1
|
Chorozian K, Karnaouri A, Tryfona T, Kondyli NG, Karantonis A, Topakas E. Characterization of a novel AA16 lytic polysaccharide monooxygenase from Thermothelomyces thermophilus and comparison of biochemical properties with an LPMO from AA9 family. Carbohydr Polym 2024; 342:122387. [PMID: 39048228 DOI: 10.1016/j.carbpol.2024.122387] [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: 02/21/2024] [Revised: 06/01/2024] [Accepted: 06/07/2024] [Indexed: 07/27/2024]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes which are categorized in the CAZy database under auxiliary activities families AA9-11, 13, 14-17. Secreted by various microorganisms, they play a crucial role in carbon recycling, particularly in fungal saprotrophs. LPMOs oxidize polysaccharides through monooxygenase/peroxygenase activities and exhibit peroxidase and oxidase activities, with variations among different families. AA16, a newly identified LPMO family, is noteworthy due to limited studies on its members, thus rendering the characterization of AA16 enzymes vital for addressing controversies around their functions. This study focused on heterologous expression and biochemical study of an AA16 LPMO from Thermothelomyces thermophilus (formerly known as Myceliophthora thermophila), namely MtLPMO16A. Substrate specificity evaluation of MtLPMO16A showed oxidative cleavage of hemicellulosic substrates and no activity on cellulose, accompanied by a strong oxidase activity. A comparative analysis with an LPMO from AA9 family explored correlations between these families, while MtLPMO16A was shown to boost the activity of some AA9 family LPMOs. The results offer new insights into the AA16 family's action mode and microbial hemicellulose decomposition mechanisms in nature.
Collapse
Affiliation(s)
- Koar Chorozian
- Ιndustrial Biotechnology & Biocatalysis Group, School of Chemical Engineering, National Technical University of Athens, Zografou Campus, 15772, Greece
| | - Anthi Karnaouri
- Laboratory of General and Agricultural Microbiology, Department of Crop Science, Agricultural University of Athens, Athens 11855, Greece.
| | - Theodora Tryfona
- Department of Biochemistry, School of Biological Sciences, University of Cambridge, Cambridge CB2 1QW, UK
| | - Nefeli Georgaki Kondyli
- Ιndustrial Biotechnology & Biocatalysis Group, School of Chemical Engineering, National Technical University of Athens, Zografou Campus, 15772, Greece; Laboratory of Physical Chemistry and Applied Electrochemistry, School of Chemical Engineering, National Technical University of Athens, Zografou Campus, 15780, Greece
| | - Antonis Karantonis
- Laboratory of Physical Chemistry and Applied Electrochemistry, School of Chemical Engineering, National Technical University of Athens, Zografou Campus, 15780, Greece
| | - Evangelos Topakas
- Ιndustrial Biotechnology & Biocatalysis Group, School of Chemical Engineering, National Technical University of Athens, Zografou Campus, 15772, Greece.
| |
Collapse
|
2
|
Munzone A, Eijsink VGH, Berrin JG, Bissaro B. Expanding the catalytic landscape of metalloenzymes with lytic polysaccharide monooxygenases. Nat Rev Chem 2024; 8:106-119. [PMID: 38200220 DOI: 10.1038/s41570-023-00565-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2023] [Indexed: 01/12/2024]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) have an essential role in global carbon cycle, industrial biomass processing and microbial pathogenicity by catalysing the oxidative cleavage of recalcitrant polysaccharides. Despite initially being considered monooxygenases, experimental and theoretical studies show that LPMOs are essentially peroxygenases, using a single copper ion and H2O2 for C-H bond oxygenation. Here, we examine LPMO catalysis, emphasizing key studies that have shaped our comprehension of their function, and address side and competing reactions that have partially obscured our understanding. Then, we compare this novel copper-peroxygenase reaction with reactions catalysed by haem iron enzymes, highlighting the different chemistries at play. We conclude by addressing some open questions surrounding LPMO catalysis, including the importance of peroxygenase and monooxygenase reactions in biological contexts, how LPMOs modulate copper site reactivity and potential protective mechanisms against oxidative damage.
Collapse
Affiliation(s)
- Alessia Munzone
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, France
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Jean-Guy Berrin
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, France
| | - Bastien Bissaro
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, France.
| |
Collapse
|
3
|
Kipping L, Jehmlich N, Moll J, Noll M, Gossner MM, Van Den Bossche T, Edelmann P, Borken W, Hofrichter M, Kellner H. Enzymatic machinery of wood-inhabiting fungi that degrade temperate tree species. THE ISME JOURNAL 2024; 18:wrae050. [PMID: 38519103 PMCID: PMC11022342 DOI: 10.1093/ismejo/wrae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/19/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
Deadwood provides habitat for fungi and serves diverse ecological functions in forests. We already have profound knowledge of fungal assembly processes, physiological and enzymatic activities, and resulting physico-chemical changes during deadwood decay. However, in situ detection and identification methods, fungal origins, and a mechanistic understanding of the main lignocellulolytic enzymes are lacking. This study used metaproteomics to detect the main extracellular lignocellulolytic enzymes in 12 tree species in a temperate forest that have decomposed for 8 ½ years. Mainly white-rot (and few brown-rot) Basidiomycota were identified as the main wood decomposers, with Armillaria as the dominant genus; additionally, several soft-rot xylariaceous Ascomycota were identified. The key enzymes involved in lignocellulolysis included manganese peroxidase, peroxide-producing alcohol oxidases, laccase, diverse glycoside hydrolases (cellulase, glucosidase, xylanase), esterases, and lytic polysaccharide monooxygenases. The fungal community and enzyme composition differed among the 12 tree species. Ascomycota species were more prevalent in angiosperm logs than in gymnosperm logs. Regarding lignocellulolysis as a function, the extracellular enzyme toolbox acted simultaneously and was interrelated (e.g. peroxidases and peroxide-producing enzymes were strongly correlated), highly functionally redundant, and present in all logs. In summary, our in situ study provides comprehensive and detailed insight into the enzymatic machinery of wood-inhabiting fungi in temperate tree species. These findings will allow us to relate changes in environmental factors to lignocellulolysis as an ecosystem function in the future.
Collapse
Affiliation(s)
- Lydia Kipping
- Department of Molecular Toxicology, Helmholtz-Centre for Environmental Research—UFZ GmbH, 04318 Leipzig, Germany
- Institute for Bioanalysis, University of Applied Sciences Coburg, 96450 Coburg, Germany
| | - Nico Jehmlich
- Department of Molecular Toxicology, Helmholtz-Centre for Environmental Research—UFZ GmbH, 04318 Leipzig, Germany
| | - Julia Moll
- Department of Soil Ecology, Helmholtz Centre for Environmental Research—UFZ GmbH, 06120 Halle (Saale), Germany
| | - Matthias Noll
- Institute for Bioanalysis, University of Applied Sciences Coburg, 96450 Coburg, Germany
- Department of Soil Ecology, University of Bayreuth, 95448 Bayreuth, Germany
| | - Martin M Gossner
- Forest Entomology, Swiss Federal Research Institute WSL, 8903 Birmensdorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, ETH Zürich, 8092 Zürich, Switzerland
| | - Tim Van Den Bossche
- VIB—UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9052 Ghent, Belgium
| | - Pascal Edelmann
- Department of Ecology and Ecosystem Management, Center of School of Life and Food Sciences Weihenstephan, TU München, 85354 Freising, Germany
| | - Werner Borken
- Department of Soil Ecology, University of Bayreuth, 95448 Bayreuth, Germany
| | - Martin Hofrichter
- Department of Bio- and Environmental Sciences, International Institute Zittau, TU Dresden, 02763 Zittau, Germany
| | - Harald Kellner
- Department of Bio- and Environmental Sciences, International Institute Zittau, TU Dresden, 02763 Zittau, Germany
| |
Collapse
|
4
|
Qin X, Yang K, Wang X, Tu T, Wang Y, Zhang J, Su X, Yao B, Huang H, Luo H. Insights into the H 2O 2-Driven Lytic Polysaccharide Monooxygenase Activity on Efficient Cellulose Degradation in the White Rot Fungus Irpex lacteus. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:8104-8111. [PMID: 37204864 DOI: 10.1021/acs.jafc.3c01777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In contrast to O2, H2O2 as the cosubstrate for lytic polysaccharide monooxygenases (LPMOs) exhibits great advantages in industrial settings for cellulose degradation. However, H2O2-driven LPMO reactions from natural microorganisms have not been fully explored and understood. Herein, secretome analysis unraveled the H2O2-driven LPMO reaction in the efficient lignocellulose-degrading fungus Irpex lacteus, including LPMOs with different oxidative regioselectivities and various H2O2-generating oxidases. Biochemical characterization of H2O2-driven LPMO catalysis showed orders of magnitude improvement in catalytic efficiency compared to that of O2-driven LPMO catalysis for cellulose degradation. Significantly, H2O2 tolerance of LPMO catalysis in I. lacteus was an order of magnitude higher than that in other filamentous fungi. In addition, natural reductants, gallic acid, in particular, presented in lignocellulosic biomass could sufficiently maintain LPMO catalytic reactions. Moreover, the H2O2-driven LPMO catalysis exhibited synergy with canonical endoglucanases for efficient cellulose degradation. Taken together, these findings demonstrate the great application potential of the H2O2-driven LPMO catalysis for upgrading cellulase cocktails to further improve cellulose degradation efficiency.
Collapse
Affiliation(s)
- Xing Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Kun Yang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuan Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jie Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoyun Su
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| |
Collapse
|
5
|
Benatti ALT, Polizeli MDLTDM. Lignocellulolytic Biocatalysts: The Main Players Involved in Multiple Biotechnological Processes for Biomass Valorization. Microorganisms 2023; 11:microorganisms11010162. [PMID: 36677454 PMCID: PMC9864444 DOI: 10.3390/microorganisms11010162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/11/2022] [Accepted: 12/26/2022] [Indexed: 01/10/2023] Open
Abstract
Human population growth, industrialization, and globalization have caused several pressures on the planet's natural resources, culminating in the severe climate and environmental crisis which we are facing. Aiming to remedy and mitigate the impact of human activities on the environment, the use of lignocellulolytic enzymes for biofuel production, food, bioremediation, and other various industries, is presented as a more sustainable alternative. These enzymes are characterized as a group of enzymes capable of breaking down lignocellulosic biomass into its different monomer units, making it accessible for bioconversion into various products and applications in the most diverse industries. Among all the organisms that produce lignocellulolytic enzymes, microorganisms are seen as the primary sources for obtaining them. Therefore, this review proposes to discuss the fundamental aspects of the enzymes forming lignocellulolytic systems and the main microorganisms used to obtain them. In addition, different possible industrial applications for these enzymes will be discussed, as well as information about their production modes and considerations about recent advances and future perspectives in research in pursuit of expanding lignocellulolytic enzyme uses at an industrial scale.
Collapse
|
6
|
Tong X, He Z, Zheng L, Pande H, Ni Y. Enzymatic treatment processes for the production of cellulose nanomaterials: A review. Carbohydr Polym 2023; 299:120199. [PMID: 36876810 DOI: 10.1016/j.carbpol.2022.120199] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/09/2022]
Abstract
Cellulose nanomaterials have attracted much attention in recent years because of their unique properties. Commercial or semi-commercial production of nanocellulose has been reported in recent years. Mechanical treatments for nanocellulose production are viable but highly energy-intensive. Chemical processes are well reported; however, these chemical processes are not only costly, but also cause environmental concerns and end-use related challenges. This review summarizes recent researches on enzymatic treatment of cellulose fibers for the production of cellulose nanomaterials, with focus on novel enzymatic processes with xylanase and lytic polysaccharide monooxygenases (LPMO) to enhance the efficacy of cellulase. Different enzymes are discussed, including endoglucanase, exoglucanase and xylanase, as well as LPMO, with emphasis on the accessibility and hydrolytic specificity of LPMO enzymes to cellulose fiber structures. LPMO acts in a synergistic way with cellulase to cause significant physical and chemical changes to the cellulose fiber cell-wall structures, which facilitate the nano-fibrillation of the fibers.
Collapse
Affiliation(s)
- Xin Tong
- Department of Chemical Engineering, Limerick Pulp and Paper Centre, University of New Brunswick, Fredericton, NB E3B5A3, Canada; Key Laboratory of Recycling and Eco-treatment of Waste Biomass of Zhejiang Province, Zhejiang University of Science and Technology, Hangzhou 310023, PR China
| | - Zhibin He
- Department of Chemical Engineering, Limerick Pulp and Paper Centre, University of New Brunswick, Fredericton, NB E3B5A3, Canada.
| | - Linqiang Zheng
- Department of Chemical Engineering, Limerick Pulp and Paper Centre, University of New Brunswick, Fredericton, NB E3B5A3, Canada
| | - Harshad Pande
- Domtar Corporation, 395 Blvd Maisonneuve West, Montreal, PQ H3A 1L6, Canada
| | - Yonghao Ni
- Department of Chemical Engineering, Limerick Pulp and Paper Centre, University of New Brunswick, Fredericton, NB E3B5A3, Canada
| |
Collapse
|
7
|
Hodge JG, Zamierowski DS, Robinson JL, Mellott AJ. Evaluating polymeric biomaterials to improve next generation wound dressing design. Biomater Res 2022; 26:50. [PMID: 36183134 PMCID: PMC9526981 DOI: 10.1186/s40824-022-00291-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 08/28/2022] [Indexed: 11/24/2022] Open
Abstract
Wound healing is a dynamic series of interconnected events with the ultimate goal of promoting neotissue formation and restoration of anatomical function. Yet, the complexity of wound healing can often result in development of complex, chronic wounds, which currently results in a significant strain and burden to our healthcare system. The advancement of new and effective wound care therapies remains a critical issue, with the current therapeutic modalities often remaining inadequate. Notably, the field of tissue engineering has grown significantly in the last several years, in part, due to the diverse properties and applications of polymeric biomaterials. The interdisciplinary cohesion of the chemical, biological, physical, and material sciences is pertinent to advancing our current understanding of biomaterials and generating new wound care modalities. However, there is still room for closing the gap between the clinical and material science realms in order to more effectively develop novel wound care therapies that aid in the treatment of complex wounds. Thus, in this review, we discuss key material science principles in the context of polymeric biomaterials, provide a clinical breadth to discuss how these properties affect wound dressing design, and the role of polymeric biomaterials in the innovation and design of the next generation of wound dressings.
Collapse
Affiliation(s)
- Jacob G Hodge
- Bioengineering Graduate Program, University of Kansas, Lawrence, KS, USA.,Department of Plastic Surgery, University of Kansas Medical Center, Kansas City, KS, USA
| | - David S Zamierowski
- Department of Plastic Surgery, University of Kansas Medical Center, Kansas City, KS, USA
| | - Jennifer L Robinson
- Department of Chemical and Petroleum Engineering, University of Kansas, Mail Stop: 3051, 3901 Rainbow Blvd, Lawrence, KS, 66160, USA
| | - Adam J Mellott
- Department of Plastic Surgery, University of Kansas Medical Center, Kansas City, KS, USA.
| |
Collapse
|
8
|
Mattoo AJ, Nonzom S. Endophytes in Lignin Valorization: A Novel Approach. Front Bioeng Biotechnol 2022; 10:895414. [PMID: 35928943 PMCID: PMC9343868 DOI: 10.3389/fbioe.2022.895414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 06/23/2022] [Indexed: 11/29/2022] Open
Abstract
Lignin, one of the essential components of lignocellulosic biomass, comprises an abundant renewable aromatic resource on the planet earth. Although 15%––40% of lignocellulose pertains to lignin, its annual valorization rate is less than 2% which raises the concern to harness and/or develop effective technologies for its valorization. The basic hindrance lies in the structural heterogeneity, complexity, and stability of lignin that collectively makes it difficult to depolymerize and yield common products. Recently, microbial delignification, an eco-friendly and cheaper technique, has attracted the attention due to the diverse metabolisms of microbes that can channelize multiple lignin-based products into specific target compounds. Also, endophytes, a fascinating group of microbes residing asymptomatically within the plant tissues, exhibit marvellous lignin deconstruction potential. Apart from novel sources for potent and stable ligninases, endophytes share immense ability of depolymerizing lignin into desired valuable products. Despite their efficacy, ligninolytic studies on endophytes are meagre with incomplete understanding of the pathways involved at the molecular level. In the recent years, improvement of thermochemical methods has received much attention, however, we lagged in exploring the novel microbial groups for their delignification efficiency and optimization of this ability. This review summarizes the currently available knowledge about endophytic delignification potential with special emphasis on underlying mechanism of biological funnelling for the production of valuable products. It also highlights the recent advancements in developing the most intriguing methods to depolymerize lignin. Comparative account of thermochemical and biological techniques is accentuated with special emphasis on biological/microbial degradation. Exploring potent biological agents for delignification and focussing on the basic challenges in enhancing lignin valorization and overcoming them could make this renewable resource a promising tool to accomplish Sustainable Development Goals (SDG’s) which are supposed to be achieved by 2030.
Collapse
Affiliation(s)
| | - Skarma Nonzom
- *Correspondence: Skarma Nonzom, , orcid.org/0000-0001-9372-7900
| |
Collapse
|
9
|
Nero G, Kivirand K, Ben Othman S, Rinken T. Amperometric method for the determination of cellulase activity and its optimization using response surface method. J Anal Sci Technol 2022. [DOI: 10.1186/s40543-022-00331-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
AbstractCellulases are a group of enzymes, which catalyse different steps of cellulose hydrolysis, and are broadly used in industry as unpurified mixtures of several enzymes. The total activity of cellulase is defined as the ability of the enzyme to produce glucose, which is the final product of cellulose hydrolysis, and is expressed in cellulase units. However, common strategies for the determination of the cellulolytic activity of industrial cellulase preparations are based on the assessment of different steps of cellulose hydrolysis, and the results obtained with different methods are not similar. The aim of the present study was to develop an assay for the determination of cellulase activity that relies on the amperometric determination of the final product of cellulose hydrolysis glucose. The assay conditions were optimized using response surface methodology (RSM) combined with Box-Behnken design. The detection limit of the proposed method was 1.71 ± 0.06 U. We compared the results of the amperometric method with the ones obtained with the spectrophotometric method and viscosimetry in a commercial cellulose preparation.
Collapse
|
10
|
Genetically related genotypes of cowpea present similar bacterial community in the rhizosphere. Sci Rep 2022; 12:3472. [PMID: 35236879 PMCID: PMC8891268 DOI: 10.1038/s41598-022-06860-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 02/08/2022] [Indexed: 12/31/2022] Open
Abstract
Plant breeding reduces the genetic diversity of plants and could influence the composition, structure, and diversity of the rhizosphere microbiome, selecting more homogeneous and specialized microbes. In this study, we used 16S rRNA sequencing to assess the bacterial community in the rhizosphere of different lines and modern cowpea cultivars, to investigate the effect of cowpea breeding on bacterial community assembly. Thus, two African lines (IT85F-2687 and IT82D-60) and two Brazilian cultivars (BRS-Guariba and BRS-Tumucumaque) of cowpea were assessed to verify if the generation advance and genetic breeding influence the bacterial community in the rhizosphere. No significant differences were found in the structure, richness, and diversity of bacterial community structure between the rhizosphere of the different cowpea genotypes, and only slight differences were found at the OTU level. The complexity of the co-occurrence network decreased from African lines to Brazilian cultivars. Regarding functional prediction, the core functions were significantly altered according to the genotypes. In general, African lines presented a more abundance of groups related to chemoheterotrophy, while the rhizosphere of the modern cultivars decreased functions related to cellulolysis. This study showed that the genetic breeding process affects the dynamics of the rhizosphere community, decreasing the complexity of interaction in one cultivar. As these cowpea genotypes are genetically related, it could suggest a new hypothesis of how genetic breeding of similar genotypes could influence the rhizosphere microbiome.
Collapse
|
11
|
Short-Term Effect of Nitrogen Fertilization on Carbon Mineralization during Corn Residue Decomposition in Soil. NITROGEN 2021. [DOI: 10.3390/nitrogen2040030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The effect of N fertilization on residue decomposition has been studied extensively; however, contrasting results reflect differences in residue quality, the form of N applied, and the type of soil studied. A 60 d laboratory incubation experiment was conducted to ascertain the effect of synthetic N addition on the decomposition of two corn (Zea mays L.) stover mixtures differing in C:N ratio by continuous monitoring of CO2 emissions and periodic measurement of microbial biomass and enzyme activities involved in C and N cycling. Cumulative CO2 production was greater for the high than low N residue treatment, and was significantly increased by the addition of exogenous N. The latter effect was prominent during the first month of incubation, whereas N-treated soils produced less CO2 in the second month, as would be expected due to more rapid substrate depletion from microbial C utilization previously enhanced by greater N availability. The stimulatory effect of exogenous N was verified with respect to active biomass, microbial biomass C and N, and cellulase and protease activities, all of which were significantly correlated with cumulative CO2 production. Intensive N fertilization in modern corn production increases the input of residues but is not conducive to soil C sequestration.
Collapse
|
12
|
Garrigues S, Kun RS, Peng M, Gruben BS, Benoit Gelber I, Mäkelä M, de Vries RP. The Cultivation Method Affects the Transcriptomic Response of Aspergillus niger to Growth on Sugar Beet Pulp. Microbiol Spectr 2021; 9:e0106421. [PMID: 34431718 PMCID: PMC8552599 DOI: 10.1128/spectrum.01064-21] [Citation(s) in RCA: 6] [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: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 11/20/2022] Open
Abstract
In nature, filamentous fungi are exposed to diverse nutritional sources and changes in substrate availability. Conversely, in submerged cultures, mycelia are continuously exposed to the existing substrates, which are depleted over time. Submerged cultures are the preferred choice for experimental setups in laboratory and industry and are often used for understanding the physiology of fungi. However, to what extent the cultivation method affects fungal physiology, with respect to utilization of natural substrates, has not been addressed in detail. Here, we compared the transcriptomic responses of Aspergillus niger grown in submerged culture and solid culture, both containing sugar beet pulp (SBP) as a carbon source. The results showed that expression of CAZy (Carbohydrate Active enZyme)-encoding and sugar catabolic genes in liquid SBP was time dependent. Moreover, additional components of SBP delayed the A. niger response to the degradation of pectin present in SBP. In addition, we demonstrated that liquid cultures induced wider transcriptome variability than solid cultures. Although there was a correlation regarding sugar metabolic gene expression patterns between liquid and solid cultures, it decreased in the case of CAZyme-encoding genes. In conclusion, the transcriptomic response of A. niger to SBP is influenced by the culturing method, limiting the value of liquid cultures for understanding the behavior of fungi in natural habitats. IMPORTANCE Understanding the interaction between filamentous fungi and their natural and biotechnological environments has been of great interest for the scientific community. Submerged cultures are preferred over solid cultures at a laboratory scale to study the natural response of fungi to different stimuli found in nature (e.g., carbon/nitrogen sources, pH). However, whether and to what extent submerged cultures introduce variation in the physiology of fungi during growth on plant biomass have not been studied in detail. In this study, we compared the transcriptomic responses of Aspergillus niger to growth on liquid and solid cultures containing sugar beet pulp (a by-product of the sugar industry) as a carbon source. We demonstrate that the transcriptomic response of A. niger was highly affected by the culture condition, since the transcriptomic response obtained in a liquid environment could not fully explain the behavior of the fungus in a solid environment. This could partially explain the differences often observed between the phenotypes on plates compared to liquid cultures.
Collapse
Affiliation(s)
- Sandra Garrigues
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Roland S. Kun
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
| | - Birgit S. Gruben
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
- Microbiology, Utrecht University, Utrecht, The Netherlands
| | - Isabelle Benoit Gelber
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
- Microbiology, Utrecht University, Utrecht, The Netherlands
| | - Miia Mäkelä
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Ronald P. de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Utrecht, The Netherlands
- Microbiology, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
13
|
Li F, Zhang J, Ma F, Chen Q, Xiao Q, Zhang X, Xie S, Yu H. Lytic polysaccharide monooxygenases promote oxidative cleavage of lignin and lignin-carbohydrate complexes during fungal degradation of lignocellulose. Environ Microbiol 2021; 23:4547-4560. [PMID: 34169632 DOI: 10.1111/1462-2920.15648] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 01/06/2023]
Abstract
Overcoming lignocellulosic biomass recalcitrance, especially the cleavage of cross-linkages in lignin-carbohydrate complexes (LCCs) and lignin, is essential for both the carbon cycle and industrial biorefinery. Lytic polysaccharide monooxygenases (LPMOs) are copper-containing enzymes that play a key role in fungal polysaccharide oxidative degradation. Nevertheless, comprehensive analysis showed that LPMOs from a white-rot fungus, Pleurotus ostreatus, correlated well with the Fenton reaction and were involved in the degradation of recalcitrant nonpolysaccharide fractions in this research. Thus, LPMOs participated in the extracellular Fenton reaction by enhancing iron reduction in quinone redox cycling. A Fenton reaction system consisting of LPMOs, hydroquinone, and ferric iron can efficiently produce hydroxy radicals and then cleave LCCs or lignin linkages. This finding indicates that LPMOs are underestimated auxiliary enzymes in eliminating biomass recalcitrance.
Collapse
Affiliation(s)
- Fei Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jialong Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Fuying Ma
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Qing Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Qiuyun Xiao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xiaoyu Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Shangxian Xie
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hongbo Yu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| |
Collapse
|
14
|
Sakhuja D, Ghai H, Rathour RK, Kumar P, Bhatt AK, Bhatia RK. Cost-effective production of biocatalysts using inexpensive plant biomass: a review. 3 Biotech 2021; 11:280. [PMID: 34094799 DOI: 10.1007/s13205-021-02847-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/11/2021] [Indexed: 12/12/2022] Open
Abstract
Enzymes are the complex protein moieties, catalyze the rate of chemical reactions by transforming various substrates to specific products and play an integral part in multiple biochemical cycles. Advancement in enzyme research and its integration with industries have reformed the biotech industries. It provides a superior monetary and ecological exchange to traditional material measures in an efficient and environmentally sustainable manner. The cost-effective production of pure and highly active enzymes is still a challenge for the biocatalyst industries. The use of high purity substrates further raises the cost of a typical biocatalyst. The use of low-cost plant-based biomasses as an enticing and sustainable substrate for enzyme production is the most cost-effective approach to these problems. Given the relevance of biomass as a substrate for enzyme development, this review article focuses on the key source, composition and major enzyme generated using various biomass residues. Furthermore, the difficulties associated with the use of biomass as a substrate and technical developments in this area, are also addressed. The use of waste biomass as a substrate lowers the ultimate cost for the production of biocatalysts while simultaneously reduces the waste burden from the environment.
Collapse
|
15
|
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.
Collapse
|
16
|
Zielińska D, Szentner K, Waśkiewicz A, Borysiak S. Production of Nanocellulose by Enzymatic Treatment for Application in Polymer Composites. MATERIALS 2021; 14:ma14092124. [PMID: 33922118 PMCID: PMC8122419 DOI: 10.3390/ma14092124] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/18/2021] [Accepted: 04/20/2021] [Indexed: 12/16/2022]
Abstract
In the last few years, the scientific community around the world has devoted a lot of attention to the search for the best methods of obtaining nanocellulose. In this work, nanocellulose was obtained in enzymatic reactions with strictly defined dispersion and structural parameters in order to use it as a filler for polymers. The controlled enzymatic hydrolysis of the polysaccharide was carried out in the presence of cellulolytic enzymes from microscopic fungi-Trichoderma reesei and Aspergillus sp. It has been shown that the efficiency of bioconversion of cellulose material depends on the type of enzymes used. The use of a complex of cellulases obtained from a fungus of the genus Trichoderma turned out to be an effective method of obtaining cellulose of nanometric dimensions with a very low polydispersity. The effect of cellulose enzymatic reactions was assessed using the technique of high-performance liquid chromatography coupled with a refractometric detector, X-ray diffraction, dynamic light scattering and Fourier transform infrared spectroscopy. In the second stage, polypropylene composites with nanometric cellulose were obtained by extrusion and injection. It was found by means of X-ray diffraction, hot stage optical microscopy and differential scanning calorimetry that nanocellulose had a significant effect on the supermolecular structure, nucleation activity and the course of phase transitions of the obtained polymer nanocomposites. Moreover, the obtained nanocomposites are characterized by very good strength properties. This paper describes for the first time that the obtained cellulose nanofillers with defined parameters can be used for the production of polymer composites with a strictly defined polymorphic structure, which in turn may influence future decision making about obtaining materials with controllable properties, e.g., high flexibility, enabling the thermoforming process of packaging.
Collapse
Affiliation(s)
- Daria Zielińska
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Berdychowo 4, 60965 Poznan, Poland;
| | - Kinga Szentner
- Department of Chemistry, Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 75, 60625 Poznan, Poland; (K.S.); (A.W.)
| | - Agnieszka Waśkiewicz
- Department of Chemistry, Faculty of Forestry and Wood Technology, Poznan University of Life Sciences, Wojska Polskiego 75, 60625 Poznan, Poland; (K.S.); (A.W.)
| | - Sławomir Borysiak
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Berdychowo 4, 60965 Poznan, Poland;
- Correspondence: ; Tel.: +48-616-653-549
| |
Collapse
|
17
|
The Reaction of Cellulolytic and Potentially Cellulolytic Spore-Forming Bacteria to Various Types of Crop Management and Farmyard Manure Fertilization in Bulk Soil. AGRONOMY-BASEL 2021. [DOI: 10.3390/agronomy11040772] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The ecology of cellulolytic bacteria in bulk soil is still relatively unknown. There is still only a handful of papers on the abundance and diversity of this group of bacteria. Our study aimed to determine the impact of various crop management systems and farmyard manure (FYM) fertilization on the abundance of cellulolytic and potentially cellulolytic spore-forming bacteria (SCB). The study site was a nearly 100-year-old fertilization experiment, one of the oldest still active field trials in Europe. The highest contents of total carbon (TC) and total nitrogen (TN) were recorded in both five-year rotations. The abundances of SCB and potential SCB were evaluated using classical microbiological methods, the most probable number (MPN), and 16S rRNA Illumina MiSeq sequencing. The highest MPN of SCB was recorded in soil with arbitrary rotation without legumes (ARP) fertilized with FYM (382 colony-forming units (CFU) mL−1). As a result of the bioinformatic analysis, the highest values of the Shannon–Wiener index and the largest number of operational taxonomic units (OTUs) were found in ARP-FYM, while the lowest in ARP treatment without FYM fertilization. In all treatments, those dominant at the order level were: Brevibacillales (13.1–43.4%), Paenibacillales (5.3–36.9%), Bacillales (4.0–0.9%). Brevibacillaceae (13.1–43.4%), Paenibacillaceae (8.2–36.9%), and Clostridiaceae (5.4–11.9%) dominated at the family level in all tested samples. Aneurinibacillaceae and Hungateiclostridiaceae families increased their overall share in FYM fertilization treatments. The results of our research show that the impact of crop management types on SCB was negligible while the actual factor shaping SCB community was the use of FYM fertilization.
Collapse
|
18
|
Role of extremophiles and their extremozymes in biorefinery process of lignocellulose degradation. Extremophiles 2021; 25:203-219. [PMID: 33768388 DOI: 10.1007/s00792-021-01225-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/10/2021] [Indexed: 12/20/2022]
Abstract
Technological advances in the field of life sciences have led to discovery of organisms that live in harsh environmental conditions referred to as extremophiles. These organisms have adapted themselves to thrive in extreme habitat giving these organisms an advantage over conventional mesophilic organisms in various industrial applications. Extremozymes produced by these extremophiles have high tolerance to inhospitable environmental conditions making them an ideal enzyme system for various industrial processes. A notable application of these extremophiles and extremozymes is their use in the degradation of recalcitrant lignocellulosic biomass and application in biorefineries. For maximum utilization of the trapped carbon source from this obstinate biomass, pretreatment is a necessary step that requires various physiochemical and enzymatic treatments. From search for novel extremophiles and extremozymes to development of various genetic and protein engineering techniques, investigation on extremozymes with enhanced stability and efficiency is been done. Since extremozymes are easily calibrated to work under such conditions, they have become an emerging topic in the research field of biofuel production. The review discusses the various extremozymes that play an important role in lignocellulose degradation along with recent studies on their molecular and genetic evolution for industrial application and production of biofuels and various value-added products.
Collapse
|
19
|
Vibrational Spectroscopic Analyses and Imaging of the Early Middle Ages Hemp Bast Fibres Recovered from Lake Sediments. Molecules 2021; 26:molecules26051314. [PMID: 33804535 PMCID: PMC7957794 DOI: 10.3390/molecules26051314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/20/2021] [Accepted: 02/25/2021] [Indexed: 02/02/2023] Open
Abstract
Fourier Transform Infrared (FT-IR) spectroscopy and imaging combined with hierarchical cluster analysis (HCA) was applied to analyse biochemical properties of Early Middle Ages hemp (Cannabis sativa L.) bast fibres collected from lake bottom sediment of lake Słone. The examined plant macrofossil material constitutes residues of the hemp retting process that took place in the 7th–8th century. By comparison of three samples: untreated isolated bast fibres, and fibres incubated overnight at 4 and 37 °C, we were able to mimic the retting conditions. Using FT-IR qualitative and semi-quantitative assessment of the primary polysaccharides content, total protein content, and their spatial distribution was performed within the hemp fibres. The concentration of cellulose remained vastly unchanged, while the concentration of lignin and pectin was the highest in the untreated sample. The spatial distributions of compounds were heterogeneous in the untreated and 4 °C-incubated samples, and homogenous in the specimen processed at 37 °C. Interestingly, a higher amide content was detected in the latter sample indicating the highest degree of enzymatic degradation. In this study, we show that the spectroscopic methods allow for a non-destructive evaluation of biochemical composition of plant fibres without preparation, which can be an appropriate approach for studying ancient plant remains.
Collapse
|
20
|
Benedetti M, Barera S, Longoni P, Guardini Z, Herrero Garcia N, Bolzonella D, Lopez‐Arredondo D, Herrera‐Estrella L, Goldschmidt‐Clermont M, Bassi R, Dall’Osto L. A microalgal-based preparation with synergistic cellulolytic and detoxifying action towards chemical-treated lignocellulose. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:124-137. [PMID: 32649019 PMCID: PMC7769238 DOI: 10.1111/pbi.13447] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/19/2020] [Accepted: 06/28/2020] [Indexed: 05/28/2023]
Abstract
High-temperature bioconversion of lignocellulose into fermentable sugars has drawn attention for efficient production of renewable chemicals and biofuels, because competing microbial activities are inhibited at elevated temperatures and thermostable cell wall degrading enzymes are superior to mesophilic enzymes. Here, we report on the development of a platform to produce four different thermostable cell wall degrading enzymes in the chloroplast of Chlamydomonas reinhardtii. The enzyme blend was composed of the cellobiohydrolase CBM3GH5 from C. saccharolyticus, the β-glucosidase celB from P. furiosus, the endoglucanase B and the endoxylanase XynA from T. neapolitana. In addition, transplastomic microalgae were engineered for the expression of phosphite dehydrogenase D from Pseudomonas stutzeri, allowing for growth in non-axenic media by selective phosphite nutrition. The cellulolytic blend composed of the glycoside hydrolase (GH) domain GH12/GH5/GH1 allowed the conversion of alkaline-treated lignocellulose into glucose with efficiencies ranging from 14% to 17% upon 48h of reaction and an enzyme loading of 0.05% (w/w). Hydrolysates from treated cellulosic materials with extracts of transgenic microalgae boosted both the biogas production by methanogenic bacteria and the mixotrophic growth of the oleaginous microalga Chlorella vulgaris. Notably, microalgal treatment suppressed the detrimental effect of inhibitory by-products released from the alkaline treatment of biomass, thus allowing for efficient assimilation of lignocellulose-derived sugars by C. vulgaris under mixotrophic growth.
Collapse
Affiliation(s)
- Manuel Benedetti
- Dipartimento di BiotecnologieUniversità di VeronaVeronaItaly
- Present address:
Dipartimento MESVAUniversità dell'AquilaCoppitoAQItaly
| | - Simone Barera
- Dipartimento di BiotecnologieUniversità di VeronaVeronaItaly
| | - Paolo Longoni
- Faculty of ScienceInstitute of BiologyUniversity of NeuchâtelNeuchâtelSwitzerland
| | - Zeno Guardini
- Dipartimento di BiotecnologieUniversità di VeronaVeronaItaly
| | | | | | - Damar Lopez‐Arredondo
- StelaGenomics MexicoS de RL de CVIrapuato, GuanajuatoMexico
- Institute of Genomics for Crop Abiotic Stress ToleranceTexas Tech UniversityLubbockTXUSA
| | - Luis Herrera‐Estrella
- Laboratorio Nacional de Genómica para la BiodiversidadCentro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalIrapuato, GuanajuatoMexico
- Institute of Genomics for Crop Abiotic Stress ToleranceTexas Tech UniversityLubbockTXUSA
| | | | - Roberto Bassi
- Dipartimento di BiotecnologieUniversità di VeronaVeronaItaly
| | - Luca Dall’Osto
- Dipartimento di BiotecnologieUniversità di VeronaVeronaItaly
| |
Collapse
|
21
|
Bernardi AV, Gerolamo LE, de Gouvêa PF, Yonamine DK, Pereira LMS, de Oliveira AHC, Uyemura SA, Dinamarco TM. LPMO AfAA9_B and Cellobiohydrolase AfCel6A from A. fumigatus Boost Enzymatic Saccharification Activity of Cellulase Cocktail. Int J Mol Sci 2020; 22:E276. [PMID: 33383972 PMCID: PMC7795096 DOI: 10.3390/ijms22010276] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/21/2020] [Accepted: 12/24/2020] [Indexed: 01/02/2023] Open
Abstract
Cellulose is the most abundant polysaccharide in lignocellulosic biomass, where it is interlinked with lignin and hemicellulose. Bioethanol can be produced from biomass. Since breaking down biomass is difficult, cellulose-active enzymes secreted by filamentous fungi play an important role in degrading recalcitrant lignocellulosic biomass. We characterized a cellobiohydrolase (AfCel6A) and lytic polysaccharide monooxygenase LPMO (AfAA9_B) from Aspergillus fumigatus after they were expressed in Pichia pastoris and purified. The biochemical parameters suggested that the enzymes were stable; the optimal temperature was ~60 °C. Further characterization revealed high turnover numbers (kcat of 147.9 s-1 and 0.64 s-1, respectively). Surprisingly, when combined, AfCel6A and AfAA9_B did not act synergistically. AfCel6A and AfAA9_B association inhibited AfCel6A activity, an outcome that needs to be further investigated. However, AfCel6A or AfAA9_B addition boosted the enzymatic saccharification activity of a cellulase cocktail and the activity of cellulase Af-EGL7. Enzymatic cocktail supplementation with AfCel6A or AfAA9_B boosted the yield of fermentable sugars from complex substrates, especially sugarcane exploded bagasse, by up to 95%. The synergism between the cellulase cocktail and AfAA9_B was enzyme- and substrate-specific, which suggests a specific enzymatic cocktail for each biomass by up to 95%. The synergism between the cellulase cocktail and AfAA9_B was enzyme- and substrate-specific, which suggests a specific enzymatic cocktail for each biomass.
Collapse
Affiliation(s)
- Aline Vianna Bernardi
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Luis Eduardo Gerolamo
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Paula Fagundes de Gouvêa
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Deborah Kimie Yonamine
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Lucas Matheus Soares Pereira
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Arthur Henrique Cavalcante de Oliveira
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| | - Sérgio Akira Uyemura
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-903, Brazil;
| | - Taisa Magnani Dinamarco
- Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil; (A.V.B.); (L.E.G.); (P.F.d.G.); (D.K.Y.); (L.M.S.P.); (A.H.C.d.O.)
| |
Collapse
|
22
|
Zhou W, Jiang C, Duan X, Song J, Yuan Y, Chen N. Fe3O4/carbonized cellulose micro-nano hybrid for high-performance microwave absorber. Carbohydr Polym 2020; 245:116531. [DOI: 10.1016/j.carbpol.2020.116531] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/01/2020] [Accepted: 05/27/2020] [Indexed: 10/24/2022]
|
23
|
Haske-Cornelius O, Hartmann A, Brunner F, Pellis A, Bauer W, Nyanhongo GS, Guebitz GM. Effects of enzymes on the refining of different pulps. J Biotechnol 2020; 320:1-10. [PMID: 32553829 DOI: 10.1016/j.jbiotec.2020.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 05/29/2020] [Accepted: 06/09/2020] [Indexed: 11/30/2022]
Abstract
Comparative studies of the effects of two commercial enzyme formulations on fiber refining were conducted. Extensive basic characterisation of the enzymes involved, assessment of their hydrolytic activities on different model substrates as well as on different pulps (softwood sulfate, softwood sulfite, hardwood sulfate) were evaluated. Both enzyme formulations showed endoglucanase as well as some xylanase and β-glucosidase activity. In addition, Enzyme A reached a CMC end viscosity of 19.5 mPa compared to 11.1 mPa for Enzyme B. Reducing sugar release almost doubled from 695 μmol mL-1 for hardwood sulfate pulp to 1300 μmol mL-1 for softwood sulfite pulp with Enzyme B under the same conditions. Enzyme A increased the degree of refining even under non-ideal conditions from 23 °SR to up to 50 °SR. Further characterization of hand sheets, made from enzyme pre-treated and refined cellulose fibers with Enzyme A and B, showed that Enzyme A had the best effects leading to hand sheets with increased tensile strength and low air permeability. In summary, the increase in the degree of refining seen for Enzyme A correlated to higher xylanase and β-glucosidase activity and lower endoglucanase activity.
Collapse
Affiliation(s)
- Oskar Haske-Cornelius
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Strasse 20, 3430, Tulln an der Donau, Austria
| | - Alexandra Hartmann
- Graz University of Technology, Institute of Paper, Pulp and Fiber Technology, Inffeldgasse 23, Graz, 8010, Austria
| | - Florian Brunner
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Strasse 20, 3430, Tulln an der Donau, Austria
| | - Alessandro Pellis
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Strasse 20, 3430, Tulln an der Donau, Austria
| | - Wolfgang Bauer
- Graz University of Technology, Institute of Paper, Pulp and Fiber Technology, Inffeldgasse 23, Graz, 8010, Austria
| | - Gibson S Nyanhongo
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Strasse 20, 3430, Tulln an der Donau, Austria.
| | - Georg M Guebitz
- Institute of Environmental Biotechnology, University of Natural Resources and Life Sciences Vienna, Konrad-Lorenz-Strasse 20, 3430, Tulln an der Donau, Austria; Austrian Centre of Industrial Biotechnology, Konrad-Lorenz-Strasse 20, 3430, Tulln an der Donau, Austria
| |
Collapse
|
24
|
Bilal M, Iqbal HMN. Recent Advancements in the Life Cycle Analysis of Lignocellulosic Biomass. ACTA ACUST UNITED AC 2020. [DOI: 10.1007/s40518-020-00153-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
25
|
Giovannoni M, Gramegna G, Benedetti M, Mattei B. Industrial Use of Cell Wall Degrading Enzymes: The Fine Line Between Production Strategy and Economic Feasibility. Front Bioeng Biotechnol 2020; 8:356. [PMID: 32411686 PMCID: PMC7200985 DOI: 10.3389/fbioe.2020.00356] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022] Open
Abstract
Cell Wall Degrading Enzymes (CWDEs) are a heterogeneous group of enzymes including glycosyl-hydrolases, oxidoreductases, lyases, and esterases. Microbes with degrading activities toward plant cell wall polysaccharides are the most relevant source of CWDEs for industrial applications. These organisms secrete a wide array of CWDEs in amounts strictly necessary for their own sustenance, nonetheless the production of CWDEs from wild type microbes can be increased at large-scale by using optimized fermentation strategies. In the last decades, advances in genetic engineering allowed the expression of recombinant CWDEs also in lab-domesticated organisms such as E. coli, yeasts and plants, dramatically increasing the available options for the large-scale production of CWDEs. The optimization of a CWDE-producing biofactory is a hard challenge that biotechnologists tackle by testing different expression strategies and expression-hosts. Although both the yield and production costs are critical factors to produce biomolecules at industrial scale, these parameters are often disregarded in basic research. This review presents the main characteristics and industrial applications of CWDEs directed toward the cell wall of plants, bacteria, fungi and microalgae. Different biofactories for CWDE expression are compared in order to highlight strengths and weaknesses of each production system and how these aspects impact the final enzyme cost and, consequently, the economic feasibility of using CWDEs for industrial applications.
Collapse
Affiliation(s)
- Moira Giovannoni
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Giovanna Gramegna
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Manuel Benedetti
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| | - Benedetta Mattei
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| |
Collapse
|
26
|
Barbosa FC, Silvello MA, Goldbeck R. Cellulase and oxidative enzymes: new approaches, challenges and perspectives on cellulose degradation for bioethanol production. Biotechnol Lett 2020; 42:875-884. [DOI: 10.1007/s10529-020-02875-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/10/2020] [Accepted: 01/13/2020] [Indexed: 01/04/2023]
|
27
|
Kumar A, Chandra R. Ligninolytic enzymes and its mechanisms for degradation of lignocellulosic waste in environment. Heliyon 2020; 6:e03170. [PMID: 32095645 PMCID: PMC7033530 DOI: 10.1016/j.heliyon.2020.e03170] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/04/2019] [Accepted: 12/31/2019] [Indexed: 12/30/2022] Open
Abstract
Ligninolytic enzymes play a key role in degradation and detoxification of lignocellulosic waste in environment. The major ligninolytic enzymes are laccase, lignin peroxidase, manganese peroxidase, and versatile peroxidase. The activities of these enzymes are enhanced by various mediators as well as some other enzymes (feruloyl esterase, aryl-alcohol oxidase, quinone reductases, lipases, catechol 2, 3-dioxygenase) to facilitate the process for degradation and detoxification of lignocellulosic waste in environment. The structurally laccase is isoenzymes with monomeric or dimeric and glycosylation levels (10–45%). This contains four copper ions of three different types. The enzyme catalyzes the overall reaction: 4 benzenediol + O2 to 4 benzosemiquinone + 2H2O. While, lignin peroxidase is a glycoprotein molecular mass of 38–46 kDa containing one mole of iron protoporphyrin IX per one mol of protein, catalyzes the H2O2 dependent oxidative depolymerization of lignin. The manganese peroxidase is a glycosylated heme protein with molecular mass of 40–50kDa. It depolymerizes the lignin molecule in the presence of manganese ion. The versatile peroxidase has broad range substrate sharing typical features of the manganese and lignin peroxidase families. Although ligninolytic enzymes have broad range of industrial application specially the degradation and detoxification of lignocellulosic waste discharged from various industrial activities, its large scale application is still limited due to lack of limited production. Further, the extremophilic properties of ligninolytic enzymes indicated their broad prospects in varied environmental conditions. Therefore it needs more extensive research for understanding its structure and mechanisms for broad range commercial applications.
Collapse
Affiliation(s)
- Adarsh Kumar
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar (A Central) University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India
| | - Ram Chandra
- Department of Environmental Microbiology, School for Environmental Sciences, Babasaheb Bhimrao Ambedkar (A Central) University, Vidya Vihar, Raebareli Road, Lucknow, Uttar Pradesh, 226025, India
| |
Collapse
|
28
|
Challacombe JF, Hesse CN, Bramer LM, McCue LA, Lipton M, Purvine S, Nicora C, Gallegos-Graves LV, Porras-Alfaro A, Kuske CR. Genomes and secretomes of Ascomycota fungi reveal diverse functions in plant biomass decomposition and pathogenesis. BMC Genomics 2019; 20:976. [PMID: 31830917 PMCID: PMC6909477 DOI: 10.1186/s12864-019-6358-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 12/01/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The dominant fungi in arid grasslands and shrublands are members of the Ascomycota phylum. Ascomycota fungi are important drivers in carbon and nitrogen cycling in arid ecosystems. These fungi play roles in soil stability, plant biomass decomposition, and endophytic interactions with plants. They may also form symbiotic associations with biocrust components or be latent saprotrophs or pathogens that live on plant tissues. However, their functional potential in arid soils, where organic matter, nutrients and water are very low or only periodically available, is poorly characterized. RESULTS Five Ascomycota fungi were isolated from different soil crust microhabitats and rhizosphere soils around the native bunchgrass Pleuraphis jamesii in an arid grassland near Moab, UT, USA. Putative genera were Coniochaeta, isolated from lichen biocrust, Embellisia from cyanobacteria biocrust, Chaetomium from below lichen biocrust, Phoma from a moss microhabitat, and Aspergillus from the soil. The fungi were grown in replicate cultures on different carbon sources (chitin, native bunchgrass or pine wood) relevant to plant biomass and soil carbon sources. Secretomes produced by the fungi on each substrate were characterized. Results demonstrate that these fungi likely interact with primary producers (biocrust or plants) by secreting a wide range of proteins that facilitate symbiotic associations. Each of the fungal isolates secreted enzymes that degrade plant biomass, small secreted effector proteins, and proteins involved in either beneficial plant interactions or virulence. Aspergillus and Phoma expressed more plant biomass degrading enzymes when grown in grass- and pine-containing cultures than in chitin. Coniochaeta and Embellisia expressed similar numbers of these enzymes under all conditions, while Chaetomium secreted more of these enzymes in grass-containing cultures. CONCLUSIONS This study of Ascomycota genomes and secretomes provides important insights about the lifestyles and the roles that Ascomycota fungi likely play in arid grassland, ecosystems. However, the exact nature of those interactions, whether any or all of the isolates are true endophytes, latent saprotrophs or opportunistic phytopathogens, will be the topic of future studies.
Collapse
Affiliation(s)
- Jean F Challacombe
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
- Present address: Colorado State University, College of Agricultural Sciences, 301 University Ave, Fort Collins, CO, 80523, USA.
| | - Cedar N Hesse
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
- Horticultural Crops Research, USDA ARS, Corvallis, OR, USA
| | - Lisa M Bramer
- Applied Statistics & Computational Modeling, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Lee Ann McCue
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, 99352, USA
| | - Mary Lipton
- Applied Statistics & Computational Modeling, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Samuel Purvine
- Applied Statistics & Computational Modeling, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Carrie Nicora
- Applied Statistics & Computational Modeling, Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | | | - Cheryl R Kuske
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| |
Collapse
|
29
|
Green Production and Biotechnological Applications of Cell Wall Lytic Enzymes. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9235012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
: Energy demand is constantly growing, and, nowadays, fossil fuels still play a dominant role in global energy production, despite their negative effects on air pollution and the emission of greenhouse gases, which are the main contributors to global warming. An alternative clean source of energy is represented by the lignocellulose fraction of plant cell walls, the most abundant carbon source on Earth. To obtain biofuels, lignocellulose must be efficiently converted into fermentable sugars. In this regard, the exploitation of cell wall lytic enzymes (CWLEs) produced by lignocellulolytic fungi and bacteria may be considered as an eco-friendly alternative. These organisms evolved to produce a variety of highly specific CWLEs, even if in low amounts. For an industrial use, both the identification of novel CWLEs and the optimization of sustainable CWLE-expressing biofactories are crucial. In this review, we focus on recently reported advances in the heterologous expression of CWLEs from microbial and plant expression systems as well as some of their industrial applications, including the production of biofuels from agricultural feedstock and of value-added compounds from waste materials. Moreover, since heterologous expression of CWLEs may be toxic to plant hosts, genetic strategies aimed in converting such a deleterious effect into a beneficial trait are discussed.
Collapse
|
30
|
A Lytic Polysaccharide Monooxygenase from a White-Rot Fungus Drives the Degradation of Lignin by a Versatile Peroxidase. Appl Environ Microbiol 2019; 85:AEM.02803-18. [PMID: 30824433 DOI: 10.1128/aem.02803-18] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 02/12/2019] [Indexed: 12/21/2022] Open
Abstract
Lytic polysaccharide monooxygenases (LPMOs), a class of copper-dependent enzymes, play a crucial role in boosting the enzymatic decomposition of polysaccharides. Here, we reveal that LPMOs might be associated with a lignin degradation pathway. An LPMO from white-rot fungus Pleurotus ostreatus, LPMO9A (PoLPMO9A), was shown to be able to efficiently drive the activity of class II lignin-degrading peroxidases in vitro through H2O2 production regardless of the presence or absence of a cellulose substrate. An LPMO-driven peroxidase reaction can degrade β-O-4 and 5-5' types of lignin dimer with 46.5% and 37.7% degradation, respectively, as well as alter the structure of natural lignin and kraft lignin. H2O2 generated by PoLPMO9A was preferentially utilized for the peroxidase from Physisporinus sp. strain P18 (PsVP) reaction rather than cellulose oxidation, indicating that white-rot fungi may have a strategy for preferential degradation of resistant lignin. This discovery shows that LPMOs may be involved in lignin oxidation as auxiliary enzymes of lignin-degrading peroxidases during the white-rot fungal decay process.IMPORTANCE The enzymatic biodegradation of structural polysaccharides is affected by the degree of delignification of lignocellulose during the white-rot fungal decay process. The lignin matrix decreases accessibility to the substrates for LPMOs. H2O2 has been studied as a cosubstrate for LPMOs, but the formation and utilization of H2O2 in the reactions still represent an intriguing focus of current research. Lignin-degrading peroxidases and LPMOs usually coexist during fungal decay, and therefore, the relationship between H2O2-dependent lignin-degrading peroxidases and LPMOs should be considered during the wood decay process. The current study revealed that white-rot fungal LPMOs may be involved in the degradation of lignin through driving a versatile form of peroxidase activity in vitro and that H2O2 generated by PoLPMO9A was preferentially used for lignin oxidation by lignin-degrading peroxidase (PsVP). These findings reveal a potential relationship between LPMOs and lignin degradation, which will be of great significance for further understanding the contribution of LPMOs to the white-rot fungal decay process.
Collapse
|
31
|
Gissibl A, Care A, Sun A, Hobba G, Nevalainen H, Sunna A. Development of screening strategies for the identification of paramylon-degrading enzymes. J Ind Microbiol Biotechnol 2019; 46:769-781. [PMID: 30806871 DOI: 10.1007/s10295-019-02157-7] [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: 12/01/2018] [Accepted: 02/17/2019] [Indexed: 10/27/2022]
Abstract
Enzymatic degradation of the β-1,3-glucan paramylon could enable the production of bioactive compounds for healthcare and renewable substrates for biofuels. However, few enzymes have been found to degrade paramylon efficiently and their enzymatic mechanisms remain poorly understood. Thus, the aim of this work was to find paramylon-degrading enzymes and ways to facilitate their identification. Towards this end, a Euglena gracilis-derived cDNA expression library was generated and introduced into Escherichia coli. A flow cytometry-based screening assay was developed to identify E. gracilis enzymes that could hydrolyse the fluorogenic substrate fluorescein di-β-D-glucopyranoside in combination with time-saving auto-induction medium. In parallel, four amino acid sequences of potential E. gracilis β-1,3-glucanases were identified from proteomic data. The open reading frame encoding one of these candidate sequences (light_m.20624) was heterologously expressed in E. coli. Finally, a Congo Red dye plate assay was developed for the screening of enzyme preparations potentially able to degrade paramylon. This assay was validated with enzymes assumed to have paramylon-degrading activity and then used to identify four commercial preparations with previously unknown paramylon degradation ability.
Collapse
Affiliation(s)
- Alexander Gissibl
- Department of Molecular Sciences, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia
- Australian Research Council Industrial Transformation Training Centre for Molecular Technology in the Food Industry, Sydney, NSW, 2109, Australia
| | - Andrew Care
- Department of Molecular Sciences, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW, 2109, Australia
| | - Angela Sun
- Department of Molecular Sciences, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia
- Australian Research Council Industrial Transformation Training Centre for Molecular Technology in the Food Industry, Sydney, NSW, 2109, Australia
| | - Graham Hobba
- Agritechnology Pty Ltd, 36 Underwood Road, Borenore, NSW, 2800, Australia
| | - Helena Nevalainen
- Department of Molecular Sciences, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia
- Australian Research Council Industrial Transformation Training Centre for Molecular Technology in the Food Industry, Sydney, NSW, 2109, Australia
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW, 2109, Australia
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, North Ryde, Sydney, NSW, 2109, Australia.
- Australian Research Council Industrial Transformation Training Centre for Molecular Technology in the Food Industry, Sydney, NSW, 2109, Australia.
- Biomolecular Discovery and Design Research Centre, Macquarie University, Sydney, NSW, 2109, Australia.
| |
Collapse
|
32
|
Highly Selective Enzymatic Recovery of Building Blocks from Wool-Cotton-Polyester Textile Waste Blends. Polymers (Basel) 2018; 10:polym10101107. [PMID: 30961032 PMCID: PMC6403871 DOI: 10.3390/polym10101107] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/04/2018] [Accepted: 10/05/2018] [Indexed: 11/17/2022] Open
Abstract
In Europe, most of the discarded and un-wearable textiles are incinerated or landfilled. In this study, we present an enzyme-based strategy for the recovery of valuable building blocks from mixed textile waste and blends as a circular economy concept. Therefore, model and real textile waste were sequentially incubated with (1) protease for the extraction of amino acids from wool components (95% efficiency) and (2) cellulases for the recovery of glucose from cotton and rayon constituents (85% efficiency). The purity of the remaining poly(ethylene terephthalate) (PET) unaltered by the enzymatic treatments was assessed via Fourier-transformed infrared spectroscopy. Amino acids recovered from wool were characterized via elementary and molecular size analysis, while the glucose resulting from the cotton hydrolysis was successfully converted into ethanol by fermentation with Saccharomyces cerevisiae. This work demonstrated that the step-wise application of enzymes can be used for the recovery of pure building blocks (glucose) and their further reuse in fermentative processes.
Collapse
|
33
|
Rodríguez Hernáez J, Cerón Cucchi ME, Cravero S, Martinez MC, Gonzalez S, Puebla A, Dopazo J, Farber M, Paniego N, Rivarola M. The first complete genomic structure of Butyrivibrio fibrisolvens and its chromid. Microb Genom 2018; 4. [PMID: 30216146 PMCID: PMC6249431 DOI: 10.1099/mgen.0.000216] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Butyrivibrio fibrisolvens forms part of the gastrointestinal microbiome of ruminants and other mammals, including humans. Indeed, it is one of the most common bacteria found in the rumen and plays an important role in ruminal fermentation of polysaccharides, yet, to date, there is no closed reference genome published for this species in any ruminant animal. We successfully assembled the nearly complete genome sequence of B. fibrisolvens strain INBov1 isolated from cow rumen using Illumina paired-end reads, 454 Roche single-end and mate pair sequencing technology. Additionally, we constructed an optical restriction map of this strain to aid in scaffold ordering and positioning, and completed the first genomic structure of this species. Moreover, we identified and assembled the first chromid of this species (pINBov266). The INBov1 genome encodes a large set of genes involved in the cellulolytic process but lacks key genes. This seems to indicate that B. fibrisolvens plays an important role in ruminal cellulolytic processes, but does not have autonomous cellulolytic capacity. When searching for genes involved in the biohydrogenation of unsaturated fatty acids, no linoleate isomerase gene was found in this strain. INBov1 does encode oleate hydratase genes known to participate in the hydrogenation of oleic acids. Furthermore, INBov1 contains an enolase gene, which has been recently determined to participate in the synthesis of conjugated linoleic acids. This work confirms the presence of a novel chromid in B. fibrisolvens and provides a new potential reference genome sequence for this species, providing new insight into its role in biohydrogenation and carbohydrate degradation.
Collapse
Affiliation(s)
- Javier Rodríguez Hernáez
- 3Skoklab - Department of Pathology, NYU Langone Health, New York, USA.,1Biotechnology Institute, CICVyA-Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Provincia de Buenos Aires, Argentina.,2Fundación Universidad Argentina de la Empresa (UADE), Buenos Aires, Argentina
| | - Maria Esperanza Cerón Cucchi
- 1Biotechnology Institute, CICVyA-Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Provincia de Buenos Aires, Argentina
| | - Silvio Cravero
- 1Biotechnology Institute, CICVyA-Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Provincia de Buenos Aires, Argentina
| | - Maria Carolina Martinez
- 1Biotechnology Institute, CICVyA-Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Provincia de Buenos Aires, Argentina
| | - Sergio Gonzalez
- 1Biotechnology Institute, CICVyA-Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Provincia de Buenos Aires, Argentina
| | - Andrea Puebla
- 1Biotechnology Institute, CICVyA-Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Provincia de Buenos Aires, Argentina
| | - Joaquin Dopazo
- 4Clinical Bioinformatics Research Area, Fundación Progreso y Salud, Hospital Virgen del Rocío, Sevilla, Spain
| | - Marisa Farber
- 1Biotechnology Institute, CICVyA-Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Provincia de Buenos Aires, Argentina.,5CONICET, Buenos Aires, Argentina
| | - Norma Paniego
- 1Biotechnology Institute, CICVyA-Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Provincia de Buenos Aires, Argentina.,5CONICET, Buenos Aires, Argentina
| | - Máximo Rivarola
- 1Biotechnology Institute, CICVyA-Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham, Provincia de Buenos Aires, Argentina.,2Fundación Universidad Argentina de la Empresa (UADE), Buenos Aires, Argentina.,5CONICET, Buenos Aires, Argentina
| |
Collapse
|
34
|
Gissibl A, Care A, Parker LM, Iqbal S, Hobba G, Nevalainen H, Sunna A. Microwave pretreatment of paramylon enhances the enzymatic production of soluble β-1,3-glucans with immunostimulatory activity. Carbohydr Polym 2018; 196:339-347. [DOI: 10.1016/j.carbpol.2018.05.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 04/18/2018] [Accepted: 05/12/2018] [Indexed: 12/31/2022]
|
35
|
|
36
|
Fungal lytic polysaccharide monooxygenases from family AA9: Recent developments and application in lignocelullose breakdown. Int J Biol Macromol 2017; 102:771-778. [DOI: 10.1016/j.ijbiomac.2017.04.077] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 04/20/2017] [Accepted: 04/21/2017] [Indexed: 11/24/2022]
|
37
|
Bhatia R, Gallagher JA, Gomez LD, Bosch M. Genetic engineering of grass cell wall polysaccharides for biorefining. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1071-1092. [PMID: 28557198 PMCID: PMC5552484 DOI: 10.1111/pbi.12764] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/17/2017] [Accepted: 05/24/2017] [Indexed: 05/10/2023]
Abstract
Grasses represent an abundant and widespread source of lignocellulosic biomass, which has yet to fulfil its potential as a feedstock for biorefining into renewable and sustainable biofuels and commodity chemicals. The inherent recalcitrance of lignocellulosic materials to deconstruction is the most crucial limitation for the commercial viability and economic feasibility of biomass biorefining. Over the last decade, the targeted genetic engineering of grasses has become more proficient, enabling rational approaches to modify lignocellulose with the aim of making it more amenable to bioconversion. In this review, we provide an overview of transgenic strategies and targets to tailor grass cell wall polysaccharides for biorefining applications. The bioengineering efforts and opportunities summarized here rely primarily on (A) reprogramming gene regulatory networks responsible for the biosynthesis of lignocellulose, (B) remodelling the chemical structure and substitution patterns of cell wall polysaccharides and (C) expressing lignocellulose degrading and/or modifying enzymes in planta. It is anticipated that outputs from the rational engineering of grass cell wall polysaccharides by such strategies could help in realizing an economically sustainable, grass-derived lignocellulose processing industry.
Collapse
Affiliation(s)
- Rakesh Bhatia
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| | - Joe A. Gallagher
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| | | | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences (IBERS)Aberystwyth UniversityAberystwythUK
| |
Collapse
|
38
|
Cavaliere M, Feng S, Soyer OS, Jiménez JI. Cooperation in microbial communities and their biotechnological applications. Environ Microbiol 2017; 19:2949-2963. [PMID: 28447371 PMCID: PMC5575505 DOI: 10.1111/1462-2920.13767] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 04/08/2017] [Accepted: 04/11/2017] [Indexed: 12/30/2022]
Abstract
Microbial communities are increasingly utilized in biotechnology. Efficiency and productivity in many of these applications depends on the presence of cooperative interactions between members of the community. Two key processes underlying these interactions are the production of public goods and metabolic cross-feeding, which can be understood in the general framework of ecological and evolutionary (eco-evo) dynamics. In this review, we illustrate the relevance of cooperative interactions in microbial biotechnological processes, discuss their mechanistic origins and analyse their evolutionary resilience. Cooperative behaviours can be damaged by the emergence of 'cheating' cells that benefit from the cooperative interactions but do not contribute to them. Despite this, cooperative interactions can be stabilized by spatial segregation, by the presence of feedbacks between the evolutionary dynamics and the ecology of the community, by the role of regulatory systems coupled to the environmental conditions and by the action of horizontal gene transfer. Cooperative interactions enrich microbial communities with a higher degree of robustness against environmental stress and can facilitate the evolution of more complex traits. Therefore, the evolutionary resilience of microbial communities and their ability to constraint detrimental mutants should be considered to design robust biotechnological applications.
Collapse
Affiliation(s)
- Matteo Cavaliere
- School of Informatics, BBSRC/EPSRC/MRC Synthetic Biology Research CentreUniversity of EdinburghEdinburghEH8 9ABUK
| | - Song Feng
- Center for Nonlinear StudiesTheoretical Division (T‐6), Los Alamos National LaboratoryLos AlamosNM 87545USA
| | - Orkun S. Soyer
- School of Life Sciences, BBSRC/EPSRC Warwick Integrative Synthetic Biology CentreUniversity of WarwickCoventryCV4 7ALUK
| | - José I. Jiménez
- Faculty of Health and Medical SciencesUniversity of SurreyGuildfordGU2 7XHUK
| |
Collapse
|
39
|
Pathak VM, Navneet. Review on the current status of polymer degradation: a microbial approach. BIORESOUR BIOPROCESS 2017. [DOI: 10.1186/s40643-017-0145-9] [Citation(s) in RCA: 308] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
|
40
|
Nemoto S, Ueno T, Watthanaphanit A, Hieda J, Saito N. Crystallinity and surface state of cellulose in wet ball-milling process. J Appl Polym Sci 2017. [DOI: 10.1002/app.44903] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shimpei Nemoto
- Department of Materials Science and Engineering, Graduate School of Engineering; Nagoya University; Furo-Cho, Chikusa-Ku Nagoya Aichi 464-8603 Japan
- CREST-JST, Nagoya University; Furo-Cho, Chikusa-Ku Nagoya Aichi 464-8603 Japan
| | - Tomonaga Ueno
- Department of Materials Science and Engineering, Graduate School of Engineering; Nagoya University; Furo-Cho, Chikusa-Ku Nagoya Aichi 464-8603 Japan
- CREST-JST, Nagoya University; Furo-Cho, Chikusa-Ku Nagoya Aichi 464-8603 Japan
| | - Anyarat Watthanaphanit
- Department of Chemistry, Faculty of Science; Mahidol University; 272 Thanon Rama VI, Thung Phaya Thai Retchathewi Bangkok 10400 Thailand
| | - Junko Hieda
- Department of Materials Science and Engineering, Graduate School of Engineering; Nagoya University; Furo-Cho, Chikusa-Ku Nagoya Aichi 464-8603 Japan
| | - Nagahiro Saito
- Department of Materials Science and Engineering, Graduate School of Engineering; Nagoya University; Furo-Cho, Chikusa-Ku Nagoya Aichi 464-8603 Japan
- CREST-JST, Nagoya University; Furo-Cho, Chikusa-Ku Nagoya Aichi 464-8603 Japan
| |
Collapse
|
41
|
Karnaouri A, Muraleedharan MN, Dimarogona M, Topakas E, Rova U, Sandgren M, Christakopoulos P. Recombinant expression of thermostable processive MtEG5 endoglucanase and its synergism with MtLPMO from Myceliophthora thermophila during the hydrolysis of lignocellulosic substrates. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:126. [PMID: 28515785 PMCID: PMC5432998 DOI: 10.1186/s13068-017-0813-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 05/08/2017] [Indexed: 05/02/2023]
Abstract
BACKGROUND Filamentous fungi are among the most powerful cellulolytic organisms in terrestrial ecosystems. To perform the degradation of lignocellulosic substrates, these microorganisms employ both hydrolytic and oxidative mechanisms that involve the secretion and synergism of a wide variety of enzymes. Interactions between these enzymes occur on the level of saccharification, i.e., the release of neutral and oxidized products, but sometimes also reflected in the substrate liquefaction. Although the synergism regarding the yield of neutral sugars has been extensively studied, further studies should focus on the oxidized sugars, as well as the effect of enzyme combinations on the viscosity properties of the substrates. RESULTS In the present study, the heterologous expression of an endoglucanase (EG) and its combined activity together with a lytic polysaccharide monooxygenase (LPMO), both from the thermophilic fungus Myceliophthora thermophila, are described. The EG gene, belonging to the glycoside hydrolase family 5, was functionally expressed in the methylotrophic yeast Pichia pastoris. The produced MtEG5A (75 kDa) featured remarkable thermal stability and showed high specific activity on microcrystalline cellulose compared to CMC, which is indicative of its processivity properties. The enzyme was capable of releasing high amounts of cellobiose from wheat straw, birch, and spruce biomass. Addition of MtLPMO9 together with MtEG5A showed enhanced enzymatic hydrolysis yields against regenerated amorphous cellulose (PASC) by improving the release not only of the neutral but also of the oxidized sugars. Assessment of activity of MtEG5A on the reduction of viscosity of PASC and pretreated wheat straw using dynamic viscosity measurements revealed that the enzyme is able to perform liquefaction of the model substrate and the natural lignocellulosic material, while when added together with MtLPMO9, no further synergistic effect was observed. CONCLUSIONS The endoglucanase MtEG5A from the thermophilic fungus M. thermophila exhibited excellent properties that render it a suitable candidate for use in biotechnological applications. Its strong synergism with LPMO was reflected in sugars release, but not in substrate viscosity reduction. Based on the level of oxidative sugar formation, this is the first indication of synergy between LPMO and EG reported.
Collapse
Affiliation(s)
- Anthi Karnaouri
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
| | - Madhu Nair Muraleedharan
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
| | - Maria Dimarogona
- Biotechnology Laboratory, Department of Synthesis and Development of Industrial Processes, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Evangelos Topakas
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
- Biotechnology Laboratory, Department of Synthesis and Development of Industrial Processes, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Ulrika Rova
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
| | - Mats Sandgren
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Paul Christakopoulos
- Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
| |
Collapse
|
42
|
Reyes-Sosa FM, López Morales M, Platero Gómez AI, Valbuena Crespo N, Sánchez Zamorano L, Rocha-Martín J, Molina-Heredia FP, Díez García B. Management of enzyme diversity in high-performance cellulolytic cocktails. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:156. [PMID: 28649275 PMCID: PMC5477296 DOI: 10.1186/s13068-017-0845-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 06/12/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Modern biorefineries require enzymatic cocktails of improved efficiency to generate fermentable sugars from lignocellulosic biomass. Cellulolytic fungi, among other microorganisms, have demonstrated the highest potential in terms of enzymatic productivity, complexity and efficiency. On the other hand, under cellulolytic-inducing conditions, they often produce a considerable diversity of carbohydrate-active enzymes which allow them to adapt to changing environmental conditions. However, industrial conditions are fixed and adjusted to the optimum of the whole cocktail, resulting in underperformance of individual enzymes. RESULTS One of these cellulolytic cocktails from Myceliophthora thermophila has been analyzed here by means of LC-MS/MS. Pure GH6 family members detected have been characterized, confirming previous studies, and added to whole cocktails to compare their contribution in the hydrolysis of industrial substrates. Finally, independent deletions of two GH6 family members, as an example of the enzymatic diversity management, led to the development of a strain producing a more efficient cellulolytic cocktail. CONCLUSIONS These data indicate that the deletion of noncontributive cellulases (here EG VI) can increase the cellulolytic efficiency of the cocktail, validating the management of cellulase diversity as a strategy to obtain improved fungal cellulolytic cocktails.
Collapse
Affiliation(s)
| | - Macarena López Morales
- Department of Biotechnology, Abengoa Research, Campus Palmas Altas, C/Energía Solar 1, 41014 Seville, Spain
| | - Ana Isabel Platero Gómez
- Department of Biotechnology, Abengoa Research, Campus Palmas Altas, C/Energía Solar 1, 41014 Seville, Spain
| | - Noelia Valbuena Crespo
- Department of Biotechnology, Abengoa Research, Campus Palmas Altas, C/Energía Solar 1, 41014 Seville, Spain
| | - Laura Sánchez Zamorano
- Department of Biotechnology, Abengoa Research, Campus Palmas Altas, C/Energía Solar 1, 41014 Seville, Spain
| | - Javier Rocha-Martín
- Department of Biotechnology, Abengoa Research, Campus Palmas Altas, C/Energía Solar 1, 41014 Seville, Spain
| | - Fernando P. Molina-Heredia
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla y CSIC, Américo Vespucio 49, 41092 Seville, Spain
| | - Bruno Díez García
- Department of Biotechnology, Abengoa Research, Campus Palmas Altas, C/Energía Solar 1, 41014 Seville, Spain
| |
Collapse
|
43
|
Corrêa TLR, dos Santos LV, Pereira GAG. AA9 and AA10: from enigmatic to essential enzymes. Appl Microbiol Biotechnol 2016; 100:9-16. [PMID: 26476647 DOI: 10.1007/s00253-015-7040-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 09/20/2015] [Accepted: 09/24/2015] [Indexed: 12/15/2022]
Abstract
The lignocellulosic biomass, comprised mainly of cellulose, hemicellulose, and lignin, is a strong competitor for petroleum to obtain fuels and other products because of its renewable nature, low cost, and non-competitiveness with food production when obtained from agricultural waste. Due to its recalcitrance, lignocellulosic material requires an arsenal of enzymes for its deconstruction and the consequent release of fermentable sugars. In this context, enzymes currently classified as auxiliary activity 9 (AA9/formerly GH61) and 10 (AA10/formerly CBM 33) or lytic polysaccharide monooxygenases (LPMO) have emerged as cellulase boosting enzymes. AA9 and AA10 are the new paradigm for deconstruction of lignocellulosic biomass by enhancing the activity and decreasing the loading of classical enzymes to the reaction and, consequently, reducing costs of the hydrolysis step in the second-generation ethanol production chain. In view of that disclosed above, the goal of this work is to review experimental data that supports the relevance of AA9 and AA10 for the biomass deconstruction field.
Collapse
|
44
|
Sekar R, Shin HD, DiChristina TJ. Direct conversion of cellulose and hemicellulose to fermentable sugars by a microbially-driven Fenton reaction. BIORESOURCE TECHNOLOGY 2016; 218:1133-1139. [PMID: 27469094 DOI: 10.1016/j.biortech.2016.07.087] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 07/18/2016] [Accepted: 07/20/2016] [Indexed: 06/06/2023]
Abstract
The aim of this work was to develop a microbially-driven Fenton reaction that fragments cellulose and hemicellulose, degrades cellodextrins and xylodextrins, and produces short-chain oligosaccharides and monomeric sugars in a single bioreactor. The lignocellulose degradation system operates at neutral pH and does not require addition of conventional lignocellulose-degrading enzymes, thus avoiding problems associated with enzyme accessibility and specificity. The ability to produce useful bioproducts was demonstrated by production of the bioplastic polyhydroxybutyrate with the xylan degradation products as starting substrate.
Collapse
Affiliation(s)
- Ramanan Sekar
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Hyun Dong Shin
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Thomas J DiChristina
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, United States.
| |
Collapse
|
45
|
Dos Santos Castro L, de Paula RG, Antoniêto ACC, Persinoti GF, Silva-Rocha R, Silva RN. Understanding the Role of the Master Regulator XYR1 in Trichoderma reesei by Global Transcriptional Analysis. Front Microbiol 2016; 7:175. [PMID: 26909077 PMCID: PMC4754417 DOI: 10.3389/fmicb.2016.00175] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 02/01/2016] [Indexed: 11/13/2022] Open
Abstract
We defined the role of the transcriptional factor—XYR1—in the filamentous fungus Trichoderma reesei during cellulosic material degradation. In this regard, we performed a global transcriptome analysis using RNA-Seq of the Δxyr1 mutant strain of T. reesei compared with the parental strain QM9414 grown in the presence of cellulose, sophorose, and glucose as sole carbon sources. We found that 5885 genes were expressed differentially under the three tested carbon sources. Of these, 322 genes were upregulated in the presence of cellulose, while 367 and 188 were upregulated in sophorose and glucose, respectively. With respect to genes under the direct regulation of XYR1, 30 and 33 are exclusive to cellulose and sophorose, respectively. The most modulated genes in the Δxyr1 belong to Carbohydrate-Active Enzymes (CAZymes), transcription factors, and transporters families. Moreover, we highlight the downregulation of transporters belonging to the MFS and ABC transporter families. Of these, MFS members were mostly downregulated in the presence of cellulose. In sophorose and glucose, the expression of these transporters was mainly upregulated. Our results revealed that MFS and ABC transporters could be new players in cellulose degradation and their role was shown to be carbon source-dependent. Our findings contribute to a better understanding of the regulatory mechanisms of XYR1 to control cellulase gene expression in T. reesei in the presence of cellulosic material, thereby potentially enhancing its application in several biotechnology fields.
Collapse
Affiliation(s)
- Lilian Dos Santos Castro
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
| | - Renato G de Paula
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
| | - Amanda C C Antoniêto
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
| | - Gabriela F Persinoti
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais Campinas, Brazil
| | - Rafael Silva-Rocha
- Systems and Synthetic Biology Laboratory, Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
| | - Roberto N Silva
- Molecular Biotechnology Laboratory, Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo Ribeirão Preto, Brazil
| |
Collapse
|
46
|
The Renaissance of Neurospora crassa: How a Classical Model System is Used for Applied Research. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27951-0_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
47
|
Montella S, Amore A, Faraco V. Metagenomics for the development of new biocatalysts to advance lignocellulose saccharification for bioeconomic development. Crit Rev Biotechnol 2015; 36:998-1009. [PMID: 26381035 DOI: 10.3109/07388551.2015.1083939] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The world economy is moving toward the use of renewable and nonedible lignocellulosic biomasses as substitutes for fossil sources in order to decrease the environmental impact of manufacturing processes and overcome the conflict with food production. Enzymatic hydrolysis of the feedstock is a key technology for bio-based chemical production, and the identification of novel, less expensive and more efficient biocatalysts is one of the main challenges. As the genomic era has shown that only a few microorganisms can be cultured under standard laboratory conditions, the extraction and analysis of genetic material directly from environmental samples, termed metagenomics, is a promising way to overcome this bottleneck. Two screening methodologies can be used on metagenomic material: the function-driven approach of expression libraries and sequence-driven analysis based on gene homology. Both techniques have been shown to be useful for the discovery of novel biocatalysts for lignocellulose conversion, and they enabled identification of several (hemi)cellulases and accessory enzymes involved in (hemi)cellulose hydrolysis. This review summarizes the latest progress in metagenomics aimed at discovering new enzymes for lignocellulose saccharification.
Collapse
Affiliation(s)
- Salvatore Montella
- a Department of Chemical Sciences , University of Naples "Federico II", Complesso Universitario Monte S. Angelo , Naples , Italy
| | - Antonella Amore
- a Department of Chemical Sciences , University of Naples "Federico II", Complesso Universitario Monte S. Angelo , Naples , Italy
| | - Vincenza Faraco
- a Department of Chemical Sciences , University of Naples "Federico II", Complesso Universitario Monte S. Angelo , Naples , Italy
| |
Collapse
|
48
|
Protein disulfide isomerase homolog TrPDI2 contributing to cellobiohydrolase production in Trichoderma reesei. Enzyme Microb Technol 2015; 77:21-8. [PMID: 26138396 DOI: 10.1016/j.enzmictec.2015.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 05/07/2015] [Accepted: 05/19/2015] [Indexed: 11/21/2022]
Abstract
The majority of the cysteine residues in the secreted proteins form disulfide bonds via protein disulfide isomerase (PDI)-mediated catalysis, stabilizing the enzyme activity. The role of PDI in cellulase production is speculative, as well as the possibility of PDI as a target for improving enzyme production efficiency of Trichoderma reesei, a widely used producer of enzyme for the production of lignocellulose-based biofuels and biochemicals. Here, we report that a PDI homolog, TrPDI2 in T. reesei exhibited a 36.94% and an 11.81% similarity to Aspergillus niger TIGA and T. reesei PDI1, respectively. The capability of TrPDI2 to recover the activity of reduced and denatured RNase by promoting refolding verified its protein disulfide isomerase activity. The overexpression of Trpdi2 increased the secretion and the activity of CBH1 at the early stage of cellulase induction. In addition, both the expression level and redox state of TrPDI2 responded to cellulase induction in T. reesei, providing sustainable oxidative power to ensure cellobiohydrolase maturation and production. The results suggest that TrPDI2 may contribute to cellobiohydrolase secretion by enhancing the capability of disulfide bond formation, which is essential for protein folding and maturation.
Collapse
|
49
|
Adsul M, Sharma B, Singhania RR, Saini JK, Sharma A, Mathur A, Gupta R, Tuli DK. Blending of cellulolytic enzyme preparations from different fungal sources for improved cellulose hydrolysis by increasing synergism. RSC Adv 2014. [DOI: 10.1039/c4ra08129c] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A prepared enzyme cocktail from different fungal enzyme preparations increases the hydrolysis of avicel/wheat straw by increasing synergism between the same or different types of cellulases.
Collapse
Affiliation(s)
- Mukund Adsul
- DBT-IOC Centre for Advanced Bioenergy Research
- Indian Oil R and D Centre
- Faridabad-121007, India
| | - Bhawna Sharma
- DBT-IOC Centre for Advanced Bioenergy Research
- Indian Oil R and D Centre
- Faridabad-121007, India
| | - Reeta Rani Singhania
- DBT-IOC Centre for Advanced Bioenergy Research
- Indian Oil R and D Centre
- Faridabad-121007, India
| | - Jitendra Kumar Saini
- DBT-IOC Centre for Advanced Bioenergy Research
- Indian Oil R and D Centre
- Faridabad-121007, India
| | - Ankita Sharma
- DBT-IOC Centre for Advanced Bioenergy Research
- Indian Oil R and D Centre
- Faridabad-121007, India
| | - Anshu Mathur
- DBT-IOC Centre for Advanced Bioenergy Research
- Indian Oil R and D Centre
- Faridabad-121007, India
| | - Ravi Gupta
- DBT-IOC Centre for Advanced Bioenergy Research
- Indian Oil R and D Centre
- Faridabad-121007, India
| | - Deepak Kumar Tuli
- DBT-IOC Centre for Advanced Bioenergy Research
- Indian Oil R and D Centre
- Faridabad-121007, India
| |
Collapse
|
50
|
Dimarogona M, Topakas E, Christakopoulos P. Recalcitrant polysaccharide degradation by novel oxidative biocatalysts. Appl Microbiol Biotechnol 2013; 97:8455-65. [PMID: 23995228 DOI: 10.1007/s00253-013-5197-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 08/09/2013] [Accepted: 08/12/2013] [Indexed: 12/13/2022]
Abstract
The classical hydrolytic mechanism for the degradation of plant polysaccharides by saprophytic microorganisms has been reconsidered after the recent landmark discovery of a new class of oxidases termed lytic polysaccharide monooxygenases (LPMOs). LPMOs are of increased biotechnological interest due to their implication in lignocellulosic biomass decomposition for the production of biofuels and high-value chemicals. They act on recalcitrant polysaccharides by a combination of hydrolytic and oxidative function, generating oxidized and non-oxidized chain ends. They are copper-dependent and require molecular oxygen and an external electron donor for their proper function. In this review, we present the recent findings concerning the mechanism of action of these oxidative enzymes and identify issues and questions to be addressed in the future.
Collapse
Affiliation(s)
- Maria Dimarogona
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str, Zografou Campus, 15700, Athens, Greece
| | | | | |
Collapse
|