Channeling of substrates and intermediates in enzyme-catalyzed reactions

Cascade Reactions in Nanozymes: Spatially Separated Active Sites inside Ag-Core-Porous-Cu-Shell Nanoparticles for Multistep Carbon Dioxide Reduction to Higher Organic Molecules

Enzymes can perform complex multistep cascade reactions by linking multiple distinct catalytic sites via substrate channeling. We mimic this feature in a generalized approach with an electrocatalytic nanoparticle for the carbon dioxide reduction reaction comprising a Ag core surrounded by a porous Cu shell, providing different active sites in nanoconfined volumes. The architecture of the nanozyme provides the basis for a cascade reaction, which promotes C-C coupling reactions. The first step occurs on the Ag core, and the subsequent steps on the porous copper shell, where a sufficiently high CO concentration due to the nanoconfinement facilitates C-C bond formation. The architecture yields the formation of n-propanol and propionaldehyde at potentials as low as -0.6 V vs RHE.

Homeostatic controllers compensating for growth and perturbations

Cells and organisms have developed homeostatic mechanisms which protect them against a changing environment. How growth and homeostasis interact is still not well understood, but of increasing interest to the molecular and synthetic biology community to recognize and design control circuits which can oppose the diluting effects of cell growth. In this paper we describe the performance of selected negative feedback controllers in response to different applied growth laws and time dependent outflow perturbations of a controlled variable. The approach taken here is based on deterministic mass action kinetics assuming that cell content is instantaneously mixed. All controllers behave ideal in the sense that they for step-wise perturbations in volume and a controlled compound A are able to drive A precisely back to the controllers' theoretical set-points. The applied growth kinetics reflect experimentally observed growth laws, which range from surface to volume ratio growth to linear and exponential growth. Our results show that the kinetic implementation of integral control and the structure of the negative feedback loop are two properties which affect controller performance. Best performance is observed for controllers based on derepression kinetics and controllers with an autocatalytic implementation of integral control. Both are able to defend exponential growth and perturbations, although the autocatalytic controller shows an offset from its theoretical set-point. Controllers with activating signaling using zero-order or bimolecular (antithetic) kinetics for integral control behave very similar but less well. Their performance can be improved by implementing negative feedback structures having repression/derepression steps or by increasing controller aggressiveness. Our results provide a guide what type of feedback structures and integral control kinetics are suitable to oppose the dilution effects by different growth laws and time dependent perturbations on a deterministic level.

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update)

MOLEonline is an interactive, web-based application for the detection and characterization of channels (pores and tunnels) within biomacromolecular structures. The updated version of MOLEonline overcomes limitations of the previous version by incorporating the recently developed LiteMol Viewer visualization engine and providing a simple, fully interactive user experience. The application enables two modes of calculation: one is dedicated to the analysis of channels while the other was specifically designed for transmembrane pores. As the application can use both PDB and mmCIF formats, it can be leveraged to analyze a wide spectrum of biomacromolecular structures, e.g. stemming from NMR, X-ray and cryo-EM techniques. The tool is interconnected with other bioinformatics tools (e.g., PDBe, CSA, ChannelsDB, OPM, UniProt) to help both setup and the analysis of acquired results. MOLEonline provides unprecedented analytics for the detection and structural characterization of channels, as well as information about their numerous physicochemical features. Here we present the application of MOLEonline for structural analyses of α-hemolysin and transient receptor potential mucolipin 1 (TRMP1) pores. The MOLEonline application is freely available via the Internet at https://mole.upol.cz.

Proximity channeling during cyanobacterial phycoerythrobilin synthesis

Substrate channeling is a widespread mechanism in metabolic pathways to avoid decomposition of unstable intermediates, competing reactions, and to accelerate catalytic turnover. During the biosynthesis of light-harvesting phycobilins in cyanobacteria, two members of the ferredoxin-dependent bilin reductases are involved in the reduction of the open-chain tetrapyrrole biliverdin IXα to the pink pigment phycoerythrobilin. The first reaction is catalyzed by 15,16-dihydrobiliverdin:ferredoxin oxidoreductase and produces the unstable intermediate 15,16-dihydrobiliverdin (DHBV). This intermediate is subsequently converted by phycoerythrobilin:ferredoxin oxidoreductase to the final product phycoerythrobilin. Although substrate channeling has been postulated already a decade ago, detailed experimental evidence was missing. Using a new on-column assay employing immobilized enzyme in combination with UV-Vis and fluorescence spectroscopy revealed that both enzymes transiently interact and that transfer of the intermediate is facilitated by a significantly higher binding affinity of DHBV toward phycoerythrobilin:ferredoxin oxidoreductase. Concluding from the presented data, the intermediate DHBV is transferred via proximity channeling.

SNZ3 Encodes a PLP Synthase Involved in Thiamine Synthesis in Saccharomyces cerevisiae

Pyridoxal 5′-phosphate (the active form of vitamin B₆) is a cofactor that is important for a broad number of biochemical reactions and is essential for all forms of life. Organisms that can synthesize pyridoxal 5′-phosphate use either the deoxyxylulose phosphate-dependent or -independent pathway, the latter is encoded by a two-component pyridoxal 5′-phosphate synthase. Saccharomyces cerevisiae contains three paralogs of the two-component SNZ/SNO pyridoxal 5′-phosphate synthase. Past work identified the biochemical activity of Snz1p, Sno1p and provided in vivo data that SNZ1 was involved in pyridoxal 5′-phosphate biosynthesis. Snz2p and Snz3p were considered redundant isozymes and no growth condition requiring their activity was reported. Genetic data herein showed that either SNZ2 or SNZ3 are required for efficient thiamine biosynthesis in Saccharomyces cerevisiae. Further, SNZ2 or SNZ3 alone could satisfy the cellular requirement for pyridoxal 5′-phosphate (and thiamine), while SNZ1 was sufficient for pyridoxal 5′-phosphate synthesis only if thiamine was provided. qRT-PCR analysis determined that SNZ2,3 are repressed ten-fold by the presence thiamine. In total, the data were consistent with a requirement for PLP in thiamine synthesis, perhaps in the Thi5p enzyme, that could only be satisfied by SNZ2 or SNZ3. Additional data showed that Snz3p is a pyridoxal 5′-phosphate synthase in vitro and is sufficient to satisfy the pyridoxal 5′-phosphate requirement in Salmonella enterica when the medium has excess ammonia.

Can enzyme proximity accelerate cascade reactions?

The last decade has seen an exponential expansion of interest in conjugating multiple enzymes of cascades in close proximity to each other, with the overarching goal being to accelerate the overall reaction rate. However, some evidence has emerged that there is no effect of proximity channeling on the reaction velocity of the popular GOx-HRP cascade, particularly in the presence of a competing enzyme (catalase). Herein, we rationalize these experimental results quantitatively. We show that, in general, proximity channeling can enhance reaction velocity in the presence of competing enzymes, but in steady state a significant enhancement can only be achieved for diffusion-limited reactions or at high concentrations of competing enzymes. We provide simple equations to estimate the effect of channeling quantitatively and demonstrate that proximity can have a more pronounced effect under crowding conditions in vivo, particularly that crowding can enhance the overall rates of channeled cascade reactions.

Regulation of carbamoylphosphate synthesis in Escherichia coli: an amazing metabolite at the crossroad of arginine and pyrimidine biosynthesis

In all organisms, carbamoylphosphate (CP) is a precursor common to the synthesis of arginine and pyrimidines. In Escherichia coli and most other Gram-negative bacteria, CP is produced by a single enzyme, carbamoylphosphate synthase (CPSase), encoded by the carAB operon. This particular situation poses a question of basic physiological interest: what are the metabolic controls coordinating the synthesis and distribution of this high-energy substance in view of the needs of both pathways? The study of the mechanisms has revealed unexpected moonlighting gene regulatory activities of enzymes and functional links between mechanisms as diverse as gene regulation and site-specific DNA recombination. At the level of enzyme production, various regulatory mechanisms were found to cooperate in a particularly intricate transcriptional control of a pair of tandem promoters. Transcription initiation is modulated by an interplay of several allosteric DNA-binding transcription factors using effector molecules from three different pathways (arginine, pyrimidines, purines), nucleoid-associated factors (NAPs), trigger enzymes (enzymes with a second unlinked gene regulatory function), DNA remodeling (bending and wrapping), UTP-dependent reiterative transcription initiation, and stringent control by the alarmone ppGpp. At the enzyme level, CPSase activity is tightly controlled by allosteric effectors originating from different pathways: an inhibitor (UMP) and two activators (ornithine and IMP) that antagonize the inhibitory effect of UMP. Furthermore, it is worth noticing that all reaction intermediates in the production of CP are extremely reactive and unstable, and protected by tunneling through a 96 Å long internal channel.

Enzymatic complexes across scales

An unprecedented opportunity to integrate ~100 years of meticulous in vitro biomolecular research is currently provided in the light of recent advances in methods to visualize closer-to-native architectures of biomolecular machines, and metabolic enzymes in particular. Traditional views of enzymes, namely biomolecular machines, only partially explain their role, organization and kinetics in the cellular milieu. Enzymes self- or hetero-associate, form fibers, may bind to membranes or cytoskeletal elements, have regulatory roles, associate into higher order assemblies (metabolons) or even actively participate in phase-separated membraneless organelles, and all the above in a transient, temporal and spatial manner in response to environmental changes or structural/functional changes of their assemblies. Here, we focus on traditional and emerging concepts in cellular biochemistry and discuss new opportunities in bridging structural, molecular and cellular analyses for metabolic pathways, accumulated over the years, highlighting functional aspects of enzymatic complexes discussed across different levels of spatial resolution.

Molecular Tunnels in Enzymes and Thermophily: A Case Study on the Relationship to Growth Temperature

Developments in protein expression, analysis and computational capabilities are decisively contributing to a better understanding of the structure of proteins and their relationship to function. Proteins are known to be adapted to the growth rate of microorganisms and some microorganisms (named (hyper)thermophiles) thrive optimally at high temperatures, even above 100 °C. Nevertheless, some biomolecules show great instability at high temperatures and some of them are universal and required substrates and cofactors in multiple enzymatic reactions for all (both mesophiles and thermophiles) living cells. Only a few possibilities have been pointed out to explain the mechanisms that thermophiles use to successfully thrive under high temperatures. As one of these alternatives, the role of molecular tunnels or channels in enzymes has been suggested but remains to be elucidated. This study presents an analysis of channels in proteins (i.e., substrate tunnels), comparing two different protein types, glutamate dehydrogenase and glutamine phosphoribosylpyrophosphate amidotransferase, which are supposed to present a different strategy on the requirement for substrate tunnels with low and high needs for tunneling, respectively. The search and comparison of molecular tunnels in these proteins from microorganisms thriving optimally from 15 °C to 100 °C suggested that those tunnels in (hyper)thermophiles are required and optimized to specific dimensions at high temperatures for the enzyme glutamine phosphoribosylpyrophosphate amidotransferase. For the enzyme glutamate dehydrogenase, a reduction of empty spaces within the protein could explain the optimization at increasing temperatures. This analysis provides further evidence on molecular channeling as a feasible mechanism in hyperthermophiles with multiple relevant consequences contributing to better understand how they live under those extreme conditions.

"Pinching" the ammonia tunnel of CTP synthase unveils coordinated catalytic and allosteric-dependent control of ammonia passage

Molecular gates within enzymes often play important roles in synchronizing catalytic events. We explored the role of a gate in cytidine-5'-triphosphate synthase (CTPS) from Escherichia coli. This glutamine amidotransferase catalyzes the biosynthesis of CTP from UTP using either l-glutamine or exogenous NH₃ as a substrate. Glutamine is hydrolyzed in the glutaminase domain, with GTP acting as a positive allosteric effector, and the nascent NH₃ passes through a gate located at the end of a ~25-Å tunnel before entering the synthase domain where CTP is generated. Substitution of the gate residue Val 60 by Ala, Cys, Asp, Trp, or Phe using site-directed mutagenesis and subsequent kinetic analyses revealed that V60-substitution impacts glutaminase activity, nucleotide binding, salt-dependent inhibition, and inter-domain NH₃ transport. Surprisingly, the increase in steric bulk present in V60F perturbed the local structure consistent with "pinching" the tunnel, thereby revealing processes that synchronize the transfer of NH₃ from the glutaminase domain to the synthase domain. V60F had a slightly reduced coupling efficiency at maximal glutaminase activity that was ameliorated by slowing down the glutamine hydrolysis reaction, consistent with a "bottleneck" effect. The inability of V60F to use exogenous NH₃ was overcome in the presence of GTP, and more so if CTPS was covalently modified by 6-diazo-5-oxo-l-norleucine. Use of NH₂OH by V60F as an alternative bulkier substrate occurred most efficiently when it was concomitant with the glutaminase reaction. Thus, the glutaminase activity and GTP-dependent activation act in concert to open the NH₃ gate of CTPS to mediate inter-domain NH₃ transport.

Globally Optimal Catalytic Fields - Inverse Design of Abstract Embeddings for Maximum Reaction Rate Acceleration

The search for, and understanding of, good catalysts for chemical reactions is a central issue for chemists. Here, we present first steps toward developing a general computational framework to better support this task. This framework combines efficient, unbiased global optimization techniques with an abstract representation of the catalytic environment, to shrink the search space. To analyze the resulting catalytic embeddings, we employ dimensionality reduction and clustering techniques. This not only provides an inverse design approach to new catalytic embeddings but also illuminates the actual interactions behind catalytic effects. All this is illustrated here with a strictly electrostatic model for the environment and with two versions of a selected example reaction. We close with detailed discussions of future improvements of our framework.

Tracking the route of molecular oxygen in O2-tolerant membrane-bound [NiFe] hydrogenase

[NiFe] hydrogenases catalyze the reversible splitting of H₂ into protons and electrons at a deeply buried active site. The catalytic center can be accessed by gas molecules through a hydrophobic tunnel network. While most [NiFe] hydrogenases are inactivated by O₂, a small subgroup, including the membrane-bound [NiFe] hydrogenase (MBH) of Ralstonia eutropha, is able to overcome aerobic inactivation by catalytic reduction of O₂ to water. This O₂ tolerance relies on a special [4Fe3S] cluster that is capable of releasing two electrons upon O₂ attack. Here, the O₂ accessibility of the MBH gas tunnel network has been probed experimentally using a "soak-and-freeze" derivatization method, accompanied by protein X-ray crystallography and computational studies. This combined approach revealed several sites of O₂ molecules within a hydrophobic tunnel network leading, via two tunnel entrances, to the catalytic center of MBH. The corresponding site occupancies were related to the O₂ concentrations used for MBH crystal derivatization. The examination of the O₂-derivatized data furthermore uncovered two unexpected structural alterations at the [4Fe3S] cluster, which might be related to the O₂ tolerance of the enzyme.

Structure and function of urea amidolyase

Urea is the degradation product of a wide range of nitrogen containing bio-molecules. Urea amidolyase (UA) catalyzes the conversion of urea to ammonium, the essential first step in utilizing urea as a nitrogen source. It is widely distributed in fungi, bacteria and other microorganisms, and plays an important role in nitrogen recycling in the biosphere. UA is composed of urea carboxylase (UC) and allophanate hydrolase (AH) domains, which catalyze sequential reactions. In some organisms UC and AH are encoded by separated genes. We present here structure of the Kluyveromyces lactis UA (KlUA). The structure revealed that KlUA forms a compact homo-dimer with a molecular weight of 400 kDa. Structure inspired biochemical experiments revealed the mechanism of its reaction intermediate translocation, and that the KlUA holo-enzyme formation is essential for its optimal activity. Interestingly, previous studies and ours suggest that UC and AH encoded by separated genes probably do not form a KlUA-like complex, consequently they might not catalyze the urea to ammonium conversion as efficiently.

Encapsulation and Controlled Release of Protein Guests by the Bacillus subtilis Lumazine Synthase Capsid

In Bacillus subtilis, the 60-subunit dodecahedral capsid formed by lumazine synthase (BsLS) acts as a container for trimeric riboflavin synthase (BsRS). To test whether the C-terminal sequence of BsRS is responsible for its encapsulation by BsLS, the green fluorescent protein (GFP) was fused to either the last 11 or the last 32 amino acids of BsRS, yielding variant GFP11 or GFP32, respectively. After purification, BsLS capsids that had been co-produced in bacteria with GFP11 and GFP32 are 15- and 6-fold more fluorescent, respectively, than BsLS co-produced with GFP lacking any BsRS fragment, indicating complex formation. Enzyme-linked immunosorbent assay experiments confirm that GFP11 is localized within the BsLS capsid. In addition, fusing the last 11 amino acids of BsRS to the C-terminus of the Abrin A chain also led to its encapsulation by BsLS at a level similar to that of GFP11. Together, these results demonstrate that the C-terminal tail of BsRS can act as an encapsulation tag capable of targeting other proteins to the BsLS capsid interior. As with the natural BsLS-BsRS complex, mild changes in pH and buffer identity trigger dissociation of the GFP11 guest, accompanied by a substantial expansion of the BsLS capsid. This system for protein encapsulation and release provides a novel tool for bionanotechnology.

Enhanced ethanol formation by Clostridium thermocellum via pyruvate decarboxylase

Background

Pyruvate decarboxylase (PDC) is a well-known pathway for ethanol production, but has not been demonstrated for high titer ethanol production at temperatures above 50 °C.

Result

Here we examined the thermostability of eight PDCs. The purified bacterial enzymes retained 20% of activity after incubation for 30 min at 55 °C. Expression of these PDC genes, except the one from Zymomonas mobilis, improved ethanol production by Clostridium thermocellum. Ethanol production was further improved by expression of the heterologous alcohol dehydrogenase gene adhA from Thermoanaerobacterium saccharolyticum.

Conclusion

The best PDC enzyme was from Acetobactor pasteurianus. A strain of C. thermocellum expressing the pdc gene from A. pasteurianus and the adhA gene from T. saccharolyticum was able to produce 21.3 g/L ethanol from 60 g/L cellulose, which is 70% of the theoretical maximum yield.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-017-0783-9) contains supplementary material, which is available to authorized users.

The advantage of channeling nucleotides for very processive functions

Nucleoside triphosphate (NTP)s, like ATP (adenosine 5'-triphosphate) and GTP (guanosine 5'-triphosphate), have long been considered sufficiently concentrated and diffusible to fuel all cellular ATPases (adenosine triphosphatases) and GTPases (guanosine triphosphatases) in an energetically healthy cell without becoming limiting for function. However, increasing evidence for the importance of local ATP and GTP pools, synthesised in close proximity to ATP- or GTP-consuming reactions, has fundamentally challenged our view of energy metabolism. It has become evident that cellular energy metabolism occurs in many specialised 'microcompartments', where energy in the form of NTPs is transferred preferentially from NTP-generating modules directly to NTP-consuming modules. Such energy channeling occurs when diffusion through the cytosol is limited, where these modules are physically close and, in particular, if the NTP-consuming reaction has a very high turnover, i.e. is very processive. Here, we summarise the evidence for these conclusions and describe new insights into the physiological importance and molecular mechanisms of energy channeling gained from recent studies. In particular, we describe the role of glycolytic enzymes for axonal vesicle transport and nucleoside diphosphate kinases for the functions of dynamins and dynamin-related GTPases.

The advantage of channeling nucleotides for very processive functions

Nucleoside triphosphate (NTP)s, like ATP (adenosine 5'-triphosphate) and GTP (guanosine 5'-triphosphate), have long been considered sufficiently concentrated and diffusible to fuel all cellular ATPases (adenosine triphosphatases) and GTPases (guanosine triphosphatases) in an energetically healthy cell without becoming limiting for function. However, increasing evidence for the importance of local ATP and GTP pools, synthesised in close proximity to ATP- or GTP-consuming reactions, has fundamentally challenged our view of energy metabolism. It has become evident that cellular energy metabolism occurs in many specialised 'microcompartments', where energy in the form of NTPs is transferred preferentially from NTP-generating modules directly to NTP-consuming modules. Such energy channeling occurs when diffusion through the cytosol is limited, where these modules are physically close and, in particular, if the NTP-consuming reaction has a very high turnover, i.e. is very processive. Here, we summarise the evidence for these conclusions and describe new insights into the physiological importance and molecular mechanisms of energy channeling gained from recent studies. In particular, we describe the role of glycolytic enzymes for axonal vesicle transport and nucleoside diphosphate kinases for the functions of dynamins and dynamin-related GTPases.

Metabolism Shapes the Cell

More than 5 decades of work support the idea that cell envelope synthesis, including the inward growth of cell division, is tightly coordinated with DNA replication and protein synthesis through central metabolism. Remarkably, no unifying model exists to account for how these fundamentally disparate processes are functionally coupled. Recent studies demonstrate that proteins involved in carbohydrate and nitrogen metabolism can moonlight as direct regulators of cell division, coordinate cell division and DNA replication, and even suppress defects in DNA replication. In this minireview, we focus on studies illustrating the intimate link between metabolism and regulation of peptidoglycan (PG) synthesis during growth and division, and we identify the following three recurring themes. (i) Nutrient availability, not growth rate, is the primary determinant of cell size. (ii) The degree of gluconeogenic flux is likely to have a profound impact on the metabolites available for cell envelope synthesis, so growth medium selection is a critical consideration when designing and interpreting experiments related to morphogenesis. (iii) Perturbations in pathways relying on commonly shared and limiting metabolites, like undecaprenyl phosphate (Und-P), can lead to pleotropic phenotypes in unrelated pathways.

Hydrolysis of peptidoglycan is modulated by amidation of meso-diaminopimelic acid and Mg2+ in Bacillus subtilis

The ability of excess Mg²⁺ to compensate the absence of cell wall related genes in Bacillus subtilis has been known for a long time, but the mechanism has remained obscure. Here, we show that the rigidity of wild‐type cells remains unaffected with excess Mg²⁺, but the proportion of amidated meso‐diaminopimelic (mDAP) acid in their peptidoglycan (PG) is significantly reduced. We identify the amidotransferase AsnB as responsible for mDAP amidation and show that the gene encoding it is essential without added Mg²⁺. Growth without excess Mg²⁺ causes ΔasnB mutant cells to deform and ultimately lyse. In cell regions with deformations, PG insertion is orderly and indistinguishable from the wild‐type. However, PG degradation is unevenly distributed along the sidewalls. Furthermore, ΔasnB mutant cells exhibit increased sensitivity to antibiotics targeting the cell wall. These results suggest that absence of amidated mDAP causes a lethal deregulation of PG hydrolysis that can be inhibited by increased levels of Mg²⁺. Consistently, we find that Mg²⁺ inhibits autolysis of wild‐type cells. We suggest that Mg²⁺ helps to maintain the balance between PG synthesis and hydrolysis in cell wall mutants where this balance is perturbed in favor of increased degradation.

Ligand diffusion in proteins via enhanced sampling in molecular dynamics

Computational simulations in biophysics describe the dynamics and functions of biological macromolecules at the atomic level. Among motions particularly important for life are the transport processes in heterogeneous media. The process of ligand diffusion inside proteins is an example of a complex rare event that can be modeled using molecular dynamics simulations. The study of physical interactions between a ligand and its biological target is of paramount importance for the design of novel drugs and enzymes. Unfortunately, the process of ligand diffusion is difficult to study experimentally. The need for identifying the ligand egress pathways and understanding how ligands migrate through protein tunnels has spurred the development of several methodological approaches to this problem. The complex topology of protein channels and the transient nature of the ligand passage pose difficulties in the modeling of the ligand entry/escape pathways by canonical molecular dynamics simulations. In this review, we report a methodology involving a reconstruction of the ligand diffusion reaction coordinates and the free-energy profiles along these reaction coordinates using enhanced sampling of conformational space. We illustrate the above methods on several ligand-protein systems, including cytochromes and G-protein-coupled receptors. The methods are general and may be adopted to other transport processes in living matter.

Does metabolite channeling accelerate enzyme-catalyzed cascade reactions?

Metabolite or substrate channeling is a direct transfer of metabolites from one enzyme to the next enzyme in a cascade. Among many potential advantages of substrate channeling, acceleration of the total reaction rate is considered as one of the most important and self-evident. However, using a simple model, supported by stochastic simulations, we show that it is not always the case; particularly at long times (i.e. in steady state) and high substrate concentrations, a channeled reaction cannot be faster, and can even be slower, than the original non-channeled cascade reaction. In addition we show that increasing the degree of channeling may lead to an increase of the metabolite pool size. We substantiate that the main advantage of channeling likely lies in protecting metabolites from degradation or competing side reactions.

Adaptation of Candida albicans to Reactive Sulfur Species

Candida albicans is an opportunistic fungal pathogen that is highly resistant to different oxidative stresses. How reactive sulfur species (RSS) such as sulfite regulate gene expression and the role of the transcription factor Zcf2 and the sulfite exporter Ssu1 in such responses are not known. Here, we show that C. albicans specifically adapts to sulfite stress and that Zcf2 is required for that response as well as induction of genes predicted to remove sulfite from cells and to increase the intracellular amount of a subset of nitrogen metabolites. Analysis of mutants in the sulfate assimilation pathway show that sulfite conversion to sulfide accounts for part of sulfite toxicity and that Zcf2-dependent expression of the SSU1 sulfite exporter is induced by both sulfite and sulfide. Mutations in the SSU1 promoter that selectively inhibit induction by the reactive nitrogen species (RNS) nitrite, a previously reported activator of SSU1, support a model for C. albicans in which Cta4-dependent RNS induction and Zcf2-dependent RSS induction are mediated by parallel pathways, different from S. cerevisiae in which the transcription factor Fzf1 mediates responses to both RNS and RSS. Lastly, we found that endogenous sulfite production leads to an increase in resistance to exogenously added sulfite. These results demonstrate that C. albicans has a unique response to sulfite that differs from the general oxidative stress response, and that adaptation to internal and external sulfite is largely mediated by one transcription factor and one effector gene.

Higher order structures in purine and pyrimidine metabolism

The recent discovery of several forms of higher order protein structures in cells has shifted the paradigm of how we think about protein organization and metabolic regulation. These dynamic and controllable protein assemblies, which are composed of dozens or hundreds of copies of an enzyme or related enzymes, have emerged as important players in myriad cellular processes. We are only beginning to appreciate the breadth of function of these types of macromolecular assemblies. These higher order structures, which can be assembled in response to varied cellular stimuli including changing metabolite concentrations or signaling cascades, give the cell the capacity to modulate levels of biomolecules both temporally and spatially. This provides an added level of control with distinct kinetics and unique features that can be harnessed as a subtle, yet powerful regulatory mechanism. Due, in large part, to advances in structural methods, such as crystallography and cryo-electron microscopy, and the advent of super-resolution microscopy techniques, a rapidly increasing number of these higher order structures are being identified and characterized. In this review, we detail what is known about the structure, function and control mechanisms of these mesoscale protein assemblies, with a particular focus on those involved in purine and pyrimidine metabolism. These structures have important implications both for our understanding of fundamental cellular processes and as fertile ground for new targets for drug discovery and development.

Spatial organization of multi-enzyme biocatalytic cascades

Multi-enzyme cascades provide a wealth of valuable chemicals. Efficiency of reaction schemes can be improved by spatial organization of biocatalysts. This review will highlight various methods of spatial organization of biocatalysts: fusion, immobilization, scaffolding and encapsulation.

Uncoupling of an ammonia channel as a mechanism of allosteric inhibition in anthranilate synthase of Serratia marcescens: dynamic and graph theoretical analysis

Network modeling and molecular dynamic studies reveal the perturbation in communication pathways as a mechanism of allosteric inhibition in anthranilate synthase.

Influence of Linker Length Variations on the Biomass-Degrading Performance of Heat-Active Enzyme Chimeras

Plant cell walls are composed of complex polysaccharides such as cellulose and hemicellulose. In order to efficiently hydrolyze cellulose, the synergistic action of several cellulases is required. Some anaerobic cellulolytic bacteria form multienzyme complexes, namely cellulosomes, while other microorganisms produce a portfolio of diverse enzymes that work in synergistic fashion. Molecular biological methods can mimic such effects through the generation of artificial bi- or multifunctional fusion enzymes. Endoglucanase and β-glucosidase from extremely thermophilic anaerobic bacteria Fervidobacterium gondwanense and Fervidobacterium islandicum, respectively, were fused end-to-end in an approach to optimize polysaccharide degradation. Both enzymes are optimally active at 90 °C and pH 6.0-7.0 representing excellent candidates for fusion experiments. The direct linkage of both enzymes led to an increased activity toward the substrate specific for β-glucosidase, but to a decreased activity of endoglucanase. However, these enzyme chimeras were superior over 1:1 mixtures of individual enzymes, because combined activities resulted in a higher final product yield. Therefore, such fusion enzymes exhibit promising features for application in industrial bioethanol production processes.

Sortase A-Mediated Metabolic Enzyme Ligation in Escherichia coli

We demonstrate metabolic enzyme ligation using a transpeptidase (Staphylococcal sortase A) in the microbial cytoplasm for the redirection of metabolic flux through metabolic channeling. Here, sortase A expression was controlled by the lac promoter to trigger metabolic channeling by the addition of isopropyl-β-d-thiogalactopyranoside (IPTG). We tested covalent linking of pyruvate-formate lyase and phosphate acetyltransferase by sortase A-mediated ligation and evaluated the production of acetate. The time point of addition of IPTG was not critical for facilitating metabolic enzyme ligation, and acetate production increased upon expression of sortase A. These results show that sortase A-mediated enzyme ligation enhances an acetate-producing flux in E. coli. We have validated that sortase A-mediated enzyme ligation offers a metabolic channeling approach to redirect a central flux to a desired flux.

Non-metabolic functions of glycolytic enzymes in tumorigenesis

Cancer cells reprogram their metabolism to meet the requirement for survival and rapid growth. One hallmark of cancer metabolism is elevated aerobic glycolysis and reduced oxidative phosphorylation. Emerging evidence showed that most glycolytic enzymes are deregulated in cancer cells and play important roles in tumorigenesis. Recent studies revealed that all essential glycolytic enzymes can be translocated into nucleus where they participate in tumor progression independent of their canonical metabolic roles. These noncanonical functions include anti-apoptosis, regulation of epigenetic modifications, modulation of transcription factors and co-factors, extracellular cytokine, protein kinase activity and mTORC1 signaling pathway, suggesting that these multifaceted glycolytic enzymes not only function in canonical metabolism but also directly link metabolism to epigenetic and transcription programs implicated in tumorigenesis. These findings underscore our understanding about how tumor cells adapt to nutrient and fuel availability in the environment and most importantly, provide insights into development of cancer therapy.

Direct Evidence for Metabolon Formation and Substrate Channeling in Recombinant TCA Cycle Enzymes

Supramolecular assembly of enzymes into metabolon structures is thought to enable efficient transport of reactants between active sites via substrate channeling. Recombinant versions of porcine citrate synthase (CS), mitochondrial malate dehydrogenase (mMDH), and aconitase (Aco) were found to adopt a homogeneous native-like metabolon structure in vitro. Site-directed mutagenesis performed on highly conserved arginine residues located in the positively charged channel connecting mMDH and CS active sites led to the identification of CS(R65A) which retained high catalytic efficiency. Substrate channeling between the CS mutant and mMDH was severely impaired and the overall channeling probability decreased from 0.99 to 0.023. This work provides direct mechanistic evidence for the channeling of reaction intermediates, and disruption of this interaction would have important implications on the control of flux in central carbon metabolism.

A roadmap for biocatalysis - functional and spatial orchestration of enzyme cascades

Advances in biological engineering and systems biology have provided new approaches and tools for the industrialization of biology. In the next decade, advanced biocatalytic systems will increasingly be used for the production of chemicals that cannot be made by current processes and/or where the use of enzyme catalysts is more resource efficient with a much reduced environmental impact. We expect that in the future, manufacture of chemicals and materials will utilize both biocatalytic and chemical synthesis synergistically. The realization of such advanced biomanufacturing processes currently faces a number of major challenges. Ready‐to‐deploy portfolios of biocatalysts for design to production must be created from biological diverse sources and through protein engineering. Robust and efficient multi‐step enzymatic reaction cascades must be developed that can operate simultaneously in one‐pot. For this to happen, bio‐orthogonal strategies for spatial and temporal control of biocatalyst activities must be developed. Promising approaches and technologies are emerging that will eventually lead to the design of in vitro biocatalytic systems that mimic the metabolic pathways and networks of cellular systems which will be discussed in this roadmap.

Systematic identification and analysis of frequent gene fusion events in metabolic pathways

Background

Gene fusions are the most powerful type of in silico-derived functional associations. However, many fusion compilations were made when <100 genomes were available, and algorithms for identifying fusions need updating to handle the current avalanche of sequenced genomes. The availability of a large fusion dataset would help probe functional associations and enable systematic analysis of where and why fusion events occur.

Results

Here we present a systematic analysis of fusions in prokaryotes. We manually generated two training sets: (i) 121 fusions in the model organism Escherichia coli; (ii) 131 fusions found in B vitamin metabolism. These sets were used to develop a fusion prediction algorithm that captured the training set fusions with only 7 % false negatives and 50 % false positives, a substantial improvement over existing approaches. This algorithm was then applied to identify 3.8 million potential fusions across 11,473 genomes. The results of the analysis are available in a searchable database at http://modelseed.org/projects/fusions/. A functional analysis identified 3,000 reactions associated with frequent fusion events and revealed areas of metabolism where fusions are particularly prevalent.

Conclusions

Customary definitions of fusions were shown to be ambiguous, and a stricter one was proposed. Exploring the genes participating in fusion events showed that they most commonly encode transporters, regulators, and metabolic enzymes. The major rationales for fusions between metabolic genes appear to be overcoming pathway bottlenecks, avoiding toxicity, controlling competing pathways, and facilitating expression and assembly of protein complexes. Finally, our fusion dataset provides powerful clues to decipher the biological activities of domains of unknown function.

Electronic supplementary material

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Solution NMR Spectroscopy for the Study of Enzyme Allostery

Allostery is a ubiquitous biological regulatory process in which distant binding sites within a protein or enzyme are functionally and thermodynamically coupled. Allosteric interactions play essential roles in many enzymological mechanisms, often facilitating formation of enzyme-substrate complexes and/or product release. Thus, elucidating the forces that drive allostery is critical to understanding the complex transformations of biomolecules. Currently, a number of models exist to describe allosteric behavior, taking into account energetics as well as conformational rearrangements and fluctuations. In the following Review, we discuss the use of solution NMR techniques designed to probe allosteric mechanisms in enzymes. NMR spectroscopy is unequaled in its ability to detect structural and dynamical changes in biomolecules, and the case studies presented herein demonstrate the range of insights to be gained from this valuable method. We also provide a detailed technical discussion of several specialized NMR experiments that are ideally suited for the study of enzymatic allostery.

Fine-tuning of microsolvation and hydrogen bond interaction regulates substrate channelling in the course of flavonoid biosynthesis

In the course of metabolite formation, some multienzymatic edifices, the so-called metabolon, are formed and lead to a more efficient production of these natural compounds. One of the major features of these enzyme complexes is the facilitation of direct transfer of the metabolite between enzyme active sites by substrate channelling. Biophysical insights into substrate channelling remain scarce because the transient nature of these macromolecular complexes prevents the observation of high resolution structures. Here, using molecular modelling, we describe the substrate channelling of a flavonoid compound between DFR (dihydroflavonol-4-reductase) and LAR (leucoanthocyanidin reductase). The simulation presents crucial details concerning the kinetic, thermodynamic, and structural aspects of this diffusion. The formation of the DFR-LAR complex leads to the opening of the DFR active site giving rise to a facilitated diffusion, in about 1 μs, of the DFR product towards LAR cavity. The theoretically observed substrate channelling is supported experimentally by the fact that this metabolite, i.e. the product of the DFR enzyme, is not stable in the media. Moreover, along this path, the influence of the solvent is crucial. The metabolite remains close to the surface of the complex avoiding full solvation. In addition, when the dynamic behaviour of the system leads to a loss of interaction between the metabolite and the enzymes, water molecules through bridging H-bonds prevent the former from escaping to the bulk.

The impact of crystallization conditions on structure-based drug design: A case study on the methylene blue/acetylcholinesterase complex

Structure-based drug design utilizes apoprotein or complex structures retrieved from the PDB. >57% of crystallographic PDB entries were obtained with polyethylene glycols (PEGs) as precipitant and/or as cryoprotectant, but <6% of these report presence of individual ethyleneglycol oligomers. We report a case in which ethyleneglycol oligomers' presence in a crystal structure markedly affected the bound ligand's position. Specifically, we compared the positions of methylene blue and decamethonium in acetylcholinesterase complexes obtained using isomorphous crystals precipitated with PEG200 or ammonium sulfate. The ligands' positions within the active-site gorge in complexes obtained using PEG200 are influenced by presence of ethyleneglycol oligomers in both cases bound to W84 at the gorge's bottom, preventing interaction of the ligand's proximal quaternary group with its indole. Consequently, both ligands are ∼3.0Å further up the gorge than in complexes obtained using crystals precipitated with ammonium sulfate, in which the quaternary groups make direct π-cation interactions with the indole. These findings have implications for structure-based drug design, since data for ligand-protein complexes with polyethylene glycol as precipitant may not reflect the ligand's position in its absence, and could result in selecting incorrect drug discovery leads. Docking methylene blue into the structure obtained with PEG200, but omitting the ethyleneglycols, yields results agreeing poorly with the crystal structure; excellent agreement is obtained if they are included. Many proteins display features in which precipitants might lodge. It will be important to investigate presence of precipitants in published crystal structures, and whether it has resulted in misinterpreting electron density maps, adversely affecting drug design.

Single-Molecule Stochastic Analysis of Channeling Enzyme Tryptophan Synthase

The channeling enzyme tryptophan synthase provides a paradigmatic example of a chemical nanomachine. It possesses two active centers and, as a single molecule, catalyzes 13 different reaction steps with a complex pattern of allosteric regulation and with an intermediate product channeled from one active center to another. Here, the first single-molecule stochastic model of the enzyme is proposed and analyzed. All its transition rate constants were deduced from the experimental data available, and no fitting parameters were thus employed. Numerical simulations reveal strong correlations in the states of the active centers and the emergent synchronization of intramolecular processes in tryptophan synthase.

All the O2 Consumed by Thermus thermophilus Cytochrome ba3 Is Delivered to the Active Site through a Long, Open Hydrophobic Tunnel with Entrances within the Lipid Bilayer

Cytochrome ba3 is a proton-pumping heme-copper oxygen reductase from the extreme thermophile Thermus thermophilus. Despite the fact that the enzyme's active site is buried deep within the protein, the apparent second order rate constant for the initial binding of O2 to the active-site heme has been experimentally found to be 10(9) M(-1) s(-1) at 298 K, at or near the diffusion limit, and 2 orders of magnitude faster than for O2 binding to myoglobin. To provide quantitative and microscopic descriptions of the O2 delivery pathway and mechanism in cytochrome ba3, extensive molecular dynamics simulations of the enzyme in its membrane-embedded form have been performed, including different protocols of explicit ligand sampling (flooding) simulations with O2, implicit ligand sampling analysis, and in silico mutagenesis. The results show that O2 diffuses to the active site exclusively via a Y-shaped hydrophobic tunnel with two 25-Å long membrane-accessible branches that coincide with the pathway previously suggested by the crystallographically identified xenon binding sites. The two entrances of the bifurcated tunnel of cytochrome ba3 are located within the lipid bilayer, where O2 is preferentially partitioned from the aqueous phase. The largest barrier to O2 migration within the tunnel is estimated to be only 1.5 kcal/mol, allowing O2 to reach the enzyme active site virtually impeded by one-dimensional diffusion once it reaches a tunnel entrance at the protein surface. Unlike other O2-utilizing proteins, the tunnel is "open" with no transient barriers observed due to protein dynamics. This unique low-barrier passage through the protein ensures that O2 transit through the protein is never rate-limiting.