Biomedical subjects

Zi-Niu Yu

Publications and source records attributed to Zi-Niu Yu.

12 recordsLinked to original sources

PubMed2006

The key DNA-binding residues in the C-terminal domain of Mycobacterium tuberculosis DNA gyrase A subunit (GyrA).

As only the type II topoisomerase is capable of introducing negative supercoiling, DNA gyrase is involved in crucial cellular processes. Although the other domains of DNA gyrase are better understood, the mechanism of DNA binding by the C-terminal domain of the DNA gyrase A subunit (GyrA-CTD) is less clear. Here, we investigated the DNA-binding sites in the GyrA-CTD of Mycobacterium tuberculosis gyrase through site-directed mutagenesis. The results show that Y577, R691 and R745 are among the key DNA-binding residues in M.tuberculosis GyrA-CTD, and that the third blade of the GyrA-CTD is the main DNA-binding region in M.tuberculosis DNA gyrase. The substitutions of Y577A, D669A, R691A, R745A and G729W led to the loss of supercoiling and relaxation activities, although they had a little effect on the drug-dependent DNA cleavage and decatenation activities, and had no effect on the ATPase activity. Taken together, these results showed that the GyrA-CTD is essential to DNA gyrase of M.tuberculosis, and promote the idea that the M.tuberculosis GyrA-CTD is a new potential target for drug design. It is the first time that the DNA-binding sites in GyrA-CTD have been identified.

Adenosine Triphosphatases↗

PubMed2006

Archaeal communities in mangrove soil characterized by 16S rRNA gene clones.

An archaeal 16S rRNA gene library was constructed from mangrove soil. Phylogenetic analysis revealed archaea in mangrove soil including the Crenarchaeota (80.4%) and Euryarchaeota (19.6%) phyla. The archaeal community in mangrove soil appears to be a mixture of organisms found in a variety of environments with the majority being of marine origin.

Archaea↗

PubMed2005

[Cloning and functional analysis of the stable plasmid pBMB175 in Bacillus thuringiensis subsp. tenebrionis strains YBT-1765].

A 15.2 kb plasmid pBMB175 from Bacillus thuringiensis subsp. tenebrionis strains YBT-1765 was cloned and the restriction map was constructed. The mini-replicating region of pBMB175 was located in a 1151 bp fragment by functional analysis. The sequence of a 4152 bp fragment which contained the mini-replicating region was analyzed and results showed that the fragment had three potential open reading frames (ORF1, ORF2 and ORF3). Sequence comparison and homology search revealed that ORF1 (767AA) has 20% approximately 30% similarity to UvrD-helicase, RecD and RecB family proteins; no homology was found between ORF2 (149AA) and other known proteins; ORF3 shared 34% identification to a potential protein (ORF7) in pGI3. Deletion and sequence analysis presumed that the protein encoded by ORF2 maybe a new replication protein. Above all, pBMB175 likely belongs to a new plasmid family with a new replicon. The recombinant plasmid harboring the mini-replicating region is very stable, even after growth for more than 40 generations without selection, so it might be used as a cloning and expression vector.

Bacillus thuringiensis↗

PubMed2005

[Co-expression of crystal protein gene cry26Aa and cry28Aa has an ability to form parasporal crystal inside exosporium in Bacillus thuringiensis subsp. finitimus].

Parasporal crystal in Bacillus thuringiensis subsp. finitimus T02 forms within the exosporium and remains attached to the spore after mother cell lysis, which leads to spore-crystal connection. According to the crystal protein gene sequence in B. thuringiensis subsp. finitimus, cry26 and cry28 were cloned from strain T02 by PCR amplification and transformed into the crystal negative Bacillus thuringiensis strain BMB171 by shuttle vectors, alone or in combination together. Crystal can be observed inside of exosporium when co-expression of these two genes. But crystal mainly formed outside of exosporium when they expressed alone. This suggests interaction between of the two crystal proteins may be involved in enclosure.

Bacillus thuringiensis↗

PubMed2004

[Isolation of 2,4-dichlorophenol degrading bacterium strain and cloning and expression of its 2,4-dichlorophenol hydroxylase gene].

2,4-Dichlorophenol is toxic and biorefratory organic pollutant. A 2,4-dichlorophenol degrading bacterial strain GT241-1, identified as Pseudomonas sp., was isolated from soil samples which was collected from drainage area of several 2,4-dichlorophenol producing factories. Strain GT241-1 had strong 2,4-dichlorophenol degrading ability, it could decompose 91% 2, 4-dichlorophenol of 90 mg/L within 48 hours at 25 - 30 degrees C, and could utilize 2,4-dichlorophenol, 2,4-dichlorophenoxyacetic acid (2,4-D), benzoate and catechol as sole carbon and energy source. Southern blot showed that 2,4-dichlorophenol hydroxylase gene (dcpA) of strain GT241-1 locates on the about 10kb EcoR I/Xba I fragment. This fragment was recovered, linked to the vecter pUC19 and transformed into the E. coli DH5alpha. A aim transformant, Z539, was obtained by dot blotting from about 1200 transformants. PCR and the sequencing results shew that the whole dcpA gene is contained within the 10kb EcoR I /Xba I fragment of pZ539. This fragment was shortened to about 2.4kb by HindmIII. The shorted fragment was subcloned to vecter pRSET-B to get a transformant BS1-12. The subcloned fragment was sequenced. Sequencing results showed that the whole length of the subcloned fragment containing dcpA is 2389bp and the nucleotide span of coding region is from number 276 to number 2072 (1797 bp), with ATG and TAA as start and stop codon respectively. The sequence analysis of dcpA and the deduced amino acid encoded by dcpA showed that they are different from the relative sequences registered in the GenBank. The subcloned fragment carry the promoter of dcpA, this can deduce from the fact that the upflow length of dcpA coding region is 275bp, and further confirmed by the 2,4-dichlorophenol hydroxylase activity measurement results. The 2,4-dichlorophenol hydroxylase activity of transformant Z539 and BS1-12 were detected, the results showed these transformants have 2,4-dichlorophenol hydroxylase activity. By comparison, the activity of these transformants were lower than that of the strain GT241-1.

Amino Acid Sequence↗

PubMed2004

[Cloning and expression of tyrosinase-encoding gene (mel) of Bacillus thuringiensis and its initial research of application].

Tyrosinase, which is encoded by Tyrosinase gene (mel), is the key enzyme in the process of melanin formation in animals, plants and microorganisms. Using the primers designed by comparing the conserved domain of tyrosinase, a DNA fragment was amplified which contain the mel gene from Bacillus thuringiensis 4D11. The recombinant E. coli EMB1179 was gained by subcloning this DNA fragment onto the vector pGEM-7zf and transformed it into E. coli DH5alpha. EMB1179 express the tyrosinase activity and produce melanin under the presence of L-tyrosin. The effect of melanin on survival of E. coli was also determined. The results showed that the melanin produced by EMB1179 effectively increased its resistance against UV light.

Bacillus thuringiensis↗

PubMed2003

Determination of the fungicide validamycin A by capillary zone electrophoresis with indirect UV detection.

Validamycin A, a main component of the antibiotic validamycin complex, which is widely used to control sheath blight disease of rice plants, can be determined by capillary zone electrophoresis with indirect UV detection. The influence of various separation conditions including background electrolyte and modifier concentration, pH, and voltage was investigated. By using 10 mM aminopyrine-2 mM ethylenediaminetetraacetic acid at pH 5.2 as the carrier electrolyte, high efficiency separation of validamycin A was achieved with the number of theoretical plates up to 350000 plates/m. The linear range was across 3 orders of magnitude. The relative standard deviations for migration times and peak areas were less than 0.5 and 3.0%, respectively. The limit of detection for validamycin A was 1.0 microg/mL. The average recoveries ranged from 103.0 to 104.8%. This method has many advantages as compared with high-performance liquid chromatography and micellar electrokinetic capillary chromatography in the determination of commercial formulations.

Chromatography, High Pressure Liquid↗

PubMed2003

[Construction of insecticidal recombinant Bacillus thuringiensis using an integrative vector].

Insecticidal crystal protein gene cry1C which is highly toxic to Spodoptera exigua was cloned into an integrative vector pBMB-F7E, which was derived from Bacillus thuringiensis transposon Tn4430. The recombinant integrative plasmid pBMB-FLC harboring the cry1C gene was gained and transformed into a wild-type Bt strain YBT803-1. A transformant BMB803-A was obtained, and grown at 46 degrees C for about 120 generations, From which three recombinants with cry1C gene integrating into the chromosome were achieved at a frequency of approximately 3.4 x 10(-5). Southern blotting revealed that the integration occurred in different sites of the chromosome. The integrated cry1C were expressed effectively. The results of bioassays showed that the toxicity of recombinants BMB803-X and BMB803-Z against Plutella xylostella were similar to that of strain YBT803-1, and their toxicity to Spodoptera exigua were higher than that of strain YBT803-1.

Animals↗

PubMed2003

[Expression of gene aiiA carrying the promoter of gene cry3Aa in Bacillus thuringiensis].

N-acyl-homoserine lactones (AHLs), are widely conserved signal molecules present in quorum-sensing systems of many Gram-negative bacteria. AHLs molecules mediate the expression of virulence genes of a range of bacterial pathogens. Recently, it has been reported that AiiA protein, which widely exists in Bacillus species, can inactivate the AHLs by hydrolyzing the lactone bond of AHLs, thus attenuate the diseases caused by the expression of virulence genes of bacterial pathogens. Bacillus thuringiensis, a type of Gram-positive bacteria, has been used extensively as a microbial insecticide in the last few decades. However, most of important insecticidal B. thuringiensis strains have not been exploited for bacterial disease control because they usually do not produce antibiotics that are effective against bacteria and fungi. The discovery of AiiA protein in B. thuringiensis shows the application potential of B. thuringiensis on biocontrol against bacterial diseases. In this study, in order to construct the B. thuringiensis recombinant strain that has high expression of AiiA protein, the promoter of insecticidal crystal protein coding gene cry3Aa of B. thuringiensis was selected. The promoter of gene cry3Aa is a non-sporulation promoter, it promotes the transcription earlier and longer than the promoters of other cry genes. The promoter of AiiA protein coding gene aiiA was replaced with the promoter of gene cry3Aa by overlapping PCR, resulting fusion gene pro3A-aiiA. The gene pro3A-aiiA was inserted into shuttle vector pHT304 at site BamH I / Sph I , resulting recombinant plasmid pBMB686. The plasmid pBMB686 was introduced into B. thuringiensis acrystalliferous strain BMB171, the resulting strain BMB686 had a higher and more stable expression level of protein AiiA comparing with the parental strain BMB171. Furthermore, the strain BMB686 exhibited stronger ability of AHLs inactivation and much more effective restraint to the potato's soft rot disease caused by Erwinia carotovora than those of the parental strain BMB171. From these results, it was concluded that the B. thuringiensis strain harvesting the fusion gene pro3A-aiiA may be utilized in the future to control bacterial diseases which are mediated by the AHL quorum-sensing signals.

Acyl-Butyrolactones↗

PubMed2002

[A novel resolution vector with Bacillus thuringiensis plasmid replicon ori44].

The resolution recognization sites of transposon Tn4430 of Bacillus thuringiensis was inserted into cloning vector pRSET B and pUC19, resulting recombinant plasmids pBMB1201 and pBMB1202. Both of the mini res fragments, BamHI/HindIII fragment in pBMB1201 and EcoRI/HindIII fragment in pBMB1202, were ligated to the 3.3 kb EcoRI/HindIII fragment of shuttle vector pHT3101, which contained the ori. Ec, ampr and emr antibiotic resistant genes, resulting recombinant plasmid pBMB1203. After deleted the BamHI and EcoRI sites which located ouside the two res sites, resolution vector pBMB1204 was resulted. There are multiple cloning sites between two copies of resolution sites which have the same direction. The plasmid replication origin ori44, which come from B. thuringiensis sub sp. kurstaki strain YBT-1520, was inserted into the multiple cloning sites of pBMB1204 and then resolution shuttle vector pBMB1205 was obtained. With spectinomycin resistant gene as target, it was found that the resolution rate is 100% and the stability of the resolved plasmid is 93%. Using this shuttle vector, antibiotic resistance markers and other non-B. thuringiensis DNA can be selectively eliminated after the selection of transformants by antibiotic resistance marker. This vector is very useful to solve the gene safety problem while has no effect on target gene expression.

Bacillus thuringiensis↗

PubMed2002

[The analysis of Bacillus thuringiensis vegetative insecticical protein gene cloning and expression].

Three kinds of Bacillus thuringiensis serotype-subsp. Leesis(H33) strain YBT-833, subsp. Aizawai(H7) strain YBT-1416 and subsp. Kurstaki(H3ab) strain YBT-1535, which were isolated by our lab, are chosen as original strain to clone vegetative insecticidal protein gene. Southern hybridization showed that vip genes are all localized at roughly 4-5 kb size-fractionated XbaI fragments of total DNA from YBT-833, YBT-1416 and YBT-1535. Three subgenomic libraries containing the vip gene fragment, were constructed with pUC19 as vector. Then, three vegetative insecticidal protein gene vip83, vip14 and vip15 are obtained from the libraries through the methods of colony-blot-in-situ screening and enzyme-cut detection. Comparision of DNA sequence made out that only vip83 gene exist five different base pairs with known vip genes. Because the sequences of vip14 and vip15 are the same, two of the three genes, vip83 and vip14, were subcloned to shuttle vehicle pHT315 to get recombinant plasmids pBMB8901 and pBMB8902 in turn. The plasmids were separately transformed into vip Bt. receptors BMB171 and 4Q7 to obtain four engineered strains BMB8901-171, BMB8902-171, BMB8901-4Q7 and BMB8902-4Q7. SDS-PAGE results indicated that all recombinant strains express 88 kD vegetative insecticidal protein. Bioassay also showed that the proteins of genes vip83 and vip14 both have certain toxicity to Lepidopteran insect larvae such as Heliochis armigera, Spodotera exigua and Plutella xylostella. While the toxicity of vip protein from four engineered strains to Plutella xylostellas are highest, whose LC50 value is 28.6, 31.6, 45.4 and 37.6 microL/mL respectively. This study will contributed to construct high efficacy and wide spectrum engineered strains on theory and reality.

Animals↗

PubMed2002

[Effects of carbon sources on the expression of cry1D -lacZ in Bacillus thuringiensis].

In order to investigate the influence of the carbon source on the expression of cry1D -lacZ in Bacillus thuringiensis with different genetic backgrounds, cry1D -lacZ was introduced into different strains and cultured in liquid medium containing different carbon sources. Analysis of activity of beta-galactosidase showed that cry1D -lacZ expressed differently in the same host because of different carbon sources and differently in different hosts utilizing same carbon sources,suggesting that metabolism pathway of carbon source in HD-133-5 was special. Sodium succinate as carbon source could lead to earlier sporulation and earlier expression of cry1D -lacZ. When sodium acetate acted as carbon source, cry1D -lacZ could keep high, stable expression in different hosts. These results are helpful for future fermentation of Bacillus thuringiensis.

English Abstract↗