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Baramee S, Thianheng P, Uke A, Cheawchanlertfa P, Tachaapaikoon C, Waeonukul R, Pason P, Ratanakhanokchai K, Liu YJ, Kosugi A. Extracytoplasmic polysaccharides control cellulosomal and non-cellulosomal systems in Herbivorax saccincola A7. Appl Microbiol Biotechnol 2024; 108:477. [PMID: 39352555 PMCID: PMC11445354 DOI: 10.1007/s00253-024-13310-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Revised: 09/09/2024] [Accepted: 09/10/2024] [Indexed: 10/04/2024]
Abstract
Herbivorax saccincola A7 is an anaerobic alkali-thermophilic lignocellulolytic bacterium that possesses a cellulosome and high xylan degradation ability. To understand the expression profile of extracellular enzymes by carbon sources, quantitative real-time PCR was performed on all cellulosomal and non-cellulosomal enzyme genes of H. saccincola A7 using cellulose and xylan as carbon sources. The results confirmed that the scaffolding proteins of H. saccincola A7 were expressed. In general, the cellulosomal genes belonging to the glycoside hydrolase families 9, 10, 11, and 48 were repressed when xylan was the sole carbon source, but these genes were significantly induced in the presence of cellulose. These results indicate that cellulose, not xylan, is a key inducer of cellulosomal genes in H. saccincola A7. The RsgI-like proteins, which regulate a carbohydrate-sensing mechanism in Clostridium thermocellum, were also found to be encoded in the H. saccincola A7 genome. To confirm the regulation by RsgI-like proteins, the relative expression of σI1-σI4 factors was analyzed on both carbon sources. The expression of alternative σI1 and σI2 factors was enhanced by the presence of cellulose. By contrast, the expression of σI3 and σI4 factors was activated by both cellulose and xylan. Taken together, the results reveal that the cellulosomal and non-cellulosomal genes of H. saccincola A7 are regulated through a carbohydrate-sensing mechanism involving anti-σ regulator RsgI-like proteins. KEY POINTS: • qRT-PCR performed on cellulosomal and non-cellulosomal genes of H. saccincola A7 • Cellulose is a key inducer of the cellulosome of H. saccincola A7 • H. saccincola A7 possesses a similar system of anti-σ regulator RsgI-like proteins.
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Affiliation(s)
- Sirilak Baramee
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Pakinee Thianheng
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
- Enzyme Technology Laboratory, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Ayaka Uke
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Pattsarun Cheawchanlertfa
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
- Enzyme Technology Laboratory, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Chakrit Tachaapaikoon
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
- Enzyme Technology Laboratory, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Rattiya Waeonukul
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
- Enzyme Technology Laboratory, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Patthra Pason
- Excellent Center of Enzyme Technology and Microbial Utilization, Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
- Enzyme Technology Laboratory, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Khanok Ratanakhanokchai
- Enzyme Technology Laboratory, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (KMUTT), Bangkok, 10150, Thailand
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, PR China
- Shandong Energy Institute, Qingdao, 266101, PR China
- Qingdao New Energy Shandong Laboratory, Qingdao, 266101, PR China
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan.
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Chaudhary A, Hussain Z, Ajmal H, Abdul Rehman R, Abbas G, Aihetasham A, Tahira SA. Efficient Bioconversion of Mango Waste into Ethanol Employing Plackett-Burman and Central Composite Models. ACS OMEGA 2024; 9:39652-39662. [PMID: 39346855 PMCID: PMC11425814 DOI: 10.1021/acsomega.4c04374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 08/31/2024] [Accepted: 09/05/2024] [Indexed: 10/01/2024]
Abstract
The current study focuses on the idea of "Energy from Waste" that intends to address energy crises and manage waste. Fruit waste is one of the most common forms of organic waste due to its inedible portion and perishable nature. In Pakistani regions, an extensive amount of mango pulp (MP)/juice waste is produced due to excessive consumption during summers, which poses huge environmental challenges. The study aims at effective valorization of perishable waste and elimination of deteriorating waste that causes a polluting environment. Experimental work has been conducted to evaluate the sucrolytic potential of Bacillus cereus FA3 for the bioconversion of sucrose from mango waste into reducing sugars for ethanologenesis. The Plackett-Burman model was designed to analyze enzymatic hydrolytic parameters for sugar conversion. The model was significant for reducing sugars with F and p values of 43.99 and 0.0013 correspondingly. 11.43 ± 0.068 g/L maximum reducing sugars were analyzed in MP after hydrolysis with 12.58 IU of crude enzyme dosage of B. cereus FA3 at 30 °C within 5 days with a 22% enzyme conversion rate. Additionally, the ethanologenic potentials of experimental Metschnikowia cibodasensis Y34 and standard Saccharomyces cerevisiae K7 yeasts were investigated from mango hydrolyzate when subjected to central composite design as a statistical optimization tool. These findings exhibited significantly higher response outcomes and good development for waste management.
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Affiliation(s)
- Asma Chaudhary
- Department
of Zoology, Division of Science and Technology, University of Education, Lahore 54770, Pakistan
| | - Zawar Hussain
- Department
of Zoology, Division of Science and Technology, University of Education, Lahore 54770, Pakistan
| | - Hafsa Ajmal
- Department
of Zoology, Division of Science and Technology, University of Education, Lahore 54770, Pakistan
| | - Rahat Abdul Rehman
- Department
of Forensic Medicine/Medical Jurisprudence, University of Health Sciences, Lahore 54600, Pakistan
| | - Ghulam Abbas
- Department
of Biotechnology, University of Agriculture, Dera Ismail Khan, Khyber
Pakhtunkhwa 29111, Pakistan
| | - Ayesha Aihetasham
- Institute
of Zoology, University of the Punjab, Lahore 54590, Pakistan
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3
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Pech-Canul A, Hammer SK, Ziegler SJ, Richardson ID, Sharma BD, Maloney MI, Bomble YJ, Lynd LR, Olson DG. The role of AdhE on ethanol tolerance and production in Clostridium thermocellum. J Biol Chem 2024; 300:107559. [PMID: 39002679 PMCID: PMC11365378 DOI: 10.1016/j.jbc.2024.107559] [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: 03/19/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/15/2024] Open
Abstract
Many anaerobic microorganisms use the bifunctional aldehyde and alcohol dehydrogenase enzyme, AdhE, to produce ethanol. One such organism is Clostridium thermocellum, which is of interest for cellulosic biofuel production. In the course of engineering this organism for improved ethanol tolerance and production, we observed that AdhE was a frequent target of mutations. Here, we characterized those mutations to understand their effects on enzymatic activity, as well ethanol tolerance and product formation in the organism. We found that there is a strong correlation between NADH-linked alcohol dehydrogenase (ADH) activity and ethanol tolerance. Mutations that decrease NADH-linked ADH activity increase ethanol tolerance; correspondingly, mutations that increase NADH-linked ADH activity decrease ethanol tolerance. We also found that the magnitude of ADH activity did not play a significant role in determining ethanol titer. Increasing ADH activity had no effect on ethanol titer. Reducing ADH activity had indeterminate effects on ethanol titer, sometimes increasing and sometimes decreasing it. Finally, this study shows that the cofactor specificity of ADH activity was found to be the primary factor affecting ethanol yield. We expect that these results will inform efforts to use AdhE enzymes in metabolic engineering approaches.
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Affiliation(s)
- Angel Pech-Canul
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Sarah K Hammer
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Samantha J Ziegler
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA; Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Isaiah D Richardson
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Bishal D Sharma
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Marybeth I Maloney
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Yannick J Bomble
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA; Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado, USA
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Daniel G Olson
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
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4
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Jamal QMS, Ahmad V. Bacterial metabolomics: current applications for human welfare and future aspects. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2024:1-24. [PMID: 39078342 DOI: 10.1080/10286020.2024.2385365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 07/31/2024]
Abstract
An imbalanced microbiome is linked to several diseases, such as cancer, inflammatory bowel disease, obesity, and even neurological disorders. Bacteria and their by-products are used for various industrial and clinical purposes. The metabolites under discussion were chosen based on their biological impacts on host and gut microbiota interactions as established by metabolome research. The separation of bacterial metabolites by using statistics and machine learning analysis creates new opportunities for applications of bacteria and their metabolites in the environmental and medical sciences. Thus, the metabolite production strategies, methodologies, and importance of bacterial metabolites for human well-being are discussed in this review.
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Affiliation(s)
- Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia
| | - Varish Ahmad
- Health Information Technology Department, The Applied College, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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Lyu H, Zhong R, Kilasara M, Hartono A, Sun Z, Funakawa S, Watanabe T. Impact of Climate on Soil Organic Matter Composition in Soils of Tropical Volcanic Regions Revealed by EGA-MS and Py-GC/MS. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:9646-9657. [PMID: 38758106 DOI: 10.1021/acs.est.3c07000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Soil organic matter (SOM) crucially influences the global carbon cycle, yet its molecular composition and determinants are understudied, especially for tropical volcanic regions. We investigated how SOM compounds change in response to climate, vegetation, soil horizon, and soil properties and the relationship between SOM composition and microbial decomposability in Tanzanian and Indonesian volcanic regions. We collected topsoil (0-15 cm) and subsoil (20-40 cm) horizons (n = 22; pH: 4.6-7.6; SOC: 10-152 g kg-1) with undisturbed vegetation and wide mean annual temperature and moisture ranges (14-26 °C; 800-3300 mm) across four elevational transects (340-2210 m asl.). Evolved gas analysis-mass spectrometry (EGA-MS) documented a simultaneous release of SOM compounds and clay mineral dehydroxylation. Subsequently applying double-shot pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) at 200 and 550 °C, we detailed the molecular composition of topsoil and subsoil SOM. A minor portion (2.7 ± 1.9%) of compounds desorbed at 200 °C, limiting its efficacy for investigating overall SOM characteristics. Pyrolyzed SOM closely aligns with the intermediate decomposable SOM pool, with most pyrolysates (550 °C) originating from this pool. Pyrolysates composition suggests tropical SOM is mainly microbial-derived and subsoil contains more degraded compounds. Higher litter inputs and attenuated SOM decomposition due to cooler temperatures and lower soil pH (<5.5) produce less-degraded SOM at higher elevations. Redundancy analyses revealed the crucial role of active Al/Fe (oxalate-extractable Al/Fe), abundant in low-temperature/high-moisture conditions, in stabilizing these less-degraded components. Our findings provide new insights into SOM molecular composition and its determinants, critical for understanding the carbon cycle in tropical ecosystems.
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Affiliation(s)
- Han Lyu
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
- Organization for WISE Program, Tokyo University of Agriculture and Technology, Fuchu 183-8509, Tokyo, Japan
| | - Ruohan Zhong
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Method Kilasara
- College of Agriculture, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Arief Hartono
- Faculty of Agriculture, Bogor Agricultural University, Bogor 16680, West Java, Indonesia
| | - Zheng Sun
- CNRS, EPHE, UMR 7619 METIS, Sorbonne Université, 4 Place Jussieu, F-75005 Paris, France
| | - Shinya Funakawa
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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6
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Chou KJ, Croft T, Hebdon SD, Magnusson LR, Xiong W, Reyes LH, Chen X, Miller EJ, Riley DM, Dupuis S, Laramore KA, Keller LM, Winkelman D, Maness PC. Engineering the cellulolytic bacterium, Clostridium thermocellum, to co-utilize hemicellulose. Metab Eng 2024; 83:193-205. [PMID: 38631458 DOI: 10.1016/j.ymben.2024.03.008] [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: 12/28/2023] [Revised: 03/15/2024] [Accepted: 03/29/2024] [Indexed: 04/19/2024]
Abstract
Consolidated bioprocessing (CBP) of lignocellulosic biomass holds promise to realize economic production of second-generation biofuels/chemicals, and Clostridium thermocellum is a leading candidate for CBP due to it being one of the fastest degraders of crystalline cellulose and lignocellulosic biomass. However, CBP by C. thermocellum is approached with co-cultures, because C. thermocellum does not utilize hemicellulose. When compared with a single-species fermentation, the co-culture system introduces unnecessary process complexity that may compromise process robustness. In this study, we engineered C. thermocellum to co-utilize hemicellulose without the need for co-culture. By evolving our previously engineered xylose-utilizing strain in xylose, an evolved clonal isolate (KJC19-9) was obtained and showed improved specific growth rate on xylose by ∼3-fold and displayed comparable growth to a minimally engineered strain grown on the bacteria's naturally preferred substrate, cellobiose. To enable full xylan deconstruction to xylose, we recombinantly expressed three different β-xylosidase enzymes originating from Thermoanaerobacterium saccharolyticum into KJC19-9 and demonstrated growth on xylan with one of the enzymes. This recombinant strain was capable of co-utilizing cellulose and xylan simultaneously, and we integrated the β-xylosidase gene into the KJC19-9 genome, creating the KJCBXint strain. The strain, KJC19-9, consumed monomeric xylose but accumulated xylobiose when grown on pretreated corn stover, whereas the final KJCBXint strain showed significantly greater deconstruction of xylan and xylobiose. This is the first reported C. thermocellum strain capable of degrading and assimilating hemicellulose polysaccharide while retaining its cellulolytic capabilities, unlocking significant potential for CBP in advancing the bioeconomy.
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Affiliation(s)
- Katherine J Chou
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA.
| | - Trevor Croft
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Skyler D Hebdon
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Lauren R Magnusson
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Wei Xiong
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Luis H Reyes
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA; Grupo de Diseño de Productos y Procesos, Department of Chemical and Food Engineering, Universidad de los Andes, Bogotá, Colombia
| | - Xiaowen Chen
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Emily J Miller
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Danielle M Riley
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Sunnyjoy Dupuis
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Kathrin A Laramore
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Lisa M Keller
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Dirk Winkelman
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
| | - Pin-Ching Maness
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80228, USA
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7
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Lau MH, Madika A, Zhang Y, Minton NP. Parageobacillus thermoglucosidasius Strain Engineering Using a Theophylline Responsive RiboCas for Controlled Gene Expression. ACS Synth Biol 2024; 13:1237-1245. [PMID: 38517011 PMCID: PMC11036489 DOI: 10.1021/acssynbio.3c00735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/23/2024]
Abstract
The relentless increase in atmospheric greenhouse gas concentrations as a consequence of the exploitation of fossil resources compels the adoption of sustainable routes to chemical and fuel manufacture based on biological fermentation processes. The use of thermophilic chassis in such processes is an attractive proposition; however, their effective exploitation will require improved genome editing tools. In the case of the industrially relevant chassis Parageobacillus thermoglucosidasius, CRISPR/Cas9-based gene editing has been demonstrated. The constitutive promoter used, however, accentuates the deleterious nature of Cas9, causing decreased transformation and low editing efficiencies, together with an increased likelihood of off-target effects or alternative mutations. Here, we rectify this issue by controlling the expression of Cas9 through the use of a synthetic riboswitch that is dependent on the nonmetabolized, nontoxic, and cheap inducer, theophylline. We demonstrate that the riboswitches are dose-dependent, allowing for controlled expression of the target gene. Through their use, we were then able to address the deleterious nature of Cas9 and produce an inducible system, RiboCas93. The benefits of RiboCas93 were demonstrated by increased transformation efficiency of the editing vectors, improved efficiency in mutant generation (100%), and a reduction of Cas9 toxicity, as indicated by a reduction in the number of single nucleotide polymorphisms (SNPs) observed. This new system provides a quick and efficient way to produce mutants in P. thermoglucosidasius.
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Affiliation(s)
- Matthew
S. H. Lau
- BBSRC/EPSRC
Synthetic Biology Research Centre (SBRC), Biodiscovery Institute,
School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K.
| | - Abubakar Madika
- BBSRC/EPSRC
Synthetic Biology Research Centre (SBRC), Biodiscovery Institute,
School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K.
- Department
of Microbiology, Faculty of Life Sciences, Ahmadu Bello University, Zaria 810107, Nigeria
| | - Ying Zhang
- BBSRC/EPSRC
Synthetic Biology Research Centre (SBRC), Biodiscovery Institute,
School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K.
| | - Nigel P. Minton
- BBSRC/EPSRC
Synthetic Biology Research Centre (SBRC), Biodiscovery Institute,
School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K.
- NIHR
Nottingham Biomedical Research Centre, Nottingham
University Hospitals NHS Trust and The University of Nottingham, Nottingham NG7 2RD, U.K.
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8
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Wang Y, Qian J, Shi T, Wang Y, Ding Q, Ye C. Application of extremophile cell factories in industrial biotechnology. Enzyme Microb Technol 2024; 175:110407. [PMID: 38341913 DOI: 10.1016/j.enzmictec.2024.110407] [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: 12/15/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/13/2024]
Abstract
Due to the extreme living conditions, extremophiles have unique characteristics in morphology, structure, physiology, biochemistry, molecular evolution mechanism and so on. Extremophiles have superior growth and synthesis capabilities under harsh conditions compared to conventional microorganisms, allowing for unsterilized fermentation processes and thus better performance in low-cost production. In recent years, due to the development and optimization of molecular biology, synthetic biology and fermentation technology, the identification and screening technology of extremophiles has been greatly improved. In this review, we summarize techniques for the identification and screening of extremophiles and review their applications in industrial biotechnology in recent years. In addition, the facts and perspectives gathered in this review suggest that next-generation industrial biotechnology (NGIBs) based on engineered extremophiles holds the promise of simplifying biofuturing processes, establishing open, non-sterilized continuous fermentation production systems, and utilizing low-cost substrates to make NGIBs attractive and cost-effective bioprocessing technologies for sustainable manufacturing.
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Affiliation(s)
- Yuzhou Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Jinyi Qian
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Tianqiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Yuetong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China
| | - Qiang Ding
- School of Life Sciences, Anhui University, Hefei 230601, PR China.
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, PR China; Ministry of Education Key Laboratory of NSLSCS.
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9
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Han CJ, Cheng CH, Yeh TF, Pauchet Y, Shelomi M. Coconut rhinoceros beetle digestive symbiosis with potential plant cell wall degrading microbes. NPJ Biofilms Microbiomes 2024; 10:34. [PMID: 38555351 PMCID: PMC10981690 DOI: 10.1038/s41522-024-00505-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 03/20/2024] [Indexed: 04/02/2024] Open
Abstract
Coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is an invasive palm pest whose larvae eat wood, yet lack the necessary digestive enzymes. This study confirmed endogenous CRB cellulase is inactive, suggesting microbial fermentation. The inner lining of the CRB hindgut has tree-like structures covered with a conspicuous biofilm. To identify possible symbionts, 16 S rRNA amplicon sequencing was used on individuals from across Taiwan. Several taxa of Clostridia, an anaerobic class including many cellulolytic bacteria, were highly abundant in most individuals from all locations. Whole metagenome sequencing further confirmed many lignocellulose degrading enzymes are derived from these taxa. Analyses of eggs, larvae, adults, and soil found these cellulolytic microbes are not transmitted vertically or transstadially. The core microbiomes of the larval CRB are likely acquired and enriched from the environment with each molt, and enable efficient digestion of wood.
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Affiliation(s)
- Chiao-Jung Han
- Department of Entomology, National Taiwan University, Taipei, Taiwan.
| | - Chih-Hsin Cheng
- School of Forestry & Resource Conservation, National Taiwan University, Taipei, Taiwan
| | - Ting-Feng Yeh
- School of Forestry & Resource Conservation, National Taiwan University, Taipei, Taiwan
| | - Yannick Pauchet
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Matan Shelomi
- Department of Entomology, National Taiwan University, Taipei, Taiwan
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10
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Datta R. Enzymatic degradation of cellulose in soil: A review. Heliyon 2024; 10:e24022. [PMID: 38234915 PMCID: PMC10792583 DOI: 10.1016/j.heliyon.2024.e24022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/13/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024] Open
Abstract
Cellulose degradation is a critical process in soil ecosystems, playing a vital role in nutrient cycling and organic matter decomposition. Enzymatic degradation of cellulosic biomass is the most sustainable and green method of producing liquid biofuel. It has gained intensive research interest with future perspective as the majority of terrestrial lignocellulose biomass has a great potential to be used as a source of bioenergy. However, the recalcitrant nature of lignocellulose limits its use as a source of energy. Noteworthy enough, enzymatic conversion of cellulose biomass could be a leading future technology. Fungal enzymes play a central role in cellulose degradation. Our understanding of fungal cellulases has substantially redirected in the past few years with the discovery of a new class of enzymes and Cellulosome. Efforts have been made from time to time to develop an economically viable method of cellulose degradation. This review provides insights into the current state of knowledge regarding cellulose degradation in soil and identifies areas where further research is needed.
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Affiliation(s)
- Rahul Datta
- Department of Geology and Pedology, Faculty of Forestry and Wood Technology. Mendel University In Brno, Czech Republic
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11
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Vasylyshyn R, Dmytruk O, Sybirnyy A, Ruchała J. Engineering of Ogataea polymorpha strains with ability for high-temperature alcoholic fermentation of cellobiose. FEMS Yeast Res 2024; 24:foae007. [PMID: 38400543 DOI: 10.1093/femsyr/foae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/30/2024] [Accepted: 02/22/2024] [Indexed: 02/25/2024] Open
Abstract
Successful conversion of cellulosic biomass into biofuels requires organisms capable of efficiently utilizing xylose as well as cellodextrins and glucose. Ogataea (Hansenula) polymorpha is the natural xylose-metabolizing organism and is one of the most thermotolerant yeasts known, with a maximum growth temperature above 50°C. Cellobiose-fermenting strains, derivatives of an improved ethanol producer from xylose O. polymorpha BEP/cat8∆, were constructed in this work by the introduction of heterologous genes encoding cellodextrin transporters (CDTs) and intracellular enzymes (β-glucosidase or cellobiose phosphorylase) that hydrolyze cellobiose. For this purpose, the genes gh1-1 of β-glucosidase, CDT-1m and CDT-2m of cellodextrin transporters from Neurospora crassa and the CBP gene coding for cellobiose phosphorylase from Saccharophagus degradans, were successfully expressed in O. polymorpha. Through metabolic engineering and mutagenesis, strains BEP/cat8∆/gh1-1/CDT-1m and BEP/cat8∆/CBP-1/CDT-2mAM were developed, showing improved parameters for high-temperature alcoholic fermentation of cellobiose. The study highlights the need for further optimization to enhance ethanol yields and elucidate cellobiose metabolism intricacies in O. polymorpha yeast. This is the first report of the successful development of stable methylotrophic thermotolerant strains of O. polymorpha capable of coutilizing cellobiose, glucose, and xylose under high-temperature alcoholic fermentation conditions at 45°C.
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Affiliation(s)
- Roksolana Vasylyshyn
- Institute of Biotechnology, College of Natural Sciences, University of Rzeszow, Cwiklinskiej 2D Street, 35-601 Rzeszow, Poland
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAN of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
| | - Olena Dmytruk
- Institute of Biotechnology, College of Natural Sciences, University of Rzeszow, Cwiklinskiej 2D Street, 35-601 Rzeszow, Poland
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAN of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
| | - Andriy Sybirnyy
- Institute of Biotechnology, College of Natural Sciences, University of Rzeszow, Cwiklinskiej 2D Street, 35-601 Rzeszow, Poland
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAN of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
| | - Justyna Ruchała
- Institute of Biotechnology, College of Natural Sciences, University of Rzeszow, Cwiklinskiej 2D Street, 35-601 Rzeszow, Poland
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAN of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
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12
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Saxena A, Hussain A, Parveen F, Ashfaque M. Current status of metabolic engineering of microorganisms for bioethanol production by effective utilization of pentose sugars of lignocellulosic biomass. Microbiol Res 2023; 276:127478. [PMID: 37625339 DOI: 10.1016/j.micres.2023.127478] [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: 05/08/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023]
Abstract
Lignocellulosic biomass, consisting of homo- and heteropolymeric sugars, acts as a substrate for the generation of valuable biochemicals and biomaterials. The readily available hexoses are easily utilized by microbes due to the presence of transporters and native metabolic pathways. But, utilization of pentose sugar viz., xylose and arabinose are still challenging due to several reasons including (i) the absence of the particular native pathways and transporters, (ii) the presence of inhibitors, and (iii) lower uptake of pentose sugars. These challenges can be overcome by manipulating metabolic pathways/glycosidic enzymes cascade by using genetic engineering tools involving inverse-metabolic engineering, ex-vivo isomerization, Adaptive Laboratory Evolution, Directed Metabolic Engineering, etc. Metabolic engineering of bacteria and fungi for the utilization of pentose sugars for bioethanol production is the focus area of research in the current decade. This review outlines current approaches to biofuel development and strategies involved in the metabolic engineering of different microbes that can uptake pentose for bioethanol production.
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Affiliation(s)
- Ayush Saxena
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| | - Akhtar Hussain
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| | - Fouziya Parveen
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| | - Mohammad Ashfaque
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
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13
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Jilani SB, Olson DG. Mechanism of furfural toxicity and metabolic strategies to engineer tolerance in microbial strains. Microb Cell Fact 2023; 22:221. [PMID: 37891678 PMCID: PMC10612203 DOI: 10.1186/s12934-023-02223-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Lignocellulosic biomass represents a carbon neutral cheap and versatile source of carbon which can be converted to biofuels. A pretreatment step is frequently used to make the lignocellulosic carbon bioavailable for microbial metabolism. Dilute acid pretreatment at high temperature and pressure is commonly utilized to efficiently solubilize the pentose fraction by hydrolyzing the hemicellulose fibers and the process results in formation of furans-furfural and 5-hydroxymethyl furfural-and other inhibitors which are detrimental to metabolism. The presence of inhibitors in the medium reduce productivity of microbial biocatalysts and result in increased production costs. Furfural is the key furan inhibitor which acts synergistically along with other inhibitors present in the hydrolysate. In this review, the mode of furfural toxicity on microbial metabolism and metabolic strategies to increase tolerance is discussed. Shared cellular targets between furfural and acetic acid are compared followed by discussing further strategies to engineer tolerance. Finally, the possibility to use furfural as a model inhibitor of dilute acid pretreated lignocellulosic hydrolysate is discussed. The furfural tolerant strains will harbor an efficient lignocellulosic carbon to pyruvate conversion mechanism in presence of stressors in the medium. The pyruvate can be channeled to any metabolite of interest by appropriate modulation of downstream pathway of interest. The aim of this review is to emphasize the use of hydrolysate as a carbon source for bioproduction of biofuels and other compounds of industrial importance.
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Affiliation(s)
- S Bilal Jilani
- Thayer School of Engineering, Dartmouth College, 15 Thayer Drive, Hanover, NH, 03755, USA.
| | - Daniel G Olson
- Thayer School of Engineering, Dartmouth College, 15 Thayer Drive, Hanover, NH, 03755, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
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14
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Seo H, Singh P, Wyman CE, Cai CM, Trinh CT. Rewiring metabolism of Clostridium thermocellum for consolidated bioprocessing of lignocellulosic biomass poplar to produce short-chain esters. BIORESOURCE TECHNOLOGY 2023:129263. [PMID: 37271458 DOI: 10.1016/j.biortech.2023.129263] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/06/2023]
Abstract
Consolidated bioprocessing (CBP) of lignocellulosic biomass uses cellulolytic microorganisms to enable enzyme production, saccharification, and fermentation to produce biofuels, biochemicals, and biomaterials in a single step. However, understanding and redirecting metabolisms of these microorganisms compatible with CBP are limited. Here, a cellulolytic thermophile Clostridium thermocellum was engineered and demonstrated to be compatible with CBP integrated with a Co-solvent Enhanced Lignocellulosic Fractionation (CELF) pretreatment for conversion of hardwood poplar into short-chain esters with industrial use as solvents, flavors, fragrances, and biofuels. The recombinant C. thermocellum engineered with deletion of carbohydrate esterases and stable overexpression of alcohol acetyltransferases improved ester production without compromised deacetylation activities. These esterases were discovered to exhibit promiscuous thioesterase activities and their deletion enhanced ester production by rerouting the electron and carbon metabolism. Ester production was further improved up to 80-fold and ester composition could be modulated by deleting lactate biosynthesis and using poplar with different pretreatment severity.
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Affiliation(s)
- Hyeongmin Seo
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, USA; Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Priyanka Singh
- Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Chemical and Environmental Engineering Department, University of California, Riverside, CA 92521, USA
| | - Charles E Wyman
- Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Chemical and Environmental Engineering Department, University of California, Riverside, CA 92521, USA
| | - Charles M Cai
- Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Chemical and Environmental Engineering Department, University of California, Riverside, CA 92521, USA
| | - Cong T Trinh
- Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN, USA; Center of Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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15
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Tamaru Y, Nakanishi S, Tanaka K, Umetsu M, Nakazawa H, Sugiyama A, Ito T, Shimokawa N, Takagi M. Recent research advances on non-linear phenomena in various biosystems. J Biosci Bioeng 2023:S1389-1723(23)00107-X. [PMID: 37246137 DOI: 10.1016/j.jbiosc.2023.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/03/2023] [Accepted: 03/22/2023] [Indexed: 05/30/2023]
Abstract
All biological phenomena can be classified as open, dissipative and non-linear. Moreover, the most typical phenomena are associated with non-linearity, dissipation and openness in biological systems. In this review article, four research topics on non-linear biosystems are described to show the examples from various biological systems. First, membrane dynamics of a lipid bilayer for the cell membrane is described. Since the cell membrane separates the inside of the cell from the outside, self-organizing systems that form spatial patterns on membranes often depend on non-linear dynamics. Second, various data banks based on recent genomics analysis supply the data including vast functional proteins from many organisms and their variable species. Since the proteins existing in nature are only a very small part of the space represented by amino acid sequence, success of mutagenesis-based molecular evolution approach crucially depends on preparing a library with high enrichment of functional proteins. Third, photosynthetic organisms depend on ambient light, the regular and irregular changes of which have a significant impact on photosynthetic processes. The light-driven process proceeds through many redox couples in the cyanobacteria constituting chain of redox reactions. Forth topics focuses on a vertebrate model, the zebrafish, which can help to understand, predict and control the chaos of complex biological systems. In particular, during early developmental stages, developmental differentiation occurs dynamically from a fertilized egg to divided and mature cells. These exciting fields of complexity, chaos, and non-linear science have experienced impressive growth in recent decades. Finally, future directions for non-liner biosystems are presented.
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Affiliation(s)
- Yutaka Tamaru
- Department of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Tsu, Mie 514-8507, Japan.
| | - Shuji Nakanishi
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Kenya Tanaka
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Mitsuo Umetsu
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aramakiazaaoba, Aoba, Sendai, Miyagi 980-8579, Japan
| | - Hikaru Nakazawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aramakiazaaoba, Aoba, Sendai, Miyagi 980-8579, Japan
| | - Aruto Sugiyama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aramakiazaaoba, Aoba, Sendai, Miyagi 980-8579, Japan
| | - Tomoyuki Ito
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aramakiazaaoba, Aoba, Sendai, Miyagi 980-8579, Japan
| | - Naofumi Shimokawa
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Masahiro Takagi
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
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16
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Ye C, Geng S, Zhang Y, Qiu H, Zhou J, Zeng Q, Zhao Y, Wu D, Yu G, Gong H, Hu B, Hong Y. The impact of culture systems on the gut microbiota and gut metabolome of bighead carp (Hypophthalmichthys nobilis). Anim Microbiome 2023; 5:20. [PMID: 37005679 PMCID: PMC10067185 DOI: 10.1186/s42523-023-00239-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/08/2023] [Indexed: 04/04/2023] Open
Abstract
BACKGROUND The gut microbiota of fish confers various effects on the host, including health, nutrition, metabolism, feeding behaviour, and immune response. Environment significantly impacts the community structure of fish gut microbiota. However, there is a lack of comprehensive research on the gut microbiota of bighead carp in culture systems. To demonstrate the impact of culture systems on the gut microbiome and metabolome in bighead carp and investigate a potential relationship between fish muscle quality and gut microbiota, we conducted a study using 16S ribosomal ribonucleic acid sequencing, gas chromatography-mass spectrometry, and liquid chromatography-mass spectrometry techniques on bighead carp in three culture systems. RESULTS Our study revealed significant differences in gut microbial communities and metabolic profiles among the three culture systems. We also observed conspicuous changes in muscle structure. The reservoir had higher gut microbiota diversity indices than the pond and lake. We detected significant differences in phyla and genera, such as Fusobacteria, Firmicutes, and Cyanobacteria at the phylum level, Clostridium sensu stricto 1, Macellibacteroides, Blvii28 wastewater sludge group at the genus level. Multivariate statistical models, including principal component analysis and orthogonal projections to latent structures-discriminant analysis, indicated significant differences in the metabolic profiles. Key metabolites were significantly enriched in metabolic pathways involved in "arginine biosynthesis" and "glycine, serine, and threonine metabolism". Variation partitioning analysis revealed that environmental factors, such as pH, ammonium nitrogen, and dissolved oxygen, were the primary drivers of differences in microbial communities. CONCLUSIONS Our findings demonstrate that the culture system significantly impacted the gut microbiota of bighead carp, resulting in differences in community structure, abundance, and potential metabolic functions, and altered the host's gut metabolism, especially in pathways related to amino acid metabolism. These differences were influenced substantially by environmental factors. Based on our study, we discussed the potential mechanisms by which gut microbes affect muscle quality. Overall, our study contributes to our understanding of the gut microbiota of bighead carp under different culture systems.
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Affiliation(s)
- Chen Ye
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Shiyu Geng
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Yingyu Zhang
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Huimin Qiu
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Jie Zhou
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Qi Zeng
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Yafei Zhao
- School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Di Wu
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Guilan Yu
- School of Life Science, Nanchang University, Nanchang, 330031, China
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China
| | - Haibo Gong
- Jiangxi Provincial Aquatic Biology Protection and Rescue Center, Nanchang, 330000, China
| | - Beijuan Hu
- School of Life Science, Nanchang University, Nanchang, 330031, China.
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China.
- Modern Agricultural Research Institute, Nanchang University, Nanchang, 330031, China.
| | - Yijiang Hong
- School of Life Science, Nanchang University, Nanchang, 330031, China.
- Jiangxi Province Key Laboratory of Aquatic Animal Resources and Utilization, Nanchang University, Nanchang, 330031, China.
- Modern Agricultural Research Institute, Nanchang University, Nanchang, 330031, China.
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17
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Taseska T, Yu W, Wilsey MK, Cox CP, Meng Z, Ngarnim SS, Müller AM. Analysis of the Scale of Global Human Needs and Opportunities for Sustainable Catalytic Technologies. Top Catal 2023; 66:338-374. [PMID: 37025115 PMCID: PMC10007685 DOI: 10.1007/s11244-023-01799-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2023] [Indexed: 03/13/2023]
Abstract
AbstractWe analyzed the enormous scale of global human needs, their carbon footprint, and how they are connected to energy availability. We established that most challenges related to resource security and sustainability can be solved by providing distributed, affordable, and clean energy. Catalyzed chemical transformations powered by renewable electricity are emerging successor technologies that have the potential to replace fossil fuels without sacrificing the wellbeing of humans. We highlighted the technical, economic, and societal advantages and drawbacks of short- to medium-term decarbonization solutions to gauge their practicability, economic feasibility, and likelihood for widespread acceptance on a global scale. We detailed catalysis solutions that enhance sustainability, along with strategies for catalyst and process development, frontiers, challenges, and limitations, and emphasized the need for planetary stewardship. Electrocatalytic processes enable the production of solar fuels and commodity chemicals that address universal issues of the water, energy and food security nexus, clothing, the building sector, heating and cooling, transportation, information and communication technology, chemicals, consumer goods and services, and healthcare, toward providing global resource security and sustainability and enhancing environmental and social justice.
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Affiliation(s)
- Teona Taseska
- Department of Chemical Engineering, University of Rochester, 14627 Rochester, NY USA
| | - Wanqing Yu
- Department of Chemical Engineering, University of Rochester, 14627 Rochester, NY USA
| | | | - Connor P. Cox
- Materials Science Program, University of Rochester, 14627 Rochester, NY USA
| | - Ziyi Meng
- Materials Science Program, University of Rochester, 14627 Rochester, NY USA
| | - Soraya S. Ngarnim
- Department of Chemistry, University of Rochester, 14627 Rochester, NY USA
| | - Astrid M. Müller
- Department of Chemical Engineering, University of Rochester, 14627 Rochester, NY USA
- Materials Science Program, University of Rochester, 14627 Rochester, NY USA
- Department of Chemistry, University of Rochester, 14627 Rochester, NY USA
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18
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Bing RG, Carey MJ, Laemthong T, Willard DJ, Crosby JR, Sulis DB, Wang JP, Adams MWW, Kelly RM. Fermentative conversion of unpretreated plant biomass: A thermophilic threshold for indigenous microbial growth. BIORESOURCE TECHNOLOGY 2023; 367:128275. [PMID: 36347479 PMCID: PMC10561188 DOI: 10.1016/j.biortech.2022.128275] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Naturally occurring, microbial contaminants were found in plant biomasses from common bioenergy crops and agricultural wastes. Unexpectedly, indigenous thermophilic microbes were abundant, raising the question of whether they impact thermophilic consolidated bioprocessing fermentations that convert biomass directly into useful bioproducts. Candidate microbial platforms for biomass conversion, Acetivibrio thermocellus (basionym Clostridium thermocellum; Topt 60 °C) and Caldicellulosiruptor bescii (Topt 78 °C), each degraded a wide variety of plant biomasses, but only A. thermocellus was significantly affected by the presence of indigenous microbial populations harbored by the biomass. Indigenous microbial growth was eliminated at ≥75 °C, conditions where C. bescii thrives, but where A. thermocellus cannot survive. Therefore, 75 °C is the thermophilic threshold to avoid sterilizing pre-treatments on the biomass that prevents native microbes from competing with engineered microbes and forming undesirable by-products. Thermophiles that naturally grow at and above 75 °C offer specific advantages as platform microorganisms for biomass conversion into fuels and chemicals.
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Affiliation(s)
- Ryan G Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Morgan J Carey
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Tunyaboon Laemthong
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Daniel J Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - James R Crosby
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States
| | - Daniel B Sulis
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, United States
| | - Jack P Wang
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, United States
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, United States
| | - Robert M Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, United States.
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19
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An Q, Chen D, Zhu Y, Feng Y, Hu Y, Chen H. Promotion of methane production and degradation of pyrolysis oil during its co-anaerobic digestion process via addition of N-doping hydro-chars. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 325:116519. [PMID: 36326522 DOI: 10.1016/j.jenvman.2022.116519] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/06/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Pyrolysis of wastes usually produces toxic pyrolysis oil (PO), which has complex ingredients, including benzene series and long-chain macromolecule organic pollutants. Co-anaerobic digestion (co-AD) can be an economic and high-efficiency method for PO degradation and recovery of methane simultaneously, but complete degradation of PO has not been achieved yet. Addition of a hydro-char in the process is beneficial to PO degradation and methane production. In this study, to further enhance the effectiveness of the hydro-char, nitrogen (N) was doped into the hydro-char by plasma modification in a NH3 atmosphere; and the effectiveness of the N-doped hydro-chars for promoting PO degradation and methane production during the co-AD process were evaluated. The experimental results indicated that all the hydro-chars can reduce the biotoxicity of the PO, improve its degradation during the co-AD process, and increase the methane yield. Compared with the plain hydro-char (HC), the hydro-chars modified at ambient temperature (HC-NH3-P-25) and at 500 °C (HC-NH3-P-500) can help achieving complete PO degradation and increasing the methane yield more effectively. The anaerobic digestor containing the HC-NH3-P-500 had the highest apparent methane yield (169.03 mLCH4/mLPO) and highest COD removal rate (79.5%). The nitrogen content, specific surface area, and electron transfer capability are found to be the key factors affecting PO degradation and methane yield; and the HC-NH3-P-500 had the highest N-doping, most specific surface area and electron transfer capability, explaining its best performance. The microbial communities of the digestate with the addition of the hydro-chars were founded to be richer with Clostridia and Methanosarcina, which could enhance the electron transfer between different microorganisms and contribute to the PO degradation.
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Affiliation(s)
- Qing An
- Thermal and Environmental Engineering Institute, School of Mechanical Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China; Shanghai Engineering Research Center of Multi-source Solid Wastes Co-processing and Energy Utilization, 1239 Siping Road, Shanghai, 200092, China
| | - Dezhen Chen
- Thermal and Environmental Engineering Institute, School of Mechanical Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China; Shanghai Engineering Research Center of Multi-source Solid Wastes Co-processing and Energy Utilization, 1239 Siping Road, Shanghai, 200092, China.
| | - Yuting Zhu
- Tongji Architectural Design (Group) Co., Ltd., Shanghai, 200092, China
| | - Yuheng Feng
- Thermal and Environmental Engineering Institute, School of Mechanical Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China; Shanghai Engineering Research Center of Multi-source Solid Wastes Co-processing and Energy Utilization, 1239 Siping Road, Shanghai, 200092, China
| | - Yuyan Hu
- Thermal and Environmental Engineering Institute, School of Mechanical Engineering, Tongji University, 1239 Siping Road, Shanghai, 200092, China; Shanghai Engineering Research Center of Multi-source Solid Wastes Co-processing and Energy Utilization, 1239 Siping Road, Shanghai, 200092, China
| | - Hui Chen
- School of Mechanical Engineering, Shanghai Dianji University, Shanghai, 201306, China
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20
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Fu L, Ju Z, Yu M, Luo H, Zhang C, Zhang X, Cheng H, Zheng M, Jin L, Ge C. Cellulose Regeneration in Imidazolium-Based Ionic Liquids and Antisolvent Mixtures: A Density Functional Theory Study. ACS OMEGA 2022; 7:42170-42180. [PMID: 36440146 PMCID: PMC9685753 DOI: 10.1021/acsomega.2c04915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Cellulose can be dissolved in ionic liquids (ILs), and it can be recovered by adding antisolvent such as water or alcohol. In addition, the regenerated cellulose can be used for textiles, degradable membranes, hydrogels/aerogels, etc. However, the regenerated mechanism of cellulose remains ambiguous. In this work, density functional theory (DFT) calculation is reported for the cellulose regeneration from a cellulose/1-n-butyl-3-methylimidazolium acetate (BmimOAc)/water mixture. To investigate the microscopic effects of the antisolvents, we analyzed the structures and H-bonds of BmimOAc-nH2O and cellobiose-ILs-nH2O (n = 0-6) clusters. It can be found that when n ≥ 5 in the BmimOAc-nH2O clusters, the solvent-separated ion pairs (SIPs) play a dominant position in the system. With the increasing numbers of water molecules, the cation-anion interaction can be separated by water to reduce the effects of ILs on cellulose dissolution. Furthermore, the BmimOAc-nH2O and cellobiose-ILs (n = 0-6) clusters tend to be a more stable structure with high hydration in an aqueous solution. When the water molecules were added to the system, H-bonds can be formed among H2O, the hydroxyl of cellulose, and the oxygen of OAc. Therefore, the interactions between cellulose and ILs will be decreased to promote cellulose regeneration. This work would provide some help to understand the mechanism of cellulose regeneration from the view of theoretical calculation.
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Affiliation(s)
- Lanlan Fu
- College
of Chemical & Material Engineering, Quzhou University, Quzhou 324000, China
| | - Zhaoyang Ju
- College
of Chemical & Material Engineering, Quzhou University, Quzhou 324000, China
| | - Mengting Yu
- College
of Chemical & Material Engineering, Quzhou University, Quzhou 324000, China
| | | | | | - Ximing Zhang
- College
of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Haixiang Cheng
- College
of Chemical & Material Engineering, Quzhou University, Quzhou 324000, China
| | - Minjia Zheng
- College
of Chemical & Material Engineering, Quzhou University, Quzhou 324000, China
| | - Lu Jin
- College
of Chemical & Material Engineering, Quzhou University, Quzhou 324000, China
| | - Chengsheng Ge
- College
of Chemical & Material Engineering, Quzhou University, Quzhou 324000, China
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21
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Re A, Mazzoli R. Current progress on engineering microbial strains and consortia for production of cellulosic butanol through consolidated bioprocessing. Microb Biotechnol 2022; 16:238-261. [PMID: 36168663 PMCID: PMC9871528 DOI: 10.1111/1751-7915.14148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/01/2022] [Accepted: 09/07/2022] [Indexed: 01/27/2023] Open
Abstract
In the last decades, fermentative production of n-butanol has regained substantial interest mainly owing to its use as drop-in-fuel. The use of lignocellulose as an alternative to traditional acetone-butanol-ethanol fermentation feedstocks (starchy biomass and molasses) can significantly increase the economic competitiveness of biobutanol over production from non-renewable sources (petroleum). However, the low cost of lignocellulose is offset by its high recalcitrance to biodegradation which generally requires chemical-physical pre-treatment and multiple bioreactor-based processes. The development of consolidated processing (i.e., single-pot fermentation) can dramatically reduce lignocellulose fermentation costs and promote its industrial application. Here, strategies for developing microbial strains and consortia that feature both efficient (hemi)cellulose depolymerization and butanol production will be depicted, that is, rational metabolic engineering of native (hemi)cellulolytic or native butanol-producing or other suitable microorganisms; protoplast fusion of (hemi)cellulolytic and butanol-producing strains; and co-culture of (hemi)cellulolytic and butanol-producing microbes. Irrespective of the fermentation feedstock, biobutanol production is inherently limited by the severe toxicity of this solvent that challenges process economic viability. Hence, an overview of strategies for developing butanol hypertolerant strains will be provided.
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Affiliation(s)
- Angela Re
- Centre for Sustainable Future TechnologiesFondazione Istituto Italiano di TecnologiaTorinoItaly,Department of Applied Science and TechnologyPolitecnico di TorinoTurinItaly
| | - Roberto Mazzoli
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems BiologyUniversity of TorinoTorinoItaly
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22
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Somayaji A, Dhanjal CR, Lingamsetty R, Vinayagam R, Selvaraj R, Varadavenkatesan T, Govarthanan M. An insight into the mechanisms of homeostasis in extremophiles. Microbiol Res 2022; 263:127115. [PMID: 35868258 DOI: 10.1016/j.micres.2022.127115] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 07/07/2022] [Accepted: 07/07/2022] [Indexed: 01/10/2023]
Abstract
The homeostasis of extremophiles is one that is a diamond hidden in the rough. The way extremophiles adapt to their extreme environments gives a clue into the true extent of what is possible when it comes to life. The discovery of new extremophiles is ever-expanding and an explosion of knowledge surrounding their successful existence in extreme environments is obviously perceived in scientific literature. The present review paper aims to provide a comprehensive view on the different mechanisms governing the extreme adaptations of extremophiles, along with insights and discussions on what the limits of life can possibly be. The membrane adaptations that are vital for survival are discussed in detail. It was found that there are many alterations in the genetic makeup of such extremophiles when compared to their mesophilic counterparts. Apart from the several proteins involved, the significance of chaperones, efflux systems, DNA repair proteins and a host of other enzymes that adapt to maintain functionality, are enlisted, and explained. A deeper understanding of the underlying mechanisms could have a plethora of applications in the industry. There are cases when certain microbes can withstand extreme doses of antibiotics. Such microbes accumulate numerous genetic elements (or plasmids) that possess genes for multiple drug resistance (MDR). A deeper understanding of such mechanisms helps in the development of potential approaches and therapeutic schemes for treating pathogen-mediated outbreaks. An in-depth analysis of the parameters - radiation, pressure, temperature, pH value and metal resistance - are discussed in this review, and the key to survival in these precarious niches is described.
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Affiliation(s)
- Adithi Somayaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Chetan Roger Dhanjal
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Rathnamegha Lingamsetty
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India; Manipal Biomachines, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Ramesh Vinayagam
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Raja Selvaraj
- Department of Chemical Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Thivaharan Varadavenkatesan
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
| | - Muthusamy Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daegu, South Korea; Department of Biomaterials, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Chennai 600077, India.
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23
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Monterrey DT, Ayuso-Fernández I, Oroz-Guinea I, García-Junceda E. Design and biocatalytic applications of genetically fused multifunctional enzymes. Biotechnol Adv 2022; 60:108016. [PMID: 35781046 DOI: 10.1016/j.biotechadv.2022.108016] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 01/01/2023]
Abstract
Fusion proteins, understood as those created by joining two or more genes that originally encoded independent proteins, have numerous applications in biotechnology, from analytical methods to metabolic engineering. The use of fusion enzymes in biocatalysis may be even more interesting due to the physical connection of enzymes catalyzing successive reactions into covalently linked complexes. The proximity of the active sites of two enzymes in multi-enzyme complexes can make a significant contribution to the catalytic efficiency of the reaction. However, the physical proximity of the active sites does not guarantee this result. Other aspects, such as the nature and length of the linker used for the fusion or the order in which the enzymes are fused, must be considered and optimized to achieve the expected increase in catalytic efficiency. In this review, we will relate the new advances in the design, creation, and use of fused enzymes with those achieved in biocatalysis over the past 20 years. Thus, we will discuss some examples of genetically fused enzymes and their application in carbon‑carbon bond formation and oxidative reactions, generation of chiral amines, synthesis of carbohydrates, biodegradation of plant biomass and plastics, and in the preparation of other high-value products.
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Affiliation(s)
- Dianelis T Monterrey
- Departamento de Química Bioorgánica, Instituto de Química Orgánica General (IQOG), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain.
| | - Iván Ayuso-Fernández
- Departamento de Química Bioorgánica, Instituto de Química Orgánica General (IQOG), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain.
| | - Isabel Oroz-Guinea
- Departamento de Química Bioorgánica, Instituto de Química Orgánica General (IQOG), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain.
| | - Eduardo García-Junceda
- Departamento de Química Bioorgánica, Instituto de Química Orgánica General (IQOG), CSIC, Juan de la Cierva 3, 28006 Madrid, Spain.
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24
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Svetlitchnyi VA, Svetlichnaya TP, Falkenhan DA, Swinnen S, Knopp D, Läufer A. Direct conversion of cellulose to L-lactic acid by a novel thermophilic Caldicellulosiruptor strain. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:44. [PMID: 35501875 PMCID: PMC9063331 DOI: 10.1186/s13068-022-02137-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 04/14/2022] [Indexed: 11/18/2022]
Abstract
Background Consolidated bioprocessing (CBP) of lignocellulosic biomass to l-lactic acid using thermophilic cellulolytic/hemicellulolytic bacteria provides a promising solution for efficient lignocellulose conversion without the need for additional cellulolytic/hemicellulolytic enzymes. Most studies on the mesophilic and thermophilic CBP of lignocellulose to lactic acid concentrate on cultivation of non-cellulolytic mesophilic and thermophilic bacteria at temperatures of 30–55 °C with external addition of cellulases/hemicellulases for saccharification of substrates. Results l-Lactic acid was generated by fermenting microcrystalline cellulose or lignocellulosic substrates with a novel thermophilic anaerobic bacterium Caldicellulosiruptor sp. DIB 104C without adding externally produced cellulolytic/hemicellulolytic enzymes. Selection of this novel bacterium strain for lactic acid production is described as well as the adaptive evolution towards increasing the l-lactic acid concentration from 6 to 70 g/l on microcrystalline cellulose. The evolved strains grown on microcrystalline cellulose show a maximum lactic acid production rate of 1.0 g/l*h and a lactic acid ratio in the total organic fermentation products of 96 wt%. The enantiomeric purity of the l-lactic acid generated is 99.4%. In addition, the lactic acid production by these strains on several other types of cellulose and lignocellulosic feedstocks is also reported. Conclusions The evolved strains originating from Caldicellulosiruptor sp. DIB 104C were capable of producing unexpectedly large amounts of l-lactic acid from microcrystalline cellulose in fermenters. These strains produce l-lactic acid also from lignocellulosic feedstocks and thus represent an ideal starting point for development of a highly integrated commercial l-lactic acid production process from such feedstocks.
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Affiliation(s)
| | | | | | - Steve Swinnen
- BluCon Biotech GmbH, Nattermannallee 1, 50829, Cologne, Germany
| | - Daniela Knopp
- BluCon Biotech GmbH, Nattermannallee 1, 50829, Cologne, Germany
| | - Albrecht Läufer
- BluCon Biotech GmbH, Nattermannallee 1, 50829, Cologne, Germany
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25
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Ye TJ, Huang KF, Ko TP, Wu SH. Synergic action of an inserted carbohydrate-binding module in a glycoside hydrolase family 5 endoglucanase. Acta Crystallogr D Struct Biol 2022; 78:633-646. [PMID: 35503211 PMCID: PMC9063844 DOI: 10.1107/s2059798322002601] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/07/2022] [Indexed: 11/24/2022] Open
Abstract
Most known cellulase-associated carbohydrate-binding modules (CBMs) are attached to the N- or C-terminus of the enzyme or are expressed separately and assembled into multi-enzyme complexes (for example to form cellulosomes), rather than being an insertion into the catalytic domain. Here, by solving the crystal structure, it is shown that MtGlu5 from Meiothermus taiwanensis WR-220, a GH5-family endo-β-1,4-glucanase (EC 3.2.1.4), has a bipartite architecture consisting of a Cel5A-like catalytic domain with a (β/α)8 TIM-barrel fold and an inserted CBM29-like noncatalytic domain with a β-jelly-roll fold. Deletion of the CBM significantly reduced the catalytic efficiency of MtGlu5, as determined by isothermal titration calorimetry using inactive mutants of full-length and CBM-deleted MtGlu5 proteins. Conversely, insertion of the CBM from MtGlu5 into TmCel5A from Thermotoga maritima greatly enhanced the substrate affinity of TmCel5A. Bound sugars observed between two tryptophan side chains in the catalytic domains of active full-length and CBM-deleted MtGlu5 suggest an important stacking force. The synergistic action of the catalytic domain and CBM of MtGlu5 in binding to single-chain polysaccharides was visualized by substrate modeling, in which additional surface tryptophan residues were identified in a cross-domain groove. Subsequent site-specific mutagenesis results confirmed the pivotal role of several other tryptophan residues from both domains of MtGlu5 in substrate binding. These findings reveal a way to incorporate a CBM into the catalytic domain of an existing enzyme to make a robust cellulase.
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Affiliation(s)
- Ting-Juan Ye
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 115, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Shih-Hsiung Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 115, Taiwan
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26
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Goussé M, Dell'Aglio E, Curien G, Borland S, Renoud S, Ranquet C, Chandor-Proust A. E. coli chromosomal-driven expression of NADK2 from A. thaliana: A preferable alternative to plasmid-driven expression for challenging proteins. Protein Expr Purif 2022; 195-196:106090. [PMID: 35346853 DOI: 10.1016/j.pep.2022.106090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 11/25/2022]
Abstract
The expression and purification of large recombinant proteins or protein complexes is problematic for some biotechnology laboratories. Indeed, it is often difficult to obtain enough active proteins to perform biological characterization or reach commercialization, when large proteins or protein complexes are expressed in E. coli via the popular T7-based plasmid-driven expression system. There is also an industrial demand to decrease our dependence on plasmid-driven expression, because of its drawbacks, such as: i) the common use of antibiotics to maintain the plasmid, ii) the issue of plasmid copy number, and iii) the risk of overloading the expression system. Despite all these issues, alternative solutions, such as gene integration in the bacterial chromosome, are rarely employed and their advantages are still a matter of debate. Plant plastidial NAD kinases (NADK; ATP:NAD 2'-phosphotransferase, EC 2.7.1.23) are a classic example of proteins with high molecular weight, that are difficult to express and purify with traditional T7-based technology. We therefore compared plasmid-driven and chromosomal-driven expression of the Arabidopsis thaliana NADK2 protein, using a proprietary counter-selection tool, COLIBELT®, that allows scar-free and marker-free chromosomal modifications. Here we show that chromosomal-driven expression allowed recovery of more active NADK2 protein than classic T7 expression systems, as well as better production, thus confirming that expression from one single chromosomal copy is preferable to plasmid-driven expression and might be appealing for both basic and applied research.
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Affiliation(s)
| | - Elisa Dell'Aglio
- Univ. Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, Grenoble, France
| | - Gilles Curien
- Univ. Grenoble Alpes, CNRS, CEA, INRAe, IRIG-LPCV, Grenoble, France
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27
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Kubis MR, Holwerda EK, Lynd LR. Declining carbohydrate solubilization with increasing solids loading during fermentation of cellulosic feedstocks by Clostridium thermocellum: documentation and diagnostic tests. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:12. [PMID: 35418299 PMCID: PMC8817502 DOI: 10.1186/s13068-022-02110-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/15/2022] [Indexed: 12/31/2022]
Abstract
Background For economically viable 2nd generation biofuels, processing of high solid lignocellulosic substrate concentrations is a necessity. The cellulolytic thermophilic anaerobe Clostridium thermocellum is one of the most effective biocatalysts for solubilization of carbohydrate harbored in lignocellulose. This study aims to document the solubilization performance of Clostridium thermocellum at increasing solids concentrations for two lignocellulosic feedstocks, corn stover and switchgrass, and explore potential effectors of solubilization performance. Results Monocultures of Clostridium thermocellum demonstrated high levels of carbohydrate solubilization for both unpretreated corn stover and switchgrass. However, fractional carbohydrate solubilization decreases with increasing solid loadings. Fermentation of model insoluble substrate (cellulose) in the presence of high solids lignocellulosic spent broth is temporarily affected but not model soluble substrate (cellobiose) fermentations. Mid-fermentation addition of cells (C. thermocellum) or model substrates did not significantly enhance overall corn stover solubilization loaded at 80 g/L, however cultures utilized the model substrates in the presence of high concentrations of corn stover. An increase in corn stover solubilization was observed when water was added, effectively diluting the solids concentration mid-fermentation. Introduction of a hemicellulose-utilizing coculture partner, Thermoanaerobacterium thermosaccharolyticum, increased the fractional carbohydrate solubilization at both high and low solid loadings. Residual solubilized carbohydrates diminished significantly in the presence of T. thermosaccharolyticum compared to monocultures of C. thermocellum, yet a small fraction of solubilized oligosaccharides of both C5 and C6 sugars remained unutilized. Conclusion Diminishing fractional carbohydrate solubilization with increasing substrate loading was observed for C. thermocellum-mediated solubilization and fermentation of unpretreated lignocellulose feedstocks. Results of experiments involving spent broth addition do not support a major role for inhibitors present in the liquid phase. Mid-fermentation addition experiments confirm that C. thermocellum and its enzymes remain capable of converting model substrates during the middle of high solids lignocellulose fermentation. An increase in fractional carbohydrate solubilization was made possible by (1) mid-fermentation solid loading dilutions and (2) coculturing C. thermocellum with T. thermosaccharolyticum, which ferments solubilized hemicellulose. Incomplete utilization of solubilized carbohydrates suggests that a small fraction of the carbohydrates is unaffected by the extracellular carbohydrate-active enzymes present in the culture. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02110-4.
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Affiliation(s)
- Matthew R Kubis
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH, 03755, USA.,The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Evert K Holwerda
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH, 03755, USA. .,The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH, 03755, USA.,The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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28
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Vandamme EJ. Professor Arnold L. (Arny) Demain's historical position in the rise of industrial microbiology and biotechnology. J Ind Microbiol Biotechnol 2021; 48:kuab034. [PMID: 34113991 PMCID: PMC8788709 DOI: 10.1093/jimb/kuab034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/19/2021] [Indexed: 11/15/2022]
Abstract
This perspective text focuses on the pivotal role and historical position that the late Prof. Arnold L. (Arny) Demain has taken since the 1950s in the rise and impact of the field of industrial microbiology and biotechnology. His drive toward academic research with industrial potential-first at Merck & Co. and later at MIT-, his feeling for establishing cordial personal contacts with his students and postdocs (Arny's Army) and his ability for worldwide networking are outlined here, intertwined with the author's personal experiences and impressions. His scientific output is legendary as to research papers, comprehensive reviews, books, and lectures at conferences worldwide. Some of his research experiences in industry and academia are mentioned in a historical context as well as his relentless efforts to advocate the importance and impact of industrial microbiology and biotechnology as an essential green technology for our planet Earth.
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Affiliation(s)
- Erick J Vandamme
- Department of Biotechnology, Centre for Industrial Biotechnology and Synthetic Biology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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29
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Cheng J, Li W, Wang Y, Cao Q, Ni Y, Zhang W, Guo J, Chen B, Zang Y, Zhu Y. Electroacupuncture modulates the intestinal microecology to improve intestinal motility in spinal cord injury rats. Microb Biotechnol 2021; 15:862-873. [PMID: 34797954 PMCID: PMC8913878 DOI: 10.1111/1751-7915.13968] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 12/14/2022] Open
Abstract
Spinal cord injury (SCI) is a disease involving gastrointestinal disorders. The underlying mechanisms of the potential protective effects of electroacupuncture (EA) and 5-hydroxytryptamine (5-HT) system on SCI remain unknown. We investigated whether EA improves gut microbial dysbiosis in SCI and regulates the 5-HT system. 16S rDNA gene sequencing was applied to investigate alterations in the gut microbiome of the rats. Faecal metabolites and the expression of the 5-HT system were detected. EA and faecal microbiota transplantation (FMT) treatment facilitated intestinal transmission functional recovery and restored the colon morphology of SCI rats. The composition of the intestinal microbiota, including numbers of phylum Proteobacteria, class Clostridia, order Bacteroidales, and genus Dorea, were amplified in SCI rats, and EA and FMT significantly reshaped the intestinal microbiota. SCI resulted in disturbed metabolic conditions in rats, and the EA and FMT group showed increased amounts of catechin compared with SCI rats. SCI inhibited 5-HT system expression in the colon, which was significantly reversed by EA and FMT treatment. Therefore, EA may ameliorate SCI by modulating microbiota and metabolites and regulate the 5-HT system. Our study provides new insights into the pathogenesis and therapy of SCI from the perspective of microbiota and 5-HT regulation.
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Affiliation(s)
- Jie Cheng
- Nanjing University of Chinese Medicine, Nanjing, China
| | - Weimin Li
- The Second Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Ying Wang
- The Ninth People's Hospital of Wuxi affiliated to Soochow University, Wuxi, China.,Department of Kinesiology, Shanghai University of Sport, Shanghai, China
| | - Qing Cao
- Department of Kinesiology, Shanghai University of Sport, Shanghai, China.,Zigong Forth People's Hospital, Zigong, China
| | - Ying Ni
- Nanjing University of Chinese Medicine, Nanjing, China
| | - Wenyi Zhang
- Zhongshan Rehabilitation Hospital Affiliated to Jiangsu Provincial People's Hospital, Nanjing, China
| | - Jiabao Guo
- The Second Clinical Medical School, Xuzhou Medical University, Xuzhou, China
| | - Binglin Chen
- The Second Clinical Medical School, Xuzhou Medical University, Xuzhou, China
| | - Yaning Zang
- Department of Kinesiology, Shanghai University of Sport, Shanghai, China
| | - Yi Zhu
- The Second Affiliated Hospital of Hainan Medical University, Haikou, China.,The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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30
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Qaiser H, Kaleem A, Abdullah R, Iqtedar M, Hoessli DC. Overview of lignocellulolytic enzyme systems with special reference to valorization of lignocellulosic biomass. Protein Pept Lett 2021; 28:1349-1364. [PMID: 34749601 DOI: 10.2174/0929866528666211105110643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/03/2021] [Accepted: 09/03/2021] [Indexed: 11/22/2022]
Abstract
Lignocellulosic biomass, one of the most valuable natural resources, is abundantly present on earth. Being a renewable feedstock, it harbors a great potential to be exploited as a raw material, to produce various value-added products. Lignocellulolytic microorganisms hold a unique position regarding the valorization of lignocellulosic biomass as they contain efficient enzyme systems capable of degrading this biomass. The ubiquitous nature of these microorganisms and their survival under extreme conditions have enabled their use as an effective producer of lignocellulolytic enzymes with improved biochemical features crucial to industrial bioconversion processes. These enzymes can prove to be an exquisite tool when it comes to the eco-friendly manufacturing of value-added products using waste material. This review focuses on highlighting the significance of lignocellulosic biomass, microbial sources of lignocellulolytic enzymes and their use in the formation of useful products.
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Affiliation(s)
- Hina Qaiser
- Department of Biology, Lahore Garrison University, Lahore. Pakistan
| | - Afshan Kaleem
- Department of Biotechnology, Lahore College for Women University, Lahore. Pakistan
| | - Roheena Abdullah
- Department of Biotechnology, Lahore College for Women University, Lahore. Pakistan
| | - Mehwish Iqtedar
- Department of Biotechnology, Lahore College for Women University, Lahore. Pakistan
| | - Daniel C Hoessli
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi. Pakistan
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31
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Li J, Chen C, Liu YJ, Cui Q, Bayer EA, Feng Y. NMR chemical shift assignments of a module of unknown function in the cellulosomal secondary scaffoldin ScaF from Clostridium thermocellum. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:329-334. [PMID: 33876380 DOI: 10.1007/s12104-021-10025-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/10/2021] [Indexed: 06/12/2023]
Abstract
The cellulosome is a highly efficient cellulolytic complex containing cellulolytic enzymes and non-catalytic subunits, i.e. scaffoldins, which are assembled by the interactions between the dockerin modules of the enzymes and the cohesin modules of the primary scaffoldins. The cellulosome attaches to the cell surface via the S-layer homology (SLH) modules of the anchoring scaffoldins. Clostridium thermocellum DSM1313 is a thermophilic cellulosome-producing bacterium with great potential in lignocellulose bioconversion and biofuel production. The bacterium contains four anchoring scaffoldins ScaB, ScaC, ScaD and ScaF, among which ScaF is the only one that contains an additional module of unknown function (ScaF-X) between the cohesin and SLH modules. The gene of ScaF is located outside the scaffoldin gene cluster of scaA, scaB, scaC and scaD. Previous studies showed unique regulation properties and function of ScaF compared to other anchoring scaffoldins, which might be related to the additional ScaF-X module. Here we report the NMR chemical shift assignments of ScaF-X from C. thermocellum DSM1313. The well-dispersed NMR spectrum and the secondary structure prediction based on the chemical shifts of ScaF-X indicated that ScaF-X is a well-folded protein module. The chemical shift assignments provide the basis for future studies on the structure of this module and its function in cellulosomes.
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Affiliation(s)
- Jie Li
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Energy Institute, Qingdao, 266101, Shandong, China
- New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Chen
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Energy Institute, Qingdao, 266101, Shandong, China
- New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Energy Institute, Qingdao, 266101, Shandong, China
- New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China
- Shandong Energy Institute, Qingdao, 266101, Shandong, China
- New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, 7610001, Rehovot, Israel
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, 8499000, Beer-Sheva, Israel
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China.
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China.
- Shandong Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, Shandong, China.
- Shandong Energy Institute, Qingdao, 266101, Shandong, China.
- New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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32
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Biorefinery Gets Hot: Thermophilic Enzymes and Microorganisms for Second-Generation Bioethanol Production. Processes (Basel) 2021. [DOI: 10.3390/pr9091583] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
To mitigate the current global energy and the environmental crisis, biofuels such as bioethanol have progressively gained attention from both scientific and industrial perspectives. However, at present, commercialized bioethanol is mainly derived from edible crops, thus raising serious concerns given its competition with feed production. For this reason, lignocellulosic biomasses (LCBs) have been recognized as important alternatives for bioethanol production. Because LCBs supply is sustainable, abundant, widespread, and cheap, LCBs-derived bioethanol currently represents one of the most viable solutions to meet the global demand for liquid fuel. However, the cost-effective conversion of LCBs into ethanol remains a challenge and its implementation has been hampered by several bottlenecks that must still be tackled. Among other factors related to the challenging and variable nature of LCBs, we highlight: (i) energy-demanding pretreatments, (ii) expensive hydrolytic enzyme blends, and (iii) the need for microorganisms that can ferment mixed sugars. In this regard, thermophiles represent valuable tools to overcome some of these limitations. Thus, the aim of this review is to provide an overview of the state-of-the-art technologies involved, such as the use of thermophilic enzymes and microorganisms in industrial-relevant conditions, and to propose possible means to implement thermophiles into second-generation ethanol biorefineries that are already in operation.
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Harlow BE, Flythe MD, Klotz JL, Harmon DL, Aiken GE. Effect of biochanin A on the rumen microbial community of Holstein steers consuming a high fiber diet and subjected to a subacute acidosis challenge. PLoS One 2021; 16:e0253754. [PMID: 34288928 PMCID: PMC8294529 DOI: 10.1371/journal.pone.0253754] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 06/11/2021] [Indexed: 11/21/2022] Open
Abstract
Subacute rumen acidosis (SARA) occurs when highly fermentable carbohydrates are introduced into the diet, decreasing pH and disturbing the microbial ecology of the rumen. Rumen amylolytic bacteria rapidly catabolize starch, fermentation acids accumulate in the rumen and reduce environmental pH. Historically, antibiotics (e.g., monensin, MON) have been used in the prevention and treatment of SARA. Biochanin A (BCA), an isoflavone produced by red clover (Trifolium pratense), mitigates changes associated with starch fermentation ex vivo. The objective of the study was to determine the effect of BCA on amylolytic bacteria and rumen pH during a SARA challenge. Twelve rumen fistulated steers were assigned to 1 of 4 treatments: HF CON (high fiber control), SARA CON, MON (200 mg d-1), or BCA (6 g d-1). The basal diet consisted of corn silage and dried distiller’s grains ad libitum. The study consisted of a 2-wk adaptation, a 1-wk HF period, and an 8-d SARA challenge (d 1–4: 40% corn; d 5–8: 70% cracked corn). Samples for pH and enumeration were taken on the last day of each period (4 h). Amylolytic, cellulolytic, and amino acid/peptide-fermenting bacteria (APB) were enumerated. Enumeration data were normalized by log transformation and data were analyzed by repeated measures ANOVA using the MIXED procedure of SAS. The SARA challenge increased total amylolytics and APB, but decreased pH, cellulolytics, and in situ DMD of hay (P < 0.05). BCA treatment counteracted the pH, microbiological, and fermentative changes associated with SARA challenge (P < 0.05). Similar results were also observed with MON (P < 0.05). These results indicate that BCA may be an effective alternative to antibiotics for mitigating SARA in cattle production systems.
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Affiliation(s)
- Brittany E. Harlow
- United States Department of Agriculture, Forage Animal Production Research Unit, Agricultural Research Service, Lexington, KY, United States of America
- * E-mail:
| | - Michael D. Flythe
- United States Department of Agriculture, Forage Animal Production Research Unit, Agricultural Research Service, Lexington, KY, United States of America
| | - James L. Klotz
- United States Department of Agriculture, Forage Animal Production Research Unit, Agricultural Research Service, Lexington, KY, United States of America
| | - David L. Harmon
- Department of Animal and Food Sciences, University of Kentucky, Lexington, KY, United States of America
| | - Glen E. Aiken
- North Florida Research and Education Center, University of Florida, Quincy, FL, United States of America
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34
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Costa P, Usai G, Re A, Manfredi M, Mannino G, Bertea CM, Pessione E, Mazzoli R. Clostridium cellulovorans Proteomic Responses to Butanol Stress. Front Microbiol 2021; 12:674639. [PMID: 34367082 PMCID: PMC8336468 DOI: 10.3389/fmicb.2021.674639] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/14/2021] [Indexed: 12/16/2022] Open
Abstract
Combination of butanol-hyperproducing and hypertolerant phenotypes is essential for developing microbial strains suitable for industrial production of bio-butanol, one of the most promising liquid biofuels. Clostridium cellulovorans is among the microbial strains with the highest potential for direct production of n-butanol from lignocellulosic wastes, a process that would significantly reduce the cost of bio-butanol. However, butanol exhibits higher toxicity compared to ethanol and C. cellulovorans tolerance to this solvent is low. In the present investigation, comparative gel-free proteomics was used to study the response of C. cellulovorans to butanol challenge and understand the tolerance mechanisms activated in this condition. Sequential Window Acquisition of all Theoretical fragment ion spectra Mass Spectrometry (SWATH-MS) analysis allowed identification and quantification of differentially expressed soluble proteins. The study data are available via ProteomeXchange with the identifier PXD024183. The most important response concerned modulation of protein biosynthesis, folding and degradation. Coherent with previous studies on other bacteria, several heat shock proteins (HSPs), involved in protein quality control, were up-regulated such as the chaperones GroES (Cpn10), Hsp90, and DnaJ. Globally, our data indicate that protein biosynthesis is reduced, likely not to overload HSPs. Several additional metabolic adaptations were triggered by butanol exposure such as the up-regulation of V- and F-type ATPases (involved in ATP synthesis/generation of proton motive force), enzymes involved in amino acid (e.g., arginine, lysine, methionine, and branched chain amino acids) biosynthesis and proteins involved in cell envelope re-arrangement (e.g., the products of Clocel_4136, Clocel_4137, Clocel_4144, Clocel_4162 and Clocel_4352, involved in the biosynthesis of saturated fatty acids) and a redistribution of carbon flux through fermentative pathways (acetate and formate yields were increased and decreased, respectively). Based on these experimental findings, several potential gene targets for metabolic engineering strategies aimed at improving butanol tolerance in C. cellulovorans are suggested. This includes overexpression of HSPs (e.g., GroES, Hsp90, DnaJ, ClpC), RNA chaperone Hfq, V- and F-type ATPases and a number of genes whose function in C. cellulovorans is currently unknown.
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Affiliation(s)
- Paolo Costa
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Giulia Usai
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.,Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy.,Department of Applied Science and Technology, Politecnico di Torino, Turin, Italy
| | - Angela Re
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
| | - Marcello Manfredi
- Center for Translational Research on Autoimmune and Allergic Diseases, Università del Piemonte Orientale, Novara, Italy.,Department of Translational Medicine, Università del Piemonte Orientale, Novara, Italy
| | - Giuseppe Mannino
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Cinzia Margherita Bertea
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Enrica Pessione
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Roberto Mazzoli
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
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35
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Lau MSH, Sheng L, Zhang Y, Minton NP. Development of a Suite of Tools for Genome Editing in Parageobacillus thermoglucosidasius and Their Use to Identify the Potential of a Native Plasmid in the Generation of Stable Engineered Strains. ACS Synth Biol 2021; 10:1739-1749. [PMID: 34197093 DOI: 10.1021/acssynbio.1c00138] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The relentless rise in the levels of atmospheric greenhouse gases caused by the exploitation of fossil fuel necessitates the development of more environmentally friendly routes to the manufacture of chemicals and fuels. The exploitation of a fermentative process that uses a thermophilic chassis represents an attractive option. Its use, however, is hindered by a dearth of genetic tools. Here we expand on those available for the engineering of the industrial chassis Parageobacillus thermoglucosidasius through the assembly and testing of a range of promoters, ribosome binding sites, reporter genes, and the implementation of CRISPR/Cas9 genome editing based on two different thermostable Cas9 nucleases. The latter were used to demonstrate that the deletion of the two native plasmids carried by P. thermoglucosidasius, pNCI001 and pNCI002, either singly or in combination, had no discernible effects on the overall phenotypic characteristics of the organism. Through the CRISPR/Cas9-mediated insertion of the gene encoding a novel fluorescent reporter, eCGP123, we showed that pNCI001 exhibited a high degree of segregational stability. As the relatively higher copy number of pNCI001 led to higher levels of eCGP123 expression than when the same gene was integrated into the chromosome, we propose that pNCI001 represents the preferred option for the integration of metabolic operons when stable commercial strains are required.
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Affiliation(s)
- Matthew S. H. Lau
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Lili Sheng
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Ying Zhang
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Nigel P. Minton
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
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36
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Bing RG, Sulis DB, Wang JP, Adams MW, Kelly RM. Thermophilic microbial deconstruction and conversion of natural and transgenic lignocellulose. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:272-293. [PMID: 33684253 PMCID: PMC10519370 DOI: 10.1111/1758-2229.12943] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/25/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
The potential to convert renewable plant biomasses into fuels and chemicals by microbial processes presents an attractive, less environmentally intense alternative to conventional routes based on fossil fuels. This would best be done with microbes that natively deconstruct lignocellulose and concomitantly form industrially relevant products, but these two physiological and metabolic features are rarely and simultaneously observed in nature. Genetic modification of both plant feedstocks and microbes can be used to increase lignocellulose deconstruction capability and generate industrially relevant products. Separate efforts on plants and microbes are ongoing, but these studies lack a focus on optimal, complementary combinations of these disparate biological systems to obtain a convergent technology. Improving genetic tools for plants have given rise to the generation of low-lignin lines that are more readily solubilized by microorganisms. Most focus on the microbiological front has involved thermophilic bacteria from the genera Caldicellulosiruptor and Clostridium, given their capacity to degrade lignocellulose and to form bio-products through metabolic engineering strategies enabled by ever-improving molecular genetics tools. Bioengineering plant properties to better fit the deconstruction capabilities of candidate consolidated bioprocessing microorganisms has potential to achieve the efficient lignocellulose deconstruction needed for industrial relevance.
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Affiliation(s)
- Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
| | - Daniel B. Sulis
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695
| | - Jack P. Wang
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695
| | - Michael W.W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695
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37
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Strategies towards Reduction of Cellulases Consumption: Debottlenecking the Economics of Lignocellulosics Valorization Processes. POLYSACCHARIDES 2021. [DOI: 10.3390/polysaccharides2020020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Lignocellulosic residues have been receiving growing interest as a promising source of polysaccharides, which can be converted into a variety of compounds, ranging from biofuels to bioplastics. Most of these can replace equivalent products traditionally originated from petroleum, hence representing an important environmental advantage. Lignocellulosic materials are theoretically unlimited, cheaper and may not compete with food crops. However, the conversion of these materials to simpler sugars usually requires cellulolytic enzymes. Being still associated with a high cost of production, cellulases are commonly considered as one of the main obstacles in the economic valorization of lignocellulosics. This work provides a brief overview of some of the most studied strategies that can allow an important reduction of cellulases consumption, hence improving the economy of lignocellulosics conversion. Cellulases recycling is initially discussed regarding the main processes to recover active enzymes and the most important factors that may affect enzyme recyclability. Similarly, the potential of enzyme immobilization is analyzed with a special focus on the contributions that some elements of the process can offer for prolonged times of operation and improved enzyme stability and robustness. Finally, the emergent concept of consolidated bioprocessing (CBP) is also described in the particular context of a potential reduction of cellulases consumption.
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38
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Najjarzadeh N, Matsakas L, Rova U, Christakopoulos P. How Carbon Source and Degree of Oligosaccharide Polymerization Affect Production of Cellulase-Degrading Enzymes by Fusarium oxysporum f. sp. lycopersici. Front Microbiol 2021; 12:652655. [PMID: 33841380 PMCID: PMC8032549 DOI: 10.3389/fmicb.2021.652655] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Cellulases are a group of enzymes responsible for the degradation of cellulose, which is one of the most abundant polymers on Earth. The three main groups of cellulases are endoglucosidases, exoglucosidases, and β-glucosidases; however, the mechanism of induction of these enzymes remains poorly characterized. Cellooligosaccharides are among the main inducers of these enzymes in filamentous fungi, yet it is not clear how their degree of polymerization may affect the strength of induction. In the present study, we investigated the effect of different carbohydrate-based inducers, such as lactose, sophorose, cellooligosaccharides, and xylooligosacharides, characterized by different concentrations and degree of polymerization, on cellulases production by the fungus Fusarium oxysporum f. sp. lycopersici, which is one of the most studied lignocellulose degrading fungi with the ability to consume both cellulose and hemicellulose. Moreover, the effect of carbon source on cellulase induction was assessed by growing the biomass on sucrose or glycerol. Results showed a correlation between induction efficiency and the cellooligosaccharides' concentration and size, as well as the carbon source available. Specifically, cellotetraose was a better inducer when sucrose was the carbon source, while cellobiose yielded a better result on glycerol. These findings can help optimize industrial cellulase production.
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Affiliation(s)
| | | | | | - Paul Christakopoulos
- Biochemical Process Engineering, Division of Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden
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39
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Ahamed F, Song HS, Ho YK. Modeling coordinated enzymatic control of saccharification and fermentation by Clostridium thermocellum during consolidated bioprocessing of cellulose. Biotechnol Bioeng 2021; 118:1898-1912. [PMID: 33547803 DOI: 10.1002/bit.27705] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/03/2021] [Accepted: 02/04/2021] [Indexed: 11/09/2022]
Abstract
Consolidated bioprocessing (CBP) of cellulose is a cost-effective route to produce valuable biochemicals by integrating saccharification, fermentation and cellulase synthesis in a single step. However, the lack of understanding of governing factors of interdependent saccharification and fermentation in CBP eludes reliable process optimization. Here, we propose a new framework that synergistically couples population balances (to simulate cellulose depolymerization) and cybernetic models (to model enzymatic regulation of fermentation) to enable improved understanding of CBP. The resulting framework, named the unified cybernetic-population balance model (UC-PBM), enables simulation of CBP driven by coordinated control of enzyme synthesis through closed-loop interactions. UC-PBM considers two key aspects in controlling CBP: (1) heterogeneity in cellulose properties and (2) cellular regulation of competing cell growth and cellulase secretion. In a case study on Clostridium thermocellum, UC-PBM not only provides a decent fit with various exometabolomic data, but also reveals that: (i) growth-decoupled cellulase-secreting pathways are only activated during famine conditions to promote the production of growth substrates, and (ii) starting cellulose concentration has a strong influence on the overall flux distribution. Equipped with mechanisms of cellulose degradation and fermentative regulations, UC-PBM is practical to explore phenotypic functions for primary evaluation of microorganisms' potential for metabolic engineering and optimal design of bioprocess.
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Affiliation(s)
- Firnaaz Ahamed
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia
| | - Hyun-Seob Song
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.,Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Yong Kuen Ho
- Chemical Engineering Discipline, School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia.,Monash-Industry Palm Oil Education and Research Platform, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor, Malaysia
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40
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Froese AG, Sparling R. Cross-feeding and wheat straw extractives enhance growth of Clostridium thermocellum-containing co-cultures for consolidated bioprocessing. Bioprocess Biosyst Eng 2021; 44:819-830. [PMID: 33392746 DOI: 10.1007/s00449-020-02490-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/24/2020] [Indexed: 01/19/2023]
Abstract
Co-cultures consisting of three thermophilic and lignocellulolytic bacteria, namely Clostridium thermocellum, C. stercorarium, and Thermoanaerobacter thermohydrosulfuricus, degrade lignocellulosic material in a synergistic manner. When cultured in a defined minimal medium two of the members appeared to be auxotrophic and unable to grow, but the growth of all species was observed in all co-culture combinations, indicating cross-feeding of unidentified growth factors between the members. Growth factors also appeared to be present in water-soluble extractives obtained from wheat straw, allowing for the growth of the auxotrophic monocultures in the defined minimal medium. Cell enumeration during growth on wheat straw in this medium revealed different growth profiles of the members that varied between the co-cultures. End-product profiles also varied substantially between the cultures, with significantly higher ethanol production in all co-cultures compared to the mono-cultures. Understanding interactions between co-culture members, and the additional nutrients provided by lignocellulosic substrates, will aid us in consolidated bioprocessing design.
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Affiliation(s)
- Alan G Froese
- Department of Microbiology, University of Manitoba, 213 Buller Building, Winnipeg, MB, R3T 2N2, Canada
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, 213 Buller Building, Winnipeg, MB, R3T 2N2, Canada.
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41
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Ye M, Ye Y, Du Z, Chen G. Cell-surface engineering of yeasts for whole-cell biocatalysts. Bioprocess Biosyst Eng 2021; 44:1003-1019. [PMID: 33389168 DOI: 10.1007/s00449-020-02484-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/16/2020] [Indexed: 01/23/2023]
Abstract
Due to the unique advantages comparing with traditional free enzymes and chemical catalysis, whole-cell biocatalysts have been widely used to catalyze reactions effectively, simply and environment friendly. Cell-surface display technology provides a novel and effective approach for improved whole-cell biocatalysts expressing heterologous enzymes on the cell surface. They can overcome the substrate transport limitation of the intracellular expression and provide the enzymes with enhanced properties. Among all the host surface-displaying microorganisms, yeast is ideally suitable for constructing whole cell-surface-displaying biocatalyst, because of the large cell size, the generally regarded as safe (GRAS) status, and the perfect post-translational processing of secreted proteins. Yeast cell-surface display system has been a promising and powerful method for development of novel and improved engineered biocatalysts. In this review, the characterization and principles of yeast cell-surface display and the applications of yeast cell-surface display in engineered whole-cell biocatalysts as well as the improvement of the enzyme efficiency are summarized and discussed.
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Affiliation(s)
- Mengqi Ye
- Marine College, Shandong University, Weihai, 264209, China
| | - Yuqi Ye
- Marine College, Shandong University, Weihai, 264209, China
| | - Zongjun Du
- Marine College, Shandong University, Weihai, 264209, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Guanjun Chen
- Marine College, Shandong University, Weihai, 264209, China.
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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42
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Ghosh S, Godoy L, Anchang KY, Achilonu CC, Gryzenhout M. Fungal Cellulases: Current Research and Future Challenges. Fungal Biol 2021. [DOI: 10.1007/978-3-030-85603-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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43
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Zafar A, Aftab MN, Asif A, Karadag A, Peng L, Celebioglu HU, Afzal MS, Hamid A, Iqbal I. Efficient biomass saccharification using a novel cellobiohydrolase from Clostridium clariflavum for utilization in biofuel industry. RSC Adv 2021; 11:9246-9261. [PMID: 35423428 PMCID: PMC8695235 DOI: 10.1039/d1ra00545f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/18/2021] [Accepted: 02/23/2021] [Indexed: 11/30/2022] Open
Abstract
The present study describes the cloning of the cellobiohydrolase gene from a thermophilic bacterium Clostridium clariflavum and its expression in Escherichia coli BL21(DE3) utilizing the expression vector pET-21a(+). The optimization of various parameters (pH, temperature, isopropyl β-d-1-thiogalactopyranoside (IPTG) concentration, time of induction) was carried out to obtain the maximum enzyme activity (2.78 ± 0.145 U ml−1) of recombinant enzyme. The maximum expression of recombinant cellobiohydrolase was obtained at pH 6.0 and 70 °C respectively. Enzyme purification was performed by heat treatment and immobilized metal anionic chromatography. The specific activity of the purified enzyme was 57.4 U mg−1 with 35.17% recovery and 3.90 purification fold. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) showed that the molecular weight of cellobiohydrolase was 78 kDa. Among metal ions, Ca2+ showed a positive impact on the cellobiohydrolase enzyme with increased activity by 115%. Recombinant purified cellobiohydrolase enzyme remained stable and exhibited 77% and 63% residual activity in comparison to control in the presence of n-butanol and after incubation at 80 °C for 1 h, respectively. Our results indicate that our purified recombinant cellobiohydrolase can be used in the biofuel industry. Successful expression of a novel cellobiohydrolase enzyme from Clostridium clariflavum with efficient saccharification potential of plant biomass for the biofuel industry.![]()
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Affiliation(s)
- Asma Zafar
- Faculty of Life Sciences
- University of Central Punjab
- Lahore
- Pakistan
| | | | - Anam Asif
- Institute of Industrial Biotechnology
- GC University
- Lahore
- Pakistan
| | - Ahmet Karadag
- Department of Chemistry
- Faculty of Arts and Sciences
- Yozgat Bozok University
- Yozgat
- Turkey
| | - Liangcai Peng
- Biomass and Bioenergy Research Center
- Huazhong Agriculture University
- Wuhan
- China
| | | | - Muhammad Sohail Afzal
- Department of Life Sciences
- School of Science
- University of Management and Technology (UMT)
- Lahore
- Pakistan
| | - Attia Hamid
- Institute of Industrial Biotechnology
- GC University
- Lahore
- Pakistan
| | - Irfana Iqbal
- Department of Zoology
- Lahore College for Women University
- Lahore
- Pakistan
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44
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Kluyveromyces marxianus: Current State of Omics Studies, Strain Improvement Strategy and Potential Industrial Implementation. FERMENTATION-BASEL 2020. [DOI: 10.3390/fermentation6040124] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bioethanol is considered an excellent alternative to fossil fuels, since it importantly contributes to the reduced consumption of crude oil, and to the alleviation of environmental pollution. Up to now, the baker yeast Saccharomyces cerevisiae is the most common eukaryotic microorganism used in ethanol production. The inability of S. cerevisiae to grow on pentoses, however, hinders its effective growth on plant biomass hydrolysates, which contain large amounts of C5 and C12 sugars. The industrial-scale bioprocessing requires high temperature bioreactors, diverse carbon sources, and the high titer production of volatile compounds. These criteria indicate that the search for alternative microbes possessing useful traits that meet the required standards of bioethanol production is necessary. Compared to other yeasts, Kluyveromyces marxianus has several advantages over others, e.g., it could grow on a broad spectrum of substrates (C5, C6 and C12 sugars); tolerate high temperature, toxins, and a wide range of pH values; and produce volatile short-chain ester. K. marxianus also shows a high ethanol production rate at high temperature and is a Crabtree-negative species. These attributes make K. marxianus promising as an industrial host for the biosynthesis of biofuels and other valuable chemicals.
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Kumar K, Singh S, Sharma K, Goyal A. Computational modeling and small-angle X-ray scattering based structure analysis and identifying ligand cleavage mechanism by processive endocellulase of family 9 glycoside hydrolase (HtGH9) from Hungateiclostridium thermocellum ATCC 27405. J Mol Graph Model 2020; 103:107808. [PMID: 33248343 DOI: 10.1016/j.jmgm.2020.107808] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/13/2020] [Accepted: 11/13/2020] [Indexed: 11/16/2022]
Abstract
The cellulases of family 9 glycoside hydrolase with subtle difference in amino acid sequence have shown different types of catalytic activities such as endo-, exo- or processive endocellulase. However, the reason behind the different types of catalytic activities still unclear. In this study, the processive endocellulase, HtGH9 of family 9 GH from Hungateiclostridium thermocellum was modeled by homology modeling. The catalytic module (HtGH9t) of HtGH9 modeled structure displayed the (α/α)6 barrel topology and associated family 3 carbohydrate binding module (HtCBM3c) displayed β-sandwich fold. Ramachandran plot of HtGH9 modeled structure displayed all the amino acid residues in allowed region except Asn225 and Asp317. Secondary structure analysis of modeled HtGH9 showed the presence of 41.3% α-helices and 11.0% β-strands which was validated through circular dichroism analysis that showed the presence of 42.6% α-helices and 14.5% β-strands. Molecular Dynamic (MD) simulation of HtGH9 structure for 50 ns showed Root Mean Square Deviation (RMSD), 0.84 nm and radius of gyration (Rg) 3.1 nm. The Small-angle X-ray scattering of HtGH9 confirmed the monodisperse state. The radius of gyration for globular shape (Rg) was 5.50 ± 0.15 nm and for rod shape (Rc) by Guinier plot was 2.0 nm. The loop formed by amino acid residues, 264-276 towards one end of the catalytic site of HtGH9 forms a barrier, that blocks the non-reducing end of the cellulose chain causing the processive cleavage resulting in the release of cellotetraose. The position of the corresponding loop in cellulases of family 9 GH is responsible for different types of cleavage patterns.
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Affiliation(s)
- Krishan Kumar
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Shubha Singh
- Division of Biological Sciences and Engineering, Netaji Subhas University of Technology, Delhi, 110078, India
| | - Kedar Sharma
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India; Laboratory of Small Molecules & Macro Molecular Crystallography, Department of Bioengineering, Indian Institute of Technology Gandhinagar, Gandhinagar, 382355, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India.
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46
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Foroozandeh Shahraki M, Ariaeenejad S, Fallah Atanaki F, Zolfaghari B, Koshiba T, Kavousi K, Salekdeh GH. MCIC: Automated Identification of Cellulases From Metagenomic Data and Characterization Based on Temperature and pH Dependence. Front Microbiol 2020; 11:567863. [PMID: 33193158 PMCID: PMC7645119 DOI: 10.3389/fmicb.2020.567863] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 09/30/2020] [Indexed: 01/03/2023] Open
Abstract
As the availability of high-throughput metagenomic data is increasing, agile and accurate tools are required to analyze and exploit this valuable and plentiful resource. Cellulose-degrading enzymes have various applications, and finding appropriate cellulases for different purposes is becoming increasingly challenging. An in silico screening method for high-throughput data can be of great assistance when combined with the characterization of thermal and pH dependence. By this means, various metagenomic sources with high cellulolytic potentials can be explored. Using a sequence similarity-based annotation and an ensemble of supervised learning algorithms, this study aims to identify and characterize cellulolytic enzymes from a given high-throughput metagenomic data based on optimum temperature and pH. The prediction performance of MCIC (metagenome cellulase identification and characterization) was evaluated through multiple iterations of sixfold cross-validation tests. This tool was also implemented for a comparative analysis of four metagenomic sources to estimate their cellulolytic profile and capabilities. For experimental validation of MCIC’s screening and prediction abilities, two identified enzymes from cattle rumen were subjected to cloning, expression, and characterization. To the best of our knowledge, this is the first time that a sequence-similarity based method is used alongside an ensemble machine learning model to identify and characterize cellulase enzymes from extensive metagenomic data. This study highlights the strength of machine learning techniques to predict enzymatic properties solely based on their sequence. MCIC is freely available as a python package and standalone toolkit for Windows and Linux-based operating systems with several functions to facilitate the screening and thermal and pH dependence prediction of cellulases.
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Affiliation(s)
- Mehdi Foroozandeh Shahraki
- Laboratory of Complex Biological Systems and Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Shohreh Ariaeenejad
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research Education and Extension Organization, Karaj, Iran
| | - Fereshteh Fallah Atanaki
- Laboratory of Complex Biological Systems and Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Behrouz Zolfaghari
- Computer Science and Engineering Department, Indian Institute of Technology Guwahati, Guwahati, India
| | - Takeshi Koshiba
- Department of Mathematics, Faculty of Education and Integrated Arts and Sciences, Waseda University, Tokyo, Japan
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research Education and Extension Organization, Karaj, Iran.,Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
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47
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Zhou J, Wang Y, Zeng X, Zhang T, Li P, Yao B, Wang L, Qiao S, Zeng X. Effect of antibiotic-free, low-protein diets with specific amino acid compositions on growth and intestinal flora in weaned pigs. Food Funct 2020; 11:493-507. [PMID: 31833513 DOI: 10.1039/c9fo02724f] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study investigated the effects of modulation of the amino acid profile on growth performance and gut health in weaned pigs fed an antibiotic-free, low-protein diet. In experiment 1, 5 treatments were included: a control diet with antibiotics; a low-protein diet with antibiotics; a low-protein diet without antibiotics (LP); a LP diet with 10% more dietary essential amino acids (LP110); and an LP110 diet with 12% more dietary Met + Cys, Thr and Trp. The intestinal digestive enzyme activity and morphology were improved with the increase in dietary essential amino acid levels, while the growth performance was decreased, indicating that the dietary amino acid level was too high. In experiment 2, all 5 treatments of experiment 1 were included, plus a LP diet with 5% more dietary essential amino acids (LP105) and an LP105 diet with 6% more dietary Met + Cys, Thr and Trp. The LP105 treatment showed optimal feed efficiency, a reduced plasma endotoxin concentration, and an increased fecal lactate concentration and increased abundances of Prevotellaceae and Roseburia bacteria. Our results demonstrate that the optimal amino acid profile in an antibiotic-free, low-protein diet can efficiently improve growth performance and gut health and modulate the fecal microbial structure in weaned pigs.
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Affiliation(s)
- Junyan Zhou
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing 100193, PR. China.
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48
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Fongaro G, Maia GA, Rogovski P, Cadamuro RD, Lopes JC, Moreira RS, Camargo AF, Scapini T, Stefanski FS, Bonatto C, Marques Souza DS, Stoco PH, Duarte RTD, Cabral da Cruz AC, Wagner G, Treichel H. Extremophile Microbial Communities and Enzymes for Bioenergetic Application Based on Multi-Omics Tools. Curr Genomics 2020; 21:240-252. [PMID: 33071618 PMCID: PMC7521039 DOI: 10.2174/1389202921999200601144137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/02/2020] [Accepted: 04/20/2020] [Indexed: 12/03/2022] Open
Abstract
Abstract: Genomic and proteomic advances in extremophile microorganism studies are increasingly demonstrating their ability to produce a variety of enzymes capable of converting biomass into bioenergy. Such microorganisms are found in environments with nutritional restrictions, anaerobic environments, high salinity, varying pH conditions and extreme natural environments such as hydrothermal vents, soda lakes, and Antarctic sediments. As extremophile microorganisms and their enzymes are found in widely disparate locations, they generate new possibilities and opportunities to explore biotechnological prospecting, including biofuels (biogas, hydrogen and ethanol) with an aim toward using multi-omics tools that shed light on biotechnological breakthroughs.
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Affiliation(s)
- Gislaine Fongaro
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Guilherme Augusto Maia
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Paula Rogovski
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Rafael Dorighello Cadamuro
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Joana Camila Lopes
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Renato Simões Moreira
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Aline Frumi Camargo
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Thamarys Scapini
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Fábio Spitza Stefanski
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Charline Bonatto
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Doris Sobral Marques Souza
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Patrícia Hermes Stoco
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Rubens Tadeu Delgado Duarte
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Ariadne Cristiane Cabral da Cruz
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Glauber Wagner
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
| | - Helen Treichel
- 1Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 2Laboratory of Microbiology and Bioprocess, Federal University of Fronteira Sul, Erechim, RS, Brazil; 3Department of Chemical and Food Engineering, Federal University of Santa Catarina, Florianópolis, SC, Brazil; 4Department of Dentistry, Federal University of Santa Catarina, Florianópolis, SC, Brazil
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49
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Dvořák P, Bayer EA, de Lorenzo V. Surface Display of Designer Protein Scaffolds on Genome-Reduced Strains of Pseudomonas putida. ACS Synth Biol 2020; 9:2749-2764. [PMID: 32877604 DOI: 10.1021/acssynbio.0c00276] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The bacterium Pseudomonas putida KT2440 is gaining considerable interest as a microbial platform for biotechnological valorization of polymeric organic materials, such as lignocellulosic residues or plastics. However, P. putida on its own cannot make much use of such complex substrates, mainly because it lacks an efficient extracellular depolymerizing apparatus. We seek to address this limitation by adopting a recombinant cellulosome strategy for this host. In this work, we report an essential step in this endeavor-a display of designer enzyme-anchoring protein "scaffoldins", encompassing cohesin binding domains from divergent cellulolytic bacterial species on the P. putida surface. Two P. putida chassis strains, EM42 and EM371, with streamlined genomes and differences in the composition of the outer membrane were employed in this study. Scaffoldin variants were optimally delivered to their surface with one of four tested autotransporter systems (Ag43 from Escherichia coli), and the efficient display was confirmed by extracellular attachment of chimeric β-glucosidase and fluorescent proteins. Our results not only highlight the value of cell surface engineering for presentation of recombinant proteins on the envelope of Gram-negative bacteria but also pave the way toward designer cellulosome strategies tailored for P. putida.
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Affiliation(s)
- Pavel Dvořák
- Department of Experimental Biology (Section of Microbiology), Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología CNB-CSIC, Cantoblanco, Darwin 3, 28049 Madrid, Spain
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50
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Jia L, Li C, Zhang Y, Chen Y, Li M, Wu S, Wu H. Microbial community responses to agricultural biomass addition in aerated constructed wetlands treating low carbon wastewater. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 270:110912. [PMID: 32721346 DOI: 10.1016/j.jenvman.2020.110912] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 04/17/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
Using agricultural biomasses as solid carbon substrates in constructed wetlands (CWs) could be an effective way to achieve sustainable nitrogen removal for carbon-limited wastewater treatments. This study investigated the response of bacteria community in CWs to the addition of agricultural biomasses (wheat straw, walnut shell and apricot pit). Results indicated that the addition of different agricultural biomasses had distinct influence on bacterial communities in CWs. Both wheat straw and walnut shell increased the diversity of microbial communities and optimized the structure of microorganisms. The effect of apricot pit on the richness and evenness of microbial communities was not significant, but the composition of microorganisms was significantly affected at the phylum level, especially the relative abundance of phylum Saccharibacteria. Moreover, the addition of agricultural biomasses in CWs acclimatized more functional bacteria including nitrifier and denitrifier, which were proved to be positively correlated with the high-rate denitrification performance. The obtained results would be beneficial to understand the underlying microbial mechanism of nitrogen removal in CWs with agricultural biomass and provide some guidance on the practical application of CWs.
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Affiliation(s)
- Lixia Jia
- School of Environment and Planning, Liaocheng University, Liaocheng, Shandong, 252000, PR China; College of Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Cong Li
- School of Environment and Planning, Liaocheng University, Liaocheng, Shandong, 252000, PR China; Shandong Liaohe Environmental Protection Technology Co., Ltd., Liaocheng, Shandong, 252000, PR China
| | - Yan Zhang
- College of Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Yingrun Chen
- College of Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Mengqi Li
- College of Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Shubiao Wu
- Department of Bioscience, Aarhus University, Aarhus, 8000C, Denmark
| | - Haiming Wu
- College of Resources and Environment, Northwest A&F University, Yangling, Shaanxi, 712100, PR China; Department of Bioscience, Aarhus University, Aarhus, 8000C, Denmark.
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