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Rawat M, Chauhan M, Pandey A. Extremophiles and their expanding biotechnological applications. Arch Microbiol 2024; 206:247. [PMID: 38713374 DOI: 10.1007/s00203-024-03981-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/16/2024] [Accepted: 04/25/2024] [Indexed: 05/08/2024]
Abstract
Microbial life is not restricted to any particular setting. Over the past several decades, it has been evident that microbial populations can exist in a wide range of environments, including those with extremes in temperature, pressure, salinity, and pH. Bacteria and Archaea are the two most reported types of microbes that can sustain in extreme environments, such as hot springs, ice caves, acid drainage, and salt marshes. Some can even grow in toxic waste, organic solvents, and heavy metals. These microbes are called extremophiles. There exist certain microorganisms that are found capable of thriving in two or more extreme physiological conditions simultaneously, and are regarded as polyextremophiles. Extremophiles possess several physiological and molecular adaptations including production of extremolytes, ice nucleating proteins, pigments, extremozymes and exopolysaccharides. These metabolites are used in many biotechnological industries for making biofuels, developing new medicines, food additives, cryoprotective agents etc. Further, the study of extremophiles holds great significance in astrobiology. The current review summarizes the diversity of microorganisms inhabiting challenging environments and the biotechnological and therapeutic applications of the active metabolites obtained as a response to stress conditions. Bioprospection of extremophiles provides a progressive direction with significant enhancement in economy. Moreover, the introduction to omics approach including whole genome sequencing, single cell genomics, proteomics, metagenomics etc., has made it possible to find many unique microbial communities that could be otherwise difficult to cultivate using traditional methods. These findings might be capable enough to state that discovery of extremophiles can bring evolution to biotechnology.
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Affiliation(s)
- Manvi Rawat
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, 248002, India
| | - Mansi Chauhan
- Department of Microbiology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, 248002, India
| | - Anita Pandey
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, 248002, India.
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Singh Y, Sharma S, Kumar U, Sihag P, Balyan P, Singh KP, Dhankher OP. Strategies for economic utilization of rice straw residues into value-added by-products and prevention of environmental pollution. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167714. [PMID: 37832665 DOI: 10.1016/j.scitotenv.2023.167714] [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: 05/12/2023] [Revised: 09/26/2023] [Accepted: 10/08/2023] [Indexed: 10/15/2023]
Abstract
Rice straw management, along with the prevalent practice of residue burning, poses multifaceted challenges with substantial environmental and human health implications. After harvest, a considerable amount of straw is left behind, often disposed of through burning, releasing several pollutants into the environment. Carbon dioxide (CO2) dominates at 70%, accompanied by methane (CH4) at 0.66%, carbon monoxide (CO) at 7%, and nitrous oxide (N2O) at 2.09%. This process further compounds issues by depleting soil nutrients like nitrogen and organic matter. This review focuses on strategies for residue management and using straw as value-added by-products. We address research gaps and offer potential recommendations for rice straw management using economically feasible and practical routes. We elaborate that to improve rice straw digestibility, utilization in mushroom cultivation, and other value-added products, low silica (Si) rice varieties must be developed using modern technologies including marker-assisted selection breeding or genome editing. Developing low Si rice could also reduce arsenic uptake by rice, as rice plants use the same transporters for the uptake of both elements. Conversely, silica is also indispensable for quality rice production; hence, optimizing silicon content in rice is worth investigating. More research is required to understand the extent of silicon's effect on the utilization of straw for various purposes. This review also discusses the importance of educating farmers about the straw burning issue and its environmental consequences. We highlight the significance of tailoring rice straw management methods to local suitability, moving away from a universal approach. More extension work is needed to encourage farmers to opt for environmentally and economically sound options for rice straw management. Policy intervention to incentivize farmers and develop technologies for the widespread use of rice straw for various industries and product development could help in the management of rice straw and will also create a circular economy.
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Affiliation(s)
- Yogita Singh
- Department of Molecular Biology & Biotechnology, College of Biotechnology, CCS Haryana Agricultural University, Hisar 125004, India
| | - Sudhir Sharma
- Stockbridge School of Agriculture, University of Massachusetts Amherst, MA 01003, USA
| | - Upendra Kumar
- Department of Molecular Biology & Biotechnology, College of Biotechnology, CCS Haryana Agricultural University, Hisar 125004, India; Department of Plant Science, Mahatma Jyotiba Phule Rohilkhand University, Bareilly-243006, India.
| | - Pooja Sihag
- Department of Molecular Biology & Biotechnology, College of Biotechnology, CCS Haryana Agricultural University, Hisar 125004, India
| | - Priyanka Balyan
- Department of Botany, Deva Nagri P.G. College, CCS University Meerut, 250001, India
| | - Krishna Pal Singh
- Biophysics Unit, College of Basic Sciences & Humanities, GB Pant University of Agriculture & Technology, Pantnagar 263145, India; Vice-Chancellor's Secretariat, Mahatma Jyotiba Phule Rohilkhand University, Bareilly 243001, India
| | - Om Parkash Dhankher
- Stockbridge School of Agriculture, University of Massachusetts Amherst, MA 01003, USA.
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Wang H, Shao T, Zhou Y, Long X, Rengel Z. The effect of biochar prepared at different pyrolysis temperatures on microbially driven conversion and retention of nitrogen during composting. Heliyon 2023; 9:e13698. [PMID: 36873514 PMCID: PMC9976328 DOI: 10.1016/j.heliyon.2023.e13698] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 01/31/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Aerobic composting is one of the most economical ways to produce organic fertilizer from agricultural wastes. In this research, we independently developed a simple composting simulation reactor. The effects of biochar pyrolysised at different pyrolysis temperatures (B1-450 °C; B2-550 °C; and B3-650 °C) on nitrogen conversion (Total nitrogen (TN), ammonium nitrogen (NH4 +-N), nitrate nitrogen (NO3 --N), cumulative amount of ammonia (CEA) and nitrous oxide (CEN) emission, nitrogen loss rate (NLR), etc.) and functional microbial community (cbbL, cbbM and nifH) structure in the composting system were studied. Results showed that the addition of biochar significantly improved the efficiency of composting, increased the NO3 --N concentration and reduced the NLR (%) in the composting system (B3 (31.4 ± 2.73)<B2=B1 (41.7 ± 3.29)<B0 (54.5 ± 3.34), p ≤ 0.05), while the loss rate of nitrogen positively correlated with compost pH. Denitrifying bacterial genera such as Pseudomonas, Alcaligenes, Paracoccus, Bacillus, Citrobacter, Mesorhizobium, Thiobacillus and Rhodococcus in this study was an important reason for nitrogen loss during composting, and the abundance of autotrophic microorganisms (such as Sulfuritalea, Hydrogenophaga, Thiobacillus, Thiomonas and Candidatus_Thioglobus) in treatments with biochar (B1, B2 and B3) were higher than that in B0. Besides, the community structure in the treatments B2 and B3 was similar at the end of composting and clearly distinguished from that in B1. Moreover, the five functions predicted by OTUs in this study with the highest proportions were chemoheterotrophy, nitrate reduction, fermentation, aerobic chemoheterotrophy and nitrogen respiration. The study provided a theoretical basis for the application of biochar to improve the compost-related processes.
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Affiliation(s)
- Haihou Wang
- Suzhou Academy of Agricultural Sciences, Institution of Agricultural Sciences Taihu Lake District, Suzhou, 215155, China.,National Soil Quality Observation and Experimental Station in Xiangcheng, Suzhou, 215131, China
| | - Tianyun Shao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yujie Zhou
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaohua Long
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zed Rengel
- Soil Science and Plant Nutrition, UWA School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia.,Institute for Adriatic Crops and Karst Reclamation, Put Duilova 11, Split, Croatia
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Eljonaid MY, Tomita H, Okazaki F, Tamaru Y. Enzymatic Characterization of Unused Biomass Degradation Using the Clostridium cellulovorans Cellulosome. Microorganisms 2022; 10:microorganisms10122514. [PMID: 36557767 PMCID: PMC9784398 DOI: 10.3390/microorganisms10122514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
The cellulolytic system of Clostridium cellulovorans mainly consisting of a cellulosome that synergistically collaborates with non-complexed enzymes was investigated using cellulosic biomass. The cellulosomes were isolated from the culture supernatants with shredded paper, rice straw and sugarcane bagasse using crystalline cellulose. Enzyme solutions, including the cellulosome fractions, were analyzed by SDS-PAGE and Western blot using an anti-CbpA antibody. As a result, C. cellulovorans was able to completely degrade shredded paper for 9 days and to be continuously cultivated by the addition of new culture medium containing shredded paper, indicating, through TLC analysis, that its degradative products were glucose and cellobiose. Regarding the rice straw and sugarcane bagasse, while the degradative activity of rice straw was most active using the cellulosome in the culture supernatant of rice straw medium, that of sugarcane bagasse was most active using the cellulosome from the supernatant of cellobiose medium. Based on these results, no alcohols were found when C. acetobutylicum was cultivated in the absence of C. cellulovorans as it cannot degrade the cellulose. While 1.5 mM of ethanol was produced with C. cellulovorans cultivation, both n-butanol (1.67 mM) and ethanol (1.89 mM) were detected with the cocultivation of C. cellulovorans and C. acetobutylicum. Regarding the enzymatic activity evaluation against rice straw and sugarcane bagasse, the rice straw cellulosome fraction was the most active when compared against rice straw. Furthermore, since we attempted to choose reaction conditions more efficiently for the degradation of sugarcane bagasse, a wet jet milling device together with L-cysteine as a reducing agent was used. As a result, we found that the degradation activity was almost twice as high with 10 mM L-cysteine compared with without it. These results will provide new insights for biomass utilization.
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Affiliation(s)
- Mohamed Yahia Eljonaid
- Department of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Tsu 514-8507, Japan
| | - Hisao Tomita
- Department of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Tsu 514-8507, Japan
| | - Fumiyoshi Okazaki
- Department of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Tsu 514-8507, Japan
- Department of Bioinfomatics, Mie University Advanced Science Research Center, Mie University, 1577 Kurimamachiya, Tsu 514-8507, Japan
- Smart Cell Innovation Research Center, Mie University, 1577 Kurimamachiya, Tsu 514-8507, Japan
| | - Yutaka Tamaru
- Department of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Tsu 514-8507, Japan
- Department of Bioinfomatics, Mie University Advanced Science Research Center, Mie University, 1577 Kurimamachiya, Tsu 514-8507, Japan
- Smart Cell Innovation Research Center, Mie University, 1577 Kurimamachiya, Tsu 514-8507, Japan
- Correspondence: ; Tel.: +81-59-231-9560
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Biomethanation of Rice Straw: A Sustainable Perspective for the Valorisation of a Field Residue in the Energy Sector. SUSTAINABILITY 2022. [DOI: 10.3390/su14095679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Rice straw represents a field waste. Indeed, only 20% of the rice straw produced is used in the pulp and paper industry. The larger amount of this field residue is burned or left in the field, which has very important environmental consequences. Recently, analogous to a barrel of oil, a metric approach to rice straw, the rice straw barrel, was introduced in order to assign economic value to this waste. In this paper, potential annual biomethane production from anaerobic digestion is evaluated, resulting in a range of biomethane created for each rice straw barrel depending on volatile solid (VS) content as a percentage of total solid (TS) content and on biomethane yield: 23.36 m3 (VS=73.8%TS, 92 L kgVS−1), 26.61 m3 (VS=84.08%TS, 186 L kgVS−1), 29.27 m3 (VS=95.26%TS, 280 L kgVS−1). The new concept of the rice straw barrel is improved based on a new indicator for sustainability, the Thermodynamic Human Development Index (THDI), which was introduced within the last three years. The improvement in sustainability by using rice straw barrels for different countries is analysed based on the THDI.
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Uetsuki K, Kawashima H, Ohno E, Ishikawa T, Iida T, Yamamoto K, Furukawa K, Nakamura M, Honda T, Ishigami M, Hirooka Y, Fujishiro M. Measurement of fasting breath hydrogen concentration as a simple diagnostic method for pancreatic exocrine insufficiency. BMC Gastroenterol 2021; 21:211. [PMID: 33971823 PMCID: PMC8111728 DOI: 10.1186/s12876-021-01776-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/20/2021] [Indexed: 12/16/2022] Open
Abstract
Background Pancreatic exocrine insufficiency (PEI) is associated with the outcome of pancreatic disease. However, there is no method for assessing PEI that can be used noninvasively and easily for outpatient. It has been reported that changes in intestinal bacteria caused by PEI may increase breath hydrogen concentration (BHC) levels during glucose or lactose loading. We have evaluated the usefulness of fasting breath hydrogen concentration (FBHC) measurement without glucose loading for the evaluation of PEI. Methods Sixty patients underwent FBHC measurement, BT-PABA testing, and microbiome analysis. They were classified into PEI group (PABA excretion rate < 73.4%, n = 30) and non-PEI group (n = 30). The FBHC of the two groups were compared, and the diagnostic ability of PEI by them was evaluated. The 16 s rRNA (V3–V4) from fecal samples was analyzed by MiSeq. Results FBHC levels was higher in the PEI group 15.70 (1.4 to 77.0) ppm than in the non-PEI group 2.80 (0.7 to 28.2) ppm (P < 0.0001). FBHC was negatively correlated with PABA excretion rate (r = − 0.523, P < 0.001). The cutoff value of FBHC of 10.7 ppm (95% CI: 0.678–0.913, P < 0.001) showed a sensitivity of 73.3% and specificity of 83.3% for PEI diagnosis. In the PEI group, there was a significant increase of relative abundance of phylum Firmicutes (P < 0.05) and the genus Clostridium (P < 0.05). Conclusion FBHC shows good potential as a simple and repeatable test for the diagnosis of PEI. The elevated FBHC levels may be caused by hydrogen-producing bacteria such as Clostridium.
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Affiliation(s)
- Kota Uetsuki
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Hiroki Kawashima
- Department of Endoscopy, Nagoya University Hospital, 65 Tsuruma-cho, Showa-ku, Nagoya, 466-8550, Japan.
| | - Eizaburo Ohno
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Takuya Ishikawa
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Tadashi Iida
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Kenta Yamamoto
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Kazuhiro Furukawa
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Masanao Nakamura
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Takashi Honda
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Masatoshi Ishigami
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Yoshiki Hirooka
- Department of Gastroenterology and Gastroenterological Oncology, Fujita Health University, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi, 470-1192, Japan
| | - Mitsuhiro Fujishiro
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsuruma-cho, Showa-ku, Nagoya, 466-8550, Japan
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Bao T, Hou W, Wu X, Lu L, Zhang X, Yang ST. Engineering Clostridium cellulovorans for highly selective n-butanol production from cellulose in consolidated bioprocessing. Biotechnol Bioeng 2021; 118:2703-2718. [PMID: 33844271 DOI: 10.1002/bit.27789] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/06/2021] [Accepted: 04/09/2021] [Indexed: 01/05/2023]
Abstract
Cellulosic n-butanol from renewable lignocellulosic biomass has gained increased interest. Previously, we have engineered Clostridium cellulovorans, a cellulolytic acidogen, to overexpress the bifunctional butyraldehyde/butanol dehydrogenase gene adhE2 from C. acetobutylicum for n-butanol production from crystalline cellulose. However, butanol production by this engineered strain had a relatively low yield of approximately 0.22 g/g cellulose due to the coproduction of ethanol and acids. We hypothesized that strengthening the carbon flux through the central butyryl-CoA biosynthesis pathway and increasing intracellular NADH availability in C. cellulovorans adhE2 would enhance n-butanol production. In this study, thiolase (thlACA ) from C. acetobutylicum and 3-hydroxybutyryl-CoA dehydrogenase (hbdCT ) from C. tyrobutyricum were overexpressed in C. cellulovorans adhE2 to increase the flux from acetyl-CoA to butyryl-CoA. In addition, ferredoxin-NAD(P)+ oxidoreductase (fnr), which can regenerate the intracellular NAD(P)H and thus increase butanol biosynthesis, was also overexpressed. Metabolic flux analyses showed that mutants overexpressing these genes had a significantly increased carbon flux toward butyryl-CoA, which resulted in increased production of butyrate and butanol. The addition of methyl viologen as an electron carrier in batch fermentation further directed more carbon flux towards n-butanol biosynthesis due to increased reducing equivalent or NADH. The engineered strain C. cellulovorans adhE2-fnrCA -thlACA -hbdCT produced n-butanol from cellulose at a 50% higher yield (0.34 g/g), the highest ever obtained in batch fermentation by any known bacterial strain. The engineered C. cellulovorans is thus a promising host for n-butanol production from cellulosic biomass in consolidated bioprocessing.
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Affiliation(s)
- Teng Bao
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Wenjie Hou
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA.,College of Life Sciences, Northwest A&F University, Yangling, Shanxi, China
| | - Xuefeng Wu
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA.,School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Li Lu
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
| | - Xian Zhang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA.,School of Biotechnology, Jiangnan University, Wuxi, China
| | - Shang-Tian Yang
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
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Tao X, Xu T, Kempher ML, Liu J, Zhou J. Precise promoter integration improves cellulose bioconversion and thermotolerance in Clostridium cellulolyticum. Metab Eng 2020; 60:110-118. [PMID: 32294528 DOI: 10.1016/j.ymben.2020.03.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/22/2020] [Accepted: 03/30/2020] [Indexed: 11/15/2022]
Abstract
Lignocellulose has been used for production of sustainable biofuels and value-added chemicals. However, the low-efficiency bioconversion of lignocellulose greatly contributes to a high production cost. Here, we employed CRISPR-Cas9 editing to improve cellulose degradation efficiency by editing a regulatory element of the cip-cel gene cluster in Clostridium cellulolyticum. Insertion of a synthetic promoter (P4) and an endogenous promoter (P2) in the mspI-deficient parental strain (Δ2866) created chromosomal integrants, P4-2866 and P2-2866, respectively. Both engineered strains increased the transcript abundance of downstream polycistronic genes and enhanced in vitro cellulolytic activities of isolated cellulosomes. A high cellulose load of 20 g/L suppressed cellulose degradation in the parental strain in the first 150 h fermentation; whereas P4-2866 and P2-2866 hydrolyzed 29% and 53% of the cellulose, respectively. Both engineered strains also demonstrated a greater growth rate and a higher cell biomass yield. Interestingly, the Δ2866 parental strain demonstrated better thermotolerance than the wildtype strain, and promoter insertion further enhanced thermotolerance. Similar improvements in cell growth and cellulose degradation were reproduced by promoter insertion in the wildtype strain and a lactate production-defective mutant (LM). P2 insertion in LM increased ethanol titer by 65%. Together, the editing of regulatory elements of catabolic gene clusters provides new perspectives on improving cellulose bioconversion in microbes.
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Affiliation(s)
- Xuanyu Tao
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA
| | - Tao Xu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA; Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.
| | - Megan L Kempher
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA
| | - Jiantao Liu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, USA; Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China.
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Yu F, Liang JF, Song J, Wang SK, Lu JK. Bacterial Community Selection of Russula griseocarnosa Mycosphere Soil. Front Microbiol 2020; 11:347. [PMID: 32269551 PMCID: PMC7109302 DOI: 10.3389/fmicb.2020.00347] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 02/17/2020] [Indexed: 11/13/2022] Open
Abstract
Russula griseocarnosa is a wild, ectomycorrhizal, edible, and medicinal fungus with high economic value in southern China. R. griseocarnosa fruiting bodies cannot be artificially cultivated. To better understand the effects of abiotic and biotic factors on R. griseocarnosa growth, the physicochemical properties of R. griseocarnosa and its associated bacterial communities were investigated in two soil types (mycosphere and bulk soil) from Fujian, Guangdong, and Guangxi Provinces. The results revealed that the diversity, community structure, and functional characteristics of the dominant mycosphere bacteria in all geographical locations were similar. Soil pH and available nitrogen (AN) are the major factors influencing the mycosphere-soil bacterial communities' structure. The diversity of soil bacteria is decreased in R. griseocarnosa mycosphere when compared with the bulk soil. Burkholderia-Paraburkholderia, Mycobacterium, Roseiarcus, Sorangium, Acidobacterium, and Singulisphaera may also be mycorrhiza helper bacteria (MHB) of R. griseocarnosa. The functional traits related to the two-component system, bacterial secretion system, tyrosine metabolism, biosynthesis of unsaturated fatty acids, and metabolism of cofactors and vitamins were more abundant in R. griseocarnosa mycosphere soil. The mycosphere soil bacteria of R. griseocarnosa play a key role in R. griseocarnosa growth. Application of management strategies, such as N fertilizer and microbial fertilizer containing MHB, may promote the conservation, propagation promotion, and sustainable utilization of R. griseocarnosa.
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Affiliation(s)
| | - Jun-Feng Liang
- Key Laboratory of State Forestry Administration on Tropical Forestry Research, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
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Aikawa S, Thianheng P, Baramee S, Ungkulpasvich U, Tachaapaikoon C, Waeonukul R, Pason P, Ratanakhanokchai K, Kosugi A. Phenotypic characterization and comparative genome analysis of two strains of thermophilic, anaerobic, cellulolytic-xylanolytic bacterium Herbivorax saccincola. Enzyme Microb Technol 2020; 136:109517. [PMID: 32331721 DOI: 10.1016/j.enzmictec.2020.109517] [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: 10/11/2019] [Revised: 01/09/2020] [Accepted: 01/25/2020] [Indexed: 11/25/2022]
Abstract
The genome sequences of thermophilic, anaerobic, and cellulolytic-xylanolytic bacterium Herbivorax saccincola strains A7 and GGR1 have recently been determined. Although both strains belong to the same species, A7 is alkaliphilic, non-endospore-forming, and ammonium-assimilating, whereas GGR1 is neutrophilic, endospore-forming, and weak-ammonium-assimilating. To better understand the phenotypic diversity among H. saccincola strains, the genome sequences of A7 and GGR1 were compared. A7 contained three additional genes showing similarity to an alkaline stress-associated ABC-transporter but lacked four endospore formation-associated genes, AUG58543 and AUG58618 (encoding SpoVT), AUG57258 (encoding SpoVS), and AUG58614 (encoding YdhD), all of which were present in GGR1. In addition, A7 contained key ammonia assimilation genes PQQ67145 and PQQ66619, encoding ornithine cyclodeaminase and arginase, respectively, which were absent in GGR1. There was no difference in the number and types of cellulosomal-scaffolding proteins and glycosyl hydrolases between the two strains. However, cellulase and xylanase enzymes from A7 demonstrated greater activity and stability at an alkaline pH compared with those from GGR1, and amino acid substitutions were identified in 11 glycosyl hydrolases from A7. This characterization though comparative genomic analysis provides useful information for understanding the genetic basis of the phenotypic differences between H. saccincola strains isolated from distinct areas and environments.
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Affiliation(s)
- Shimpei Aikawa
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Phakhinee Thianheng
- Enzyme Technology Laboratory, School of Bioresources and Technology, King Mongkut's University of Technology, Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Sirilak Baramee
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Umbhorn Ungkulpasvich
- Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Chakrit Tachaapaikoon
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology, Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Rattiya Waeonukul
- Pilot Plant Development and Training Institute (PDTI), King Mongkut's University of Technology, Thonburi (KMUTT), Bangkok 10150, Thailand
| | - Patthra Pason
- Pilot Plant Development and Training Institute (PDTI), 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
| | - Akihiko Kosugi
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
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11
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Fan L, Li M, Li Y, Fan X, Liu Y, Lv Y. Draft Genome Sequence of Thermophilic Bacillus sp. TYF-LIM-B05 Directly Producing Ethanol from Various Carbon Sources Including Lignocellulose. Curr Microbiol 2019; 77:491-499. [PMID: 31832840 DOI: 10.1007/s00284-019-01833-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 11/29/2019] [Indexed: 12/01/2022]
Abstract
Bacillus sp. TYF-LIM-B05, which is isolated from spoilage vinegar, is resistant to high temperature, high concentrated alcohol, acid, and salt, and can produce ethanol from mono-, di-, polysaccharide, and complex biomass as the sole carbon source. Thus, this strain is a potential candidate for consolidated bioprocessing (CBP) of fermenting lignocellulose to ethanol in a single step. To provide insight into the key enzymes involved in lignocellulose degradation and ethanol production, a draft genome of TYF-LIM-B05 was developed in this study. The results indicated that 348 genes are related to carbohydrate transport and metabolism according to the clusters of orthologous groups of proteins and annotated 187 CAZy domains from a total of 61 different families. The presence of genes encoding laccases, quinone oxidoreductases/reductases, and aryl-alcohol dehydrogenases further implies that TYF-LIM-B05 has the potential to degrade lignin. Remarkably, this strain has the ability to catalyze the oxidative decarboxylation of pyruvate to acetyl-CoA by pyruvate dehydrogenase complexes. The genomic information provided in this study will help researchers to better understand the mechanisms of the lignocellulose degradation and ethanol production pathway in thermophiles.
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Affiliation(s)
- Lulu Fan
- College of Environmental Science and Engineering, Taiyuan University of Technology, No. 209 of University Street, Yuci District, Jinzhong, 030600, Shanxi, China
| | - Min Li
- College of Biomedical Engineering, Taiyuan University of Technology, No. 209 of University Street, Yuci District, Jinzhong, 030600, Shanxi, China
| | - Yao Li
- College of Biomedical Engineering, Taiyuan University of Technology, No. 209 of University Street, Yuci District, Jinzhong, 030600, Shanxi, China
| | - Xiaojun Fan
- College of Environmental Science and Engineering, Taiyuan University of Technology, No. 209 of University Street, Yuci District, Jinzhong, 030600, Shanxi, China. .,Innovation Institute of Environmental Industry, Taiyuan University of Technology, No. 209 of University Street, Yuci District, Jinzhong, 030600, Shanxi, China.
| | - Yuxiang Liu
- College of Environmental Science and Engineering, Taiyuan University of Technology, No. 209 of University Street, Yuci District, Jinzhong, 030600, Shanxi, China.
| | - Yongkang Lv
- Key Laboratory of Coal Science and Technology, Ministry of Education and Shanxi Province, Taiyuan University of Technology, Taiyuan, 030024, Shanxi, China
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12
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The Second-Generation Biomethane from Mandarin Orange Peel under Cocultivation with Methanogens and the Armed Clostridium cellulovorans. FERMENTATION-BASEL 2019. [DOI: 10.3390/fermentation5040095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This study demonstrates that the consortium, which consists of the microbial flora of methane production (MFMP) and Clostridium cellulovorans grown with cellulose, can perform the direct conversion of cellulosic biomass to methane. The MFMP was taken from a commercial methane fermentation tank and was extremely complicated. Therefore, C. cellulovorans grown with cellobiose could not perform high degradation ability on cellulosic biomass due to competition by various microorganisms in MFMP. Focusing on the fact that C. cellulovorans was cultivated with cellulose, which is armed with cellulosome, so that it is now armed C. cellulovorans; the direct conversion was carried out by the consortium which consisted of MFMP and the armed C. cellulovorans. As a result, the consortium of C. cellulovorans grown with cellobiose and MFMP (CCeM) could not degrade the purified cellulose and mandarin orange peel. However, MFMP and the armed C. cellulovorans reduced 78.4% of the total sugar of the purified cellulose such as MN301, and produced 6.89 mL of methane simultaneously. Furthermore, the consortium consisted of MFMP and the armed C. cellulovorans degraded mandarin orange peel without any pretreatments and produced methane that was accounting for 66.2% of the total produced gas.
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Wang Y, Leng L, Islam MK, Liu F, Lin CSK, Leu SY. Substrate-Related Factors Affecting Cellulosome-Induced Hydrolysis for Lignocellulose Valorization. Int J Mol Sci 2019; 20:ijms20133354. [PMID: 31288425 PMCID: PMC6651384 DOI: 10.3390/ijms20133354] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/30/2019] [Accepted: 07/03/2019] [Indexed: 11/22/2022] Open
Abstract
Cellulosomes are an extracellular supramolecular multienzyme complex that can efficiently degrade cellulose and hemicelluloses in plant cell walls. The structural and unique subunit arrangement of cellulosomes can promote its adhesion to the insoluble substrates, thus providing individual microbial cells with a direct competence in the utilization of cellulosic biomass. Significant progress has been achieved in revealing the structures and functions of cellulosomes, but a knowledge gap still exists in understanding the interaction between cellulosome and lignocellulosic substrate for those derived from biorefinery pretreatment of agricultural crops. The cellulosomic saccharification of lignocellulose is affected by various substrate-related physical and chemical factors, including native (untreated) wood lignin content, the extent of lignin and xylan removal by pretreatment, lignin structure, substrate size, and of course substrate pore surface area or substrate accessibility to cellulose. Herein, we summarize the cellulosome structure, substrate-related factors, and regulatory mechanisms in the host cells. We discuss the latest advances in specific strategies of cellulosome-induced hydrolysis, which can function in the reaction kinetics and the overall progress of biorefineries based on lignocellulosic feedstocks.
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Affiliation(s)
- Ying Wang
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, China
- Department of Civil and Environmental Engineering, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Ling Leng
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8566, Japan
| | - Md Khairul Islam
- Department of Civil and Environmental Engineering, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China
| | - Fanghua Liu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Guangdong Institute of Eco-Environmental Science & Technology, Guangzhou 510650, China
| | - Carol Sze Ki Lin
- School of Energy and Environment, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Shao-Yuan Leu
- Department of Civil and Environmental Engineering, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, China.
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Aburaya S, Aoki W, Kuroda K, Minakuchi H, Ueda M. Temporal proteome dynamics of Clostridium cellulovorans cultured with major plant cell wall polysaccharides. BMC Microbiol 2019; 19:118. [PMID: 31159733 PMCID: PMC6547498 DOI: 10.1186/s12866-019-1480-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 05/07/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Clostridium cellulovorans is a mesophilic, cellulosome-producing bacterium containing 57 genomic cellulosomal enzyme-encoding genes. In addition to cellulosomal proteins, C. cellulovorans also secretes non-cellulosomal proteins to degrade plant cell wall polysaccharides. Unlike other cellulosome-producing Clostridium species, C. cellulovorans can metabolize all major plant cell wall polysaccharides (cellulose, hemicelluloses, and pectins). In this study, we performed a temporal proteome analysis of C. cellulovorans to reveal strategies underlying plant cell wall polysaccharide degradation. RESULTS We cultured C. cellulovorans with five different carbon sources (glucose, cellulose, xylan, galactomannan, and pectin) and performed proteome analysis on cellular and secreted proteins. In total, we identified 1895 cellular proteins and 875 secreted proteins. The identified unique carbohydrate-degrading enzymes corresponding to each carbon source were annotated to have specific activity against each carbon source. However, we identified pectate lyase as a unique enzyme in C. cellulovorans cultivated on xylan, which was not previously associated with xylan degradation. We performed k-means clustering analysis for elucidation of temporal changes of the cellular and secreted proteins in each carbon sources. We found that cellular proteins in most of the k-means clusters are involved in carbohydrate metabolism, amino acid metabolism, translation, or membrane transport. When xylan and pectin were used as the carbon sources, the most increasing k-means cluster contained proteins involved in the metabolism of cofactors and vitamins. In case of secreted proteins of C. cellulovorans cultured either on cellulose or xylan, galactomannan, and pectin, the clusters with the most increasing trend contained either 25 cellulosomal proteins and five non-cellulosomal proteins or 8-19 cellulosomal proteins and 9-16 non-cellulosomal proteins, respectively. These differences might reflect mechanisms for degrading cellulose of other carbon source. Co-abundance analysis of the secreted proteins revealed that proteases and protease inhibitors accumulated coordinately. This observation implies that the secreted protease inhibitors and proteases protect carbohydrate-degrading enzymes from an attack from the plant. CONCLUSION In this study, we clarified, for the first time, the temporal proteome dynamics of cellular and secreted proteins in C. cellulovorans. This data will be valuable in understanding strategies employed by C. cellulovorans for degrading major plant cell wall polysaccharides.
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Affiliation(s)
- Shunsuke Aburaya
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan.,Research Fellow of the Japan Society for the Promotion of Science, Sakyo-ku, Kyoto, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan.,Kyoto Integrated Science and Technology Bio-Analysis Center, Shimogyo-ku, Kyoto, Japan.,JST-PRESTO, Chiyoda-ku, Tokyo, Japan
| | - Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Hiroshi Minakuchi
- Kyoto-monotech, 1095, Shuzei-cho, Kamigyo-ku, Kyoto-shi, Kyoto, 602-8155, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan. .,Kyoto Integrated Science and Technology Bio-Analysis Center, Shimogyo-ku, Kyoto, Japan. .,JST-PRESTO, Chiyoda-ku, Tokyo, Japan.
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Tomita H, Okazaki F, Tamaru Y. Biomethane production from sugar beet pulp under cocultivation with Clostridium cellulovorans and methanogens. AMB Express 2019; 9:28. [PMID: 30778890 PMCID: PMC6379495 DOI: 10.1186/s13568-019-0752-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 02/08/2019] [Indexed: 12/11/2022] Open
Abstract
This study was demonstrated with a coculture fermentation system using sugar beet pulp (SBP) as a carbon source combining the cellulose-degrading bacterium Clostridium cellulovorans with microbial flora of methane production (MFMP) for the direct conversion of cellulosic biomass to methane (CH4). The MFMP was taken from a commercial methane fermentation plant and extremely complicated. Therefore, the MFMP was analyzed by a next-generation sequencing system and the microbiome was identified and classified based on several computer programs. As a result, Methanosarcina mazei (1.34% of total counts) and the other methanogens were found in the MFMP. Interestingly, the simultaneous utilization of hydrogen (H2) and carbon dioxide (CO2) for methanogenesis was observed in the coculture with Consortium of C. cellulovorans with the MFMP (CCeM) including M. mazei. Furthermore, the CCeM degraded 87.3% of SBP without any pretreatment and produced 34.0 L of CH4 per 1 kg of dry weight of SBP. Thus, a gas metabolic shift in the fermentation pattern of C. cellulovorans was observed in the CCeM coculture. These results indicated that degradation of agricultural wastes was able to be carried out simultaneously with CH4 production by C. cellulovorans and the MFMP.
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16
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Xin F, Dong W, Zhang W, Ma J, Jiang M. Biobutanol Production from Crystalline Cellulose through Consolidated Bioprocessing. Trends Biotechnol 2019; 37:167-180. [DOI: 10.1016/j.tibtech.2018.08.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/22/2018] [Accepted: 08/24/2018] [Indexed: 01/08/2023]
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17
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Tomita H, Okazaki F, Tamaru Y. Direct IBE fermentation from mandarin orange wastes by combination of Clostridium cellulovorans and Clostridium beijerinckii. AMB Express 2019; 9:1. [PMID: 30607514 PMCID: PMC6318158 DOI: 10.1186/s13568-018-0728-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/26/2018] [Indexed: 11/18/2022] Open
Abstract
For a resolution of reducing carbon dioxide emission and increasing food production to respond to the growth of global population, production of biofuels from non-edible biomass is urgently required. Abundant orange wastes, such as peel and strained lees, are produced as by-product of orange juice, which is available non-edible biomass. However, d-limonene included in citrus fruits often inhibits yeast growth and makes the ethanol fermentation difficult. This study demonstrated that isopropanol-butanol-ethanol fermentation ability of Clostridium beijerinckii and cellulosic biomass degrading ability of C. cellulovorans were cultivated under several concentrations of limonene. As a result, C. cellulovorans was able to grow even in the medium containing 0.05% limonene (v/v) and degraded 85% of total sugar from mandarin peel and strained lees without any pretreatments. More interestingly, C. beijerinckii produced 0.046 g butanol per 1 g of dried strained lees in the culture supernatant together with C. cellulovorans.
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18
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Ren Z, You W, Wu S, Poetsch A, Xu C. Secretomic analyses of Ruminiclostridium papyrosolvens reveal its enzymatic basis for lignocellulose degradation. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:183. [PMID: 31338125 PMCID: PMC6628489 DOI: 10.1186/s13068-019-1522-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 07/05/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Efficient biotechnological conversion of lignocellulosic biomass to valuable products, such as transportation biofuels, is ecologically attractive, yet requires substantially improved mechanistic understanding and optimization to become economically feasible. Cellulolytic clostridia, such as Ruminiclostridium papyrosolvens (previously Clostridium papyrosolvens), produce a wide variety of carbohydrate-active enzymes (CAZymes) including extracellular multienzyme complexes-cellulosomes with different specificities for enhanced cellulosic biomass degradation. Identification of the secretory components, especially CAZymes, during bacterial growth on lignocellulose and their influence on bacterial catalytic capabilities provide insight into construction of potent cellulase systems of cell factories tuned or optimized for the targeted substrate by matching the type and abundance of enzymes and corresponding transporters. RESULTS In this study, we firstly predicted a total of 174 putative CAZymes from the genome of R. papyrosolvens, including 74 cellulosomal components. To explore profile of secreted proteins involved in lignocellulose degradation, we compared the secretomes of R. papyrosolvens grown on different substrates using label-free quantitative proteomics. CAZymes, extracellular solute-binding proteins (SBPs) of transport systems and proteins involved in spore formation were enriched in the secretome of corn stover for lignocellulose degradation. Furthermore, compared with free CAZymes, complex CAZymes (cellulosomal components) had larger fluctuations in variety and abundance of enzymes among four carbon sources. In particular, cellulosomal proteins encoded by the cip-cel operon and the xyl-doc gene cluster had the highest abundance with corn stover as substrate. Analysis of differential expression of CAZymes revealed a substrate-dependent secretion pattern of CAZymes, which was consistent with their catalytic activity from each secretome determined on different cellulosic substrates. The results suggest that the expression of CAZymes is regulated by the type of substrate in the growth medium. CONCLUSIONS In the present study, our results demonstrated the complexity of the lignocellulose degradation systems of R. papyrosolvens and showed the potency of its biomass degradation activity. Differential proteomic analyses and activity assays of CAZymes secreted by R. papyrosolvens suggested a distinct environment-sensing strategy for cellulose utilization in which R. papyrosolvens modulated the composition of the CAZymes, especially cellulosome, according to the degradation state of its natural substrate.
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Affiliation(s)
- Zhenxing Ren
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 Shanxi China
- Institute of Applied Chemistry, Shanxi University, Taiyuan, 030006 Shanxi China
| | - Wuxin You
- Department of Plant Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Shasha Wu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 Shanxi China
| | - Ansgar Poetsch
- Department of Plant Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
- School of Biomedical and Healthcare Sciences, University of Plymouth, Plymouth, PL48AA UK
| | - Chenggang Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 Shanxi China
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Shikata A, Sermsathanaswadi J, Thianheng P, Baramee S, Tachaapaikoon C, Waeonukul R, Pason P, Ratanakhanokchai K, Kosugi A. Characterization of an Anaerobic, Thermophilic, Alkaliphilic, High Lignocellulosic Biomass-Degrading Bacterial Community, ISHI-3, Isolated from Biocompost. Enzyme Microb Technol 2018; 118:66-75. [DOI: 10.1016/j.enzmictec.2018.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/25/2018] [Accepted: 07/02/2018] [Indexed: 11/29/2022]
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Aikawa S, Baramee S, Sermsathanaswadi J, Thianheng P, Tachaapaikoon C, Shikata A, Waeonukul R, Pason P, Ratanakhanokchai K, Kosugi A. Characterization and high-quality draft genome sequence of Herbivorax saccincola A7, an anaerobic, alkaliphilic, thermophilic, cellulolytic, and xylanolytic bacterium. Syst Appl Microbiol 2018; 41:261-269. [DOI: 10.1016/j.syapm.2018.01.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 10/18/2022]
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Widyasti E, Shikata A, Hashim R, Sulaiman O, Sudesh K, Wahjono E, Kosugi A. Biodegradation of fibrillated oil palm trunk fiber by a novel thermophilic, anaerobic, xylanolytic bacterium Caldicoprobacter sp. CL-2 isolated from compost. Enzyme Microb Technol 2018; 111:21-28. [DOI: 10.1016/j.enzmictec.2017.12.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/29/2017] [Accepted: 12/29/2017] [Indexed: 10/18/2022]
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Nakajima D, Shibata T, Tanaka R, Kuroda K, Ueda M, Miyake H. Characterization of the cellulosomal scaffolding protein CbpC from Clostridium cellulovorans 743B. J Biosci Bioeng 2017; 124:376-380. [PMID: 28533157 DOI: 10.1016/j.jbiosc.2017.04.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 04/18/2017] [Accepted: 04/20/2017] [Indexed: 12/15/2022]
Abstract
Clostridium cellulovorans 743B, an anaerobic and mesophilic bacterium, produces an extracellular enzyme complex called the cellulosome on the cell surface. Recently, we have reported the whole genome sequence of C. cellulovorans, which revealed that a total of 4 cellulosomal scaffolding proteins: CbpA, HbpA, CbpB, and CbpC were encoded in the C. cellulovorans genome. In particular, cbpC encoded a 429-residue polypeptide that includes a carbohydrate-binding module (CBM), an S-layer homology module, and a cohesin. CbpC was also detected in the culture supernatant of C. cellulovorans. Genomic DNA coding for CbpC was subcloned into a pET-22b+ vector in order to express and produce the recombinant protein in Escherichia coli BL21(DE3). Measurement of CbpC adsorption to crystalline cellulose indicated a dissociation constant of 0.60 μM, which is a similar to that of CBM from CbpA. We also subcloned the region encoding xylanase B (XynB) with the dockerin from C. cellulovorans and analyzed the interaction between XynB and CbpC by GST pull-down assay. It was observed that GST-CbpC assembles with XynB to form a minimal cellulosome. The activity of XynB against rice straw tended to be increased in the presence of CbpC. These results showed a synergistic effect on rice straw as a representative cellulosic biomass through the formation of a minimal cellulosome containing XynB bound to CbpC. Thus, our findings provide a foundation for the development of cellulosic biomass saccharification using a minimal cellulosome.
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Affiliation(s)
- Daichi Nakajima
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
| | - Toshiyuki Shibata
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
| | - Reiji Tanaka
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan
| | - Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hideo Miyake
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan; Life Science Research Center, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan.
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Mendes CVT, Rocha JMDS, de Menezes FF, Carvalho MDGVS. Batch and fed-batch simultaneous saccharification and fermentation of primary sludge from pulp and paper mills. ENVIRONMENTAL TECHNOLOGY 2017; 38:1498-1506. [PMID: 27611735 DOI: 10.1080/09593330.2016.1235230] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 09/05/2016] [Indexed: 06/06/2023]
Abstract
Primary sludge from a Portuguese pulp and paper mill, containing 60% of carbohydrates, and unbleached pulp (as reference material), with 93% of carbohydrates, were used to produce ethanol by simultaneous saccharification and fermentation (SSF). SSF was performed in batch or fed-batch conditions without the need of a pretreatment. Cellic® CTec2 was the cellulolytic enzymatic complex used and Saccharomyces cerevisiae (baker's yeast or ATCC 26602 strain) or the thermotolerant yeast Kluyveromyces marxianus NCYC 1426 were employed. Primary sludge was successfully converted to ethanol and the best results in SSF efficiency were obtained with S. cerevisiae. An ethanol concentration of 22.7 g L-1 was produced using a content of 50 g L-1 of carbohydrates from primary sludge, in batch conditions, with a global conversion yield of 81% and a production rate of 0.94 g L-1 h-1. Fed-batch operation enabled higher solids content (total carbohydrate concentration of 200 g L-1, equivalent to a consistency of 33%) and a reduction of three-quarters of cellulolytic enzyme load, leading to an ethanol concentration of 40.7 g L-1, although with lower yield and productivity. Xylitol with a concentration up to 7 g L-1 was also identified as by-product in the primary sludge bioconversion process.
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Affiliation(s)
- Cátia Vanessa Teixeira Mendes
- a CIEPQPF, Department of Chemical Engineering, Faculty of Sciences and Technology , University of Coimbra , Coimbra , Portugal
| | - Jorge Manuel Dos Santos Rocha
- a CIEPQPF, Department of Chemical Engineering, Faculty of Sciences and Technology , University of Coimbra , Coimbra , Portugal
| | - Fabrícia Farias de Menezes
- a CIEPQPF, Department of Chemical Engineering, Faculty of Sciences and Technology , University of Coimbra , Coimbra , Portugal
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Schwede S, Thorin E, Lindmark J, Klintenberg P, Jääskeläinen A, Suhonen A, Laatikainen R, Hakalehto E. Using slaughterhouse waste in a biochemical-based biorefinery - results from pilot scale tests. ENVIRONMENTAL TECHNOLOGY 2017; 38:1275-1284. [PMID: 27575339 DOI: 10.1080/09593330.2016.1225128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/11/2016] [Indexed: 06/06/2023]
Abstract
A novel biorefinery concept was piloted using protein-rich slaughterhouse waste, chicken manure and straw as feedstocks. The basic idea was to provide a proof of concept for the production of platform chemicals and biofuels from organic waste materials at non-septic conditions. The desired biochemical routes were 2,3-butanediol and acetone-butanol fermentation. The results showed that hydrolysis resulted only in low amounts of easily degradable carbohydrates. However, amino acids released from the protein-rich slaughterhouse waste were utilized and fermented by the bacteria in the process. Product formation was directed towards acidogenic compounds rather than solventogenic products due to increasing pH-value affected by ammonia release during amino acid fermentation. Hence, the process was not effective for 2,3-butanediol production, whereas butyrate, propionate, γ-aminobutyrate and valerate were predominantly produced. This offered fast means for converting tedious protein-rich waste mixtures into utilizable chemical goods. Furthermore, the residual liquid from the bioreactor showed significantly higher biogas production potential than the corresponding substrates. The combination of the biorefinery approach to produce chemicals and biofuels with anaerobic digestion of the residues to recover energy in form of methane and nutrients that can be utilized for animal feed production could be a feasible concept for organic waste utilization.
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Affiliation(s)
- Sebastian Schwede
- a School of Business Society and Engineering , Mälardalen University , Västerås , Sweden
| | - Eva Thorin
- a School of Business Society and Engineering , Mälardalen University , Västerås , Sweden
| | - Johan Lindmark
- a School of Business Society and Engineering , Mälardalen University , Västerås , Sweden
| | - Patrik Klintenberg
- a School of Business Society and Engineering , Mälardalen University , Västerås , Sweden
| | - Ari Jääskeläinen
- b Environmental Engineering , Savonia University of Applied Sciences , Kuopio , Finland
| | - Anssi Suhonen
- b Environmental Engineering , Savonia University of Applied Sciences , Kuopio , Finland
| | - Reino Laatikainen
- c School of Pharmacy , University of Eastern Finland , Kuopio , Finland
| | - Elias Hakalehto
- c School of Pharmacy , University of Eastern Finland , Kuopio , Finland
- d Finnoflag Oy , Kuopio , Finland
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Ábrego U, Chen Z, Wan C. Consolidated Bioprocessing Systems for Cellulosic Biofuel Production. ADVANCES IN BIOENERGY 2017. [DOI: 10.1016/bs.aibe.2017.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Inamori T, Aburaya S, Morisaka H, Kuroda K, Ueda M. Characteristic strategy of assimilation of various saccharides by Clostridium cellulovorans. AMB Express 2016; 6:64. [PMID: 27586595 PMCID: PMC5009059 DOI: 10.1186/s13568-016-0237-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 08/24/2016] [Indexed: 11/10/2022] Open
Abstract
Clostridium cellulovorans can effectively assimilate not only cellulose but also hemicellulose by producing cellulosomal and non-cellulosomal enzymes. However, little is known about how C. cellulovorans assimilates various saccharides in media containing polysaccharides and oligosaccharides. In this research, we investigated the property of saccharide incorporation and assimilation by C. cellulovorans. Faster growth in media containing xylan and cellulose was achieved by switching polysaccharides, in which xylan was first assimilated, followed by cellulose. Furthermore, the presence of polysaccharides that can be easily degraded might increase the assimilation rate of lignocellulose by promoting growth. These properties of C. cellulovorans could be suitable for the effective utilization of lignocellulosic biomass.
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Isolation and Cultivation of Anaerobes. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 156:35-53. [DOI: 10.1007/10_2016_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
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Restriction modification system analysis and development of in vivo methylation for the transformation of Clostridium cellulovorans. Appl Microbiol Biotechnol 2015; 100:2289-99. [PMID: 26590584 DOI: 10.1007/s00253-015-7141-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 10/28/2015] [Accepted: 11/02/2015] [Indexed: 12/11/2022]
Abstract
Clostridium cellulovorans, a cellulolytic bacterium producing butyric and acetic acids as main fermentation products, is a promising host for biofuel production from cellulose. However, the transformation method of C. cellulovorans was not available, hindering its genetic engineering. To overcome this problem, its restriction modification (RM) systems were analyzed and a novel in vivo methylation was established for its successful transformation in the present study. Specifically, two RM systems, Cce743I and Cce743II, were determined. R. Cce743I has the same specificity as LlaJI, recognizing 5'-GACGC-3' and 5'-GCGTC-3', while M. Cce743I methylates the external cytosine in the strand (5'-GACG(m)C-3'). R. Cce743II, has the same specificity as LlaI, recognizing 5'-CCAGG-3' and 5'-CCTGG-3', while M. Cce743II methylates the external cytosine of both strands. An in vivo methylation system, expressing M. Cce743I and M. Cce743II from C. cellulovorans in Escherichia coli, was then established to protect plasmids used in electrotransformation. Transformants expressing an aldehyde/alcohol dehydrogenase (adhE2), which converted butyryl-CoA to n-butanol and acetyl-CoA to ethanol, were obtained. For the first time, an effective transformation method was developed for metabolic engineering of C. cellulovorans for biofuel production directly from cellulose.
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Nogueira KMV, Costa MDN, de Paula RG, Mendonça-Natividade FC, Ricci-Azevedo R, Silva RN. Evidence of cAMP involvement in cellobiohydrolase expression and secretion by Trichoderma reesei in presence of the inducer sophorose. BMC Microbiol 2015; 15:195. [PMID: 26424592 PMCID: PMC4590280 DOI: 10.1186/s12866-015-0536-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/25/2015] [Indexed: 01/08/2023] Open
Abstract
Background The signaling second messenger cyclic AMP (cAMP) regulates many aspects of cellular function in all organisms. Previous studies have suggested a role for cAMP in the regulation of gene expression of cellulolytic enzymes in Trichoderma reesei (anamorph of Hypocrea jecorina). Methods The effects of cAMP in T. reesei were analyzed through both activity and expression of cellulase, intracellular cAMP level measurement, western blotting, indirect immunofluorescence and confocal microscopy. Results To elucidate the involvement of cAMP in the cellulase expression, we analyzed the growth of the mutant strain ∆acy1 and its parental strain QM9414 in the presence of the inducers cellulose, cellobiose, lactose, or sophorose, and the repressor glucose. Our results indicated that cAMP regulates the expression of cellulase in a carbon source-dependent manner. The expression cel7a, and cel6a genes was higher in the presence of sophorose than in the presence of cellulose, lactose, cellobiose, or glucose. Moreover, intracellular levels of cAMP were up to four times higher in the presence of sophorose compared to other carbon sources. Concomitantly, our immunofluorescence microscopy and western blot data suggest that in the presence of sophorose, cAMP may regulate secretion of cellulolytic enzymes in T. reesei. Conclusions These results allow us to better understand the role of cAMP and expand our knowledge on the signal transduction pathways involved in the regulation of cellulase expression in T. reesei. Finally, our data may help develop new strategies to improve the expression of cel7a and cel6a genes, and therefore, favor their application in several biotechnology fields. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0536-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Karoline Maria Vieira Nogueira
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, 14049-900, Ribeirão Preto, SP, Brazil.
| | - Mariana do Nascimento Costa
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, 14049-900, Ribeirão Preto, SP, Brazil.
| | - Renato Graciano de Paula
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, 14049-900, Ribeirão Preto, SP, Brazil.
| | - Flávia Costa Mendonça-Natividade
- Department of Cell Biology and Molecular and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, 14049-900, Ribeirão Preto, SP, Brazil.
| | - Rafael Ricci-Azevedo
- Department of Cell Biology and Molecular and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, 14049-900, Ribeirão Preto, SP, Brazil.
| | - Roberto Nascimento Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, 14049-900, Ribeirão Preto, SP, Brazil.
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Yang X, Xu M, Yang ST. Metabolic and process engineering of Clostridium cellulovorans for biofuel production from cellulose. Metab Eng 2015; 32:39-48. [PMID: 26365585 DOI: 10.1016/j.ymben.2015.09.001] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 08/27/2015] [Accepted: 09/02/2015] [Indexed: 11/28/2022]
Abstract
Production of cellulosic biofuels has drawn increasing attention. However, currently no microorganism can produce biofuels, particularly butanol, directly from cellulosic biomass efficiently. Here we engineered a cellulolytic bacterium, Clostridium cellulovorans, for n-butanol and ethanol production directly from cellulose by introducing an aldehyde/alcohol dehydrogenase (adhE2), which converts butyryl-CoA to n-butanol and acetyl-CoA to ethanol. The engineered strain was able to produce 1.42 g/L n-butanol and 1.60 g/L ethanol directly from cellulose. Moreover, the addition of methyl viologen as an artificial electron carrier shifted the metabolic flux from acid production to alcohol production, resulting in a high biofuel yield of 0.39 g/g from cellulose, comparable to ethanol yield from corn dextrose by yeast fermentation. This study is the first metabolic engineering of C. cellulovorans for n-butanol and ethanol production directly from cellulose with significant titers and yields, providing a promising consolidated bioprocessing (CBP) platform for biofuel production from cellulosic biomass.
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Affiliation(s)
- Xiaorui Yang
- Department of Chemical and Biomolecular Engineering and Department of Molecular Genetics, The Ohio State University, 151 West Woodruff Avenue, Columbus, OH 43210, USA
| | - Mengmeng Xu
- Department of Chemical and Biomolecular Engineering and Department of Molecular Genetics, The Ohio State University, 151 West Woodruff Avenue, Columbus, OH 43210, USA
| | - Shang-Tian Yang
- Department of Chemical and Biomolecular Engineering and Department of Molecular Genetics, The Ohio State University, 151 West Woodruff Avenue, Columbus, OH 43210, USA.
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Arora R, Behera S, Sharma NK, Kumar S. Bioprospecting thermostable cellulosomes for efficient biofuel production from lignocellulosic biomass. BIORESOUR BIOPROCESS 2015. [DOI: 10.1186/s40643-015-0066-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Tomazetto G, Hahnke S, Koeck DE, Wibberg D, Maus I, Pühler A, Klocke M, Schlüter A. Complete genome analysis of Clostridium bornimense strain M2/40(T): A new acidogenic Clostridium species isolated from a mesophilic two-phase laboratory-scale biogas reactor. J Biotechnol 2015; 232:38-49. [PMID: 26256097 DOI: 10.1016/j.jbiotec.2015.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 07/23/2015] [Accepted: 08/04/2015] [Indexed: 12/17/2022]
Abstract
Taxonomic and functional profiling based on metagenome analyses frequently revealed that members of the class Clostridia dominate biogas reactor communities and perform different essential metabolic pathways in the biogas fermentation process. Clostridium bornimense strain M2/40(T) was recently isolated from a mesophilic two-phase lab-scale biogas reactor continuously fed with maize silage and wheat straw. The genome of the strain was completely sequenced and manually annotated to reconstruct its metabolic potential regarding carbohydrate active enzyme production and fermentation of organic compounds for consolidated biofuel production from biomass. The C. bornimense M2/40(T) genome consists of a chromosome (2,917,864bp in size) containing 2613 protein coding sequences, and a 699,161bp chromid (secondary replicon) harboring 680 coding sequences. Both replicons feature very similar GC-contents of approximately 29%. The complex genome comprises three prophage regions, two CRISPR-cas systems and a putative cellulosomal gene cluster that is located on the second replicon (chromid) of the strain. The overexpressed glycosyl hydrolases (GH) CelK (GH9) and CelA (GH48) encoded in the cellulosomal gene cluster were shown to be active on the substrates xylan and xyloglucan whereas XghA (GH74) is highly active on xyloglucan. Reconstruction of fermentation pathways from genome sequence data revealed that strain M2/40(T) encodes all enzymes for hydrogen, acetate, formate, lactate, butyrate, and ethanol production, leading to the classification of the isolate as acidogenic bacterium. Phylogenetic analyses uncovered that the closest characterized relative of C. bornimense is C. cellulovorans. Comparative analyses of the C. bornimense and C. cellulovorans genomes revealed considerable rearrangements within their chromosomes suggesting that both species evolved separately for a relatively long period of time and adapted to specific tasks within microbial consortia responsible for anaerobic digestion.
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Affiliation(s)
- Geizecler Tomazetto
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Sarah Hahnke
- Department of Bioengineering, Leibniz Institute for Agricultural Engineering Potsdam-Bornim (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Daniela E Koeck
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Michael Klocke
- Department of Bioengineering, Leibniz Institute for Agricultural Engineering Potsdam-Bornim (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Institute for Genome Research and Systems Biology, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany.
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Tanaka T, Kondo A. Cell surface engineering of industrial microorganisms for biorefining applications. Biotechnol Adv 2015; 33:1403-11. [PMID: 26070720 DOI: 10.1016/j.biotechadv.2015.06.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 06/04/2015] [Accepted: 06/06/2015] [Indexed: 11/19/2022]
Abstract
In order to decrease carbon emissions and negative environmental impacts of various pollutants, biofuel/biochemical production should be promoted for replacing fossil-based industrial processes. Utilization of abundant lignocellulosic biomass as a feedstock has recently become an attractive option. In this review, we focus on recent efforts of cell surface display using industrial microorganisms such as Escherichia coli and yeast. Cell surface display is used primarily for endowing cellulolytic activity on the host cells, and enables direct fermentation to generate useful fuels and chemicals from lignocellulosic biomass. Cell surface display systems are systematically summarized, and the drawbacks/perspectives as well as successful application of surface display for industrial biotechnology are discussed.
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Affiliation(s)
- Tsutomu Tanaka
- Department of Chemical Science and Technology, Graduate School of Engineering, Kobe University, 1-1, Rokkodaicho, Nada, Kobe 657-8501 Japan
| | - Akihiko Kondo
- Department of Chemical Science and Technology, Graduate School of Engineering, Kobe University, 1-1, Rokkodaicho, Nada, Kobe 657-8501 Japan.
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Amore A, Parameswaran B, Kumar R, Birolo L, Vinciguerra R, Marcolongo L, Ionata E, La Cara F, Pandey A, Faraco V. Application of a new xylanase activity from Bacillus amyloliquefaciens XR44A in brewer's spent grain saccharification. JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY (OXFORD, OXFORDSHIRE : 1986) 2015; 90:573-581. [PMID: 25866429 PMCID: PMC4384805 DOI: 10.1002/jctb.4589] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 11/05/2014] [Accepted: 11/13/2014] [Indexed: 05/12/2023]
Abstract
BACKGROUND Cellulases and xylanases are the key enzymes involved in the conversion of lignocelluloses into fermentable sugars. Western Ghat region (India) has been recognized as an active hot spot for the isolation of new microorganisms. The aim of this work was to isolate new microorganisms producing cellulases and xylanases to be applied in brewer's spent grain saccharification. RESULTS 93 microorganisms were isolated from Western Ghat and screened for the production of cellulase and xylanase activities. Fourteen cellulolytic and seven xylanolytic microorganisms were further screened in liquid culture. Particular attention was focused on the new isolate Bacillus amyloliquefaciens XR44A, producing xylanase activity up to 10.5 U mL-1. A novel endo-1,4-beta xylanase was identified combining zymography and proteomics and recognized as the main enzyme responsible for B. amyloliquefaciens XR44A xylanase activity. The new xylanase activity was partially characterized and its application in saccharification of brewer's spent grain, pretreated by aqueous ammonia soaking, was investigated. CONCLUSION The culture supernatant of B. amyloliquefaciens XR44A with xylanase activity allowed a recovery of around 43% xylose during brewer's spent grain saccharification, similar to the value obtained with a commercial xylanase from Trichoderma viride, and a maximum arabinose yield of 92%, around 2-fold higher than that achieved with the commercial xylanase. © 2014 The Authors. Journal of Chemical Technology & Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Antonella Amore
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelovia Cintia, 4, 80126, Naples, Italy
| | - Binod Parameswaran
- CSIR-National Institute for Interdisciplinary Science and Technology (NIIST)Trivandrum, 695 019, India
| | - Ramesh Kumar
- CSIR-National Institute for Interdisciplinary Science and Technology (NIIST)Trivandrum, 695 019, India
| | - Leila Birolo
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelovia Cintia, 4, 80126, Naples, Italy
| | - Roberto Vinciguerra
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelovia Cintia, 4, 80126, Naples, Italy
| | - Loredana Marcolongo
- Institute of Biosciences and BioResources - National Research CouncilNapoli, Italy
| | - Elena Ionata
- Institute of Biosciences and BioResources - National Research CouncilNapoli, Italy
| | - Francesco La Cara
- Institute of Biosciences and BioResources - National Research CouncilNapoli, Italy
| | - Ashok Pandey
- CSIR-National Institute for Interdisciplinary Science and Technology (NIIST)Trivandrum, 695 019, India
| | - Vincenza Faraco
- Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelovia Cintia, 4, 80126, Naples, Italy
- * Correspondence to: V. Faraco, Department of Chemical Sciences, University of Naples “Federico II”, Complesso Universitario Monte S. Angelo, via Cintia, 4 80126 Napoli, Italy. E-mail:
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Ashfaque M, Solomon S, Pathak N. Optimization of pretreatment and fermentation conditions for production of extracellular cellulase complex using sugarcane bagasse. Bioinformation 2014; 10:606-10. [PMID: 25489168 PMCID: PMC4248341 DOI: 10.6026/97320630010606] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 09/23/2014] [Indexed: 11/23/2022] Open
Abstract
Sugarcane bagasse (SCB), a lignocellulosic byproduct of juice extraction from sugarcane, is rich in cellulose (40-42%). This could be used as a substrate for the production of cellulase complex. Fermentation conditions were optimized for production of cellulase complex (CMCase, Cellulobiase and FPase) by wild type Trichoderma sp. using sugarcane bagasse as sole carbon source. Alkaline treatment (2% NaOH) of bagasse (AlSCB) was found suitable for the production of reducing sugar over the acidic pretreatment method. After 5 days of incubation period, 5% substrate concentration at pH 5.0 and 400C resulted in maximum production of CMCase (0.622 U), while maximum (3.388 U) production of cellulobiase was obtained at 300C. The CMCase was precipitated and purified to the extent of 59.06 fold by affinity chromatography with 49.09% recovery. On 12% SDS-PAGE, a single band corresponding to 33 kDa was observed. The Km and Vmax for CMCase from Trichoderma was found 507.04 mg/ml and 65.32 mM/min, respectively. The enzyme exhibited maximum activity at 300C at pH-5.0 (0.363 U) and was stable over range of 20-60°C and pH 5.0-7.5.
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Affiliation(s)
- Mohammad Ashfaque
- Department of Biotechnology, Integral University, Dasauli, Kursi Road, Lucknow 226 026, Uttar Pradesh, India ; Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow - 226 002, Uttar Pradesh, India
| | - Sushil Solomon
- Indian Institute of Sugarcane Research, Raibareli Road, P.O. Dilkusha, Lucknow - 226 002, Uttar Pradesh, India
| | - Neelam Pathak
- Department of Biotechnology, Integral University, Dasauli, Kursi Road, Lucknow 226 026, Uttar Pradesh, India
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Wang J, Yang X, Chen CC, Yang ST. Engineering clostridia for butanol production from biorenewable resources: from cells to process integration. Curr Opin Chem Eng 2014. [DOI: 10.1016/j.coche.2014.09.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Ikeda Y, Parashar A, Bressler DC. Highly retained enzymatic activities of two different cellulases immobilized on non-porous and porous silica particles. BIOTECHNOL BIOPROC E 2014. [DOI: 10.1007/s12257-014-0191-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Costa M, Fernandes VO, Ribeiro T, Serrano L, Cardoso V, Santos H, Lordelo M, Ferreira LMA, Fontes CMGA. Construction of GH16 β-glucanase mini-cellulosomes to improve the nutritive value of barley-based diets for broilers. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:7496-7506. [PMID: 25010714 DOI: 10.1021/jf502157y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Anaerobic cellulolytic bacteria organize a comprehensive range of cellulases and hemicellulases in high molecular weight multienzyme complexes termed cellulosomes. Integration of cellulosomal components occurs via highly ordered protein-protein interactions between cohesins and dockerins. This paper reports the production of mini-cellulosomes containing one (GH16-1C) or three (GH16-3C) copies of Clostridium thermocellum glucanase 16A (CtGlc16A). Barley β-1,3-1,4-glucans are known to be antinutritive for monogastric animals, particularly for poultry. GH16-1C and GH16-3C were used to supplement barley-based diets for broilers. The data revealed that the two mini-cellulosomes effectively improved the nutritive value of barley-based diets for broilers. Analysis of mini-cellulosome molecular integrity revealed that linker sequences separating protein domains in scaffoldins and cellulosomal catalytic units are highly susceptible to proteolytic attack in vivo. The data suggest that linker protection could result in further improvements in enzyme efficacy to improve the nutritive value of barley-based diets for monogastric animals.
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Affiliation(s)
- Mónica Costa
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa , Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
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Mussoline W, Esposito G, Lens P, Spagni A, Giordano A. Enhanced methane production from rice straw co-digested with anaerobic sludge from pulp and paper mill treatment process. BIORESOURCE TECHNOLOGY 2013; 148:135-143. [PMID: 24045200 DOI: 10.1016/j.biortech.2013.08.107] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 08/16/2013] [Accepted: 08/19/2013] [Indexed: 06/02/2023]
Abstract
Rice straw is a widely available lignocellulosic waste with potential for energy recovery through anaerobic digestion. Lignin slows the hydrolysis phase, resulting in low methane recovery and long digestion periods. Although pretreatment is effective, it often requires high energy inputs or chemicals that are not feasible for farm-scale systems. This study investigates a unique co-digestion strategy to improve methane yields and reduce digestion times for farm-scale systems. By adding both piggery wastewater and paper mill sludge, specific methane yields in laboratory-scale digesters reached the theoretical value for rice straw (i.e. 330LNCH4/kgVS) over the 92-day period. Accelerated hydrolysis of the straw was directly related to the quantity of sludge added. The most stable digester, with sufficient buffering capacity and nutrients, contained equal parts of straw, wastewater and sludge. This approach is feasible for farm-scale applications since it requires no additional energy inputs or changes to existing infrastructure for dry systems.
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Affiliation(s)
- Wendy Mussoline
- University of Cassino, via Di Biasio 43, 03043 Cassino, Italy.
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Fixation of CO2 in Clostridium cellulovorans analyzed by 13C-isotopomer-based target metabolomics. AMB Express 2013; 3:61. [PMID: 24103325 PMCID: PMC4124662 DOI: 10.1186/2191-0855-3-61] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 10/05/2013] [Indexed: 12/21/2022] Open
Abstract
Clostridium cellulovorans has been one of promising microorganisms to use biomass efficiently; however the basic metabolic pathways have not been completely known. We carried out 13C-isotopomer-based target metabolome analysis, or carbohydrate conversion process analysis, for more profound understanding of metabolic pathways of the bacterium. Our findings that pyruvate + oxaloacetate, fumarate, and malate inside and outside cells exhibited 13C incorporation suggest that C. cellulovorans exactly fixed CO2 and partly operated the TCA cycle in a reductive manner. Accompanied with CO2 fixation, the microorganism was also found to produce and secrete lactate. Overall, our study demonstrates that a part of C. cellulovorans metabolic pathways related to glycolysis and the TCA cycle are involved in CO2 fixation.
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Vijayalaxmi S, Anu Appaiah KA, Jayalakshmi SK, Mulimani VH, Sreeramulu K. Production of bioethanol from fermented sugars of sugarcane bagasse produced by lignocellulolytic enzymes of Exiguobacterium sp. VSG-1. Appl Biochem Biotechnol 2013; 171:246-60. [PMID: 23832861 DOI: 10.1007/s12010-013-0366-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Accepted: 06/23/2013] [Indexed: 11/26/2022]
Abstract
Exiguobacterium sp. VSG-1 was isolated from the soil sample and characterized for the production of lignocellulolytic enzymes. Production of these enzymes by the strain VSG-1 was carried out using steam-exploded sugarcane bagasse (SCB) and found to secrete cellulase, pectinase, mannanase, xylanase, and tannase. The growth and enzyme production were found to be optimum at pH 9.0 and 37 °C. Upon steam explosion of SCB, the cellulose increased by 42 %, whereas hemicelluloses and lignin decreased by 40 and 62 %, respectively. Enzymatic hydrolysis of steam-exploded SCB yielded 640 g/l of total sugars. Fermentation of sugars produced from pretreated SCB was carried out by using Saccharomyces cerevisiae at pH 5.0 and 30 °C. The alcohol produced was calculated and found to be 62.24 g/l corresponding to 78 % of the theoretical yield of ethanol. Hence, the strain VSG-1 has an industrial importance for the production of fermentable sugars for biofuels.
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Affiliation(s)
- S Vijayalaxmi
- Department of Biochemistry, Gulbarga University, Gulbarga, 585106, Karnataka, India
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Ota M, Sakuragi H, Morisaka H, Kuroda K, Miyake H, Tamaru Y, Ueda M. Display ofClostridium cellulovoransxylose isomerase on the cell surface ofSaccharomyces cerevisiaeand its direct application to xylose fermentation. Biotechnol Prog 2013; 29:346-51. [DOI: 10.1002/btpr.1700] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 01/11/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Miki Ota
- Div. of Applied Life Sciences, Graduate School of Agriculture; Kyoto University; Sakyo Kyoto 606-8502 Japan
| | - Hiroshi Sakuragi
- Div. of Applied Life Sciences, Graduate School of Agriculture; Kyoto University; Sakyo Kyoto 606-8502 Japan
| | - Hironobu Morisaka
- Div. of Applied Life Sciences, Graduate School of Agriculture; Kyoto University; Sakyo Kyoto 606-8502 Japan
| | - Kouichi Kuroda
- Div. of Applied Life Sciences, Graduate School of Agriculture; Kyoto University; Sakyo Kyoto 606-8502 Japan
| | - Hideo Miyake
- Dept. of Life Sciences, Graduate School of Bioresources; Mie University 1577 Kurimamachiya, Tsu, Mie, 514-8507 Japan
| | - Yutaka Tamaru
- Dept. of Life Sciences, Graduate School of Bioresources; Mie University 1577 Kurimamachiya, Tsu, Mie, 514-8507 Japan
| | - Mitsuyoshi Ueda
- Div. of Applied Life Sciences, Graduate School of Agriculture; Kyoto University; Sakyo Kyoto 606-8502 Japan
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Yamada R, Hasunuma T, Kondo A. Endowing non-cellulolytic microorganisms with cellulolytic activity aiming for consolidated bioprocessing. Biotechnol Adv 2013; 31:754-63. [PMID: 23473971 DOI: 10.1016/j.biotechadv.2013.02.007] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 02/19/2013] [Accepted: 02/24/2013] [Indexed: 11/17/2022]
Abstract
With the exhaustion of fossil fuels and with the environmental issues they pose, utilization of abundant lignocellulosic biomass as a feedstock for biofuels and bio-based chemicals has recently become an attractive option. Lignocellulosic biomass is primarily composed of cellulose, hemicellulose, and lignin and has a very rigid and complex structure. It is accordingly much more expensive to process than starchy grains because of the need for extensive pretreatment and relatively large amounts of cellulases for efficient hydrolysis. Efficient and cost-effective methods for the production of biofuels and chemicals from lignocellulose are required. A consolidated bioprocess (CBP), which integrates all biological steps consisting of enzyme production, saccharification, and fermentation, is considered a promising strategy for reducing production costs. Establishing an efficient CBP using lignocellulosic biomass requires both lignocellulose degradation into glucose and efficient production of biofuels or chemicals from glucose. With this aim, many researchers are attempting to endow selected microorganisms with lignocellulose-assimilating ability. In this review, we focus on studies aimed at conferring lignocellulose-assimilating ability not only to yeast strains but also to bacterial strains by recombinant technology. Recent developments in improvement of enzyme productivity by microorganisms and in improvement of the specific activity of cellulase are emphasized.
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Affiliation(s)
- Ryosuke Yamada
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
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Aerobic deconstruction of cellulosic biomass by an insect-associated Streptomyces. Sci Rep 2013; 3:1030. [PMID: 23301151 PMCID: PMC3538285 DOI: 10.1038/srep01030] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 11/01/2012] [Indexed: 12/16/2022] Open
Abstract
Streptomyces are best known for producing antimicrobial secondary metabolites, but they are also recognized for their contributions to biomass utilization. Despite their importance to carbon cycling in terrestrial ecosystems, our understanding of the cellulolytic ability of Streptomyces is currently limited to a few soil-isolates. Here, we demonstrate the biomass-deconstructing capability of Streptomyces sp. SirexAA-E (ActE), an aerobic bacterium associated with the invasive pine-boring woodwasp Sirex noctilio. When grown on plant biomass, ActE secretes a suite of enzymes including endo- and exo-cellulases, CBM33 polysaccharide-monooxygenases, and hemicellulases. Genome-wide transcriptomic and proteomic analyses, and biochemical assays have revealed the key enzymes used to deconstruct crystalline cellulose, other pure polysaccharides, and biomass. The mixture of enzymes obtained from growth on biomass has biomass-degrading activity comparable to a cellulolytic enzyme cocktail from the fungus Trichoderma reesei, and thus provides a compelling example of high cellulolytic capacity in an aerobic bacterium.
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Amore A, Pepe O, Ventorino V, Birolo L, Giangrande C, Faraco V. Industrial waste based compost as a source of novel cellulolytic strains and enzymes. FEMS Microbiol Lett 2012. [PMID: 23181595 DOI: 10.1111/1574-6968.12057] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Ninety bacteria isolated from raw composting materials were screened for their cellulolytic activity on solid medium containing carboxymethylcellulose. The bacteria producing the highest cellulolytic activity levels were identified by 16S rRNA sequencing as Bacillus licheniformis strain 1, Bacillus subtilis subsp. subtilis strain B7B, Bacillus subtilis subsp. spizizenii strain 6, and Bacillus amyloliquefaciens strain B31C. Cellulase activity production by the most productive strain B. amyloliquefaciens B31C was optimized in liquid culture varying the carbon source. Comparison of growth curves of B. amyloliquefaciens B31C at temperatures from 28 to 47 °C indicated its thermotolerant nature. Moreover, analysis of time courses of cellulase activity production in this thermal range showed that increase of temperature from 28 to 37 °C causes an increase of cellulase activity levels. Investigating the enzymes responsible for cellulase activity produced by B. amyloliquefaciens B31C by proteomic analyses, an endoglucanase was identified. It was shown that the purified enzyme catalyzes carboxymethylcellulose's hydrolysis following Michaelis-Menten kinetics with a K(M) of 9.95 mg ml(-1) and a v(max) of 284 μM min(-1) . It shows a retention of 90% of its activity for at least 144 h of incubation at 40 °C and exhibits a range of optimum temperatures from 50 to 70 °C.
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Affiliation(s)
- Antonella Amore
- Department of Chemical Sciences, University of Naples 'Federico II', Complesso Universitario Monte S. Angelo, Naples, Italy
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Trujillo-Cabrera Y, Ponce-Mendoza A, Vásquez-Murrieta MS, Rivera-Orduña FN, Wang ET. Diverse cellulolytic bacteria isolated from the high humus, alkaline-saline chinampa soils. ANN MICROBIOL 2012. [DOI: 10.1007/s13213-012-0533-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Morisaka H, Matsui K, Tatsukami Y, Kuroda K, Miyake H, Tamaru Y, Ueda M. Profile of native cellulosomal proteins of Clostridium cellulovorans adapted to various carbon sources. AMB Express 2012; 2:37. [PMID: 22839966 PMCID: PMC3444338 DOI: 10.1186/2191-0855-2-37] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 07/20/2012] [Indexed: 12/04/2022] Open
Abstract
We performed a focused proteome analysis of cellulosomal proteins predicted by a genome analysis of Clostridium cellulovorans [Tamaru, Y., et al.. 2010. J. Bacteriol. 192:901–902]. Our system employed a long monolithic column (300 cm), which provides better performance and higher resolution than conventional systems. Twenty-three cellulosomal proteins were, without purification, identified by direct analysis of the culture medium. Proteome analysis of the C. cellulovorans cellulosome after culture in various carbon sources demonstrated the production of carbon source-adapted cellulosome components.
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Akao S, Maeda K, Nakatani S, Hosoi Y, Nagare H, Maeda M, Fujiwara T. Comparison of simultaneous and separate processes: saccharification and thermophilic L-lactate fermentation of catch crop and aquatic plant biomass. ENVIRONMENTAL TECHNOLOGY 2012; 33:1523-1529. [PMID: 22988611 DOI: 10.1080/09593330.2012.669412] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Catch crop candidates (corn, guinea grass) for recovering nutrients from farm soil and aquatic plants (water caltrop, water hyacinth) were utilized to produce L-lactic acid. The efficiencies ofpre-treatment methods for enzymatic saccharification and L-lactate production of two fermentation processes, thermophilic simultaneous saccharification and fermentation (SSF), as well as separate saccharification and fermentation, were compared. Conditions were set at 55 degrees C and pH 5.5 for non-sterile fermentation. Alkaline/peroxide pre-treatment proved the most effective for saccharification in pre-treated corn, guinea grass, water caltrop and water hyacinth with glucose yields of 0.23, 0.20, 0.11 and 0.14 g/g-dry native biomass (24-hour incubation period), respectively. Examination of the two types of thermophilic L-lactate fermentation employed following alkaline/peroxide pre-treatment and saccharification demonstrated that the L-lactate yield obtained using SSF (0.15 g/g in the case of corn) was lower than that obtained using separate saccharification and fermentation (0.28 g/g in the case of corn). The lower yield obtained from SSF is likely to have resulted from the saccharification conditions used in the present study, as the possibility of cellulase deactivation during SSF by thermophilic L-lactate producing bacteria existed. A cellulase that retains high activity levels under non-sterile conditions and a L-lactate producer without cellulose hydrolysis activity would be required in order for SSF to serve as an effective method of L-lactate production.
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Affiliation(s)
- Satoshi Akao
- Management of Social Systems Course, Graduate School of Engineering, Tottori University, 4-101, Koyama-minami, Tottori 680-8552, Japan.
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50
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Recent developments in yeast cell surface display toward extended applications in biotechnology. Appl Microbiol Biotechnol 2012; 95:577-91. [DOI: 10.1007/s00253-012-4175-0] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 05/13/2012] [Accepted: 05/14/2012] [Indexed: 10/28/2022]
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