A direct and efficient PAGE-mediated overlap extension PCR method for gene multiple-site mutagenesis.

Abstract:

:A simple, two-step efficient method to perform multiple-site mutagenesis of a gene from bacterial genome was developed. The method was named polyacrylamide gel electrophoresis (PAGE)-mediated overlap extension polymerase chain reaction (PCR) (POEP). The first step involves synthesis of individual fragments containing mutant sites with 15- to 25-bp overlap between two adjacent fragments. Mutations were introduced into the overlapping oligonucleotide primers which ensured the particular primer-template annealing. PAGE was used to remove contaminating parental templates, mispriming fragments, and leftover primers. The second step involves synthesis of the mutant full-length fragment. All purified PCR products from the first step were combined and used as the template for a second PCR using high-fidelity DNA polymerase, with the two outermost flanking oligonucleotides as primers. Using the POEP method, we have successfully introduced eight EcoRI sites into the Escherichia coli beta-galactosidase (Lac Z) gene. The overall rate of obtaining the multiple mutant sites was 100%. The POEP method is simple, involving only two steps, and reliable for multiple-site mutagenesis and is promising to be widely used in gene modification.

authors

Peng RH,Xiong AS,Yao QH

doi

10.1007/s00253-006-0583-3

subject

Has Abstract

pub_date

2006-11-01 00:00:00

pages

234-40

issue

1

eissn

0175-7598

issn

1432-0614

journal_volume

73

pub_type

杂志文章
  • Increased intracellular calcium level and impaired nutrient absorption are important pathogenicity traits in the chicken intestinal epithelium during Campylobacter jejuni colonization.

    abstract::Although a high number of chickens carry Campylobacter jejuni, the mechanistic action of colonization in the intestine is still poorly understood. The current study was therefore designed to investigate the effects of C. jejuni on glucose uptake, amino acids availability in digesta, and intracellular calcium [Ca(2+)]i...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-015-6543-z

    authors: Awad WA,Smorodchenko A,Hess C,Aschenbach JR,Molnár A,Dublecz K,Khayal B,Pohl EE,Hess M

    更新日期:2015-08-01 00:00:00

  • Soluble expression and stability enhancement of transcription factors using 30Kc19 cell-penetrating protein.

    abstract::Transcription factors have been studied as an important drug candidate. Ever since the successful generation of induced pluripotent stem cells (iPSCs), there has been tremendous interest in reprogramming transcription factors. Because of the safety risks involved in a virus-based approach, many researchers have been t...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-015-7199-4

    authors: Ryu J,Park HH,Park JH,Lee HJ,Rhee WJ,Park TH

    更新日期:2016-04-01 00:00:00

  • Streptomyces sp. JS520 produces exceptionally high quantities of undecylprodigiosin with antibacterial, antioxidative, and UV-protective properties.

    abstract::A Gram-positive, red-pigment-producing bacterial strain, designated JS520 was isolated from the pristine sediment from the cave on mountain Miroc in Serbia. Strain was confirmed to belong to Streptomyces genus based on phenotypic and genetic analysis. Streptomyces sp. JS520 has the ability to produce exceptionally hig...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-012-4237-3

    authors: Stankovic N,Radulovic V,Petkovic M,Vuckovic I,Jadranin M,Vasiljevic B,Nikodinovic-Runic J

    更新日期:2012-12-01 00:00:00

  • Use of real time PCR to determine population profiles of individual species of lactic acid bacteria in alfalfa silage and stored corn stover.

    abstract::Real-time polymerase chain reaction (RT-PCR) was used to quantify seven species of lactic acid bacteria (LAB) in alfalfa silage prepared in the presence or absence of four commercial inoculants and in uninoculated corn stover harvested and stored under a variety of field conditions. Species-specific PCR primers were d...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-005-0170-z

    authors: Stevenson DM,Muck RE,Shinners KJ,Weimer PJ

    更新日期:2006-07-01 00:00:00

  • An impaired ubiquitin ligase complex favors initial growth of auxotrophic yeast strains in synthetic grape must.

    abstract::We used experimental evolution in order to identify genes involved in the adaptation of Saccharomyces cerevisiae to the early stages of alcoholic fermentation. Evolution experiments were run for about 200 generations, in continuous culture conditions emulating the initial stages of wine fermentation. We performed whol...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-014-6126-4

    authors: Mangado A,Tronchoni J,Morales P,Novo M,Quirós M,Gonzalez R

    更新日期:2015-02-01 00:00:00

  • Batch, design optimization, and DNA sequencing study for continuous 1,3-propanediol production from waste glycerol by a soil-based inoculum.

    abstract::1,3-propanediol (1,3-PD) was produced with a robust fermentation process using waste glycerol feedstock from biodiesel production and a soil-based bacterial inoculum. An iterative inoculation method was developed to achieve independence from soil and selectively breed bacterial populations capable of glycerol metaboli...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-014-6259-5

    authors: Kanjilal B,Noshadi I,Bautista EJ,Srivastava R,Parnas RS

    更新日期:2015-03-01 00:00:00

  • Metabolic activity of Corynebacterium glutamicum grown on L: -lactic acid under stress.

    abstract::Respiration measurement in shake flasks is introduced as a new method to characterize the metabolic activity of microorganisms during and after stress exposure. The major advantage of the new method is the possibility to determine the metabolic activity independent of manual sampling without the necessity to change th...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-006-0436-0

    authors: Seletzky JM,Noack U,Fricke J,Hahn S,Büchs J

    更新日期:2006-10-01 00:00:00

  • Transcriptional changes involved in inhibition of biofilm formation by ε-polylysine in Salmonella Typhimurium.

    abstract::The pathogenicity of Salmonella Typhimurium, a foodborne pathogen, is mainly attributed to its ability to form biofilm on food contact surfaces. ε-polylysine, a polymer of positively charged lysine, is reported to inhibit biofilm formation of both gram-positive and gram-negative bacteria. To elucidate the mechanism un...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-020-10575-2

    authors: Shen C,Islam MT,Masuda Y,Honjoh KI,Miyamoto T

    更新日期:2020-06-01 00:00:00

  • Lipids as renewable resources: current state of chemical and biotechnological conversion and diversification.

    abstract::Oils and fats are the most important renewable raw materials of the chemical industry. They make available fatty acids in such purity that they may be used for chemical conversions and for the synthesis of chemically pure compounds. Oleic acid (1) from "new sunflower," linoleic acid (2) from soybean, linolenic acid (3...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章,评审

    doi:10.1007/s00253-006-0335-4

    authors: Metzger JO,Bornscheuer U

    更新日期:2006-06-01 00:00:00

  • Improved inhibitor tolerance in xylose-fermenting yeast Spathaspora passalidarum by mutagenesis and protoplast fusion.

    abstract::The xylose-fermenting yeast Spathaspora passalidarum showed excellent fermentation performance utilizing glucose and xylose under anaerobic conditions. But this yeast is highly sensitive to the inhibitors such as furfural present in the pretreated lignocellulosic biomass. In order to improve the inhibitor tolerance of...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-011-3693-5

    authors: Hou X,Yao S

    更新日期:2012-03-01 00:00:00

  • Humic analog AQDS and AQS as an electron mediator can enhance chromate reduction by Bacillus sp. strain 3C3.

    abstract::Humus as an electron mediator is recognized as an effective strategy to improve the biological transformation and degradation of toxic substances, yet the action of humus in microbial detoxification of chromate is still unknown. In this study, a humus-reducing strain 3C(3) was isolated from mangrove sediment. Based on...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-011-3577-8

    authors: Hong Y,Wu P,Li W,Gu J,Duan S

    更新日期:2012-03-01 00:00:00

  • Manipulating the expression of SARP family regulator BulZ and its target gene product to increase tacrolimus production.

    abstract::Tacrolimus (FK506), an effective immunosuppressant, is widely used in the treatment of autoimmune diseases. In this study, we identified that BulZ, a Streptomyces antibiotic regulatory protein (SARP) family regulator, acted as a positive regulator for spore differentiation and tacrolimus production. A knockout of bulZ...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-018-8979-4

    authors: Ma D,Wang C,Chen H,Wen J

    更新日期:2018-06-01 00:00:00

  • Novel nano-composite hydrogels with honey effective against multi-resistant clinical strains of Acinetobacter baumannii and Pseudomonas aeruginosa.

    abstract::Novel alginate hydrogels with silver nanoparticles (AgNPs) and honey components were produced with the aim to target multidrug-resistant bacterial strains causing nosocomial wound infections. AgNP synthesis was optimized in highly concentrated honey solutions so that a 5-month stable, colloid solution with 50% of hone...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-019-10055-2

    authors: Stojkovska J,Petrovic P,Jancic I,Milenkovic MT,Obradovic B

    更新日期:2019-10-01 00:00:00

  • Molecular basis of Cd+2 stress response in Candida tropicalis.

    abstract::This study examines the bioremediation potential and cadmium-induced cellular response on a molecular level in Candida tropicalis 3Aer. Spectroscopic analysis clearly illustrated the involvement of yeast cell wall components in biosorption. Cadmium bioaccumulation was confirmed by TEM, SEM, and EDX examination. TEM im...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-017-8503-2

    authors: Khan Z,Rehman A,Nisar MA,Zafar S,Hussain SZ,Zerr I,Hussain I,Waseem M,Arif M

    更新日期:2017-10-01 00:00:00

  • Behavioral response of dissimilatory perchlorate-reducing bacteria to different electron acceptors.

    abstract::The response behavior of three dissimilatory perchlorate-reducing bacteria to different electron acceptors (nitrate, chlorate, and perchlorate) was investigated with two different assays. The observed response was species-specific, dependent on the prior growth conditions, and was inhibited by oxygen. We observed attr...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-009-2051-3

    authors: Sun Y,Gustavson RL,Ali N,Weber KA,Westphal LL,Coates JD

    更新日期:2009-10-01 00:00:00

  • Application of recombinant Pediococcus acidilactici BD16 (fcs +/ech +) for bioconversion of agrowaste to vanillin.

    abstract::Biotechnological production of vanillin is gaining momentum as the natural synthesis of vanillin that is very expensive. Ferulic acid (FA), a costly compound, is used as the substrate to produce vanillin biotechnologically and the making process is still expensive. Therefore, this study investigated the practical use ...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-017-8283-8

    authors: Chakraborty D,Selvam A,Kaur B,Wong JWC,Karthikeyan OP

    更新日期:2017-07-01 00:00:00

  • Enzymatic reduction of azo and indigoid compounds.

    abstract::A customer- and environment-friendly method for the decolorization azo dyes was developed. Azoreductases could be used both to bleach hair dyed with azo dyes and to reduce dyes in vat dyeing of textiles. A new reduced nicotinamide adenine dinucleotide-dependent azoreductase of Bacillus cereus, which showed high potent...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-007-1165-8

    authors: Pricelius S,Held C,Murkovic M,Bozic M,Kokol V,Cavaco-Paulo A,Guebitz GM

    更新日期:2007-11-01 00:00:00

  • Dynamic change of surface microbiota with different environmental cleaning methods between two wards in a hospital.

    abstract::Terminal disinfection and daily cleaning have been performed in hospitals in Taiwan for many years to reduce the risks of healthcare-associated infections. However, the effectiveness of these cleaning approaches and dynamic changes of surface microbiota upon cleaning remain unclear. Here, we report the surface changes...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-016-7846-4

    authors: Chen CH,Tu CC,Kuo HY,Zeng RF,Yu CS,Lu HH,Liou ML

    更新日期:2017-01-01 00:00:00

  • Generation of biologically contained, readily transformable, and genetically manageable mutants of the biotechnologically important Bacillus pumilus.

    abstract::Bacillus pumilus mutants were generated by targeted deletion of a set of genes eventually facilitating genetic handling and assuring biological containment. The well-defined and stable mutants do not form functional endospores due to the deletion of yqfD, an essential sporulation gene; they are affected in DNA repair,...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-013-4935-5

    authors: Wemhoff S,Meinhardt F

    更新日期:2013-09-01 00:00:00

  • β-glucosidase from Penicillium aculeatum hydrolyzes exo-, 3-O-, and 6-O-β-glucosides but not 20-O-β-glucoside and other glycosides of ginsenosides.

    abstract::A novel β-glucosidase from Penicillium aculeatum was purified as a single 110.5-kDa band on SDS-PAGE with a specific activity of 75.4 U mg⁻¹ by salt precipitation and Hi-Trap Q HP and Resource Q ion exchange chromatographies. The purified enzyme was identified as a member of the glycoside hydrolase 3 family based on i...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-013-4828-7

    authors: Lee GW,Yoo MH,Shin KC,Kim KR,Kim YS,Lee KW,Oh DK

    更新日期:2013-07-01 00:00:00

  • Biodetoxification of fungal mycotoxins zearalenone by engineered probiotic bacterium Lactobacillus reuteri with surface-displayed lactonohydrolase.

    abstract::Zearalenone (ZEN) is one of the common mycotoxins with quite high occurrence rate and is harmful to animal and human health. Lactobacillus reuteri is known as a probiotic bacterium with active immune stimulating and high inhibitory activity against pathogenic microorganisms. In this study, we expressed the lactonohydr...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-019-10153-1

    authors: Liu F,Malaphan W,Xing F,Yu B

    更新日期:2019-11-01 00:00:00

  • Cloning and functional expression of a nitrile hydratase (NHase) from Rhodococcus equi TG328-2 in Escherichia coli, its purification and biochemical characterisation.

    abstract::The nitrile hydratase (NHase, EC 4.2.1.84) genes (alpha and beta subunit) and the corresponding activator gene from Rhodococcus equi TG328-2 were cloned and sequenced. This Fe-type NHase consists of 209 amino acids (alpha subunit, M(r) 23 kDa) and 218 amino acids (beta subunit, M(r) 24 kDa) and the NHase activator of ...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-009-2153-y

    authors: Rzeznicka K,Schätzle S,Böttcher D,Klein J,Bornscheuer UT

    更新日期:2010-02-01 00:00:00

  • Robust NADH-regenerator: improved alpha-haloketone-resistant formate dehydrogenase.

    abstract::Formate dehydrogenases (FDH) are useful for the regeneration of NADH, which is required for asymmetric reduction by several dehydrogenases and reductases. FDHs have relatively low activity and are labile, especially to alpha-haloketones, thus FDH cannot be applied to the industrial manufacture of optically active alph...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-004-1728-x

    authors: Yamamoto H,Mitsuhashi K,Kimoto N,Kobayashi Y,Esaki N

    更新日期:2005-04-01 00:00:00

  • Environmental evaluation of coexistence of denitrifying anaerobic methane-oxidizing archaea and bacteria in a paddy field.

    abstract::The nitrate-dependent denitrifying anaerobic methane oxidation (DAMO) process, which is metabolized together by anaerobic methanotrophic archaea and NC10 phylum bacteria, is expected to be important for the global carbon and nitrogen cycles. However, there are little studies about the existence of this process and the...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-015-6986-2

    authors: Ding J,Fu L,Ding ZW,Lu YZ,Cheng SH,Zeng RJ

    更新日期:2016-01-01 00:00:00

  • Deciphering bacterial xylose metabolism and metabolic engineering of industrial microorganisms for use as efficient microbial cell factories.

    abstract::The goal of sustainable production of biochemicals and biofuels has driven the engineering of microbial cell as factories that convert low-value substrates to high-value products. Xylose is the second most abundant sugar substrate in lignocellulosic hydrolysates. We analyzed the mechanisms of xylose metabolism using g...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章,评审

    doi:10.1007/s00253-018-9353-2

    authors: Kim D,Woo HM

    更新日期:2018-11-01 00:00:00

  • Modulation of calcium carbonate precipitation by exopolysaccharide in Bacillus sp. JH7.

    abstract::Extracellular polymeric substance (EPS) is proposed to facilitate calcium ion supersaturation through its nucleation effect during the microbially induced calcium carbonate precipitation (MICP) process. However, the supersaturation effect of Ca2+ via EPS in MICP has not been clearly demonstrated. Enhanced exopolysacch...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-017-8372-8

    authors: Kim HJ,Shin B,Lee YS,Park W

    更新日期:2017-08-01 00:00:00

  • Pyrosequencing analysis of bacterial communities in biofilms from different pipe materials in a city drinking water distribution system of East China.

    abstract::Biofilms in drinking water distribution systems (DWDSs) could cause several types of problems, such as the deterioration of water quality, corrosion of pipe walls, and potential proliferation of opportunistic pathogens. In this study, ten biofilm samples from different pipe materials, including ductile cast iron pipe ...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-015-6885-6

    authors: Ren H,Wang W,Liu Y,Liu S,Lou L,Cheng D,He X,Zhou X,Qiu S,Fu L,Liu J,Hu B

    更新日期:2015-12-01 00:00:00

  • Biotransformations of organic compounds mediated by cultures of Aspergillus niger.

    abstract::Many different organic compounds may be converted by microbial biotransformation to high-value products for the chemical and pharmaceutical industries. This review summarizes the use of strains of Aspergillus niger, a well-known filamentous fungus used in numerous biotechnological processes, for biochemical transforma...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章,评审

    doi:10.1007/s00253-015-6765-0

    authors: Parshikov IA,Woodling KA,Sutherland JB

    更新日期:2015-09-01 00:00:00

  • Selective enrichment and characterization of a phosphorus-removing bacterial consortium from activated sludge.

    abstract::Under alternating aerobic/anaerobic conditions and without additional carbon sources, a bacterial consortium consisting initially of 18 bacterial strains was obtained in a sequence batch reactor. The phosphorus removal capability could only be maintained using sterile filtrate of activated sludge as medium. The additi...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-001-0847-x

    authors: Hollender J,Dreyer U,Kornberger L,Kämpfer P,Dott W

    更新日期:2002-01-01 00:00:00

  • Display of both N- and C-terminal target fusion proteins on the Aspergillus oryzae cell surface using a chitin-binding module.

    abstract::A novel cell surface display system in Aspergillus oryzae was established by using a chitin-binding module (CBM) from Saccharomyces cerevisiae as an anchor protein. CBM was fused to the N or C terminus of green fluorescent protein (GFP) and the fusion proteins (GFP-CBM and CBM-GFP) were expressed using A. oryzae as a ...

    journal_title:Applied microbiology and biotechnology

    pub_type: 杂志文章

    doi:10.1007/s00253-010-2664-6

    authors: Tabuchi S,Ito J,Adachi T,Ishida H,Hata Y,Okazaki F,Tanaka T,Ogino C,Kondo A

    更新日期:2010-08-01 00:00:00