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Nyathi M, Dhlamini Z, Ncube T. Cloning Cellulase Genes from Victoria Falls Rainforest Decaying Logs Metagenome. Pol J Microbiol 2024; 0:pjm-2024-029. [PMID: 39074063 DOI: 10.33073/pjm-2024-029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/28/2022] [Indexed: 07/31/2024] Open
Abstract
The Victoria Falls rainforest is a protected site whose forest floors harbor a host of cellulolytic microorganisms involved in biomass degradation. This study collected decaying logs and soil from the rainforest for bioprospecting cellulases from their metagenomes. Metagenomic DNA was isolated from the compound sample. Degenerate cellulase primers were used to amplify cellulase genes in the metagenome. The resulting amplicons cloned into Z-competent Escherichia coli DH5α were analyzed by functional screening for the production of cellulase extracellularly. Functional screening of the clones resulted in one clone (Clone-i) testing positive for extracellular cellulase production. Submerged fermentation of Clone-i was carried out for cellulase production. The cellulases were characterized to determine their activity's optimum pH and temperature. The diversity of the cellulases produced by Clone-i was determined. Clone-i's optimum enzyme activity was observed after 72 hours of incubation at 50°C and pH 5. Clone-i produced 80% more exoglucanases as compared to endoglucanases. The cellulolytic Clone-i' isolate shows Victoria Falls rainforest's potential as an enzyme bioprospecting site, reflecting that metagenomics is a valuable tool in microbial ecology.
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Affiliation(s)
- Makhosazana Nyathi
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Zephaniah Dhlamini
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Thembekile Ncube
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
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2
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Mon ML, Romano N, Farace PD, Tortone CA, Oriani DS, Picariello G, Zumárraga MJ, Gioffré AK, Talia PM. Exploring the cellulolytic activity of environmental mycobacteria. Tuberculosis (Edinb) 2024; 147:102516. [PMID: 38735123 DOI: 10.1016/j.tube.2024.102516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024]
Abstract
Although studies on non-tuberculous mycobacteria have increased in recent years because they cause a considerable proportion of infections, their cellulolytic system is still poorly studied. This study presents a characterization of the cellulolytic activities of environmental mycobacterial isolates derived from soil and water samples from the central region of Argentina, aimed to evaluate the conservation of the mechanism for the degradation of cellulose in this group of bacteria. The molecular and genomic identification revealed identity with Mycolicibacterium septicum. The endoglucanase and total cellulase activities were assessed both qualitatively and quantitatively and the optimal enzymatic conditions were characterized. A specific protein of around 56 kDa with cellulolytic activity was detected in a zymogram. Protein sequences possibly arising from a cellulase were identified by mass spectrometry-based shotgun proteomics. Results showed that M. septicum encodes for cellulose- and hemicellulose-related degrading enzymes, including at least an active β-1,4 endoglucanase enzyme that could be useful to improve its survival in the environment. Given the important health issues related to mycobacteria, the results of the present study may contribute to the knowledge of their cellulolytic system, which could be important for their ability to survive in many different types of environments.
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Affiliation(s)
- María Laura Mon
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Nelson Romano
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Pablo Daniel Farace
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Claudia A Tortone
- Cátedra de Bacteriología y Micología, Facultad de Ciencias Veterinarias, Universidad Nacional de La Pampa, General Pico, La Pampa, Argentina.
| | - Delia S Oriani
- Cátedra de Bacteriología y Micología, Facultad de Ciencias Veterinarias, Universidad Nacional de La Pampa, General Pico, La Pampa, Argentina.
| | - Gianluca Picariello
- Istituto di Scienze Dell'Alimentazione, Consiglio Nazionale Delle Ricerche, Via Roma 64, 83100, Avellino, Italy.
| | - Martín José Zumárraga
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Andrea Karina Gioffré
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - Paola M Talia
- Instituto de Agrobiotecnología y Biología Molecular IABIMO, UEDD INTA-CONICET, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, provincia de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
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3
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Okon P, Liebscher S, Simon AH, Wensch-Dorendorf M, Bachmann M, Bordusa F, Zeyner A. The Impact of Streptomyces griseus Protease Reserved for Protein Evaluation of Ruminant Feed on Carbohydrase Activity during Co-Incubation. Animals (Basel) 2024; 14:1931. [PMID: 38998042 PMCID: PMC11240829 DOI: 10.3390/ani14131931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/17/2024] [Accepted: 06/27/2024] [Indexed: 07/14/2024] Open
Abstract
For protein evaluation of feedstuffs for ruminants, the Streptomyces griseus protease test provides a solely enzymatic method for estimating ruminal protein degradation. Since plant proteins are often structured in carbohydrate complexes, the use of carbohydrase during the test might improve its accuracy. It is advisable to co-incubate protease and carbohydrase, risking that the carbohydrase activity is reduced under the influence of the protease. The present study was conducted to investigate this impact by using α-amylase or the multi-enzyme complex Viscozym® L as carbohydrase. The detection of active protease was determined fluorescence photometrically using internally quenched fluorogenic substrates (IQFS). Cellulose, pectin, and starch degradation were determined spectrophotometrically using 3,5-dinitro salicylic acid as a colorimetric agent. The Streptomyces griseus protease mixture proved to be active for the selected IQFS immediately after the start of measurements (p < 0.05). Starch hydrolysis catalyzed by α-amylase or Viscozym® L, respectively, was decreased by co-incubation with protease mixture by maximal 3% or 37%, respectively, at 5 h incubation time (p > 0.05). Pectin and cellulose hydrolysis catalyzed by Viscozym® L, respectively, was not significantly influenced by co-incubation with a protease mixture (p > 0.05). Although a decrease in carbohydrase activity during co-incubation with Streptomyces griseus protease occurred, it was only numerical and might be counteracted by an adapted carbohydrase activity.
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Affiliation(s)
- Paul Okon
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Sandra Liebscher
- Charles Tanford Protein Centre, Institute of Biochemistry/Biotechnology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Andreas Hans Simon
- Charles Tanford Protein Centre, Institute of Biochemistry/Biotechnology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Monika Wensch-Dorendorf
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Martin Bachmann
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Frank Bordusa
- Charles Tanford Protein Centre, Institute of Biochemistry/Biotechnology, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Annette Zeyner
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
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Carreira de Paula J, García Olmedo P, Gómez-Moracho T, Buendía-Abad M, Higes M, Martín-Hernández R, Osuna A, de Pablos LM. Promastigote EPS secretion and haptomonad biofilm formation as evolutionary adaptations of trypanosomatid parasites for colonizing honeybee hosts. NPJ Biofilms Microbiomes 2024; 10:27. [PMID: 38514634 PMCID: PMC10957890 DOI: 10.1038/s41522-024-00492-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/22/2024] [Indexed: 03/23/2024] Open
Abstract
Bees are major pollinators involved in the maintenance of all terrestrial ecosystems. Biotic and abiotic factors placing these insects at risk is a research priority for ecological and agricultural sustainability. Parasites are one of the key players of this global decline and the study of their mechanisms of action is essential to control honeybee colony losses. Trypanosomatid parasites and particularly the Lotmaria passim are widely spread in honeybees, however their lifestyle is poorly understood. In this work, we show how these parasites are able to differentiate into a new parasitic lifestyle: the trypanosomatid biofilms. Using different microscopic techniques, we demonstrated that the secretion of Extracellular Polymeric Substances by free-swimming unicellular promastigote forms is a prerequisite for the generation and adherence of multicellular biofilms to solid surfaces in vitro and in vivo. Moreover, compared to human-infective trypanosomatid parasites our study shows how trypanosomatid parasites of honeybees increases their resistance and thus resilience to drastic changes in environmental conditions such as ultralow temperatures and hypoosmotic shock, which would explain their success thriving within or outside their hosts. These results set up the basis for the understanding of the success of this group of parasites in nature and to unveil the impact of such pathogens in honeybees, a keystones species in most terrestrial ecosystems.
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Affiliation(s)
- Jéssica Carreira de Paula
- Department of Parasitology, Biochemical and Molecular Parasitology Group CTS-183, University of Granada, Granada, Spain
- Institute of Biotechnology, University of Granada, Granada, Spain
| | - Pedro García Olmedo
- Department of Parasitology, Biochemical and Molecular Parasitology Group CTS-183, University of Granada, Granada, Spain
- Institute of Biotechnology, University of Granada, Granada, Spain
| | - Tamara Gómez-Moracho
- Department of Parasitology, Biochemical and Molecular Parasitology Group CTS-183, University of Granada, Granada, Spain
- Institute of Biotechnology, University of Granada, Granada, Spain
| | - María Buendía-Abad
- Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), IRIAF - Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal, Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, Marchamalo, Spain
- Instituto de Recursos Humanos para la Ciencia y la Tecnología, Fundación Parque Científico y Tecnológico de Castilla-La Mancha, 02006, Albacete, Spain
| | - Mariano Higes
- Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), IRIAF - Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal, Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, Marchamalo, Spain
- Instituto de Recursos Humanos para la Ciencia y la Tecnología, Fundación Parque Científico y Tecnológico de Castilla-La Mancha, 02006, Albacete, Spain
| | - Raquel Martín-Hernández
- Laboratorio de Patología Apícola, Centro de Investigación Apícola y Agroambiental (CIAPA), IRIAF - Instituto Regional de Investigación y Desarrollo Agroalimentario y Forestal, Consejería de Agricultura de la Junta de Comunidades de Castilla-La Mancha, Marchamalo, Spain
- Instituto de Recursos Humanos para la Ciencia y la Tecnología, Fundación Parque Científico y Tecnológico de Castilla-La Mancha, 02006, Albacete, Spain
| | - Antonio Osuna
- Department of Parasitology, Biochemical and Molecular Parasitology Group CTS-183, University of Granada, Granada, Spain
- Institute of Biotechnology, University of Granada, Granada, Spain
| | - Luis Miguel de Pablos
- Department of Parasitology, Biochemical and Molecular Parasitology Group CTS-183, University of Granada, Granada, Spain.
- Institute of Biotechnology, University of Granada, Granada, Spain.
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Castañeda-Barreto A, Olivera-Gonzales P, Tamariz-Angeles C. A natural consortium of thermophilic bacteria from Huancarhuaz hot spring (Ancash-Peru) for promising lignocellulose bioconversion. Heliyon 2024; 10:e27272. [PMID: 38486736 PMCID: PMC10937689 DOI: 10.1016/j.heliyon.2024.e27272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/14/2024] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
The lignocellulose bioconversion process is an eco-friendly and green-economy alternative technology that allows the reduction of pollution and global warming, so it is necessary for thermophilic and thermostable hydrolytic enzymes from natural sources. This research aimed to isolate cellulolytic and xylanolytic microbial consortia from Huancarhuaz hot spring (Peru) from sludge or in situ baiting cultured with or without sugarcane bagasse. According to the hydrolytic activities consortium T4 from in situ baiting was selected. It was cultivated in submerged fermentation at 65 °C, pH 6.5 for eight days using LB supplemented with sugar cane bagasse (SCB), pine wood sawdust (PWS), CMC, xylan of birchwood, or micro granular cellulose. Crude extract of culture supplemented with SCB (T4B) showed better endoglucanase and xylanase activities with higher activities at 75 °C and pH 6. In these conditions, cellulase activity was kept up to 57% after 1 h of incubation, while xylanase activity was up to 63% after 72 h. Furthermore, this crude extract released reduced sugars from pretreated SCB and PWS. According to metagenomic analysis of 16S rDNA, Geobacillus was the predominant genus. It was found thermostable genes: a type of endoglucanase (GH5), an endo-xylanase (GH10), and alkali xylanase (GH10) previously reported in Geobacillus sp. strains. Finally, Huancarhuaz hot spring harbors a genetic microbial diversity for lignocellulosic waste bioconversion in high temperatures, and the T4B consortium will be a promising source of novel extreme condition stable enzymes for the saccharification process.
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Affiliation(s)
- Alberto Castañeda-Barreto
- Facultad de Ciencias del Ambiente, Universidad Nacional Santiago Antúnez de Mayolo, Av. Centenario 200, 02002, Independencia, Huaraz, Ancash, Peru
| | - Percy Olivera-Gonzales
- Centro de Investigación de la Biodiversidad y Recursos Genéticos de Ancash, Facultad de Ciencias, Universidad Nacional Santiago Antúnez de Mayolo, Av. Centenario 200, 02002, Independencia, Huaraz, Ancash, Peru
| | - Carmen Tamariz-Angeles
- Centro de Investigación de la Biodiversidad y Recursos Genéticos de Ancash, Facultad de Ciencias, Universidad Nacional Santiago Antúnez de Mayolo, Av. Centenario 200, 02002, Independencia, Huaraz, Ancash, Peru
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6
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Nowinski D, Czapka T, Maliszewska I. Effect of multiple nonthermal plasma treatments of filamentous fungi on cellular phenotypic changes and phytopathogenicity. Int J Food Microbiol 2024; 408:110428. [PMID: 37837937 DOI: 10.1016/j.ijfoodmicro.2023.110428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 07/26/2023] [Accepted: 10/03/2023] [Indexed: 10/16/2023]
Abstract
The effect of multiple sublethal doses of non-thermal plasma treatments on fungal cells phenotypical changes and the reduction in phytopathogenicity of Fusarium oxysporum, Botrytis cinerea, and Alternaria alternata was examined. The intensity of these changes depended on the species of fungus and the number of exposures of the mycelia to the DBD plasma. Microscopic observations showed that the plasma damaged the surface of the hyphae, increased their thickness and decreased overall dry biomass of the organisms. A decrease in pectinolytic activity was found in F. oxysporum and A. alternata, in contrast to B. cinerea, where an increase in pectinolytic activity was observed after the fifth plasma treatment. Changes in specific xylanase activity varied and were dependent on the species of fungus. The percentage of cucumber seeds germinated artificially infected with mycelium after multiple plasma treatments increased compared to those that were mycelium infected prior to plasma exposure. Plants that developed from seeds after plasma exposure were characterized by a higher biomass and longer roots and stems. Multiple treatments of the studied fungi with plasma, followed by seed infection, increased the SWVI and SWVI indexes of cucumber seedlings, but they did not reach the characteristic value of the control seeds (not infected with fungi). The reduced phytopathogenicity of the tested fungi was confirmed by artificial infestation of tomato fruits.
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Affiliation(s)
- Daria Nowinski
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Tomasz Czapka
- Department of Electrical Engineering Fundamentals, Faculty of Electrical Engineering, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Irena Maliszewska
- Department of Organic and Medicinal Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
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7
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Dementiev A, Lillington SP, Jin S, Kim Y, Jedrzejczak R, Michalska K, Joachimiak A, O'Malley MA. Structure and enzymatic characterization of CelD endoglucanase from the anaerobic fungus Piromyces finnis. Appl Microbiol Biotechnol 2023; 107:5999-6011. [PMID: 37548665 PMCID: PMC10485095 DOI: 10.1007/s00253-023-12684-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/24/2023] [Accepted: 06/29/2023] [Indexed: 08/08/2023]
Abstract
Anaerobic fungi found in the guts of large herbivores are prolific biomass degraders whose genomes harbor a wealth of carbohydrate-active enzymes (CAZymes), of which only a handful are structurally or biochemically characterized. Here, we report the structure and kinetic rate parameters for a glycoside hydrolase (GH) family 5 subfamily 4 enzyme (CelD) from Piromyces finnis, a modular, cellulosome-incorporated endoglucanase that possesses three GH5 domains followed by two C-terminal fungal dockerin domains (double dockerin). We present the crystal structures of an apo wild-type CelD GH5 catalytic domain and its inactive E154A mutant in complex with cellotriose at 2.5 and 1.8 Å resolution, respectively, finding the CelD GH5 catalytic domain adopts the (β/α)8-barrel fold common to many GH5 enzymes. Structural superimposition of the apo wild-type structure with the E154A mutant-cellotriose complex supports a catalytic mechanism in which the E154 carboxylate side chain acts as an acid/base and E278 acts as a complementary nucleophile. Further analysis of the cellotriose binding pocket highlights a binding groove lined with conserved aromatic amino acids that when docked with larger cellulose oligomers is capable of binding seven glucose units and accommodating branched glucan substrates. Activity analyses confirm P. finnis CelD can hydrolyze mixed linkage glucan and xyloglucan, as well as carboxymethylcellulose (CMC). Measured kinetic parameters show the P. finnis CelD GH5 catalytic domain has CMC endoglucanase activity comparable to other fungal endoglucanases with kcat = 6.0 ± 0.6 s-1 and Km = 7.6 ± 2.1 g/L CMC. Enzyme kinetics were unperturbed by the addition or removal of the native C-terminal dockerin domains as well as the addition of a non-native N-terminal dockerin, suggesting strict modularity among the domains of CelD. KEY POINTS: • Anaerobic fungi host a wealth of industrially useful enzymes but are understudied. • P. finnis CelD has endoglucanase activity and structure common to GH5_4 enzymes. • CelD's kinetics do not change with domain fusion, exhibiting high modularity.
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Affiliation(s)
- Alexey Dementiev
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Stephen P Lillington
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA
| | - Shiyan Jin
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA
| | - Youngchang Kim
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Robert Jedrzejczak
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Karolina Michalska
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Andrzej Joachimiak
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA.
- Biological Engineering Program, University of California, Santa Barbara, CA, USA.
- Joint BioEnergy Institute (JBEI), Emeryville, CA, 94608, USA.
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Zhang X, Tang G, Zhou Z, Wang H, Li X, Yan G, Liu Y, Huang Y, Wang J, Cao Y. Fabrication of Enzyme-Responsive Prodrug Self-Assembly Based on Fluazinam for Reducing Toxicity to Aquatic Organisms. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:12678-12687. [PMID: 37595273 DOI: 10.1021/acs.jafc.3c03762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
Abstract
Prodrug-based nanodrug delivery systems were drug formulations by covalently conjugating drugs with inversely polar groups via a cleavable bond to self-assemble into nanoparticles for efficient drug delivery. To improve the utilization efficiency of fluazinam (FZN), enzyme-responsive prodrugs were prepared by conjugating FZN with different alkyl aliphatic acids through a nucleophilic substitution reaction and subsequently self-assembled into nanoparticles (FZNP NPs) without using any harmful adjuvant. The obtained FZNP NPs exhibited excellent efficacies against Sclerotinia sclerotiorum as a result of improved physicochemical properties, including low surface tension, high retention, and enhanced photostability. The LC50 values of FZNP NPs toward zebrafish were 3-8 times that of FZN, which illustrated that the FZNP NPs reduced the detriments of FZN to the aquatic organisms while retaining good biological activity. Therefore, prodrug self-assembly technology would offer a potential method for improving the utilization efficiency of pesticides and lowering the risks to the ecological environment.
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Affiliation(s)
- Xiaohong Zhang
- College of Plant Protection, China Agricultural University, 2 Yuanmingyuan West Road, Beijing 100193, People's Republic of China
| | - Gang Tang
- College of Plant Protection, China Agricultural University, 2 Yuanmingyuan West Road, Beijing 100193, People's Republic of China
| | - Zhiyuan Zhou
- College of Plant Protection, China Agricultural University, 2 Yuanmingyuan West Road, Beijing 100193, People's Republic of China
| | - Huachen Wang
- College of Plant Protection, China Agricultural University, 2 Yuanmingyuan West Road, Beijing 100193, People's Republic of China
| | - Xuan Li
- College of Plant Protection, China Agricultural University, 2 Yuanmingyuan West Road, Beijing 100193, People's Republic of China
| | - Guangyao Yan
- College of Plant Protection, China Agricultural University, 2 Yuanmingyuan West Road, Beijing 100193, People's Republic of China
| | - Yulu Liu
- College of Plant Protection, China Agricultural University, 2 Yuanmingyuan West Road, Beijing 100193, People's Republic of China
| | - Yuqi Huang
- College of Plant Protection, China Agricultural University, 2 Yuanmingyuan West Road, Beijing 100193, People's Republic of China
| | - Jialu Wang
- College of Plant Protection, China Agricultural University, 2 Yuanmingyuan West Road, Beijing 100193, People's Republic of China
| | - Yongsong Cao
- College of Plant Protection, China Agricultural University, 2 Yuanmingyuan West Road, Beijing 100193, People's Republic of China
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9
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Hernalsteens S, Cong HH, Chen XD. Soymilk modification by immobilized bacteria in a soft elastic tubular reactor's wall. J FOOD ENG 2023. [DOI: 10.1016/j.jfoodeng.2023.111536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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10
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Dar A, Were E, Hilger T, Zahir ZA, Ahmad M, Hussain A, Rasche F. Bacterial secondary metabolites: possible mechanism for weed suppression in wheat. Can J Microbiol 2023; 69:103-116. [PMID: 36379032 DOI: 10.1139/cjm-2022-0181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chemical weed control is an effective method, but has proved hazardous for humans, environment, and soil biodiversity. Use of allelopathic bacteria may be more efficient and sustainable weed control measure. The bacterial inoculants have never been studied in context of their interaction with weed root exudates and precursor-dependent production of the natural phytotoxins (cyanide, cytolytic enzymes and auxin) by these strains to understand their weed suppression and wheat growth promotion abilities. Therefore, root exudates of Avena fatua, Phalaris minor, Rumex dentatus, and wheat were quantified and their role in microbial root colonization and secondary metabolite production, i.e., cyanide, cytolytic enzymes, phenolics, and elevated auxin concentration, was studied. The results depicted l-tryptophan and glycine as major contributors of elevated cyanide and elevated levels in weed rhizosphere by the studied Pseudomonas strains, through their higher root colonization ability in weeds as compared with wheat. Furthermore, the higher root colonization also enhanced p-coumaric acid (photosynthesis inhibitor by impairing cytochrome c oxidase activity in plants) and cytolytic enzyme (root cell wall degradation) concentration in weed rhizosphere. In conclusion, the differential root colonization of wheat and weeds by these strains is responsible for enhancing weed suppression (enhancing phytotoxic effect) and wheat growth promotion (lowering phytotoxic effect).
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Affiliation(s)
- Abubakar Dar
- Department of Soil Science, The Islamia University of Bahawalpur, Bahawalpur, Punjab 63100, Pakistan
| | - Evans Were
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Germany
| | - Thomas Hilger
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Germany
| | - Zahir Ahmad Zahir
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, Punjab 38040, Pakistan
| | - Maqshoof Ahmad
- Department of Soil Science, The Islamia University of Bahawalpur, Bahawalpur, Punjab 63100, Pakistan
| | - Azhar Hussain
- Department of Soil Science, The Islamia University of Bahawalpur, Bahawalpur, Punjab 63100, Pakistan
| | - Frank Rasche
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Germany
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11
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Tom LM, Aulitto M, Wu YW, Deng K, Gao Y, Xiao N, Rodriguez BG, Louime C, Northen TR, Eudes A, Mortimer JC, Adams PD, Scheller HV, Simmons BA, Ceja-Navarro JA, Singer SW. Low-abundance populations distinguish microbiome performance in plant cell wall deconstruction. MICROBIOME 2022; 10:183. [PMID: 36280858 PMCID: PMC9594917 DOI: 10.1186/s40168-022-01377-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 09/19/2022] [Indexed: 05/23/2023]
Abstract
BACKGROUND Plant cell walls are interwoven structures recalcitrant to degradation. Native and adapted microbiomes can be particularly effective at plant cell wall deconstruction. Although most understanding of biological cell wall deconstruction has been obtained from isolates, cultivated microbiomes that break down cell walls have emerged as new sources for biotechnologically relevant microbes and enzymes. These microbiomes provide a unique resource to identify key interacting functional microbial groups and to guide the design of specialized synthetic microbial communities. RESULTS To establish a system assessing comparative microbiome performance, parallel microbiomes were cultivated on sorghum (Sorghum bicolor L. Moench) from compost inocula. Biomass loss and biochemical assays indicated that these microbiomes diverged in their ability to deconstruct biomass. Network reconstructions from gene expression dynamics identified key groups and potential interactions within the adapted sorghum-degrading communities, including Actinotalea, Filomicrobium, and Gemmatimonadetes populations. Functional analysis demonstrated that the microbiomes proceeded through successive stages that are linked to enzymes that deconstruct plant cell wall polymers. The combination of network and functional analysis highlighted the importance of cellulose-degrading Actinobacteria in differentiating the performance of these microbiomes. CONCLUSIONS The two-tier cultivation of compost-derived microbiomes on sorghum led to the establishment of microbiomes for which community structure and performance could be assessed. The work reinforces the observation that subtle differences in community composition and the genomic content of strains may lead to significant differences in community performance. Video Abstract.
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Affiliation(s)
- Lauren M Tom
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Martina Aulitto
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, 110, Taiwan
| | - Kai Deng
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yu Gao
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Systems and Genome Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Naijia Xiao
- Institute of Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | | | - Clifford Louime
- College of Natural Sciences, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - Trent R Northen
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Systems and Genome Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aymerick Eudes
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Systems and Genome Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jenny C Mortimer
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Systems and Genome Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- School of Agriculture, Food and Wine, & Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, CA, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Henrik V Scheller
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Systems and Genome Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Javier A Ceja-Navarro
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, USA.
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, USA.
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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12
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Tian Y, Huang Y, Zhang X, Tang G, Gao Y, Zhou Z, Li Y, Wang H, Yu X, Li X, Liu Y, Yan G, Wang J, Cao Y. Self-Assembled Nanoparticles of a Prodrug Conjugate Based on Pyrimethanil for Efficient Plant Disease Management. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11901-11910. [PMID: 36111893 DOI: 10.1021/acs.jafc.2c04489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Self-assembled nanotechnology is a promising strategy for improving the effective utilization of pesticides due to its distinct advantages. Herein, an amide-bonded prodrug conjugate based on pyrimethanil (PYR) and butyric acid (BA) was successfully synthesized by the nucleophilic substitution reaction and subsequently self-assembled into spherical nanoparticles (PB NPs) with an average size of 85 nm through the solvent exchange method without using any toxic adjuvant. The results showed that PB NPs based on PYR and BA had a synergistic antimicrobial activity against S. sclerotiorum on plant leaves due to good photostability, low volatilization, good surface activity, and improved retention. Additionally, PB NPs could be used by plant cells as nutrients to promote the growth of plants and thus reduced the toxicity of PYR to plant. Therefore, this prodrug conjugate self-assembly nanotechnology would provide a promising strategy for improving the effective utilization rates of pesticides and reducing their toxicities to plants.
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Affiliation(s)
- Yuyang Tian
- College of Plant Protection, China Agricultural University, Beijing 100093, China
| | - Yuqi Huang
- College of Plant Protection, China Agricultural University, Beijing 100093, China
| | - Xiaohong Zhang
- College of Plant Protection, China Agricultural University, Beijing 100093, China
| | - Gang Tang
- College of Plant Protection, China Agricultural University, Beijing 100093, China
| | - Yunhao Gao
- College of Plant Protection, China Agricultural University, Beijing 100093, China
| | - Zhiyuan Zhou
- College of Plant Protection, China Agricultural University, Beijing 100093, China
| | - Yan Li
- College of Plant Protection, China Agricultural University, Beijing 100093, China
| | - Huachen Wang
- College of Plant Protection, China Agricultural University, Beijing 100093, China
| | - Xueyang Yu
- College of Plant Protection, China Agricultural University, Beijing 100093, China
| | - Xuan Li
- College of Plant Protection, China Agricultural University, Beijing 100093, China
| | - Yulu Liu
- College of Plant Protection, China Agricultural University, Beijing 100093, China
| | - Guangyao Yan
- College of Plant Protection, China Agricultural University, Beijing 100093, China
| | - Jialu Wang
- College of Plant Protection, China Agricultural University, Beijing 100093, China
| | - Yongsong Cao
- College of Plant Protection, China Agricultural University, Beijing 100093, China
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Chancharoonpong C, Hsieh PC. Effect of Black Bean Koji Enzyme on Fermentation, Chemical Properties and Biogenic Amine Formation of Fermented Fish Sauce. JOURNAL OF AQUATIC FOOD PRODUCT TECHNOLOGY 2022. [DOI: 10.1080/10498850.2022.2035879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Chuenjit Chancharoonpong
- Department of Food Technology and Nutrition, Faculty of Natural Resources and Agro-Industry, Kasetsart University, Chalermphrakiat Sakon Nakhon Province Campus,Sakon Nakhon, Thailand
| | - Pao-Chuan Hsieh
- Department of Food Science, National Pingtung University of Science and Technology, Pingtung, Taiwan
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14
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Boock JT, Taw M, King BC, Conrado RJ, Gibson DM, DeLisa MP. Two-Tiered Selection and Screening Strategy to Increase Functional Enzyme Production in E. coli. Methods Mol Biol 2022; 2406:169-187. [PMID: 35089557 DOI: 10.1007/978-1-0716-1859-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Development of recombinant enzymes as industrial biocatalysts or metabolic pathway elements requires soluble expression of active protein. Here we present a two-step strategy, combining a directed evolution selection with an enzyme activity screen, to increase the soluble production of enzymes in the cytoplasm of E. coli. The directed evolution component relies on the innate quality control of the twin-arginine translocation pathway coupled with antibiotic selection to isolate point mutations that promote intracellular solubility. A secondary screen is applied to ensure the solubility enhancement has not compromised enzyme activity. This strategy has been successfully applied to increase the soluble production of a fungal endocellulase by 30-fold in E. coli without change in enzyme specific activity through two rounds of directed evolution.
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Affiliation(s)
- Jason T Boock
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA.
- Department of Chemical, Paper and Biomedical Engineering, Miami University (OH), Oxford, OH, USA.
| | - May Taw
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Brian C King
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, USA
| | - Robert J Conrado
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Donna M Gibson
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, USA
- USDA Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA
| | - Matthew P DeLisa
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
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15
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Effect of edible coating on physical and chemical properties of potato tubers under different storage conditions. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112580] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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16
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Dou Y, Yang Y, Mund NK, Wei Y, Liu Y, Wei L, Wang Y, Du P, Zhou Y, Liesche J, Huang L, Fang H, Zhao C, Li J, Wei Y, Chen S. Comparative Analysis of Herbaceous and Woody Cell Wall Digestibility by Pathogenic Fungi. Molecules 2021; 26:molecules26237220. [PMID: 34885803 PMCID: PMC8659149 DOI: 10.3390/molecules26237220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 11/21/2021] [Accepted: 11/25/2021] [Indexed: 11/16/2022] Open
Abstract
Fungal pathogens have evolved combinations of plant cell-wall-degrading enzymes (PCWDEs) to deconstruct host plant cell walls (PCWs). An understanding of this process is hoped to create a basis for improving plant biomass conversion efficiency into sustainable biofuels and bioproducts. Here, an approach integrating enzyme activity assay, biomass pretreatment, field emission scanning electron microscopy (FESEM), and genomic analysis of PCWDEs were applied to examine digestibility or degradability of selected woody and herbaceous biomass by pathogenic fungi. Preferred hydrolysis of apple tree branch, rapeseed straw, or wheat straw were observed by the apple-tree-specific pathogen Valsa mali, the rapeseed pathogen Sclerotinia sclerotiorum, and the wheat pathogen Rhizoctonia cerealis, respectively. Delignification by peracetic acid (PAA) pretreatment increased PCW digestibility, and the increase was generally more profound with non-host than host PCW substrates. Hemicellulase pretreatment slightly reduced or had no effect on hemicellulose content in the PCW substrates tested; however, the pretreatment significantly changed hydrolytic preferences of the selected pathogens, indicating a role of hemicellulose branching in PCW digestibility. Cellulose organization appears to also impact digestibility of host PCWs, as reflected by differences in cellulose microfibril organization in woody and herbaceous PCWs and variation in cellulose-binding domain organization in cellulases of pathogenic fungi, which is known to influence enzyme access to cellulose. Taken together, this study highlighted the importance of chemical structure of both hemicelluloses and cellulose in host PCW digestibility by fungal pathogens.
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Affiliation(s)
- Yanhua Dou
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yan Yang
- College of Chemistry and Chemical Engineering, Shanxi Datong University, Datong 037009, China;
| | - Nitesh Kumar Mund
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yanping Wei
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yisong Liu
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Linfang Wei
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yifan Wang
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Panpan Du
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yunheng Zhou
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Johannes Liesche
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Lili Huang
- College of Plant Protection, Northwest A&F University, Yangling, Xianyang 712100, China;
| | - Hao Fang
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Chen Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Jisheng Li
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yahong Wei
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Northwest A&F University, Yangling, Xianyang 712100, China
- Correspondence: (Y.W.); (S.C.); Tel.: +86-029-87091021 (S.C.)
| | - Shaolin Chen
- College of Life Sciences, Northwest A&F University, Yangling, Xianyang 712100, China; (Y.D.); (N.K.M.); (Y.W.); (Y.L.); (L.W.); (Y.W.); (P.D.); (Y.Z.); (J.L.); (H.F.); (C.Z.); (J.L.)
- Biomass Energy Center for Arid and Semi-Arid Lands, Northwest A&F University, Yangling, Xianyang 712100, China
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Northwest A&F University, Yangling, Xianyang 712100, China
- Correspondence: (Y.W.); (S.C.); Tel.: +86-029-87091021 (S.C.)
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Improved saccharification of Chlorella vulgaris biomass by fungal secreted enzymes for bioethanol production. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102402] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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18
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Gabriel R, Mueller R, Floerl L, Hopson C, Harth S, Schuerg T, Fleissner A, Singer SW. CAZymes from the thermophilic fungus Thermoascus aurantiacus are induced by C5 and C6 sugars. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:169. [PMID: 34384463 PMCID: PMC8359064 DOI: 10.1186/s13068-021-02018-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Filamentous fungi are excellent lignocellulose degraders, which they achieve through producing carbohydrate active enzymes (CAZymes). CAZyme production is highly orchestrated and gene expression analysis has greatly expanded understanding of this important biotechnological process. The thermophilic fungus Thermoascus aurantiacus secretes highly active thermostable enzymes that enable saccharifications at higher temperatures; however, the genome-wide measurements of gene expression in response to CAZyme induction are not understood. RESULTS A fed-batch system with plant biomass-derived sugars D-xylose, L-arabinose and cellobiose established that these sugars induce CAZyme expression in T. aurantiacus. The C5 sugars induced both cellulases and hemicellulases, while cellobiose specifically induced cellulases. A minimal medium formulation was developed to enable gene expression studies of T. aurantiacus with these inducers. It was found that d-xylose and L-arabinose strongly induced a wide variety of CAZymes, auxiliary activity (AA) enzymes and carbohydrate esterases (CEs), while cellobiose facilitated lower expression of mostly cellulase genes. Furthermore, putative orthologues of different unfolded protein response genes were up-regulated during the C5 sugar feeding together with genes in the C5 sugar assimilation pathways. CONCLUSION This work has identified two additional CAZyme inducers for T. aurantiacus, L-arabinose and cellobiose, along with D-xylose. A combination of biochemical assays and RNA-seq measurements established that C5 sugars induce a suite of cellulases and hemicellulases, providing paths to produce broad spectrum thermotolerant enzymatic mixtures.
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Affiliation(s)
- Raphael Gabriel
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Institut Für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Rebecca Mueller
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Institut Für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Lena Floerl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 18, 1190, Vienna, Austria
- Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Cynthia Hopson
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Department of Chemical Engineering and Materials, Faculty of Chemistry, Complutense University of Madrid, Av. Complutense s/n, 28040, Madrid, Spain
| | - Simon Harth
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Frankfurt Institute of Molecular Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Timo Schuerg
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Andre Fleissner
- Institut Für Genetik, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Rebenring 56, 38106, Braunschweig, Germany
| | - Steven W Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 9720, USA.
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.
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Skin Color Retention in Red Potatoes during Long-Term Storage with Edible Coatings. Foods 2021; 10:foods10071531. [PMID: 34359400 PMCID: PMC8307985 DOI: 10.3390/foods10071531] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/15/2021] [Accepted: 06/28/2021] [Indexed: 11/17/2022] Open
Abstract
In this study, we aimed to investigate the effect of edible coatings and cold storage conditions on the skin color of red potatoes (Ciklamen and Modoc) stored for six months at 4 ± 2 °C and 90 ± 5% relative humidity (RH). The four different formulations used were sodium alginate (F1), sodium alginate and potato starch (F2), zein and chitosan (F3), and chitosan, sodium alginate and potato starch (F4), in addition to the control treatment with distilled water. The treated samples were assessed periodically during six months of storage for changes in color, levels of reducing sugars, total phenolics and sensory qualities. The results indicated that the treatment with edible coatings significantly enhanced the chroma value of skin color, especially F1 and F2 formulations. However, these coatings instilled a limited effect on the level of reducing sugars. Moreover, F1 and F4 formulations exerted a significant effect (p < 0.05) on anthocyanin content examined after three months of storage. Alginate-based edible coatings significantly improved sensory evaluation, especially in terms of the color, gloss, and general acceptability of red skin potatoes.
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Oszust K, Pylak M, Frąc M. Trichoderma-Based Biopreparation with Prebiotics Supplementation for the Naturalization of Raspberry Plant Rhizosphere. Int J Mol Sci 2021; 22:ijms22126356. [PMID: 34198606 PMCID: PMC8232080 DOI: 10.3390/ijms22126356] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 11/16/2022] Open
Abstract
The number of raspberry plants dying from a sudden outbreak of gray mold, verticillium wilt, anthracnosis, and phytophthora infection has increased in recent times, leading to crop failure. The plants suffer tissue collapse and black roots, symptoms similar to a Botrytis-Verticillium-Colletotrichum-Phytophthora disease complex. A sizeable number of fungal isolates were acquired from the root and rhizosphere samples of wild raspberries from different locations. Subsequent in vitro tests revealed that a core consortium of 11 isolates of selected Trichoderma spp. was the most essential element for reducing in phytopathogen expansion. For this purpose, isolates were characterized by the efficiency of their antagonistic properties against Botrytis, Verticillium, Colletotrichum and Phytophthora isolates and with hydrolytic properties accelerating the decomposition of organic matter in the soil and thus making nutrients available to plants. Prebiotic additive supplementation with a mixture of adonitol, arabitol, erythritol, mannitol, sorbitol, and adenosine was proven in a laboratory experiment to be efficient in stimulating the growth of Trichoderma isolates. Through an in vivo pathosystem experiment, different raspberry naturalization-protection strategies (root inoculations and watering with native Trichoderma isolates, applied separately or simultaneously) were tested under controlled phytotron conditions. The experimental application of phytopathogens attenuated raspberry plant and soil properties, while Trichoderma consortium incorporation exhibited a certain trend of improving these features in terms of a short-term response, depending on the pathosystem and naturalization strategy. What is more, a laboratory-scale development of a biopreparation for the naturalization of the raspberry rhizosphere based on the Trichoderma consortium was proposed in the context of two application scenarios. The first was a ready-to-use formulation to be introduced while planting (pellets, gel). The second was a variant to be applied with naturalizing watering (soluble powder).
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Consolidated Bioprocessing: Synthetic Biology Routes to Fuels and Fine Chemicals. Microorganisms 2021; 9:microorganisms9051079. [PMID: 34069865 PMCID: PMC8157379 DOI: 10.3390/microorganisms9051079] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/27/2021] [Accepted: 05/14/2021] [Indexed: 11/17/2022] Open
Abstract
The long road from emerging biotechnologies to commercial “green” biosynthetic routes for chemical production relies in part on efficient microbial use of sustainable and renewable waste biomass feedstocks. One solution is to apply the consolidated bioprocessing approach, whereby microorganisms convert lignocellulose waste into advanced fuels and other chemicals. As lignocellulose is a highly complex network of polymers, enzymatic degradation or “saccharification” requires a range of cellulolytic enzymes acting synergistically to release the abundant sugars contained within. Complications arise from the need for extracellular localisation of cellulolytic enzymes, whether they be free or cell-associated. This review highlights the current progress in the consolidated bioprocessing approach, whereby microbial chassis are engineered to grow on lignocellulose as sole carbon sources whilst generating commercially useful chemicals. Future perspectives in the emerging biofoundry approach with bacterial hosts are discussed, where solutions to existing bottlenecks could potentially be overcome though the application of high throughput and iterative Design-Build-Test-Learn methodologies. These rapid automated pathway building infrastructures could be adapted for addressing the challenges of increasing cellulolytic capabilities of microorganisms to commercially viable levels.
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22
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Deng Y, Beahm DR, Ionov S, Sarpeshkar R. Measuring and modeling energy and power consumption in living microbial cells with a synthetic ATP reporter. BMC Biol 2021; 19:101. [PMID: 34001118 PMCID: PMC8130387 DOI: 10.1186/s12915-021-01023-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 04/10/2021] [Indexed: 11/29/2022] Open
Abstract
Background Adenosine triphosphate (ATP) is the main energy carrier in living organisms, critical for metabolism and essential physiological processes. In humans, abnormal regulation of energy levels (ATP concentration) and power consumption (ATP consumption flux) in cells is associated with numerous diseases from cancer, to viral infection and immune dysfunction, while in microbes it influences their responses to drugs and other stresses. The measurement and modeling of ATP dynamics in cells is therefore a critical component in understanding fundamental physiology and its role in pathology. Despite the importance of ATP, our current understanding of energy dynamics and homeostasis in living cells has been limited by the lack of easy-to-use ATP sensors and the lack of models that enable accurate estimates of energy and power consumption related to these ATP dynamics. Here we describe a dynamic model and an ATP reporter that tracks ATP in E. coli over different growth phases. Results The reporter is made by fusing an ATP-sensing rrnB P1 promoter with a fast-folding and fast-degrading GFP. Good correlations between reporter GFP and cellular ATP were obtained in E. coli growing in both minimal and rich media and in various strains. The ATP reporter can reliably monitor bacterial ATP dynamics in response to nutrient availability. Fitting the dynamics of experimental data corresponding to cell growth, glucose, acetate, dissolved oxygen, and ATP yielded a mathematical and circuit model. This model can accurately predict cellular energy and power consumption under various conditions. We found that cellular power consumption varies significantly from approximately 0.8 and 0.2 million ATP/s for a tested strain during lag and stationary phases to 6.4 million ATP/s during exponential phase, indicating ~ 8–30-fold changes of metabolic rates among different growth phases. Bacteria turn over their cellular ATP pool a few times per second during the exponential phase and slow this rate by ~ 2–5-fold in lag and stationary phases. Conclusion Our rrnB P1-GFP reporter and kinetic circuit model provide a fast and simple way to monitor and predict energy and power consumption dynamics in bacterial cells, which can impact fundamental scientific studies and applied medical treatments in the future.
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Affiliation(s)
- Yijie Deng
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA
| | | | - Steven Ionov
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA
| | - Rahul Sarpeshkar
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA. .,Departments of Engineering, Microbiology & Immunology, Physics, and Molecular and Systems Biology, Dartmouth College, Hanover, NH, 03755, USA.
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Chang TH, Lin YH, Wan YL, Chen KS, Huang JW, Chang PFL. Degenerated Virulence and Irregular Development of Fusarium oxysporum f. sp. niveum Induced by Successive Subculture. J Fungi (Basel) 2020; 6:jof6040382. [PMID: 33371239 PMCID: PMC7767292 DOI: 10.3390/jof6040382] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/27/2020] [Accepted: 12/12/2020] [Indexed: 11/17/2022] Open
Abstract
Successive cultivation of fungi on artificial media has been reported to cause the sectorization, which leads to degeneration of developmental phenotype, and virulence. Fusarium oxysporum f. sp. niveum (Fon), the causal agent of watermelon Fusarium wilt, forms degenerated sectors after successive cultivation. In the present research, we demonstrated that subculture with aged mycelia increased the incidence of degenerations. To further investigate the differences between the Fon wild type (sporodochial type, ST) and variants (MT: mycelial type and PT: pionnotal type), developmental phenotypes and pathogenicity to watermelon were examined. Results in variants (PT2, PT3, PT11, and MT6) were different from ST with mycelia growth, conidia production and chlamydospore formation. Virulence of degenerated variants on susceptible watermelon Grand Baby (GB) cultivar was determined after inoculation with Fon variants and Fon ST. In root dipping methods, Fon variants showed no significant differences in disease progress compared with ST. Fon variants showed a significant decrease in disease progression compared with ST through infested soil inoculation. The contrasting results of two inoculation methods suggest that the degenerative changes due to repeated successive cultivation may lead to the loss of pathogen virulence-related factors of the early stage of Fon infection process. Therefore, cell wall-degrading enzymes (CWDEs; cellulase, pectinase, and xylanase) activities of different variants were analyzed. All Fon degenerated variants demonstrated significant decreases of CWDEs activities compared with ST. Additionally, transcript levels of 9 virulence-related genes (fmk1, fgb1, pacC, xlnR, pl1, rho1, gas1, wc1, and fow1) were assessed in normal state. The degenerated variants demonstrated a significantly low level of tested virulence-related gene transcripts except for fmk1, xlnR, and fow1. In summary, the degeneration of Fon is triggered with successive subculture through aged mycelia. The degeneration showed significant impacts on virulence to watermelon, which was correlated with the reduction of CWDEs activities and declining expression of a set of virulence-related genes.
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Affiliation(s)
- Tao-Ho Chang
- Department of Plant Pathology, National Chung Hsing University, Taichung City 402204, Taiwan; (T.-H.C.); (Y.-L.W.); (J.-W.H.)
- Innovation and Development Center of Sustainable Agriculture (IDCSA), National Chung Hsing University, Taichung City 402204, Taiwan
| | - Ying-Hong Lin
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan;
- Plant Medicine Teaching Hospital, General Research Service Center, National Pingtung University of Science and Technology, Pingtung 912301, Taiwan
| | - Yu-Ling Wan
- Department of Plant Pathology, National Chung Hsing University, Taichung City 402204, Taiwan; (T.-H.C.); (Y.-L.W.); (J.-W.H.)
| | - Kan-Shu Chen
- Chiayi Experiment Branch, Taiwan Agricultural Research Institute, Chiayi 611002, Taiwan;
| | - Jenn-Wen Huang
- Department of Plant Pathology, National Chung Hsing University, Taichung City 402204, Taiwan; (T.-H.C.); (Y.-L.W.); (J.-W.H.)
- Innovation and Development Center of Sustainable Agriculture (IDCSA), National Chung Hsing University, Taichung City 402204, Taiwan
| | - Pi-Fang Linda Chang
- Department of Plant Pathology, National Chung Hsing University, Taichung City 402204, Taiwan; (T.-H.C.); (Y.-L.W.); (J.-W.H.)
- Innovation and Development Center of Sustainable Agriculture (IDCSA), National Chung Hsing University, Taichung City 402204, Taiwan
- Correspondence: ; Tel.: +886-422840780 (ext. 330)
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24
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Ben Guerrero E, Salvador R, Talia P. Evaluation of hydrolytic enzyme activities from digestive fluids of Anthonomus grandis (Coleoptera: Curculionidae). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2020; 105:e21730. [PMID: 32737998 DOI: 10.1002/arch.21730] [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: 06/05/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
The cotton boll weevil, Anthonomus grandis, is a major pest of cotton crops in South America. In this work, partial biochemical characterizations of (hemi) cellulases and pectinases activities in the digestive system (head- and gut- extracts) of A. grandis were evaluated. Gut extract section from third instar larvae exhibited endoglucanase, xylanase, β-glucosidase, and pectinase activities. The endoglucanase and xylanase activities were localized in the foregut, whereas β-glucosidase activity was mainly detected in the hindgut. In addition, no difference in pectinase activity was observed across the gut sections. Thus, A. grandis digestive system is a potentially interesting reservoir for further lignocellulolytic enzymes research.
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Affiliation(s)
- Emiliano Ben Guerrero
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Provincia de Buenos Aires, Argentina
| | - Ricardo Salvador
- Instituto de Microbiología y Zoología Agrícola (IMYZA), Hurlingham, Provincia de Buenos Aires, Argentina
| | - Paola Talia
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Provincia de Buenos Aires, Argentina
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25
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Hefferon K, Cantero-Tubilla B, Badar U, Wilson DW. Plant-Based Cellulase Assay Systems as Alternatives for Synthetic Substrates. Appl Biochem Biotechnol 2020; 192:1318-1330. [PMID: 32734581 DOI: 10.1007/s12010-020-03395-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/16/2020] [Indexed: 11/25/2022]
Abstract
Dissociative enzymes such as cellulases are greatly desired for a variety of applications in the food, fuel, and fiber industries. Cellulases and other cell wall-degrading enzymes are currently being engineered with improved traits for application in the breakdown of lignocellulosic biomass. Biochemical assays using these "designer" enzymes have traditionally been carried out using synthetic substrates such as crystalline bacterial microcellulose (BMCC). However, the use of synthetic substrates may not reflect the actual action of these cellulases on real plant biomass. We examined the potential of suspension cell walls from several plant species as possible alternatives for synthetic cellulose substrates. Suspension cells grow synchronously; hence, their cell walls are more uniform than those derived from mature plants. This work will help to establish a new assay system that is more genuine than using synthetic substrates. In addition to this, we have demonstrated that it is feasible to produce cellulases inexpensively and at high concentrations and activities in plants using a recombinant plant virus expression system. Our long-term goals are to use this system to develop tailored cocktails of cellulases that have been engineered to function optimally for specific tasks (i.e., the conversion of biomass into biofuel or the enhancement of nutrients available in livestock feed). The broad impact would be to provide a facile and economic system for generating industrial enzymes that offer green solutions to valorize biomass in industrialized communities and specifically in developing countries.
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Affiliation(s)
- Kathleen Hefferon
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA.
| | - Borja Cantero-Tubilla
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14850, USA
| | - Uzma Badar
- Cell and Systems Biology, University of Toronto, Toronto, Canada
| | - David W Wilson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
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26
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Lopez C, Zhao Y, Masonbrink R, Shao Z. Modulating Pathway Performance by Perturbing Local Genetic Context. ACS Synth Biol 2020; 9:706-717. [PMID: 32207925 DOI: 10.1021/acssynbio.9b00445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Combinatorial engineering is a preferred strategy for attaining optimal pathway performance. Previous endeavors have been concentrated on regulatory elements (e.g., promoters, terminators, and ribosomal binding sites) and/or open reading frames. Accumulating evidence indicates that noncoding DNA sequences flanking a transcriptional unit on the genome strongly impact gene expression. Here, we sought to mimic the effect imposed on expression cassettes by the genome. We created variants of the model yeast Saccharomyces cerevisiae with significantly improved fluorescence or cellobiose consumption rate by randomizing the sequences adjacent to the GFP expression cassette or the cellobiose-utilization pathway, respectively. Interestingly, nucleotide specificity was observed at certain positions and showed to be essential for achieving optimal cellobiose assimilation. Further characterization suggested that the modulation effects of the short sequences flanking the expression cassettes could be potentially mediated by remodeling DNA packaging and/or recruiting transcription factors. Collectively, these results indicate that the often-overlooked contiguous DNA sequences can be exploited to rapidly achieve balanced pathway expression, and the corresponding approach could be easily stacked with other combinatorial engineering strategies.
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Affiliation(s)
- Carmen Lopez
- Interdepartmental Microbiology Program, Iowa State University, Ames, Iowa 50011, United States
| | - Yuxin Zhao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin 300071, China
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Rick Masonbrink
- Office of Biotechnology, Iowa State University, Ames, Iowa 50011, United States
| | - Zengyi Shao
- Interdepartmental Microbiology Program, Iowa State University, Ames, Iowa 50011, United States
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
- NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa 50011, United States
- Ames Laboratory, Ames, Iowa 50011, United States
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27
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Hefferon KL, Cantero‐Tubilla B, Brady J, Wilson D. Aromatic residues surrounding the active site tunnel of TfCel48A influence activity, processivity, and synergistic interactions with other cellulases. Biotechnol Bioeng 2019; 116:2463-2472. [DOI: 10.1002/bit.27086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 05/29/2019] [Accepted: 06/02/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Kathleen L. Hefferon
- Department of Cellular and Molecular GeneticsCornell University Ithaca New York
- Department of Food Science and TechnologyCornell University Ithaca New York
| | - Borja Cantero‐Tubilla
- Robert Frederick Smith School of Chemical and Biomolecular EngineeringCornell University Ithaca New York
| | - John Brady
- Department of Food Science and TechnologyCornell University Ithaca New York
| | - David Wilson
- Department of Cellular and Molecular GeneticsCornell University Ithaca New York
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28
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Borkowska M, Białas W, Kubiak M, Celińska E. Rapid micro-assays for amylolytic activities determination: customization and validation of the tests. Appl Microbiol Biotechnol 2019; 103:2367-2379. [PMID: 30675636 PMCID: PMC6420461 DOI: 10.1007/s00253-018-09610-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/27/2018] [Accepted: 12/28/2018] [Indexed: 02/07/2023]
Abstract
High-throughput function-based screening techniques remain the major bottleneck in the novel biocatalysts development pipeline. In the present study, we customized protocols for amylolytic activity determination (Somogyi-Nelson and starch-iodine tests) to micro-volume thermalcycler-based assays (linearity range 60-600 μM of reducing sugar, R2 = 0.9855; 0-2 mg/mL of starch, R2 = 0.9921, respectively). Exploitation of a thermalcycler enabled rapid and accurate temperature control, further reduction of reagents and samples volumes, and limited evaporation of the reaction mixtures, meeting several crucial requirements of an adequate enzymatic assay. In the optimized micro-volume Somogyi-Nelson protocol, we were able to reduce the time required for high-temperature heating sixfold (down to 5 min) and further increase sensitivity of the assay (tenfold), when compared to the previous MTP-based protocol. The optimized microassays have complementary scope of specificities: micro-starch-iodine test for endoglucanases, micro-Somogyi-Nelson test for exoglucanases. Due to rapid, micro-volume and high-throughput character, the methods can complement toolbox assisting development of novel biocatalysts and analysis of saccharides-containing samples.
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Affiliation(s)
- Monika Borkowska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Wojciech Białas
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Monika Kubiak
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland.
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29
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Chan YW, Acquah C, Obeng EM, Dullah EC, Jeevanandam J, Ongkudon CM. Parametric study of immobilized cellulase-polymethacrylate particle for the hydrolysis of carboxymethyl cellulose. Biochimie 2019; 157:204-212. [DOI: 10.1016/j.biochi.2018.11.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/30/2018] [Indexed: 12/16/2022]
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30
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Chow YY, Ting ASY. Influence of fungal infection on plant tissues: FTIR detects compositional changes to plant cell walls. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2018.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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31
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Truskewycz A, Shukla R, Ball AS. Phytofabrication of Iron Nanoparticles for Hexavalent Chromium Remediation. ACS OMEGA 2018; 3:10781-10790. [PMID: 30411070 PMCID: PMC6199743 DOI: 10.1021/acsomega.8b00410] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 08/07/2018] [Indexed: 05/08/2023]
Abstract
Hexavalent chromium is a genotoxic and carcinogenic byproduct of a number of industrial processes, which is discharged into the environment in excessive and toxic concentrations worldwide. In this paper, the synthesis of green iron oxide nanoparticles using extracts of four novel plant species [Pittosporum undulatum, Melia azedarach, Schinus molle, and Syzygium paniculatum (var. australe)] using a "bottom-up approach" has been implemented for hexavalent chromium remediation. Nanoparticle characterizations show that different plant extracts lead to the formation of nanoparticles with different sizes, agglomeration tendencies, and shapes but similar amorphous nature and elemental makeup. Hexavalent chromium removal is linked with the particle size and monodispersity. Nanoparticles with sizes between 5 and 15 nm from M. azedarach and P. undulatum showed enhanced chromium removal capacities (84.1-96.2%, respectively) when compared to the agglomerated particles of S. molle and S. paniculatum with sizes between 30 and 100 nm (43.7-58.7%, respectively) in over 9 h. This study has shown that the reduction of iron salts with plant extracts is unlikely to generate vast quantities of stable zero valent iron nanoparticles but rather favor the formation of iron oxide nanoparticles. In addition, plant extracts with higher antioxidant concentrations may not produce nanoparticles with morphologies optimal for pollutant remediation.
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Affiliation(s)
- Adam Truskewycz
- Centre
for Environmental Sustainability and Remediation, School of Science, RMIT University, GPO Box 71, Bundoora, Victoria 3083, Australia
- Nanobiotechnology
Research Laboratory and Centre for Advanced Materials & Industrial
Chemistry, School of Science, RMIT University, GPO Box 2476, Melbourne, Victoria 3000, Australia
- E-mail: (A.T.)
| | - Ravi Shukla
- Nanobiotechnology
Research Laboratory and Centre for Advanced Materials & Industrial
Chemistry, School of Science, RMIT University, GPO Box 2476, Melbourne, Victoria 3000, Australia
| | - Andrew S. Ball
- Centre
for Environmental Sustainability and Remediation, School of Science, RMIT University, GPO Box 71, Bundoora, Victoria 3083, Australia
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The workability of Escherichia coli BL21 (DE3) and Pseudomonas putida KT2440 expression platforms with autodisplayed cellulases: a comparison. Appl Microbiol Biotechnol 2018; 102:4829-4841. [DOI: 10.1007/s00253-018-8987-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 04/02/2018] [Accepted: 04/05/2018] [Indexed: 02/07/2023]
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Autotransporter-Based Surface Display of Hemicellulases onPseudomonas putida: Whole-Cell Biocatalysts for the Degradation of Biomass. ChemCatChem 2017. [DOI: 10.1002/cctc.201700577] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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34
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Palacios S, Ruiz HA, Ramos-Gonzalez R, Martínez J, Segura E, Aguilar M, Aguilera A, Michelena G, Aguilar C, Ilyina A. Comparison of physicochemical pretreatments of banana peels for bioethanol production. Food Sci Biotechnol 2017; 26:993-1001. [PMID: 30263629 DOI: 10.1007/s10068-017-0128-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/21/2017] [Accepted: 05/01/2017] [Indexed: 11/24/2022] Open
Abstract
Pretreatments with different concentrations of sulfuric acid (0, 0.5, and 1% v/v) and temperatures (28 and 121 °C at 103 kPa in an autoclave) were performed on banana peels (BP) milled by mechanical grinding and grinding in a blender as well as without grinding. Cellulose, hemicellulose, lignin, ash, and total and reducing sugar contents were evaluated. The highest yields of cellulose enzymatic hydrolysis (99%) were achieved with liquefied autoclaved BP treated with 0.5 and 1% acid after 48 h of hydrolysis. Ethanol production by Kluyveromyces marxianus fermentation was assayed using hydrolyzed BP at 10, 15, and 20% (w/w). The highest ethanol level (21 g/L) was reached after 24 h of fermentation with 20% (w/w) BP. Kinetics of the consumption of reducing sugars under this fermentation condition demonstrates the presence of a lag period (about 8 h). Thus, BP are a good source for ethanol production.
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Affiliation(s)
- Sócrates Palacios
- 1Nanobioscience and Biorefinery Groups, Food Research Department, Chemistry School, Autonomous University of Coahuila, Blvd. V. Carranza e Ing. José Cárdenas Valdés, 25280 Saltillo, Coahuila Mexico.,Faculty of Engineering in Mechanics and Production Sciences, Polytechnic School of Litoral, Km. 30.5 Perimetral Road, Guayaquil, Ecuador
| | - Héctor A Ruiz
- 1Nanobioscience and Biorefinery Groups, Food Research Department, Chemistry School, Autonomous University of Coahuila, Blvd. V. Carranza e Ing. José Cárdenas Valdés, 25280 Saltillo, Coahuila Mexico
| | - Rodolfo Ramos-Gonzalez
- 3CONACYT- Autonomous University of Coahuila, Blvd. V. Carranza e Ing. José Cárdenas Valdés, 25280 Saltillo, Coahuila Mexico
| | - José Martínez
- 1Nanobioscience and Biorefinery Groups, Food Research Department, Chemistry School, Autonomous University of Coahuila, Blvd. V. Carranza e Ing. José Cárdenas Valdés, 25280 Saltillo, Coahuila Mexico
| | - Elda Segura
- 1Nanobioscience and Biorefinery Groups, Food Research Department, Chemistry School, Autonomous University of Coahuila, Blvd. V. Carranza e Ing. José Cárdenas Valdés, 25280 Saltillo, Coahuila Mexico
| | - Miguel Aguilar
- Research Center and Advanced Studies of IPN (CINVESTAV-IPN), 25903 Ramos Arizpe, Coahuila Mexico
| | - Antonio Aguilera
- Antonio Narro Agrarian Autonomous University, Calzada Antonio Narro, 25315 Buenavista, Coahuila Mexico
| | - Georgina Michelena
- ICIDCA - Cuban Research Institute of Derivatives Sugarcane, vía Blanca, S.M. del Padron, La Habana, Cuba
| | - Cristóbal Aguilar
- 1Nanobioscience and Biorefinery Groups, Food Research Department, Chemistry School, Autonomous University of Coahuila, Blvd. V. Carranza e Ing. José Cárdenas Valdés, 25280 Saltillo, Coahuila Mexico
| | - Anna Ilyina
- 1Nanobioscience and Biorefinery Groups, Food Research Department, Chemistry School, Autonomous University of Coahuila, Blvd. V. Carranza e Ing. José Cárdenas Valdés, 25280 Saltillo, Coahuila Mexico
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35
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Obeng EM, Budiman C, Ongkudon CM. Identifying additives for cellulase enhancement—A systematic approach. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2017. [DOI: 10.1016/j.bcab.2017.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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36
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Automated multiplex genome-scale engineering in yeast. Nat Commun 2017; 8:15187. [PMID: 28469255 PMCID: PMC5418614 DOI: 10.1038/ncomms15187] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 03/08/2017] [Indexed: 12/23/2022] Open
Abstract
Genome-scale engineering is indispensable in understanding and engineering microorganisms, but the current tools are mainly limited to bacterial systems. Here we report an automated platform for multiplex genome-scale engineering in Saccharomyces cerevisiae, an important eukaryotic model and widely used microbial cell factory. Standardized genetic parts encoding overexpression and knockdown mutations of >90% yeast genes are created in a single step from a full-length cDNA library. With the aid of CRISPR-Cas, these genetic parts are iteratively integrated into the repetitive genomic sequences in a modular manner using robotic automation. This system allows functional mapping and multiplex optimization on a genome scale for diverse phenotypes including cellulase expression, isobutanol production, glycerol utilization and acetic acid tolerance, and may greatly accelerate future genome-scale engineering endeavours in yeast.
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37
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Alcázar M, Kind T, Gschaedler A, Silveria M, Arrizon J, Fiehn O, Vallejo A, Higuera I, Lugo E. Effect of steroidal saponins from Agave on the polysaccharide cell wall composition of Saccharomyces cerevisiae and Kluyveromyces marxianus. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2016.11.048] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Santos AAD, Deoti JR, Müller G, Dário MG, Stambuk BU, Alves Junior SL. Dosagem de açúcares redutores com o reativo DNS em microplaca. BRAZILIAN JOURNAL OF FOOD TECHNOLOGY 2017. [DOI: 10.1590/1981-6723.11315] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Resumo O método colorimétrico mais amplamente empregado para a determinação de açúcares redutores utiliza o ácido 3,5-dinitrosalicílico (DNS) como agente oxidante. No entanto, essa metodologia clássica demanda grande quantidade de reagente (DNS), amostra e tempo. No intuito de reduzir custo e tempo empregados nos ensaios, adaptamos o método clássico de DNS, realizado em tubos, a um rápido e econômico experimento em microplacas de 96 poços. Os resultados obtidos com essa nova metodologia foram comparados a análises por HPLC em 60 amostras, oriundas de cultivos laboratoriais de leveduras vinícolas, e diferiram em menos de 10%. Assim sendo, esse novo método, que pode ser considerado validado em relação ao método padrão e a análises cromatográficas, revela-se um ensaio rápido e de baixo custo para a determinação de açúcares redutores.
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Ben Guerrero E, Soria M, Salvador R, Ceja-Navarro JA, Campos E, Brodie EL, Talia P. Effect of Different Lignocellulosic Diets on Bacterial Microbiota and Hydrolytic Enzyme Activities in the Gut of the Cotton Boll Weevil ( Anthonomus grandis). Front Microbiol 2016; 7:2093. [PMID: 28082962 PMCID: PMC5186755 DOI: 10.3389/fmicb.2016.02093] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 12/09/2016] [Indexed: 11/13/2022] Open
Abstract
Cotton boll weevils, Anthonomus grandis, are omnivorous coleopteran that can feed on diets with different compositions, including recalcitrant lignocellulosic materials. We characterized the changes in the prokaryotic community structure and the hydrolytic activities of A. grandis larvae fed on different lignocellulosic diets. A. grandis larvae were fed on three different artificial diets: cottonseed meal (CM), Napier grass (NG) and corn stover (CS). Total DNA was extracted from the gut samples for amplification and sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Proteobacteria and Firmicutes dominated the gut microbiota followed by Actinobacteria, Spirochaetes and a small number of unclassified phyla in CM and NG microbiomes. In the CS feeding group, members of Spirochaetes were the most prevalent, followed by Proteobacteria and Firmicutes. Bray-Curtis distances showed that the samples from the CS community were clearly separated from those samples of the CM and NG diets. Gut extracts from all three diets exhibited endoglucanase, xylanase, β-glucosidase and pectinase activities. These activities were significantly affected by pH and temperature across different diets. We observed that the larvae reared on a CM showed significantly higher activities than larvae reared on NG and CS. We demonstrated that the intestinal bacterial community structure varies depending on diet composition. Diets with more variable and complex compositions, such as CS, showed higher bacterial diversity and richness than the two other diets. In spite of the detected changes in composition and diversity, we identified a core microbiome shared between the three different lignocellulosic diets. These results suggest that feeding with diets of different lignocellulosic composition could be a viable strategy to discover variants of hemicellulose and cellulose breakdown systems.
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Affiliation(s)
- Emiliano Ben Guerrero
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Centro Nacional de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria Castelar Hurlingham, Argentina
| | - Marcelo Soria
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales-Consejo Nacional de Investigaciones Científicas y Técnicas, Cátedra de Microbiología Agrícola, Facultad de Agronomía, Universidad de Buenos Aires Buenos Aires, Argentina
| | - Ricardo Salvador
- Instituto de Microbiología y Zoología Agrícola, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Centro Nacional de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria Castelar Hurlingham, Argentina
| | - Javier A Ceja-Navarro
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Eleonora Campos
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Centro Nacional de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria CastelarHurlingham, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Buenos Aires, Argentina
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Paola Talia
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Centro Nacional de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria CastelarHurlingham, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Buenos Aires, Argentina
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Tozakidis IEP, Brossette T, Lenz F, Maas RM, Jose J. Proof of concept for the simplified breakdown of cellulose by combining Pseudomonas putida strains with surface displayed thermophilic endocellulase, exocellulase and β-glucosidase. Microb Cell Fact 2016; 15:103. [PMID: 27287198 PMCID: PMC4901517 DOI: 10.1186/s12934-016-0505-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 06/01/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The production and employment of cellulases still represents an economic bottleneck in the conversion of lignocellulosic biomass to biofuels and other biocommodities. This process could be simplified by displaying the necessary enzymes on a microbial cell surface. Such an approach, however, requires an appropriate host organism which on the one hand can withstand the rough environment coming along with lignocellulose hydrolysis, and on the other hand does not consume the generated glucose so that it remains available for subsequent fermentation steps. RESULTS The robust soil bacterium Pseudomonas putida showed a strongly reduced uptake of glucose above a temperature of 50 °C, while remaining structurally intact hence recyclable, which makes it suitable for cellulose hydrolysis at elevated temperatures. Consequently, three complementary, thermophilic cellulases from Ruminiclostridium thermocellum were displayed on the surface of the bacterium. All three enzymes retained their activity on the cell surface. A mixture of three strains displaying each one of these enzymes was able to synergistically hydrolyze filter paper at 55 °C, producing 20 μg glucose per mL cell suspension in 24 h. CONCLUSION We could establish Pseudomonas putida as host for the surface display of cellulases, and provided proof-of-concept for a fast and simple cellulose breakdown process at elevated temperatures. This study opens up new perspectives for the application of P. putida in the production of biofuels and other biotechnological products.
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Affiliation(s)
- Iasson E P Tozakidis
- Institute of Pharmaceutical and Medicinal Chemistry, Westfälische Wilhelms-Universität Münster, PharmaCampus, Corrensstraße 48, 48149, Münster, Germany.,NRW Graduate School of Chemistry, Westfälische Wilhelms-Universität Münster, PharmaCampus, Corrensstraße 48, 48149, Münster, Germany
| | - Tatjana Brossette
- Autodisplay Biotech GmbH, Merowingerplatz 1a, 40225, Düsseldorf, Germany
| | - Florian Lenz
- Institute of Pharmaceutical and Medicinal Chemistry, Westfälische Wilhelms-Universität Münster, PharmaCampus, Corrensstraße 48, 48149, Münster, Germany
| | - Ruth M Maas
- Autodisplay Biotech GmbH, Merowingerplatz 1a, 40225, Düsseldorf, Germany
| | - Joachim Jose
- Institute of Pharmaceutical and Medicinal Chemistry, Westfälische Wilhelms-Universität Münster, PharmaCampus, Corrensstraße 48, 48149, Münster, Germany. .,NRW Graduate School of Chemistry, Westfälische Wilhelms-Universität Münster, PharmaCampus, Corrensstraße 48, 48149, Münster, Germany.
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Willson BJ, Kovács K, Wilding-Steele T, Markus R, Winzer K, Minton NP. Production of a functional cell wall-anchored minicellulosome by recombinant Clostridium acetobutylicum ATCC 824. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:109. [PMID: 27222664 PMCID: PMC4877998 DOI: 10.1186/s13068-016-0526-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 05/10/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND The use of fossil fuels is no longer tenable. Not only are they a finite resource, their use is damaging the environment through pollution and global warming. Alternative, environmentally friendly, renewable sources of chemicals and fuels are required. To date, the focus has been on using lignocellulose as a feedstock for microbial fermentation. However, its recalcitrance to deconstruction is making the development of economic processes extremely challenging. One solution is the generation of an organism suitable for use in consolidated bioprocessing (CBP), i.e. one able to both hydrolyse lignocellulose and ferment the released sugars, and this represents an important goal for synthetic biology. We aim to use synthetic biology to develop the solventogenic bacterium C. acetobutylicum as a CBP organism through the introduction of a cellulosome, a complex of cellulolytic enzymes bound to a scaffold protein called a scaffoldin. In previous work, we were able to demonstrate the in vivo production of a C. thermocellum-derived minicellulosome by recombinant strains of C. acetobutylicum, and aim to develop on this success, addressing potential issues with the previous strategy. RESULTS The genes for the cellulosomal enzymes Cel9G, Cel48F, and Xyn10A from C. cellulolyticum were integrated into the C. acetobutylicum genome using Allele-Coupled Exchange (ACE) technology, along with a miniscaffoldin derived from C. cellulolyticum CipC. The possibility of anchoring the recombinant cellulosome to the cell surface using the native sortase system was assessed, and the cellulolytic properties of the recombinant strains were assayed via plate growth, batch fermentation and sugar release assays. CONCLUSIONS We have been able to demonstrate the synthesis and in vivo assembly of a four-component minicellulosome by recombinant C. acetobutylicum strains. Furthermore, we have been able to anchor a minicellulosome to the C. acetobutylicum cell wall by the use of the native sortase system. The recombinant strains display an improved growth phenotype on xylan and an increase in released reducing sugar from several substrates including untreated powdered wheat straw. This constitutes an important milestone towards the development of a truly cellulolytic strain suitable for CBP.
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Affiliation(s)
- Benjamin J. Willson
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Katalin Kovács
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Tom Wilding-Steele
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Robert Markus
- />SLIM Imaging Unit, Faculty of Medicine and Health Sciences, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Klaus Winzer
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
| | - Nigel P. Minton
- />Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD UK
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Visvanathan R, Jayathilake C, Liyanage R. A simple microplate-based method for the determination of α-amylase activity using the glucose assay kit (GOD method). Food Chem 2016; 211:853-9. [PMID: 27283705 DOI: 10.1016/j.foodchem.2016.05.090] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 05/11/2016] [Accepted: 05/13/2016] [Indexed: 11/17/2022]
Abstract
For the first time, a reliable, simple, rapid and high-throughput analytical method for the detection and quantification of α-amylase inhibitory activity using the glucose assay kit was developed. The new method facilitates rapid screening of a large number of samples, reduces labor, time and reagents and is also suitable for kinetic studies. This method is based on the reaction of maltose with glucose oxidase (GOD) and the development of a red quinone. The test is done in microtitre plates with a total volume of 260μL and an assay time of 40min including the pre-incubation steps. The new method is tested for linearity, sensitivity, precision, reproducibility and applicability. The new method is also compared with the most commonly used 3,5-dinitrosalicylic acid (DNSA) method for determining α-amylase activity.
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Affiliation(s)
- Rizliya Visvanathan
- Division of Nutritional Biochemistry, National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka; Postgraduate Institute of Science, University of Peradeniya, Sri Lanka.
| | - Chathuni Jayathilake
- Division of Nutritional Biochemistry, National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka.
| | - Ruvini Liyanage
- Division of Nutritional Biochemistry, National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka.
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Hildebrand A, Bennett Addison J, Kasuga T, Fan Z. Cellobionic acid inhibition of cellobiohydrolase I and cellobiose dehydrogenase. Biochem Eng J 2016. [DOI: 10.1016/j.bej.2016.01.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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44
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Cellulases: Classification, Methods of Determination and Industrial Applications. Appl Biochem Biotechnol 2016; 179:1346-80. [PMID: 27068832 DOI: 10.1007/s12010-016-2070-3] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 03/31/2016] [Indexed: 10/22/2022]
Abstract
Microbial cellulases have been receiving worldwide attention, as they have enormous potential to process the most abundant cellulosic biomass on this planet and transform it into sustainable biofuels and other value added products. The synergistic action of endoglucanases, exoglucanases, and β-glucosidases is required for the depolymerization of cellulose to fermentable sugars for transformation in to useful products using suitable microorganisms. The lack of a better understanding of the mechanisms of individual cellulases and their synergistic actions is the major hurdles yet to be overcome for large-scale commercial applications of cellulases. We have reviewed various microbial cellulases with a focus on their classification with mechanistic aspects of cellulase hydrolytic action, insights into novel approaches for determining cellulase activity, and potential industrial applications of cellulases.
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45
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Production control and characterization of antibacterial carotenoids from the yeast Rhodotorula mucilaginosa AY-01. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.01.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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46
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Solomon KV, Haitjema CH, Henske JK, Gilmore SP, Borges-Rivera D, Lipzen A, Brewer HM, Purvine SO, Wright AT, Theodorou MK, Grigoriev IV, Regev A, Thompson DA, O'Malley MA. Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes. Science 2016; 351:1192-5. [PMID: 26912365 PMCID: PMC5098331 DOI: 10.1126/science.aad1431] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/09/2016] [Indexed: 01/22/2023]
Abstract
The fungal kingdom is the source of almost all industrial enzymes in use for lignocellulose bioprocessing. We developed a systems-level approach that integrates transcriptomic sequencing, proteomics, phenotype, and biochemical studies of relatively unexplored basal fungi. Anaerobic gut fungi isolated from herbivores produce a large array of biomass-degrading enzymes that synergistically degrade crude, untreated plant biomass and are competitive with optimized commercial preparations from Aspergillus and Trichoderma. Compared to these model platforms, gut fungal enzymes are unbiased in substrate preference due to a wealth of xylan-degrading enzymes. These enzymes are universally catabolite-repressed and are further regulated by a rich landscape of noncoding regulatory RNAs. Additionally, we identified several promising sequence-divergent enzyme candidates for lignocellulosic bioprocessing.
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Affiliation(s)
- Kevin V Solomon
- Department of Chemical Engineering, University of California, Santa Barbara (UCSB), Santa Barbara, CA 93106, USA
| | - Charles H Haitjema
- Department of Chemical Engineering, University of California, Santa Barbara (UCSB), Santa Barbara, CA 93106, USA
| | - John K Henske
- Department of Chemical Engineering, University of California, Santa Barbara (UCSB), Santa Barbara, CA 93106, USA
| | - Sean P Gilmore
- Department of Chemical Engineering, University of California, Santa Barbara (UCSB), Santa Barbara, CA 93106, USA
| | | | - Anna Lipzen
- U.S. Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Heather M Brewer
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA. Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Samuel O Purvine
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA. Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Aaron T Wright
- Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Michael K Theodorou
- Animal Production, Welfare and Veterinary Sciences, Harper Adams University, Newport, Shropshire TF10 8NB, UK
| | - Igor V Grigoriev
- U.S. Department of Energy (DOE) Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02143, USA
| | - Dawn A Thompson
- Broad Institute of MIT and Harvard, Cambridge, MA 02143, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara (UCSB), Santa Barbara, CA 93106, USA.
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Yu X, Liu Y, Cui Y, Cheng Q, Zhang Z, Lu JH, Meng Q, Teng L, Ren X. Measurement of filter paper activities of cellulase with microplate-based assay. Saudi J Biol Sci 2016; 23:S93-8. [PMID: 26858572 PMCID: PMC4705267 DOI: 10.1016/j.sjbs.2015.06.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 06/19/2015] [Accepted: 06/20/2015] [Indexed: 11/05/2022] Open
Abstract
It is always a challenge to determine the total cellulase activity efficiently without reducing accuracy. The most common total cellulase activity assay is the filter paper assay (FPA) established by the International Union of Pure and Applied Chemistry (IUPAC). A new procedure to measure the FPA with microplate-based assay was studied in this work, which followed the main idea of IUPAC to dilute cellulase preparation to get fixed glucose release. FPAs of six cellulase preparations were determined with the microplate-based assay. It is shown that FPAs of cellulase Youtell, RCconc, R-10, Lerkam, Yishui and Sinopharm were 67.9, 46.0, 46.1, 27.4, 7.6 and 8.0 IU/ml respectively. There was no significant difference at the 95% confidence level between the FPA determined with IUPAC and the microplate-based assay. It could be concluded that the FPA could be determined by the microplate-based assay with the same accuracy and much more efficiency compared with that by IUPAC.
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Affiliation(s)
- Xiaoxiao Yu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun 130023, China
| | - Yan Liu
- School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Yuxiao Cui
- School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Qiyue Cheng
- School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Zaixiao Zhang
- School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Jia Hui Lu
- School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Qingfan Meng
- School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Lirong Teng
- School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
| | - Xiaodong Ren
- School of Life Sciences, Jilin University, Changchun, Jilin 130012, China
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Puente-Garza CA, Gutiérrez-Mora A, García-Lara S. Micropropagation of Agave salmiana: Means to Production of Antioxidant and Bioactive Principles. FRONTIERS IN PLANT SCIENCE 2015; 6:1026. [PMID: 26635850 PMCID: PMC4655248 DOI: 10.3389/fpls.2015.01026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 11/05/2015] [Indexed: 05/30/2023]
Abstract
Maguey, Agave salmiana, is an important plant for the "pulque" beverage and functional food industries; however, it has several constraints for elite and homogeneous plant production. In this study, a micropropagation process was established to generate in vitro plants. The effect of the method on metabolite content and antioxidant (AOX) activity in regenerated plants was evaluated. Young germinated plantlets were micropropagated from axillary shoots using Murashige and Skoog medium supplemented with L2 vitamins, 0.04 mg/L 2,4-dichlorophenoxyacetic acid and 10 mg/L 6-benzylaminopurine. Total soluble sugars from the aqueous fraction and total phenolic acids, total saponins, and AOX activity of the methanol fraction were determined in wild-type (WT) plants, in in vitro (IN) plants, and ex vitro acclimated plants (EN). The results showed that IN plants have a 50% lower soluble sugar content compared to WT, and EN. The total phenolic acids content was at least 30% higher in micropropagated (IN) and regenerated (EN) plants compared to WT. The total saponin content in IN, and EN plants was 36 and 25 times higher compared to WT. The AOX capacity of IN plants was on average three times higher compared to other treatments. However, no correlation was found between the AOX activity and total phenolic acids or total saponins. A negative and significant correlation (r = -0.927; p = 0.003) was found between the AOX activity and the total soluble sugars content. Micropropagated plants of A. salmiana have a different phytochemical content and bioactivity after the in vitro process compared to WT plants. The micropropagation process could be used as a platform for phytochemical enhancement of Agave plants.
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Affiliation(s)
- César A. Puente-Garza
- Plant-Food Molecular Breeding Unit, Escuela de Ingenieria y Ciencias, Tecnologico de Monterrey, Campus MonterreyMonterrey, Mexico
| | - Antonia Gutiérrez-Mora
- Unidad de Biotecnología Vegetal, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de JaliscoGuadalajara, Mexico
| | - Silverio García-Lara
- Plant-Food Molecular Breeding Unit, Escuela de Ingenieria y Ciencias, Tecnologico de Monterrey, Campus MonterreyMonterrey, Mexico
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49
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Prospection and Evaluation of (Hemi) Cellulolytic Enzymes Using Untreated and Pretreated Biomasses in Two Argentinean Native Termites. PLoS One 2015; 10:e0136573. [PMID: 26313257 PMCID: PMC4552170 DOI: 10.1371/journal.pone.0136573] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 08/04/2015] [Indexed: 01/30/2023] Open
Abstract
Saccharum officinarum bagasse (common name: sugarcane bagasse) and Pennisetum purpureum (also known as Napier grass) are among the most promising feedstocks for bioethanol production in Argentina and Brazil. In this study, both biomasses were assessed before and after acid pretreatment and following hydrolysis with Nasutitermes aquilinus and Cortaritermes fulviceps termite gut digestome. The chemical composition analysis of the biomasses after diluted acid pretreatment showed that the hemicellulose fraction was partially removed. The (hemi) cellulolytic activities were evaluated in bacterial culture supernatants of termite gut homogenates grown in treated and untreated biomasses. In all cases, we detected significantly higher endoglucanase and xylanase activities using pretreated biomasses compared to untreated biomasses, carboxymethylcellulose and xylan. Several protein bands with (hemi) cellulolytic activity were detected in zymograms and two-dimensional gel electrophoresis. Some proteins of these bands or spots were identified as xylanolytic peptides by mass spectrometry. Finally, the diversity of cultured cellulolytic bacterial endosymbionts associated to both Argentinean native termite species was analyzed. This study describes, for the first time, bacterial endosymbionts and endogenous (hemi) cellulases of two Argentinean native termites as well as their potential application in degradation of lignocellulosic biomass for bioethanol production.
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50
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Malinowska KH, Rind T, Verdorfer T, Gaub HE, Nash MA. Quantifying Synergy, Thermostability, and Targeting of Cellulolytic Enzymes and Cellulosomes with Polymerization-Based Amplification. Anal Chem 2015; 87:7133-40. [DOI: 10.1021/acs.analchem.5b00936] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Klara H. Malinowska
- Lehrstuhl für Angewandte
Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Thomas Rind
- Lehrstuhl für Angewandte
Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Tobias Verdorfer
- Lehrstuhl für Angewandte
Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Hermann E. Gaub
- Lehrstuhl für Angewandte
Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
| | - Michael A. Nash
- Lehrstuhl für Angewandte
Physik and Center for Nanoscience, Ludwig-Maximilians-Universität, 80799 Munich, Germany
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