scholarly journals Pollutant Degrading Enzyme: Catalytic Mechanisms and Their Expanded Applications

Molecules ◽  
2021 ◽  
Vol 26 (16) ◽  
pp. 4751
Author(s):  
Anming Xu ◽  
Xiaoxiao Zhang ◽  
Shilei Wu ◽  
Ning Xu ◽  
Yan Huang ◽  
...  
Keyword(s):  
Gene Editing ◽  
High Efficiency ◽  
Catalytic Mechanism ◽  
Enzyme Level ◽  
Environmental Pollutants ◽  
Degrading Enzyme ◽  
Degrading Enzymes ◽  
Microbial Biodegradation ◽  
Catalytic Mechanisms ◽  
External Intervention

The treatment of environmental pollution by microorganisms and their enzymes is an innovative and socially acceptable alternative to traditional remediation approaches. Microbial biodegradation is often characterized with high efficiency as this process is catalyzed via degrading enzymes. Various naturally isolated microorganisms were demonstrated to have considerable ability to mitigate many environmental pollutants without external intervention. However, only a small fraction of these strains are studied in detail to reveal the mechanisms at the enzyme level, which strictly limited the enhancement of the degradation efficiency. Accordingly, this review will comprehensively summarize the function of various degrading enzymes with an emphasis on catalytic mechanisms. We also inspect the expanded applications of these pollutant-degrading enzymes in industrial processes. An in-depth understanding of the catalytic mechanism of enzymes will be beneficial for exploring and exploiting more degrading enzyme resources and thus ameliorate concerns associated with the ineffective biodegradation of recalcitrant and xenobiotic contaminants with the help of gene-editing technology and synthetic biology.

scholarly journals Cuticle degrading enzyme production by some isolates of the entomopathogenic fungus, Metarhizium anisopliae (Metsch.)

2014 ◽  
Vol 20 ◽  
pp. 25-32
Author(s):  
N Sapna Bai ◽  
OK Remadevi ◽  
TO Sasidharan ◽  
M Balachander ◽  
Priyadarsanan Dharmarajan
Keyword(s):  
Pest Control ◽  
Entomopathogenic Fungi ◽  
Enzyme Production ◽  
Insect Pest ◽  
Strong Relationship ◽  
Control Agent ◽  
Mechanical Pressure ◽  
Degrading Enzyme ◽  
Insect Pest Control ◽  
Degrading Enzymes

Context: Entomopathogenic fungi have been recognized as viable alternate options to chemicals in insect pest control. Unlike other potential biocontrol agents, fungi do not have to be ingested to infect their hosts but invade directly through the cuticle. Entry into the host involves both enzymic degradation of the cuticle barrier and mechanical pressure. Production of a range of cuticle degrading enzymes is an important event in the interaction of entomopathogenic fungi and host. Enzyme secretion is believed to be a key contributor for the virulence of a fungal isolate. Objectives: The potentiality of nine isolates of M. anisopliae were tested to produce to produce three important cuticle degrading enzymes, viz., chitinase, protease and lipase. Materials and Methods: Nine isolates of M. anisopliae were evaluated for chitinase, protease and lipase enzyme production by determining the enzyme index and activities. Results: Chitinase index of these isolates were ranged from 1.5 to 2.2 and chitinolytic activity from 0.525 to 1.560 U/ml. The isolates showed protease index in the range of 1.2 to 3.3 and the activity ranged from 0.020 to 0.114 U/ml. Lipase index ranged from 1.15 to 7.0 and the enzyme activity ranged from 0.153 to 0.500 U/ml. A strong relationship was observed between virulence of the isolates and cuticle degrading enzyme production as increased enzyme production was observed for virulent isolates. Conclusion: In the present study three isolates as (MIS2, MIS7 and MIS13) demonstrated cuticle degrading enzyme (CDE) that indicate higher virulence based on the bioassay conducted earlier by the authors as strongly substantiating the role of CDEs is considered the virulence of Metarhizium isolates. So, these isolates may be as ecofriendly insect-pest control agent in future. DOI: http://dx.doi.org/10.3329/jbs.v20i0.17648 J. bio-sci. 20: 25-32, 2012

scholarly journals Functional dissection of the catalytic mechanism of mammalian RNA polymerase II

2005 ◽  
Vol 83 (4) ◽  
pp. 497-504 ◽  
Author(s):  
Benoit Coulombe ◽  
Marie-France Langelier
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Catalytic Mechanism ◽  
Mutational Analysis ◽  
Structural Elements ◽  
Catalytic Mechanisms ◽  
Rnap Ii ◽  
Affinity Peptide

High resolution X-ray crystal structures of multisubunit RNA polymerases (RNAP) have contributed to our understanding of transcriptional mechanisms. They also provided a powerful guide for the design of experiments aimed at further characterizing the molecular stages of the transcription reaction. Our laboratory used tandem-affinity peptide purification in native conditions to isolate human RNAP II variants that had site-specific mutations in structural elements located strategically within the enzyme's catalytic center. Both in vitro and in vivo analyses of these mutants revealed novel features of the catalytic mechanisms involving this enzyme.Key words: RNA polymerase II, transcriptional mechanisms, mutational analysis, mRNA synthesis.

scholarly journals In vivo genome editing in mouse restores dystrophin expression in Duchenne muscular dystrophy patient muscle fibers

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Menglong Chen ◽  
Hui Shi ◽  
Shixue Gou ◽  
Xiaomin Wang ◽  
Lei Li ◽  
...  
Keyword(s):  
Duchenne Muscular Dystrophy ◽  
Muscular Dystrophy ◽  
Mouse Model ◽  
Genome Editing ◽  
Large Scale ◽  
Gene Editing ◽  
High Efficiency ◽  
Muscle Fibers ◽  
Muscle Cells

Abstract Background Mutations in the DMD gene encoding dystrophin—a critical structural element in muscle cells—cause Duchenne muscular dystrophy (DMD), which is the most common fatal genetic disease. Clustered regularly interspaced short palindromic repeat (CRISPR)-mediated gene editing is a promising strategy for permanently curing DMD. Methods In this study, we developed a novel strategy for reframing DMD mutations via CRISPR-mediated large-scale excision of exons 46–54. We compared this approach with other DMD rescue strategies by using DMD patient-derived primary muscle-derived stem cells (DMD-MDSCs). Furthermore, a patient-derived xenograft (PDX) DMD mouse model was established by transplanting DMD-MDSCs into immunodeficient mice. CRISPR gene editing components were intramuscularly delivered into the mouse model by adeno-associated virus vectors. Results Results demonstrated that the large-scale excision of mutant DMD exons showed high efficiency in restoring dystrophin protein expression. We also confirmed that CRISPR from Prevotella and Francisella 1(Cas12a)-mediated genome editing could correct DMD mutation with the same efficiency as CRISPR-associated protein 9 (Cas9). In addition, more than 10% human DMD muscle fibers expressed dystrophin in the PDX DMD mouse model after treated by the large-scale excision strategies. The restored dystrophin in vivo was functional as demonstrated by the expression of the dystrophin glycoprotein complex member β-dystroglycan. Conclusions We demonstrated that the clinically relevant CRISPR/Cas9 could restore dystrophin in human muscle cells in vivo in the PDX DMD mouse model. This study demonstrated an approach for the application of gene therapy to other genetic diseases.

scholarly journals Highly efficient generation of canker resistant sweet orange enabled by an improved CRISPR/Cas9 system

2021 ◽  
Author(s):  
Xiaoen Huang ◽  
Nian Wang
Keyword(s):  
Genome Editing ◽  
Gene Editing ◽  
Target Genes ◽  
High Efficiency ◽  
Sweet Orange ◽  
Susceptibility Gene ◽  
Transformation Rate ◽  
Biallelic Mutation ◽  
Important Species ◽  
Citrus Production

Sweet orange (Citrus sinensis) is the most economically important species for the citrus industry. However, it is susceptible to many diseases including citrus bacterial canker caused by Xanthomonas citri subsp. citri (Xcc) that triggers devastating effects on citrus production. Conventional breeding has not met the challenge to improve disease resistance of sweet orange due to the long juvenility and other limitations. CRISPR-mediated genome editing has shown promising potentials for genetic improvements of plants. Generation of biallelic/homozygous mutants remains difficult for sweet orange due to low transformation rate, existence of heterozygous alleles for target genes and low biallelic editing efficacy using the CRISPR technology. Here, we report improvements in the CRISPR/Cas9 system for citrus gene editing. Based on the improvements we made previously (dicot codon optimized Cas9, tRNA for multiplexing, a modified sgRNA scaffold with high efficiency, CsU6 to drive sgRNA expression), we further improved our CRISPR/Cas9 system by choosing superior promoters (CmYLCV or CsUbi promoter) to drive Cas9 and optimizing culture temperature. This system was able to generate a biallelic mutation rate of up to 89% for Carrizo citrange and 79% for Hamlin sweet orange. Consequently, this system was used to generate canker resistant Hamlin sweet orange by mutating the effector binding element (EBE) of canker susceptibility gene CsLOB1, which is required for causing canker symptoms by Xcc. Six biallelic Hamlin sweet orange mutant lines in the EBE were generated. The biallelic mutants are resistant to Xcc. Biallelic mutation of the EBE region abolishes the induction of CsLOB1 by Xcc. This study represents a significant improvement in sweet orange gene editing efficacy and generating disease resistant varieties via CRISPR-mediated genome editing. This improvement in citrus genome editing makes genetic studies and manipulations of sweet orange more feasible.

scholarly journals Sustainable Use of Biochar in Environmental Management

2021 ◽  
Author(s):  
Ammal Abukari ◽  
Ziblim Abukari Imoro ◽  
Abubakari Zarouk Imoro ◽  
Abudu Ballu Duwiejuah
Keyword(s):  
High Efficiency ◽  
Low Cost ◽  
Sustainable Use ◽  
Environmental Pollutants ◽  
Growth Yield ◽  
Soil Nutrient ◽  
Environmental Pollutant ◽  
Exchange Capacity ◽  
Agricultural Wastes ◽  
Preparation Conditions

Conversion of agricultural wastes into eco-friendly and low cost biochar is not only a smart recycling strategy but a panacea to environmental pollution management. Agricultural wastes biochar can be an effective alternative technique for controlling contaminants due to its low cost, high-efficiency, simple to use, ecological sustainability and reliability in terms of public safety. Biochars have made substantial breakthroughs in reducing greenhouse gases emissions, reducing soil nutrient leaching, sequester atmospheric carbon into the soil, increasing agricultural productivity, and reducing bioavailability of environmental contaminants. Recent advances in the understanding of biochars warrant a proper scientific evaluation of the relationship between its properties and impact on soil properties, environmental pollutant remediation, plant growth, yield, and resistance to biotic and abiotic stresses. The main factors controlling biochar properties include the nature of feedstock, heat transfer rate, residence time and pyrolysis temperature. Biochar efficacy in pollutants management largely depends on its elemental composition, ion-exchange capacity, pore size distribution and surface area, which vary with the nature of feedstock, preparation conditions and procedures. The chapter explored the possibility of using biochar from agricultural wastes as a suitable alternative for the remediation of environmental pollutants, soil conditioning and the long-term biochar application in the environment.

scholarly journals A QM/MM Study of Acylphosphatase Reveals the Nucleophilic-Attack and Ensuing Carbonyl-Assisted Catalytic Mechanisms

2020 ◽  
Author(s):  
zheng zhao ◽  
Phil bourne ◽  
Hao Hu ◽  
Huanyu Chu
Keyword(s):  
Energy Barrier ◽  
Potential Energy Surfaces ◽  
Catalytic Mechanism ◽  
Interaction Networks ◽  
Nucleophilic Attack ◽  
Reaction Coordinates ◽  
Transition State Stabilization ◽  
Catalytic Mechanisms ◽  
Energy Surfaces

Acylphosphatase is one of the vital enzymes in many organs/tissues to catalyze an acylphosphate molecule into carboxylate and phosphate. Here we use a combined <i>ab initio</i> QM/MM approach to reveal the catalytic mechanism of the benzoylphosphate-bound acylphosphatase system. Using a multi-dimensional reaction-coordinates-driving scheme, we obtained a detailed catalytic process including one nucleophilic-attack and then an ensuing carbonyl-shuttle catalytic mechanism by calculating two-dimensional potential energy surfaces. We also obtained an experiment-agreeable energy barrier and validated the role of the key amino acid Asn38. Additionally, we qualified the transition state stabilization strategy based on the amino acids-contributed interaction networks revealed in the enzymatic environment. This study provided usefule insights into the underlying catalytic mechanism to contribute to disease-involved research.

scholarly journals Development of a CRISPR-SaCas9 system for projection- and function-specific gene editing in the rat brain

2020 ◽  
Vol 6 (12) ◽  
pp. eaay6687 ◽  
Author(s):  
Haojie Sun ◽  
Su Fu ◽  
Shuang Cui ◽  
Xiangsha Yin ◽  
Xiaoyan Sun ◽  
...  
Keyword(s):  
Rat Brain ◽  
Gene Editing ◽  
High Efficiency ◽  
Protein A ◽  
Cell Types ◽  
Cell Labeling ◽  
Specific Gene ◽  
Creb Binding Protein ◽  
A Genome ◽  
And Function

A genome editing technique based on the clustered regularly interspaced short palindromic repeats (CRISPR)–associated endonuclease Cas9 enables efficient modification of genes in various cell types, including neurons. However, neuronal ensembles even in the same brain region are not anatomically or functionally uniform but divide into distinct subpopulations. Such heterogeneity requires gene editing in specific neuronal populations. We developed a CRISPR-SaCas9 system–based technique, and its combined application with anterograde/retrograde AAV vectors and activity-dependent cell-labeling techniques achieved projection- and function-specific gene editing in the rat brain. As a proof-of-principle application, we knocked down the cbp (CREB-binding protein), a sample target gene, in specific neuronal subpopulations in the medial prefrontal cortex, and demonstrated the significance of the projection- and function-specific CRISPR-SaCas9 system in revealing neuronal and circuit basis of memory. The high efficiency and specificity of our projection- and function-specific CRISPR-SaCas9 system could be widely applied in neural circuitry studies.

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