appearance. Thus, signals such as the location or translation direction of an ambiguously rotating wire frame cube, which are normally uninformative, can be learned as cues to determine the rotation direction. This perceptual learning occurs when the formerly uninformative signal is statistically associated with long-trusted visual cues (such as binocular disparity) that disambiguate appearance during training. In previous demonstrations, the newly learned cue was intrinsic to the perceived object, in that the signal was conveyed by the same image elements as the object itself. Here we used extrinsic new signals and observed no learning. We correlated three new signals with long-trusted cues in the rotating cube paradigm: one crossmodal (an auditory signal) and two within modality (visual). Cue recruitment did not occur in any of these conditions, either in single sessions or in ten sessions across as many days. These results suggest that the intrinsic/extrinsic distinction is important for the perceptual system in determining whether it can learn and use new information from the environment to construct appearance. Extrinsic cues do have perceptual effects (e.g. the "bounce-pass" illusion and McGurk effect), so we speculate that extrinsic signals must be recruited for perception, but only if certain conditions are met. These conditions might specify the age of the observer, the strength of the long-trusted cues, or the amount of exposure to the correlation.     

AN INTEGRATED MORPHOLOGICAL AND BIOCHEMICAL STUDY OF A PURIFIED PREPARATION OF THE SUCCINATE AND DPNH OXIDASE SYSTEM

Electron micrographs of a purified succinate and DPNH oxidase system prepared from heart muscle reveal that it has a vesicular appearance and is membranous in nature. In keeping with its vesicular appearance is the fact that light scattering by this preparation shows marked changes as the molarity of the suspending medium is altered. Treatment of this preparation with 0.5 per cent deoxycholate solutions removes a large part of the lipide material, which comprises almost half of the dry weight of the preparation. The residue, which still contains the "core" of the cytochrome electron transmitter system, as shown by spectroscopic and enzymatic experiments, is still structured and is membranous in morphological appearance. It is concluded that the enzyme preparation is largely composed of fragmented mitochondrial membranes, and some of the consequences of the localization of the succinate and DPNH oxidase systems in or on these membranes are discussed.     

Acid ceramidase and human disease

Acid ceramidase (N-acylsphingosine deacylase, EC 3.5.1.23; AC) is the lipid hydrolase responsible for the degradation of ceramide into sphingosine and free fatty acids within lysosomes. The enzymatic activity was first identified over four decades ago, and is deficient in the inherited lipid storage disorder, Farber Lipogranulomatosis (Farber disease). Importantly, AC not only hydrolyzes ceramide into sphingosine, but also can synthesize ceramide from sphingosine and free fatty acids in vitro and in situ. This “reverse” enzymatic activity occurs at a distinct pH from the hydrolysis (“forward”) reaction (6.0 vs. 4.5, respectively), suggesting that the enzyme may have diverse functions within cells dependent on its subcellular location and the local pH. Most information concerning the role of AC in human disease stems from work on Farber disease. This lipid storage disease is caused by mutations in the gene encoding AC, leading to a profound reduction in enzymatic activity. Recent studies have also shown that AC activity is aberrantly expressed in several human cancers, and that the enzyme may be a useful cancer drug target. For example, AC inhibitors have been used to slow the growth of cancer cells, alone or in combination with other established, anti-oncogenic treatments. Aberrant AC activity also has been described in Alzheimer's disease, and overexpression of AC may prevent insulin resistant (Type II) diabetes induced by free fatty acids. Current information concerning the biology of this enzyme and its role in human disease is reviewed within.     

Enzyme mechanism as a kinetic control element for designing synthetic biofuel pathways

Living systems have evolved remarkable molecular functions that can be redesigned for in vivo chemical synthesis as we gain a deeper understanding of the underlying biochemical principles for de novo construction of synthetic pathways. We have focused on developing pathways for next-generation biofuels as they require carbon to be channeled to product at quantitative yields. However, these fatty acid-inspired pathways must manage the highly reversible nature of the enzyme components. For targets in the biodiesel range, the equilibrium can be driven to completion by physical sequestration of an insoluble product, which is a mechanism unavailable to soluble gasoline-sized products. In this work, we report the construction of a chimeric pathway assembled from three different organisms for the high-level production of n-butanol (4,650 ± 720 mg l?1) that uses an enzymatic chemical reaction mechanism in place of a physical step as a kinetic control element to achieve high yields from glucose (28%).     

JmjC-domain-containing proteins and histone demethylation

Histone methylation has important roles in regulating gene expression and forms part of the epigenetic memory system that regulates cell fate and identity. Enzymes that directly remove methyl marks from histones have recently been identified, revealing a new level of plasticity within this epigenetic modification system. Here we analyse the evolutionary relationship between Jumonji C (JmjC)-domain-containing proteins and discuss their cellular functions in relation to their potential enzymatic activities.