Likui Zhang

Likui Zhang
Yangzhou University · Marine Science

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59
Publications
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709
Citations

Publications

Publications (59)
Article
Mismatch glycosylase (MIG) can excise thymine and uracil from mutagenic T:G and U:G mispairs, which arise from cytosine and 5-methylcytosine deamination, respectively. Here, we present evidence that a thermostable MIG from the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5 (Tb-MIG) can remove thymine and uracil from T:G and U:G mispairs...
Article
RecJ is ubiquitous in bacteria and Archaea, and play an important role in DNA replication and repair. Currently, our understanding on biochemical function of archaeal RecJ is incomplete due to limited reports. The genome of the hyperthermophilic and radioresistant euryarchaeon Thermococcus gammatolerans encodes one putative RecJ protein (Tga-RecJ)....
Article
Flap endonuclease 1 (FEN1) plays important roles in DNA replication, repair and recombination. Herein, we report the biochemical characteristics and catalytic mechanism of a novel FEN1 from the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5 (Tb-FEN1). As expected, the recombinant Tb-FEN1 can cleave 5′-flap DNA. However, the enzyme has n...
Article
Endonuclease III (EndoIII), which is ubiquitous in bacteria, Archaea and eukaryotes, plays an important role in excising thymine glycol (Tg) from DNA. Herein, we present evidence that an EndoIII from the hyperthermophilic crenarchaeon Sulfolobus islandicus REY15A (Sis-EndoIII) is capable of removing Tg from DNA at high temperature. Biochemical data...
Article
Full-text available
Since hyperthermophilic Archaea (HA) thrive in high-temperature environments, which accelerate the rates of deamination of base in DNA, their genomic stability is facing a severe challenge. Hypoxanthine (Hx) is one of the common deaminated bases in DNA. Generally, replication of Hx in DNA before repaired causes AT → GC mutation. Biochemical data ha...
Article
Full-text available
Genomes of hyperthermophiles are facing a severe challenge due to increased deamination rates of cytosine induced by high temperature, which could be counteracted by base excision repair mediated by uracil DNA glycosylase (UDG) or other repair pathways. Our previous work has shown that the two UDGs (Tba UDG247 and Tba UDG194) encoded by the genome...
Article
The genome of the hyperthermophilic and piezophilic euryarchaeaon Thermococcus barophilus Ch5 encodes three putative alcohol dehydrogenases (Tba ADHs). Herein, we characterized Tba ADH547 biochemically and probed its mechanism by mutational studies. Our data demonstrate that Tba ADH547 can oxidize ethanol and reduce acetaldehyde at high temperature...
Article
The genome of the thermophilic bacteriophage GVE2 encodes a putative tailspike protein (GVE2 TSP). Here we report the crystal structure of the truncated GVE2 TSP at 2.0-Å resolution lacking 204 amino acid residues at its N-terminus (ΔnGVE2 TSP), possessing a "vase" outline similar to other TSP's structures. However, ΔnGVE2 TSP displays structural c...
Article
The hyperthermophilic and radioresistant euryarchaeon Thermococcus gammatolerans encodes a putative 3-methlyadenine DNA glycosylase II (Tg-AlkA). Herein, we report biochemical characterization and catalytic mechanism of Tg-AlkA. The recombinant Tg-AlkA can excise hypoxanthine (Hx) and 1-methlyadenine (1-meA) from dsDNA with varied efficiencies at h...
Article
Full-text available
Hyperthermophilic Archaea (HA) thrive in high temperature environments and their genome is facing severe stability challenge due to the increased DNA damage levels caused by high temperature. Surprisingly, HA display spontaneous mutation frequencies similar to mesophilic microorganisms, thereby indicating that the former must possess more efficient...
Article
Full-text available
Plant rhizosphere-associated bacterial communities play key roles in affecting host health in response to diverse biotic stresses. Currently, the effect of continuous cropping of potato on soil bacterial communities and physiochemical parameters has not been well documented. Herein, we compared bacterial composition and diversity in rotationally an...
Article
Thermococcus gammatolerans is anaerobic euryarchaeon which grows optimally at 88 °C and its genome encodes a Family B DNA polymerase (Tga PolB). Herein, we cloned the gene of Tga PolB, expressed and purified the gene product, and characterized the enzyme biochemically. The recombinant Tga PolB can efficiently synthesize DNA at high temperature, and...
Article
The hyperthermophilic euryarchaeon Thermococcus barophilus Ch5 encodes two uracil DNA glycosylases (UDGs): Tba UDG247 and Tba UDG194. Herein, we characterized biochemically Tba UDG194. Compared with Tba UDG247, Tba UDG194 exhibits different biochemical characteristics. At >85 °C, >90 cleavage percentage was observed, suggesting that Tba UDG194 can...
Article
Full-text available
8-oxoguanine (GO) is a major lesion found in DNA that arises from guanine oxidation. The hyperthermophilic and radioresistant euryarchaeon Thermococcus gammatolerans encodes an archaeal GO DNA glycosylase (Tg-AGOG). Here, we characterized biochemically Tg-AGOG and probed its GO removal mechanism by mutational studies. Tg-AGOG can remove GO from DNA...
Article
Recent studies show that NucS endonucleases participate in mismatch repair in several archaea and bacteria. However, the function of archaeal NucS endonucleases has not been completely clarified. Here, we describe a NucS endonuclease from the hyperthermophilic and radioresistant archaeon Thermococcus gammatolerans (Tga NucS) that can cleave uracil...
Article
Purpose Archaea have important roles in global biogeochemical circulation. Although archaeal diversity and their ecological significance in deep-sea environments in the South China Sea (SCS) have been investigated, archaeal communities in deep-sea sediments below 2000 m water depth in the SCS are not well documented. The objective of our work was t...
Article
Full-text available
DNA ligases are essential enzymes for DNA replication, repair, and recombination processes by catalyzing a nick-joining reaction in double-stranded DNA. The genome of the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5 encodes a putative ATP-dependent DNA ligase (Tba ligase). Herein, we characterized the biochemical properties of the rec...
Article
Uracil DNA glycosylases (UDGs)play an important role in removing uracil from DNA to initiate DNA base excision repair. Here, we characterized biochemically a thermostable UDG from the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5 (Tba UDG), and probed its mechanism by mutational analysis. The recombinant Tba UDG cleaves exclusively ura...
Article
Full-text available
Exopolysaccharide (EPS) of two benthic diatoms, Amphora sp. and Stauroneis sp., with different biofilm formation abilities were investigated. The ratio of suspension-cells/biofilm-cells was employed to indicate the diatom biofilm formation abilities. The soluble EPS from the supernatant of whole culture, tightly bound EPS from floating cells, loose...
Article
Site-directed mutagenesis is a powerful method to introduce mutation(s) into DNA sequences. A number of methods have been developed over the years with a main goal being to create a high number of mutant genes. The single-mutagenic primer method for site-directed mutagenesis is the most direct method that yields mutant genes in about 25–50 % of tra...
Article
The bacteriophage T4 DNA polymerase (pol) and the closely related RB69 DNA pol have been developed into model enzymes to study family B DNA pols. While all family B DNA pols have similar structures and share conserved protein motifs, the molecular mechanism underlying natural drug resistance of non-herpes family B DNA pols and drug sensitivity of h...
Article
Full-text available
Translesion synthesis (TLS) DNA polymerases (pols) are often mutagenic for lesion bypass due to their low fidelity. Here, we isolated a weak yeast DNA pol δ mutant that possessed amino acid substitution V592G by genetic selection. The pol3-V592G cells were sensitive to hydroxyurea (HU), which increases the requirement for dNTPs, and their HU sensit...
Article
Full-text available
HNH endonucleases in bacteriophages play a variety of roles in the phage lifecycle as key components of phage DNA packaging machines. The deep-sea thermophilic bacteriophage Geobacillus virus E2 (GVE2) encodes an HNH endonuclease (GVE2 HNHE). Here, the crystal structure of GVE2 HNHE is reported. This is the first structural study of a thermostable...
Article
Full-text available
His-Asn-His (HNH) proteins are a very common family of small nucleic acid-binding proteins that are generally associated with endonuclease activity and are found in all kingdoms of life. Although HNH endonucleases from mesophiles have been widely investigated, the biochemical functions of HNH endonucleases from thermophilic bacteriophages remain un...
Article
Full-text available
Active deep-sea hydrothermal vents harbor abundant thermophilic and hyperthermophilic microorganisms. However, microbial communities in inactive hydrothermal vents have not been well documented. Here, we investigated bacterial and archaeal communities in the two deep-sea sediments (named as TVG4 and TVG11) collected from inactive hydrothermal vents...
Article
Full-text available
The diversity and ecological significance of bacteria and archaea in deep-sea environments have been thoroughly investigated, but eukaryotic microorganisms in these areas, such as fungi, are poorly understood. To elucidate fungal diversity in calcareous deep-sea sediments in the Southwest India Ridge (SWIR), the internal transcribed spacer (ITS) re...
Article
Full-text available
DNA polymerase (pol) is a ubiquitous enzyme that synthesizes DNA strands in all living cells. In vitro, DNA pol is used for DNA manipulation, including cloning, PCR, site-directed mutagenesis, sequencing, and several other applications. Family B archaeal DNA pols have been widely used for molecular biological methods. Biochemical and structural stu...
Article
Mutational analysis is a powerful experimental method to probe gene function. Gene deletions and mutations conferring loss of function or conditional lethality indicate if a gene is essential or not under a variety of experimental conditions. Point mutations can reveal information about function that is not possible from studies of the wild-type ge...
Article
Replication factor C (RFC) is known to function in loading proliferating cell nuclear antigen (PCNA) onto primed DNA, allowing PCNA to tether DNA polymerase for highly processive DNA synthesis in eukaryotic and archaeal replication. In this report, we show that an RFC complex from the hyperthermophilic archaea of the genus Sulfolobus physically int...
Chapter
Each time a cell divides, the genetic information contained in long DNA strands is copied by enzymes called ‘DNA polymerases’. The template strand provides instruction for DNA polymerases to synthesize a complementary strand. DNA polymerases, however, cannot initiate DNA synthesis on their own and require a primer, which can be RNA, DNA, or even a...
Chapter
Organisms have numerous nucleases that cleave the phosphodiester bonds of DNA and RNA for a variety of biological processes that include DNA replication, removing DNA damage, repairing DNA double-strand breaks, synthesis of active messenger RNA, processing of ribosomal and transfer RNAs, and gene regulation. In addition, DNases degrade DNA for prog...
Chapter
Each time a cell divides, the genetic information contained in long DNA strands is copied by enzymes called DNA polymerases. Each DNA strand provides a template that is used to synthesize a complementary strand. The replication fork is the site of ongoing DNA replication. Double-stranded DNA is unzipped to produce a Y-shaped or fork structure; lead...
Chapter
Each time a cell divides, the genetic information contained in long DNA strands is copied by enzymes called DNA polymerases. Each DNA strand provides a template that is used by DNA polymerases to synthesize a complementary strand. At a replication fork, one DNA strand is synthesized continuously in the 5' to 3' direction; this is the leading strand...
Article
Full-text available
Many gene engineering methods are reported to require highly transformable bacteria. We observed that one of the highly transformable strains that is commonly used for site-directed-mutagenesis (SDM), XL10-Gold®, produces bacteriophage.
Article
Full-text available
Understanding polymerase fidelity is an important objective towards ascertaining the overall stability of an organism's genome. Saccharomyces cerevisiae DNA polymerase eta (yPoleta), a Y-family DNA polymerase, is known to efficiently bypass DNA lesions (e.g., pyrimidine dimers) in vivo. Using pre-steady-state kinetic methods, we examined both full-...
Article
The accuracy of DNA synthesis by DNA polymerase B1 from the hyperthermophilic archaeon Sulfolobus solfataricus (Sso pol B1) at near the physiological temperature was investigated using M13-based mutational assays. Sso pol B1 showed replication fidelity similar to or higher than most viral, bacterial, and eukaryotic replicases. The fidelity of the e...
Data
Circular dichroism spectra of wild-type Dpo4 and Dpo4 mutants at 37°C. Circular dichroism spectra were collected on Model 62A DS Spectrometer (Aviv, Lakewood, NJ) in a 1-mm path-length cuvette at 37°C. The spectra were taken in the buffer (25 mM sodium phosphate, pH 7.5, 50 mM NaCl, and 5 mM MgCl2). Data points were recorded from 270 to 200 nm at 1...
Data
Stopped-flow kinetics of dTTP incorporation into a normal DNA substrate S-1 at 20°C. Dpo4 mutant•S-1 DNA complexes were reacted with dTTP and the fluorescence of the donor (green) and acceptor (red) was recorded individually. The traces are shown for (A) the finger (E49C), (B) palm (S96C), (C) palm (N130C), (D) LF (R267C), and (E) thumb (K172C). Ea...
Data
Stopped-flow kinetics of dTTP incorporation into a normal DNA substrate S-1 catalyzed by a Dpo4 mutant (S112C) at different temperatures. Dpo4 mutant (S112C)•S-1 DNA complexes were reacted with dTTP. The stopped-flow experiments were performed at (A) 17°C, (B) 20°C, (C) 24°C, (D) 32°C, and (E) 37°C. The traces monitoring donor and acceptor fluoresc...
Data
Measured motion distances of each Alexa594-labelled amino acid residue of Dpo4 during correct nucleotide binding at 20°C using steady-state FRET data. (0.05 MB DOC)
Data
Stopped-flow kinetics of dTTP incorporation into a dideoxy-terminated DNA substrate S-2 at 20°C. Dpo4 mutant•S-2 DNA complexes were reacted with dTTP and the fluorescence was monitored using a stopped-flow apparatus. Donor (green) and acceptor (red) traces are shown for the (A) finger (E49C), (B) palm (S96C), (C) palm (N130C), (D) LF (R267C), and (...
Data
Finger domain motions relative to the LF domain during a single, correct nucleotide incorporation. The domains of Dpo4 are shown in blue (finger), red (palm), green (thumb), and purple (LF); the DNA is in gold; acceptor CPM-labeled mutant residues are in yellow and the single mutant tryptophan donor is in cyan. The arrows (black for CPM-labeled res...
Data
Dpo4 mutants for monitoring the domain motions relative to DNA. (0.04 MB DOC)
Data
Dpo4 mutants for monitoring the finger domain motions relative to the little finger domain. (0.03 MB DOC)
Data
The rates of correct nucleotide incorporation catalyzed by unlabeled- and dye-labeled Dpo4 mutants under single-turnover conditions. The radioactive experiments were performed in a rapid-chemical quench apparatus. (0.05 MB DOC)
Data
The phase rates (s−1) derived from stopped-flow kinetic assays are the average from multiple independent experiments and are reported as mean ± standard deviation. (0.08 MB DOC)
Data
Control experiments of finger domain mutant (N70C) by steady-state and stopped-flow FRET under the same reaction conditions at 20°C. The reaction condition: 600 nM protein, 100 nM DNA, and 1 mM dTTP. The mixture was excited at a wavelength of 493 nm. Steady-state control experiments of (A) the unlabeled protein and labeled DNA and (B) the labeled p...
Data
Predicted motion distances of each selected amino acid residue of Dpo4 during correct nucleotide binding on the basis of the binary and ternary crystal structures of Dpo4. (0.05 MB DOC)
Article
Full-text available
Replicative DNA polymerases are stalled by damaged DNA while the newly discovered Y-family DNA polymerases are recruited to rescue these stalled replication forks, thereby enhancing cell survival. The Y-family DNA polymerases, characterized by low fidelity and processivity, are able to bypass different classes of DNA lesions. A variety of kinetic a...
Article
Sulfolobus solfataricus P2 is an aerobic crenarchaeon which grows optimally at 80 degrees C and pH 2-4. This organism encodes a B-family DNA polymerase, DNA polymerase B1 (PolB1), which faithfully replicates its genome of 3 million base pairs. Using pre-steady-state kinetic methods, we estimated the fidelity of PolB1 to be in the range of 10(-6) to...
Article
Response surface methodology was used to evaluate the effect of three selected factors (chlorine concentration, washing time and water-to-lettuce ratio) on reducing aerobic mesophilic bacteria on fresh-cut lettuce. According to statistical analysis, the model established was effective in predicting the reduction of aerobic mesophilic bacteria on fr...
Article
Various Gompertz models of the growth of bacteria on fresh-cut lettuce were established in order to predict the shelf life of fresh-cut lettuce untreated and treated with chlorinated water in storage under different temperatures. The sensory quality of fresh-cut lettuce treated with water containing 75 µg/L of available chlorine was also examined d...
Article
The effects of irradiation on microorganisms and physiological quality of fresh-cut lettuce were evaluated during storage at 4°C. The total bacterial counts on fresh-cut lettuce irradiated with 1.0kGy were reduced by the order of 2.35 Log CFU/g, and the total coliform group were lowered to less than 30 MPN (most probably number)/100g. The polypheno...
Article
Fresh-cut lettuce was irradiated and microbiological and sensory quality was examined during storage at 4 degrees C. Experimental results showed that the number of aerobic mesophilic bacteria on fresh-cut lettuce irradiated with 1.0 kGy was reduced by 2.35 logs and sensory quality was maintained best during storage for 8 days at 4 degrees C. It was...
Article
When celery is mechanically cut, contamination with microorganisms will occur as well as enzyme activity in the cut tissue. The gamma irradiation was utilized in order to extend shelf-life and to ensure the safety of fresh-cut celery. The results showed that the number of bacteria and fungi in fresh-cut celery was decreased by the order of 102 and...
Article
Fresh-cut celery was dipped with ozonated water and evaluated for changes of microbiological population and physiological quality during storage at 4 °C. The polyphenoloxidase (PPO) activity and respiration rate of fresh-cut celery was much inhibited by treatment of ozonated water and sensory quality of fresh-cut celery treated with ozonated water...

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