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Parmar AS, Rahi DK. Cutinase production from Fusarium verticillioides using response surface methodology and its application as potential insecticide degrader. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:86484-86497. [PMID: 37450178 DOI: 10.1007/s11356-023-28635-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 07/02/2023] [Indexed: 07/18/2023]
Abstract
Cutinase, a multifunctional enzyme, has shown great potential in environmental applications such as degradation of plastics and some commonly used insecticides. To overcome these environmental threatening problems, attempts should be made to enhance enzyme production. In the present study, a cutinolytic fungus was isolated from the soil. Based on 18 s rDNA sequencing, it was found that isolate AR08 belongs to the genus Fusarium and clades with Fusarium verticillioides. Optimization of medium composition for enhancement in cutinase production was done using. classical and statistical methods. Firstly, key factors were selected by one variable at a time (OVAT) method, then by Plackett- Burman design. Concentration of these important factors was optimized by Central Composite design. A total of 30 experiments were conducted and the optimized concentration of sodium nitrate, dipotassium hydrogen phosphate, flaxseed oil and zinc sulphate were found to be 0.455%, 0.305%, 2% and 0.0355% respectively. The result of ANOVA (analysis of variance) test revealed that p value was significant for the model. Interaction between flaxseed oil and sodium nitrate was found to have a positive effect on cutinase production. A 14.57 fold increase in enzyme activity was found under optimized conditions with the maximum cutinase activity of 626.6 IUml-1.
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Affiliation(s)
| | - Deepak K Rahi
- Department of Microbiology, Panjab University, Chandigarh, India
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2
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Parashiva J, Nuthan BR, Bharatha M, Praveen R, Tejashwini P, Satish S. Response surface methodology based optimized production, purification, and characterization of L-asparaginase from Fusarium foetens. World J Microbiol Biotechnol 2023; 39:252. [PMID: 37442849 DOI: 10.1007/s11274-023-03684-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023]
Abstract
L-asparaginase is used as one of the prime chemotherapeutic agents to treat acute lymphoblastic leukemia. L-asparaginase obtained from bacteria exhibits hypersensitive reactions including various side effects. The present work aimed to optimize growth parameters for maximum production of L-asparaginase by Fusarium foetens through response surface methodology, its purification, and characterization. The optimization of L-asparaginase production by Fusarium foetens was initially done through a one-factor-at-a-time method. L-asparaginase production was further optimized using a central composite design based response surface methodology. The maximum L-asparaginase activity of 12.83 IU/ml was obtained under the following growth conditions; temperature-27.5 °C, pH-8, inoculum concentration-1.5 × 106 spores/ml, and incubation period-7 days. In comparison with the unoptimized growth conditions (4.58 IU/ml), the optimization led to a 2.65-fold increase in the L-asparaginase activity. The L-asparaginase from Fusarium foetens was purified 15.60-fold, with a yield of 39.89% using DEAE-cellulose column chromatography. After purification, the L-asparaginase activity was determined to be 127.26 IU/ml and the specific activity was found to be 231.38 IU/mg. The molecular mass was estimated to be approximately 37 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The purified enzyme showed optimum activity at pH 5, and a temperature of 40 °C. The enzyme showed 100% specificity towards L-asparagine and no activity towards L-glutamine. Its activity was enhanced by Mn2+, Fe2+, and Mg2, while it was inhibited by β-mercaptoethanol and EDTA. The Km and Vmax of the purified L-asparaginase were found to be 23.82 mM and 210.3 IU/ml respectively. The results suggest that Fusarium foetens could be a potent candidate for the bioprocessing of L-asparaginase at a large scale.
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Affiliation(s)
- Javaraiah Parashiva
- Department of Studies in Microbiology, University of Mysore, Manasagangotri, Mysuru, Karnataka, 570 006, India
| | | | - Madeva Bharatha
- Department of Studies in Biochemistry, University of Mysore, Manasagangotri, Mysuru, Karnataka, 570 005, India
| | - Raju Praveen
- Department of Studies in Biochemistry, University of Mysore, Manasagangotri, Mysuru, Karnataka, 570 005, India
| | - Purushotham Tejashwini
- Department of Studies in Microbiology, University of Mysore, Manasagangotri, Mysuru, Karnataka, 570 006, India
| | - Sreedharamurthy Satish
- Department of Studies in Microbiology, University of Mysore, Manasagangotri, Mysuru, Karnataka, 570 006, India.
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Mohammadi FS, Arabian D. Optimization of
Chlorella vulgaris
cultivation grown in waste molasses syrup using mixture design. J AM OIL CHEM SOC 2022. [DOI: 10.1002/aocs.12656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Fahimeh Sadat Mohammadi
- Department of Bioscience and Biotechnology Malek Ashtar University of Technology Tehran Iran
| | - Daryush Arabian
- Faculty of Applied Science Malek Ashtar University of Technology Tehran Iran
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4
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Identification of Copper-Containing Oxidoreductases in the Secretomes of Three Colletotrichum Species with a Focus on Copper Radical Oxidases for the Biocatalytic Production of Fatty Aldehydes. Appl Environ Microbiol 2021; 87:e0152621. [PMID: 34613753 DOI: 10.1128/aem.01526-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Copper radical alcohol oxidases (CRO-AlcOx), which have been recently discovered among fungal phytopathogens, are attractive for the production of fragrant fatty aldehydes. With the initial objective to investigate the secretion of CRO-AlcOx by natural fungal strains, we undertook time course analyses of the secretomes of three Colletotrichum species (C. graminicola, C. tabacum, and C. destructivum) using proteomics. The addition of a copper-manganese-ethanol mixture in the absence of any plant-biomass mimicking compounds to Colletotrichum cultures unexpectedly induced the secretion of up to 400 proteins, 29 to 52% of which were carbohydrate-active enzymes (CAZymes), including a wide diversity of copper-containing oxidoreductases from the auxiliary activities (AA) class (AA1, AA3, AA5, AA7, AA9, AA11, AA12, AA13, and AA16). Under these specific conditions, while a CRO-glyoxal oxidase from the AA5_1 subfamily was among the most abundantly secreted proteins, the targeted AA5_2 CRO-AlcOx were secreted at lower levels, suggesting heterologous expression as a more promising strategy for CRO-AlcOx production and utilization. C. tabacum and C. destructivum CRO-AlcOx were thus expressed in Pichia pastoris, and their preference toward both aromatic and aliphatic primary alcohols was assessed. The CRO-AlcOx from C. destructivum was further investigated in applied settings, revealing a full conversion of C6 and C8 alcohols into their corresponding fragrant aldehydes. IMPORTANCE In the context of the industrial shift toward greener processes, the biocatalytic production of aldehydes is of utmost interest owing to their importance for their use as flavor and fragrance ingredients. Copper radical alcohol oxidases (CRO-AlcOx) have the potential to become platform enzymes for the oxidation of alcohols to aldehydes. However, the secretion of CRO-AlcOx by natural fungal strains has never been explored, while the use of crude fungal secretomes is an appealing approach for industrial applications to alleviate various costs pertaining to biocatalyst production. While investigating this primary objective, the secretomics studies revealed unexpected results showing that under the oxidative stress conditions we probed, Colletotrichum species can secrete a broad diversity of copper-containing enzymes (laccases, sugar oxidoreductases, and lytic polysaccharide monooxygenases [LPMOs]) usually assigned to "plant cell wall degradation," despite the absence of any plant-biomass mimicking compound. However, in these conditions, only small amounts of CRO-AlcOx were secreted, pointing out recombinant expression as the most promising path for their biocatalytic application.
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Gururaj P, Khushbu S, Monisha B, Selvakumar N, Chakravarthy M, Gautam P, Nandhini Devi G. Production, purification and application of Cutinase in enzymatic scouring of cotton fabric isolated from Acinetobacter baumannii AU10. Prep Biochem Biotechnol 2020; 51:550-561. [PMID: 33108946 DOI: 10.1080/10826068.2020.1836655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Conventional cotton scouring in the textile industry using alkali results in huge environmental impact which can be overcome by using enzymes. Pectinase along with cutinase gives enhanced bioscouring results. Cutin was extracted from tomato peels and was used as substrate in the microbial media. The strain isolated from tomato peel was identified as Acinetobacter baumannii AU10 by 16S rDNA sequencing. The cutinase production was optimized by Placket-Burman and Response Surface Methodology (RSM) and the maximum production of 82.75 U/mL obtained at sucrose 6.68% (w/v), gelatin 2.74 g/L at a temperature of 35.93 °C. Cutinase was purified by ammonium sulfate precipitation, hydrophobic interaction chromatography and ion exchange chromatography with a recovery of 25.6% and specific activity of 38030 U/mg. The confirmation test for the purity of cutinase was analyzed by RP-HPLC. The molecular mass of cutinase was determined as 28.9 kDa by SDS-PAGE technique. Scanning electron microscopic analysis showed a rough and open primary wall surface on the cutinase bioscoured fabric which confirmed its activity on cutin present in the cotton fabric. Additionally, the cutinase-bioscoured samples showed better absorbency than the untreated samples. Therefore, enzymatic scouring increases wetting capacity of scoured cotton and also helps to reduce environmental pollution.
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Affiliation(s)
- P Gururaj
- Centre for Food Technology, Department of Biotechnology, Anna University, Chennai, India
| | - S Khushbu
- Centre for Food Technology, Department of Biotechnology, Anna University, Chennai, India
| | - B Monisha
- Centre for Food Technology, Department of Biotechnology, Anna University, Chennai, India
| | - N Selvakumar
- Centre for Food Technology, Department of Biotechnology, Anna University, Chennai, India
| | - M Chakravarthy
- Centre for Food Technology, Department of Biotechnology, Anna University, Chennai, India
| | - P Gautam
- Centre for Food Technology, Department of Biotechnology, Anna University, Chennai, India
| | - G Nandhini Devi
- Centre for Food Technology, Department of Biotechnology, Anna University, Chennai, India
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Shariati S, Zare D, Mirdamadi S. Screening of carbon and nitrogen sources using mixture analysis designs for carotenoid production by Blakeslea trispora. Food Sci Biotechnol 2019; 28:469-479. [PMID: 30956859 DOI: 10.1007/s10068-018-0484-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 08/26/2018] [Accepted: 09/10/2018] [Indexed: 10/28/2022] Open
Abstract
The production of many secondary metabolites such as carotenoids is influenced by the type of carbon and nitrogen sources and C:N ratio applied in culture medium. The present study discusses the role of C:N ratio and screening of carbon and nitrogen sources using mixture analysis design in carotenoids production by Blakeslea trispora. The C:N ratios of 20, 40, and 60 with six nitrogen sources were evaluated. Results indicated that limitation of nitrogen source (C:N of 60) could improve carotenoids production. Six nitrogen and carbon sources were then screened using mixture analysis design. The most effective nitrogen and carbon sources were soybean powder and glucose, respectively. The productivity of carotenoids (983.8 ± 31.5 mg/L) based on consumed nitrogen and carbon source was 189.10 mg/g soybean powder and 19.66 mg/g glucose. Mixture analysis design indicated single carbon and nitrogen source were more effective than a mixture of sources for carotenoids production.
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Affiliation(s)
- Sepideh Shariati
- 1Pharmaceutical Sciences Branch, Islamic Azad University, 1941933111 Tehran, Islamic Republic of Iran
| | - Davood Zare
- 2Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), P. O. Box 33535111, Tehran, Islamic Republic of Iran
| | - Saeed Mirdamadi
- 2Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), P. O. Box 33535111, Tehran, Islamic Republic of Iran
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Mixture Design of Experiments for the Optimization of Carbon Source for Promoting Undecylprodigiosin and Actinorhodin Production. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.4.11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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8
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Optimization of solid substrate mixture and process parameters for the production of L-asparaginase and scale-up using tray bioreactor. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2018.01.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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9
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Adıgüzel AO, Tunçer M. Purification and characterization of cutinase from Bacillus sp. KY0701 isolated from plastic wastes. Prep Biochem Biotechnol 2017; 47:925-933. [DOI: 10.1080/10826068.2017.1365245] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Münir Tunçer
- Department of Biology, University of Mersin, Mersin, Turkey
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10
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Van Noi N, Chung YC. Optimization of expression and purification of recombinant S1 domain of the porcine epidemic diarrhea virus spike (PEDV- S1) protein in Escherichia coli. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1308231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Nguyen Van Noi
- Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Pingtung, Taiwan, ROC
- Institute of Life Science, Thai Nguyen University of Agriculture and Forestry, Thai Nguyen, Vietnam
| | - Yao-Chi Chung
- Graduate Institute of Animal Vaccine Technology, National Pingtung University of Science and Technology, Pingtung, Taiwan, ROC
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11
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Sathish T, Uppuluri KB, Veera Bramha Chari P, Kezia D. Sequential Optimization Methods for Augmentation of Marine Enzymes Production in Solid-State Fermentation: l-Glutaminase Production a Case Study. ADVANCES IN FOOD AND NUTRITION RESEARCH 2017; 78:95-114. [PMID: 27452167 DOI: 10.1016/bs.afnr.2016.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
There is an increased l-glutaminase market worldwide due to its relevant industrial applications. Salt tolerance l-glutaminases play a vital role in the increase of flavor of different types of foods like soya sauce and tofu. This chapter is presenting the economically viable l-glutaminases production in solid-state fermentation (SSF) by Aspergillus flavus MTCC 9972 as a case study. The enzyme production was improved following a three step optimization process. Initially mixture design (MD) (augmented simplex lattice design) was employed to optimize the solid substrate mixture. Such solid substrate mixture consisted of 59:41 of wheat bran and Bengal gram husk has given higher amounts of l-glutaminase. Glucose and l-glutamine were screened as a finest additional carbon and nitrogen sources for l-glutaminase production with help of Plackett-Burman Design (PBD). l-Glutamine also acting as a nitrogen source as well as inducer for secretion of l-glutaminase from A. flavus MTCC 9972. In the final step of optimization various environmental and nutritive parameters such as pH, temperature, moisture content, inoculum concentration, glucose, and l-glutamine levels were optimized through the use of hybrid feed forward neural networks (FFNNs) and genetic algorithm (GA). Through sequential optimization methods MD-PBD-FFNN-GA, the l-glutaminase production in SSF could be improved by 2.7-fold (453-1690U/g).
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Affiliation(s)
- T Sathish
- Bioengineering and Environmental Centre, Indian Institute of Chemical Technology, Hyderabad, India.
| | - K B Uppuluri
- Bioprospecting Laboratory, School of Chemical and Biotechnology, SASTRA University, Thanjavur, India
| | | | - D Kezia
- Center for Biotechnology, Andhra University, Visakhapatnam, India
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12
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Agro-industrial wastes utilization for the generation of fibrinolytic metalloprotease by Serratia marcescens RSPB11. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2016.11.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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13
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Ohara A, Soares de Castro RJ, Goia Nishide T, Gonçalves Dias FF, Pavan Bagagli M, Harumi Sato H. Invertase production by Aspergillus niger under solid state fermentation: Focus on physical–chemical parameters, synergistic and antagonistic effects using agro-industrial wastes. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2015. [DOI: 10.1016/j.bcab.2015.06.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Malik A, Alsenaidy AM, Elrobh M, Khan W, Alanazi MS, Bazzi MD. Optimization of expression and purification of HSPA6 protein from Camelus dromedarius in E. coli. Saudi J Biol Sci 2015; 23:410-9. [PMID: 27081368 PMCID: PMC4818323 DOI: 10.1016/j.sjbs.2015.04.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 04/23/2015] [Accepted: 04/26/2015] [Indexed: 11/29/2022] Open
Abstract
The HSPA6, one of the members of large family of HSP70, is significantly up-regulated and has been targeted as a biomarker of cellular stress in several studies. Herein, conditions were optimized to increase the yield of recombinant camel HSPA6 protein in its native state, primarily focusing on the optimization of upstream processing parameters that lead to an increase in the specific as well as volumetric yield of the protein. The results showed that the production of cHSPA6 was increased proportionally with increased incubation temperature up to 37 °C. Induction with 10 μM IPTG was sufficient to induce the expression of cHSPA6 which was 100 times less than normally used IPTG concentration. Furthermore, the results indicate that induction during early to late exponential phase produced relatively high levels of cHSPA6 in soluble form. In addition, 5 h of post-induction incubation was found to be optimal to produce folded cHSPA6 with higher specific and volumetric yield. Subsequently, highly pure and homogenous cHSPA6 preparation was obtained using metal affinity and size exclusion chromatography. Taken together, the results showed successful production of electrophoretically pure recombinant HSPA6 protein from Camelus dromedarius in Escherichia coli in milligram quantities from shake flask liquid culture.
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Key Words
- 2× LB, double strength Luria–Bertani
- DTT, dithiothreitol
- EDTA, ethylenediaminetetraacetic acid
- Expression optimization
- FPLC, fast protein liquid chromatography
- Fast protein liquid chromatography
- Heat shock protein
- Hsp70
- IPTG, isopropyl β-d-1-thiogalactopyranoside
- LB, Luria–Bertani
- Molecular chaperone
- NB, nutrient broth
- Ni–NTA, nickel–nitrilotriacetic acid
- OD600, optical density at 600 nm
- PMSF, phenylmethylsulfonyl fluoride
- Recombinant
- TB, terrific broth
- amp, ampicillin
- rpm, rotations per minute
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Affiliation(s)
- Ajamaluddin Malik
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdulrahman M Alsenaidy
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Mohamed Elrobh
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia; Biochemistry Department, Faculty of Science, Ain-Shams University, Abbassia 11381, Cairo, Egypt
| | - Wajahatullah Khan
- Department of Basic Sciences, College of Science and Health Professions, King Saud Bin Abdulaziz University for Health Sciences, PO Box 3660, Riyadh 11426, Saudi Arabia
| | - Mohammed S Alanazi
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Mohammad D Bazzi
- Protein Research Chair, Department of Biochemistry, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia; Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
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Brooks JP, Edwards DJ, Harwich MD, Rivera MC, Fettweis JM, Serrano MG, Reris RA, Sheth NU, Huang B, Girerd P, Strauss JF, Jefferson KK, Buck GA. The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies. BMC Microbiol 2015; 15:66. [PMID: 25880246 PMCID: PMC4433096 DOI: 10.1186/s12866-015-0351-6] [Citation(s) in RCA: 300] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 01/16/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Characterizing microbial communities via next-generation sequencing is subject to a number of pitfalls involving sample processing. The observed community composition can be a severe distortion of the quantities of bacteria actually present in the microbiome, hampering analysis and threatening the validity of conclusions from metagenomic studies. We introduce an experimental protocol using mock communities for quantifying and characterizing bias introduced in the sample processing pipeline. We used 80 bacterial mock communities comprised of prescribed proportions of cells from seven vaginally-relevant bacterial strains to assess the bias introduced in the sample processing pipeline. We created two additional sets of 80 mock communities by mixing prescribed quantities of DNA and PCR product to quantify the relative contribution to bias of (1) DNA extraction, (2) PCR amplification, and (3) sequencing and taxonomic classification for particular choices of protocols for each step. We developed models to predict the "true" composition of environmental samples based on the observed proportions, and applied them to a set of clinical vaginal samples from a single subject during four visits. RESULTS We observed that using different DNA extraction kits can produce dramatically different results but bias is introduced regardless of the choice of kit. We observed error rates from bias of over 85% in some samples, while technical variation was very low at less than 5% for most bacteria. The effects of DNA extraction and PCR amplification for our protocols were much larger than those due to sequencing and classification. The processing steps affected different bacteria in different ways, resulting in amplified and suppressed observed proportions of a community. When predictive models were applied to clinical samples from a subject, the predicted microbiome profiles were better reflections of the physiology and diagnosis of the subject at the visits than the observed community compositions. CONCLUSIONS Bias in 16S studies due to DNA extraction and PCR amplification will continue to require attention despite further advances in sequencing technology. Analysis of mock communities can help assess bias and facilitate the interpretation of results from environmental samples.
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Affiliation(s)
- J Paul Brooks
- Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, 23284-3083, Richmond, VA, USA. .,Center for the Study of Biological Complexity, Virginia Commonwealth University, 23284, Richmond, VA, USA.
| | - David J Edwards
- Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, 23284-3083, Richmond, VA, USA.
| | - Michael D Harwich
- Department of Microbiology and Immunology, Virginia Commonwealth University, 23284, Richmond, VA, USA.
| | - Maria C Rivera
- Department of Biology, Virginia Commonwealth University, 23284, Richmond, VA, USA.
| | - Jennifer M Fettweis
- Department of Microbiology and Immunology, Virginia Commonwealth University, 23284, Richmond, VA, USA.
| | - Myrna G Serrano
- Center for the Study of Biological Complexity, Virginia Commonwealth University, 23284, Richmond, VA, USA. .,Department of Microbiology and Immunology, Virginia Commonwealth University, 23284, Richmond, VA, USA.
| | - Robert A Reris
- Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, 23284-3083, Richmond, VA, USA.
| | - Nihar U Sheth
- Center for the Study of Biological Complexity, Virginia Commonwealth University, 23284, Richmond, VA, USA.
| | - Bernice Huang
- Department of Microbiology and Immunology, Virginia Commonwealth University, 23284, Richmond, VA, USA.
| | - Philippe Girerd
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, 23284, Richmond, VA, USA.
| | | | - Jerome F Strauss
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, 23284, Richmond, VA, USA.
| | - Kimberly K Jefferson
- Center for the Study of Biological Complexity, Virginia Commonwealth University, 23284, Richmond, VA, USA. .,Department of Microbiology and Immunology, Virginia Commonwealth University, 23284, Richmond, VA, USA.
| | - Gregory A Buck
- Center for the Study of Biological Complexity, Virginia Commonwealth University, 23284, Richmond, VA, USA. .,Department of Microbiology and Immunology, Virginia Commonwealth University, 23284, Richmond, VA, USA.
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16
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Setoodeh P, Jahanmiri A, Eslamloueyan R, Niazi A, Ayatollahi SS, Aram F, Mahmoodi M, Hortamani A. Statistical screening of medium components for recombinant production of Pseudomonas aeruginosa ATCC 9027 rhamnolipids by nonpathogenic cell factory Pseudomonas putida KT2440. Mol Biotechnol 2014; 56:175-91. [PMID: 23943464 DOI: 10.1007/s12033-013-9693-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Rhamnolipids (RLs) produced by the opportunistic human pathogen Pseudomonas aeruginosa are considered as potential candidates for the next generation of surfactants. Large-scale production of RLs depends on progress in strain engineering, medium design, operating strategies, and purification procedures. In this work, the rhlAB genes extracted from a mono_RLs_producing strain of P. aeruginosa (ATCC 9027) were introduced to an appropriate safety host Pseudomonas putida KT2440. The capability of the recombinant strain was evaluated in various media. As a prerequisite for optimal medium design, a set of 32 experiments was performed in two steps for screening a number of macro-nutritional compounds. In the experiments, a two-level fractional factorial design resolution IV was followed by a two-level full factorial one. By means of this approach, it was observed that glycerol, yeast extract, and peptone have significant positive influence on recombinant RLs production while the yeast extract/peptone two-factor and glycerol/yeast extract/peptone three-factor interactions have considerable negative effects. A wide range of variation from 0 to 570 mg/l was obtained for RLs production during the screening experiments indicating the importance of medium optimization. The results point out the opportunity for possible higher yields of RLs through further screening, mixture/combined mixture designs, and high-cell-density cultivations.
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Affiliation(s)
- Payam Setoodeh
- School of Chemical and Petroleum Engineering, Shiraz University, Molasadra St., Shiraz, Iran
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17
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Production Optimization and Characterization of Recombinant Cutinases from Thermobifida fusca sp. NRRL B-8184. Appl Biochem Biotechnol 2013; 170:654-75. [DOI: 10.1007/s12010-013-0219-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 04/01/2013] [Indexed: 11/30/2022]
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Sathish T, Prakasham RS. Intensification of Fructosyltransferases and Fructo-Oligosaccharides Production in Solid State Fermentation by Aspergillus awamori GHRTS. Indian J Microbiol 2013; 53:337-42. [PMID: 24426134 DOI: 10.1007/s12088-013-0380-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Accepted: 02/25/2013] [Indexed: 10/27/2022] Open
Abstract
The present work was aimed to investigate the impact of the solid substrates mixture on Fructosyltransferases (FTase) and Fructo-oligosaccharides (FOS) production. An augmented simplex lattice design was used to optimize a three component mixture for FTase production. Among selected substrates corn cobs has highest impact on FTase production followed by wheat bran and rice bran. All two substrates and three substrate combinations showed the highest enzyme production than their individual levels. Among the tested various models quadratic model was found to be the best suitable model to explain mixture design. Corncobs, wheat bran and rice bran in a ratio of approximately 45:29:26 is best suitable for the FTase production by isolated Aspergillus awamori GHRTS. This study signifies mixture design could be effective utilize for selection of best combination of multi substrate for improved production of high value products under solid state fermentation.
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Affiliation(s)
- Thadikamala Sathish
- Bioengineering and Environmental Centre, Indian Institute of Chemical Technology, Hyderabad, India ; Department of Marine Biotechnology, ANCOST, NIOT, Port-Blair, Andaman Nicobar Islands India
| | - Reddy Shetty Prakasham
- Bioengineering and Environmental Centre, Indian Institute of Chemical Technology, Hyderabad, India
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Delabona PDS, Farinas CS, Lima DJDS, Pradella JGDC. Experimental mixture design as a tool to enhance glycosyl hydrolases production by a new Trichoderma harzianum P49P11 strain cultivated under controlled bioreactor submerged fermentation. BIORESOURCE TECHNOLOGY 2013; 132:401-5. [PMID: 23265822 DOI: 10.1016/j.biortech.2012.11.087] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 11/19/2012] [Accepted: 11/20/2012] [Indexed: 06/01/2023]
Abstract
This work investigates the glycosyl hydrolase (GH) profile of a new Trichoderma harzianum strain cultivated under controlled bioreactor submerged fermentation. The influence of different medium components (delignified steam-exploded sugarcane bagasse, sucrose, and soybean flour) on GH biosynthesis was assessed using experimental mixture design (EMD). Additionally, the effect of increased component concentrations in culture media selected from the EMD was studied. It was found that that a mixed culture medium could significantly maximize GH biosynthesis rate, especially for xylanase enzymes which achieved a 2-fold increment. Overall, it was demonstrated that T. harzianumP49P11 enzymes have a great potential to be used in the deconstruction of biomass.
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Affiliation(s)
- Priscila da Silva Delabona
- Brazilian Bioethanol Science and Technology Laboratory - CTBE, Rua Giuseppe Maximo Scolfaro 10000, Pólo II de Alta Tecnologia, Caixa Postal 6192, CEP 13083-970 Campinas, São Paulo, Brazil
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20
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Dutta K, Dasu VV, Hegde K. Development of Medium and Kinetic Modeling for Enhanced Production of Cutinase from Pseudomonas cepacia NRRL B-2320. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/aim.2013.36064] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Dutta K, Krishnamoorthy H, Venkata Dasu V. Novel cutinase from Pseudomonas cepacia NRRL B 2320: Purification, characterization and identification of cutinase encoding genes. J GEN APPL MICROBIOL 2013; 59:171-84. [DOI: 10.2323/jgam.59.171] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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22
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Kotlar CE, Agüero MV, Roura SI. Statistical optimization of a novel low-cost medium based on regional agro-industrial by-products for the production of proteolytic enzymes by Bacillus cereus. Prep Biochem Biotechnol 2012; 42:406-25. [PMID: 22897765 DOI: 10.1080/10826068.2011.635739] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Bacillus sp. are specific producers of peptidase amongst bacteria and peptidase enzymes and are of significant ones due to their multifarious applications. Advances in industrial biotechnology offer potential opportunities for economic utilization of agro-industrial by-products for many biochemical reactions. Due to their rich organic nature, they can serve as an ideal substrate for the production of different value added products like peptidases. In the present work, an attempt was made to optimize different variables by Taguchi methodology for the production of peptidase using agro-industrial by-products hydrolyzed by a Bacillus cereus strain, resulting in brewer's spent grain (BSG) being the optimal organic substrate. Subsequently, operative variables for the BSG were investigated using Taguchi methodology in order to maximize the enzyme production. Additionally, the main medium components were optimized using a mixture design. Finally, the production of peptidase by B. cereus was investigated; also the possible interaction with other proteolytic microbial strains was evaluated. A notorious synergistic effect was observed when B. cereus was inoculated with Pseudomonas sp. These brought a triple benefit, first, opening the possibility to produce technical enzymes at low cost, second, giving greater value to a food industry by-product, and third, reducing the environmental impact caused by the product removal directly into the environment.
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Affiliation(s)
- C E Kotlar
- Research Group on Food Engineering, Department of Chemical & Food Engineering, Faculty of Engineering, National University of Mar del Plata, Mar del Plata, Argentina.
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23
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A marked enhancement in production of amylase by Bacillus amyloliquefaciens in flask fermentation using statistical methods. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11771-011-0803-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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24
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Agüero MV, Kotlar CE, Roura SI. METHODS: Simultaneous optimization of biomass and protease biosynthesis by a local isolatedPseudomonassp. — Selection of main medium components and operating conditions. Ind Biotechnol (New Rochelle N Y) 2011. [DOI: 10.1089/ind.2011.7.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- María Victoria Agüero
- Research Group on Food Engineering, Department of Chemical & Food Engineering, Faculty of Engineering, National University of Mar del Plata, Juan B. Justo 4302, 7600 Mar del Plata, Argentina; and National Council of Scientific and Technical Research (CONICET), Argentina
| | - Catalina Elena Kotlar
- Research Group on Food Engineering, Department of Chemical & Food Engineering, Faculty of Engineering, National University of Mar del Plata, Juan B. Justo 4302, 7600 Mar del Plata, Argentina; and National Council of Scientific and Technical Research (CONICET), Argentina
| | - Sara Inés Roura
- Research Group on Food Engineering, Department of Chemical & Food Engineering, Faculty of Engineering, National University of Mar del Plata, Juan B. Justo 4302, 7600 Mar del Plata, Argentina; and National Council of Scientific and Technical Research (CONICET), Argentina
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Kotlar CE, Agüero MV, Roura SI. METHODS: Simultaneous optimization of biomass and protease biosynthesis by a local isolated Pseudomonas sp. — Response surface optimization using Box-Behnken design. Ind Biotechnol (New Rochelle N Y) 2010. [DOI: 10.1089/ind.2010.6.364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Catalina Elena Kotlar
- Research Group on Food Engineering, Department of Chemical & Food Engineering, Faculty of Engineering, National University of Mar del Plata, Juan B. Justo 4302, 7600 Mar del Plata, Argentina
- National Council of Scientific and Technical Research (CONICET), Argentina
| | - María Victoria Agüero
- Research Group on Food Engineering, Department of Chemical & Food Engineering, Faculty of Engineering, National University of Mar del Plata, Juan B. Justo 4302, 7600 Mar del Plata, Argentina
- National Council of Scientific and Technical Research (CONICET), Argentina
| | - Sara Inés Roura
- Research Group on Food Engineering, Department of Chemical & Food Engineering, Faculty of Engineering, National University of Mar del Plata, Juan B. Justo 4302, 7600 Mar del Plata, Argentina
- National Council of Scientific and Technical Research (CONICET), Argentina
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Pimenta EF, Vita-Marques AM, Tininis A, Seleghim MHR, Sette LD, Veloso K, Ferreira AG, Williams DE, Patrick BO, Dalisay DS, Andersen RJ, Berlinck RGS. Use of experimental design for the optimization of the production of new secondary metabolites by two Penicillium species. JOURNAL OF NATURAL PRODUCTS 2010; 73:1821-1832. [PMID: 21053938 DOI: 10.1021/np100470h] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A fractional factorial design approach has been used to enhance secondary metabolite production by two Penicillium strains. The method was initially used to improve the production of bioactive extracts as a whole and subsequently to optimize the production of particular bioactive metabolites. Enhancements of over 500% in secondary metabolite production were observed for both P. oxalicum and P. citrinum. Two new alkaloids, citrinalins A (5) and B (6), were isolated and identified from P. citrinum cultures optimized for production of minor metabolites.
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Affiliation(s)
- Eli F Pimenta
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil
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Hydrolytic Enzyme of Cellulose for Complex Formulation Applied Research. Appl Biochem Biotechnol 2010; 164:23-33. [DOI: 10.1007/s12010-010-9111-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 10/11/2010] [Indexed: 11/26/2022]
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28
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Modeling and optimization of cutinase production by recombinant Escherichia coli based on statistical experimental designs. KOREAN J CHEM ENG 2010. [DOI: 10.1007/s11814-010-0195-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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29
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Rispoli F, Shah V. A new efficient mixture screening design for optimization of media. Biotechnol Prog 2009; 25:980-5. [DOI: 10.1002/btpr.225] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Sathish T, Lakshmi G, Rao C, Brahmaiah P, Prakasham R. Mixture design as first step for improved glutaminase production in solid-state fermentation by isolatedBacillussp. RSP-GLU. Lett Appl Microbiol 2008; 47:256-62. [DOI: 10.1111/j.1472-765x.2008.02413.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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32
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Cutinase production by Fusarium oxysporum in liquid medium using central composite design. J Ind Microbiol Biotechnol 2007; 35:59-67. [DOI: 10.1007/s10295-007-0266-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2007] [Accepted: 09/20/2007] [Indexed: 10/22/2022]
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33
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Optimizing the production of cutinase by Fusarium oxysporum using response surface methodology. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2007.05.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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