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Biomedical subjects

Huimin Zhao

Publications and source records attributed to Huimin Zhao.

At least 19 recordsLinked to original sources
PubMed2026

Accelerating natural product discovery, characterization and engineering by biofoundries.

Covering: From early developments to the presentNatural product (NP) discovery is increasingly constrained by low-throughput screening, repeated rediscovery, and challenges in scaling genome mining-guided validation workflows. This highlight examines how automated biofoundries are accelerating NP discovery, characterization, and engineering through integrated design-build-test-learn (DBTL) cycles. We discuss recent advances in phenotype-first and genome-first discovery strategies enabled by robotics, high-throughput pathway reconstitution, and automated screening platforms. We further highlight emerging technologies, including cell-free biosynthesis, automated culturomics, programmable chassis engineering, and AI-assisted workflow orchestration, that may enable increasingly autonomous biofoundries for scalable exploration of NP chemical space and therapeutic discovery.

Journal Article↗
PubMed2026

Discovery and engineering of enzymes for new-to-nature photobiocatalysis.

Photobiocatalysis integrates enzymatic catalysis with photochemistry, enabling challenging radical transformations with high selectivity under mild conditions. Early developments in this field were largely driven by the discovery that enzyme-bound cofactors can form photoactive charge-transfer complexes with substrates, thereby initiating radical chemistry upon light irradiation. Recent advances, however, have substantially expanded the mechanistic landscape of photobiocatalysis through diverse mechanisms. This review summarizes major developments in photobiocatalysis reported since 2024. Rather than cataloging individual reactions, we focus on the fundamental mechanisms of radical generation and interception within enzyme active sites, and discuss how these mechanistic principles guide the discovery, engineering, and design of enzymes for new-to-nature photobiocatalysis.

Protein Engineering↗
PubMed2026

Acidic transcription factors position the genome at nuclear speckles through transcription-dependent and -independent mechanisms.

A small fraction of the genome reproducibly positions near nuclear speckles (NSs), increasing the expression and/or splicing efficiency of NS-associated genes. How specific genomic regions in mammalian cells are targeted to NSs remains unclear. Here, we demonstrate the establishment of genome-wide NS association without active transcription. We show that DNA sequences derived from NS-associated regions, when integrated as transgenes, are autonomously targeted to NSs. By systematically dissecting one such genomic locus, the COL1A1-SGCA locus, we identified redundant NS-targeting cis-regulatory elements, including an ∼600-bp fragment with 17 binding motifs for 8 transcription factors (TFs). Four NS-targeting TFs within this fragment contain acidic activation domains (AADs) that provide both chromatin-context and transcription-dependent NS targeting, properties that appear to be common among several other tested AADs. A subset of acidic activator TFs contains an additional, transcription-independent NS-targeting activity. Our findings establish diverse and partially redundant NS-targeting activities, which may facilitate dynamic gene positioning at the NS periphery for context-specific transcriptional responses.

Transcription, Genetic↗
PubMed2025

Synteny plot quality control with SyntenyQC.

SUMMARY: SyntenyQC is a data pre-processing tool for the construction of synteny plots. It supports genomic data collection, annotation and dereplication to facilitate (and in some cases fundamentally enable) the construction of informative synteny plots. AVAILABILITY AND IMPLEMENTATION: SyntenyQC is a command line app developed using Python version 3.10 and tested using pytest. SyntenyQC is available on PyPI (https://pypi.org/project/SyntenyQC) under the MIT License, along with a detailed user tutorial. Package tests can be viewed at https://github.com/Tim-Kirkwood/SyntenyQC.

Synteny↗
PubMed2007

Efficient regeneration of NADPH using an engineered phosphite dehydrogenase.

The in situ regeneration of reduced nicotinamide cofactors (NAD(P)H) is necessary for practical synthesis of many important chemicals. Here, we report the engineering of a highly stable and active mutant phosphite dehydrogenase (12x-A176R PTDH) from Pseudomonas stutzeri and evaluation of its potential as an effective NADPH regeneration system in an enzyme membrane reactor. Two practically important enzymatic reactions including xylose reductase-catalyzed xylitol synthesis and alcohol dehydrogenase-catalyzed (R)-phenylethanol synthesis were used as model systems, and the mutant PTDH was directly compared to the commercially available NADP(+)-specific Pseudomonas sp. 101 formate dehydrogenase (mut Pse-FDH) that is widely used for NADPH regeneration. In both model reactions, the two regeneration enzymes showed similar rates of enzyme activity loss; however, the mutant PTDH showed higher substrate conversion and higher total turnover numbers for NADP(+) than mut Pse-FDH. The space-time yields of the product with the mutant PTDH were also up to fourfold higher than those with mut Pse-FDH. In particular, a space-time yield of 230 g L(-1) d(-1) xylitol was obtained with the mutant PTDH using a charged nanofiltration membrane, representing the highest productivity compared to other existing biological processes for xylitol synthesis based on yeast D-xylose converting strains or similar in vitro enzyme membrane reactor systems.

Enzyme Activation↗
PubMed2006

Fabrication and characterization of silica/titania nanotubes composite membrane with photocatalytic capability.

Silica/titania nanotubes composite membranes were successfully prepared from silica/titania sols using porous alumina support membranes. XRD patterns of the composite membranes confirmed that the embedding of amorphous silica into nanophase titania matrix helped to increase the thermal stability of titania which suppressed the phase transformation from anatase to rutile and decreased the size of titania particles. Ninety-five percent of the pore volume of composite membrane was located in mesopores with diameters ranging from 1.4 to 10 nm. The surface of these composite membranes exhibited extremely high affinity for water under UV irradiation with water contact angle decreased from 62 degrees to nearly 5 degrees within 80 min. By coupling membrane separation with photocatalysis technique, the removal efficiency of Direct Black 168 was improved remarkably; being 85% within 100 min, while the values were 66% and 73% with photocatalysis alone or membrane separation alone during the same time, respectively. Good photocatalytic activity and wettability of composite membrane under UV irradiation helped to obtain high permeate flux across the composite membrane. The silica/titania nanotubes composite membrane had the multifunctions of separation, degradation, and improvement of membrane flux in photooxidation of organic contaminants in wastewater.

Aluminum Oxide↗
PubMed2006

Engineering and characterization of human manganese superoxide dismutase mutants with high activity and low product inhibition.

Human manganese superoxide dismutase is a mitochondrial metalloenzyme that is involved in protecting aerobic organisms against superoxide toxicity, and has been implicated in slowing tumor growth. Unfortunately, this enzyme exhibits strong product inhibition, which limits its potential biomedical applications. Previous efforts to alleviate human manganese superoxide dismutase product inhibition utilized rational protein design and site-directed mutagenesis. These efforts led to variants of human manganese superoxide dismutase at residue 143 with dramatically reduced product inhibition, but also reduced catalytic activity and efficiency. Here, we report the use of a directed evolution approach to engineer two variants of the Q143A human manganese superoxide dismutase mutant enzyme with improved catalytic activity and efficiency. Two separate activity-restoring mutations were found--C140S and N73S--that increase the catalytic efficiency of the parent Q143A human manganese superoxide dismutase enzyme by up to five-fold while maintaining low product inhibition. Interestingly, C140S is a context-dependent mutation, and the C140S-Q143A human manganese superoxide dismutase did not follow Michaelis-Menten kinetics. The re-engineered human manganese superoxide dismutase mutants should be useful for biomedical applications, and our kinetic and structural studies also provide new insights into the structure-function relationships of human manganese superoxide dismutase.

Catalysis↗
PubMed2006

Characterization of the substrate specificity of PhlD, a type III polyketide synthase from Pseudomonas fluorescens.

PhlD, a type III polyketide synthase from Pseudomonas fluorescens, catalyzes the synthesis of phloroglucinol from three molecules of malonyl-CoA. Kinetic analysis by direct measurement of the appearance of the CoASH product (k(cat) = 24 +/- 4 min(-1) and Km = 13 +/- 1 microM) gave a k(cat) value more than an order of magnitude higher than that of any other known type III polyketide synthase. PhlD exhibits broad substrate specificity, accepting C4-C12 aliphatic acyl-CoAs and phenylacetyl-CoA as the starters to form C6-polyoxoalkylated alpha-pyrones from sequential condensation with malonyl-CoA. Interestingly, when primed with long chain acyl-CoAs, PhlD catalyzed extra polyketide elongation to form up to heptaketide products. A homology structural model of PhlD showed the presence of a buried tunnel extending out from the active site to assist the binding of long chain acyl-CoAs. To probe the structural basis for the unusual ability of PhlD to accept long chain acyl-CoAs, both site-directed mutagenesis and saturation mutagenesis were carried out on key residues lining the tunnel. Three mutations, M21I, H24V, and L59M, were found to significantly reduce the reactivity of PhlD with lauroyl-CoA while still retaining its physiological activity to synthesize phloroglucinol. Our homology modeling and mutational studies indicated that even subtle changes in the tunnel volume could affect the ability of PhlD to accept long chain acyl-CoAs. This suggested novel strategies for combinatorial biosynthesis of unnatural pharmaceutically important polyketides.

Bacterial Proteins↗
PubMed2006

Degradation of p-nitrophenol in aqueous solution by microwave assisted oxidation process through a granular activated carbon fixed bed.

A microwave (MW) assisted oxidation process was investigated for degradation of p-nitrophenol (PNP) from aqueous solution. The process consisted of a granular activated carbon (GAC) fixed bed reactor, a MW source, solution and air supply system, and a heat exchanger. The process was operated in continuous flow mode. Air was applied for oxygen supply. GAC acted as a MW energy absorption material as well as the catalyst for PNP degradation. MW power, air flow, GAC dose, and influent flow proved to be major factors which influenced PNP degradation. The results showed that PNP was degraded effectively by this new process. Under a given condition (PNP concentration 1330mg/L, MW power 500 W, influent flow 6.4 mL/min, air flow 100 mL/min), PNP removed 90%, corresponding to 80% of TOC removal. The pathway of PNP degradation was deduced based on GC-MS identification of course products. PNP experienced sequential oxidation steps and mineralized ultimately. Nitro-group of PNP converted to nitrite and nitrate. Biodegradability of the solution was improved apparently after treatment by MW assisted oxidation process, which benefit to further treatment of the solution using biochemical method.

Adsorption↗
PubMed2006

Photoelectrocatalytic degradation of pentachlorophenol in aqueous solution using a TiO2 nanotube film electrode.

Titanium dioxide (TiO2) nanotube film electrodes are fabricated by the anodic oxidation method. Scanning electron microscopy (SEM) showed that these tubes were well aligned and organized into high-density uniform arrays. XRD analysis showed the TiO2 nanotubes to be in the anatase crystal form. The TiO2 nanotube film electrode exhibited increased photoelectrocatalytic (PEC) capability compared to a traditional TiO2 film electrode fabricated using the anodizing method for pentachlorophenol (PCP) degradation in aqueous solution. The bias potential, pH value, and electrolyte concentration were shown to be important factors influencing the degradation of PCP by the PEC method using the TiO2 nanotube film electrode as the working electrode.

Catalysis↗
PubMed2006

Directed evolution of enzymes and biosynthetic pathways.

Directed evolution is an important tool for overcoming the limitations of natural enzymes as biocatalysts. Recent advances have focused on applying directed evolution to a variety of enzymes, such as epoxide hydrolase, glyphosate N-acetyltransferase, xylanase and phosphotriesterase, in order to improve their activity, selectivity, stability and solubility. The focus has also shifted to manipulating biosynthetic pathways for the production of many naturally synthesized compounds, as well as the production of novel 'unnatural' compounds. A combined directed evolution and computational design approach is becoming increasingly important in exploring enzyme sequence-space and creating improved or novel enzymes. Fueled by recent breakthroughs in genomics and metagenomics, these developments should help expand the use of biocatalysts in industry.

Anti-Infective Agents↗
PubMed2006

Electrochemically enhanced adsorption of phenol on activated carbon fibers in basic aqueous solution.

Electrosorption isotherms and thermodynamics of phenol on activated carbon fibers (ACFs) in basic solution, as well as the factors (bias potential, initial concentration, and electrolyte) affecting adsorption/electrosorption kinetics, were investigated. The kinetics, which followed the Lagergren adsorption rate law, exhibited a variety of responses depending on bias potential, initial concentration, and electrolyte. The electrosorption isotherms were in agreement with the classical models of Langmuir and Freundlich, but the former gave more satisfactory correlation coefficients. With electrosorption at a bias potential of 700 mV from the basic solution, a nearly 10-fold enhancement of maximum adsorption capacity was achievable. The electrosorption free energy (DeltaG(ads)), enthalpy (DeltaH(ads)), and entropy (DeltaS(ads)) of phenol on the ACFs were calculated from adsorption isotherms at different temperatures. The results indicated that electrosorption of phenol in basic solution was spontaneous and exothermic. Furthermore, it was assessed that electrosorption occurred by dipole-dipole interaction with DeltaH(ads) of -20.14 kJ mol(-1) besides suppositional electrostatic interaction.

Journal Article↗
PubMed2006

Atmospheric PCDD/F and PCB levels implicated by pine (Cedrus deodara) needles at Dalian, China.

Dalian is a seaside city situated in the northeastern monsoon area of China. For the first time, levels of PCDD/F and PCB congeners in pine (Cedrus deodara) needles of Dalian urban areas were investigated. Two sampling campaigns with 17 sampling points were performed in 2002. The summation of tetra- to octachlorinated PCDD/Fs and summation of 209 PCB congeners in Dalian pine needles averaged 127+/-40 ng/kg (dry) and 4389+/-1575 ng/kg (dry), respectively. Average toxic equivalence (TEQ) for PCDD/Fs and PCBs are 2.1 and 0.4 ng/kg (dry), respectively. The pine needles can differentiate spatial variation of the pollutants. The PCDD/F and PCB levels in Dalian pine needles are low or comparable with other international regions that were not impacted by evident point sources. The data can serve as a base for long-term spatial and temporal studies of PCDD/Fs and PCBs in China.

China↗
PubMed2006

Microbial synthesis of triacetic acid lactone.

Native g2ps1-encoded 2-pyrone synthase (2-PS) from Gerbera hybrida, a mutant Brevibacterium ammoniagenes fatty acid synthase B (FAS-B) and two different mutants of Penicillium patulum 6-methylsalycilic acid synthase (6-MSAS) are examined to identify the best enzyme to recruit for the microbial synthesis of triacetic acid lactone (TAL). To identify the best microbial host for these evaluations, the native TAL-synthesizing activity of g2ps1-encoded 2-PS is expressed in recombinant Escherichia coli and Saccharomyces cerevisiae constructs. Five-fold higher expression levels of 2-PS are observed in S. cerevisiae. Consequently, microbial synthesis of TAL focuses on S. cerevisiae constructs. Comparison of different promoters for the expression of g2ps1 in S. cerevisiae indicates that the alcohol dehydrogenase II promoter (P(ADH2)) affords the highest expression levels of 2-PS. As a result, the genes encoding the various TAL-synthesizing enzyme activities are expressed in S. cerevisiae from a P(ADH2) promoter. To extend TAL-synthesizing activity beyond g2ps1-encoded 2-PS, the ketoreductase domains of fasB-encoded FAS-B and 6-MSAS-encoded 6-MSAS are modified using a single mutation. Modification of the nicotinamide cofactor-binding site of 6-MSAS with a triple mutation is also examined. Separate S. cerevisiae constructs expressing native g2ps1, mutant Y2226F fasB, mutant Y1572F 6-MSAS, and mutant G1419A-G1421P-G1424A 6-MSAS are cultured under the same fermentor-controlled conditions. The highest concentration (1.8 g/L) and yield (6%) of TAL are synthesized from glucose by S. cerevisiae expressing the Y1572F mutant of 6-MSAS.

Acyltransferases↗
PubMed2006

Heterologous production of fosfomycin and identification of the minimal biosynthetic gene cluster.

Fosfomycin is a clinically utilized, highly effective antibiotic, which is active against methicillin- and vancomycin-resistant pathogens. Here we report the cloning and characterization of a complete fosfomycin biosynthetic cluster from Streptomyces fradiae and heterologous production of fosfomycin in S. lividans. Sequence analysis coupled with gene deletion and disruption revealed that the minimal cluster consists of fom1-4, fomA-D. A LuxR-type activator that was apparently required for heterologous fosfomycin production was also discovered approximately 13 kb away from the cluster and was named fomR. The genes fomE and fomF, previously thought to be involved in fosfomycin biosynthesis, were shown not to be essential by gene disruption. This work provides new insights into fosfomycin biosynthesis and opens the door for fosfomycin overproduction and creation of new analogs via biomolecular pathway engineering.

Alkyl and Aryl Transferases↗