Accumulation of d-glucose from pentoses by metabolically engineered Escherichia coli

Functional consequences of lysine acetylation of phosphofructokinase isozymes

Phosphofructokinase (Pfk) catalyzes the phosphorylation of fructose 6-phosphate and is a key regulatory point in the glycolysis pathway. Multiple lysine residues in both Pfk isozymes, PfkA and PfkB, have been identified to be acetylated in Escherichia coli by proteomic studies, but no studies have been implemented to further characterize these acetylation events. To investigate the role of Pfk acetylation, the genetic code expansion strategy was used to generate homogeneously acetylated Pfk variants at target lysine sites that have been reported to be acetylated in nature. We found that acetylation of K309 of PfkA and K27 of PfkB decreased PfK enzyme activities significantly. We further investigated the deacetylation and acetylation processes of Pfk isozymes biochemically and genetically. Acetyl phosphate-mediated non-enzymatic acetylation could be the major mechanism of Pfk isozyme acetylation in E. coli, whereas NAD-dependent protein deacylase CobB can remove most of the acetylated lysine residues but not K309 of PfkA and K27 of PfkB, which affect enzyme activities. Because of the important role of Pfk in cellular metabolism, the results of the present study are expected to facilitate studies in the fields of metabolic engineering and research.

Structural basis of collagen glucosyltransferase function and its serendipitous role in kojibiose synthesis

Collagen glucosyltransferases catalyze a unique type of collagen glucosylation that is critical for biological processes and disease mechanisms. However, the structural regulation of collagen glucosyltransferases remains poorly understood. Here, we report the crystal structures of a mimiviral collagen glucosyltransferase in its apo form and in complexes with uridine diphosphate (UDP) and the disaccharide product. Our findings reveal that the enzyme functions as a homodimer, stabilized by a loop from one subunit locking into a cleft on the opposite subunit. This dimerization enables UDP-glucose binding cooperativity and enzymatic activity, a property conserved in the human homolog. Further structural analyses suggest an induced fit model for UDP interaction, mediated by Lysine 222. The dimerization also forms an extended cleft flanked by two active sites, which likely facilitates collagen recognition. Unexpectedly, we discovered that the mimiviral collagen glucosyltransferase can also synthesize the prebiotic disaccharide kojibiose. An elongated pocket adjacent to the UDP-binding site allows the enzyme to use UDP-glucose as the sugar donor and glucose as the acceptor for kojibiose production. Enzymatic activity assays confirmed the enzyme's novel kojibiose synthesis activity in vitro and in vivo. These structural insights not only inform glucosyltransferase function but also open new avenues for biomedicine.

Compositional and temporal division of labor modulates mixed sugar fermentation by an engineered yeast consortium

Synthetic microbial communities have emerged as an attractive route for chemical bioprocessing. They are argued to be superior to single strains through microbial division of labor (DOL), but the exact mechanism by which DOL confers advantages remains unclear. Here, we utilize a synthetic Saccharomyces cerevisiae consortium along with mathematical modeling to achieve tunable mixed sugar fermentation to overcome the limitations of single-strain fermentation. The consortium involves two strains with each specializing in glucose or xylose utilization for ethanol production. By controlling initial community composition, DOL allows fine tuning of fermentation dynamics and product generation. By altering inoculation delay, DOL provides additional programmability to parallelly regulate fermentation characteristics and product yield. Mathematical models capture observed experimental findings and further offer guidance for subsequent fermentation optimization. This study demonstrates the functional potential of DOL in bioprocessing and provides insight into the rational design of engineered ecosystems for various applications.

Whole genome sequencing and analysis of selenite-reducing bacteria Bacillus paralicheniformis SR14 in response to different sugar supplements

The biosynthetic process of selenium nanoparticles (SeNPs) by specific bacterial strain, whose growth directly affects the synthesis efficiency, has attracted great attentions. We previously reported that Bacillus paralicheniformis SR14, a SeNPs-producing bacteria, could improve intestinal antioxidative function in vitro. To further analyze the biological characteristics of SR14, whole genome sequencing was used to reveal the genetic characteristics in selenite reduction and sugar utilization. The results reviewed that the genome size of SR14 was 4,448,062 bp, with a GC content of 45.95%. A total of 4300 genes into 49 biological pathways was annotated to the KEGG database. EC: 1.1.1.49 (glucose-6-phosphate 1-dehydrogenase) and EC: 5.3.1.9 (glucose-6-phosphate isomerase), were found to play a potential role in glucose degradation and EC:2.7.1.4 (fructokinase) might be involved in the fructose metabolism. Growth profile and selenite-reducing ability of SR14 under different sugar supplements were determined and the results reviewed that glucose had a better promoting effect on the reduction of selenite and growth of bacteria than fructose, sucrose, and maltose. Moreover, RT-qPCR experiment proved that glucose supplement remarkably promoted the expressions of thioredoxin, fumarate reductase, and the glutathione peroxidase in SR14. Analysis of mRNA expression showed levels of glucose-6-phosphate dehydrogenase and fructokinase significantly upregulated under the supplement of glucose. Overall, our data demonstrated the genomic characteristics of SR14 and preliminarily determined that glucose supplement was most beneficial for strain growth and SeNPs synthesis.

Direct conversion of carbon dioxide to glucose using metabolically engineered Cupriavidus necator

Artificial synthesis of glucose, the monomer of starch, from renewable resources and CO₂ is a promising method for addressing food crisis and alleviating climate change. Here, the construction of a microbial biocatalyst for glucose production from renewable resources and CO₂ was reported. Initially, blocking the glucose catabolic pathway via deletion of glk gene generated a glucose-producing strain of Cupriavidus necator with titers of 24.7, 47.5 and 180.1 mg/L from fructose, glycerol and CO₂, respectively. Subsequently, the Entner-Doudoroff pathway and polyhydroxybutyrate biosynthesis pathway were disrupted to further increase glucose accumulation. The maximum glucose titer and yield on biomass from CO₂ reached 253.3 mg/L and 91.6 mg/L/OD₆₀₀, respectively. Finally, the phosphatases that mediate the dephosphorylation of phosphorylated glucose were identified. Overexpression of HAD1 and cbbY2 could enhance glucose titer by 5.5-fold when fructose was used as sole carbon source. This study demonstrates a feasible route for microbial-based synthesis of glucose from CO₂.

Phosphatases and phosphate affect the formation of glucose from pentoses in Escherichia coli

Metabolically engineered Escherichia coli MEC143 with deletions of the ptsG, manZ, glk, pfkA, and zwf genes converts pentoses such as arabinose and xylose into glucose, with the dephosphorylation of glucose-6-phosphate serving as the final step. To determine which phosphatase mediates this conversion, we examined glucose formation from pentoses in strains containing knockouts of six different phosphatases singly and in combination. Deletions of single phosphatases and combinations of multiple phosphatases did not eliminate the accumulation of glucose from xylose or arabinose. Overexpression of one phosphatase, haloacid dehalogenase-like phosphatase 12 coded by the ybiV gene, increased glucose yield significantly from 0.26 to 0.30 g/g (xylose) and from 0.32 to 0.35 g/g (arabinose). Growing cells under phosphate-limited steady-state conditions increased the glucose yield to 0.39 g glucose/g xylose, but did not affect glucose yield from arabinose (0.31 g/g). No single phosphatase is exclusively responsible for the conversion of glucose-6-phosphate to glucose in E. coli MEC143. Phosphate-limited conditions are indeed able to enhance glucose formation in some cases, with this effect likely influenced by the different phosphate demands when E. coli metabolizes different carbon sources.

Structural Basis for the Interconversion of Maltodextrins by MalQ, the Amylomaltase of Escherichia coli

Amylomaltase MalQ is essential for the metabolism of maltose and maltodextrins in Escherichia coli. It catalyzes transglycosylation/disproportionation reactions in which glycosyl or dextrinyl units are transferred among linear maltodextrins of various lengths. To elucidate the molecular basis of transglycosylation by MalQ, we have determined three crystal structures of this enzyme, i.e. the apo-form, its complex with maltose, and an inhibitor complex with the transition state analog acarviosine-glucose-acarbose, at resolutions down to 2.1 Å. MalQ represents the first example of a mesophilic bacterial amylomaltase with known structure and exhibits an N-terminal extension of about 140 residues, in contrast with previously described thermophilic enzymes. This moiety seems unique to amylomaltases from Enterobacteriaceae and folds into two distinct subdomains that associate with different parts of the catalytic core. Intriguingly, the three MalQ crystal structures appear to correspond to distinct states of this enzyme, revealing considerable conformational changes during the catalytic cycle. In particular, the inhibitor complex highlights the requirement of both a 3-OH group and a 4-OH group (or α1-4-glycosidic bond) at the acceptor subsite +1 for the catalytically competent orientation of the acid/base catalyst Glu-496. Using an HPLC-based MalQ enzyme assay, we could demonstrate that the equilibrium concentration of maltodextrin products depends on the length of the initial substrate; with increasing numbers of glycosidic bonds, less glucose is formed. Thus, both structural and enzymatic data are consistent with the extremely low hydrolysis rates observed for amylomaltases and underline the importance of MalQ for the metabolism of maltodextrins in E. coli.