1
|
Hecko S, Schiefer A, Badenhorst CPS, Fink MJ, Mihovilovic MD, Bornscheuer UT, Rudroff F. Enlightening the Path to Protein Engineering: Chemoselective Turn-On Probes for High-Throughput Screening of Enzymatic Activity. Chem Rev 2023; 123:2832-2901. [PMID: 36853077 PMCID: PMC10037340 DOI: 10.1021/acs.chemrev.2c00304] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Many successful stories in enzyme engineering are based on the creation of randomized diversity in large mutant libraries, containing millions to billions of enzyme variants. Methods that enabled their evaluation with high throughput are dominated by spectroscopic techniques due to their high speed and sensitivity. A large proportion of studies relies on fluorogenic substrates that mimic the chemical properties of the target or coupled enzymatic assays with an optical read-out that assesses the desired catalytic efficiency indirectly. The most reliable hits, however, are achieved by screening for conversions of the starting material to the desired product. For this purpose, functional group assays offer a general approach to achieve a fast, optical read-out. They use the chemoselectivity, differences in electronic and steric properties of various functional groups, to reduce the number of false-positive results and the analytical noise stemming from enzymatic background activities. This review summarizes the developments and use of functional group probes for chemoselective derivatizations, with a clear focus on screening for enzymatic activity in protein engineering.
Collapse
Affiliation(s)
- Sebastian Hecko
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Astrid Schiefer
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Christoffel P S Badenhorst
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Michael J Fink
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Marko D Mihovilovic
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Uwe T Bornscheuer
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Florian Rudroff
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| |
Collapse
|
2
|
Osifalujo EA, Preston‐Herrera C, Betts PC, Satterwhite LR, Froese JT. Improving Toluene Dioxygenase Activity for Ester‐Functionalized Substrates through Enzyme Engineering. ChemistrySelect 2022. [DOI: 10.1002/slct.202200753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Cristina Preston‐Herrera
- Department of Chemistry Ball State University 1600 W Ashland Avenue Muncie IN USA 47306
- Cristina Preston-Herrera Department of Chemistry and Chemical Biology Cornell University 122 Baker Laboratory Ithaca NY USA 14853
| | - Phillip C. Betts
- Department of Chemistry Ball State University 1600 W Ashland Avenue Muncie IN USA 47306
| | - Louis R. Satterwhite
- Department of Chemistry Ball State University 1600 W Ashland Avenue Muncie IN USA 47306
| | - Jordan T. Froese
- Department of Chemistry Ball State University 1600 W Ashland Avenue Muncie IN USA 47306
| |
Collapse
|
3
|
Current and emerging tools of computational biology to improve the detoxification of mycotoxins. Appl Environ Microbiol 2021; 88:e0210221. [PMID: 34878810 DOI: 10.1128/aem.02102-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Biological organisms carry a rich potential for removing toxins from our environment, but identifying suitable candidates and improving them remain challenging. We explore the use of computational tools to discover strains and enzymes that detoxify harmful compounds. In particular, we will focus on mycotoxins-fungi-produced toxins that contaminate food and feed-and biological enzymes that are capable of rendering them less harmful. We discuss the use of established and novel computational tools to complement existing empirical data in three directions: discovering the prospect of detoxification among underexplored organisms, finding important cellular processes that contribute to detoxification, and improving the performance of detoxifying enzymes. We hope to create a synergistic conversation between researchers in computational biology and those in the bioremediation field. We showcase open bioremediation questions where computational researchers can contribute and highlight relevant existing and emerging computational tools that could benefit bioremediation researchers.
Collapse
|
4
|
Preston-Herrera C, Jackson AS, Bachmann BO, Froese JT. Development and application of a high throughput assay system for the detection of Rieske dioxygenase activity. Org Biomol Chem 2021; 19:775-784. [PMID: 33439179 DOI: 10.1039/d0ob02412k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Herein we report the development of a new periodate-based reactive assay system for the fluorescent detection of the cis-diol metabolites produced by Rieske dioxygenases. This sensitive and diastereoselective assay system successfully evaluates the substrate scope of Rieske dioxygenases and determines the relative activity of a rationally designed Rieske dioxygenase variant library. The high throughput capacity of the assay system enables rapid and efficient substrate scope investigations and screening of large dioxygenase variant libraries.
Collapse
Affiliation(s)
| | - Aaron S Jackson
- Department of Chemistry, Ball State University, 2000 W Riverside Ave, Muncie, IN 47306, USA.
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
| | - Jordan T Froese
- Department of Chemistry, Ball State University, 2000 W Riverside Ave, Muncie, IN 47306, USA.
| |
Collapse
|
5
|
Joshi DR, Zhang Y, Zhang H, Gao Y, Yang M. Characteristics of microbial community functional structure of a biological coking wastewater treatment system. J Environ Sci (China) 2018; 63:105-115. [PMID: 29406094 DOI: 10.1016/j.jes.2017.07.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/18/2017] [Accepted: 07/19/2017] [Indexed: 06/07/2023]
Abstract
Nitrogenous heterocyclic compounds are key pollutants in coking wastewater; however, the functional potential of microbial communities for biodegradation of such contaminants during biological treatment is still elusive. Herein, a high throughput functional gene array (GeoChip 5.0) in combination with Illumina HiSeq2500 sequencing was used to compare and characterize the microbial community functional structure in a long run (500days) bench scale bioreactor treating coking wastewater, with a control system treating synthetic wastewater. Despite the inhibitory toxic pollutants, GeoChip 5.0 detected almost all key functional gene (average 61,940 genes) categories in the coking wastewater sludge. With higher abundance, aromatic ring cleavage dioxygenase genes including multi ring1,2diox; one ring2,3diox; catechol represented significant functional potential for degradation of aromatic pollutants which was further confirmed by Illumina HiSeq2500 analysis results. Response ratio analysis revealed that three nitrogenous compound degrading genes- nbzA (nitro-aromatics), tdnB (aniline), and scnABC (thiocyanate) were unique for coking wastewater treatment, which might be strong cause to increase ammonia level during the aerobic process. Additionally, HiSeq2500 elucidated carbozole and isoquinoline degradation genes in the system. These findings expanded our understanding on functional potential of microbial communities to remove organic nitrogenous pollutants; hence it will be useful in optimization strategies for biological treatment of coking wastewater.
Collapse
Affiliation(s)
- Dev Raj Joshi
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Hong Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yingxin Gao
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
6
|
Lin J, Sharma V, Milase R, Mbhense N. Simultaneous enhancement of phenolic compound degradations byAcinetobacterstrain V2via a step-wise continuous acclimation process. J Basic Microbiol 2015; 56:627-34. [DOI: 10.1002/jobm.201500263] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 09/29/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Johnson Lin
- School of Life Sciences; University of KwaZulu-Natal (Westville); Durban Republic of South Africa
| | - Vikas Sharma
- School of Life Sciences; University of KwaZulu-Natal (Westville); Durban Republic of South Africa
| | - Ridwaan Milase
- School of Life Sciences; University of KwaZulu-Natal (Westville); Durban Republic of South Africa
| | - Ntuthuko Mbhense
- School of Life Sciences; University of KwaZulu-Natal (Westville); Durban Republic of South Africa
| |
Collapse
|
7
|
Factors affecting the activation and inhibition of intracellular enzymes for degradation of 1,2 diamino benzene: kinetics and thermodynamic studies. Bioprocess Biosyst Eng 2015; 38:2221-30. [PMID: 26334986 DOI: 10.1007/s00449-015-1460-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 08/13/2015] [Indexed: 10/23/2022]
Abstract
Citrobacter freundii, the bacterium isolated from marine sediments was capable of degrading 1,2 diamino benzene (DAB), an endocrine disruptor. The mixed intracellular enzymes from C. freundii were extracted and purified. The mixed intracellular enzymes were used for the degradation of DAB and degree of degradation was evaluated in terms of pyruvic acid, the end product, formed. The variables such as effect of pH, temperature and metal ions on the degradation of DAB using mixed intracellular enzymes (MICE) were investigated. The maximum amount of pyruvic acid formed was found to be 569 ± 5 µg with 96% degradation efficiency at pH 7; temperature 25 °C; zinc nitrate 0.1 mM; and copper sulphate ions 0.15 mM. The stability of MICE at different temperatures and the interaction of MICE with metal ions were confirmed using FT-IR spectroscopy. The formation of pyruvic acid from degradation of DAB followed pseudo-second-order rate kinetics and it was a spontaneous, exothermic process. The activation energy of degradation of DAB by MICE was found to be 82.55 kJ/mol.
Collapse
|
8
|
Lang W, Sirisansaneeyakul S, Ngiwsara L, Mendes S, Martins LO, Okuyama M, Kimura A. Characterization of a new oxygen-insensitive azoreductase from Brevibacillus laterosporus TISTR1911: toward dye decolorization using a packed-bed metal affinity reactor. BIORESOURCE TECHNOLOGY 2013; 150:298-306. [PMID: 24177163 DOI: 10.1016/j.biortech.2013.09.124] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/24/2013] [Accepted: 09/26/2013] [Indexed: 06/02/2023]
Abstract
This study reports the identification of a new bacterial azoreductase from Brevibacillus laterosporus TISTR1911, its heterologous production in Escherichia coli, the biochemical characterization and immobilization for use in dye biodegradation processes. The recombinant azoreductase (BrAzo) is a monomeric FMN oxygen-insensitive enzyme with a molecular mass of 23 kDa showing a broad specificity for the reduction of synthetic azo dyes. Double hexahistidine-tagged BrAzo was immobilized onto a nickel chelating column and methyl orange was used to assess its degradation potential using a packed-bed reactor. The dye degradation is described by an exponential model in a downstream batchwise continuous flow mode operated with recycling. The complete degradation of methyl orange (170 μM at 600 mL/h) was achieved in 3 h and continued over 9 cycles. Coupling the immobilized BrAzo with glucose dehydrogenase for NADH regeneration yielded a shorter 1.5 h-degradation period that was maintained throughout 16 cycles.
Collapse
Affiliation(s)
- Weeranuch Lang
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | | | | | | | | | | | | |
Collapse
|
9
|
Improvement of biocatalysts for industrial and environmental purposes by saturation mutagenesis. Biomolecules 2013; 3:778-811. [PMID: 24970191 PMCID: PMC4030971 DOI: 10.3390/biom3040778] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 09/22/2013] [Accepted: 09/23/2013] [Indexed: 11/16/2022] Open
Abstract
Laboratory evolution techniques are becoming increasingly widespread among protein engineers for the development of novel and designed biocatalysts. The palette of different approaches ranges from complete randomized strategies to rational and structure-guided mutagenesis, with a wide variety of costs, impacts, drawbacks and relevance to biotechnology. A technique that convincingly compromises the extremes of fully randomized vs. rational mutagenesis, with a high benefit/cost ratio, is saturation mutagenesis. Here we will present and discuss this approach in its many facets, also tackling the issue of randomization, statistical evaluation of library completeness and throughput efficiency of screening methods. Successful recent applications covering different classes of enzymes will be presented referring to the literature and to research lines pursued in our group. The focus is put on saturation mutagenesis as a tool for designing novel biocatalysts specifically relevant to production of fine chemicals for improving bulk enzymes for industry and engineering technical enzymes involved in treatment of waste, detoxification and production of clean energy from renewable sources.
Collapse
|
10
|
Kayashima T, Suzuki H, Maeda T, Ogawa HI. Real-time PCR for rapidly detecting aniline-degrading bacteria in activated sludge. CHEMOSPHERE 2013; 91:1338-1343. [PMID: 23466276 DOI: 10.1016/j.chemosphere.2013.01.114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 01/23/2013] [Accepted: 01/24/2013] [Indexed: 06/01/2023]
Abstract
We developed a detection method that uses quantitative real-time PCR (qPCR) and the TaqMan system to easily and rapidly assess the population of aniline-degrading bacteria in activated sludge prior to conducting a biodegradability test on a chemical compound. A primer and probe set for qPCR was designed by a multiple alignment of conserved amino acid sequences encoding the large (α) subunit of aniline dioxygenase. PCR amplification tests showed that the designed primer and probe set targeted aniline-degrading strains such as Acidovorax sp., Gordonia sp., Rhodococcus sp., and Pseudomonas putida, thereby suggesting that the developed method can detect a wide variety of aniline-degrading bacteria. There was a strong correlation between the relative copy number of the α-aniline dioxygenase gene in activated sludge obtained with the developed qPCR method and the number of aniline-degrading bacteria measured by the Most Probable Number method, which is the conventional method, and a good correlation with the lag time of the BOD curve for aniline degradation produced by the biodegradability test in activated sludge samples collected from eight different wastewater treatment plants in Japan. The developed method will be valuable for the rapid and accurate evaluation of the activity of inocula prior to conducting a ready biodegradability test.
Collapse
Affiliation(s)
- Takakazu Kayashima
- Chemicals Evaluation and Research Institute, Kurume Laboratory, 3-2-7 Miyanojin, Kurume-shi, Fukuoka 839-0801, Japan.
| | | | | | | |
Collapse
|
11
|
Shainsky J, Bernath-Levin K, Isaschar-Ovdat S, Glaser F, Fishman A. Protein engineering of nirobenzene dioxygenase for enantioselective synthesis of chiral sulfoxides. Protein Eng Des Sel 2013; 26:335-45. [PMID: 23442445 DOI: 10.1093/protein/gzt005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Nitrobenzene dioxygenase (NBDO) from Comamonas sp. is shown here to perform enantioselective oxidation of aromatic sulfides. Several para-substituted alkyl aryl sulfides were examined and it was found that the activity of the enzyme is dependent on the size of the substrate. Saturation mutagenesis was performed on different residues in the active site in order to improve activity and selectivity. Mutagenesis at position 258 in the α-hydroxylase subunit of NBDO improved both activity and enantioselectivity. Substitutions in position 293 improved the activity on all substrates and had diverse influence on enantioselectivity. Mutagenesis in position 207 provided two interesting variants, V207I and V207A, with opposite enantioselectivities. Furthermore, combining two favorable mutations, N258A and F293H, provided an improved variant with both higher activity (5.20 ± 0.01, 2.12 ± 0.21, 2.64 ± 0.14 and 4.01 ± 0.34 nmol min(-1) mg protein(-1) on thioanisole, ptolyl, Cl-thioanisole and Br-thioanisole, respectively, which is 1.7, 4.6, 7.1 and 26.7-fold compared with wild type) and improved enantioselectivity (e.g. 67% enantiomeric excess for Cl-thioanisole vs. 5% for wild type). Molecular docking and active site volume calculations were used to correlate between the structure of the substrates and the function of the enzymes. The results from this work suggest that the location of pro-chiral sulfides in the active site is coordinated by hydrophobic interactions and by steric considerations, which in turn influences the activity and enantioselectivity of NBDO.
Collapse
Affiliation(s)
- Janna Shainsky
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | | | | | | | | |
Collapse
|
12
|
Baboshin MA, Golovleva LA. Aerobic bacterial degradation of polycyclic aromatic hydrocarbons (PAHs) and its kinetic aspects. Microbiology (Reading) 2012. [DOI: 10.1134/s0026261712060021] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
13
|
Pourmir A, Johannes TW. Directed evolution: selection of the host organism. Comput Struct Biotechnol J 2012; 2:e201209012. [PMID: 24688653 PMCID: PMC3962113 DOI: 10.5936/csbj.201209012] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 10/06/2012] [Accepted: 10/12/2012] [Indexed: 11/29/2022] Open
Abstract
Directed evolution has become a well-established tool for improving proteins and biological systems. A critical aspect of directed evolution is the selection of a suitable host organism for achieving functional expression of the target gene. To date, most directed evolution studies have used either Escherichia coli or Saccharomyces cerevisiae as a host; however, other bacterial and yeast species, as well as mammalian and insect cell lines, have also been successfully used. Recent advances in synthetic biology and genomics have opened the possibility of expanding the use of directed evolution to new host organisms such as microalgae. This review focuses on the different host organisms used in directed evolution and highlights some of the recent directed evolution strategies used in these organisms.
Collapse
Affiliation(s)
- Azadeh Pourmir
- Department of Chemical Engineering, The University of Tulsa, 800 S. Tucker Dr, Tulsa, OK 74104, United States
| | - Tyler W Johannes
- Department of Chemical Engineering, The University of Tulsa, 800 S. Tucker Dr, Tulsa, OK 74104, United States
| |
Collapse
|
14
|
Dror A, Fishman A. Engineering non-heme mono- and dioxygenases for biocatalysis. Comput Struct Biotechnol J 2012; 2:e201209011. [PMID: 24688652 PMCID: PMC3962191 DOI: 10.5936/csbj.201209011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Revised: 10/02/2012] [Accepted: 10/12/2012] [Indexed: 11/25/2022] Open
Abstract
Oxygenases are ubiquitous enzymes that catalyze the introduction of one or two oxygen atoms to unreactive chemical compounds. They require reduction equivalents from NADH or NADPH and comprise metal ions, metal ion complexes, or coenzymes in their active site. Thus, for industrial purposes, oxygenases are most commonly employed using whole cell catalysis, to alleviate the need for co-factor regeneration. Biotechnological applications include bioremediation, chiral synthesis, biosensors, fine chemicals, biofuels, pharmaceuticals, food ingredients and polymers. Controlling activity and selectivity of oxygenases is therefore of great importance and of growing interest to the scientific community. This review focuses on protein engineering of non-heme monooxygenases and dioxygenases for generating improved or novel functionalities. Rational mutagenesis based on x-ray structures and sequence alignment, as well as random methods such as directed evolution, have been utilized. It is concluded that knowledge-based protein engineering accompanied with targeted libraries, is most efficient for the design and tuning of biocatalysts towards novel substrates and enhanced catalytic activity while minimizing the screening efforts.
Collapse
Affiliation(s)
- Adi Dror
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Ayelet Fishman
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| |
Collapse
|
15
|
Restriction enzyme-free construction of random gene mutagenesis libraries in Escherichia coli. Anal Biochem 2011; 421:640-8. [PMID: 22155067 DOI: 10.1016/j.ab.2011.11.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 11/07/2011] [Accepted: 11/10/2011] [Indexed: 11/22/2022]
Abstract
Directed evolution relies on both random and site-directed mutagenesis of individual genes and regulatory elements to create variants with altered activity profiles for engineering applications. Central to these experiments is the construction of large libraries of related variants. However, a number of technical hurdles continue to limit routine construction of random mutagenesis libraries in Escherichia coli, in particular, inefficiencies during digestion and ligation steps. Here, we report a restriction enzyme-free approach to library generation using megaprimers termed MegAnneal. Target DNA is first exponentially amplified using error-prone polymerase chain reaction (PCR) and then linearly amplified with a single 3' primer to generate long, randomly mutated, single-stranded megaprimers. These are annealed to single-stranded dUTP-containing template plasmid and extended with T7 polymerase to create a complementary strand, and the resulting termini are ligated with T4 DNA ligase. Using this approach, we are able to reliably generate libraries of approximately 10⁷ colony-forming units (cfu)/μg DNA/transformation in a single day. We have created MegAnneal libraries based on three different single-chain antibodies and identified variants with enhanced expression and ligand-binding affinity. The key advantages of this approach include facile amplification, restriction enzyme-free library generation, and a significantly reduced risk of mutations outside the targeted region and wild-type contamination as compared with current methods.
Collapse
|
16
|
Gündoğdu A, Long YB, Vollmerhausen TL, Katouli M. Antimicrobial resistance and distribution of sul genes and integron-associated intI genes among uropathogenic Escherichia coli in Queensland, Australia. J Med Microbiol 2011; 60:1633-1642. [DOI: 10.1099/jmm.0.034140-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Aycan Gündoğdu
- Faculty of Science, Health and Education, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Ysanne Beverley Long
- Faculty of Science, Health and Education, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Tara Leigh Vollmerhausen
- Faculty of Science, Health and Education, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Mohammad Katouli
- Faculty of Science, Health and Education, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| |
Collapse
|
17
|
Behrens GA, Hummel A, Padhi SK, Schätzle S, Bornscheuer UT. Discovery and Protein Engineering of Biocatalysts for Organic Synthesis. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201100446] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
18
|
Xiong AS, Peng RH, Zhuang J, Davies J, Zhang J, Yao QH. Advances in directed molecular evolution of reporter genes. Crit Rev Biotechnol 2011; 32:133-42. [DOI: 10.3109/07388551.2011.593503] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
19
|
Hongsawat P, Vangnai AS. Biodegradation pathways of chloroanilines by Acinetobacter baylyi strain GFJ2. JOURNAL OF HAZARDOUS MATERIALS 2011; 186:1300-1307. [PMID: 21177022 DOI: 10.1016/j.jhazmat.2010.12.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 11/26/2010] [Accepted: 12/01/2010] [Indexed: 05/30/2023]
Abstract
The Acinetobacter baylyi strain GFJ2 was isolated from soil that was potentially contaminated with herbicides. It exhibited complete biodegradations of 4-chlroaniline (4CA) and 3,4-dichloroaniline (34DCA), a wide range of monohalogenated anilines (chloro-, bromo-, and fluoro-anilines) and other dichloroanilines. An in-depth investigation of the biodegradation pathway revealed that a dechlorination reaction may be involved in 34DCA biodegradation, which forms 4CA as the first intermediate. By detecting the transient intermediates and characterizing the relevant enzymes, this investigation is also the first to report that A. baylyi strain GFJ2 has two distinct 4CA degradation pathways that yield 4-chlorocatechol (4CC) and aniline as the first intermediate in each route, which are further metabolized through an ortho-cleavage pathway. Analysis of biodegradation kinetics analysis illustrated that A. baylyi GFJ2 utilized aniline and 4CC at significantly slower rates than it used 4CA, suggesting that the transformations of aniline and 4CC were probably the limiting steps during 4CA biodegradation. Our results suggest the potential application of A. baylyi strain GFJ2 in bioremediation and waste treatment, and the kinetic data provide the insights into the degradation mechanism, dynamics and possible limitations of the biodegradation which include substrate and product inhibitions.
Collapse
Affiliation(s)
- Parnuch Hongsawat
- International Postgraduate Program in Environmental Management, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | | |
Collapse
|
20
|
Jez JM. Toward protein engineering for phytoremediation: possibilities and challenges. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2011; 13 Suppl 1:77-89. [PMID: 22046752 DOI: 10.1080/15226514.2011.568537] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The combination of rational protein engineering and directed evolution techniques allow for the redesign of enzymes with tailored properties for use in environmental remediation. This review summarizes current molecular methods for either altering or improving protein function and highlights examples of how these methods can address bioremediation problems. Although much of the protein engineering applied to environmental clean-up employs microbial systems, there is great potential for and significant challenges to translating these approaches to plant systems for phytoremediation purposes. Protein engineering technologies combined with genomic information and metabolic engineering strategies hold promise for the design of plants and microbes to remediate organic and inorganic pollutants.
Collapse
Affiliation(s)
- Joseph M Jez
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA.
| |
Collapse
|
21
|
Xu Z, Yu J. A novel solid-state electrochemiluminescence sensor based on Ru(bpy)(3)(2+) immobilization on TiO(2) nanotube arrays and its application for detection of amines in water. NANOTECHNOLOGY 2010; 21:245501. [PMID: 20484789 DOI: 10.1088/0957-4484/21/24/245501] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Many amines are proven or suspected to be carcinogenic and have been implicated in inducing cancer of the bladder. Therefore, the monitoring of their levels in environmental samples is important for the protection of health and the environment. Herein, a novel method for effective immobilization of Ru(bpy)(3)(2+) on the electrode surface of TiO(2) nanotube arrays (TNs) is developed for the first time. The method involves Ru(bpy)(3)(2+) spontaneously adsorbed on the surface of negatively charged TiO(2) nanotubes due to electrostatic interaction to produce a Ru(bpy)(3)(2+) /TNs/Ti (Ru-TNs-Ti) solid-state electrochemiluminescence (ECL) sensor. The prepared solid-state sensor was used to detect the changes of concentrations of pollutant tripropylamine (TPA) in water. The sensor exhibits excellent ECL behavior, very good stability and high sensitivity. This study may provide new insight into the design and preparation of an advanced solid-state ECL sensor for monitoring of amines in water.
Collapse
Affiliation(s)
- Zhihua Xu
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070, People's Republic of China
| | | |
Collapse
|