Xin Yan

• Coventry University

Soluble methane monooxygenase (sMMO) from methanotrophs has been extensively investigated for decades. However, major knowledge gaps persist regarding the synthesis mechanism of sMMO, particularly concerning the ambiguous roles of mmoD and mmoG in the sMMO gene cluster. Here, the functions of mmoD and mmoG were investigated in a model methanotrophi...

Replacement of nitrate with ammonium at large scale cultivation of methanotrophs can improve the economic feasibility of these bacteria in methane-based biomanufacturing and methane removal. However, ammonia toxicity and N 2 O emission impede this option. The mechanism of ammonia oxidation in methanotrophs remains elusive, limiting the effort to de...

Methanotrophs of the genus Methylocystis are frequently found in rice paddies. Although more than ten facultative methanotrophs have been reported since 2005, none of these strains was isolated from paddy soil. Here, a facultative methane-oxidizing bacterium, Methylocystis iwaonis SD4, was isolated and characterized from rhizosphere samples of rice...

17β-estradiol (E2) is a natural endocrine disruptor that is frequently detected in surface and groundwater sources, thereby threatening ecosystems and human health. The newly isolated E2-degrading strain Sphingomonas colocasiae C3-2 can degrade E2 through both the 4,5-seco pathway and the 9,10-seco pathway; the former is the primary pathway support...

Due to the extensive utilization of poly (ethylene terephthalate) (PET), a significant amount of PET waste has been discharged into the environment, endangering both human health and the ecology. As an eco-friendly approach to PET waste treatment, biodegradation is dependent on efficient strains and enzymes. In this study, a screening method was fi...

In a previous study, the novel gene cluster cehGHI was found to be involved in salicylate degradation through the CoA-mediated pathway in Rhizobium sp. strain X9 (Mol Microbiol 116:783–793, 2021). In this study, an IclR family transcriptional regulator CehR4 was identified. In contrast to other regulators involved in salicylate degradation, cehR4 f...

Background Mussel foot proteins (Mfps) are considered as remarkable materials due to their extraordinary adhesive capability. Recombinant expression is an ideal way to synthesis these proteins at large scale. However, secretory expression of Mfps into culture medium has not been achieved in a heterologous host. Methods and Results Here, to realize...

Although polyurethane (PUR) plastics play important roles in daily life, its wastes bring serious environmental pollutions. Biological (enzymatic) degradation is considered as an environmentally friendly and low-cost method for PUR waste recycling, in which the efficient PUR-degrading strains or enzymes are crucial. In this work, a polyester PUR-de...

Polyurethane (PUR) plastics is widely used because of its unique physical and chemical properties. However, unreasonable disposal of the vast amount of used PUR plastics has caused serious environmental pollution. The efficient degradation and utilization of used PUR plastics by means of microorganisms has become one of the current research hotspot...

2,3,5-Trimethylhydroquinone (2,3,5-TMHQ) is the key precursor in the synthesis of vitamin E. It is still a major challenge to produce 2,3,5-TMHQ under mild reaction conditions by chemical methods. The monooxygenase system MpdAB can specifically catalyze the conversion of 2,3,6-trimethylphenol (2,3,6-TMP) to 2,3,5-TMHQ. However, the weak catalytic c...

Methanotrophs play key roles in global methane cycling and are promising platforms for methane bioconversion. However, major gaps existing in fundamental knowledge undermines understanding of these methane-consuming microorganisms. To associate genes with a phenotype at the genome-wide level, we developed a Cre/lox-mediated method for constructing...

Residues of iprodione, used for the control of fungal diseases in crops, endanger both human health and ecosystem functioning. In this study, we isolated an iprodione-degrading bacteria, Pseudarthrobacter sp. Y-5, able to grow on iprodione as the sole carbon source. To achieve the high-level stable synthesis of iprodione hydrolase (IpaH), an unmark...

Bacillus subtilis is a robust industrial workhorse for the production of heterologous proteins. Chromosomal integration-based protein production has advantages over plasmid-based methods. Considering that the expression level of a gene is affected by its location in the chromosome, it is important to find an optimal integration site for the gene to...

The worldwide use of the carbamate insecticide carbofuran has caused considerable concern about its environmental fate. Degradation of carbofuran by Sphingobium sp. strain CFD-1 is initiated via the hydrolysis of its ester bond by carbamate hydrolase CehA to form carbofuran phenol. In this study, another carbofuran-degrading strain, Sphingobium sp....

Dipicolinic acid (DPA), an essential pyridine derivative biosynthesized in Bacillus spores, constitutes a major proportion of global biomass carbon pool. Alcaligenes faecalis strain JQ135 could catabolize DPA through the "3HDPA (3-hydroxydipicolinic acid) pathway." However, the genes involved in this 3HDPA pathway are still unknown. In this study,...

The pic gene cluster was found to be responsible for PA degradation and widely distributed in Alpha- , Beta- , and Gammaproteobacteria . Thus, it is very necessary to understand the regulation mechanism of the pic cluster in these strains.

Although the microbial degradation of the six isomers of dimethylphenol has been extensively studied, the genetic and biochemical mechanisms of 2,6-DMP degradation remain unclear. This study identified the genes responsible for the initial step in the 2,6-DMP catabolic pathway in M. neoaurum B5-4.

The bacterial hydrolytic dehalogenation of 4-chlorobenzoate (4CBA) is a CoA-activation type catabolic pathway that is usually a common part of the microbial mineralization of chlorinated aromatic compounds. Previous studies have shown that the transport and dehalogenation genes for 4CBA are typically clustered as an fcbBAT1T2T3C operon and are indu...

Based on the structural characteristic, carbamate insecticides can be classified into oxime carbamates (methomyl, aldicarb, oxamyl, etc.) and N -methyl carbamates (carbaryl, carbofuran, isoprocarb, etc.). So far, research on the degradation of carbamate pesticides has mainly focused on the detoxification step and hydrolysis of their carbamate bond....

A gammaproteobacterial methanotroph, strain GJ1T, was isolated from a rhizosphere soil sample of rice in Nanjing, China. The cells were Gram-negative, motile rods with a single polar flagellum, and they contained type I intracytoplasmic membranes. The cells formed pink colonies. The strain possessed both the particulate methane monooxygenase enzyme...

Bacillus subtilis is an attractive host for the directed evolution of the enzymes whose substrates cannot be transported across cell membrane. However, the generation of a mutant library in B. subtilis suffers problems of small library size, plasmid instability, and heterozygosity. Here, a large library of random mutant was created by inserting err...

To achieve the high-level stable expression of chlorothalonil hydrolytic dehalogenase (Chd), the gene chd was first integrated into the chromosome of Bacillus subtilis WB800. High generation stability was achieved by almost no gene lost after six generations but Chd activity decreased. aprE promoter alteration, translation initiation region modific...

Due to their fast growth rate and robustness, some haloalkalitolerant methanotrophs from the genus Methylotuvimicrobium have recently become not only promising biocatalysts for methane conversion but also favorable materials for obtaining fundamental knowledge on methanotrophs. Here, to realize unmarked genome modification in Methylotuvimicrobium b...

2,6-Dimethylphenol (2,6-DMP), an important chemical intermediate and the monomer of plastic polyphenylene oxide, is widely used in chemical and plastics industry. However, the pollution problem of 2,6-DMP residues is becoming increasingly serious, which is harmful to some aquatic animals. Microbial degradation provided an effective approach to elim...

The environmental fate of the extensively used chloroacetanilide herbicides (CH) has been a cause of increasing concern in the past decade because of their carcinogenic properties. Although microbes play important roles in CH degradation, Sphingomonas wittichii DC-6 was the first reported CH-mineralizing bacterium. In this study, the complete genom...

The residues of aniline and its derivatives are serious environment pollutants. Aniline dioxygenase (AD) derived from aerobic bacteria catalyzes the conversion of aniline to catechol, which has potential use in the bioremediation of aromatic amines and biorefining process. AD contains four components: a glutamine synthetase (GS)-like enzyme, a glut...

Background: Bacillus subtilis is developed to be an attractive expression host to produce both secreted and cytoplasmic proteins owing to its prominent biological characteristics. Chromosomal integration is a stable expression strategy while the expression level is not ideal compared with plasmid expression. Thus, to meet the requirement of protei...

Although one of the major factors limiting the application of Bacillus subtilis as an expression host has been its production of at least eight extracellular proteases, researchers have also noticed that some proteases benefited the secretion of foreign proteins at times. Therefore, to maximize the yield of a foreign protein, the proteases should b...

Dicamba is an important herbicide, and its use and leakage into the environment have dramatically increased since the large-scale planting of genetically modified (GM) dicamba-resistant crops in 2015. However, the complete catabolic pathway of dicamba has remained unknown, which limits ecotoxicological studies of this herbicide. Our previous study...

Due to the extensive use of carbofuran over the past 50 years, bacteria have evolved catabolic pathways to mineralize this insecticide, which plays an important role in eliminating carbofuran residue in the environment. This study revealed the genetic determinants of carbofuran degradation in Sphingomonas sp. strain CDS-1. We speculate that the clo...

Bacillus subtilis is well known as both a model organism and as a microbial cell factory. Simple and scarless gene modification is a desirable tool for basic research and industrial applications of B. subtilis. It has been demonstrated that naturally competent strains of B. subtilis can uptake multiple different DNA molecules, a phenomenon called c...

Unlike the benzene ring, the uneven distribution of the electron density of the pyridine ring influences the positional reactivity and interaction with enzymes; e.g., the ortho and para oxidations are more difficult than the meta oxidations. Hydroxylation is an important oxidation process for the pyridine derivative metabolism. In previous reports,...

The synergistic relationships between plants and their rhizospheric microbes can be used to develop a combinational bioremediation method, overcoming the constraints of individual phytoremediation or a bioaugmentation method. Here, we provide a combinational transgenic plant-microbe remediation system for a more efficient removal of phenylurea herb...

Microbial inoculant preparation is a prerequisite for its application in large-scale bioremediation. In the present study, Sphingomonas sp. DC-6, an efficient acetochlor-degrading strain, was used to investigate the process of preparing the inoculant. Optimization of submerged fermentation (SmF) by response surface methodology (RSM) resulted in a f...

Alkyl-substituted aniline is an important aniline derivative that may be associated with serious environmental risks. Previously, Sphingobium baderi DE-13, a bacterium that can mineralize alkyl substituted anilines such as 2,6-dimethylaniline, 2,6-diethylaniline, 2-methyl-6-ethylaniline, 2-methylaniline, and 2-ethylaniline, was isolated from active...

Thiobencarb is a thiocarbamate herbicide used in rice paddies worldwide. Microbial degradation plays a crucial role in the dissipation of thiobencarb in the environment. However, the physiological and genetic mechanisms underlying thiobencarb degradation remain unknown. In this study, a novel thiobencarb degradation pathway was proposed in Acidovor...

Buprofezin is a widely used insect growth regulator whose residue has been frequently detected in the environment, posing a threat to aquatic organisms and nontarget insects. Microorganisms play an important role in the degradation of buprofezin in the natural environment. However, the relevant catabolic pathway has not been fully characterized, an...

5-hydroxypicolinic acid (5HPA) is a natural pyridine derivative that can be microbially degraded. However, the physiological, biochemical, and genetic foundation of the microbial catabolism of 5HPA remains unknown. In this study, a gene cluster hpa (which is involved in degradation of 5HPA in Alcaligenes faecalis JQ135) was cloned and HpaM was iden...

Importance: Much attention has been paid to the environmental fate of chloroacetanilide herbicides used for the past sixty years. Microbial degradation is considered an important mechanism in the degradation of these compounds. Bacterial degradation of chloroacetanilide herbicides have been investigated in many recent studies. Pure cultures or con...

In this study, a bacterial strain of Achromobacter sp. LZ35, which was capable of utilizing 2,4-dichlorophenoxyacetic acid (2,4-D) and 2-methyl-4-chlorophenoxy acetic acid (MCPA) as the sole sources of carbon and energy for growth, was isolated from the soil in a disused pesticide factory in Suzhou, China. The optimal 2,4-D degradation by strain LZ...

Aside from applications in the production of commercial enzymes and metabolites, Bacillus amyloliquefaciens is also an important group of plant growth-promoting rhizobacteria that supports plant growth and suppresses phytopathogens. A host-genotype-independent counter-selectable marker would enable rapid genetic manipulation and metabolic engineeri...

Background: To reduce the fermentation cost for industrialization of chlorothalonil hydrolytic dehalogenase (Chd), agro-industrial wastewater including molasses, corn steep liquor (CSL) and fermentation wastewater were used to substitute the expensive carbon and nitrogen sources and fresh water for lab preparation. Results: The results showed th...

Importance: Dicamba is a very important herbicide that is widely used to control more than 200 types of broadleaf weeds and is a suitable target herbicide for the engineering of herbicide-resistant transgenic crops. Study of the mechanism of dicamba metabolism by soil microorganisms will benefit studies of its dissipation, transformation and migra...

The worldwide use of the phenylurea herbicide, isoproturon (IPU), has resulted in considerable concern about its environmental fate. Though many microbial metabolites of IPU are known and IPU-mineralizing bacteria have been isolated, the molecular mechanism of IPU catabolism has not been elucidated yet. In this study, complete genes that encode the...

Methane is becoming a major candidate for a prominent carbon feedstock in the future and bioconversion of methane into valuable products has drawn increasing attention. To facilitate the use of methanotrophic organisms as industrial strains and accelerate our ability to metabolically engineer methanotrophs, simple and rapid genetic tools are needed...

To achieve the secretory expression of chlorothalonil hydrolytic dehalogenase (Chd), the chd gene was cloned into the vector pP43NMK under the control of the P43 promoter and the NprB signal peptide-encoding sequence and extracellularly expressed in the protease-deficient strain Bacillus subtilis WB800. The optimization of Chd production in submerg...

Strain Y1(T), a Gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from activated sludge. This strain is able to degrade several commonly used chloroacetamide herbicides, such as butachlor, acetochlor and alachlor. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Y1(T) is a member of the genus Sphingomon...

Strain YF-2(T), a Gram-staining-negative, non-motile, non-spore-forming, light-yellow-pigmented bacterium, was isolated from soil samples collected in the city of Yuncheng, Shanxi province of China. Strain YF-2(T) grew over a temperature range of 25-37 °C, at pH 5.0-8.0 and with 0-5 % (w/v) NaCl. Phylogenetic analysis based on sequence of the 16S r...

Sphingomonads DC-6 and DC-2 degrade the chloroacetanilide herbicides alachlor, acetochlor, and butachlor via N-dealkylation. In this study, we report a three-component Rieske non-heme iron oxygenase (RHO) system catalyzing the N-dealkylation of these herbicides. The oxygenase component gene cndA is located in a transposable element that is highly c...

Sphingobium wenxiniae JZ-1 utilizes a wide range of pyrethroids and their metabolic product, 3-phenoxybenzoate, as sources of carbon and energy. A mutant JZ-1 strain, MJZ-1, defective in the degradation of 3-phenoxybenzoate was obtained by successive streaking on LB agar. Comparison of the draft genomes of strains JZ-1 and MJZ-1 revealed that a 29,...

A structural model is proposed for designing an electro-optic polymer microring resonator (MRR) switch array. This device consists of 1 horizontal channel, N vertical channels and N switching elements. Every switching element contains triple series-coupled microrings with identical radii. Parameter optimization and characteristic analysis of the de...

The environmental fate of phenylurea herbicides has received considerable attention in recent decades. The microbial metabolism of N,N-dimethyl-substituted phenylurea herbicides can generally be initiated by mono-N-demethylation. In this study, the molecular basis for this process was revealed. The pdmAB genes in Sphingobium sp. strain YBL2 were sh...

Bacterial strain GB-01 was isolated from abamectin-contaminated soils by continuous enrichment culture. The preliminary identification of strain GB-01 as a Burkholderia species was based mainly on simple biochemical and substrate utilization tests; however, these tests alone cannot accurately differentiate all the species within the genus Burkholde...

Rhodococcus sp. strain B1 could degrade 100 mg/L butachlor within 5 d. Butachlor was firstly hydrolyzed by strain B1 through N-dealkylation, which resulted in the production of butoxymethanol and 2-chloro-N-(2,6-dimethylphenyl) acetamide. Butoxymethanol could be further degraded and utilized as the carbon source for the growth of strain B1, while 2...

Bacillus amyloliquefaciens strains are capable of suppressing soilborne pathogens through the secretion of an array of lipopeptides and root colonization, and biofilm formation ability is considered a prerequisite for efficient root colonization. In this study, we report that one of the lipopeptide compounds (bacillomycin D) produced by the rhizosp...

A bacterial strain, Cupriavidus sp. DT-1, capable of degrading chlorpyrifos and 3,5,6-trichloro-2-pyridinol (TCP) and using these compounds as sole carbon source was isolated and characterized. Investigation of the degradation pathway showed that chlorpyrifos was first hydrolyzed to TCP, successively dechlorinated to 2-pyridinol, and then subjected...

A novel kind of wavelength-insensitive wide-spectrum polymer electro-optic (EO) switch is proposed by employing two symmetric active Mach-Zehnder interferometers (MZIs), a passive middle directional coupler and a pair of passive phase-generating couplers. Extinction ratio compensation condition under off-state and insertion loss compensation condit...

One rhamnolipid-producing bacterial strain named Pseudomonas aeruginosa BSFD5 was isolated and characterized. Its rhlABRI cassette including necessary genes for rhamnolipid synthesis was cloned and transformed into the chromosome of P. putida KT2440 by a new random transposon vector without introducing antibiotic-resistance marker, generating a gen...

In our previous study, a phenylurea herbicides degrading strain Sphingobium sp. YBL2 was isolated. In the present study, the degradation pathway of IPU (Isoproturon) in strain YBL2 was investigated by intermediate metabolites identification. HPLC and/or MS/MS analysis showed that, three intermediate metabolites, MDIPU (1-(4-isopropylphenyl)-3-methy...

A strain designated as XY-1, capable of degrading nitrobenzene efficiently, was isolated from the sludge in an chemical factory wastewater treatment plant. Strain XY-1 was identified preliminarily as Pseudomonas sp. based on its physiological and biochemical characters and the result of 16S rDNA homologue sequence analysis. Strain XY-1 could grow w...

A buprofezin-degrading bacterium, YL-1, was isolated from rice field soil. YL-1 was identified as Rhodococcus sp. on the basis of the comparative analysis of 16S rDNA sequences. The strain could use buprofezin as the sole source of carbon and nitrogen for growth and was able to degrade 92.4% of 50 mg L(-1) buprofezin within 48 h in liquid culture....

In our previous study, the isoproturon-degrading strain Sphingomonas sp. Y57 was isolated from the wastewater treatment system of an herbicide factory. Interestingly, this strain also showed the ability to degrade propanil (3,4-dichloropropionamilide). The present work reveals that Y57 degrades propanil via the following pathway: propanil was initi...

A novel amidase gene, designated pamh, was cloned from Paracoccus sp. M-1. Site-directed mutagenesis and bioinformatic analysis showed that the PamH protein belonged to the amidase signature enzyme family. PamH was expressed in Escherichia coli, purified, and characterized. The molecular mass of PamH was determined to be 52 kDa with an isoelectric...

A rapid and convenient method is presented for unmarked gene deletions in Pichia pastoris. Cre/mutated lox system, Zeocin(®) (Invitrogen) resistance marker and homologous arms were spliced together by fusion PCR to generate the gene disruption cassettes (homologous region-lox71-Cre-ZeoR-lox66-homologous region), which could be integrated into the P...

To enhance the electro-optic (EO) modulation efficiency and realize the impedance-matching, a polymer-on-silicon multimode interference (MMI) Mach-Zehnder interferometer (MZI) -based electro-optic (EO) switch is designed and optimized. Under the central operation wavelength of 1550 nm, the driving voltages of the designed switch are 0 and ±1.375 V,...

To enlarge the output spectrum, a novel reasonable structure of one kind of Mach-Zehnder interferometer (MZI) electro-optic (EO) switches containing two symmetric N-th order phase generating couplers (PGCs) is presented, and thorough model, analysis and design technique are proposed. A non-linear least square method is investigated for optimizing t...

By using the proposed 3-D mode propagation analysis method and point-matching method, a polymer multimode interference (MMI) Mach-Zehnder interferometer (MZI) electro-optic (EO) switch is designed and optimized for enhancing the EO modulating efficiency and matching the impedance and the velocity. The designed switch possesses low driving voltages...

A novel technique and related formulations are proposed for analyzing the influences of the skin-effect on the performances of a polymer Y-fed coupler electro-optic modulator with shielded push-pull micro-strip electrodes. Using the extended point-matching method, coupled mode theory and electro-optic modulation theory, thorough design and optimiza...

Detailed model, analysis and design technique are presented for simulating a high-speed polymer Mach–Zehnder interferometer (MZI) electro-optic switch with push-pull dual driving electrodes and rib waveguides. The novel formulas of the time-domain response are derived. Thorough optimization and simulation for the designed device are performed. The...

The structure and the principle for the polymer electro-optic microring resonator (MRR) switch are proposed as well as the transfer functions. The structural parameters are optimized; the transmission characteristics are analyzed including the output power, switching time, switching voltage, insertion loss, and crosstalk. When the operation voltage...

Formulas of the transfer functions and the output power gains are presented, amplifying characteristics are analyzed, and simulation is performed for an Er3+–Yb3+-co-doped microring resonator. Under the pump wavelength of 980 nm and the central signal wavelength of 1550 nm, the dependence of the output power gain on the amplitude coupling ratio, pu...

We have developed an efficient and precise method for genome manipulations in Bacillus subtilis that allows rapid alteration of gene sequence or multiple gene sequences without altering the chromosome in any other way. In our approach, the Escherichia coli toxin gene mazF, which was used as a counter-selectable marker, was placed under the control...

In the Pichia pastoris expression system, increasing the copy number of the expression cassette often has the effect of increasing the amount of protein expressed. To improve the expression level of methyl parathion hydrolase (MPH), we constructed two integration vectors with four and eight direct repeats of the expression cassette using an in vitr...

In terms of the coupled mode theory, formulas of the transfer function and the output power gain are presented for an Er/Yb co-doped parallel-cascaded double microring resonator. Around the pump wavelength of 0.98 μm and the central signal wavelength of 1.55 μm, analysis is performed for the dependence of the output power gain on the pump power, si...

Formulas for the transfer function and the output power gain are presented for an Er³⁺/Yb³⁺ codoped series-cascaded double microring resonator (MRR). Around the pumping wavelength of 974 nm and the central signal wavelength of 1530 nm, the effects of the pump power, signal power, Er³⁺/Yb³⁺ dopant concentrations and amplitude coupling ratios on the...

A packaged polymer electro-optic switch using double-section reversed electrodes based on the Y-fed coupler structure is investigated in terms of the conformal transforming method, image method, coupled mode theory and electro-optic modulation theory. The structure and principle are described, and unique formulations are proposed for simulating the...

The release of malachite green, a commonly used triphenylmethane dye, into the environment is causing increasing concern due to its toxicity, mutagenicity, and carcinogenicity. A bacterial strain that could degrade malachite green was isolated from the water of an aquatic hatchery. It was identified as a Pseudomonas sp. based on the morphological,...

A dual-driving polymer Mach-Zehnder interferometer (MZI) electro-optic switch is designed and optimized, which consists of a phase-generating coupler (PGC) and a 3-dB directional coupler. Structural schematics and principles of the PGC and the switch are described. Novel formulas of the switching time are presented. Under the central operation wave...

Two integrated 1 × 2 and 1 × 4 polymer electro-optic switches based on Y-fed directional couplers are designed and optimized in terms of the coupled mode theory, electro-optic modulation theory, conformal transforming method and image method. The principle of the 1 × 2 electro-optic switch is described. Parameters including the core size, buffer la...