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Chang C, Guo Y, Tang K, Hu Y, Xu W, Chen W, McLaughlin N, Wang Z. Straw from Different Crop Species Recruits Different Communities of Lignocellulose-Degrading Microorganisms in Black Soil. Microorganisms 2024; 12:938. [PMID: 38792768 PMCID: PMC11123855 DOI: 10.3390/microorganisms12050938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024] Open
Abstract
The biological degradation of plant residues in the soil or on the soil surface is an integral part of the natural life cycle of annual plants and does not have adverse effects on the environment. Crop straw is characterized by a complex structure and exhibits stability and resistance to rapid microbial decomposition. In this study, we conducted a microcosm experiment to investigate the dynamic succession of the soil microbial community and the functional characteristics associated with lignocellulose-degrading pathways. Additionally, we aimed to identify lignocellulose-degrading microorganisms from the straw of three crop species prevalent in Northeast China: soybean (Glycine max Merr.), rice (Oryza sativa L.), and maize (Zea mays L.). Our findings revealed that both the type of straw and the degradation time influenced the bacterial and fungal community structure and composition. Metagenome sequencing results demonstrated that during degradation, different straw types assembled carbohydrate-active enzymes (CAZymes) and KEGG pathways in distinct manners, contributing to lignocellulose and hemicellulose degradation. Furthermore, isolation of lignocellulose-degrading microbes yielded 59 bacterial and 14 fungal strains contributing to straw degradation, with fungi generally exhibiting superior lignocellulose-degrading enzyme production compared to bacteria. Experiments were conducted to assess the potential synergistic effects of synthetic microbial communities (SynComs) comprising both fungi and bacteria. These SynComs resulted in a straw weight loss of 42% at 15 days post-inoculation, representing a 22% increase compared to conditions without any SynComs. In summary, our study provides novel ecological insights into crop straw degradation by microbes.
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Affiliation(s)
- Chunling Chang
- College of Life Science and Agroforestry, Qiqihar University, Qiqihar 161006, China; (C.C.); (Y.G.); (K.T.); (Y.H.); (W.X.); (W.C.)
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
- Heilongjiang Provincial Collaborative Innovation Center of Agrobiological Preparation Industrialization, Qiqihar 161006, China
| | - Yue Guo
- College of Life Science and Agroforestry, Qiqihar University, Qiqihar 161006, China; (C.C.); (Y.G.); (K.T.); (Y.H.); (W.X.); (W.C.)
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
- Heilongjiang Provincial Collaborative Innovation Center of Agrobiological Preparation Industrialization, Qiqihar 161006, China
| | - Kuanqiang Tang
- College of Life Science and Agroforestry, Qiqihar University, Qiqihar 161006, China; (C.C.); (Y.G.); (K.T.); (Y.H.); (W.X.); (W.C.)
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
- Heilongjiang Provincial Collaborative Innovation Center of Agrobiological Preparation Industrialization, Qiqihar 161006, China
| | - Yunlong Hu
- College of Life Science and Agroforestry, Qiqihar University, Qiqihar 161006, China; (C.C.); (Y.G.); (K.T.); (Y.H.); (W.X.); (W.C.)
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
- Heilongjiang Provincial Collaborative Innovation Center of Agrobiological Preparation Industrialization, Qiqihar 161006, China
| | - Weihui Xu
- College of Life Science and Agroforestry, Qiqihar University, Qiqihar 161006, China; (C.C.); (Y.G.); (K.T.); (Y.H.); (W.X.); (W.C.)
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
- Heilongjiang Provincial Collaborative Innovation Center of Agrobiological Preparation Industrialization, Qiqihar 161006, China
| | - Wenjing Chen
- College of Life Science and Agroforestry, Qiqihar University, Qiqihar 161006, China; (C.C.); (Y.G.); (K.T.); (Y.H.); (W.X.); (W.C.)
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
- Heilongjiang Provincial Collaborative Innovation Center of Agrobiological Preparation Industrialization, Qiqihar 161006, China
| | - Neil McLaughlin
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada;
| | - Zhigang Wang
- College of Life Science and Agroforestry, Qiqihar University, Qiqihar 161006, China; (C.C.); (Y.G.); (K.T.); (Y.H.); (W.X.); (W.C.)
- Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar 161006, China
- Heilongjiang Provincial Collaborative Innovation Center of Agrobiological Preparation Industrialization, Qiqihar 161006, China
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The production and application of bacterial exopolysaccharides as biomaterials for bone regeneration. Carbohydr Polym 2022; 291:119550. [DOI: 10.1016/j.carbpol.2022.119550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/19/2022] [Accepted: 04/26/2022] [Indexed: 11/18/2022]
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Jo Y, Cayetano RDA, Kim GB, Park J, Kim SH. The effects of ammonia acclimation on biogas recovery and the microbial population in continuous anaerobic digestion of swine manure. ENVIRONMENTAL RESEARCH 2022; 212:113483. [PMID: 35588770 DOI: 10.1016/j.envres.2022.113483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/25/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
This study investigated the ammonia toxicity and the acclimation of anaerobic microbiome in continuous anaerobic digestion of swine manure using unacclimated inoculum. When the total ammonia nitrogen concentration (TAN) reached 2.5 g N/L, the methane yield decreased from 254.1 ± 9.6 to 154.6 ± 9.9 mL/g COD. The free ammonia nitrogen concentration of the inhibited condition was 190 mg N/L. The methane yield was eventually recovered as 269.6 ± 3.6 mL/g COD with a further operation. Anaerobic toxicity assay (ATA) showed that mixed liquor from the recovered phase possessed enhanced tolerance to ammonia, not only within the exposed level in continuous operation (<2.5 g NH3/L) but also over the range (>2.5 g NH3/L). Microbial analysis revealed that continuous operation under ammonia stress resulted in the change of both bacterial and archaeal populations. The ammonia adaptation was concurrent with the archaeal population shift from Methanosaeta to Methanosarcina and Methanobacterium. The dominancy of Clostridia in bacterial population was found in the recovered phase. It is highly recommended to use an inoculum acclimated to a target ammonia level which can be pre-checked by ATA and to secure a start-up period for ammonia adaptation in the field application of anaerobic digestion for swine manure.
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Affiliation(s)
- Yura Jo
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Roent Dune A Cayetano
- Department of Environmental Engineering, Seoul National University of Science and Technology, Seoul 01811, Republic of Korea
| | - Gi-Beom Kim
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jungsu Park
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Sang-Hyoun Kim
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea.
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Ichikawa S, Ito D, Asaoka S, Abe R, Katsuo N, Ito T, Ito D, Karita S. The expression of alternative sigma-I7 factor induces the transcription of cellulosomal genes in the cellulolytic bacterium Clostridium thermocellum. Enzyme Microb Technol 2022; 156:110002. [DOI: 10.1016/j.enzmictec.2022.110002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/12/2022] [Accepted: 01/31/2022] [Indexed: 01/07/2023]
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Khosravi F, Khaleghi M, Naghavi H. Screening and identification of cellulose-degrading bacteria from soil and leaves at Kerman province, Iran. Arch Microbiol 2021; 204:88. [PMID: 34961888 DOI: 10.1007/s00203-021-02713-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 11/25/2022]
Abstract
Cellulosic biomass is considered one of the most promising sources for the production of alternative renewable bioenergy and other valuable products. Identification and optimization of strains with high enzymatic activity that can overcome constraints imposed by the cellulosic structure is an essential step in the development of new biotechnologies. The aim of this study was to isolate and identify thermophilic (50 °C) and mesophilic (37 °C) cellulolytic bacteria from soil and leaves samples at Kerman, Iran. Degrader bacteria were isolated using serial dilution and pour plate method. Media contained carboxymethylcellulose (CMC), and filter paper was used as sources of carbon. Totally 22 mesophilic and 17 thermophilic bacterial strains which produced clear zones were further identified by morphological and biochemical tests. Screening of purified bacteria was performed to identify cellulase-producing bacteria by Congo red test. These bacteria were compared to each other based on cellulase activity, the percentage of growth, and extracellular protein amounts. The strains with the highest enzymatic activity were determined by the DNS method. The isolated US5 and US7 grew rapidly, and produced cellulase. The US5 created the largest clear zones (7 mm). Besides, these strains were selected for analysis of 16S rRNA sequence. The results showed that selected bacteria strains belong to Brevibacillus borstelensis. The B. borstelensis strains isolated in this study showed a suitable cellulase enzyme activity.
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Affiliation(s)
- Farshid Khosravi
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran.
| | - Mouj Khaleghi
- Department of Biology, Faculty of Science, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Hormazd Naghavi
- Soil and Water Research, Kerman Agricultural and Natural Resources Research and Education Center, AREEO, Kerman, Iran
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Fatani S, Saito Y, Alarawi M, Gojobori T, Mineta K. Genome sequencing and identification of cellulase genes in Bacillus paralicheniformis strains from the Red Sea. BMC Microbiol 2021; 21:254. [PMID: 34548024 PMCID: PMC8456639 DOI: 10.1186/s12866-021-02316-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 09/08/2021] [Indexed: 11/23/2022] Open
Abstract
Background Cellulolytic microorganisms are considered a key player in the degradation of plant biomass in various environments. These microorganisms can be isolated from various environments, such as soils, the insect gut, the mammalian rumen and oceans. The Red Sea exhibits a unique environment in terms of presenting a high seawater temperature, high salinity, low nutrient levels and high biodiversity. However, there is little information regarding cellulase genes in the Red Sea environment. This study aimed to examine whether the Red Sea can be a resource for the bioprospecting of microbial cellulases by isolating cellulase-producing microorganisms from the Red Sea environment and characterizing cellulase genes. Results Three bacterial strains were successfully isolated from the plankton fraction and the surface of seagrass. The isolated strains were identified as Bacillus paralicheniformis and showed strong cellulase activity. These results suggested that these three isolates secreted active cellulases. By whole genome sequencing, we found 10 cellulase genes from the three isolates. We compared the expression of these cellulase genes under cellulase-inducing and non-inducing conditions and found that most of the cellulase genes were generally upregulated during cellulolysis in the isolates. Our operon structure analysis also showed that cellulase genes form operons with genes involved in various kinds of cellular reactions, such as protein metabolism, which suggests the existence of crosstalk between cellulolysis and other metabolic pathways in the bacterial isolates. These results suggest that multiple cellulases are playing important roles in cellulolysis. Conclusions Our study reports the isolation and characterization of cellulase-producing bacteria from the Red Sea. Our whole-genome sequencing classified our three isolates as Bacillus paralicheniformis, and we revealed the presence of ten cellulase orthologues in each of three isolates’ genomes. Our comparative expression analysis also identified that most of the cellulase genes were upregulated under the inducing conditions in general. Although cellulases have been roughly classified into three enzyme groups of beta-glucosidase, endo-β-1,4-glucanase and exoglucanase, these findings suggest the importance to consider microbial cellulolysis as a more complex reaction with various kinds of cellulase enzymes. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02316-w.
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Affiliation(s)
- Siham Fatani
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Yoshimoto Saito
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Marine Open Innovation Institute (MaOI), Shizuoka, Japan
| | - Mohammed Alarawi
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Katsuhiko Mineta
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Froese AG, Sparling R. Cross-feeding and wheat straw extractives enhance growth of Clostridium thermocellum-containing co-cultures for consolidated bioprocessing. Bioprocess Biosyst Eng 2021; 44:819-830. [PMID: 33392746 DOI: 10.1007/s00449-020-02490-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/24/2020] [Indexed: 01/19/2023]
Abstract
Co-cultures consisting of three thermophilic and lignocellulolytic bacteria, namely Clostridium thermocellum, C. stercorarium, and Thermoanaerobacter thermohydrosulfuricus, degrade lignocellulosic material in a synergistic manner. When cultured in a defined minimal medium two of the members appeared to be auxotrophic and unable to grow, but the growth of all species was observed in all co-culture combinations, indicating cross-feeding of unidentified growth factors between the members. Growth factors also appeared to be present in water-soluble extractives obtained from wheat straw, allowing for the growth of the auxotrophic monocultures in the defined minimal medium. Cell enumeration during growth on wheat straw in this medium revealed different growth profiles of the members that varied between the co-cultures. End-product profiles also varied substantially between the cultures, with significantly higher ethanol production in all co-cultures compared to the mono-cultures. Understanding interactions between co-culture members, and the additional nutrients provided by lignocellulosic substrates, will aid us in consolidated bioprocessing design.
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Affiliation(s)
- Alan G Froese
- Department of Microbiology, University of Manitoba, 213 Buller Building, Winnipeg, MB, R3T 2N2, Canada
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, 213 Buller Building, Winnipeg, MB, R3T 2N2, Canada.
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8
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Comparing Low-Temperature Hydrothermal Pretreatments through Convective Heating versus Microwave Heating for Napier Grass Digestion. Processes (Basel) 2020. [DOI: 10.3390/pr8101221] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
This study investigates the effects of convective hydrothermal pretreatment (CHTP) compared to microwave pretreatment (MWP) on the anaerobic digestion of hybrid Napier grass for biomethane production. For rapid estimation of methane yield (YCH4), enzymatic hydrolyzability (EH), whose test lasts only 2 days was used as a surrogate parameter instead of the biochemical methane potential (BMP) assay that normally takes 45–60 days. The relationship between EH and BMP was successfully modeled with satisfactory accuracy (R2 = 0.9810). From CHTP results, quadratic regression characterised by p < 0.0001 and R2 = 0.8364 shows that YCH4 increase was clearly sensitive to detention time at all CHTP temperatures. The maximal YCH4 achieved of 301.5 ± 3.0 mL CH4/gVSadd was 53.2% higher than the control. Then, MWP was employed at various power levels and microwave exposure times. Changes in lignocellulosic structure by Fourier-transform infrared spectroscopy (FTIR) and energy balance demonstrate that MWP caused more damage to plant cells, which proved more effective than CHTP. In the best conditions, approximately 50% of energy was needed for MWP to achieve the equivalent improvement in YCH4. However, CHTP is a more suitable option since waste heat, i.e., from a biogas CHP (combined heat and power) unit, could be used, as opposed to the electricity required for MWP.
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Wei Z, Chen C, Liu YJ, Dong S, Li J, Qi K, Liu S, Ding X, Ortiz de Ora L, Muñoz-Gutiérrez I, Li Y, Yao H, Lamed R, Bayer EA, Cui Q, Feng Y. Alternative σI/anti-σI factors represent a unique form of bacterial σ/anti-σ complex. Nucleic Acids Res 2019; 47:5988-5997. [PMID: 31106374 PMCID: PMC6582324 DOI: 10.1093/nar/gkz355] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/21/2019] [Accepted: 04/26/2019] [Indexed: 12/18/2022] Open
Abstract
The σ70 family alternative σI factors and their cognate anti-σI factors are widespread in Clostridia and Bacilli and play a role in heat stress response, virulence, and polysaccharide sensing. Multiple σI/anti-σI factors exist in some lignocellulolytic clostridial species, specifically for regulation of components of a multienzyme complex, termed the cellulosome. The σI and anti-σI factors are unique, because the C-terminal domain of σI (SigIC) and the N-terminal inhibitory domain of anti-σI (RsgIN) lack homology to known proteins. Here, we report structure and interaction studies of a pair of σI and anti-σI factors, SigI1 and RsgI1, from the cellulosome-producing bacterium, Clostridium thermocellum. In contrast to other known anti-σ factors that have N-terminal helical structures, RsgIN has a β-barrel structure. Unlike other anti-σ factors that bind both σ2 and σ4 domains of the σ factors, RsgIN binds SigIC specifically. Structural analysis showed that SigIC contains a positively charged surface region that recognizes the promoter -35 region, and the synergistic interactions among multiple interfacial residues result in the specificity displayed by different σI/anti-σI pairs. We suggest that the σI/anti-σI factors represent a distinctive mode of σ/anti-σ complex formation, which provides the structural basis for understanding the molecular mechanism of the intricate σI/anti-σI system.
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Affiliation(s)
- Zhen Wei
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Chen
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Ya-Jun Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Sheng Dong
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Jie Li
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuan Qi
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shiyue Liu
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoke Ding
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Lizett Ortiz de Ora
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Iván Muñoz-Gutiérrez
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Yifei Li
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Hongwei Yao
- High-Field Nuclear Magnetic Resonance Center, Xiamen University, 422 South Siming Road, Xiamen 361005, China
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Qiu Cui
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Yingang Feng
- CAS Key Laboratory of Biofuels, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- To whom correspondence should be addressed. Tel: +86 532 80662706; Fax: +86 532 80662707;
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Pavlenko OS, Gra OA, Mustafaev ON, Kabarbaeva KV, Sadovskaya NS, Tyurin AA, Fadeev VS, Goldenkova-Pavlova IV. Thermostable Lichenase from Clostridium thermocellum as a Host Protein in the Domain Insertion Approach. BIOCHEMISTRY. BIOKHIMIIA 2019; 84:931-940. [PMID: 31522675 DOI: 10.1134/s0006297919080091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 12/17/2023]
Abstract
Clostridium thermocellum lichenase (endo-β-1,3;1,4-glucan-D-glycosyl hydrolase, EC 3.2.1.73 (P29716)) has been tested for the insertion of two model fluorescent proteins (EGFP and TagRFP) into two regions of this enzyme. Functional folding of the resulting proteins was confirmed by retention of lichenase activity and EGFP and TagRFP fluorescence. These results convincingly demonstrate that (i) the two experimentally selected lichenase loop regions may serve as the areas for domain insertion without disturbing enzyme folding in vivo; (ii) lichenase permits not only single but also tandem insertions of large protein domains. High specific activity, outstanding thermostability, and efficient in vitro refolding of thermostable lichenase make it an attractive new host protein for the insertional fusion of domains in the engineering of multifunctional proteins.
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Affiliation(s)
- O S Pavlenko
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia.
| | - O A Gra
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - O N Mustafaev
- Baku State University, Department of Biophysics and Molecular Biology, Baku, AZ1106, Azerbaijan.
| | - K V Kabarbaeva
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - N S Sadovskaya
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - A A Tyurin
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - V S Fadeev
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - I V Goldenkova-Pavlova
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia.
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11
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Ichikawa S, Ogawa S, Nishida A, Kobayashi Y, Kurosawa T, Karita S. Cellulosomes localise on the surface of membrane vesicles from the cellulolytic bacterium Clostridium thermocellum. FEMS Microbiol Lett 2019; 366:5526221. [DOI: 10.1093/femsle/fnz145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/27/2019] [Indexed: 12/21/2022] Open
Abstract
ABSTRACTMembrane vesicles released from bacteria contribute to cell–cell communication by carrying various cargos such as proteins, nucleic acids and signaling molecules. Cellulolytic bacteria have been isolated from many environments, yet the function of membrane vesicles for cellulolytic ability has been rarely described. Here, we show that a Gram-positive cellulolytic bacterium Clostridium thermocellum released membrane vesicles, each approximately 50–300 nm in diameter, into the broth. The observations with immunoelectron microscopy also revealed that cellulosomes, which are carbohydrate-active enzyme complexes that give C. thermocellum high cellulolytic activity, localized on the surface of the membrane vesicles. The membrane vesicles collected by ultracentrifugation maintained the cellulolytic activity. Supplementation with the biosurfactant surfactin or sonication treatment disrupted the membrane vesicles in the exoproteome of C. thermocellum and significantly decreased the degradation activity of the exoproteome for microcrystalline cellulose. However, these did not affect the degradation activity for soluble carboxymethyl cellulose. These results suggest a novel function of membrane vesicles: C. thermocellum releases cellulolytic enzymes on the surface of membrane vesicles to enhance the cellulolytic activity of C. thermocellum for crystalline cellulose.
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Affiliation(s)
- Shunsuke Ichikawa
- Graduate School of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Satoru Ogawa
- Faculty of Medicine, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Ayami Nishida
- Graduate School of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Yuzuki Kobayashi
- Faculty of Education, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Toshihito Kurosawa
- Advanced Science Research Promotion Center, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
| | - Shuichi Karita
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho Tsu, Mie 514-8507, Japan
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Liu Q, Li J, Zhao J, Wu J, Shao T. Enhancement of lignocellulosic degradation in high-moisture alfalfa via anaerobic bioprocess of engineered Lactococcus lactis with the function of secreting cellulase. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:88. [PMID: 31015862 PMCID: PMC6469111 DOI: 10.1186/s13068-019-1429-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Butyric fermentation and a substantial loss of dry matter (DM) often occur in alfalfa silage during the rainy season, which is not conducive to subsequent biofuel production. Currently, there have been negative effects on the combination of cellulases and lactic acid bacteria (LAB) on processing high-moisture alfalfa silage; however, transgenically engineered LAB strains that secrete cellulase have been proposed as an alternative approach to avoid the above problem. The objective of the present study was to construct engineered Lactococcus lactis strains with high-efficiency secretory-expressing cellulase genes from Trichoderma reesei and to investigate the effects of the combination of transgenically engineered L. lactis strains HT1/pMG36e-usp45-bgl1, HT1/pMG36e-usp45-cbh2, and HT1/pMG36e-usp45-egl3 (HT2) on fermentation quality, structural carbohydrate degradability and nonstructural carbohydrate fermentation kinetics of high-moisture alfalfa silage treated without additive as a negative control (Control), or/and with cellulase (EN), wild-type L. lactis subsp. lactis MG1363 (HT1) and the combination of HT1 and EN (HT1 + EN) as positive additive controls. RESULTS Engineered L. lactis strains were successfully constructed and efficiently secreted endoglucanase (1118 mU/mL), cellobiohydrolase (222 mU/mL), and β-glucosidase (131 mU/mL) and had high filter paper activity (236 mU/mL). Ensiling experiments verified that HT2 obtained the highest fermentation quality score (83.6) and most efficiently processed high-moisture alfalfa silage, demonstrated by a low pH (4.49) and ammonia-N content (106 g/kg nitrogen) and a high lactic acid content (67.1 g/kg DM) and without butyric acid. Change curves of structural carbohydrates revealed that HT2 degraded more lignocelluloses, demonstrated by the lowest contents of neutral detergent fibre, acid detergent fibre, cellulose and hemicellulose after ensiling for 60 days. Kinetic analysis showed that the most residual water-soluble carbohydrates, glucose, fructose and xylose generated by lignocellulose degradation were produced by HT2, followed by HT1 + EN. The HT2-treated silages had the highest DM recovery, had the fewest Clostridia spores, emitted a fragrance and were not sticky. CONCLUSION HT2 improved the conversion of lignocellulose to sugars and processed high-moisture alfalfa silage efficiently. This is a novel strategy that can be used to enhance lignocellulosic degradation in high-moisture alfalfa via a bioprocess with transgenically engineered L. lactis strains, which could enhance the development of alfalfa as a biomass feedstock and promote second-generation biofuel development in the rainy season.
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Affiliation(s)
- Qinhua Liu
- Institute of Ensiling and Processing of Grass, Nanjing Agricultural University, Weigang 1, Nanjing, 210095 China
| | - Junfeng Li
- Institute of Ensiling and Processing of Grass, Nanjing Agricultural University, Weigang 1, Nanjing, 210095 China
| | - Jie Zhao
- Institute of Ensiling and Processing of Grass, Nanjing Agricultural University, Weigang 1, Nanjing, 210095 China
| | - Jingxing Wu
- Institute of Ensiling and Processing of Grass, Nanjing Agricultural University, Weigang 1, Nanjing, 210095 China
| | - Tao Shao
- Institute of Ensiling and Processing of Grass, Nanjing Agricultural University, Weigang 1, Nanjing, 210095 China
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Froese A, Schellenberg J, Sparling R. Enhanced depolymerization and utilization of raw lignocellulosic material by co-cultures of Ruminiclostridium thermocellum with hemicellulose-utilizing partners. Can J Microbiol 2019; 65:296-307. [PMID: 30608879 DOI: 10.1139/cjm-2018-0535] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Ruminiclostridium thermocellum is one of the most promising candidates for consolidated bioprocessing (CBP) of low-cost lignocellulosic materials to biofuels but it still shows poor performance in its ability to deconstruct untreated lignocellulosic substrates. One promising approach to increase R. thermocellum's rate of hydrolysis is to co-culture this cellulose-specialist with partners that possess synergistic hydrolysis enzymes and metabolic capabilities. We have created co-cultures of R. thermocellum with two hemicellulose utilizers, Ruminiclostridium stercorarium and Thermoanaerobacter thermohydrosulfuricus, both of which secrete xylanolytic enzymes and utilize the pentose oligo- and monosaccharides that inhibit R. thermocellum's hydrolysis and metabolism. When grown on milled wheat straw, the co-cultures were able to solubilize up to 58% more of the total polysaccharides than the R. thermocellum mono-culture control. Repeated passaging of the co-cultures on wheat straw yielded stable populations with reduced R. thermocellum cell numbers, indicating competition for cellodextrins released from cellulose hydrolysis, although these stabilized co-cultures were still able to outperform the mono-culture controls. Repeated passaging on Avicel cellulose also yielded stable populations. Overall, the observed synergism suggests that co-culturing R. thermocellum with other members is a viable option for increasing the rate and extent of untreated lignocellulose deconstruction by R. thermocellum for CBP purposes.
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Affiliation(s)
- Alan Froese
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.,Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - John Schellenberg
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.,Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Richard Sparling
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Broeker J, Mechelke M, Baudrexl M, Mennerich D, Hornburg D, Mann M, Schwarz WH, Liebl W, Zverlov VV. The hemicellulose-degrading enzyme system of the thermophilic bacterium Clostridium stercorarium: comparative characterisation and addition of new hemicellulolytic glycoside hydrolases. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:229. [PMID: 30159029 PMCID: PMC6106730 DOI: 10.1186/s13068-018-1228-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/14/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND The bioconversion of lignocellulosic biomass in various industrial processes, such as the production of biofuels, requires the degradation of hemicellulose. Clostridium stercorarium is a thermophilic bacterium, well known for its outstanding hemicellulose-degrading capability. Its genome comprises about 50 genes for partially still uncharacterised thermostable hemicellulolytic enzymes. These are promising candidates for industrial applications. RESULTS To reveal the hemicellulose-degrading potential of 50 glycoside hydrolases, they were recombinantly produced and characterised. 46 of them were identified in the secretome of C. stercorarium cultivated on cellobiose. Xylanases Xyn11A, Xyn10B, Xyn10C, and cellulase Cel9Z were among the most abundant proteins. The secretome of C. stercorarium was active on xylan, β-glucan, xyloglucan, galactan, and glucomannan. In addition, the recombinant enzymes hydrolysed arabinan, mannan, and galactomannan. 20 enzymes are newly described, degrading xylan, galactan, arabinan, mannan, and aryl-glycosides of β-d-xylose, β-d-glucose, β-d-galactose, α-l-arabinofuranose, α-l-rhamnose, β-d-glucuronic acid, and N-acetyl-β-d-glucosamine. The activities of three enzymes with non-classified glycoside hydrolase (GH) family modules were determined. Xylanase Xyn105F and β-d-xylosidase Bxl31D showed activities not described so far for their GH families. 11 of the 13 polysaccharide-degrading enzymes were most active at pH 5.0 to pH 6.5 and at temperatures of 57-76 °C. Investigation of the substrate and product specificity of arabinoxylan-degrading enzymes revealed that only the GH10 xylanases were able to degrade arabinoxylooligosaccharides. While Xyn10C was inhibited by α-(1,2)-arabinosylations, Xyn10D showed a degradation pattern different to Xyn10B and Xyn10C. Xyn11A released longer degradation products than Xyn10B. Both tested arabinose-releasing enzymes, Arf51B and Axh43A, were able to hydrolyse single- as well as double-arabinosylated xylooligosaccharides. CONCLUSIONS The obtained results lead to a better understanding of the hemicellulose-degrading capacity of C. stercorarium and its involved enzyme systems. Despite similar average activities measured by depolymerisation tests, a closer look revealed distinctive differences in the activities and specificities within an enzyme class. This may lead to synergistic effects and influence the enzyme choice for biotechnological applications. The newly characterised glycoside hydrolases can now serve as components of an enzyme platform for industrial applications in order to reconstitute synthetic enzyme systems for complete and optimised degradation of defined polysaccharides and hemicellulose.
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Affiliation(s)
- Jannis Broeker
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Matthias Mechelke
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Melanie Baudrexl
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Denise Mennerich
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Daniel Hornburg
- Present Address: School of Medicine, Stanford University, Stanford, CA 94305 USA
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Matthias Mann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Wolfgang H. Schwarz
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Wolfgang Liebl
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Vladimir V. Zverlov
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising, Germany
- Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, Moscow, 123182 Russia
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15
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Leis B, Held C, Andreeßen B, Liebl W, Graubner S, Schulte LP, Schwarz WH, Zverlov VV. Optimizing the composition of a synthetic cellulosome complex for the hydrolysis of softwood pulp: identification of the enzymatic core functions and biochemical complex characterization. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:220. [PMID: 30116297 PMCID: PMC6083626 DOI: 10.1186/s13068-018-1220-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/31/2018] [Indexed: 05/30/2023]
Abstract
BACKGROUND The development of efficient cellulase blends is a key factor for cost-effectively valorizing biomass in a new bio-economy. Today, the enzymatic hydrolysis of plant-derived polysaccharides is mainly accomplished with fungal cellulases, whereas potentially equally effective cellulose-degrading systems from bacteria have not been developed. Particularly, a thermostable multi-enzyme cellulase complex, the cellulosome from the anaerobic cellulolytic bacterium Clostridium thermocellum is promising of being applied as cellulolytic nano-machinery for the production of fermentable sugars from cellulosic biomass. RESULTS In this study, 60 cellulosomal components were recombinantly produced in E. coli and systematically permuted in synthetic complexes to study the function-activity relationship of all available enzymes on Kraft pulp from pine wood as the substrate. Starting from a basic exo/endoglucanase complex, we were able to identify additional functional classes such as mannanase and xylanase for optimal activity on the substrate. Based on these results, we predicted a synthetic cellulosome complex consisting of seven single components (including the scaffoldin protein and a β-glucosidase) and characterized it biochemically. We obtained a highly thermostable complex with optimal activity around 60-65 °C and an optimal pH in agreement with the optimum of the native cellulosome (pH 5.8). Remarkably, a fully synthetic complex containing 47 single cellulosomal components showed comparable activity with a commercially available fungal enzyme cocktail on the softwood pulp substrate. CONCLUSIONS Our results show that synthetic bacterial multi-enzyme complexes based on the cellulosome of C. thermocellum can be applied as a versatile platform for the quick adaptation and efficient degradation of a substrate of interest.
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Affiliation(s)
- Benedikt Leis
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
- Present Address: Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Winchester Str. 2, 35394 Gießen, Germany
| | - Claudia Held
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Björn Andreeßen
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Wolfgang Liebl
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Sigrid Graubner
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Louis-Philipp Schulte
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Wolfgang H. Schwarz
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Vladimir V. Zverlov
- Department of Microbiology, Technische Universität München, TUM School of Life Sciences Weihenstephan, Emil-Ramann-Str. 4, 85354 Freising, Germany
- Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, Moscow, 123182 Russia
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Tomazetto G, Hahnke S, Wibberg D, Pühler A, Klocke M, Schlüter A. Proteiniphilum saccharofermentans str. M3/6 T isolated from a laboratory biogas reactor is versatile in polysaccharide and oligopeptide utilization as deduced from genome-based metabolic reconstructions. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2018; 18:e00254. [PMID: 29892569 PMCID: PMC5993710 DOI: 10.1016/j.btre.2018.e00254] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 12/16/2022]
Abstract
Proteiniphilum saccharofermentans str. M3/6T is a recently described species within the family Porphyromonadaceae (phylum Bacteroidetes), which was isolated from a mesophilic laboratory-scale biogas reactor. The genome of the strain was completely sequenced and manually annotated to reconstruct its metabolic potential regarding biomass degradation and fermentation pathways. The P. saccharofermentans str. M3/6T genome consists of a 4,414,963 bp chromosome featuring an average GC-content of 43.63%. Genome analyses revealed that the strain possesses 3396 protein-coding sequences. Among them are 158 genes assigned to the carbohydrate-active-enzyme families as defined by the CAZy database, including 116 genes encoding glycosyl hydrolases (GHs) involved in pectin, arabinogalactan, hemicellulose (arabinan, xylan, mannan, β-glucans), starch, fructan and chitin degradation. The strain also features several transporter genes, some of which are located in polysaccharide utilization loci (PUL). PUL gene products are involved in glycan binding, transport and utilization at the cell surface. In the genome of strain M3/6T, 64 PUL are present and most of them in association with genes encoding carbohydrate-active enzymes. Accordingly, the strain was predicted to metabolize several sugars yielding carbon dioxide, hydrogen, acetate, formate, propionate and isovalerate as end-products of the fermentation process. Moreover, P. saccharofermentans str. M3/6T encodes extracellular and intracellular proteases and transporters predicted to be involved in protein and oligopeptide degradation. Comparative analyses between P. saccharofermentans str. M3/6T and its closest described relative P. acetatigenes str. DSM 18083T indicate that both strains share a similar metabolism regarding decomposition of complex carbohydrates and fermentation of sugars.
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Affiliation(s)
- Geizecler Tomazetto
- Brazilian Bioethanol Science and Technology Laboratory – CTBE/CNPEM, 10000 Giuseppe Maximo Scolfaro St, Zip Code 13083-852 Campinas, SP, Brazil
| | - Sarah Hahnke
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Alfred Pühler
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Michael Klocke
- Department Bioengineering, Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Andreas Schlüter
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
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The features that distinguish lichenases from other polysaccharide-hydrolyzing enzymes and the relevance of lichenases for biotechnological applications. Appl Microbiol Biotechnol 2018; 102:3951-3965. [DOI: 10.1007/s00253-018-8904-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 01/16/2023]
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Tyurin AA, Kabardaeva KV, Mustafaev ON, Pavlenko OS, Sadovskaya NS, Fadeev VS, Zvonova EA, Goldenkova-Pavlova IV. Expression of Soluble Active Interferon αA in Escherichia coli Periplasm by Fusion with Thermostable Lichenase Using the Domain Insertion Approach. BIOCHEMISTRY (MOSCOW) 2018; 83:259-269. [DOI: 10.1134/s0006297918030069] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Schwarz WH, Brunecky R, Broeker J, Liebl W, Zverlov VV. Handling gene and protein names in the age of bioinformatics: the special challenge of secreted multimodular bacterial enzymes such as the cbhA/cbh9A gene of Clostridium thermocellum. World J Microbiol Biotechnol 2018; 34:42. [PMID: 29480332 DOI: 10.1007/s11274-018-2424-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 02/20/2018] [Indexed: 01/11/2023]
Abstract
An increasing number of researchers working in biology, biochemistry, biotechnology, bioengineering, bioinformatics and other related fields of science are using biological molecules. As the scientific background of the members of different scientific communities is more diverse than ever before, the number of scientists not familiar with the rules for non-ambiguous designation of genetic elements is increasing. However, with biological molecules gaining importance through biotechnology, their functional and unambiguous designation is vital. Unfortunately, naming genes and proteins is not an easy task. In addition, the traditional concepts of bioinformatics are challenged with the appearance of proteins comprising different modules with a respective function in each module. This article highlights basic rules and novel solutions in designation recently used within the community of bacterial geneticists, and we discuss the present-day handling of gene and protein designations. As an example we will utilize a recent mischaracterization of gene nomenclature. We make suggestions for better handling of names in future literature as well as in databases and annotation projects. Our methodology emphasizes the hydrolytic function of multi-modular genes and extracellular proteins from bacteria.
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Affiliation(s)
- Wolfgang H Schwarz
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil‑Ramann‑Str. 4, 85354, Freising, Germany.
| | - Roman Brunecky
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO, 80401, USA
| | - Jannis Broeker
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil‑Ramann‑Str. 4, 85354, Freising, Germany
| | - Wolfgang Liebl
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil‑Ramann‑Str. 4, 85354, Freising, Germany
| | - Vladimir V Zverlov
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil‑Ramann‑Str. 4, 85354, Freising, Germany. .,Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, 123182, Moscow, Russia.
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Herlet J, Kornberger P, Roessler B, Glanz J, Schwarz WH, Liebl W, Zverlov VV. A new method to evaluate temperature vs. pH activity profiles for biotechnological relevant enzymes. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:234. [PMID: 29046720 PMCID: PMC5637330 DOI: 10.1186/s13068-017-0923-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/03/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Glycoside hydrolases are important for various industrial and scientific applications. Determination of their temperature as well as pH optima and range is crucial to evaluate whether an enzyme is suitable for application in a biotechnological process. These basic characteristics of enzymes are generally determined by two separate measurements. However, these lead to a two-dimensional assessment of the pH range at one temperature (and vice versa) and do not allow prediction of the relative enzymatic performance at any pH/temperature combination of interest. In this work, we demonstrate a new method that is based on experimental data and visualizes the relationship among pH, temperature, and activity at a glance in a three-dimensional contour plot. RESULTS In this study, we present a method to determine the relative activity of an enzyme at 96 different combinations of pH and temperature in parallel. For this purpose, we used a gradient PCR cycler and a citrate-phosphate-based buffer system in microtiter plates. The approach was successfully tested with various substrates and diverse assays for glycoside hydrolases. Furthermore, its applicability was demonstrated for single enzymes using the endoglucanase Cel8A from Clostridium thermocellum as well as the commercially available complex enzyme mixture Celluclast®. Thereby, we developed a fast and adaptable method to determine simultaneously both pH and temperature ranges of enzymes over a wide range of conditions, an easy transformation of the experimental data into a contour plot for visualization, and the necessary controls. With our method, the suitability of an enzyme or enzyme mixture for any chosen combination of temperature and pH can easily be assessed at a glance. CONCLUSIONS We propose a method that offers significant advantages over commonly used methods to determine the pH and temperature ranges of enzymes. The overall relationship among pH, temperature, and activity is visualized. Our method could be applied to evaluate exactly what conditions have to be met for optimal utilization of an enzyme or enzyme mixture for both lab-scale and industrial processes. Adaptation to other enzymes, including proteases, should be possible and the method may also lead to a platform for additional applications, such as inactivation kinetics analysis.
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Affiliation(s)
- J. Herlet
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - P. Kornberger
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - B. Roessler
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - J. Glanz
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - W. H. Schwarz
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - W. Liebl
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - V. V. Zverlov
- Department of Microbiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
- Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, 123182 Moscow, Russia
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Ichikawa S, Nishida A, Yasui S, Karita S. Characterization of lignocellulose particles during lignocellulose solubilization by Clostridium thermocellum. Biosci Biotechnol Biochem 2017; 81:2028-2033. [PMID: 28831850 DOI: 10.1080/09168451.2017.1364619] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Clostridium thermocellum is a candidate bacterium for lignocellulose utilization due to its efficient lignocellulose solubilization ability. It has been reported that C. thermocellum efficiently degrades purified cellulose substrates, but cannot completely degrade milled lignocellulose powders. Evaluation of cellulose and hemicellulose contents in a lignocellulose residue after the cultivation of C. thermocellum indicated that C. thermocellum degraded cellulose and hemicellulose equally. Microscopic observations demonstrated that C. thermocellum significantly degraded small-sized lignocellulose particles, but it only partially degraded the larger sized particles. The lignin content of the large-sized particles was higher than that of the small particles. The remained large-sized particles included vascular tissues. These results suggest that the lignified structures such as vascular tissues in milled lignocellulose were less susceptible to bacterial lignocellulose solubilization.
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Affiliation(s)
| | - Ayami Nishida
- a Faculty of Education , Mie University , Tsu city , Japan
| | - Saori Yasui
- b Faculty of Bioresources , Mie University , Tsu city , Japan
| | - Shuichi Karita
- c Graduate School of Bioresources , Mie University , Tsu city , Japan
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Nisha M, Saranyah K, Shankar M, Saleena LM. Enhanced saccharification of lignocellulosic agricultural biomass and increased bioethanol titre using acclimated Clostridium thermocellum DSM1313. 3 Biotech 2017; 7:35. [PMID: 28409424 PMCID: PMC5391369 DOI: 10.1007/s13205-017-0606-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 01/07/2017] [Indexed: 12/29/2022] Open
Abstract
Consolidated bioprocess assures an efficient lignocellulosic conversion to fermentable sugars and subsequently to bioethanol. Such a single-step hydrolysis and anaerobic fermentation was achieved with acclimated Clostridium thermocellum DSM 1313 on different mildly pre-treated agricultural lignocellulosic residues without any additional enzymes/and strains. Acclimation was achieved by serially sub-culturing in increasing concentration of individual substrates, such as rice husk, sugarcane bagasse, and banana pseudostem in the standard media, with cellobiose as an adjunct. The acclimated cellulolytic thermophile exhibited an early log phase entry with enhanced growth compared to the direct inoculation experiments with unacclimated culture. Around 672 mg/g of reducing sugar was produced from sugarcane bagasse media and 636 mg/g from rice husk media and 513 mg/g from banana pseudostem media with the acclimated organism. Bioethanol production also doubled in experiments with serially acclimated cultures, with a maximum of 1.21 and 1.0 g/L ethanol titre from sugarcane bagasse and rice husk, respectively. The serial acclimation experiments have increased the saccharification potentials of the organism towards the respective lignocellulosic substrates and also enhanced the bioethanol production.
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Affiliation(s)
- M. Nisha
- Department of Biotechnology, School of Bioengineering, SRM University, Kattankulathur, Chennai, Tamil Nadu 603203 India
| | - K. Saranyah
- Department of Biotechnology, School of Bioengineering, SRM University, Kattankulathur, Chennai, Tamil Nadu 603203 India
| | - Mukund Shankar
- Department of Chemical Engineering, School of Bioengineering, SRM University, Kattankulathur, Chennai, Tamil Nadu 603203 India
| | - L. M. Saleena
- Department of Biotechnology, School of Bioengineering, SRM University, Kattankulathur, Chennai, Tamil Nadu 603203 India
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Mechelke M, Koeck DE, Broeker J, Roessler B, Krabichler F, Schwarz WH, Zverlov VV, Liebl W. Characterization of the arabinoxylan-degrading machinery of the thermophilic bacterium Herbinix hemicellulosilytica-Six new xylanases, three arabinofuranosidases and one xylosidase. J Biotechnol 2017; 257:122-130. [PMID: 28450260 DOI: 10.1016/j.jbiotec.2017.04.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 04/20/2017] [Accepted: 04/20/2017] [Indexed: 10/19/2022]
Abstract
Herbinix hemicellulosilytica is a newly isolated, gram-positive, anaerobic bacterium with extensive hemicellulose-degrading capabilities obtained from a thermophilic biogas reactor. In order to exploit its potential as a source for new industrial arabinoxylan-degrading enzymes, six new thermophilic xylanases, four from glycoside hydrolase family 10 (GH10) and two from GH11, three arabinofuranosidases (1x GH43, 2x GH51) and one β-xylosidase (GH43) were selected. The recombinantly produced enzymes were purified and characterized. All enzymes were active on different xylan-based polysaccharides and most of them showed temperature-vs-activity profiles with maxima around 55-65°C. HPAEC-PAD analysis of the hydrolysates of wheat arabinoxylan and of various purified xylooligosaccharides (XOS) and arabinoxylooligosaccharides (AXOS) was used to investigate their substrate and product specificities: among the GH10 xylanases, XynB showed a different product pattern when hydrolysing AXOS compared to XynA, XynC, and XynD. None of the GH11 xylanases was able to degrade any of the tested AXOS. All three arabinofuranosidases, ArfA, ArfB and ArfC, were classified as type AXH-m,d enzymes. None of the arabinofuranosidases was able to degrade the double-arabinosylated xylooligosaccharides XA2+3XX. β-Xylosidase XylA (GH43) was able to degrade unsubstituted XOS, but showed limited activity to degrade AXOS.
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Affiliation(s)
- M Mechelke
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - D E Koeck
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - J Broeker
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - B Roessler
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - F Krabichler
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - W H Schwarz
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany
| | - V V Zverlov
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany; Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, 123182 Moscow Russia
| | - W Liebl
- Department of Microbiology, Technical University of Munich, Emil-Ramann-Str. 4, 85354 Freising-Weihenstephan, Germany.
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Osiro KO, de Camargo BR, Satomi R, Hamann PRV, Silva JP, de Sousa MV, Quirino BF, Aquino EN, Felix CR, Murad AM, Noronha EF. Characterization of Clostridium thermocellum (B8) secretome and purified cellulosomes for lignocellulosic biomass degradation. Enzyme Microb Technol 2017; 97:43-54. [DOI: 10.1016/j.enzmictec.2016.11.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 11/04/2016] [Accepted: 11/05/2016] [Indexed: 11/16/2022]
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Differences in biomass degradation between newly isolated environmental strains of Clostridium thermocellum and heterogeneity in the size of the cellulosomal scaffoldin. Syst Appl Microbiol 2015; 38:424-32. [DOI: 10.1016/j.syapm.2015.06.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 06/05/2015] [Accepted: 06/05/2015] [Indexed: 11/21/2022]
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Abstract
Clostridium clariflavum is an anaerobic, cellulosome-forming thermophile, containing in its genome genes for a large number of cellulosomal enzyme and a complex scaffoldin system. Previously, we described the major cohesin-dockerin interactions of the cellulosome components, and on this basis a model of diverse cellulosome assemblies was derived. In this work, we cultivated C. clariflavum on cellobiose-, microcrystalline cellulose-, and switchgrass-containing media and isolated cell-free cellulosome complexes from each culture. Gel filtration separation of the cellulosome samples revealed two major fractions, which were analyzed by label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) in order to identify the key players of the cellulosome assemblies therein. From the 13 scaffoldins present in the C. clariflavum genome, 11 were identified, and a variety of enzymes from different glycoside hydrolase and carbohydrate esterase families were identified, including the glycoside hydrolase families GH48, GH9, GH5, GH30, GH11, and GH10. The expression level of the cellulosomal proteins varied as a function of the carbon source used for cultivation of the bacterium. In addition, the catalytic activity of each cellulosome was examined on different cellulosic substrates, xylan and switchgrass. The cellulosome isolated from the microcrystalline cellulose-containing medium was the most active of all the cellulosomes that were tested. The results suggest that the expression of the cellulosome proteins is regulated by the type of substrate in the growth medium. Moreover, both cell-free and cell-bound cellulosome complexes were produced which together may degrade the substrate in a synergistic manner. These observations are compatible with our previously published model of cellulosome assemblies in this bacterium. Because the reservoir of unsustainable fossil fuels, such as coal, petroleum, and natural gas, is overutilized and continues to contribute to environmental pollution and CO2 emission, the need for appropriate alternative energy sources becomes more crucial. Bioethanol produced from dedicated crops and cellulosic waste can provide a partial answer, yet a cost-effective production method must be developed. The cellulosome system of the anaerobic thermophile C. clariflavum comprises a large number of cellulolytic and hemicellulolytic enzymes, which self-assemble in a number of different cellulosome architectures for enhanced cellulosic biomass degradation. Identification of the major cellulosomal components expressed during growth of the bacterium and their influence on its catalytic capabilities provide insight into the performance of the remarkable cellulosome of this intriguing bacterium. The findings, together with the thermophilic characteristics of the proteins, render C. clariflavum of great interest for future use in industrial cellulose conversion processes.
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Tyurin А, Sadovskaya N, Nikiforova K, Mustafaev О, Komakhin R, Fadeev V, Goldenkova-Pavlova I. Clostridium thermocellum thermostable lichenase with circular permutations and modifications in the N-terminal region retains its activity and thermostability. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:10-9. [DOI: 10.1016/j.bbapap.2014.10.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 09/25/2014] [Accepted: 10/15/2014] [Indexed: 11/30/2022]
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Koeck DE, Pechtl A, Zverlov VV, Schwarz WH. Genomics of cellulolytic bacteria. Curr Opin Biotechnol 2014; 29:171-83. [PMID: 25104562 DOI: 10.1016/j.copbio.2014.07.002] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 07/10/2014] [Accepted: 07/15/2014] [Indexed: 10/24/2022]
Abstract
The heterogeneous plant biomass is efficiently decomposed by the interplay of a great number of different enzymes. The enzyme systems in cellulolytic bacteria have been investigated by sequencing and bioinformatic analysis of genomes from plant biomass degrading microorganisms with valuable insights into the variety of the involved enzymes. This broadened our understanding of the biochemical mechanisms of plant polymer degradation and made the enzymes applicable for modern biotechnology. A list of the truly cellulolytic bacteria described and the available genomic information was examined for proteins with cellulolytic and hemicellulolytic capability. The importance of the isolation, characterization and genomic sequencing of cellulolytic microorganisms and their usage for sustainable energy production from biomass and other residues, is emphasized.
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Affiliation(s)
- Daniela E Koeck
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, D-85350 Freising-Weihenstephan, Germany
| | - Alexander Pechtl
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, D-85350 Freising-Weihenstephan, Germany
| | - Vladimir V Zverlov
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, D-85350 Freising-Weihenstephan, Germany; Institute of Molecular Genetics, Russian Academy of Science, Kurchatov Sq. 2, 123182 Moscow, Russia
| | - Wolfgang H Schwarz
- Department of Microbiology, Technische Universität München, Emil-Ramann-Str. 4, D-85350 Freising-Weihenstephan, Germany.
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Schellenberg JJ, Verbeke TJ, McQueen P, Krokhin OV, Zhang X, Alvare G, Fristensky B, Thallinger GG, Henrissat B, Wilkins JA, Levin DB, Sparling R. Enhanced whole genome sequence and annotation of Clostridium stercorarium DSM8532T using RNA-seq transcriptomics and high-throughput proteomics. BMC Genomics 2014; 15:567. [PMID: 24998381 PMCID: PMC4102724 DOI: 10.1186/1471-2164-15-567] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 06/26/2014] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Growing interest in cellulolytic clostridia with potential for consolidated biofuels production is mitigated by low conversion of raw substrates to desired end products. Strategies to improve conversion are likely to benefit from emerging techniques to define molecular systems biology of these organisms. Clostridium stercorarium DSM8532T is an anaerobic thermophile with demonstrated high ethanol production on cellulose and hemicellulose. Although several lignocellulolytic enzymes in this organism have been well-characterized, details concerning carbohydrate transporters and central metabolism have not been described. Therefore, the goal of this study is to define an improved whole genome sequence (WGS) for this organism using in-depth molecular profiling by RNA-seq transcriptomics and tandem mass spectrometry-based proteomics. RESULTS A paired-end Roche/454 WGS assembly was closed through application of an in silico algorithm designed to resolve repetitive sequence regions, resulting in a circular replicon with one gap and a region of 2 kilobases with 10 ambiguous bases. RNA-seq transcriptomics resulted in nearly complete coverage of the genome, identifying errors in homopolymer length attributable to 454 sequencing. Peptide sequences resulting from high-throughput tandem mass spectrometry of trypsin-digested protein extracts were mapped to 1,755 annotated proteins (68% of all protein-coding regions). Proteogenomic analysis confirmed the quality of annotation and improvement pipelines, identifying a missing gene and an alternative reading frame. Peptide coverage of genes hypothetically involved in substrate hydrolysis, transport and utilization confirmed multiple pathways for glycolysis, pyruvate conversion and recycling of intermediates. No sequences homologous to transaldolase, a central enzyme in the pentose phosphate pathway, were observed by any method, despite demonstrated growth of this organism on xylose and xylan hemicellulose. CONCLUSIONS Complementary omics techniques confirm the quality of genome sequence assembly, annotation and error-reporting. Nearly complete genome coverage by RNA-seq likely indicates background DNA in RNA extracts, however these preps resulted in WGS enhancement and transcriptome profiling in a single Illumina run. No detection of transaldolase by any method despite xylose utilization by this organism indicates an alternative pathway for sedoheptulose-7-phosphate degradation. This report combines next-generation omics techniques to elucidate previously undefined features of substrate transport and central metabolism for this organism and its potential for consolidated biofuels production from lignocellulose.
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Affiliation(s)
| | - Tobin J Verbeke
- />Department of Microbiology, University of Manitoba, Winnipeg, Canada
| | - Peter McQueen
- />Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Canada
| | - Oleg V Krokhin
- />Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Canada
| | - Xiangli Zhang
- />Department of Plant Sciences, University of Manitoba, Winnipeg, Canada
| | - Graham Alvare
- />Department of Plant Sciences, University of Manitoba, Winnipeg, Canada
| | - Brian Fristensky
- />Department of Plant Sciences, University of Manitoba, Winnipeg, Canada
| | - Gerhard G Thallinger
- />Core Facility Bioinformatics, Austrian Centre of Industrial Biotechnology (ACIB), Graz, Austria
- />Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria
| | - Bernard Henrissat
- />Architecture et Fonction des Macromolécules Biologiques, Université Aix-Marseille, Marseille, France
- />UMR 7257, Centre National de Recherche Scientifique, 163 ave. de Luminy, Marseille, 13288 France
| | - John A Wilkins
- />Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, Canada
| | - David B Levin
- />Department of Biosystems Engineering, University of Manitoba, Winnipeg, Canada
| | - Richard Sparling
- />Department of Microbiology, University of Manitoba, Winnipeg, Canada
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Blumer-Schuette SE, Brown SD, Sander KB, Bayer EA, Kataeva I, Zurawski JV, Conway JM, Adams MWW, Kelly RM. Thermophilic lignocellulose deconstruction. FEMS Microbiol Rev 2014; 38:393-448. [DOI: 10.1111/1574-6976.12044] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 08/20/2013] [Accepted: 08/28/2013] [Indexed: 11/28/2022] Open
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Synergism of glycoside hydrolase secretomes from two thermophilic bacteria cocultivated on lignocellulose. Appl Environ Microbiol 2014; 80:2592-601. [PMID: 24532065 DOI: 10.1128/aem.00295-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two cellulolytic thermophilic bacterial strains, CS-3-2 and CS-4-4, were isolated from decayed cornstalk by the addition of growth-supporting factors to the medium. According to 16S rRNA gene-sequencing results, these strains belonged to the genus Clostridium and showed 98.87% and 98.86% identity with Clostridium stercorarium subsp. leptospartum ATCC 35414(T) and Clostridium cellulosi AS 1.1777(T), respectively. The endoglucanase and exoglucanase activities of strain CS-4-4 were approximately 3 to 5 times those of strain CS-3-2, whereas the β-glucosidase activity of strain CS-3-2 was 18 times higher than that of strain CS-4-4. The xylanase activity of strain CS-3-2 was 9 times that of strain CS-4-4, whereas the β-xylosidase activity of strain CS-4-4 was 27 times that of strain CS-3-2. The enzyme activities in spent cultures following cocultivation of the two strains with cornstalk as the substrate were much greater than those in pure cultures or an artificial mixture of samples, indicating synergism of glycoside hydrolase secretomes between the two strains. Quantitative measurement of the two strains in the cocultivation system indicated that strain CS-3-2 grew robustly during the initial stages, whereas strain CS-4-4 dominated the system in the late-exponential phase. Liquid chromatography-tandem mass spectrometry analysis of protein bands appearing in the native zymograms showed that ORF3880 and ORF3883 from strain CS-4-4 played key roles in the lignocellulose degradation process. Both these open reading frames (ORFs) exhibited endoglucanase and xylanase activities, but ORF3880 showed tighter adhesion to insoluble substrates at 4, 25, and 60°C owing to its five carbohydrate-binding modules (CBMs).
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Izquierdo JA, Pattathil S, Guseva A, Hahn MG, Lynd LR. Comparative analysis of the ability of Clostridium clariflavum strains and Clostridium thermocellum to utilize hemicellulose and unpretreated plant material. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:136. [PMID: 25426163 PMCID: PMC4243297 DOI: 10.1186/s13068-014-0136-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 09/03/2014] [Indexed: 05/11/2023]
Abstract
BACKGROUND Among themophilic consolidated bioprocessing (CBP) candidate organisms, environmental isolates of Clostridium clariflavum have demonstrated the ability to grow on xylan, and the genome of C. clariflavum DSM 19732 has revealed a number of mechanisms that foster solubilization of hemicellulose that are distinctive relative to the model cellulolytic thermophile Clostridium thermocellum. RESULTS Growth experiments on xylan, xylooligosaccharides, and xylose reveal that C. clariflavum strains are able to completely break down xylan to xylose and that the environmental strain C. clariflavum sp. 4-2a is able to grow on monomeric xylose. C. clariflavum strains were able to utilize a larger proportion of unpretreated switchgrass, and solubilize a higher proportion of glucan, xylan, and arabinan, with strain 4-2a reaching the highest extent of solubilization of these components (64.7 to 69.4%) compared to C. thermocellum (29.5 to 42.5%). In addition, glycome immunoanalyses of residual plant biomass reveal differences in the extent of degradation of easily accessible xylans, with C. clariflavum strains having increased solubilization of this fraction of xylans relative to C. thermocellum. CONCLUSIONS C. clariflavum strains exhibit higher activity than C. thermocellum in the breakdown of hemicellulose and are capable of degrading xylan to xylooligomers and xylose. This capability seems to also play a role in the higher levels of utilization of unpretreated plant material.
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Affiliation(s)
- Javier A Izquierdo
- />Thayer School of Engineering, Dartmouth College, Hanover, NH USA
- />BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge, Oak Ridge, TN USA
- />Department of Biology, Hofstra University, Hempstead, NY USA
| | - Sivakumar Pattathil
- />BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge, Oak Ridge, TN USA
- />Complex Carbohydrate Research Center, University of Georgia, Athens, GA USA
| | - Anna Guseva
- />Thayer School of Engineering, Dartmouth College, Hanover, NH USA
- />BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge, Oak Ridge, TN USA
| | - Michael G Hahn
- />BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge, Oak Ridge, TN USA
- />Complex Carbohydrate Research Center, University of Georgia, Athens, GA USA
| | - Lee R Lynd
- />Thayer School of Engineering, Dartmouth College, Hanover, NH USA
- />BioEnergy Science Center Oak Ridge National Laboratory Oak Ridge, Oak Ridge, TN USA
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Wilson CM, Yang S, Rodriguez M, Ma Q, Johnson CM, Dice L, Xu Y, Brown SD. Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:131. [PMID: 24028713 PMCID: PMC3848806 DOI: 10.1186/1754-6834-6-131] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 09/04/2013] [Indexed: 05/23/2023]
Abstract
BACKGROUND The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. It is capable of both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. Intolerance to stresses routinely encountered during industrial fermentations may hinder the commercial development of this organism. A previous C. thermocellum ethanol stress study showed that the largest transcriptomic response was in genes and proteins related to nitrogen uptake and metabolism. RESULTS In this study, C. thermocellum was grown to mid-exponential phase and treated with furfural or heat to a final concentration of 3 g.L-1 or 68°C respectively to investigate general and specific physiological and regulatory stress responses. Samples were taken at 10, 30, 60 and 120 min post-shock, and from untreated control fermentations, for transcriptomic analyses and fermentation product determinations and compared to a published dataset from an ethanol stress study. Urea uptake genes were induced following furfural stress, but not to the same extent as ethanol stress and transcription from these genes was largely unaffected by heat stress. The largest transcriptomic response to furfural stress was genes for sulfate transporter subunits and enzymes in the sulfate assimilatory pathway, although these genes were also affected late in the heat and ethanol stress responses. Lactate production was higher in furfural treated culture, although the lactate dehydrogenase gene was not differentially expressed under this condition. Other redox related genes such as a copy of the rex gene, a bifunctional acetaldehyde-CoA/alcohol dehydrogenase and adjacent genes did show lower expression after furfural stress compared to the control, heat and ethanol fermentation profiles. Heat stress induced expression from chaperone related genes and overlap was observed with the responses to the other stresses. This study suggests the involvement of C. thermocellum genes with functions in oxidative stress protection, electron transfer, detoxification, sulfur and nitrogen acquisition, and DNA repair mechanisms in its stress responses and the use of different regulatory networks to coordinate and control adaptation. CONCLUSIONS This study has identified C. thermocellum gene regulatory motifs and aspects of physiology and gene regulation for further study. The nexus between future systems biology studies and recently developed genetic tools for C. thermocellum offers the potential for more rapid strain development and for broader insights into this organism's physiology and regulation.
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Affiliation(s)
- Charlotte M Wilson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Shihui Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Present address: National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Miguel Rodriguez
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Qin Ma
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, Computational Systems Biology Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Courtney M Johnson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Lezlee Dice
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Ying Xu
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, Computational Systems Biology Laboratory, University of Georgia, Athens, GA 30602, USA
- College of Computer Science and Technology, Jilin University, Changchun, Jilin, China
| | - Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Microbial community structure of a pilot-scale thermophilic anaerobic digester treating poultry litter. Appl Microbiol Biotechnol 2013; 98:2321-34. [PMID: 23989973 DOI: 10.1007/s00253-013-5144-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/17/2013] [Accepted: 07/19/2013] [Indexed: 10/26/2022]
Abstract
The microbial community structure of a stable pilot-scale thermophilic continuous stirred tank reactor digester stabilized on poultry litter was investigated. This 40-m(3) digester produced biogas with 57% methane, and chemical oxygen demand removal of 54%. Bacterial and archaeal diversity were examined using both cloning and pyrosequencing that targeted 16S rRNA genes. The bacterial community was dominated by phylum Firmicutes, constituting 93% of the clones and 76% of the pyrotags. Of the Firmicutes, class Clostridia (52% pyrotags) was most abundant followed by class Bacilli (13% pyrotags). The bacterial libraries identified 94 operational taxonomic units (OTUs) and pyrosequencing identified 577 OTUs at the 97% minimum similarity level. Fifteen OTUs were dominant (≥2% abundance), and nine of these were novel unclassified Firmicutes. Several of the dominant OTUs could not be classified more specifically than Clostridiales, but were most similar to plant biomass degraders, including Clostridium thermocellum. Of the rare pyrotag OTUs (<0.5% abundance), 75% were Firmicutes. The dominant methanogen was Methanothermobacter which has hydrogenotrophic metabolism, and accounted for >99% of the archaeal clones. Based on the primary methanogen, as well as digester chemistry (high VA and ammonia levels), we propose that bacterial acetate oxidation is the primary pathway in this digester for the control of acetate levels.
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Kovács K, Willson BJ, Schwarz K, Heap JT, Jackson A, Bolam DN, Winzer K, Minton NP. Secretion and assembly of functional mini-cellulosomes from synthetic chromosomal operons in Clostridium acetobutylicum ATCC 824. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:117. [PMID: 23962085 PMCID: PMC3765823 DOI: 10.1186/1754-6834-6-117] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 08/02/2013] [Indexed: 05/31/2023]
Abstract
BACKGROUND Consolidated bioprocessing (CBP) is reliant on the simultaneous enzyme production, saccharification of biomass, and fermentation of released sugars into valuable products such as butanol. Clostridial species that produce butanol are, however, unable to grow on crystalline cellulose. In contrast, those saccharolytic species that produce predominantly ethanol, such as Clostridium thermocellum and Clostridium cellulolyticum, degrade crystalline cellulose with high efficiency due to their possession of a multienzyme complex termed the cellulosome. This has led to studies directed at endowing butanol-producing species with the genetic potential to produce a cellulosome, albeit by localising the necessary transgenes to unstable autonomous plasmids. Here we have explored the potential of our previously described Allele-Coupled Exchange (ACE) technology for creating strains of the butanol producing species Clostridium acetobutylicum in which the genes encoding the various cellulosome components are stably integrated into the genome. RESULTS We used BioBrick2 (BB2) standardised parts to assemble a range of synthetic genes encoding C. thermocellum cellulosomal scaffoldin proteins (CipA variants) and glycoside hydrolases (GHs, Cel8A, Cel9B, Cel48S and Cel9K) as well as synthetic cellulosomal operons that direct the synthesis of Cel8A, Cel9B and a truncated form of CipA. All synthetic genes and operons were integrated into the C. acetobutylicum genome using the recently developed ACE technology. Heterologous protein expression levels and mini-cellulosome self-assembly were assayed by western blot and native PAGE analysis. CONCLUSIONS We demonstrate the successful expression, secretion and self-assembly of cellulosomal subunits by the recombinant C. acetobutylicum strains, providing a platform for the construction of novel cellulosomes.
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Affiliation(s)
- Katalin Kovács
- Clostridia Research Group, BBSRC Sustainable BioEnergy Centre, School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Benjamin J Willson
- Clostridia Research Group, BBSRC Sustainable BioEnergy Centre, School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Katrin Schwarz
- Clostridia Research Group, BBSRC Sustainable BioEnergy Centre, School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - John T Heap
- Clostridia Research Group, BBSRC Sustainable BioEnergy Centre, School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
- Current address: Centre for Synthetic Biology and Innovation, Division of Molecular Biosciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Adam Jackson
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - David N Bolam
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Klaus Winzer
- Clostridia Research Group, BBSRC Sustainable BioEnergy Centre, School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Nigel P Minton
- Clostridia Research Group, BBSRC Sustainable BioEnergy Centre, School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
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Draft genome sequence of the cellulolytic Clostridium thermocellum wild-type strain BC1 playing a role in cellulosic biomass degradation. J Biotechnol 2013; 168:62-3. [PMID: 23968723 DOI: 10.1016/j.jbiotec.2013.08.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 08/09/2013] [Indexed: 01/14/2023]
Abstract
The bacterium Clostridium thermocellum BC1, a thermophilic, anaerobic bacterium of the family Clostridiaceae, was isolated from a compost treatment site in Germany. It is able to grow efficiently on cellulose and cellodextrins. The draft genome sequence of C. thermocellum BC1 has been established and provides the genetic basis for application of this microorganism in thermophilic degradation of cellulosic biomass.
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Hanreich A, Schimpf U, Zakrzewski M, Schlüter A, Benndorf D, Heyer R, Rapp E, Pühler A, Reichl U, Klocke M. Metagenome and metaproteome analyses of microbial communities in mesophilic biogas-producing anaerobic batch fermentations indicate concerted plant carbohydrate degradation. Syst Appl Microbiol 2013; 36:330-8. [PMID: 23694815 DOI: 10.1016/j.syapm.2013.03.006] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 03/01/2013] [Accepted: 03/07/2013] [Indexed: 11/27/2022]
Abstract
Microbial communities in biogas batch fermentations, using straw and hay as co-substrates, were analyzed at the gene and protein level by metagenomic and metaproteomic approaches. The analysis of metagenomic data revealed that the Clostridiales and Bacteroidales orders were prevalent in the community. However, the number of sequences assigned to the Clostridiales order decreased during fermentation, whereas the number of sequences assigned to the Bacteroidales order increased. In addition, changes at the functional level were monitored and the metaproteomic analyses detected transporter proteins and flagellins, which were expressed mainly by members of the Bacteroidetes and Firmicutes phyla. A high number of sugar transporters, expressed by members of the Bacteroidetes, proved their potential to take up various glycans efficiently. Metagenome data also showed that methanogenic organisms represented less than 4% of the community, while 20-30% of the identified proteins were of archeal origin. These data suggested that methanogens were disproportionally active. In conclusion, the community studied was capable of digesting the recalcitrant co-substrate. Members of the Firmicutes phylum seemed to be the main degraders of cellulose, even though expression of only a few glycoside hydrolases was detected. The Bacteroidetes phylum expressed a high number of sugar transporters and seemed to specialize in the digestion of other polysaccharides. Finally, it was found that key enzymes of methanogenesis were expressed in high quantities, indicating the high metabolic activity of methanogens, although they only represented a minor group within the microbial community.
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Affiliation(s)
- Angelika Hanreich
- Leibniz-Institut für Agrartechnik Potsdam-Bornim e.V., Abteilung Bioverfahrenstechnik, Max-Eyth-Allee 100, 14469 Potsdam, Germany
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van der Veen D, Lo J, Brown SD, Johnson CM, Tschaplinski TJ, Martin M, Engle NL, van den Berg RA, Argyros AD, Caiazza NC, Guss AM, Lynd LR. Characterization of Clostridium thermocellum strains with disrupted fermentation end-product pathways. J Ind Microbiol Biotechnol 2013; 40:725-34. [PMID: 23645383 DOI: 10.1007/s10295-013-1275-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 04/15/2013] [Indexed: 10/26/2022]
Abstract
Clostridium thermocellum is a thermophilic, cellulolytic anaerobe that is a candidate microorganism for industrial biofuels production. Strains with mutations in genes associated with production of L-lactate (Δldh) and/or acetate (Δpta) were characterized to gain insight into the intracellular processes that convert cellobiose to ethanol and other fermentation end-products. Cellobiose-grown cultures of the Δldh strain had identical biomass accumulation, fermentation end-products, transcription profile, and intracellular metabolite concentrations compared to its parent strain (DSM1313 Δhpt Δspo0A). The Δpta-deficient strain grew slower and had 30 % lower final biomass concentration compared to the parent strain, yet produced 75 % more ethanol. A Δldh Δpta double-mutant strain evolved for faster growth had a growth rate and ethanol yield comparable to the parent strain, whereas its biomass accumulation was comparable to Δpta. Free amino acids were secreted by all examined strains, with both Δpta strains secreting higher amounts of alanine, valine, isoleucine, proline, glutamine, and threonine. Valine concentration for Δldh Δpta reached 5 mM by the end of growth, or 2.7 % of the substrate carbon utilized. These secreted amino acid concentrations correlate with increased intracellular pyruvate concentrations, up to sixfold in the Δpta and 16-fold in the Δldh Δpta strain. We hypothesize that the deletions in fermentation end-product pathways result in an intracellular redox imbalance, which the organism attempts to relieve, in part by recycling NADP⁺ through increased production of amino acids.
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Complete Genome Sequence of Clostridium stercorarium subsp. stercorarium Strain DSM 8532, a Thermophilic Degrader of Plant Cell Wall Fibers. GENOME ANNOUNCEMENTS 2013; 1:e0007313. [PMID: 23516204 PMCID: PMC3593316 DOI: 10.1128/genomea.00073-13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Clostridium stercorarium strain DSM 8532 is a thermophilic bacterium capable of efficiently degrading polysaccharides in plant biomass and converting the resulting sugars to ethanol and acetate. The complete genome sequence of 2.96 Mbp reveals a multitude of genes for hydrolytic enzymes and enables further study of the organism and its enzymes, and their exploitation for biotechnological processes.
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40
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The osteogenesis of bacterial cellulose scaffold loaded with bone morphogenetic protein-2. Biomaterials 2012; 33:6644-9. [DOI: 10.1016/j.biomaterials.2012.05.071] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 05/29/2012] [Indexed: 11/22/2022]
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Rydzak T, McQueen PD, Krokhin OV, Spicer V, Ezzati P, Dwivedi RC, Shamshurin D, Levin DB, Wilkins JA, Sparling R. Proteomic analysis of Clostridium thermocellum core metabolism: relative protein expression profiles and growth phase-dependent changes in protein expression. BMC Microbiol 2012; 12:214. [PMID: 22994686 PMCID: PMC3492117 DOI: 10.1186/1471-2180-12-214] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 09/11/2012] [Indexed: 01/21/2023] Open
Abstract
Background Clostridium thermocellum produces H2 and ethanol, as well as CO2, acetate, formate, and lactate, directly from cellulosic biomass. It is therefore an attractive model for biofuel production via consolidated bioprocessing. Optimization of end-product yields and titres is crucial for making biofuel production economically feasible. Relative protein expression profiles may provide targets for metabolic engineering, while understanding changes in protein expression and metabolism in response to carbon limitation, pH, and growth phase may aid in reactor optimization. We performed shotgun 2D-HPLC-MS/MS on closed-batch cellobiose-grown exponential phase C. thermocellum cell-free extracts to determine relative protein expression profiles of core metabolic proteins involved carbohydrate utilization, energy conservation, and end-product synthesis. iTRAQ (isobaric tag for relative and absolute quantitation) based protein quantitation was used to determine changes in core metabolic proteins in response to growth phase. Results Relative abundance profiles revealed differential levels of putative enzymes capable of catalyzing parallel pathways. The majority of proteins involved in pyruvate catabolism and end-product synthesis were detected with high abundance, with the exception of aldehyde dehydrogenase, ferredoxin-dependent Ech-type [NiFe]-hydrogenase, and RNF-type NADH:ferredoxin oxidoreductase. Using 4-plex 2D-HPLC-MS/MS, 24% of the 144 core metabolism proteins detected demonstrated moderate changes in expression during transition from exponential to stationary phase. Notably, proteins involved in pyruvate synthesis decreased in stationary phase, whereas proteins involved in glycogen metabolism, pyruvate catabolism, and end-product synthesis increased in stationary phase. Several proteins that may directly dictate end-product synthesis patterns, including pyruvate:ferredoxin oxidoreductases, alcohol dehydrogenases, and a putative bifurcating hydrogenase, demonstrated differential expression during transition from exponential to stationary phase. Conclusions Relative expression profiles demonstrate which proteins are likely utilized in carbohydrate utilization and end-product synthesis and suggest that H2 synthesis occurs via bifurcating hydrogenases while ethanol synthesis is predominantly catalyzed by a bifunctional aldehyde/alcohol dehydrogenase. Differences in expression profiles of core metabolic proteins in response to growth phase may dictate carbon and electron flux towards energy storage compounds and end-products. Combined knowledge of relative protein expression levels and their changes in response to physiological conditions may aid in targeted metabolic engineering strategies and optimization of fermentation conditions for improvement of biofuels production.
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Affiliation(s)
- Thomas Rydzak
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Peng S, Zheng Y, Wu J, Wu Y, Ma Y, Song W, Xi T. Preparation and characterization of degradable oxidized bacterial cellulose reacted with nitrogen dioxide. Polym Bull (Berl) 2011. [DOI: 10.1007/s00289-011-0550-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Cellulose- and xylan-degrading thermophilic anaerobic bacteria from biocompost. Appl Environ Microbiol 2011; 77:2282-91. [PMID: 21317267 DOI: 10.1128/aem.01219-10] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nine thermophilic cellulolytic clostridial isolates and four other noncellulolytic bacterial isolates were isolated from self-heated biocompost via preliminary enrichment culture on microcrystalline cellulose. All cellulolytic isolates grew vigorously on cellulose, with the formation of either ethanol and acetate or acetate and formate as principal fermentation products as well as lactate and glycerol as minor products. In addition, two out of nine cellulolytic strains were able to utilize xylan and pretreated wood with roughly the same efficiency as for cellulose. The major products of xylan fermentation were acetate and formate, with minor contributions of lactate and ethanol. Phylogenetic analyses of 16S rRNA and glycosyl hydrolase family 48 (GH48) gene sequences revealed that two xylan-utilizing isolates were related to a Clostridium clariflavum strain and represent a distinct novel branch within the GH48 family. Both isolates possessed high cellulase and xylanase activity induced independently by either cellulose or xylan. Enzymatic activity decayed after growth cessation, with more-rapid disappearance of cellulase activity than of xylanase activity. A mixture of xylan and cellulose was utilized simultaneously, with a significant synergistic effect observed as a reduction of lag phase in cellulose degradation.
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Zverlov VV, Hiegl W, Köck DE, Kellermann J, Köllmeier T, Schwarz WH. Hydrolytic bacteria in mesophilic and thermophilic degradation of plant biomass. Eng Life Sci 2010. [DOI: 10.1002/elsc.201000059] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Kalluri UC, Keller M. Bioenergy research: a new paradigm in multidisciplinary research. J R Soc Interface 2010; 7:1391-401. [PMID: 20542958 PMCID: PMC3227023 DOI: 10.1098/rsif.2009.0564] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Accepted: 05/10/2010] [Indexed: 12/28/2022] Open
Abstract
The field of biology is becoming increasingly interdisciplinary and cross-cutting. This changing research atmosphere is creating the way for a new kind of enquiry that while building upon the traditional research establishment is providing a new multidisciplinary framework to more effectively address scientific grand challenges. Using the US Department of Energy sponsored BioEnergy Science Center as an example, we highlight how impactful breakthroughs in biofuel science can be achieved within a large cross-disciplinary team environment. Such transformational insights are key to furthering our understanding and in generating models, theories and processes that can be used to overcome recalcitrance of biomass for sustainable biofuel production. Multidisciplinary approaches have an increasingly greater role to play in meeting rising demands for food, fibre, energy, clean environment and good health. Discoveries achieved by diverse minds and cross-applications of tools and analytical approaches have tremendous potential to fill existing knowledge gaps, clear roadblocks and facilitate translation of basic sciences discoveries as solutions towards addressing some of the most pressing global issues.
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Affiliation(s)
- Udaya C. Kalluri
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- BESC BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Martin Keller
- Biological and Environmental Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- BESC BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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Cellulosilyticum ruminicola, a newly described rumen bacterium that possesses redundant fibrolytic-protein-encoding genes and degrades lignocellulose with multiple carbohydrate- borne fibrolytic enzymes. Appl Environ Microbiol 2010; 76:3818-24. [PMID: 20400560 DOI: 10.1128/aem.03124-09] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cellulosilyticum ruminicola H1 is a newly described bacterium isolated from yak (Bos grunniens) rumen and is characterized by its ability to grow on a variety of hemicelluloses and degrade cellulosic materials. In this study, we performed the whole-genome sequencing of C. ruminicola H1 and observed a comprehensive set of genes encoding the enzymes essential for hydrolyzing plant cell wall. The corresponding enzymatic activities were also determined in strain H1; these included endoglucanases, cellobiohydrolases, xylanases, mannanase, pectinases, and feruloyl esterases and acetyl esterases to break the interbridge cross-link, as well as the enzymes that degrade the glycosidic bonds. This bacterium appears to produce polymer hydrolases that act on both soluble and crystal celluloses. Approximately half of the cellulytic activities, including cellobiohydrolase (50%), feruloyl esterase (45%), and one third of xylanase (31%) and endoglucanase (36%) activities were bound to cellulosic fibers. However, only a minority of mannase (6.78%) and pectinase (1.76%) activities were fiber associated. Strain H1 seems to degrade the plant-derived polysaccharides by producing individual fibrolytic enzymes, whereas the majority of polysaccharide hydrolases contain carbohydrate-binding module. Cellulosome or cellulosomelike protein complex was never isolated from this bacterium. Thus, the fibrolytic enzyme production of strain H1 may represent a different strategy in cellulase organization used by most of other ruminal microbes, but it applies the fungal mode of cellulose production.
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Niu D, Zhou XX, Yuan TY, Lin ZW, Ruan H, Li WF. Effect of the C-terminal domains and terminal residues of catalytic domain on enzymatic activity and thermostability of lichenase from Clostridium thermocellum. Biotechnol Lett 2010; 32:963-7. [DOI: 10.1007/s10529-010-0241-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Accepted: 02/19/2010] [Indexed: 11/29/2022]
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Raman B, Pan C, Hurst GB, Rodriguez M, McKeown CK, Lankford PK, Samatova NF, Mielenz JR. Impact of pretreated Switchgrass and biomass carbohydrates on Clostridium thermocellum ATCC 27405 cellulosome composition: a quantitative proteomic analysis. PLoS One 2009; 4:e5271. [PMID: 19384422 PMCID: PMC2668762 DOI: 10.1371/journal.pone.0005271] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 02/12/2009] [Indexed: 11/30/2022] Open
Abstract
Background Economic feasibility and sustainability of lignocellulosic ethanol production requires the development of robust microorganisms that can efficiently degrade and convert plant biomass to ethanol. The anaerobic thermophilic bacterium Clostridium thermocellum is a candidate microorganism as it is capable of hydrolyzing cellulose and fermenting the hydrolysis products to ethanol and other metabolites. C. thermocellum achieves efficient cellulose hydrolysis using multiprotein extracellular enzymatic complexes, termed cellulosomes. Methodology/Principal Findings In this study, we used quantitative proteomics (multidimensional LC-MS/MS and 15N-metabolic labeling) to measure relative changes in levels of cellulosomal subunit proteins (per CipA scaffoldin basis) when C. thermocellum ATCC 27405 was grown on a variety of carbon sources [dilute-acid pretreated switchgrass, cellobiose, amorphous cellulose, crystalline cellulose (Avicel) and combinations of crystalline cellulose with pectin or xylan or both]. Cellulosome samples isolated from cultures grown on these carbon sources were compared to 15N labeled cellulosome samples isolated from crystalline cellulose-grown cultures. In total from all samples, proteomic analysis identified 59 dockerin- and 8 cohesin-module containing components, including 16 previously undetected cellulosomal subunits. Many cellulosomal components showed differential protein abundance in the presence of non-cellulose substrates in the growth medium. Cellulosome samples from amorphous cellulose, cellobiose and pretreated switchgrass-grown cultures displayed the most distinct differences in composition as compared to cellulosome samples from crystalline cellulose-grown cultures. While Glycoside Hydrolase Family 9 enzymes showed increased levels in the presence of crystalline cellulose, and pretreated switchgrass, in particular, GH5 enzymes showed increased levels in response to the presence of cellulose in general, amorphous or crystalline. Conclusions/Significance Overall, the quantitative results suggest a coordinated substrate-specific regulation of cellulosomal subunit composition in C. thermocellum to better suit the organism's needs for growth under different conditions. To date, this study provides the most comprehensive comparison of cellulosomal compositional changes in C. thermocellum in response to different carbon sources. Such studies are vital to engineering a strain that is best suited to grow on specific substrates of interest and provide the building blocks for constructing designer cellulosomes with tailored enzyme composition for industrial ethanol production.
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Affiliation(s)
- Babu Raman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Chongle Pan
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Gregory B. Hurst
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Miguel Rodriguez
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Catherine K. McKeown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Patricia K. Lankford
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Nagiza F. Samatova
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Department of Computer Science, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Jonathan R. Mielenz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- * E-mail:
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Eneyskaya EV, Sundqvist G, Golubev AM, Ibatullin FM, Ivanen DR, Shabalin KA, Brumer H, Kulminskaya AA. Transglycosylating and hydrolytic activities of the beta-mannosidase from Trichoderma reesei. Biochimie 2009; 91:632-8. [PMID: 19327384 DOI: 10.1016/j.biochi.2009.03.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Accepted: 03/13/2009] [Indexed: 11/17/2022]
Abstract
A purified beta-mannosidase (EC 3.2.1.25) from the fungus Trichoderma reesei has been identified as a member of glycoside hydrolase family 2 through mass spectrometry analysis of tryptic peptides. In addition to hydrolysis, the enzyme catalyzes substrate transglycosylation with p-nitrophenyl beta-mannopyranoside. Structures of the major and minor products of this reaction were identified by NMR analysis as p-nitrophenyl mannobiosides and p-nitrophenyl mannotriosides containing beta-(1-->4) and beta-(1-->3) linkages. The rate of donor substrate hydrolysis increased in presence of acetonitrile and dimethylformamide, while transglycosylation was weakly suppressed by these organic solvents. Differential ultraviolet spectra of the protein indicate that a rearrangement of the hydrophobic environment of the active site following the addition of the organic solvents may be responsible for this hydrolytic activation.
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Affiliation(s)
- Elena V Eneyskaya
- Petersburg Nuclear Physics Institute, Russian Academy of Science, Molecular and Radiation Biophysics Division, Gatchina, Leningrad District, Russia
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