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Klauer RR, Hansen DA, Wu D, Monteiro LMO, Solomon KV, Blenner MA. Biological Upcycling of Plastics Waste. Annu Rev Chem Biomol Eng 2024. [PMID: 38621232 DOI: 10.1146/annurev-chembioeng-100522-115850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Plastic wastes accumulate in the environment, impacting wildlife and human health and representing a significant pool of inexpensive waste carbon that could form feedstock for the sustainable production of commodity chemicals, monomers, and specialty chemicals. Current mechanical recycling technologies are not economically attractive due to the lower-quality plastics that are produced in each iteration. Thus, the development of a plastics economy requires a solution that can deconstruct plastics and generate value from the deconstruction products. Biological systems can provide such value by allowing for the processing of mixed plastics waste streams via enzymatic specificity and using engineered metabolic pathways to produce upcycling targets. We focus on the use of biological systems for waste plastics deconstruction and upcycling. We highlight documented and predicted mechanisms through which plastics are biologically deconstructed and assimilated and provide examples of upcycled products from biological systems. Additionally, we detail current challenges in the field, including the discovery and development of microorganisms and enzymes for deconstructing non-polyethylene terephthalate plastics, the selection of appropriate target molecules to incentivize development of a plastic bioeconomy, and the selection of microbial chassis for the valorization of deconstruction products.
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Affiliation(s)
- Ross R Klauer
- Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA; ,
| | - D Alex Hansen
- Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA; ,
| | - Derek Wu
- Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA; ,
| | | | - Kevin V Solomon
- Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA; ,
| | - Mark A Blenner
- Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA; ,
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Gomez GVB, Lourenço GJ, Monteiro LMO, Rocha RS, Fernández KAM, Recio JA, Torricelli C, Coser LO, Oliveira ALR, Carron J, Moraes AM, Lima CSP. Association of JAK/STAT genetic variants with cutaneous melanoma. Front Oncol 2022; 12:943483. [PMID: 35982955 PMCID: PMC9379289 DOI: 10.3389/fonc.2022.943483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/01/2022] [Indexed: 11/13/2022] Open
Abstract
Background The Janus-activated kinase (JAK)-signal transducer and activator of transcription (STAT) signaling pathway regulates cutaneous melanoma (CM) development and progression. The JAK1, JAK2, and STAT3 proteins are encoded by polymorphic genes. This study aimed to verify whether single-nucleotide variants (SNVs) in JAK1 (c.1648+1272G>A, c.991-27C>T), JAK2 (c.-1132G>T, c.-139G>A), and STAT3 (c.*1671T>C, c.-1937C>G) altered the risk, clinicopathological aspects, and survival of CM patients as well as protein activity. Methods CM patients (N = 248) and controls (N = 274) were enrolled in this study. Genotyping was performed by real-time polymerase chain reaction (PCR), and JAK1, JAK2, and STAT3 expression was assessed by quantitative PCR (qPCR). STAT3 c.-1937C>G SNV was investigated by luciferase, qPCR, western blot, apoptosis, and cell cycle assays in SKMEL-28 cells with CC or GG genotype. Results Individuals with STAT3 c.*1671TT and c.-1937CC genotypes and TC haplotype of both SNVs were under about 2.0-fold increased risk of CM. Specific JAK1, JAK2, and STAT3 combined genotypes were associated with up to 4.0-fold increased risk of CM. Higher luciferase activity [4,013.34 vs. 2,463.32 arbitrary units (AU); p = 0.004], STAT3 expression by qPCR (649.20 vs. 0.03 AU; p = 0.003) and western blot (1.69 vs. 1.16 AU; p = 0.01), and percentage of cells in the S phase of the cell cycle (57.54 vs. 30.73%; p = 0.04) were more frequent in SKMEL-28 with STAT3 c.-1937CC than with GG genotype. CM cell line with CC genotype presented higher STAT3 protein levels than the one with GG genotype (1.93 versus 1.27 AU, p = 0.0027). Conclusion Our data present preliminary evidence that inherited abnormalities in the JAK/STAT pathway can be used to identify individuals at a high risk of CM, who deserve additional attention for tumor prevention and early detection.
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Affiliation(s)
- Gabriela Vilas Bôas Gomez
- Laboratory of Cancer Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Gustavo Jacob Lourenço
- Laboratory of Cancer Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Lummy Maria Oliveira Monteiro
- Department of Cellular and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Rafael Silva Rocha
- Department of Cellular and Molecular Biology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Kimberly Anne McGrail Fernández
- Animal Models and Cancer Laboratory, Vall d’Hebron Research Institute, Hospital Universitari Vall d’Hebron, Barcelona, Spain
| | - Juan Angel Recio
- Animal Models and Cancer Laboratory, Vall d’Hebron Research Institute, Hospital Universitari Vall d’Hebron, Barcelona, Spain
| | - Caroline Torricelli
- Laboratory of Cancer Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Lilian Oliveira Coser
- Laboratory of Nerve Regeneration, Department of Structural and Functional Biology, Institute of Biology, University of Campinas, São Paulo, Brazil
| | - Alexandre Leite Rodrigues Oliveira
- Laboratory of Nerve Regeneration, Department of Structural and Functional Biology, Institute of Biology, University of Campinas, São Paulo, Brazil
| | - Juliana Carron
- Laboratory of Cancer Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Aparecida Machado Moraes
- Department of Anesthesiology, Oncology and Radiology, Faculty of Medical Sciences, University of Campinas, São Paulo, Brazil
| | - Carmen Silvia Passos Lima
- Laboratory of Cancer Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
- Department of Anesthesiology, Oncology and Radiology, Faculty of Medical Sciences, University of Campinas, São Paulo, Brazil
- *Correspondence: Carmen Silvia Passos Lima,
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Oliveira Monteiro LM, Saraiva JP, Brizola Toscan R, Stadler PF, Silva-Rocha R, Nunes da Rocha U. PredicTF: prediction of bacterial transcription factors in complex microbial communities using deep learning. Environ Microbiome 2022; 17:7. [PMID: 35135629 PMCID: PMC8822659 DOI: 10.1186/s40793-021-00394-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Transcription factors (TFs) are proteins controlling the flow of genetic information by regulating cellular gene expression. A better understanding of TFs in a bacterial community context may open novel revenues for exploring gene regulation in ecosystems where bacteria play a key role. Here we describe PredicTF, a platform supporting the prediction and classification of novel bacterial TF in single species and complex microbial communities. PredicTF is based on a deep learning algorithm. RESULTS To train PredicTF, we created a TF database (BacTFDB) by manually curating a total of 11,961 TF distributed in 99 TF families. Five model organisms were used to test the performance and the accuracy of PredicTF. PredicTF was able to identify 24-62% of the known TFs with an average precision of 88% in our five model organisms. We demonstrated PredicTF using pure cultures and a complex microbial community. In these demonstrations, we used (meta)genomes for TF prediction and (meta)transcriptomes for determining the expression of putative TFs. CONCLUSION PredicTF demonstrated high accuracy in predicting transcription factors in model organisms. We prepared the pipeline to be easily implemented in studies profiling TFs using (meta)genomes and (meta)transcriptomes. PredicTF is an open-source software available at https://github.com/mdsufz/PredicTF .
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Affiliation(s)
- Lummy Maria Oliveira Monteiro
- Helmholtz Center for Environmental Research (UFZ), Leipzig, Germany
- Bioinformatics Group, Institute of Computer Science, Universität Leipzig, Leipzig, Germany
- Ribeirão Preto Medical School (FMRP), University of São Paulo (USP), Ribeirão Prêto, Brazil
| | | | | | - Peter F. Stadler
- Bioinformatics Group, Institute of Computer Science, Universität Leipzig, Leipzig, Germany
| | - Rafael Silva-Rocha
- Ribeirão Preto Medical School (FMRP), University of São Paulo (USP), Ribeirão Prêto, Brazil
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Oliveira Monteiro LM, Vici AC, Messias JM, Heinen PR, Pinheiro VE, Vargas Rechia CG, Buckeridge MS, Teixeira de Moraes Polizeli MDL. Increased Malbranchea pulchella β-glucosidase production and its application in agroindustrial residue hydrolysis: A research based on experimental designs. ACTA ACUST UNITED AC 2021; 30:e00618. [PMID: 33981591 PMCID: PMC8081928 DOI: 10.1016/j.btre.2021.e00618] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 09/07/2020] [Accepted: 04/08/2021] [Indexed: 11/25/2022]
Abstract
β-Glucosidases are a limiting factor for the biomass saccharification. β-Glucosidase was produced from thermophilic fungus Malbranchea pulchella. Enzyme production was optimized using composite central designs and response surface. Optimal production was obtained with 0.6 % cellobiose plus 4.0 % sugarcane bagasse (SCB). Application of Mixture Design with SCB, soybean hull and barley bagasse were tested.
β-Glucosidases are a limiting factor in the conversion of cellulose to glucose for the subsequent ethanol production. Here, β-glucosidase production by Malbranchea pulchella was optimized using Composite Central Designs and Response Surface Methodologies from a medium designed. The coefficient of determination (R2) was 0.9960, F-value was very high, and the lack of fit was found to be non-significant. This indicates a statistic valid and predictive result. M. pulchella enzymatic extract was successfully tested as an enzymatic cocktail in a mixture design using sugarcane bagasse, soybean hull and barley bagasse. We proved that the optimization of the β-glucosidase production and the application in hydrolysis using unexpansive biomass and agricultural wastes can be accomplished by means of statistical methodologies. The strategy presented here can be useful for the improvement of enzyme production and the hydrolysis process, arising as an alternative for bioeconomy.
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Affiliation(s)
- Lummy Maria Oliveira Monteiro
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Bandeirantes Av., 3.900, 14049-900, Ribeirão Preto, SP, Brazil
| | - Ana Claudia Vici
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Bandeirantes Av., 3.900, 14040-900, Ribeirão Preto, SP, Brazil
| | - Josana Maria Messias
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Bandeirantes Av., 3.900, 14040-900, Ribeirão Preto, SP, Brazil
| | - Paulo Ricardo Heinen
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Bandeirantes Av., 3.900, 14049-900, Ribeirão Preto, SP, Brazil
| | - Vanessa Elisa Pinheiro
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Bandeirantes Av., 3.900, 14049-900, Ribeirão Preto, SP, Brazil
| | - Carem Gledes Vargas Rechia
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Bandeirantes Av., 3.900, 14040-903, Ribeirão Preto, SP, Brazil
| | - Marcos S Buckeridge
- Instituto de Biociências, Universidade de São Paulo, Matão Street, 277, 05508-090, São Paulo, SP, Brazil
| | - Maria de Lourdes Teixeira de Moraes Polizeli
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Bandeirantes Av., 3.900, 14049-900, Ribeirão Preto, SP, Brazil.,Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Bandeirantes Av., 3.900, 14040-900, Ribeirão Preto, SP, Brazil
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Monteiro LMO, Sanches-Medeiros A, Westmann CA, Silva-Rocha R. Unraveling the Complex Interplay of Fis and IHF Through Synthetic Promoter Engineering. Front Bioeng Biotechnol 2020; 8:510. [PMID: 32626694 PMCID: PMC7314903 DOI: 10.3389/fbioe.2020.00510] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/30/2020] [Indexed: 02/03/2023] Open
Abstract
Bacterial promoters are usually formed by multiple cis-regulatory elements recognized by a plethora of transcriptional factors (TFs). From those, global regulators are key elements since these TFs are responsible for the regulation of hundreds of genes in the bacterial genome. For instance, Fis and IHF are global regulators that play a major role in gene expression control in Escherichia coli, and usually, multiple cis-regulatory elements for these proteins are present at target promoters. Here, we investigated the relationship between the architecture of the cis-regulatory elements for Fis and IHF in E. coli. For this, we analyze 42 synthetic promoter variants harboring consensus cis-elements for Fis and IHF at different distances from the core -35/-10 region and in various numbers and combinations. We first demonstrated that although Fis preferentially recognizes its consensus cis-element, it can also recognize, to some extent, the consensus-binding site for IHF, and the same was true for IHF, which was also able to recognize Fis binding sites. However, changing the arrangement of the cis-elements (i.e., the position or number of sites) can completely abolish the non-specific binding of both TFs. More remarkably, we demonstrated that combining cis-elements for both TFs could result in Fis and IHF repressed or activated promoters depending on the final architecture of the promoters in an unpredictable way. Taken together, the data presented here demonstrate how small changes in the architecture of bacterial promoters could result in drastic changes in the final regulatory logic of the system, with important implications for the understanding of natural complex promoters in bacteria and their engineering for novel applications.
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Affiliation(s)
| | | | - Cauã Antunes Westmann
- Ribeirão Preto Medical School (FMRP), University of São Paulo, Ribeirão Preto, Brazil
| | - Rafael Silva-Rocha
- Ribeirão Preto Medical School (FMRP), University of São Paulo, Ribeirão Preto, Brazil
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Monteiro LMO, Vici AC, Pinheiro MP, Heinen PR, de Oliveira AHC, Ward RJ, Prade RA, Buckeridge MS, Polizeli MDLTDM. A Highly Glucose Tolerant ß-Glucosidase from Malbranchea pulchella (MpBg3) Enables Cellulose Saccharification. Sci Rep 2020; 10:6998. [PMID: 32332833 PMCID: PMC7181827 DOI: 10.1038/s41598-020-63972-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 03/13/2020] [Indexed: 02/07/2023] Open
Abstract
β-glucosidases catalyze the hydrolysis β-1,4, β-1,3 and β-1,6 glucosidic linkages from non-reducing end of short chain oligosaccharides, alkyl and aryl β-D-glucosides and disaccharides. They catalyze the rate-limiting reaction in the conversion of cellobiose to glucose in the saccharification of cellulose for second-generation ethanol production, and due to this important role the search for glucose tolerant enzymes is of biochemical and biotechnological importance. In this study we characterize a family 3 glycosyl hydrolase (GH3) β-glucosidase (Bgl) produced by Malbranchea pulchella (MpBgl3) grown on cellobiose as the sole carbon source. Kinetic characterization revealed that the MpBgl3 was highly tolerant to glucose, which is in contrast to many Bgls that are completely inhibited by glucose. A 3D model of MpBgl3 was generated by molecular modeling and used for the evaluation of structural differences with a Bgl3 that is inhibited by glucose. Taken together, our results provide new clues to understand the glucose tolerance in GH3 β-glucosidases.
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Affiliation(s)
- Lummy Maria Oliveira Monteiro
- Faculdade de Medicina de Ribeirão Preto. Universidade de São Paulo. Bandeirantes Av., 3.900, 14049-900, Ribeirão Preto, SP, Brazil
| | - Ana Claudia Vici
- Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto. Universidade de São Paulo. Bandeirantes Av., 3.900, 14040-901, Ribeirão Preto, SP, Brazil
| | - Matheus Pinto Pinheiro
- Laboratório Nacional de Biociência (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil
| | - Paulo Ricardo Heinen
- Faculdade de Medicina de Ribeirão Preto. Universidade de São Paulo. Bandeirantes Av., 3.900, 14049-900, Ribeirão Preto, SP, Brazil
| | | | - Richard John Ward
- Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto. Universidade de São Paulo. Bandeirantes Av., 3.900, 14040-901, Ribeirão Preto, SP, Brazil
| | - Rolf Alexander Prade
- Department of Microbiology and Molecular Genetics. Oklahoma State University, Stillwater, USA
| | - Marcos S Buckeridge
- Instituto de Biociências, Universidade de São Paulo. Matão Street, 277, 05508-090, São Paulo, SP, Brazil
| | - Maria de Lourdes Teixeira de Moraes Polizeli
- Faculdade de Medicina de Ribeirão Preto. Universidade de São Paulo. Bandeirantes Av., 3.900, 14049-900, Ribeirão Preto, SP, Brazil. .,Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto. Universidade de São Paulo. Bandeirantes Av., 3.900, 14040-901, Ribeirão Preto, SP, Brazil.
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Monteiro LMO, Arruda LM, Sanches-Medeiros A, Martins-Santana L, Alves LDF, Defelipe L, Turjanski AG, Guazzaroni ME, de Lorenzo V, Silva-Rocha R. Reverse Engineering of an Aspirin-Responsive Transcriptional Regulator in Escherichia coli. ACS Synth Biol 2019; 8:1890-1900. [PMID: 31362496 DOI: 10.1021/acssynbio.9b00191] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Bacterial transcription factors (TFs) are key devices for the engineering of complex circuits in many biotechnological applications, yet there are few well-characterized inducer-responsive TFs that could be used in the context of an animal or human host. We have deciphered the inducer recognition mechanism of two AraC/XylS regulators from Pseudomonas putida (BenR and XylS) for creating a novel expression system responsive to acetyl salicylate (i.e., aspirin). Using protein homology modeling and molecular docking with the cognate inducer benzoate and a suite of chemical analogues, we identified the conserved binding pocket of BenR and XylS. By means of site-directed mutagenesis, we identified a single amino acid position required for efficient inducer recognition and transcriptional activation. Whereas this modification in BenR abolishes protein activity, in XylS, it increases the response to several inducers, including acetyl salicylic acid, to levels close to those achieved by the canonical inducer. Moreover, by constructing chimeric proteins with swapped N-terminal domains, we created novel regulators with mixed promoter and inducer recognition profiles. As a result, a collection of engineered TFs was generated with an enhanced response to benzoate, 3-methylbenzoate, 2-methylbenzoate, 4-methylbenzoate, salicylic acid, aspirin, and acetylsalicylic acid molecules for eliciting gene expression in E. coli.
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Affiliation(s)
| | - Letı́cia Magalhães Arruda
- Cell and Molecular Biology Department, FMRP − University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - Ananda Sanches-Medeiros
- Cell and Molecular Biology Department, FMRP − University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - Leonardo Martins-Santana
- Cell and Molecular Biology Department, FMRP − University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - Luana de Fátima Alves
- Biology Department, FFCLRP − University of São Paulo, Ribeirão Preto, São Paulo 14040-901, Brazil
| | - Lucas Defelipe
- Departamento de Quı́mica Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires 1428, Argentina
- IQUIBICEN/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires 1428, Argentina
| | - Adrian Gustavo Turjanski
- Departamento de Quı́mica Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires 1428, Argentina
- IQUIBICEN/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires 1428, Argentina
| | | | - Vı́ctor de Lorenzo
- Systems Biology Program, National Center of Biotechnology − CSIC, Madrid 28049, Spain
| | - Rafael Silva-Rocha
- Cell and Molecular Biology Department, FMRP − University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
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Monteiro LMO, Pereira MG, Vici AC, Heinen PR, Buckeridge MS, Polizeli MDLTDM. Efficient hydrolysis of wine and grape juice anthocyanins by Malbranchea pulchella β-glucosidase immobilized on MANAE-agarose and ConA-Sepharose supports. Int J Biol Macromol 2019; 136:1133-1141. [PMID: 31220494 DOI: 10.1016/j.ijbiomac.2019.06.106] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 06/06/2019] [Accepted: 06/15/2019] [Indexed: 12/19/2022]
Abstract
β-glucosidases (BGLs) hydrolyze short-chain cellulooligosaccharides. Some BGLs can hydrolyze anthocyanins and be applied in the clarification process of food industries, especially grape juice and wine. Enzyme immobilization is a valuable tool to increase enzyme stabilization. In this work, Malbranchea pulchella BGL was immobilized on Monoaminoethyl-N-ethyl-agarose ionic support, MANAE-agarose, and Concanavalin A-Sepharose affinity support, Con-A-Sepharose. The formed biocatalysts, denominated BLG-MANAE and BLG-ConA, were applied in the grape juice and red wine clarification. BGL-MANAE and BGL-ConA hyperactivated M. pulchella BGL 10- and 3-fold, respectively. Both biocatalysts showed at least 70% activity at pH range 2-11, until 24 h incubation. BGL-MANAE and BGL-ConA showed activity of 60% and 100%, respectively, at 50 °C, up to 24 h. Both biocatalysts were efficiently reused 20-fold. They were stable in the presence of up to 0.1 M glucose for 24 h incubation, and with 5%, 10% and 15% ethanol kept up to 70% activity. BGL-MANAE biocatalyst was 11% and 25% more efficient than BGL-ConA in clarification of concentrate and diluted wines, respectively. Likewise, BGL-MANAE biocatalysts were 14% and 33% more efficient than the BGL-ConA in clarification of diluted and concentrated juices, respectively. Therefore, the BGL-MANAE biocatalyst was especially effective in red wine and grape juice clarification.
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Affiliation(s)
- Lummy Maria Oliveira Monteiro
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Bandeirantes Av., 3.900, 14049-900 Ribeirão Preto, SP, Brazil
| | - Marita Gimenez Pereira
- Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Bandeirantes Av., 3.900, 14040-901 Ribeirão Preto, SP, Brazil
| | - Ana Claudia Vici
- Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Bandeirantes Av., 3.900, 14040-901 Ribeirão Preto, SP, Brazil
| | - Paulo Ricardo Heinen
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Bandeirantes Av., 3.900, 14049-900 Ribeirão Preto, SP, Brazil
| | - Marcos S Buckeridge
- Instituto de Biociências, Universidade de São Paulo, Matão Street, 277, 05508-090 São Paulo, SP, Brazil
| | - Maria de Lourdes Teixeira de Moraes Polizeli
- Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Bandeirantes Av., 3.900, 14049-900 Ribeirão Preto, SP, Brazil; Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Bandeirantes Av., 3.900, 14040-901 Ribeirão Preto, SP, Brazil.
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Nora LC, Westmann CA, Martins‐Santana L, Alves LDF, Monteiro LMO, Guazzaroni M, Silva‐Rocha R. The art of vector engineering: towards the construction of next-generation genetic tools. Microb Biotechnol 2019; 12:125-147. [PMID: 30259693 PMCID: PMC6302727 DOI: 10.1111/1751-7915.13318] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 08/29/2018] [Accepted: 08/31/2018] [Indexed: 12/20/2022] Open
Abstract
When recombinant DNA technology was developed more than 40 years ago, no one could have imagined the impact it would have on both society and the scientific community. In the field of genetic engineering, the most important tool developed was the plasmid vector. This technology has been continuously expanding and undergoing adaptations. Here, we provide a detailed view following the evolution of vectors built throughout the years destined to study microorganisms and their peculiarities, including those whose genomes can only be revealed through metagenomics. We remark how synthetic biology became a turning point in designing these genetic tools to create meaningful innovations. We have placed special focus on the tools for engineering bacteria and fungi (both yeast and filamentous fungi) and those available to construct metagenomic libraries. Based on this overview, future goals would include the development of modular vectors bearing standardized parts and orthogonally designed circuits, a task not fully addressed thus far. Finally, we present some challenges that should be overcome to enable the next generation of vector design and ways to address it.
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Affiliation(s)
- Luísa Czamanski Nora
- Ribeirão Preto Medical SchoolUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
| | - Cauã Antunes Westmann
- Ribeirão Preto Medical SchoolUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
| | | | - Luana de Fátima Alves
- Ribeirão Preto Medical SchoolUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
- School of Philosophy, Science and Letters of Ribeirão PretoUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
| | | | - María‐Eugenia Guazzaroni
- School of Philosophy, Science and Letters of Ribeirão PretoUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
| | - Rafael Silva‐Rocha
- Ribeirão Preto Medical SchoolUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
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Abstract
Regulation of gene expression in bacteria results from the interplay between hundreds of transcriptional factors (TFs) at target promoters. However, how the arrangement of binding sites for TFs generates the regulatory logic of promoters is not well-known. Here, we generated and fully characterized a library of synthetic complex promoters for the global regulators, CRP and IHF, in Escherichia coli, which are formed by a weak -35/-10 consensus sequence preceded by four combinatorial binding sites for these two TFs. Using this approach, we found that while cis-elements for CRP preferentially activate promoters when located immediately upstream of the promoter consensus, binding sites for IHF mainly function as "UP" elements and stimulate transcription in several different architectures in the absence of this protein. However, the combination of CRP- and IHF-binding sites resulted in emergent properties in these complex promoters, where the activity of combinatorial promoters cannot be predicted from the individual behavior of its components. Taken together, the results presented here add to the information on architecture-logic of complex promoters in bacteria.
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Affiliation(s)
- Lummy Maria Oliveira Monteiro
- Systems and Synthetic Biology Lab,
Ribeirao Preto Medical School, University of São Paulo, Ribeirão
Preto, São Paulo, Brazil
| | - Letícia Magalhães Arruda
- Systems and Synthetic Biology Lab,
Ribeirao Preto Medical School, University of São Paulo, Ribeirão
Preto, São Paulo, Brazil
| | - Rafael Silva-Rocha
- Systems and Synthetic Biology Lab,
Ribeirao Preto Medical School, University of São Paulo, Ribeirão
Preto, São Paulo, Brazil
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11
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Almeida PZ, Messias JM, Pereira MG, Pinheiro VE, Monteiro LMO, Heinen PR, Cardoso GC, Jorge JA, Polizeli MDLTDM. Mixture design of starchy substrates hydrolysis by an immobilized glucoamylase fromAspergillus brasiliensis. BIOCATAL BIOTRANSFOR 2018. [DOI: 10.1080/10242422.2017.1423059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Paula Zaghetto Almeida
- Departamento de Bioquímica e Imunologia, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, Brazil
| | - Josana Maria Messias
- Departamento de Química, Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Ribeirão Preto, Brazil
| | - Marita Gimenez Pereira
- Departamento de Biologia, Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Ribeirão Preto, Brazil
| | - Vanessa Elisa Pinheiro
- Departamento de Bioquímica e Imunologia, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, Brazil
| | - Lummy Maria Oliveira Monteiro
- Departamento de Bioquímica e Imunologia, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, Brazil
| | - Paulo Ricardo Heinen
- Departamento de Bioquímica e Imunologia, Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, Brazil
| | - George Cunha Cardoso
- Departamento de Física, Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Ribeirão Preto, Brazil
| | - João Atílio Jorge
- Departamento de Biologia, Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Ribeirão Preto, Brazil
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12
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Pinheiro VE, Desagiacomo CCV, Michelin M, Maller A, Monteiro LMO, Jorge JA, Polizeli MDLTDM. Neosartorya glabra polygalacturonase produced from fruit peels as inducers has the potential for application in passion fruit and apple juices. Braz J Food Technol 2017. [DOI: 10.1590/1981-6723.16316] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Summary Polygalacturonases are enzymes with the biotechnological potential for use in fruit juice clarification and for the enhancement of filtration efficiency. The aim of this work was to assess the production of polygalacturonase by the fungus Neosartorya glabra by means of solid-state and submerged fermentation using fruit peel residues as the carbon source, and also apply the enzyme in the clarification and decrease in viscosity of passion fruit and apple juices. The highest polygalacturonase (4.52 U/g/h) production was obtained by means of submerged fermentation in Vogel´s medium (1964) containing orange peel – Bahia variety (Citrus sinensis), at a concentration of 1.5% (w/v, dried mass) at 30-35°C for 72 h. The polygalacturonase of the crude extract presented optimal activity at 60°C and pH 5.5. The enzyme retained around 90% of the initial activity after 180 minutes at 40°C, and 50% of the initial activity after 150 minutes at 50°C. The enzyme was shown to be stable at acid pH values (3.0-6.5) after 120 minutes at 25oC. All these favourable enzymatic properties make the polygalacturonase attractive for potential uses in the industry of pectin-rich fruit juices, since the application of the crude extract to passion fruit (Passiflora edulis) juice caused an 80% reduction in viscosity and 75% decrease in light absorbance. In the processing of apple pulp juice (Malus domestica), there was a 50% reduction in viscosity and 78% decrease in light absorbance.
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