Kinetic characterization of acetone monooxygenase from Gordonia sp. strain TY-5

Co-metabolic biodegradation of chlorinated ethene in an oxygen- and ethane-based membrane biofilm reactor

Groundwater contamination by chlorinated ethenes is an urgent concern worldwide. One approach for detoxifying chlorinated ethenes is aerobic co-metabilims using ethane (C2H6) as the primary substrate. This study evaluated long-term continuous biodegradation of three chlorinated alkenes in a membrane biofilm reactor (MBfR) that delivered C2H6 and O2 via gas-transfer membranes. During 133 days of continuous operation, removals of dichloroethane (DCE), trichloroethene (TCE), and tetrachloroethene (PCE) were as high as 94 % and with effluent concentrations below 5 μM. In situ batch tests showed that the co-metabolic kinetics were faster with more chlorination. C2H6-oxidizing Comamonadaceae and "others," such as Methylococcaceae, oxidized C2H6 via monooxyenation reactions. The abundant non-ethane monooxygenases, particularly propane monooxygenase, appears to have been responsible for C2H6 aerobic metabolism and co-metabolism of chlorinated ethenes. This work proves that the C2H6 + O2 MBfR is a platform for ex-situ bioremediation of chlorinated ethenes, and the generalized action of the monooxygenases may make it applicable for other chlorinated organic contaminants.

On-chip-based electrochemical biosensor for the sensitive and label-free detection of Cryptosporidium

Cryptosporidium, an intestinal protozoan pathogen, is one of the leading causes of death in children and diarrhea in healthy adults. Detection of Cryptosporidium has become a high priority to prevent potential outbreaks. In this paper, a simple, easy to fabricate, and cost-effective on-chip-based electrochemical biosensor has been developed for the sensitive and label-free detection of Cryptosporidium oocysts in water samples. The sensor was fabricated using standard lithography using a mask with a 3-electrode design and modified by self-assembling a hybrid of a thiolated protein/G and the specific anti-Cryptosporidium monoclonal antibodies (IgG3). The electrochemical impedance spectroscopy (EIS) was employed to quantitate C. parvum in the range of 0 to 300 oocysts, with a detection limit of approximately 20 oocysts/5 µL. The high sensitivity and specificity of the developed label-free electrochemical biosensor suggest that this novel platform is a significant step towards the development of fast, real-time, inexpensive and label-free sensing tool for early warning and immediate on-site detection of C. parvum oocysts in water samples, as compared to the traditional methods (such as PCR and microscopy). Furthermore, under optimized conditions, this label-free biosensor can be extended to detect other analytes and biomarkers for environmental and biomedical analyses.

Immobilization of Baeyer-Villiger monooxygenase from acetone grown Fusarium sp

OBJECTIVE

A novel biocatalyst for Baeyer-Villiger oxidations is necessary for pharmaceutical and chemical industries, so this study aims to find a Baeyer-Villiger monooxygenase (BVMO) and to improve its stability by immobilization.

RESULTS

Acetone, the simplest ketone, was selected as the only carbon source for the screening of microorganisms with a BVMO. A eukaryote, Fusarium sp. NBRC 109816, with a BVMO (FBVMO), was isolated from a soil sample. FBVMO was overexpressed in E. coli and successfully immobilized by the organic-inorganic nanocrystal formation method. The immobilization improved the thermostability of FBVMO. Substrate specificity investigation revealed that both free and immobilized FBVMO were found to show catalytic activities not only for Baeyer-Villiger oxidation of ketones to esters but also for oxidation of sulfides to sulfoxides. Furthermore, a preparative scale reaction using immobilized FBVMO was successfully conducted.

CONCLUSIONS

FBVMO was discovered from an environmental sample, overexpressed in E. coli, and immobilized by the organic-inorganic nanocrystal formation method. The immobilization successfully improved its thermostability.

Comprehensive review of conventional and state-of-the-art detection methods of Cryptosporidium

Cryptosporidium is a critical waterborne protozoan pathogen found in water resources that have been a major cause of death and serious illnesses worldwide, costing millions of dollars annually for its detection and treatment. Over the past several decades, substantial efforts have been made towards developing techniques for the detection of Cryptosporidium. Early diagnostic techniques were established based on the existing tools in laboratories, such as microscopes. Advancements in fluorescence microscopy, immunological, and molecular techniques have led to the development of several kits for the detection of Cryptosporidium spp. However, these methods have several limitations, such as long processing times, large sample volumes, the requirement for bulky and expensive laboratory tools, and the high cost of reagents. There is an urgent need to improve these existing techniques and develop low-cost, portable and rapid detection tools for applications in the water quality industry. In this review, we compare recent advances in nanotechnology, biosensing and microfluidics that have facilitated the development of sophisticated tools for the detection of Cryptosporidium spp.Finally, we highlight the advantages and disadvantages, of these state-of-the-art detection methods compared to current analytical methodologies and discuss the need for future developments to improve such methods for detecting Cryptosporidium in the water supply chain to enable real-time and on-site monitoring in water resources and remote areas.

Portable on-chip colorimetric biosensing platform integrated with a smartphone for label/PCR-free detection of Cryptosporidium RNA

Cryptosporidium, a protozoan pathogen, is a leading threat to public health and the economy. Herein, we report the development of a portable, colorimetric biosensing platform for the sensitive, selective and label/PCR-free detection of Cryptosporidium RNA using oligonucleotides modified gold nanoparticles (AuNPs). A pair of specific thiolated oligonucleotides, complementary to adjacent sequences on Cryptosporidium RNA, were attached to AuNPs. The need for expensive laboratory-based equipment was eliminated by performing the colorimetric assay on a micro-fabricated chip in a 3D-printed holder assembly. A smartphone camera was used to capture an image of the color change for quantitative analysis. The detection was based on the aggregation of the gold nanoparticles due to the hybridization between the complementary Cryptosporidium RNA and the oligonucleotides immobilized on the AuNPs surface. In the complementary RNA's presence, a distinctive color change of the AuNPs (from red to blue) was observed by the naked eye. However, in the presence of non-complementary RNA, no color change was observed. The sensing platform showed wide linear responses between 5 and 100 µM with a low detection limit of 5 µM of Cryptosporidium RNA. Additionally, the sensor developed here can provide information about different Cryptosporidium species present in water resources. This cost-effective, easy-to-use, portable and smartphone integrated on-chip colorimetric biosensor has great potential to be used for real-time and portable POC pathogen monitoring and molecular diagnostics.

Complete Genome Sequence and Function Gene Identify of Prometryne-Degrading Strain Pseudomonas sp. DY-1

The genus Pseudomonas is widely recognized for its potential for environmental remediation and plant growth promotion. Pseudomonas sp. DY-1 was isolated from the agricultural soil contaminated five years by prometryne, it manifested an outstanding prometryne degradation efficiency and an untapped potential for plant resistance improvement. Thus, it is meaningful to comprehend the genetic background for strain DY-1. The whole genome sequence of this strain revealed a series of environment adaptive and plant beneficial genes which involved in environmental stress response, heavy metal or metalloid resistance, nitrate dissimilatory reduction, riboflavin synthesis, and iron acquisition. Detailed analyses presented the potential of strain DY-1 for degrading various organic compounds via a homogenized pathway or the protocatechuate and catechol branches of the β-ketoadipate pathway. In addition, heterologous expression, and high efficiency liquid chromatography (HPLC) confirmed that prometryne could be oxidized by a Baeyer-Villiger monooxygenase (BVMO) encoded by a gene in the chromosome of strain DY-1. The result of gene knock-out suggested that the sulfate starvation-induced (SSI) genes in this strain might also involve in the process of prometryne degradation. These results would provide the molecular basis for the application of strain DY-1 in various fields and would contribute to the study of prometryne biodegradation mechanism as well.

Characterization of different biocatalyst formats for BVMO-catalyzed cyclohexanone oxidation

Cyclohexanone monooxygenase (CHMO), a member of the Baeyer-Villiger monooxygenase family, is a versatile biocatalyst that efficiently catalyzes the conversion of cyclic ketones to lactones. In this study, an Acidovorax-derived CHMO gene was expressed in Pseudomonas taiwanensis VLB120. Upon purification, the enzyme was characterized in vitro and shown to feature a broad substrate spectrum and up to 100% conversion in 6 h. Furthermore, we determined and compared the cyclohexanone conversion kinetics for different CHMO-biocatalyst formats, that is, isolated enzyme, suspended whole cells, and biofilms, the latter two based on recombinant CHMO-containing P. taiwanensis VLB120. Biofilms showed less favorable values for K_S (9.3-fold higher) and k_cat (4.8-fold lower) compared with corresponding K_M and k_cat values of isolated CHMO, but a favorable K_I for cyclohexanone (5.3-fold higher). The unfavorable K_S and k_cat values are related to mass transfer- and possibly heterogeneity issues and deserve further investigation and engineering, to exploit the high potential of biofilms regarding process stability. Suspended cells showed only 1.8-fold higher K_S , but 1.3- and 4.2-fold higher k_cat and K_I values than isolated CHMO. This together with the efficient NADPH regeneration via glucose metabolism makes this format highly promising from a kinetics perspective.

Structure-Based Redesign of a Self-Sufficient Flavin-Containing Monooxygenase towards Indigo Production

Indigo is currently produced by a century-old petrochemical-based process, therefore it is highly attractive to develop a more environmentally benign and efficient biotechnological process to produce this timeless dye. Flavin-containing monooxygenases (FMOs) are able to oxidize a wide variety of substrates. In this paper we show that the bacterial mFMO can be adapted to improve its ability to convert indole into indigo. The improvement was achieved by a combination of computational and structure-inspired enzyme redesign. We showed that the thermostability and the k_cat for indole could be improved 1.5-fold by screening a relatively small number of enzyme mutants. This project not only resulted in an improved biocatalyst but also provided an improved understanding of the structural elements that determine the activity of mFMO and provides hints for further improvement of the monooxygenase as biocatalyst.