Tracking the Evolution of Porphobilinogen Synthase Metal Dependence in Vitro

Formulation of Zinc oxide/Gum acacia nanocomposite as a novel slow-release fertilizer for enhancing Zn uptake and growth performance of Spinacia oleracea L

Zinc (Zn) deficiency has caused nutritional disorders in 17% of the world's population; thus, producing Zn-enriched plants as a dietary source is necessary. Recently, nanofertilizers have gained much attention as a substitute for conventional fertilizers; however, soil application of polymer-coated Zn-based nanofertilizer has not been explored much. The present study depicts the green synthesis of ZnO nanoparticles using Melia azedarach L. leaf extract, whose phytoconstituents have reducing abilities. The synthesized nanoparticles were combined with gum acacia (GA) to form a ZnOGA nanocomposite. The structural and morphological properties of ZnOGA were studied using XRD, FTIR, FESEM, and EDX. A pot experiment study was carried out with Spinacia oleracea L. at various doses (3, 5, and 10 mg/kg) of the synthesized ZnOGA to evaluate its effectiveness as a slow-release fertilizer and was compared with a commercial Zn fertilizer. The plant growth studies revealed a significant increase in the phyto-morphological traits of the plants fertilized with ZnOGA compared to commercial fertilizer. The plants also displayed significantly higher contents of protein (17-47%), phenols (25-60%), proline (82-94%), total soluble sugar (20-31%), DPPH activity (70-72%), and Zn uptake (91-106%). The doses of ZnOGA played an imperative role in determining the growth and productivity of the plant. Soil column studies showed that ZnOGA reduces Zn leaching by 52% compared to commercial Zn fertilizer. This study signifies the potential of ZnOGA to be applied as an eco-friendly and sustainable substitute for conventional Zn fertilizer minimizing Zn losses and Zn deficiency-related health problems in human populations.

Biochemical and molecular characterization of a novel porphobilinogen synthase from Corynebacterium glutamicum

Corynebacterium glutamicum porphobilinogen synthase (PBGS) is a metal enzyme with a hybrid active site metal binding sequence. In this study, the porphobilinogen synthase gene of C. glutamicum was cloned and heterogeneously expressed in Escherichia coli. C. glutamicum PBGS was purified, and its enzymatic characteristics were analyzed. The results showed that C. glutamicum PBGS is a Zn²⁺-dependent enzyme, and Mg²⁺ has allosteric regulation. The allosteric Mg²⁺ plays a vital role in forming the quaternary structure of C. glutamicum PBGS. Based on the ab initio predictive structure modeling of the enzyme and the molecular docking model of 5-aminolevulinic acid (5-ALA), 11 sites were selected for site-directed mutagenesis. When the hybrid active site metal binding site of C. glutamicum PBGS is converted into a cysteine-rich motif (Zn²⁺-dependent) or an aspartic acid-rich motif (Mg²⁺/K⁺-dependent), the enzyme activity is basically lost. Four residues, D128, C130, D132, and C140, in the metal binding site, were the binding sites of Zn²⁺ and the active center of the enzyme. The band migration, from the native PAGE, of five variants with mutations in the center of enzyme activity was the same as that of the variant enzymes as purified, individually adding two metal ion chelating agents. Their Zn²⁺ active center structures were abnormal, and the quaternary structure equilibrium was altered. The destroyed active center affects the construction of its quaternary structure. The quaternary structural balance between octamer and hexamer through dimers was regulated by the allosteric regulation of C. glutamicum PBGS. The enzyme activity was also affected by the change of the active site lid structure and (α β)₈-barrel structure caused by mutation. Structural changes in the variants were analyzed to understand C. glutamicum PBGS better.

Exploring human porphobilinogen synthase metalloprotein by quantum biochemistry and evolutionary methods

Previous studies have shown the porphobilinogen synthase (PBGS) zinc-binding mechanism and its conservation among the living cells. However, the precise molecular interaction of zinc with the active center of the enzyme is unknown. In particular, quantum chemistry techniques within the density functional theory (DFT) framework have been the key methodology to describe metalloproteins, when one is looking for a compromise between accuracy and computational feasibility. Considering this, we used DFT-based models within the molecular fractionation with conjugate caps scheme to evaluate the binding energy features of zinc interacting with the human PBGS. Besides, phylogenetic and clustering analyses were successfully employed in extracting useful information from protein sequences to identify groups of conserved residues that build the ions-binding site. Our results also report a conservative assessment of the relevant amino acids, as well as the benchmark analysis of the calculation models used. The most relevant intermolecular interactions in Zn2+-PBGS are due to the amino acids CYS0122, CYS0124, CYS0132, ASP0169, SER0168, ARG0221, HIS0131, ASP0120, GLY0133, VAL0121, ARG0209, and ARG0174. Among these residues, we highlighted ASP0120, GLY0133, HIS0131, SER0168, and ARG0209 by co-occurring in all clusters generated by unsupervised clustering analysis. On the other hand, the triple cysteines at 2.5 Å from zinc (CYS0122, CYS0124, and CYS0132) have the highest energy attraction and are absent in the taxa Viridiplantae, Sar, Rhodophyta, and some Bacteria. Additionally, the performance of the DFT-based models shows that the processing time-dependence is more associated with the choice of the basis set than the exchange-correlation functional.

Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product

The advent of heme during evolution allowed organisms possessing this compound to safely and efficiently carry out a variety of chemical reactions that otherwise were difficult or impossible. While it was long assumed that a single heme biosynthetic pathway existed in nature, over the past decade, it has become clear that there are three distinct pathways among prokaryotes, although all three pathways utilize a common initial core of three enzymes to produce the intermediate uroporphyrinogen III. The most ancient pathway and the only one found in the Archaea converts siroheme to protoheme via an oxygen-independent four-enzyme-step process. Bacteria utilize the initial core pathway but then add one additional common step to produce coproporphyrinogen III. Following this step, Gram-positive organisms oxidize coproporphyrinogen III to coproporphyrin III, insert iron to make coproheme, and finally decarboxylate coproheme to protoheme, whereas Gram-negative bacteria first decarboxylate coproporphyrinogen III to protoporphyrinogen IX and then oxidize this to protoporphyrin IX prior to metal insertion to make protoheme. In order to adapt to oxygen-deficient conditions, two steps in the bacterial pathways have multiple forms to accommodate oxidative reactions in an anaerobic environment. The regulation of these pathways reflects the diversity of bacterial metabolism. This diversity, along with the late recognition that three pathways exist, has significantly slowed advances in this field such that no single organism's heme synthesis pathway regulation is currently completely characterized.

Elemental economy: microbial strategies for optimizing growth in the face of nutrient limitation

Microorganisms play a dominant role in the biogeochemical cycling of nutrients. They are rightly praised for their facility for fixing both carbon and nitrogen into organic matter, and microbial driven processes have tangibly altered the chemical composition of the biosphere and its surrounding atmosphere. Despite their prodigious capacity for molecular transformations, microorganisms are powerless in the face of the immutability of the elements. Limitations for specific elements, either fleeting or persisting over eons, have left an indelible trace on microbial genomes, physiology, and their very atomic composition. We here review the impact of elemental limitation on microbes, with a focus on selected genetic model systems and representative microbes from the ocean ecosystem. Evolutionary adaptations that enhance growth in the face of persistent or recurrent elemental limitations are evident from genome and proteome analyses. These range from the extreme (such as dispensing with a requirement for a hard to obtain element) to the extremely subtle (changes in protein amino acid sequences that slightly, but significantly, reduce cellular carbon, nitrogen, or sulfur demand). One near-universal adaptation is the development of sophisticated acclimation programs by which cells adjust their chemical composition in response to a changing environment. When specific elements become limiting, acclimation typically begins with an increased commitment to acquisition and a concomitant mobilization of stored resources. If elemental limitation persists, the cell implements austerity measures including elemental sparing and elemental recycling. Insights into these fundamental cellular properties have emerged from studies at many different levels, including ecology, biological oceanography, biogeochemistry, molecular genetics, genomics, and microbial physiology. Here, we present a synthesis of these diverse studies and attempt to discern some overarching themes.

The tetrapyrrole biosynthetic pathway and its regulation in Rhodobacter capsulatus

The purple anoxygenic photosynthetic bacterium Rhodobacter capsulatus is capable of growing in aerobic or anaerobic conditions, in the dark or using light, etc. Achieving versatile metabolic adaptations from respiration to photosynthesis requires the use of tetrapyrroles such as heme and bacteriochlorophyll, in order to carry oxygen, to transfer electrons, and to harvest light energy. A third tetrapyrrole, cobalamin (vitamin B(12)), is synthesized and used as a cofactor for many enzymes. Heme, bacteriochlorophyll, and vitamin B(12) constitute three major end products of the tetrapyrrole biosynthetic pathway in purple bacteria. Their respective synthesis involves a plethora of enzymes, several that have been characterized and several that are uncharacterized, as described in this review. To respond to changes in metabolic requirements, the pathway undergoes complex regulation to direct the flow of tetrapyrrole intermediates into a specific branch(s) at the expense of other branches of the pathway. Transcriptional regulation of the tetrapyrrole synthesizing enzymes by redox conditions and pathway intermediates is reviewed. In addition, we discuss the involvement of several transcription factors (RegA, CrtJ, FnrL, AerR, HbrL, Irr) as well as the role of riboswitches. Finally, the interdependence of the tetrapyrrole branches on each other synthesis is discussed.

Structure of the heme biosynthetic Pseudomonas aeruginosa porphobilinogen synthase in complex with the antibiotic alaremycin

The recently discovered antibacterial compound alaremycin, produced by Streptomyces sp. A012304, structurally closely resembles 5-aminolevulinic acid, the substrate of porphobilinogen synthase. During the initial steps of heme biosynthesis, two molecules of 5-aminolevulinic acid are asymmetrically condensed to porphobilinogen. Alaremycin was found to efficiently inhibit the growth of both Gram-negative and Gram-positive bacteria. Using the newly created heme-permeable strain Escherichia coli CSA1, we are able to uncouple heme biosynthesis from bacterial growth and demonstrate that alaremycin targets the heme biosynthetic pathway. Further studies focused on the activity of alaremycin against the opportunistic pathogenic bacterium Pseudomonas aeruginosa. The MIC of alaremycin was determined to be 12 mM. Alaremycin was identified as a direct inhibitor of recombinant purified P. aeruginosa porphobilinogen synthase and had a K(i) of 1.33 mM. To understand the molecular basis of alaremycin's antibiotic activity at the atomic level, the P. aeruginosa porphobilinogen synthase was cocrystallized with the alaremycin. At 1.75-A resolution, the crystal structure reveals that the antibiotic efficiently blocks the active site of porphobilinogen synthase. The antibiotic binds as a reduced derivative of 5-acetamido-4-oxo-5-hexenoic acid. The corresponding methyl group is, however, not coordinated by any amino acid residues of the active site, excluding its functional relevance for alaremycin inhibition. Alaremycin is covalently bound by the catalytically important active-site lysine residue 260 and is tightly coordinated by several active-site amino acids. Our data provide a solid structural basis to further improve the activity of alaremycin for rational drug design. Potential approaches are discussed.

The biochemistry of heme biosynthesis

Heme is an integral part of proteins involved in multiple electron transport chains for energy recovery found in almost all forms of life. Moreover, heme is a cofactor of enzymes including catalases, peroxidases, cytochromes of the P(450) class and part of sensor molecules. Here the step-by-step biosynthesis of heme including involved enzymes, their mechanisms and detrimental health consequences caused by their failure are described. Unusual and challenging biochemistry including tRNA-dependent reactions, radical SAM enzymes and substrate derived cofactors are reported.

Probing the active site of Pseudomonas aeruginosa porphobilinogen synthase using newly developed inhibitors

Porphobilinogen synthase catalyzes the first committed step of the tetrapyrrole biosynthesis pathway. In an aldol-like condensation, two molecules of 5-aminolevulinic acid (ALA) form the first pyrrole, porphobilinogen. Newly synthesized analogues of a reaction intermediate of porphobilinogen synthase have been employed in studying the active site and the catalytic mechanism of this early enzyme of tetrapyrrole biosynthesis. This study combines structural and kinetic evaluation of the inhibition potency of these inhibitors. In addition, one of the determined protein structures provides for the first time structural evidence of a magnesium ion in the active site. From these results, we can corroborate an earlier postulated enzymatic mechanism that starts with formation of a C-C bond, linking C3 of the A-side ALA to C4 of the P-side ALA through an aldole addition. The obtained data are discussed with respect to the current literature.