Concerted proton transfer mechanism of Clostridium thermocellum ribose-5-phosphate isomerase

D-allose, a typical rare sugar: properties, applications, and biosynthetic advances and challenges

D-allose, a C-3 epimer of D-glucose and an aldose-ketose isomer of D-allulose, exhibits 80% of sucrose's sweetness while being remarkably low in calories and nontoxic, making it an appealing sucrose substitute. Its diverse physiological functions, particularly potent anticancer and antitumor effects, render it a promising candidate for clinical treatment, garnering sustained attention. However, its limited availability in natural sources and the challenges associated with chemical synthesis necessitate exploring biosynthetic strategies to enhance production. This overview encapsulates recent advancements in D-allose's physicochemical properties, physiological functions, applications, and biosynthesis. It also briefly discusses the crucial role of understanding aldoketose isomerase structure and optimizing its performance in D-allose synthesis. Furthermore, it delves into the challenges and future perspectives in D-allose bioproduction. Early efforts focused on identifying and characterizing enzymes responsible for D-allose production, followed by detailed crystal structure analysis to improve performance through molecular modification. Strategies such as enzyme immobilization and implementing multi-enzyme cascade reactions, utilizing more cost-effective feedstocks, were explored. Despite progress, challenges remain, including the lack of efficient high-throughput screening methods for enzyme modification, the need for food-grade expression systems, the establishment of ordered substrate channels in multi-enzyme cascade reactions, and the development of downstream separation and purification processes.

Metabolomic and transcriptomic investigation of the mechanism involved in enantioselective toxicity of imazamox in Lemna minor

Imazamox (IM) is a chiral pesticide that has been widely used in agriculture. Currently, few studies have investigated the toxicity mechanisms of imazamox to aquatic macrophyte from the enantiomer level. In this study, the enantioselective effects of IM on the toxicity and physiological and biochemical system of aquatic macrophyte Lemna minor were systematically investigated. Metabolomic and transcriptomic for Lemna minor were used to identify potential mechanisms of toxicity. 7 d EC₅₀s for racemic-, R-, and S-IM were 0.036, 0.035, and 0.203 mg/L, respectively, showing enantioselective toxicity. In addition, IM caused Lemna minor lipid peroxidation and antioxidant damage, and inhibited the activities of the target enzymes. Metabolomic and transcriptomic data indicated that R-IM interferenced differentially expressed genes and metabolites of Lemna minor which were enriched in carbon fixation during photosynthesis, glutathione metabolic pathway, pentose phosphate pathway, zeatin biosynthesis, and porphyrin and chlorophyll metabolism. S-IM affected phenylalanine metabolism, phenylpropanoid biosynthesis, zeatin biosynthesis and secondary metabolite biosynthesis. Racemic-IM influenced carbon fixation during operation, glutathione metabolic pathway, zeatin biosynthesis and pentose phosphate pathway. The results provide new insights into the enantioselective toxicity mechanisms of IM to Lemna minor, and lay the foundation for conducting environmental risk assessments.

Engineering ribose-5-phosphate isomerase B from a central carbon metabolic enzyme to a promising sugar biocatalyst

Ribose-5-phosphate isomerase B (RpiB) was first identified in the pentose phosphate pathway responsible for the inter-conversion of ribose-5-phosphate and ribulose-5-phosphate. Though there are seldom key enzymes in central carbon metabolic system developed as useful biocatalysts, RpiB with the advantages of wide substrate scope and high stereoselectivity has become a potential biotechnological tool to fulfill the demand of rare sugars currently. In this review, the pivotal roles of RpiB in carbon metabolism are summarized, and their sequence identity and structural similarity are discussed. Substrate binding and catalytic mechanisms are illustrated to provide solid foundations for enzyme engineering. Interesting differences in origin, physiological function, structure, and catalytic mechanism between RpiB and ribose-5-phosphate isomerase A are introduced. Moreover, enzyme engineering efforts for rare sugar production are stressed, and prospects of future development are concluded briefly in the viewpoint of biocatalysis. Aided by the progresses of structural and computational biology, the application of RpiB will be promoted greatly in the preparation of valuable molecules. KEY POINTS: • Detailed illustration of RpiB's vital function in central carbon metabolism. • Potential of RpiB in sequence, substrate scope, and mechanism for application. • Enzyme engineering efforts to promote RpiB in the preparation of rare sugars.

Ribose-5-phosphate isomerases: characteristics, structural features, and applications

Ribose-5-phosphate isomerase (Rpi, EC 5.3.1.6) is widespread in microorganisms, animals, and plants. It has a pivotal role in the pentose phosphate pathway and responsible for catalyzing the isomerization between D-ribulose 5-phosphate and D-ribose 5-phosphate. In recent years, Rpi has received considerable attention as a multipurpose biocatalyst for production of rare sugars, including D-allose, L-rhamnulose, L-lyxose, and L-tagatose. Besides, it has been thought of as a potential drug target in the treatment of trypanosomatid-caused diseases such as Chagas' disease, leishmaniasis, and human African trypanosomiasis. Despite increased research activities, up to now, no systematic review of Rpi has been published. To fill this gap, this paper provides detailed information about the enzymatic properties of various Rpis. Furthermore, structural features, catalytic mechanism, and molecular modifications of Rpis are summarized based on extensive crystal structure research. Additionally, the applications of Rpi in rare sugar production and the role of Rpi in trypanocidal drug design are reviewed. Key points • Fundamental properties of various ribose-5-phosphate isomerases (Rpis). • Differences in crystal structure and catalytic mechanism between RpiA and RpiB. • Application of Rpi as a rare sugar producer and a potential drug target.

Exploring Multifunctional Residues of Ribose-5-phosphate Isomerase B from Ochrobactrum sp. CSL1 Enhancing Isomerization of d-Allose

Ribose-5-phosphate isomerase B is of great importance for biocatalysis and biosynthesis, but the multifunctional residues in active sites hinder the research efforts. This study employed rational design strategies to locate the key residues of RpiB from Ochrobactrum sp. CSL1 (OsRpiB). A single-mutant S9T of a noncontact residue showed 80% activity improvement toward d-allose. A double-mutant S98H/S134H further increased the activity to 3.6-fold. The mutations were analyzed by kinetics and molecular dynamics analyses, indicating that S9T might enhance the substrate binding and catalysis by inducing a steric effect, and S98H/S134H could strengthen both ring opening and binding of d-allose. Though S98H/S134H showed low temperature stability, its potential was explored by isomerizing d-allose to d-psicose with higher conversion and in less reaction time. The findings of this study were beneficial for illustrating the complex functions of key residues in RpiBs and applying OsRpiB in preparing rare sugars.

Studying effects of different protonation states of His11 and His102 in ribose-5-phosphate isomerase of Trypanosoma cruzi: an example of cooperative behavior

The Trypanosoma cruzi ribose-5-phosphate isomerase B (TcRpiB) is a crucial piece in the pentose phosphate pathway and thus is a potential drug target for treatment of Chagas' disease. TcRpiB residues, such as Cys69, Asp45, Glu149 and Pro47, have confirmed their roles in substrate recognition, catalytic reaction and binding site conformation. However, the joint performance of His11 and His102, in the D-ribose-5-phosphate (R5P) in the catalysis is not well understood. In this work, we probed the influence of different protonation states of His11 and His102 on the behavior of the ligand R5P using molecular dynamics simulations, network analysis and thermodynamic integration. Simulations revealed that a protonated His11 combined with a neutral His102 (His11⁺‒His102) was able to stabilize the ligand R5P in the binding site. Moreover, calculated relative free energy differences showed that when protonated His11 was coupled to a neutral His102 an exergonic process takes place. On the other hand, neutral His11 combined with a protonated His102 (His11‒His102⁺), sampled conformations that resembled the catalyzed product D-ribulose-5-phosphate (Ru5P). Network analysis also demonstrated some peculiarities for these systems with some negatively correlated nodes in the binding site for His11‒His102⁺, and exclusive suboptimal paths for His11⁺‒His102. Therefore, the combined approach presented in this paper proposes two suitable protonation states for the TcRpiB catalytic mechanism, where an extra proton in either histidines might favor R5P binding or influence isomerization reaction to Ru5P. Our results may guide further in silico drug discovery studies. Communicated by Ramaswamy H. Sarma.

In silico identification of inhibitors of ribose 5-phosphate isomerase from Trypanosoma cruzi using ligand and structure based approaches

Chagas disease, caused by the protozoan Trypanosoma cruzi, affects approximately seven million people, mainly in Latin America, and causes about 7000 deaths annually. The available treatments are unsatisfactory and search for more effective drugs against this pathogen is critical. In this context, the ribose 5-phosphate isomerase (Rpi) enzyme is a potential drug target mainly due to its function in the pentose phosphate pathway and its essentiality (previously shown in other trypanosomatids). In this study, we propose novel potential inhibitors for the Rpi of T. cruzi (TcRpi) based on a computer-aided approach, including structure-based and ligand-based pharmacophore modeling. Along with a substructural and similarity search, the selected pharmacophore hypotheses were used to screen the purchasable subset of the ZINC Database, yielding 20,183 candidate compounds. These compounds were submitted to molecular docking studies in the TcRpi and Human Rpi (HsRpi) active sites in order to identify potential selective inhibitors for the T. cruzi enzyme. After the molecular docking and ADME-T (absorption, distribution, metabolism, excretion and toxicity)/PAINS (pan-assay interference compounds) screenings, 211 molecules were selected as potential TcRpi inhibitors. Out of these, three compounds - ZINC36975961, ZINC63480117, and ZINC43763931 - were submitted to molecular dynamics simulations and two of them - ZINC36975961 and ZINC43763931- had good performance and made interactions with important active site residues over all the simulation time. These compounds could be considered potential TcRpi inhibitors candidates and also may be used as leads for developing new TcRpi inhibitors.